From d8ef35b97a98d1d3a023dc5f5b8eefa139fa9187 Mon Sep 17 00:00:00 2001
From: John Duddy <jduddy@illumina.com>
Date: Tue, 24 May 2011 15:15:03 -0700
Subject: [PATCH 001/362] Added new "multi" parallelism option for tools

---
 lib/galaxy/datatypes/data.py       | 102 +++++++++++++++++++-
 lib/galaxy/datatypes/sequence.py   |  89 +++++++++++++++++
 lib/galaxy/jobs/__init__.py        |  56 +++++++----
 lib/galaxy/jobs/runners/tasks.py   |  73 ++++++--------
 lib/galaxy/jobs/splitters/basic.py | 104 ++++----------------
 lib/galaxy/jobs/splitters/multi.py | 149 +++++++++++++++++++++++++++++
 lib/galaxy/model/__init__.py       |  11 +++
 lib/galaxy/tools/__init__.py       |  17 +++-
 8 files changed, 449 insertions(+), 152 deletions(-)
 create mode 100644 lib/galaxy/jobs/splitters/multi.py

diff --git a/lib/galaxy/datatypes/data.py b/lib/galaxy/datatypes/data.py
index e37744b69d3..9e0cf4c0b41 100644
--- a/lib/galaxy/datatypes/data.py
+++ b/lib/galaxy/datatypes/data.py
@@ -1,4 +1,4 @@
-import logging, os, sys, time, tempfile
+import logging, os, sys, time, tempfile,  gzip
 from galaxy import util
 from galaxy.util.odict import odict
 from galaxy.util.bunch import Bunch
@@ -351,6 +351,32 @@ class Data( object ):
     @property
     def has_resolution(self):
         return False
+    
+    
+
+    def merge( split_files, output_file): 
+        """
+        Export files are usually compressed, but it doesn't have to be so. In the case that they are, use
+        zcat to cat the files and gzip -c to recompress the result, otherwise use cat
+        TODO: Move to a faster gzjoin-based technique
+        """
+        #TODO: every time I try to import this from sniff, the parser dies
+        def is_gzip( filename ):
+            temp = open( filename, "U" )
+            magic_check = temp.read( 2 )
+            temp.close()
+            if magic_check != util.gzip_magic:
+                return False
+            return True
+        
+        if len(split_files) == 1:
+            os.system( 'mv -f %s %s' % ( split_files[0], output_file ) )
+            return
+        if is_gzip(split_files[0]):
+            os.system( 'zcat %s | gzip -c > %s' % ( ' '.join(split_files), output_file ) )
+        else:
+            os.system( 'cat %s > %s' % ( ' '.join(split_files), output_file ) )
+    merge = staticmethod(merge)
 
 class Text( Data ):
     file_ext = 'txt'
@@ -446,6 +472,80 @@ class Text( Data ):
             dataset.peek = 'file does not exist'
             dataset.blurb = 'file purged from disk'
 
+    def split( input_files, subdir_generator_function, split_params): 
+        """
+        Split the input files by line.
+        """
+        if split_params is None:
+            return
+            
+        if len(input_files) > 1:
+            raise Exception("Text file splitting does not support multiple files")
+        
+        lines_per_file = None
+        chunk_size = None
+        if split_params['split_mode'] == 'number_of_parts':
+            lines_per_file = []
+            # Computing the length is expensive!
+            def _file_len(fname):
+                i = 0
+                f = open(fname)
+                for i, l in enumerate(f):
+                    pass
+                f.close()
+                return i + 1
+            length = _file_len(input_files[0])
+            parts = int(split_params['split_size'])
+            if length < parts:
+                parts = length
+            len_each, remainder = divmod(length, parts)
+            while length > 0:
+                chunk = len_each
+                if remainder > 0:
+                    chunk += 1
+                lines_per_file.append(chunk)
+                remainder=- 1
+                length -= chunk
+        elif split_params['split_mode'] == 'to_size':
+            chunk_size = int(split_params['split_size'])
+        else:
+            raise Exception('Unsupported split mode %s' % split_params['split_mode'])
+        
+        f = open(input_files[0], 'rt')
+        try:
+            chunk_idx = 0
+            file_done = False
+            part_file = None
+            while not file_done:
+                if lines_per_file is None:
+                    this_chunk_size = chunk_size
+                elif chunk_idx < len(lines_per_file):
+                    this_chunk_size = lines_per_file[chunk_idx]
+                    chunk_idx += 1
+                lines_remaining = this_chunk_size
+                part_file = None
+                while lines_remaining > 0:
+                    a_line = f.readline()
+                    if a_line == '':
+                        file_done = True
+                        break
+                    if part_file is None:
+                        part_dir = subdir_generator_function()
+                        part_path = os.path.join(part_dir, os.path.basename(input_files[0]))
+                        part_file = open(part_path, 'w')
+                    part_file.write(a_line)
+                    lines_remaining -= 1
+                if part_file is not None:
+                    part_file.close()
+        except Exception,  e:
+            log.error('Unable to split files: %s' % str(e))
+            f.close()
+            if part_file is not None:
+                part_file.close()
+            raise
+        f.close()
+    split = staticmethod(split)
+
 class Newick( Text ):
     pass
 
diff --git a/lib/galaxy/datatypes/sequence.py b/lib/galaxy/datatypes/sequence.py
index 10780555af3..42bace94afc 100644
--- a/lib/galaxy/datatypes/sequence.py
+++ b/lib/galaxy/datatypes/sequence.py
@@ -49,6 +49,95 @@ class Sequence( data.Text ):
         else:
             dataset.peek = 'file does not exist'
             dataset.blurb = 'file purged from disk'
+    
+    def split( input_files, subdir_generator_function, split_params):
+        """
+        FASTQ files are split on cluster boundaries, in increments of 4 lines
+        """
+        if split_params is None:
+            return
+        
+        def split_one( input_file, get_dir, clusters_per_file,  default_clusters=None):
+            in_file = open(input_file, 'rt')
+            part_file = None
+            part = 0
+            if clusters_per_file is None:
+                local_clusters_per_file = [default_clusters]
+            else:
+                local_clusters_per_file = [x for x in clusters_per_file] 
+                
+            for i, line in enumerate(in_file):
+                cluster_number,  line_in_cluster = divmod(i, 4)
+                current_part, remainder = divmod(cluster_number, local_clusters_per_file[part])
+                
+                if (current_part != part or part_file is None):
+                    if (part_file):
+                        part_file.close()
+                    part = current_part
+                    part_dir = get_dir()
+                    part_path = os.path.join(part_dir, os.path.basename(input_file))
+                    part_file = open(part_path, 'w')
+                    if clusters_per_file is None:
+                        local_clusters_per_file.append(default_clusters)
+                part_file.write(line)
+            if (part_file):
+                part_file.close()
+            in_file.close()
+            local_clusters_per_file[part] = remainder + 1
+            return local_clusters_per_file
+    
+        directories = []
+        def create_subdir():
+            dir = subdir_generator_function()
+            directories.append(dir)
+            return dir
+        
+        clusters_per_file = None
+        if split_params['split_mode'] == 'number_of_parts':
+            # legacy splitting. To keep things simple, just scan the 0th file and count the clusters,
+            # then split it
+            clusters_per_file = []
+            in_file = open(input_files[0], 'rt')
+            for i, line in enumerate(in_file):
+                pass
+            in_file.close()
+            length = (i+1)/4
+            
+            if length <= 0:
+                raise Exception('Invalid sequence file %s' % input_files[0])
+            parts = int(split_params['split_size'])
+            if length < parts:
+                parts = length
+            len_each, remainder = divmod(length, parts)
+            while length > 0:
+                chunk = len_each
+                if remainder > 0:
+                    chunk += 1
+                clusters_per_file.append(chunk)
+                remainder=- 1
+                length -= chunk
+            split_one(input_files[0],  create_subdir,  clusters_per_file)
+        elif split_params['split_mode'] == 'to_size':
+            # split one file and see what the cluster sizes turn out to be
+            clusters_per_file = split_one(input_files[0],  create_subdir,  None,  int(split_params['split_size']))
+        else:
+            raise Exception('Unsupported split mode %s' % split_params['split_mode'])
+        
+        # split the rest, using the same number of clusters for each file
+        current_dir_idx = [0] # use a list to get around Python 2.x lame closure support
+        def get_subdir():
+            if len(directories) <= current_dir_idx[0]:
+                raise Exception('FASTQ files do not have the same number of clusters - splitting failed')
+            result = directories[current_dir_idx[0]]
+            current_dir_idx[0] = current_dir_idx[0] + 1
+            return result
+            
+        for i in range(1,  len(input_files)):
+            current_dir_idx[0] = 0
+            split_one(input_files[i],  get_subdir,  clusters_per_file)
+    split = staticmethod(split)
+
+
 
 class Alignment( data.Text ):
     """Class describing an alignment"""
diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 0ffc29ae223..64566d3a6d0 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -291,6 +291,7 @@ class JobWrapper( object ):
         self.working_directory = \
             os.path.join( self.app.config.job_working_directory, str( self.job_id ) )
         self.output_paths = None
+        self.output_dataset_paths = None
         self.tool_provided_job_metadata = None
         # Wrapper holding the info required to restore and clean up from files used for setting metadata externally
         self.external_output_metadata = metadata.JobExternalOutputMetadataWrapper( job )        
@@ -657,23 +658,35 @@ class JobWrapper( object ):
     def get_session_id( self ):
         return self.session_id
 
+    def get_input_dataset_fnames( self,  ds ):
+        filenames = []
+        filenames = [ ds.file_name ]
+        #we will need to stage in metadata file names also
+        #TODO: would be better to only stage in metadata files that are actually needed (found in command line, referenced in config files, etc.)
+        for key, value in ds.metadata.items():
+            if isinstance( value, model.MetadataFile ):
+                filenames.append( value.file_name )
+        return filenames
+    
     def get_input_fnames( self ):
         job = self.get_job()
         filenames = []
         for da in job.input_datasets: #da is JobToInputDatasetAssociation object
             if da.dataset:
-                filenames.append( da.dataset.file_name )
-                #we will need to stage in metadata file names also
-                #TODO: would be better to only stage in metadata files that are actually needed (found in command line, referenced in config files, etc.)
-                for key, value in da.dataset.metadata.items():
-                    if isinstance( value, model.MetadataFile ):
-                        filenames.append( value.file_name )
+                filenames.extend(self.get_input_dataset_fnames(da.dataset))
         return filenames
 
     def get_output_fnames( self ):
-        if self.output_paths is not None:
-            return self.output_paths
+        if self.output_paths is None:
+            self.compute_outputs()
+        return self.output_paths
 
+    def get_output_datasets_and_fnames( self ):
+        if self.output_dataset_paths is None:
+            self.compute_outputs()
+        return self.output_dataset_paths
+
+    def compute_outputs( self ) :
         class DatasetPath( object ):
             def __init__( self, dataset_id, real_path, false_path = None ):
                 self.dataset_id = dataset_id
@@ -688,19 +701,25 @@ class JobWrapper( object ):
         job = self.get_job()
         # Job output datasets are combination of output datasets, library datasets, and jeha datasets.
         jeha = self.sa_session.query( model.JobExportHistoryArchive ).filter_by( job=job ).first()
+        jeha_false_path = None
         if self.app.config.outputs_to_working_directory:
             self.output_paths = []
+            output_dataset_paths = {}
             for name, data in [ ( da.name, da.dataset.dataset ) for da in job.output_datasets + job.output_library_datasets ]:
                 false_path = os.path.abspath( os.path.join( self.working_directory, "galaxy_dataset_%d.dat" % data.id ) )
-                self.output_paths.append( DatasetPath( data.id, data.file_name, false_path ) )
+                dsp = DatasetPath( data.id, data.file_name, false_path )
+                self.output_paths.append( dsp )
+                self.output_dataset_paths[name] = data,  dsp
             if jeha:
-                false_path = os.path.abspath( os.path.join( self.working_directory, "galaxy_dataset_%d.dat" % jeha.dataset.id ) )
-                self.output_paths.append( DatasetPath( jeha.dataset.id, jeha.dataset.file_name, false_path ) )
+                jeha_false_path = os.path.abspath( os.path.join( self.working_directory, "galaxy_dataset_%d.dat" % jeha.dataset.id ) )
         else:
-            self.output_paths = [ DatasetPath( da.dataset.dataset.id, da.dataset.file_name ) for da in job.output_datasets + job.output_library_datasets ]
-            if jeha:
-                self.output_paths.append( DatasetPath( jeha.dataset.id, jeha.dataset.file_name ) )
-
+            results = [ (da.name,  da.dataset,  DatasetPath( da.dataset.dataset.id, da.dataset.file_name )) for da in job.output_datasets + job.output_library_datasets ]
+            self.output_paths = [t[2] for t in results]
+            self.output_dataset_paths = dict([(t[0],  t[1:]) for t in results])
+            
+        if jeha:
+            dsp = DatasetPath( jeha.dataset.id, jeha.dataset.file_name, jeha_false_path )
+            self.output_paths.append( dsp )
         return self.output_paths
 
     def get_output_file_id( self, file ):
@@ -807,12 +826,7 @@ class TaskWrapper(JobWrapper):
     def __init__(self, task, queue):
         super(TaskWrapper, self).__init__(task.job, queue)
         self.task_id = task.id
-        self.parallelism = None
-        if task.part_file:
-            #do this better
-            self.working_directory = os.path.dirname(task.part_file)
-        else:
-            self.working_directory = None
+        self.working_directory = task.working_directory
         self.status = task.states.NEW
 
     def get_job( self ):
diff --git a/lib/galaxy/jobs/runners/tasks.py b/lib/galaxy/jobs/runners/tasks.py
index ff2238d2383..26726456002 100644
--- a/lib/galaxy/jobs/runners/tasks.py
+++ b/lib/galaxy/jobs/runners/tasks.py
@@ -60,71 +60,58 @@ class TaskedJobRunner( object ):
         if command_line:
             try:
                 # DBTODO read tool info and use the right kind of parallelism.  
-                # For now, the only splitter is the 'basic' one, n-ways split on one input, one output.
-                # This is incredibly simplified.  Parallelism ultimately needs to describe which inputs, how, etc.
+                # For now, the only splitter is the 'basic' one
                 job_wrapper.change_state( model.Job.states.RUNNING )
                 self.sa_session.flush()
-                parent_job = job_wrapper.get_job()
                 # Split with the tool-defined method.
-                if job_wrapper.tool.parallelism == "basic":
-                    from galaxy.jobs.splitters import basic
-                    if len(job_wrapper.get_input_fnames()) > 1 or len(job_wrapper.get_output_fnames()) > 1:
-                        log.error("The basic splitter is not capable of handling jobs with multiple inputs or outputs.")
-                        job_wrapper.change_state( model.Job.states.ERROR )
-                        job_wrapper.fail("Job Splitting Failed, the basic splitter only handles tools with one input and one output")
-                        # Requeue as a standard job?
-                        return
-                    input_file = job_wrapper.get_input_fnames()[0]
-                    working_directory = job_wrapper.working_directory
-                    # DBTODO execute an external task to do the splitting, this should happen at refactor.
-                    # Regarding number of ways split, use "hints" in tool config?
-                    # If the number of tasks is sufficiently high, we can use it to calculate job completion % and give a running status.
-                    basic.split(input_file, working_directory, 
-                                        20, #Needs serious experimentation to find out what makes the most sense.
-                                        parent_job.input_datasets[0].dataset.ext)
-                    # Tasks in this parts list are in alphabetical listdir order (15 before 5), but that should not matter.
-                    parts = [os.path.join(os.path.abspath(job_wrapper.working_directory), p, os.path.basename(input_file)) 
-                                for p in os.listdir(job_wrapper.working_directory) 
-                                if p.startswith('task_')]
-                else:
+                try:
+                    splitter = getattr(__import__('galaxy.jobs.splitters',  globals(),  locals(),  [job_wrapper.tool.parallelism.method]),  job_wrapper.tool.parallelism.method)
+                except:   
                     job_wrapper.change_state( model.Job.states.ERROR )
                     job_wrapper.fail("Job Splitting Failed, no match for '%s'" % job_wrapper.tool.parallelism)
-                # Assemble parts into task_wrappers
+                    return
+                tasks = splitter.do_split(job_wrapper)
 
                 # Not an option for now.  Task objects don't *do* anything useful yet, but we'll want them tracked outside this thread to do anything.
                 # if track_tasks_in_database:
-                tasks = []
                 task_wrappers = []
-                for part in parts:
-                    task = model.Task(parent_job, part)
+                for task in tasks:
                     self.sa_session.add(task)
-                    tasks.append(task)
                 self.sa_session.flush()
+                
                 # Must flush prior to the creation and queueing of task wrappers.
                 for task in tasks:
                     tw = TaskWrapper(task, job_wrapper.queue)
                     task_wrappers.append(tw)
                     self.app.job_manager.dispatcher.put(tw)
                 tasks_incomplete = False
+                count_complete = 0
                 sleep_time = 1
+                # sleep/loop until no more progress can be made. That is when
+                # all tasks are one of { OK, ERROR, DELETED }
+                completed_states = [ model.Task.states.OK, \
+                                    model.Task.states.ERROR, \
+                                    model.Task.states.DELETED ]
+                # TODO: Should we report an error (and not merge outputs) if one of the subtasks errored out?
+                # Should we prevent any that are pending from being started in that case?
                 while tasks_incomplete is False:
+                    count_complete = 0
                     tasks_incomplete = True
                     for tw in task_wrappers:
-                        if not tw.get_state() == model.Task.states.OK:
+                        task_state = tw.get_state()
+                        if not task_state in completed_states:
                             tasks_incomplete = False
-                    sleep( sleep_time )
-                    if sleep_time < 8:
-                        sleep_time *= 2
-                output_filename = job_wrapper.get_output_fnames()[0].real_path
-                basic.merge(working_directory, output_filename)
-                log.debug('execution finished: %s' % command_line)
-                for tw in task_wrappers:
-                    # Prevent repetitive output, e.g. "Sequence File Aligned"x20
-                    # Eventually do a reduce for jobs that output "N reads mapped", combining all N for tasks.
-                    if stdout.strip() != tw.get_task().stdout.strip():
-                        stdout += tw.get_task().stdout
-                    if stderr.strip() != tw.get_task().stderr.strip():                        
-                        stderr += tw.get_task().stderr
+                        else:
+                            count_complete = count_complete + 1
+                    if tasks_incomplete is False:
+                        # log.debug('Tasks complete: %s. Sleeping %s' % (count_complete, sleep_time))
+                        sleep( sleep_time )
+                        if sleep_time < 8:
+                            sleep_time *= 2
+                
+                log.debug('execution finished - beginning merge: %s' % command_line)
+                stdout,  stderr = splitter.do_merge(job_wrapper,  task_wrappers)
+                
             except Exception:
                 job_wrapper.fail( "failure running job", exception=True )
                 log.exception("failure running job %d" % job_wrapper.job_id)
diff --git a/lib/galaxy/jobs/splitters/basic.py b/lib/galaxy/jobs/splitters/basic.py
index 4d1756c67e6..4ddbc83d429 100644
--- a/lib/galaxy/jobs/splitters/basic.py
+++ b/lib/galaxy/jobs/splitters/basic.py
@@ -1,91 +1,23 @@
-import os, logging
+import logging
+import multi
+
 log = logging.getLogger( __name__ )
 
-def _file_len(fname):
-    i = 0
-    f = open(fname)
-    for i, l in enumerate(f):
-        pass
-    f.close()
-    return i + 1
+def set_basic_defaults(job_wrapper):
+    parent_job = job_wrapper.get_job()
+    job_wrapper.tool.parallelism.attributes['split_inputs'] = parent_job.input_datasets[0].name
+    job_wrapper.tool.parallelism.attributes['merge_outputs'] = job_wrapper.get_output_datasets_and_fnames().keys()[0]
 
-def _fq_seq_count(fname):
-    count = 0
-    f = open(fname)
-    for i, l in enumerate(f):
-        if l.startswith('@'):
-            count += 1
-    f.close()
-    return count
-
-def split_fq(input_file, working_directory, parts):
-    # Temporary, switch this to use the fq reader in lib/galaxy_utils/sequence.
-    outputs = []
-    length = _fq_seq_count(input_file)
-    if length < 1:
-        return outputs
-    if length < parts:
-        parts = length
-    len_each, remainder = divmod(length, parts)
-    f = open(input_file, 'rt')
-    for p in range(0, parts):
-        part_dir = os.path.join( os.path.abspath(working_directory), 'task_%s' % p)
-        if not os.path.exists( part_dir ):
-            os.mkdir( part_dir )
-        part_path = os.path.join(part_dir, os.path.basename(input_file))
-        part_file = open(part_path, 'w')
-        for l in range(0, len_each):
-            part_file.write(f.readline())
-            part_file.write(f.readline())
-            part_file.write(f.readline())
-            part_file.write(f.readline())
-        if remainder > 0:
-            part_file.write(f.readline())
-            part_file.write(f.readline())
-            part_file.write(f.readline())
-            part_file.write(f.readline())
-            remainder -= 1
-        outputs.append(part_path)
-        part_file.close()
-    f.close()
-    return outputs
-
-def split_txt(input_file, working_directory, parts):
-    outputs = []
-    length = _file_len(input_file)
-    if length < parts:
-        parts = length
-    len_each, remainder = divmod(length, parts)
-    f = open(input_file, 'rt')
-    for p in range(0, parts):
-        part_dir = os.path.join( os.path.abspath(working_directory), 'task_%s' % p)
-        if not os.path.exists( part_dir ):
-            os.mkdir( part_dir )
-        part_path = os.path.join(part_dir, os.path.basename(input_file))
-        part_file = open(part_path, 'w')
-        for l in range(0, len_each):
-            part_file.write(f.readline())
-        if remainder > 0:
-            part_file.write(f.readline())
-            remainder -= 1
-        outputs.append(part_path)
-        part_file.close()
-    f.close()
-    return outputs
+def do_split (job_wrapper):
+    if len(job_wrapper.get_input_fnames()) > 1 or len(job_wrapper.get_output_fnames()) > 1:
+        log.error("The basic splitter is not capable of handling jobs with multiple inputs or outputs.")
+        raise Exception,  "Job Splitting Failed, the basic splitter only handles tools with one input and one output"
+    # add in the missing information for splitting the one input and merging the one output
+    set_basic_defaults(job_wrapper)
+    return multi.do_split(job_wrapper)
     
-def split( input_file, working_directory, parts, file_type = None):
-    #Implement a better method for determining how to split.
-    if file_type.startswith('fastq'):
-        return split_fq(input_file, working_directory, parts)
-    else:
-        return split_txt(input_file, working_directory, parts)
+def do_merge( job_wrapper,  task_wrappers):
+    # add in the missing information for splitting the one input and merging the one output
+    set_basic_defaults(job_wrapper)
+    return multi.do_merge(job_wrapper,  task_wrappers)
     
-def merge( working_directory, output_file ):
-    output_file_name = os.path.basename(output_file)
-    task_dirs = [os.path.join(working_directory, x) for x in os.listdir(working_directory) if x.startswith('task_')]
-    task_dirs.sort(key = lambda x: int(x.split('task_')[-1]))
-    for task_dir in task_dirs:
-        try:
-            os.system( 'cat %s >> %s' % ( os.path.join(task_dir, output_file_name), output_file ) )
-        except Exception, e:
-            log.error(str(e))
diff --git a/lib/galaxy/jobs/splitters/multi.py b/lib/galaxy/jobs/splitters/multi.py
new file mode 100644
index 00000000000..71df3058e76
--- /dev/null
+++ b/lib/galaxy/jobs/splitters/multi.py
@@ -0,0 +1,149 @@
+import os, logging,  shutil
+from galaxy import model
+
+log = logging.getLogger( __name__ )
+    
+def do_split (job_wrapper):
+    parent_job = job_wrapper.get_job()
+    working_directory = os.path.abspath(job_wrapper.working_directory)
+
+    parallel_settings = job_wrapper.tool.parallelism.attributes
+    # Syntax: split_inputs="input1,input2" shared_inputs="genome" 
+    # Designates inputs to be split or shared
+    split_inputs=parallel_settings.get("split_inputs")
+    if split_inputs is None:
+        split_inputs = []
+    else:
+        split_inputs = [x.strip() for x in split_inputs.split(",")]
+
+    shared_inputs=parallel_settings.get("shared_inputs")
+    if shared_inputs is None:
+        shared_inputs = []
+    else:
+        shared_inputs = [x.strip() for x in shared_inputs.split(",")]
+    illegal_inputs = [x for x in shared_inputs if x in split_inputs]
+    if len(illegal_inputs) > 0:
+        raise Exception("Inputs have conflicting parallelism attributes: %s" % str( illegal_inputs ))
+    
+    subdir_index = [0] # use a list to get around Python 2.x lame closure support
+    task_dirs = []
+    def get_new_working_directory_name():
+        dir=os.path.join(working_directory,  'task_%d' % subdir_index[0])
+        subdir_index[0] = subdir_index[0] + 1
+        if not os.path.exists(dir):
+            os.makedirs(dir)
+        task_dirs.append(dir)
+        return dir
+    
+    # For things like paired end alignment, we need two inputs to be split. Since all inputs to all
+    # derived subtasks need to be correlated, allow only one input type to be split
+    type_to_input_map = {}
+    for input in parent_job.input_datasets:
+        if input.name in split_inputs:
+            type_to_input_map.setdefault(input.dataset.datatype,  []).append(input.name)
+        elif input.name in shared_inputs:
+            pass # pass original file name
+        else:
+            log_error = "The input '%s' does not define a method for implementing parallelism" % str(input.name)
+            log.error(log_error)
+            raise Exception(log_error)
+
+    if len(type_to_input_map) > 1:
+        log_error = "The multi splitter does not support splitting inputs of more than one type"
+        log.error(log_error)
+        raise Exception(log_error)
+    
+    # split the first one to build up the task directories
+    input_files = []
+    for input in parent_job.input_datasets:
+        if input.name in split_inputs:
+            this_input_files = job_wrapper.get_input_dataset_fnames(input.dataset)
+            if len(this_input_files) > 1:
+                log_error = "The input '%s' is composed of multiple files - splitting is not allowed" % str(input.name)
+                log.error(log_error)
+                raise Exception(log_error)
+            input_files.extend(this_input_files)    
+    
+    input_type = type_to_input_map.keys()[0]
+    # DBTODO execute an external task to do the splitting, this should happen at refactor.
+    # If the number of tasks is sufficiently high, we can use it to calculate job completion % and give a running status.
+    try:
+        input_type.split(input_files, get_new_working_directory_name, parallel_settings)
+    except AttributeError:
+        log_error = "The type '%s' does not define a method for splitting files" % str(input_type)
+        log.error(log_error)
+        raise
+    log.debug('do_split created %d parts' % len(task_dirs))
+    # next, after we know how many divisions there are, add the shared inputs via soft links
+    for input in parent_job.input_datasets:
+        if input and input.name in shared_inputs:
+            names = job_wrapper.get_input_dataset_fnames(input.dataset)
+            for dir in task_dirs:
+                for file in names:
+                    os.symlink(file, os.path.join(dir,  os.path.basename(file)))
+    tasks = []
+    for dir in task_dirs:
+        task = model.Task(parent_job, dir)
+        tasks.append(task)
+    return tasks
+                               
+
+def do_merge( job_wrapper,  task_wrappers):
+    parent_job = job_wrapper.get_job()
+    parallel_settings = job_wrapper.tool.parallelism.attributes
+    # Syntax: merge_outputs="export" pickone_outputs="genomesize"
+    # Designates outputs to be merged, or selected from as a representative
+    merge_outputs = parallel_settings.get("merge_outputs")
+    if merge_outputs is None:
+        merge_outputs = []
+    else:
+        merge_outputs = [x.strip() for x in merge_outputs.split(",")]
+    pickone_outputs = parallel_settings.get("pickone_outputs")
+    if pickone_outputs is None:
+        pickone_outputs = []
+    else:
+        pickone_outputs = [x.strip() for x in pickone_outputs.split(",")]
+    
+    illegal_outputs = [x for x in merge_outputs if x in pickone_outputs]
+    if len(illegal_outputs) > 0:
+        raise Exception("Outputs have conflicting parallelism attributes: %s" % str( illegal_outputs ))
+
+    
+    working_directory = job_wrapper.working_directory
+    task_dirs = [os.path.join(working_directory, x) for x in os.listdir(working_directory) if x.startswith('task_')]
+    # TODO: Output datasets can be very complex. This doesn't handle metadata files
+    outputs = job_wrapper.get_output_datasets_and_fnames()
+    pickone_done = []
+    task_dirs = [os.path.join(working_directory, x) for x in os.listdir(working_directory) if x.startswith('task_')]
+    for output in outputs:
+        output_file_name = str(outputs[output][1])
+        base_output_name = os.path.basename(output_file_name)
+        if output in merge_outputs:
+            output_type = outputs[output][0].datatype
+            output_files = [os.path.join(dir,base_output_name) for dir in task_dirs]
+            log.debug('files %s ' % output_files)
+            output_type.merge(output_files, output_file_name)
+            log.debug('merge finished: %s' % output_file_name)
+            pass # TODO: merge all the files
+        elif output in pickone_outputs:
+            # just pick one of them
+            if output not in pickone_done:
+                task_file_name = os.path.join(task_dirs[0], base_output_name)
+                shutil.move( task_file_name,  output_file_name )
+                pickone_done.append(output)
+        else:
+            log_error = "The output '%s' does not define a method for implementing parallelism" % output
+            log.error(log_error)
+            raise Exception(log_error)
+
+    stdout = ''
+    stderr=''
+    for tw in task_wrappers:
+        # Prevent repetitive output, e.g. "Sequence File Aligned"x20
+        # Eventually do a reduce for jobs that output "N reads mapped", combining all N for tasks.
+        if stdout.strip() != tw.get_task().stdout.strip():
+            stdout += tw.get_task().stdout
+        if stderr.strip() != tw.get_task().stderr.strip():                        
+            stderr += tw.get_task().stderr
+    return (stdout,  stderr)
+    
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 98448694c65..b2be39f43e2 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -176,12 +176,23 @@ class Task( object ):
         self.parameters = []
         self.state = Task.states.NEW
         self.info = None
+        # TODO: Rename this to working_directory
+        # Does this necessitate a DB migration step?
         self.part_file = part_file
         self.task_runner_name = None
         self.task_runner_external_id = None
         self.job = job
         self.stdout = None
         self.stderr = None
+    
+    @property
+    def working_directory(self):
+        if self.part_file is not None:
+            if not os.path.isdir(self.part_file):
+                return os.path.dirname(self.part_file)
+            else:
+                return self.part_file
+        return None
 
     def set_state( self, state ):
         self.state = state
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index c03b2df4e33..da6a6fd3b08 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -321,6 +321,21 @@ class ToolRequirement( object ):
         self.type = None
         self.version = None
 
+class ToolParallelismInfo(object):
+    """
+    Stores the information (if any) for running multiple instances of the tool in parallel
+    on the same set of inputs.
+    """
+    def __init__(self, tag):
+        self.method = tag.get('method')
+        self.attributes = dict([item for item in tag.attrib.items() if item[0] != 'method' ])
+        if len(self.attributes) == 0:
+            # legacy basic mode - provide compatible defaults
+            self.attributes['split_size'] = 20
+            self.attributes['split_mode'] = 'number_of_parts'
+            
+        
+    
 class Tool:
     """
     Represents a computational tool that can be executed through Galaxy. 
@@ -403,7 +418,7 @@ class Tool:
         # Parallelism for tasks, read from tool config.
         parallelism = root.find("parallelism")
         if parallelism is not None and parallelism.get("method"):
-            self.parallelism = parallelism.get("method")
+            self.parallelism = ToolParallelismInfo(parallelism)
         else:
             self.parallelism = None
         if self.app.config.start_job_runners is None:

From 4c06b01d209aca07e947113434fa822047edbcd9 Mon Sep 17 00:00:00 2001
From: John Duddy <jduddy@illumina.com>
Date: Wed, 25 May 2011 10:45:53 -0700
Subject: [PATCH 002/362] Remove zcat + gzip -c for merging gz files. Go with
 cat for now

---
 lib/galaxy/datatypes/data.py | 19 +++----------------
 1 file changed, 3 insertions(+), 16 deletions(-)

diff --git a/lib/galaxy/datatypes/data.py b/lib/galaxy/datatypes/data.py
index 9e0cf4c0b41..77983cc59dc 100644
--- a/lib/galaxy/datatypes/data.py
+++ b/lib/galaxy/datatypes/data.py
@@ -1,4 +1,4 @@
-import logging, os, sys, time, tempfile,  gzip
+import logging, os, sys, time, tempfile
 from galaxy import util
 from galaxy.util.odict import odict
 from galaxy.util.bunch import Bunch
@@ -356,24 +356,11 @@ class Data( object ):
 
     def merge( split_files, output_file): 
         """
-        Export files are usually compressed, but it doesn't have to be so. In the case that they are, use
-        zcat to cat the files and gzip -c to recompress the result, otherwise use cat
-        TODO: Move to a faster gzjoin-based technique
+        TODO: Do we need to merge gzip files using gzjoin? cat seems to work,
+        but might be brittle. Need to revisit this.
         """
-        #TODO: every time I try to import this from sniff, the parser dies
-        def is_gzip( filename ):
-            temp = open( filename, "U" )
-            magic_check = temp.read( 2 )
-            temp.close()
-            if magic_check != util.gzip_magic:
-                return False
-            return True
-        
         if len(split_files) == 1:
             os.system( 'mv -f %s %s' % ( split_files[0], output_file ) )
-            return
-        if is_gzip(split_files[0]):
-            os.system( 'zcat %s | gzip -c > %s' % ( ' '.join(split_files), output_file ) )
         else:
             os.system( 'cat %s > %s' % ( ' '.join(split_files), output_file ) )
     merge = staticmethod(merge)

From 97660b81d623b2dc41034d41bc7e604061380847 Mon Sep 17 00:00:00 2001
From: John Duddy <jduddy@illumina.com>
Date: Thu, 16 Jun 2011 12:19:07 -0700
Subject: [PATCH 003/362] Add ability to split compressed input Fix off by one
 error on number_of_parts splitting

---
 lib/galaxy/datatypes/sequence.py | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/datatypes/sequence.py b/lib/galaxy/datatypes/sequence.py
index 42bace94afc..0988cb64f35 100644
--- a/lib/galaxy/datatypes/sequence.py
+++ b/lib/galaxy/datatypes/sequence.py
@@ -2,6 +2,7 @@
 Sequence classes
 """
 
+import gzip
 import data
 import logging
 import re
@@ -58,17 +59,22 @@ class Sequence( data.Text ):
             return
         
         def split_one( input_file, get_dir, clusters_per_file,  default_clusters=None):
-            in_file = open(input_file, 'rt')
+            compress = is_gzip(input_file)
+            if compress:
+# TODO: Python 2.4, 2.5 don't have io.BufferedReader!!!
+# add a buffered reader because gzip is really slow before python 2.7
+                in_file = gzip.GzipFile(input_file, 'r')
+            else:
+                in_file = open(input_file, 'rt')
             part_file = None
             part = 0
             if clusters_per_file is None:
                 local_clusters_per_file = [default_clusters]
             else:
                 local_clusters_per_file = [x for x in clusters_per_file] 
-                
             for i, line in enumerate(in_file):
                 cluster_number,  line_in_cluster = divmod(i, 4)
-                current_part, remainder = divmod(cluster_number, local_clusters_per_file[part])
+                current_part, remainder = divmod(cluster_number, local_clusters_per_file[part]+1)
                 
                 if (current_part != part or part_file is None):
                     if (part_file):
@@ -76,6 +82,7 @@ class Sequence( data.Text ):
                     part = current_part
                     part_dir = get_dir()
                     part_path = os.path.join(part_dir, os.path.basename(input_file))
+# TODO: If the input was compressed, compress the output?
                     part_file = open(part_path, 'w')
                     if clusters_per_file is None:
                         local_clusters_per_file.append(default_clusters)

From 3d43bbc2e38e50356439ac9ab9173a8467644c8f Mon Sep 17 00:00:00 2001
From: John Duddy <jduddy@illumina.com>
Date: Thu, 16 Jun 2011 14:06:06 -0700
Subject: [PATCH 004/362] Fix issues related to splitting multiple inputs and
 handling Files split evenly

---
 lib/galaxy/datatypes/sequence.py | 66 ++++++++++++++++++++++++++------
 1 file changed, 55 insertions(+), 11 deletions(-)

diff --git a/lib/galaxy/datatypes/sequence.py b/lib/galaxy/datatypes/sequence.py
index 0988cb64f35..80e1324965e 100644
--- a/lib/galaxy/datatypes/sequence.py
+++ b/lib/galaxy/datatypes/sequence.py
@@ -58,7 +58,10 @@ class Sequence( data.Text ):
         if split_params is None:
             return
         
-        def split_one( input_file, get_dir, clusters_per_file,  default_clusters=None):
+        def split_calculate_clusters( input_file, get_dir, default_clusters):
+            """
+            Split the 0th file into even sized chunks, and return the number of clusters in each
+            """
             compress = is_gzip(input_file)
             if compress:
 # TODO: Python 2.4, 2.5 don't have io.BufferedReader!!!
@@ -68,13 +71,10 @@ class Sequence( data.Text ):
                 in_file = open(input_file, 'rt')
             part_file = None
             part = 0
-            if clusters_per_file is None:
-                local_clusters_per_file = [default_clusters]
-            else:
-                local_clusters_per_file = [x for x in clusters_per_file] 
+            local_clusters_per_file = []
             for i, line in enumerate(in_file):
                 cluster_number,  line_in_cluster = divmod(i, 4)
-                current_part, remainder = divmod(cluster_number, local_clusters_per_file[part]+1)
+                current_part, remainder = divmod(cluster_number, default_clusters)
                 
                 if (current_part != part or part_file is None):
                     if (part_file):
@@ -84,8 +84,7 @@ class Sequence( data.Text ):
                     part_path = os.path.join(part_dir, os.path.basename(input_file))
 # TODO: If the input was compressed, compress the output?
                     part_file = open(part_path, 'w')
-                    if clusters_per_file is None:
-                        local_clusters_per_file.append(default_clusters)
+                    local_clusters_per_file.append(default_clusters)
                 part_file.write(line)
             if (part_file):
                 part_file.close()
@@ -93,6 +92,50 @@ class Sequence( data.Text ):
             local_clusters_per_file[part] = remainder + 1
             return local_clusters_per_file
     
+        def split_to_size(input_file, get_dir, clusters_per_file):
+            """
+            Split the files beyond the 0th to the same number of clusters as the 0th.
+            This is used to split in a variety of ways, so these are both legal for
+            clusters_per_file:
+                [ 10000, 10000, 10000, 10000, 2 ] # to_size=10000, 40002 total
+                [ 10001, 10001, 10000, 10000 ] # number_of_parts = 4, 40002 total
+
+            """
+            compress = is_gzip(input_file)
+            if compress:
+# TODO: Python 2.4, 2.5 don't have io.BufferedReader!!!
+# add a buffered reader because gzip is really slow before python 2.7
+                in_file = gzip.GzipFile(input_file, 'r')
+            else:
+                in_file = open(input_file, 'rt')
+            part_file = None
+            part = 0
+            clusters_this_part = 0
+            for i, line in enumerate(in_file):
+                cluster_number,  line_in_cluster = divmod(i, 4)
+                if clusters_this_part  == clusters_per_file[part]:
+                    current_part = part + 1
+                else:
+                    current_part = part
+                
+                if (current_part != part or part_file is None):
+                    if (part_file):
+                        part_file.close()
+                    part = current_part
+                    clusters_this_part = 0
+                    part_dir = get_dir()
+                    part_path = os.path.join(part_dir, os.path.basename(input_file))
+# TODO: If the input was compressed, compress the output?
+                    part_file = open(part_path, 'w')
+                    if clusters_per_file is None and part > 0:
+                        local_clusters_per_file.append(default_clusters)
+                part_file.write(line)
+                if line_in_cluster == 3:
+                    clusters_this_part += 1
+            if (part_file):
+                part_file.close()
+            in_file.close()
+
         directories = []
         def create_subdir():
             dir = subdir_generator_function()
@@ -123,10 +166,11 @@ class Sequence( data.Text ):
                 clusters_per_file.append(chunk)
                 remainder=- 1
                 length -= chunk
-            split_one(input_files[0],  create_subdir,  clusters_per_file)
+            split_to_size(input_files[0],  create_subdir,  clusters_per_file)
         elif split_params['split_mode'] == 'to_size':
             # split one file and see what the cluster sizes turn out to be
-            clusters_per_file = split_one(input_files[0],  create_subdir,  None,  int(split_params['split_size']))
+            clusters_per_file = split_calculate_clusters(input_files[0],  create_subdir,  
+                int(split_params['split_size']))
         else:
             raise Exception('Unsupported split mode %s' % split_params['split_mode'])
         
@@ -141,7 +185,7 @@ class Sequence( data.Text ):
             
         for i in range(1,  len(input_files)):
             current_dir_idx[0] = 0
-            split_one(input_files[i],  get_subdir,  clusters_per_file)
+            split_to_size(input_files[i],  get_subdir,  clusters_per_file)
     split = staticmethod(split)
 
 

From aec48bd6a8f04cb3f7c1e4da00a3e96902b83c65 Mon Sep 17 00:00:00 2001
From: Enis Afgan <afgane@gmail.com>
Date: Tue, 5 Jul 2011 17:48:22 -0400
Subject: [PATCH 005/362] A very much in-progress code implementation of the
 ObjectStore - most of the functionality exists and works for interaction with
 a local file system and S3. Setting of the metadata does not work (empty
 files are created but never filled with content). Not sure if rerunning jobs
 with dependent datasets that have been deleted from cache works - some tools
 at least do.

---
 lib/galaxy/app.py                             |   6 +-
 lib/galaxy/config.py                          |   6 +
 lib/galaxy/datatypes/genetics.py              |   2 +-
 lib/galaxy/jobs/__init__.py                   |  12 +-
 lib/galaxy/model/__init__.py                  | 100 +-
 lib/galaxy/model/mapping.py                   |   4 +-
 lib/galaxy/objectstore/__init__.py            | 859 ++++++++++++++++++
 lib/galaxy/objectstore/s3_multipart_upload.py |  85 ++
 lib/galaxy/tools/__init__.py                  |  43 +-
 lib/galaxy/tools/actions/__init__.py          |   3 +-
 lib/galaxy/tools/actions/upload.py            |   1 -
 lib/galaxy/tools/actions/upload_common.py     |   8 +-
 lib/galaxy/web/controllers/dataset.py         |  42 +-
 lib/galaxy/web/controllers/history.py         |   2 +-
 templates/dataset/display.mako                |  18 +-
 templates/root/history.mako                   |  28 +
 templates/root/history_common.mako            |   2 +-
 17 files changed, 1127 insertions(+), 94 deletions(-)
 create mode 100644 lib/galaxy/objectstore/__init__.py
 create mode 100644 lib/galaxy/objectstore/s3_multipart_upload.py

diff --git a/lib/galaxy/app.py b/lib/galaxy/app.py
index 77e26a37d19..63c65059d99 100644
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -7,6 +7,7 @@ from galaxy.web import security
 import galaxy.model
 import galaxy.datatypes.registry
 import galaxy.security
+from galaxy.objectstore import build_object_store_from_config
 from galaxy.tags.tag_handler import GalaxyTagHandler
 from galaxy.tools.imp_exp import load_history_imp_exp_tools
 from galaxy.sample_tracking import external_service_types
@@ -30,12 +31,15 @@ class UniverseApplication( object ):
         # Initialize database / check for appropriate schema version
         from galaxy.model.migrate.check import create_or_verify_database
         create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options )
+        # Object store manager
+        self.object_store = build_object_store_from_config(self)
         # Setup the database engine and ORM
         from galaxy.model import mapping
         self.model = mapping.init( self.config.file_path,
                                    db_url,
                                    self.config.database_engine_options,
-                                   database_query_profiling_proxy = self.config.database_query_profiling_proxy )
+                                   database_query_profiling_proxy = self.config.database_query_profiling_proxy,
+                                   object_store = self.object_store )
         # Security helper
         self.security = security.SecurityHelper( id_secret=self.config.id_secret )
         # Tag handler
diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py
index ff69704f8a9..3987d495826 100644
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -131,6 +131,12 @@ class Configuration( object ):
         self.nginx_upload_path = kwargs.get( 'nginx_upload_path', False )
         if self.nginx_upload_store:
             self.nginx_upload_store = os.path.abspath( self.nginx_upload_store )
+        self.object_store = kwargs.get( 'object_store', 'disk' )
+        self.aws_access_key = kwargs.get( 'aws_access_key', None )
+        self.aws_secret_key = kwargs.get( 'aws_secret_key', None )
+        self.s3_bucket = kwargs.get( 's3_bucket', None)
+        self.use_reduced_redundancy = kwargs.get( 'use_reduced_redundancy', False )
+        self.object_store_cache_size = float(kwargs.get( 'object_store_cache_size', -1 ))
         # Parse global_conf and save the parser
         global_conf = kwargs.get( 'global_conf', None )
         global_conf_parser = ConfigParser.ConfigParser()
diff --git a/lib/galaxy/datatypes/genetics.py b/lib/galaxy/datatypes/genetics.py
index 5f9d8b4f712..8a5059b84cc 100644
--- a/lib/galaxy/datatypes/genetics.py
+++ b/lib/galaxy/datatypes/genetics.py
@@ -636,7 +636,7 @@ class RexpBase( Html ):
     def set_peek( self, dataset, **kwd ):
         """
         expects a .pheno file in the extra_files_dir - ugh
-        note that R is wierd and does not include the row.name in
+        note that R is weird and does not include the row.name in
         the header. why?"""
         if not dataset.dataset.purged:
             pp = os.path.join(dataset.extra_files_path,'%s.pheno' % dataset.metadata.base_name)
diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 649e38eff7f..1f7ff18d6d2 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -208,7 +208,7 @@ class JobQueue( object ):
                     log.error( "unknown job state '%s' for job %d" % ( job_state, job.id ) )
                     if not self.track_jobs_in_database:
                         new_waiting_jobs.append( job.id )
-            except Exception, e:
+            except Exception:
                 log.exception( "failure running job %d" % job.id )
         # Update the waiting list
         self.waiting_jobs = new_waiting_jobs
@@ -332,7 +332,6 @@ class JobWrapper( object ):
         out_data = dict( [ ( da.name, da.dataset ) for da in job.output_datasets ] )
         inp_data.update( [ ( da.name, da.dataset ) for da in job.input_library_datasets ] )
         out_data.update( [ ( da.name, da.dataset ) for da in job.output_library_datasets ] )
-        
         # Set up output dataset association for export history jobs. Because job 
         # uses a Dataset rather than an HDA or LDA, it's necessary to set up a 
         # fake dataset association that provides the needed attributes for
@@ -428,6 +427,10 @@ class JobWrapper( object ):
                 dataset.dataset.set_total_size()
                 if dataset.ext == 'auto':
                     dataset.extension = 'data'
+                # Update (non-library) job output datasets through the object store
+                if dataset not in job.output_library_datasets:
+                    print "====== Handing failed job's dataset '%s' with name '%s' to object store" % (dataset.id, dataset.file_name)
+                    self.app.object_store.update_from_file(dataset.id, create=True)
                 self.sa_session.add( dataset )
                 self.sa_session.flush()
             job.state = model.Job.states.ERROR
@@ -538,11 +541,14 @@ class JobWrapper( object ):
                             else:
                                 # Security violation.
                                 log.exception( "from_work_dir specified a location not in the working directory: %s, %s" % ( source_file, self.working_directory ) )
-            
                 dataset.blurb = 'done'
                 dataset.peek  = 'no peek'
                 dataset.info  = context['stdout'] + context['stderr']
                 dataset.set_size()
+                # Update (non-library) job output datasets through the object store
+                if dataset not in job.output_library_datasets:
+                    print "===+=== Handing dataset '%s' with name '%s' to object store" % (dataset.id, dataset.file_name)
+                    self.app.object_store.update_from_file(dataset.id, create=True)
                 if context['stderr']:
                     dataset.blurb = "error"
                 elif dataset.has_data():
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 0219ff09256..493f64ce91e 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -522,6 +522,7 @@ class Dataset( object ):
                     FAILED_METADATA = 'failed_metadata' )
     permitted_actions = get_permitted_actions( filter='DATASET' )
     file_path = "/tmp/"
+    object_store = None # This get initialized in mapping.py (method init) by app.py
     engine = None
     def __init__( self, id=None, state=None, external_filename=None, extra_files_path=None, file_size=None, purgable=True ):
         self.id = id
@@ -535,17 +536,14 @@ class Dataset( object ):
     def get_file_name( self ):
         if not self.external_filename:
             assert self.id is not None, "ID must be set before filename used (commit the object)"
-            # First try filename directly under file_path
-            filename = os.path.join( self.file_path, "dataset_%d.dat" % self.id )
-            # Only use that filename if it already exists (backward compatibility),
-            # otherwise construct hashed path
-            if not os.path.exists( filename ):
-                dir = os.path.join( self.file_path, *directory_hash_id( self.id ) )
+            assert self.object_store is not None, "Object Store has not been initialized for dataset %s" % self.id
+            print "Calling get_filename 1", self.object_store
+            filename = self.object_store.get_filename( self.id )
+            # print 'getting filename: ', filename
+            if not self.object_store.exists( self.id ):
                 # Create directory if it does not exist
-                if not os.path.exists( dir ):
-                    os.makedirs( dir )
-                # Return filename inside hashed directory
-                return os.path.abspath( os.path.join( dir, "dataset_%d.dat" % self.id ) )
+                self.object_store.create( self.id, dir_only=True )
+            return filename
         else:
             filename = self.external_filename
         # Make filename absolute
@@ -558,15 +556,8 @@ class Dataset( object ):
     file_name = property( get_file_name, set_file_name )
     @property
     def extra_files_path( self ):
-        if self._extra_files_path: 
-            path = self._extra_files_path
-        else:
-            path = os.path.join( self.file_path, "dataset_%d_files" % self.id )
-            #only use path directly under self.file_path if it exists
-            if not os.path.exists( path ):
-                path = os.path.join( os.path.join( self.file_path, *directory_hash_id( self.id ) ), "dataset_%d_files" % self.id )
-        # Make path absolute
-        return os.path.abspath( path )
+        print "Calling get_filename 2", self.object_store
+        return self.object_store.get_filename( self.id, dir_only=True, extra_dir=self._extra_files_path or "dataset_%d_files" % self.id)
     def get_size( self, nice_size=False ):
         """Returns the size of the data on disk"""
         if self.file_size:
@@ -575,20 +566,14 @@ class Dataset( object ):
             else:
                 return self.file_size
         else:
-            try:
-                if nice_size:
-                    return galaxy.datatypes.data.nice_size( os.path.getsize( self.file_name ) )
-                else:
-                    return os.path.getsize( self.file_name )
-            except OSError:
-                return 0
+            if nice_size:
+                return galaxy.datatypes.data.nice_size( self.object_store.size(self.id) )
+            else:
+                return self.object_store.size(self.id)
     def set_size( self ):
         """Returns the size of the data on disk"""
-        try:
-            if not self.file_size:
-                self.file_size = os.path.getsize( self.file_name )
-        except OSError:
-            self.file_size = 0
+        if not self.file_size:
+            self.file_size = self.object_store.size(self.id)
     def get_total_size( self ):
         if self.total_size is not None:
             return self.total_size
@@ -603,8 +588,9 @@ class Dataset( object ):
         if self.file_size is None:
             self.set_size()
         self.total_size = self.file_size or 0
-        for root, dirs, files in os.walk( self.extra_files_path ):
-            self.total_size += sum( [ os.path.getsize( os.path.join( root, file ) ) for file in files ] )
+        if self.object_store.exists(self.id, extra_dir=self._extra_files_path or "dataset_%d_files" % self.id, dir_only=True):
+            for root, dirs, files in os.walk( self.extra_files_path ):
+                self.total_size += sum( [ os.path.getsize( os.path.join( root, file ) ) for file in files ] )
     def has_data( self ):
         """Detects whether there is any data"""
         return self.get_size() > 0
@@ -620,10 +606,7 @@ class Dataset( object ):
     # FIXME: sqlalchemy will replace this
     def _delete(self):
         """Remove the file that corresponds to this data"""
-        try:
-            os.remove(self.data.file_name)
-        except OSError, e:
-            log.critical('%s delete error %s' % (self.__class__.__name__, e))
+        self.object_store.delete(self.id)
     @property
     def user_can_purge( self ):
         return self.purged == False \
@@ -631,9 +614,12 @@ class Dataset( object ):
                 and len( self.history_associations ) == len( self.purged_history_associations )
     def full_delete( self ):
         """Remove the file and extra files, marks deleted and purged"""
-        os.unlink( self.file_name )
-        if os.path.exists( self.extra_files_path ):
-            shutil.rmtree( self.extra_files_path )
+        # os.unlink( self.file_name )
+        self.object_store.delete(self.id)
+        if self.object_store.exists(self.id, extra_dir=self._extra_files_path or "dataset_%d_files" % self.id, dir_only=True):
+            self.object_store.delete(self.id, entire_dir=True, extra_dir=self._extra_files_path or "dataset_%d_files" % self.id, dir_only=True)
+        # if os.path.exists( self.extra_files_path ):
+        #     shutil.rmtree( self.extra_files_path )
         # TODO: purge metadata files
         self.deleted = True
         self.purged = True
@@ -1595,16 +1581,32 @@ class MetadataFile( object ):
     @property
     def file_name( self ):
         assert self.id is not None, "ID must be set before filename used (commit the object)"
-        path = os.path.join( Dataset.file_path, '_metadata_files', *directory_hash_id( self.id ) )
-        # Create directory if it does not exist
+        # Ensure the directory structure and the metadata file object exist
         try:
-            os.makedirs( path )
-        except OSError, e:
-            # File Exists is okay, otherwise reraise
-            if e.errno != errno.EEXIST:
-                raise
-        # Return filename inside hashed directory
-        return os.path.abspath( os.path.join( path, "metadata_%d.dat" % self.id ) )
+            # self.history_dataset
+            # print "Dataset.file_path: %s, self.id: %s, self.history_dataset.dataset.object_store: %s" \
+            #     % (Dataset.file_path, self.id, self.history_dataset.dataset.object_store)
+            self.history_dataset.dataset.object_store.create( self.id, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name="metadata_%d.dat" % self.id )
+            print "Calling get_filename 3", self.object_store
+            path = self.history_dataset.dataset.object_store.get_filename( self.id, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name="metadata_%d.dat" % self.id )
+            print "Created metadata file at path: %s" % path
+            self.library_dataset
+            # raise
+            return path
+        except AttributeError:
+            # In case we're not working with the history_dataset
+            # print "Caught AttributeError"
+            path = os.path.join( Dataset.file_path, '_metadata_files', *directory_hash_id( self.id ) )
+            # Create directory if it does not exist
+            try:
+                os.makedirs( path )
+            except OSError, e:
+                # File Exists is okay, otherwise reraise
+                if e.errno != errno.EEXIST:
+                    raise
+            # Return filename inside hashed directory
+            return os.path.abspath( os.path.join( path, "metadata_%d.dat" % self.id ) )
+    
 
 class FormDefinition( object, APIItem ):
     # The following form_builder classes are supported by the FormDefinition class.
diff --git a/lib/galaxy/model/mapping.py b/lib/galaxy/model/mapping.py
index 06c1ae2d245..7f0837682ce 100644
--- a/lib/galaxy/model/mapping.py
+++ b/lib/galaxy/model/mapping.py
@@ -1709,10 +1709,12 @@ def load_egg_for_url( url ):
         # Let this go, it could possibly work with db's we don't support
         log.error( "database_connection contains an unknown SQLAlchemy database dialect: %s" % dialect )
 
-def init( file_path, url, engine_options={}, create_tables=False, database_query_profiling_proxy=False ):
+def init( file_path, url, engine_options={}, create_tables=False, database_query_profiling_proxy=False, object_store=None ):
     """Connect mappings to the database"""
     # Connect dataset to the file path
     Dataset.file_path = file_path
+    # Connect dataset to object store
+    Dataset.object_store = object_store
     # Load the appropriate db module
     load_egg_for_url( url )
     # Should we use the logging proxy?
diff --git a/lib/galaxy/objectstore/__init__.py b/lib/galaxy/objectstore/__init__.py
new file mode 100644
index 00000000000..076ca8cfbd1
--- /dev/null
+++ b/lib/galaxy/objectstore/__init__.py
@@ -0,0 +1,859 @@
+"""
+objectstore package, abstraction for storing blobs of data for use in Galaxy,
+all providers ensure that data can be accessed on the filesystem for running
+tools
+"""
+
+import os
+import time
+import shutil
+import logging
+import threading
+import subprocess
+import multiprocessing
+from datetime import datetime
+
+from galaxy import util
+from galaxy.jobs import Sleeper
+from galaxy.model import directory_hash_id
+from galaxy.objectstore.s3_multipart_upload import multipart_upload
+
+from boto.s3.key import Key
+from boto.s3.connection import S3Connection
+from boto.exception import S3ResponseError
+
+log = logging.getLogger( __name__ )
+logging.getLogger('boto').setLevel(logging.INFO) # Otherwise boto is quite noisy
+
+
+class ObjectNotFound(Exception):
+    """ Accessed object was not found """
+    pass
+
+
+class ObjectStore(object):
+    """
+    ObjectStore abstract interface
+    """
+    def __init__(self):
+        self.running = True
+    
+    def shutdown(self):
+        self.running = False
+    
+    def exists(self, dataset_id, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None):
+        """
+        Returns True if the object identified by `dataset_id` exists in this 
+        file store, False otherwise.
+        
+        FIELD DESCRIPTIONS (these apply to all the methods in this class):
+        :type dataset_id: int
+        :param dataset_id: Galaxy-assigned database ID of the dataset to be checked.
+        
+        :type dir_only: bool
+        :param dir_only: If True, check only the path where the file
+                         identified by `dataset_id` should be located, not the
+                         dataset itself. This option applies to `extra_dir`
+                         argument as well.
+        
+        :type extra_dir: string
+        :param extra_dir: Append `extra_dir` to the directory structure where
+                          the dataset identified by `dataset_id` should be located.
+                          (e.g., 000/extra_dir/dataset_id)
+        
+        :type extra_dir_at_root: bool
+        :param extra_dir_at_root: Applicable only if `extra_dir` is set.
+                                  If True, the `extra_dir` argument is placed at
+                                  root of the created directory structure rather
+                                  than at the end (e.g., extra_dir/000/dataset_id
+                                  vs. 000/extra_dir/dataset_id)
+        
+        :type alt_name: string
+        :param alt_name: Use this name as the alternative name for the created
+                         dataset rather than the default.
+        """
+        raise NotImplementedError()
+    
+    def file_ready(self, dataset_id, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None):
+        """ A helper method that checks if a file corresponding to a dataset 
+        is ready and available to be used. Return True if so, False otherwise."""
+        return True
+    
+    def create(self, dataset_id, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None):
+        """
+        Mark the object identified by `dataset_id` as existing in the store, but
+        with no content. This method will create a proper directory structure for
+        the file if the directory does not already exist.
+        See `exists` method for the description of the fields.
+        """
+        raise NotImplementedError()
+    
+    def empty(self, dataset_id, extra_dir=None, extra_dir_at_root=False, alt_name=None):
+        """
+        Test if the object identified by `dataset_id` has content.
+        If the object does not exist raises `ObjectNotFound`.
+        See `exists` method for the description of the fields.
+        """
+        raise NotImplementedError()
+    
+    def size(self, dataset_id, extra_dir=None, extra_dir_at_root=False, alt_name=None):
+        """
+        Return size of the object identified by `dataset_id`.
+        If the object does not exist, return 0.
+        See `exists` method for the description of the fields.
+        """
+        raise NotImplementedError()
+    
+    def delete(self, dataset_id, entire_dir=False, extra_dir=None, extra_dir_at_root=False, alt_name=None):
+        """
+        Deletes the object identified by `dataset_id`.
+        See `exists` method for the description of other fields.
+        :type entire_dir: bool
+        :param entire_dir: If True, delete the entire directory pointed to by 
+                           extra_dir. For safety reasons, this option applies
+                           only for and in conjunction with the extra_dir option.
+        """
+        raise NotImplementedError()
+    
+    def get_data(self, dataset_id, start=0, count=-1, extra_dir=None, extra_dir_at_root=False, alt_name=None):
+        """
+        Fetch `count` bytes of data starting at offset `start` from the
+        object identified uniquely by `dataset_id`.
+        If the object does not exist raises `ObjectNotFound`.
+        See `exists` method for the description of other fields.
+        
+        :type start: int
+        :param start: Set the position to start reading the dataset file
+        
+        :type count: int
+        :param count: Read at most `count` bytes from the dataset
+        """
+        raise NotImplementedError()
+    
+    def get_filename(self, dataset_id, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None):
+        """
+        Get the expected filename (including the absolute path) which can be used
+        to access the contents of the object uniquely identified by `dataset_id`.
+        See `exists` method for the description of the fields.
+        """
+        raise NotImplementedError()
+    
+    def update_from_file(self, dataset_id, extra_dir=None, extra_dir_at_root=False, alt_name=None, filename=None, create=False):
+        """
+        Inform the store that the file associated with the object has been
+        updated. If `filename` is provided, update from that file instead
+        of the default.
+        If the object does not exist raises `ObjectNotFound`.
+        See `exists` method for the description of other fields.
+        
+        :type filename: string
+        :param filename: Use file pointed to by `filename` as the source for 
+                         updating the dataset identified by `dataset_id`
+        
+        :type create: bool
+        :param create: If True and the default dataset does not exist, create it first.
+        """
+        raise NotImplementedError()
+    
+    def get_object_url(self, dataset_id, extra_dir=None, extra_dir_at_root=False, alt_name=None):
+        """
+        If the store supports direct URL access, return a URL. Otherwise return
+        None.
+        Note: need to be careful to to bypass dataset security with this.
+        See `exists` method for the description of the fields.
+        """
+        raise NotImplementedError()
+    
+    ## def get_staging_command( id ):
+    ##     """
+    ##     Return a shell command that can be prepended to the job script to stage the
+    ##     dataset -- runs on worker nodes.
+    ##
+    ##     Note: not sure about the interface here. Should this return a filename, command
+    ##     tuple? Is this even a good idea, seems very useful for S3, other object stores?
+    ##     """
+
+
+class DiskObjectStore(ObjectStore):
+    """
+    Standard Galaxy object store, stores objects in files under a specific
+    directory on disk.
+    """
+    def __init__(self, app):
+        super(DiskObjectStore, self).__init__()
+        self.file_path = app.config.file_path
+    
+    def _get_filename(self, dataset_id, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None):
+        """Class method that returns the absolute path for the file corresponding
+        to the `dataset_id` regardless of whether the file exists. 
+        """
+        path = self._construct_path(dataset_id, dir_only=dir_only, extra_dir=extra_dir, extra_dir_at_root=extra_dir_at_root, alt_name=alt_name, old_style=True)
+        # For backward compatibility, check the old style root path first; otherwise, 
+        # construct hashed path
+        if not os.path.exists(path):
+            return self._construct_path(dataset_id, dir_only=dir_only, extra_dir=extra_dir, extra_dir_at_root=extra_dir_at_root, alt_name=alt_name)
+    
+    def _construct_path(self, dataset_id, old_style=False, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None):
+        """ Construct the expected absolute path for accessing the object
+            identified by `dataset_id`.
+        
+        :type dir_only: bool
+        :param dir_only: If True, return only the absolute path where the file
+                         identified by `dataset_id` should be located
+        
+        :type extra_dir: string
+        :param extra_dir: Append the value of this parameter to the expected path
+                          used to access the object identified by `dataset_id`
+                          (e.g., /files/000/<extra_dir>/dataset_10.dat).
+        
+        :type alt_name: string
+        :param alt_name: Use this name as the alternative name for the returned
+                         dataset rather than the default.
+        
+        :type old_style: bool
+        param old_style: This option is used for backward compatibility. If True
+                         the composed directory structure does not include a hash id
+                         (e.g., /files/dataset_10.dat (old) vs. /files/000/dataset_10.dat (new))
+        """
+        if old_style:
+            if extra_dir is not None:
+                path = os.path.join(self.file_path, extra_dir)
+            else:
+                path = self.file_path
+        else:
+            rel_path = os.path.join(*directory_hash_id(dataset_id))
+            if extra_dir is not None:
+                if extra_dir_at_root:
+                    rel_path = os.path.join(extra_dir, rel_path)
+                else:
+                    rel_path = os.path.join(rel_path, extra_dir)
+            path = os.path.join(self.file_path, rel_path)
+        if not dir_only:
+            path = os.path.join(path, alt_name if alt_name else "dataset_%s.dat" % dataset_id)
+        return os.path.abspath(path)
+    
+    def exists(self, dataset_id, **kwargs):
+        path = self._construct_path(dataset_id, old_style=True, **kwargs)
+        # For backward compatibility, check root path first; otherwise, construct 
+        # and check hashed path
+        if not os.path.exists(path):
+            path = self._construct_path(dataset_id, **kwargs)
+        return os.path.exists(path)
+    
+    def create(self, dataset_id, **kwargs):
+        if not self.exists(dataset_id, **kwargs):
+            # Pull out locally used fields
+            extra_dir = kwargs.get('extra_dir', None)
+            extra_dir_at_root = kwargs.get('extra_dir_at_root', False)
+            dir_only = kwargs.get('dir_only', False)
+            alt_name = kwargs.get('alt_name', None)
+            # Construct hashed path
+            path = os.path.join(*directory_hash_id(dataset_id))
+            # Optionally append extra_dir
+            if extra_dir is not None:
+                if extra_dir_at_root:
+                    path = os.path.join(extra_dir, path)
+                else:
+                    path = os.path.join(path, extra_dir)
+            # Combine the constructted path with the root dir for all files
+            path = os.path.join(self.file_path, path)
+            # Create directory if it does not exist
+            if not os.path.exists(path):
+                os.makedirs(path)
+            if not dir_only:
+                path = os.path.join(path, alt_name if alt_name else "dataset_%s.dat" % dataset_id)
+                open(path, 'w').close() 
+    
+    def empty(self, dataset_id, **kwargs):
+        return os.path.getsize(self.get_filename(dataset_id, **kwargs)) > 0
+    
+    def size(self, dataset_id, **kwargs):
+        if self.exists(dataset_id, **kwargs):
+            try:
+                return os.path.getsize(self.get_filename(dataset_id, **kwargs))
+            except OSError:
+                return 0
+        else:
+            return 0
+    
+    def delete(self, dataset_id, entire_dir=False, **kwargs):
+        path = self.get_filename(dataset_id, **kwargs)
+        extra_dir = kwargs.get('extra_dir', None)
+        try:
+            if entire_dir and extra_dir:
+                shutil.rmtree(path)
+                return True
+            if self.exists(dataset_id, **kwargs):
+                    os.remove(path)
+                    return True
+        except OSError, ex:
+            log.critical('%s delete error %s' % (self._get_filename(dataset_id, **kwargs), ex))
+        return False
+    
+    def get_data(self, dataset_id, start=0, count=-1, **kwargs):
+        data_file = open(self.get_filename(dataset_id, **kwargs), 'r')
+        data_file.seek(start)
+        content = data_file.read(count)
+        data_file.close()
+        return content
+    
+    def get_filename(self, dataset_id, **kwargs):
+        path = self._construct_path(dataset_id, old_style=True, **kwargs)
+        # For backward compatibility, check root path first; otherwise, construct 
+        # and check hashed path
+        if os.path.exists(path):
+            return path
+        else:
+            path = self._construct_path(dataset_id, **kwargs)
+        print "Checking it %s exists: %s" %(path, os.path.exists(path))
+        if os.path.exists(path):
+            return path
+        else:
+            raise ObjectNotFound()
+    
+    def update_from_file(self, dataset_id, file_name=None, create=False, **kwargs):
+        """ `create` parameter is not used in this implementation """
+        if create:
+            self.create(dataset_id, **kwargs)
+        if file_name and self.exists(dataset_id, **kwargs):
+            try:
+                shutil.copy(file_name, self.get_filename(dataset_id, **kwargs))
+            except IOError, ex:
+                log.critical('Error copying %s to %s: %s' % (file_name, 
+                    self._get_filename(dataset_id, **kwargs), ex))
+    
+    def get_object_url(self, dataset_id, **kwargs):
+        return None
+    
+
+
+class CachingObjectStore(ObjectStore):
+    """
+    Object store that uses a directory for caching files, but defers and writes
+    back to another object store.
+    """
+    
+    def __init__(self, path, backend):
+        super(CachingObjectStore, self).__init__(self, path, backend)
+    
+
+
+class S3ObjectStore(ObjectStore):
+    """
+    Object store that stores objects as items in an AWS S3 bucket. A local
+    cache exists that is used as an intermediate location for files between
+    Galaxy and S3.
+    """
+    def __init__(self, app):
+        super(S3ObjectStore, self).__init__()
+        self.app = app
+        self.staging_path = self.app.config.file_path
+        self.s3_conn = S3Connection()
+        self.bucket = self._get_bucket(self.app.config.s3_bucket)
+        self.use_rr = self.app.config.use_reduced_redundancy
+        self.cache_size = self.app.config.object_store_cache_size * 1073741824 # Convert GBs to bytes
+        self.transfer_progress = 0
+        # Clean cache only if value is set in universe_wsgi.ini
+        if self.cache_size != -1:
+            # Helper for interruptable sleep
+            self.sleeper = Sleeper()
+            self.cache_monitor_thread = threading.Thread(target=self.__cache_monitor)
+            self.cache_monitor_thread.start()
+            log.info("Cache cleaner manager started")
+    
+    def __cache_monitor(self):
+        time.sleep(2) # Wait for things to load before starting the monitor
+        while self.running:
+            total_size = 0
+            # Is this going to be too expensive of an operation to be done frequently?
+            file_list = []
+            for dirpath, dirnames, filenames in os.walk(self.staging_path):
+                for f in filenames:
+                    fp = os.path.join(dirpath, f)
+                    file_size = os.path.getsize(fp)
+                    total_size += file_size
+                    # Get the time given file was last accessed
+                    last_access_time = time.localtime(os.stat(fp)[7])
+                    # Compose a tuple of the access time and the file path
+                    file_tuple = last_access_time, fp, file_size
+                    file_list.append(file_tuple)
+            # Sort the file list (based on access time)
+            file_list.sort()
+            # Initiate cleaning once within 10% of the defined cache size?
+            cache_limit = self.cache_size * 0.9
+            if total_size > cache_limit:
+                log.info("Initiating cache cleaning: current cache size: %s; clean until smaller than: %s" \
+                    % (convert_bytes(total_size), convert_bytes(cache_limit)))
+                # How much to delete? If simply deleting up to the cache-10% limit,
+                # is likely to be deleting frequently and may run the risk of hitting
+                # the limit - maybe delete additional #%?
+                # For now, delete enough to leave at least 10% of the total cache free
+                delete_this_much = total_size - cache_limit
+                self.__clean_cache(file_list, delete_this_much)
+            self.sleeper.sleep(30) # Test cache size every 30 seconds?
+    
+    def __clean_cache(self, file_list, delete_this_much):
+        """ Keep deleting files from the file_list until the size of the deleted
+        files is greater than the value in delete_this_much parameter.
+        
+        :type file_list: list
+        :param file_list: List of candidate files that can be deleted. This method
+            will start deleting files from the beginning of the list so the list
+            should be sorted accordingly. The list must contains 3-element tuples,
+            positioned as follows: position 0 holds file last accessed timestamp
+            (as time.struct_time), position 1 holds file path, and position 2 has 
+            file size (e.g., (<access time>, /mnt/data/dataset_1.dat), 472394)
+        
+        :type delete_this_much: int
+        :param delete_this_much: Total size of files, in bytes, that should be deleted.
+        """
+        # Keep deleting datasets from file_list until deleted_amount does not
+        # exceed delete_this_much; start deleting from the front of the file list,
+        # which assumes the oldest files come first on the list.
+        deleted_amount = 0
+        for i, f in enumerate(file_list):
+            if deleted_amount < delete_this_much:
+                deleted_amount += f[2]
+                os.remove(f[1])
+                # Debugging code for printing deleted files' stats
+                # folder, file_name = os.path.split(f[1])
+                # file_date = time.strftime("%m/%d/%y %H:%M:%S", f[0])
+                # log.debug("%s. %-25s %s, size %s (deleted %s/%s)" \
+                #     % (i, file_name, convert_bytes(f[2]), file_date, \
+                #     convert_bytes(deleted_amount), convert_bytes(delete_this_much)))
+            else:
+                log.debug("Cache cleaning done. Total space freed: %s" % convert_bytes(deleted_amount))
+                return
+    
+    def _get_bucket(self, bucket_name):
+        """ Sometimes a handle to a bucket is not established right away so try
+        it a few times. Raise error is connection is not established. """
+        for i in range(5):
+            try:
+                bucket = self.s3_conn.get_bucket(bucket_name)
+                log.debug("Using S3 object store; got bucket '%s'" % bucket.name)
+                return bucket
+            except S3ResponseError: 
+                log.debug("Could not get bucket '%s', attempt %s/5" % (bucket_name, i+1))
+                time.sleep(2)
+        # All the attempts have been exhausted and connection was not established,
+        # raise error
+        raise S3ResponseError
+    
+    def _fix_permissions(self, rel_path):
+        """ Set permissions on rel_path"""
+        for basedir, dirs, files in os.walk( rel_path ):
+            util.umask_fix_perms( basedir, self.app.config.umask, 0777, self.app.config.gid )
+            for f in files:
+                path = os.path.join( basedir, f )
+                # Ignore symlinks
+                if os.path.islink( path ):
+                    continue 
+                util.umask_fix_perms( path, self.app.config.umask, 0666, self.app.config.gid )
+    
+    def _construct_path(self, dataset_id, dir_only=None, extra_dir=None, extra_dir_at_root=False, alt_name=None):
+        rel_path = os.path.join(*directory_hash_id(dataset_id))
+        if extra_dir is not None:
+            if extra_dir_at_root:
+                rel_path = os.path.join(extra_dir, rel_path)
+            else:
+                rel_path = os.path.join(rel_path, extra_dir)
+        # S3 folders are marked by having trailing '/' so add it now
+        rel_path = '%s/' % rel_path
+        if not dir_only:
+            rel_path = os.path.join(rel_path, alt_name if alt_name else "dataset_%s.dat" % dataset_id)
+        return rel_path
+    
+    def _get_cache_path(self, rel_path):
+        return os.path.abspath(os.path.join(self.staging_path, rel_path))
+    
+    def _get_transfer_progress(self):
+        return self.transfer_progress
+    
+    def _get_size_in_s3(self, rel_path):
+        try:
+            key = self.bucket.get_key(rel_path)
+            if key:
+                return key.size
+        except S3ResponseError, ex:
+            log.error("Could not get size of key '%s' from S3: %s" % (rel_path, ex))
+        except Exception, ex:
+            log.error("Could not get reference to the key object '%s'; returning -1 for key size: %s" % (rel_path, ex))
+        return -1
+    
+    def _key_exists(self, rel_path):
+        exists = False
+        try:
+            # A hackish way of testing if the rel_path is a folder vs a file
+            is_dir = rel_path[-1] == '/'
+            if is_dir:
+                rs = self.bucket.get_all_keys(prefix=rel_path)
+                if len(rs) > 0:
+                    exists = True
+                else:
+                    exists = False
+            else:
+                key = Key(self.bucket, rel_path)
+                exists = key.exists()
+        except S3ResponseError, ex:
+            log.error("Trouble checking existence of S3 key '%s': %s" % (rel_path, ex))
+            return False
+        print "Checking if '%s' exists in S3: %s" % (rel_path, exists)
+        if rel_path[0] == '/':
+            raise
+        return exists
+    
+    def _in_cache(self, rel_path):
+        """ Check if the given dataset is in the local cache and return True if so. """
+        # log.debug("------ Checking cache for rel_path %s" % rel_path)
+        cache_path = self._get_cache_path(rel_path)
+        exists = os.path.exists(cache_path)
+        # print "Checking chache for %s; returning %s" % (cache_path, exists)
+        return exists
+        # EATODO: Part of checking if a file is in cache should be to ensure the 
+        # size of the cached file matches that on S3. Once the upload tool explicitly
+        # creates, this check sould be implemented- in the mean time, it's not
+        # looking likely to be implementable reliably.
+        # if os.path.exists(cache_path):
+        #     # print "***1 %s exists" % cache_path
+        #     if self._key_exists(rel_path):
+        #         # print "***2 %s exists in S3" % rel_path
+        #         # Make sure the size in cache is available in its entirety
+        #         # print "File '%s' cache size: %s, S3 size: %s" % (cache_path, os.path.getsize(cache_path), self._get_size_in_s3(rel_path))
+        #         if os.path.getsize(cache_path) == self._get_size_in_s3(rel_path):
+        #             # print "***2.1 %s exists in S3 and the size is the same as in cache (in_cache=True)" % rel_path
+        #             exists = True
+        #         else:
+        #             # print "***2.2 %s exists but differs in size from cache (in_cache=False)" % cache_path
+        #             exists = False
+        #     else:
+        #         # Although not perfect decision making, this most likely means
+        #         # that the file is currently being uploaded
+        #         # print "***3 %s found in cache but not in S3 (in_cache=True)" % cache_path
+        #         exists = True
+        # else:
+        #     # print "***4 %s does not exist (in_cache=False)" % cache_path
+        #     exists = False
+        # # print "Checking cache for %s; returning %s" % (cache_path, exists)
+        # return exists
+        # # return False
+    
+    def _pull_into_cache(self, rel_path):
+        # Ensure the cache directory structure exists (e.g., dataset_#_files/)
+        rel_path_dir = os.path.dirname(rel_path)
+        if not os.path.exists(self._get_cache_path(rel_path_dir)):
+            os.makedirs(self._get_cache_path(rel_path_dir))
+        # Now pull in the file
+        ok = self._download(rel_path)
+        self._fix_permissions(rel_path)
+        return ok
+    
+    def _transfer_cb(self, complete, total):
+        self.transfer_progress += 10
+        # print "Dataset transfer progress: %s" % self.transfer_progress
+    
+    def _download(self, rel_path):
+        try:
+            log.debug("Pulling key '%s' into cache to %s" % (rel_path, self._get_cache_path(rel_path)))
+            key = self.bucket.get_key(rel_path)
+            # Test is cache is large enough to hold the new file
+            if key.size > self.cache_size:
+                log.critical("File %s is larger (%s) than the cache size (%s). Cannot download." \
+                    % (rel_path, key.size, self.cache_size))
+                return False
+            # Test if 'axel' is available for parallel download and pull the key into cache
+            try:
+                ret_code = subprocess.call('axel')
+            except OSError:
+                ret_code = 127
+            if ret_code == 127:
+                self.transfer_progress = 0 # Reset transfer progress counter
+                key.get_contents_to_filename(self._get_cache_path(rel_path), cb=self._transfer_cb, num_cb=10)
+                print "(ssss) Pulled key '%s' into cache to %s" % (rel_path, self._get_cache_path(rel_path))
+                return True
+            else:
+                ncores = multiprocessing.cpu_count()
+                url = key.generate_url(7200)
+                ret_code = subprocess.call("axel -a -n %s '%s'" % (ncores, url))
+                if ret_code == 0:
+                    print "(ssss) Parallel pulled key '%s' into cache to %s" % (rel_path, self._get_cache_path(rel_path))
+                    return True
+        except S3ResponseError, ex:
+            log.error("Problem downloading key '%s' from S3 bucket '%s': %s" % (rel_path, self.bucket.name, ex))
+        return False
+    
+    def _push_to_s3(self, rel_path, source_file=None, from_string=None):
+        """ 
+        Push the file pointed to by `rel_path` to S3 naming the key `rel_path`. 
+        If `source_file` is provided, push that file instead while still using 
+        `rel_path` as the key name.
+        If `from_string` is provided, set contents of the file to the value of
+        the string
+        """
+        try:
+            source_file = source_file if source_file else self._get_cache_path(rel_path)
+            if os.path.exists(source_file):
+                key = Key(self.bucket, rel_path)
+                if from_string:
+                    key.set_contents_from_string(from_string, reduced_redundancy=self.use_rr)
+                    log.debug("Pushed data from string '%s' to key '%s'" % (from_string, rel_path))
+                else:
+                    start_time = datetime.now()
+                    print "[%s] Pushing cache file '%s' to key '%s'" % (start_time, source_file, rel_path)
+                    mb_size = os.path.getsize(source_file) / 1e6
+                    if mb_size < 60:
+                        self.transfer_progress = 0 # Reset transfer progress counter
+                        key.set_contents_from_filename(source_file, reduced_redundancy=self.use_rr,
+                            cb=self._transfer_cb, num_cb=10)
+                    else:
+                        multipart_upload(self.bucket, key.name, source_file, mb_size, use_rr=self.use_rr)
+                        # self._multipart_upload(key.name, source_file, mb_size)
+                    end_time = datetime.now()
+                    print "Push ended at '%s'; it lasted '%s'" % (end_time, end_time-start_time)
+                    log.debug("Pushed cache file '%s' to key '%s'" % (source_file, rel_path))
+                return True
+            else:
+                log.error("Tried updating key '%s' from source file '%s', but source file does not exist."
+                    % (rel_path, source_file))
+        except S3ResponseError, ex:
+            log.error("Trouble pushing S3 key '%s' from file '%s': %s" % (rel_path, source_file, ex))
+        return False
+    
+    def file_ready(self, dataset_id, **kwargs):
+        """ A helper method that checks if a file corresponding to a dataset 
+        is ready and available to be used. Return True if so, False otherwise."""
+        rel_path = self._construct_path(dataset_id, **kwargs)
+        # Make sure the size in cache is available in its entirety
+        if self._in_cache(rel_path) and os.path.getsize(self._get_cache_path(rel_path)) == self._get_size_in_s3(rel_path):
+            return True
+        return False
+    
+    def exists(self, dataset_id, **kwargs):
+        in_cache = in_s3 = False
+        rel_path = self._construct_path(dataset_id, **kwargs)
+        # Check cache
+        if self._in_cache(rel_path):
+            in_cache = True
+        # Check S3
+        in_s3 = self._key_exists(rel_path)
+        # log.debug("~~~~~~ File '%s' exists in cache: %s; in s3: %s" % (rel_path, in_cache, in_s3))
+        # dir_only does not get synced so shortcut the decision
+        dir_only = kwargs.get('dir_only', False)
+        if dir_only:
+            if in_cache or in_s3:
+                return True
+            else:
+                return False
+        # TODO: Sync should probably not be done here. Add this to an async upload stack?
+        if in_cache and not in_s3:
+            self._push_to_s3(rel_path, source_file=self._get_cache_path(rel_path))
+            return True
+        elif in_s3:
+            return True
+        else:
+            return False
+    
+    def create(self, dataset_id, **kwargs):
+        if not self.exists(dataset_id, **kwargs):
+            print "S3 OS creating a dataset with ID %s" % dataset_id
+            # Pull out locally used fields
+            extra_dir = kwargs.get('extra_dir', None)
+            extra_dir_at_root = kwargs.get('extra_dir_at_root', False)
+            dir_only = kwargs.get('dir_only', False)
+            alt_name = kwargs.get('alt_name', None)
+            # print "---- Processing: %s; %s" % (alt_name, locals())
+            # Construct hashed path
+            rel_path = os.path.join(*directory_hash_id(dataset_id))
+            # Optionally append extra_dir
+            if extra_dir is not None:
+                if extra_dir_at_root:
+                    rel_path = os.path.join(extra_dir, rel_path)
+                else:
+                    rel_path = os.path.join(rel_path, extra_dir)
+            # Create given directory in cache
+            cache_dir = os.path.join(self.staging_path, rel_path)
+            if not os.path.exists(cache_dir):
+                os.makedirs(cache_dir)
+            # Although not really necessary to create S3 folders (because S3 has
+            # flat namespace), do so for consistency with the regular file system
+            # S3 folders are marked by having trailing '/' so add it now
+            # s3_dir = '%s/' % rel_path
+            # self._push_to_s3(s3_dir, from_string='')
+            # If instructed, create the dataset in cache & in S3
+            if not dir_only:
+                rel_path = os.path.join(rel_path, alt_name if alt_name else "dataset_%s.dat" % dataset_id)
+                open(os.path.join(self.staging_path, rel_path), 'w').close()
+                self._push_to_s3(rel_path, from_string='')
+    
+    def empty(self, dataset_id, **kwargs):
+        if self.exists(dataset_id, **kwargs):
+            return bool(self.size(dataset_id, **kwargs) > 0)
+        else:
+            raise ObjectNotFound()
+    
+    def size(self, dataset_id, **kwargs):
+        rel_path = self._construct_path(dataset_id, **kwargs)
+        if self._in_cache(rel_path):
+            try:
+                return os.path.getsize(self._get_cache_path(rel_path))
+            except OSError, ex:
+                log.info("Could not get size of file '%s' in local cache, will try S3. Error: %s" % (rel_path, ex))
+        elif self.exists(dataset_id, **kwargs):
+            return self._get_size_in_s3(rel_path)
+        log.warning("Did not find dataset '%s', returning 0 for size" % rel_path)
+        return 0
+    
+    def delete(self, dataset_id, entire_dir=False, **kwargs):
+        rel_path = self._construct_path(dataset_id, **kwargs)
+        extra_dir = kwargs.get('extra_dir', None)
+        try:
+            # For the case of extra_files, because we don't have a reference to
+            # individual files/keys we need to remove the entire directory structure
+            # with all the files in it. This is easy for the local file system,
+            # but requires iterating through each individual key in S3 and deleing it.
+            if entire_dir and extra_dir:
+                shutil.rmtree(self._get_cache_path(rel_path))
+                rs = self.bucket.get_all_keys(prefix=rel_path)
+                for key in rs:
+                    log.debug("Deleting key %s" % key.name)
+                    key.delete()
+                return True
+            else:
+                # Delete from cache first
+                os.unlink(self._get_cache_path(rel_path))
+                # Delete from S3 as well
+                if self._key_exists(rel_path):
+                        key = Key(self.bucket, rel_path)
+                        log.debug("Deleting key %s" % key.name)
+                        key.delete()
+                        return True
+        except S3ResponseError, ex:
+            log.error("Could not delete key '%s' from S3: %s" % (rel_path, ex))
+        except OSError, ex:
+            log.error('%s delete error %s' % (self._get_filename(dataset_id, **kwargs), ex))
+        return False
+    
+    def get_data(self, dataset_id, start=0, count=-1, **kwargs):
+        rel_path = self._construct_path(dataset_id, **kwargs)
+        # Check cache first and get file if not there
+        if not self._in_cache(rel_path):
+            self._pull_into_cache(rel_path)
+        else:
+            print "(cccc) Getting '%s' from cache" % self._get_cache_path(rel_path)
+        # Read the file content from cache
+        data_file = open(self._get_cache_path(rel_path), 'r')
+        data_file.seek(start)
+        content = data_file.read(count)
+        data_file.close()
+        return content
+    
+    def get_filename(self, dataset_id, **kwargs):
+        print "S3 get_filename for dataset: %s" % dataset_id
+        dir_only = kwargs.get('dir_only', False)
+        rel_path = self._construct_path(dataset_id, **kwargs)
+        cache_path = self._get_cache_path(rel_path)
+        # S3 does not recognize directories as files so cannot check if those exist.
+        # So, if checking dir only, ensure given dir exists in cache and return
+        # the expected cache path.
+        # dir_only = kwargs.get('dir_only', False)
+        # if dir_only:
+        #     if not os.path.exists(cache_path):
+        #         os.makedirs(cache_path)
+        #     return cache_path
+        # Check if the file exists in the cache first
+        if self._in_cache(rel_path):
+            return cache_path
+        # Check if the file exists in persistent storage and, if it does, pull it into cache
+        elif self.exists(dataset_id, **kwargs):
+            if dir_only: # Directories do not get pulled into cache
+                return cache_path
+            else:
+                if self._pull_into_cache(rel_path):
+                    return cache_path
+        # For the case of retrieving a directory only, return the expected path
+        # even if it does not exist.
+        # if dir_only:
+        #     return cache_path
+        raise ObjectNotFound()
+        # return cache_path # Until the upload tool does not explicitly create the dataset, return expected path
+    
+    def update_from_file(self, dataset_id, file_name=None, create=False, **kwargs): 
+        if create:
+            self.create(dataset_id, **kwargs)
+        if self.exists(dataset_id, **kwargs):
+            rel_path = self._construct_path(dataset_id, **kwargs)
+            # Chose whether to use the dataset file itself or an alternate file
+            if file_name:
+                source_file = os.path.abspath(file_name)
+                # Copy into cache
+                cache_file = self._get_cache_path(rel_path)
+                try:
+                    # FIXME? Should this be a `move`?
+                    shutil.copy2(source_file, cache_file)
+                    self._fix_permissions(cache_file)
+                except OSError, ex:
+                    log.error("Trouble copying source file '%s' to cache '%s': %s" % (source_file, cache_file, ex))
+            else:
+                source_file = self._get_cache_path(rel_path)
+            # Update the file on S3
+            self._push_to_s3(rel_path, source_file)
+        else:
+            raise ObjectNotFound()
+    
+    def get_object_url(self, dataset_id, **kwargs):
+        if self.exists(dataset_id, **kwargs):
+            rel_path = self._construct_path(dataset_id, **kwargs)
+            try:
+                key = Key(self.bucket, rel_path)
+                return key.generate_url(expires_in = 86400) # 24hrs
+            except S3ResponseError, ex:
+                log.warning("Trouble generating URL for dataset '%s': %s" % (rel_path, ex))
+        return None
+    
+
+
+class HierarchicalObjectStore(ObjectStore):
+    """
+    ObjectStore that defers to a list of backends, for getting objects the
+    first store where the object exists is used, objects are always created
+    in the first store.
+    """
+    
+    def __init__(self, backends=[]):
+        super(HierarchicalObjectStore, self).__init__()
+    
+
+def build_object_store_from_config(app):
+    """ Depending on the configuration setting, invoke the appropriate object store
+    """
+    store = app.config.object_store
+    if store == 'disk':
+        return DiskObjectStore(app=app)
+    elif store == 's3':
+        os.environ['AWS_ACCESS_KEY_ID'] = app.config.aws_access_key
+        os.environ['AWS_SECRET_ACCESS_KEY'] = app.config.aws_secret_key
+        return S3ObjectStore(app=app)
+    elif store == 'hierarchical':
+        return HierarchicalObjectStore()
+
+def convert_bytes(bytes):
+    """ A helper function used for pretty printing disk usage """
+    if bytes is None:
+        bytes = 0
+    bytes = float(bytes)
+    
+    if bytes >= 1099511627776:
+        terabytes = bytes / 1099511627776
+        size = '%.2fTB' % terabytes
+    elif bytes >= 1073741824:
+        gigabytes = bytes / 1073741824
+        size = '%.2fGB' % gigabytes
+    elif bytes >= 1048576:
+        megabytes = bytes / 1048576
+        size = '%.2fMB' % megabytes
+    elif bytes >= 1024:
+        kilobytes = bytes / 1024
+        size = '%.2fKB' % kilobytes
+    else:
+        size = '%.2fb' % bytes
+    return size
diff --git a/lib/galaxy/objectstore/s3_multipart_upload.py b/lib/galaxy/objectstore/s3_multipart_upload.py
new file mode 100644
index 00000000000..85b6b3e34a1
--- /dev/null
+++ b/lib/galaxy/objectstore/s3_multipart_upload.py
@@ -0,0 +1,85 @@
+#!/usr/bin/env python
+"""
+Split large file into multiple pieces for upload to S3.
+This parallelizes the task over available cores using multiprocessing.
+Code mostly taken form CloudBioLinux.
+"""
+import os
+import glob
+import subprocess
+import contextlib
+import functools
+import multiprocessing
+from multiprocessing.pool import IMapIterator
+
+import boto
+
+def map_wrap(f):
+    @functools.wraps(f)
+    def wrapper(*args, **kwargs):
+        return apply(f, *args, **kwargs)
+    return wrapper
+
+def mp_from_ids(mp_id, mp_keyname, mp_bucketname):
+    """Get the multipart upload from the bucket and multipart IDs.
+
+    This allows us to reconstitute a connection to the upload
+    from within multiprocessing functions.
+    """
+    conn = boto.connect_s3()
+    bucket = conn.lookup(mp_bucketname)
+    mp = boto.s3.multipart.MultiPartUpload(bucket)
+    mp.key_name = mp_keyname
+    mp.id = mp_id
+    return mp
+
+@map_wrap
+def transfer_part(mp_id, mp_keyname, mp_bucketname, i, part):
+    """Transfer a part of a multipart upload. Designed to be run in parallel.
+    """
+    mp = mp_from_ids(mp_id, mp_keyname, mp_bucketname)
+    print " Transferring", i, part
+    with open(part) as t_handle:
+        mp.upload_part_from_file(t_handle, i+1)
+    os.remove(part)
+
+def multipart_upload(bucket, s3_key_name, tarball, mb_size, use_rr=True):
+    """Upload large files using Amazon's multipart upload functionality.
+    """
+    cores = multiprocessing.cpu_count()
+    print "Initiating multipart upload using %s cores" % cores
+    def split_file(in_file, mb_size, split_num=5):
+        prefix = os.path.join(os.path.dirname(in_file),
+                              "%sS3PART" % (os.path.basename(s3_key_name)))
+        # Split chunks so they are 5MB < chunk < 250MB
+        split_size = int(max(min(mb_size / (split_num * 2.0), 250), 5))
+        if not os.path.exists("%saa" % prefix):
+            cl = ["split", "-b%sm" % split_size, in_file, prefix]
+            subprocess.check_call(cl)
+        return sorted(glob.glob("%s*" % prefix))
+
+    mp = bucket.initiate_multipart_upload(s3_key_name, reduced_redundancy=use_rr)
+    with multimap(cores) as pmap:
+        for _ in pmap(transfer_part, ((mp.id, mp.key_name, mp.bucket_name, i, part)
+                                      for (i, part) in
+                                      enumerate(split_file(tarball, mb_size, cores)))):
+            pass
+    mp.complete_upload()
+
+@contextlib.contextmanager
+def multimap(cores=None):
+    """Provide multiprocessing imap like function.
+    
+    The context manager handles setting up the pool, worked around interrupt issues
+    and terminating the pool on completion.
+    """
+    if cores is None:
+        cores = max(multiprocessing.cpu_count() - 1, 1)
+    def wrapper(func):
+        def wrap(self, timeout=None):
+            return func(self, timeout=timeout if timeout is not None else 1e100)
+        return wrap
+    IMapIterator.next = wrapper(IMapIterator.next)
+    pool = multiprocessing.Pool(cores)
+    yield pool.imap
+    pool.terminate()
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index ebbdbed9fcf..31922acd39d 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1701,23 +1701,38 @@ class Tool:
         Find extra files in the job working directory and move them into
         the appropriate dataset's files directory
         """
+        # print "Working in collect_associated_files"
         for name, hda in output.items():
             temp_file_path = os.path.join( job_working_directory, "dataset_%s_files" % ( hda.dataset.id ) )
             try:
-                if len( os.listdir( temp_file_path ) ) > 0:
-                    store_file_path = os.path.join( 
-                        os.path.join( self.app.config.file_path, *directory_hash_id( hda.dataset.id ) ), 
-                        "dataset_%d_files" % hda.dataset.id )
-                    shutil.move( temp_file_path, store_file_path )
-                    # Fix permissions
-                    for basedir, dirs, files in os.walk( store_file_path ):
-                        util.umask_fix_perms( basedir, self.app.config.umask, 0777, self.app.config.gid )
-                        for file in files:
-                            path = os.path.join( basedir, file )
-                            # Ignore symlinks
-                            if os.path.islink( path ):
-                                continue 
-                            util.umask_fix_perms( path, self.app.config.umask, 0666, self.app.config.gid )
+                a_files = os.listdir( temp_file_path )
+                if len( a_files ) > 0:
+                    for f in a_files:
+                        # print "------ Instructing ObjectStore to update/create file: %s from %s" \
+                        #     % (hda.dataset.id, os.path.join(temp_file_path, f))
+                        self.app.object_store.update_from_file(hda.dataset.id,
+                            extra_dir="dataset_%d_files" % hda.dataset.id, 
+                            alt_name = f,
+                            file_name = os.path.join(temp_file_path, f),
+                            create = True)
+                    # Clean up after being handled by object store. 
+                    # FIXME: If the object (e.g., S3) becomes async, this will 
+                    # cause issues so add it to the object store functionality?
+                    # shutil.rmtree(temp_file_path)
+
+                    # store_file_path = os.path.join( 
+                    #     os.path.join( self.app.config.file_path, *directory_hash_id( hda.dataset.id ) ), 
+                    #     "dataset_%d_files" % hda.dataset.id )
+                    # shutil.move( temp_file_path, store_file_path )
+                    # # Fix permissions
+                    # for basedir, dirs, files in os.walk( store_file_path ):
+                    #     util.umask_fix_perms( basedir, self.app.config.umask, 0777, self.app.config.gid )
+                    #     for file in files:
+                    #         path = os.path.join( basedir, file )
+                    #         # Ignore symlinks
+                    #         if os.path.islink( path ):
+                    #             continue 
+                    #         util.umask_fix_perms( path, self.app.config.umask, 0666, self.app.config.gid )
             except:
                 continue
     
diff --git a/lib/galaxy/tools/actions/__init__.py b/lib/galaxy/tools/actions/__init__.py
index 000b6980716..533db36f3a8 100644
--- a/lib/galaxy/tools/actions/__init__.py
+++ b/lib/galaxy/tools/actions/__init__.py
@@ -282,7 +282,8 @@ class DefaultToolAction( object ):
                     trans.sa_session.flush()
                     trans.app.security_agent.set_all_dataset_permissions( data.dataset, output_permissions )
                 # Create an empty file immediately
-                open( data.file_name, "w" ).close()
+                # open( data.file_name, "w" ).close()
+                trans.app.object_store.create( data.id )
                 # Fix permissions
                 util.umask_fix_perms( data.file_name, trans.app.config.umask, 0666 )
                 # This may not be neccesary with the new parent/child associations
diff --git a/lib/galaxy/tools/actions/upload.py b/lib/galaxy/tools/actions/upload.py
index 757f7fba866..0f39a299d0d 100644
--- a/lib/galaxy/tools/actions/upload.py
+++ b/lib/galaxy/tools/actions/upload.py
@@ -1,4 +1,3 @@
-import os
 from __init__ import ToolAction
 from galaxy.tools.actions import upload_common
 
diff --git a/lib/galaxy/tools/actions/upload_common.py b/lib/galaxy/tools/actions/upload_common.py
index c6b7bb3f53e..b27b0a70377 100644
--- a/lib/galaxy/tools/actions/upload_common.py
+++ b/lib/galaxy/tools/actions/upload_common.py
@@ -324,13 +324,17 @@ def create_job( trans, params, tool, json_file_path, data_list, folder=None, ret
             job.add_output_library_dataset( 'output%i' % i, dataset )
             # Create an empty file immediately
             if not dataset.dataset.external_filename:
-                open( dataset.file_name, "w" ).close()
+                trans.app.object_store.create( dataset.id )
+                print "---> Upload tool created a folder(?) %s with ID %s? %s" % (dataset.file_name, dataset.id, trans.app.object_store.exists(dataset.id))
+                # open( dataset.file_name, "w" ).close()
     else:
         for i, dataset in enumerate( data_list ):
             job.add_output_dataset( 'output%i' % i, dataset )
             # Create an empty file immediately
             if not dataset.dataset.external_filename:
-                open( dataset.file_name, "w" ).close()
+                trans.app.object_store.create( dataset.id )
+                print "---> Upload tool created a file %s with ID %s? %s" % (dataset.file_name, dataset.id, trans.app.object_store.exists(dataset.id))
+                # open( dataset.file_name, "w" ).close()
     job.state = job.states.NEW
     trans.sa_session.add( job )
     trans.sa_session.flush()
diff --git a/lib/galaxy/web/controllers/dataset.py b/lib/galaxy/web/controllers/dataset.py
index 44552e3af7b..8bec4f465d5 100644
--- a/lib/galaxy/web/controllers/dataset.py
+++ b/lib/galaxy/web/controllers/dataset.py
@@ -217,7 +217,7 @@ class DatasetInterface( BaseController, UsesAnnotations, UsesHistory, UsesHistor
         outfname = data.name[0:150]
         outfname = ''.join(c in valid_chars and c or '_' for c in outfname)
         if (params.do_action == None):
-     	    params.do_action = 'zip' # default
+            params.do_action = 'zip' # default
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
         if not data:
@@ -300,8 +300,7 @@ class DatasetInterface( BaseController, UsesAnnotations, UsesHistory, UsesHistor
                         archive.wsgi_headeritems = trans.response.wsgi_headeritems()
                         return archive.stream
         return trans.show_error_message( msg )
-
-
+    
     @web.expose
     def get_metadata_file(self, trans, hda_id, metadata_name):
         """ Allows the downloading of metadata files associated with datasets (eg. bai index for bam files) """
@@ -316,12 +315,8 @@ class DatasetInterface( BaseController, UsesAnnotations, UsesHistory, UsesHistor
         trans.response.headers["Content-Type"] = "application/octet-stream"
         trans.response.headers["Content-Disposition"] = "attachment; filename=Galaxy%s-[%s].%s" % (data.hid, fname, file_ext)
         return open(data.metadata.get(metadata_name).file_name)
-        
-    @web.expose
-    def display(self, trans, dataset_id=None, preview=False, filename=None, to_ext=None, **kwd):
-        """Catches the dataset id and displays file contents as directed"""
-        composite_extensions = trans.app.datatypes_registry.get_composite_extensions( )
-        composite_extensions.append('html') # for archiving composite datatypes
+    
+    def _check_dataset(self, trans, dataset_id):
         # DEPRECATION: We still support unencoded ids for backward compatibility
         try:
             data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( dataset_id ) )
@@ -340,9 +335,36 @@ class DatasetInterface( BaseController, UsesAnnotations, UsesHistory, UsesHistor
         if data.state == trans.model.Dataset.states.UPLOAD:
             return trans.show_error_message( "Please wait until this dataset finishes uploading before attempting to view it." )
         
+        return data
+    
+    @web.expose
+    @web.json
+    def transfer_status(self, trans, dataset_id, filename=None):
+        """ Primarily used for the S3ObjectStore - get the status of data transfer
+        if the file is not in cache """
+        data = self._check_dataset(trans, dataset_id)
+        print "dataset.py -> transfer_status: Checking transfer status for dataset %s..." % data.id
+        
+        # Pulling files in extra_files_path into cache is not handled via this
+        # method but that's primarily because those files are typically linked to
+        # through tool's output page anyhow so tying a JavaScript event that will
+        # call this method does not seem doable?
+        if trans.app.object_store.file_ready(data.id):
+            return True
+        else:
+            return False
+    
+    @web.expose
+    def display(self, trans, dataset_id=None, preview=False, filename=None, to_ext=None, **kwd):
+        """Catches the dataset id and displays file contents as directed"""
+        composite_extensions = trans.app.datatypes_registry.get_composite_extensions( )
+        composite_extensions.append('html') # for archiving composite datatypes
+        data = self._check_dataset(trans, dataset_id)
+        
         if filename and filename != "index":
             # For files in extra_files_path
-            file_path = os.path.join( data.extra_files_path, filename )
+            file_path = os.path.join( data.extra_files_path, filename ) # remove after debugging
+            file_path = trans.app.object_store.get_filename(data.id, extra_dir='dataset_%s_files' % data.id, alt_name=filename)
             if os.path.exists( file_path ):
                 if os.path.isdir( file_path ):
                     return trans.show_error_message( "Directory listing is not allowed." ) #TODO: Reconsider allowing listing of directories?
diff --git a/lib/galaxy/web/controllers/history.py b/lib/galaxy/web/controllers/history.py
index 15c4032539a..5b236a0632d 100644
--- a/lib/galaxy/web/controllers/history.py
+++ b/lib/galaxy/web/controllers/history.py
@@ -581,7 +581,7 @@ class HistoryController( BaseController, Sharable, UsesAnnotations, UsesItemRati
                     trans.response.set_content_type( 'application/x-gzip' )
                 else:
                     trans.response.set_content_type( 'application/x-tar' )
-                return open( jeha.dataset.file_name )
+                return trans.app.object_store.get_data(jeha.dataset.id)
             elif jeha.job.state in [ model.Job.states.RUNNING, model.Job.states.QUEUED, model.Job.states.WAITING ]:
                 return trans.show_message( "Still exporting history %(n)s; please check back soon. Link: <a href='%(s)s'>%(s)s</a>" \
                         % ( { 'n' : history.name, 's' : url_for( action="export_archive", id=id, qualified=True ) } ) )
diff --git a/templates/dataset/display.mako b/templates/dataset/display.mako
index c1b925638b7..4085fadbc2d 100755
--- a/templates/dataset/display.mako
+++ b/templates/dataset/display.mako
@@ -9,11 +9,11 @@
 
 <%def name="init()">
 <%
-	self.has_left_panel=False
-	self.has_right_panel=True
-	self.message_box_visible=False
-	self.active_view="user"
-	self.overlay_visible=False
+    self.has_left_panel=False
+    self.has_right_panel=True
+    self.message_box_visible=False
+    self.active_view="user"
+    self.overlay_visible=False
 %>
 </%def>
 
@@ -44,10 +44,10 @@
 
 <%def name="center_panel()">
     <div class="unified-panel-header" unselectable="on">
-		<div class="unified-panel-header-inner">
-				${get_class_display_name( item.__class__ )}
-			| ${get_item_name( item ) | h}
-	    </div>
+        <div class="unified-panel-header-inner">
+                ${get_class_display_name( item.__class__ )}
+            | ${get_item_name( item ) | h}
+        </div>
     </div>
     
     <div class="unified-panel-body">
diff --git a/templates/root/history.mako b/templates/root/history.mako
index 13962bd6488..1f35a1954ab 100755
--- a/templates/root/history.mako
+++ b/templates/root/history.mako
@@ -140,6 +140,34 @@ $(function() {
                 return false;
             });
         });
+        
+        // Check to see if the dataset data is cached or needs to be pulled in
+        // via objectstore
+        $(this).find("a.display").each( function() {
+            var history_item = $(this).parents(".historyItem")[0];
+            var history_id = history_item.id.split( "-" )[1];
+            $(this).click(function() {
+                check_transfer_status($(this), history_id);
+            });
+        });
+        
+        // If dataset data is not cached, keep making ajax calls to check on the
+        // data status and update the dataset UI element accordingly
+        function check_transfer_status(link, history_id) {
+            $.getJSON("${h.url_for( controller='dataset', action='transfer_status', dataset_id='XXX' )}".replace( 'XXX', link.attr("dataset_id") ), 
+                function(ready) {
+                    if (ready === false) {
+                        // $("<div/>").text("Data is loading from S3... please be patient").appendTo(link.parent());
+                        $( '#historyItem-' + history_id).removeClass( "historyItem-ok" );
+                        $( '#historyItem-' + history_id).addClass( "historyItem-running" );
+                        setTimeout(function(){check_transfer_status(link, history_id)}, 1000);
+                    } else {
+                        $( '#historyItem-' + history_id).removeClass( "historyItem-running" );
+                        $( '#historyItem-' + history_id).addClass( "historyItem-ok" );
+                    }
+                }
+            );
+        }
 
         // Undelete link
         $(this).find("a.historyItemUndelete").each( function() {
diff --git a/templates/root/history_common.mako b/templates/root/history_common.mako
index fc79712e098..c4af0948e15 100755
--- a/templates/root/history_common.mako
+++ b/templates/root/history_common.mako
@@ -98,7 +98,7 @@
                 %if data.purged:
                     <span class="icon-button display_disabled tooltip" title="Cannoy display datasets removed from disk"></span>
                 %else:
-                    <a class="icon-button display tooltip" title="Display data in browser" href="${display_url}"
+                    <a class="icon-button display tooltip" dataset_id="${dataset_id}" title="Display data in browser" href="${display_url}"
                     %if for_editing:
                         target="galaxy_main"
                     %endif

From 7a1cd47f1225db03a6ec15dd423bbf06b0a1dad4 Mon Sep 17 00:00:00 2001
From: Enis Afgan <afgane@gmail.com>
Date: Thu, 21 Jul 2011 10:44:27 -0400
Subject: [PATCH 006/362] Added config options to universe_wsgi.ini.sample

---
 universe_wsgi.ini.sample | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/universe_wsgi.ini.sample b/universe_wsgi.ini.sample
index c136c0879e1..473711d2457 100644
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -414,6 +414,17 @@ use_interactive = True
 
 # -- Beta features
 
+# Object store mode (valid options are: disk, s3, hierarchical)
+#object_store = s3
+#aws_access_key = <AWS access key>
+#aws_secret_key = <AWS secret key>
+#s3_bucket = <name of an existing S3 bucket>
+#use_reduced_redundancy = True
+# Size (in GB) that the cache used by object store should be limited to.
+# If the value is not specified, the cache size will be limited only by the file
+# system size.
+#object_store_cache_size = 100
+
 # Enable Galaxy to communicate directly with a sequencer
 #enable_sequencer_communication = False
 

From dac2bbf1f5706c74d3666fec8f0d79283e37a6fa Mon Sep 17 00:00:00 2001
From: Enis Afgan <afgane@gmail.com>
Date: Mon, 25 Jul 2011 14:19:51 -0400
Subject: [PATCH 007/362] Fix for permission setting on files downloaded from
 S3 into cache

---
 lib/galaxy/objectstore/__init__.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/lib/galaxy/objectstore/__init__.py b/lib/galaxy/objectstore/__init__.py
index 076ca8cfbd1..cbf3bbd83e3 100644
--- a/lib/galaxy/objectstore/__init__.py
+++ b/lib/galaxy/objectstore/__init__.py
@@ -442,12 +442,12 @@ class S3ObjectStore(ObjectStore):
     
     def _fix_permissions(self, rel_path):
         """ Set permissions on rel_path"""
-        for basedir, dirs, files in os.walk( rel_path ):
-            util.umask_fix_perms( basedir, self.app.config.umask, 0777, self.app.config.gid )
+        for basedir, dirs, files in os.walk(rel_path):
+            util.umask_fix_perms(basedir, self.app.config.umask, 0777, self.app.config.gid)
             for f in files:
-                path = os.path.join( basedir, f )
+                path = os.path.join(basedir, f)
                 # Ignore symlinks
-                if os.path.islink( path ):
+                if os.path.islink(path):
                     continue 
                 util.umask_fix_perms( path, self.app.config.umask, 0666, self.app.config.gid )
     
@@ -545,7 +545,7 @@ class S3ObjectStore(ObjectStore):
             os.makedirs(self._get_cache_path(rel_path_dir))
         # Now pull in the file
         ok = self._download(rel_path)
-        self._fix_permissions(rel_path)
+        self._fix_permissions(self._get_cache_path(rel_path_dir))
         return ok
     
     def _transfer_cb(self, complete, total):
@@ -569,14 +569,14 @@ class S3ObjectStore(ObjectStore):
             if ret_code == 127:
                 self.transfer_progress = 0 # Reset transfer progress counter
                 key.get_contents_to_filename(self._get_cache_path(rel_path), cb=self._transfer_cb, num_cb=10)
-                print "(ssss) Pulled key '%s' into cache to %s" % (rel_path, self._get_cache_path(rel_path))
+                print "(ssss1) Pulled key '%s' into cache to %s" % (rel_path, self._get_cache_path(rel_path))
                 return True
             else:
                 ncores = multiprocessing.cpu_count()
                 url = key.generate_url(7200)
                 ret_code = subprocess.call("axel -a -n %s '%s'" % (ncores, url))
                 if ret_code == 0:
-                    print "(ssss) Parallel pulled key '%s' into cache to %s" % (rel_path, self._get_cache_path(rel_path))
+                    print "(ssss2) Parallel pulled key '%s' into cache to %s" % (rel_path, self._get_cache_path(rel_path))
                     return True
         except S3ResponseError, ex:
             log.error("Problem downloading key '%s' from S3 bucket '%s': %s" % (rel_path, self.bucket.name, ex))

From ab6e0d30b1b288f0f3a35516ea663954bacbba31 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Wed, 27 Jul 2011 10:48:03 -0400
Subject: [PATCH 008/362] Closed the feature/ws branch, changes from this
 branch were merged in 5827:f3a1086fac91.


From 29253409ac6a83b3a2da17342419233c66dd78b3 Mon Sep 17 00:00:00 2001
From: Enis Afgan <afgane@gmail.com>
Date: Mon, 1 Aug 2011 17:35:26 -0400
Subject: [PATCH 009/362] Metadata is now being handled by the ObjectStore as
 well

---
 lib/galaxy/app.py                         |  3 +-
 lib/galaxy/datatypes/metadata.py          |  6 ++-
 lib/galaxy/jobs/__init__.py               |  2 +-
 lib/galaxy/jobs/runners/local.py          |  2 +-
 lib/galaxy/model/__init__.py              | 11 +-----
 lib/galaxy/objectstore/__init__.py        | 48 ++++++++++++-----------
 lib/galaxy/tools/actions/upload_common.py |  2 -
 scripts/set_metadata.py                   | 30 +++++++++++++-
 8 files changed, 64 insertions(+), 40 deletions(-)

diff --git a/lib/galaxy/app.py b/lib/galaxy/app.py
index 63c65059d99..fa5e5e0ad18 100644
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -32,7 +32,7 @@ class UniverseApplication( object ):
         from galaxy.model.migrate.check import create_or_verify_database
         create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options )
         # Object store manager
-        self.object_store = build_object_store_from_config(self)
+        self.object_store = build_object_store_from_config(self.config)
         # Setup the database engine and ORM
         from galaxy.model import mapping
         self.model = mapping.init( self.config.file_path,
@@ -94,5 +94,6 @@ class UniverseApplication( object ):
         
     def shutdown( self ):
         self.job_manager.shutdown()
+        self.object_store.shutdown()
         if self.heartbeat:
             self.heartbeat.shutdown()
diff --git a/lib/galaxy/datatypes/metadata.py b/lib/galaxy/datatypes/metadata.py
index 174aae0c5c4..f4713d8f1de 100644
--- a/lib/galaxy/datatypes/metadata.py
+++ b/lib/galaxy/datatypes/metadata.py
@@ -411,6 +411,7 @@ class FileParameter( MetadataParameter ):
             mf = galaxy.model.MetadataFile()
             mf.id = value #we assume this is a valid id, since we cannot check it
             return mf
+    
     def make_copy( self, value, target_context, source_context ):
         value = self.wrap( value )
         if value:
@@ -438,8 +439,11 @@ class FileParameter( MetadataParameter ):
             if mf is None:
                 mf = self.new_file( dataset = parent, **value.kwds )
             shutil.move( value.file_name, mf.file_name )
+            # Ensure the metadata file gets updated with content
+            parent.dataset.object_store.update_from_file( parent.dataset.id, file_name=mf.file_name, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name=os.path.basename(mf.file_name) )
             value = mf.id
         return value
+    
     def to_external_value( self, value ):
         """
         Turns a value read from a metadata into its value to be pushed directly into the external dict.
@@ -461,7 +465,7 @@ class FileParameter( MetadataParameter ):
             #we will be copying its contents into the MetadataFile objects filename after restoring from JSON
             #we do not include 'dataset' in the kwds passed, as from_JSON_value() will handle this for us
             return MetadataTempFile( **kwds )
-
+    
 #This class is used when a database file connection is not available
 class MetadataTempFile( object ):
     tmp_dir = 'database/tmp' #this should be overwritten as necessary in calling scripts
diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 00cd5026165..6dac9cb54d5 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -560,7 +560,7 @@ class JobWrapper( object ):
                 dataset.set_size()
                 # Update (non-library) job output datasets through the object store
                 if dataset not in job.output_library_datasets:
-                    print "===+=== Handing dataset '%s' with name '%s' to object store" % (dataset.id, dataset.file_name)
+                    print "===++=== Job finish method handing dataset '%s' to object store" % dataset.file_name
                     self.app.object_store.update_from_file(dataset.id, create=True)
                 if context['stderr']:
                     dataset.blurb = "error"
diff --git a/lib/galaxy/jobs/runners/local.py b/lib/galaxy/jobs/runners/local.py
index e5357a27ed2..ff509dab5fe 100644
--- a/lib/galaxy/jobs/runners/local.py
+++ b/lib/galaxy/jobs/runners/local.py
@@ -118,7 +118,7 @@ class LocalJobRunner( BaseJobRunner ):
                                          preexec_fn = os.setpgrp )
             job_wrapper.external_output_metadata.set_job_runner_external_pid( external_metadata_proc.pid, self.sa_session )
             external_metadata_proc.wait()
-            log.debug( 'execution of external set_meta finished for job %d' % job_wrapper.job_id )
+            log.debug( 'execution of external set_meta for job %d finished' % job_wrapper.job_id )
         
         # Finish the job                
         try:
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 493f64ce91e..46e55589422 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -533,13 +533,12 @@ class Dataset( object ):
         self.external_filename = external_filename
         self._extra_files_path = extra_files_path
         self.file_size = file_size
+        
     def get_file_name( self ):
         if not self.external_filename:
             assert self.id is not None, "ID must be set before filename used (commit the object)"
             assert self.object_store is not None, "Object Store has not been initialized for dataset %s" % self.id
-            print "Calling get_filename 1", self.object_store
             filename = self.object_store.get_filename( self.id )
-            # print 'getting filename: ', filename
             if not self.object_store.exists( self.id ):
                 # Create directory if it does not exist
                 self.object_store.create( self.id, dir_only=True )
@@ -556,7 +555,6 @@ class Dataset( object ):
     file_name = property( get_file_name, set_file_name )
     @property
     def extra_files_path( self ):
-        print "Calling get_filename 2", self.object_store
         return self.object_store.get_filename( self.id, dir_only=True, extra_dir=self._extra_files_path or "dataset_%d_files" % self.id)
     def get_size( self, nice_size=False ):
         """Returns the size of the data on disk"""
@@ -1583,15 +1581,8 @@ class MetadataFile( object ):
         assert self.id is not None, "ID must be set before filename used (commit the object)"
         # Ensure the directory structure and the metadata file object exist
         try:
-            # self.history_dataset
-            # print "Dataset.file_path: %s, self.id: %s, self.history_dataset.dataset.object_store: %s" \
-            #     % (Dataset.file_path, self.id, self.history_dataset.dataset.object_store)
             self.history_dataset.dataset.object_store.create( self.id, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name="metadata_%d.dat" % self.id )
-            print "Calling get_filename 3", self.object_store
             path = self.history_dataset.dataset.object_store.get_filename( self.id, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name="metadata_%d.dat" % self.id )
-            print "Created metadata file at path: %s" % path
-            self.library_dataset
-            # raise
             return path
         except AttributeError:
             # In case we're not working with the history_dataset
diff --git a/lib/galaxy/objectstore/__init__.py b/lib/galaxy/objectstore/__init__.py
index cbf3bbd83e3..d318a1f4b5b 100644
--- a/lib/galaxy/objectstore/__init__.py
+++ b/lib/galaxy/objectstore/__init__.py
@@ -179,9 +179,9 @@ class DiskObjectStore(ObjectStore):
     Standard Galaxy object store, stores objects in files under a specific
     directory on disk.
     """
-    def __init__(self, app):
+    def __init__(self, config):
         super(DiskObjectStore, self).__init__()
-        self.file_path = app.config.file_path
+        self.file_path = config.file_path
     
     def _get_filename(self, dataset_id, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None):
         """Class method that returns the absolute path for the file corresponding
@@ -344,14 +344,14 @@ class S3ObjectStore(ObjectStore):
     cache exists that is used as an intermediate location for files between
     Galaxy and S3.
     """
-    def __init__(self, app):
+    def __init__(self, config):
         super(S3ObjectStore, self).__init__()
-        self.app = app
-        self.staging_path = self.app.config.file_path
+        self.config = config
+        self.staging_path = self.config.file_path
         self.s3_conn = S3Connection()
-        self.bucket = self._get_bucket(self.app.config.s3_bucket)
-        self.use_rr = self.app.config.use_reduced_redundancy
-        self.cache_size = self.app.config.object_store_cache_size * 1073741824 # Convert GBs to bytes
+        self.bucket = self._get_bucket(self.config.s3_bucket)
+        self.use_rr = self.config.use_reduced_redundancy
+        self.cache_size = self.config.object_store_cache_size * 1073741824 # Convert GBs to bytes
         self.transfer_progress = 0
         # Clean cache only if value is set in universe_wsgi.ini
         if self.cache_size != -1:
@@ -443,13 +443,13 @@ class S3ObjectStore(ObjectStore):
     def _fix_permissions(self, rel_path):
         """ Set permissions on rel_path"""
         for basedir, dirs, files in os.walk(rel_path):
-            util.umask_fix_perms(basedir, self.app.config.umask, 0777, self.app.config.gid)
+            util.umask_fix_perms(basedir, self.config.umask, 0777, self.config.gid)
             for f in files:
                 path = os.path.join(basedir, f)
                 # Ignore symlinks
                 if os.path.islink(path):
                     continue 
-                util.umask_fix_perms( path, self.app.config.umask, 0666, self.app.config.gid )
+                util.umask_fix_perms( path, self.config.umask, 0666, self.config.gid )
     
     def _construct_path(self, dataset_id, dir_only=None, extra_dir=None, extra_dir_at_root=False, alt_name=None):
         rel_path = os.path.join(*directory_hash_id(dataset_id))
@@ -594,12 +594,16 @@ class S3ObjectStore(ObjectStore):
             source_file = source_file if source_file else self._get_cache_path(rel_path)
             if os.path.exists(source_file):
                 key = Key(self.bucket, rel_path)
+                if os.path.getsize(source_file) == 0 and key.exists():
+                    log.debug("Wanted to push file '%s' to S3 key '%s' but its size is 0; skipping." % (source_file, rel_path))
+                    return True
                 if from_string:
                     key.set_contents_from_string(from_string, reduced_redundancy=self.use_rr)
                     log.debug("Pushed data from string '%s' to key '%s'" % (from_string, rel_path))
                 else:
                     start_time = datetime.now()
-                    print "[%s] Pushing cache file '%s' to key '%s'" % (start_time, source_file, rel_path)
+                    # print "Pushing cache file '%s' of size %s bytes to key '%s'" % (source_file, os.path.getsize(source_file), rel_path)
+                    # print "+ Push started at '%s'" % start_time
                     mb_size = os.path.getsize(source_file) / 1e6
                     if mb_size < 60:
                         self.transfer_progress = 0 # Reset transfer progress counter
@@ -607,10 +611,9 @@ class S3ObjectStore(ObjectStore):
                             cb=self._transfer_cb, num_cb=10)
                     else:
                         multipart_upload(self.bucket, key.name, source_file, mb_size, use_rr=self.use_rr)
-                        # self._multipart_upload(key.name, source_file, mb_size)
                     end_time = datetime.now()
-                    print "Push ended at '%s'; it lasted '%s'" % (end_time, end_time-start_time)
-                    log.debug("Pushed cache file '%s' to key '%s'" % (source_file, rel_path))
+                    # print "+ Push ended at   '%s'; %s bytes transfered in %ssec" % (end_time, os.path.getsize(source_file), end_time-start_time)
+                    log.debug("Pushed cache file '%s' to key '%s' (%s bytes transfered in %s sec)" % (source_file, rel_path, os.path.getsize(source_file), end_time-start_time))
                 return True
             else:
                 log.error("Tried updating key '%s' from source file '%s', but source file does not exist."
@@ -788,8 +791,9 @@ class S3ObjectStore(ObjectStore):
                 # Copy into cache
                 cache_file = self._get_cache_path(rel_path)
                 try:
-                    # FIXME? Should this be a `move`?
-                    shutil.copy2(source_file, cache_file)
+                    if source_file != cache_file:
+                        # FIXME? Should this be a `move`?
+                        shutil.copy2(source_file, cache_file)
                     self._fix_permissions(cache_file)
                 except OSError, ex:
                     log.error("Trouble copying source file '%s' to cache '%s': %s" % (source_file, cache_file, ex))
@@ -823,16 +827,16 @@ class HierarchicalObjectStore(ObjectStore):
         super(HierarchicalObjectStore, self).__init__()
     
 
-def build_object_store_from_config(app):
+def build_object_store_from_config(config):
     """ Depending on the configuration setting, invoke the appropriate object store
     """
-    store = app.config.object_store
+    store = config.object_store
     if store == 'disk':
-        return DiskObjectStore(app=app)
+        return DiskObjectStore(config=config)
     elif store == 's3':
-        os.environ['AWS_ACCESS_KEY_ID'] = app.config.aws_access_key
-        os.environ['AWS_SECRET_ACCESS_KEY'] = app.config.aws_secret_key
-        return S3ObjectStore(app=app)
+        os.environ['AWS_ACCESS_KEY_ID'] = config.aws_access_key
+        os.environ['AWS_SECRET_ACCESS_KEY'] = config.aws_secret_key
+        return S3ObjectStore(config=config)
     elif store == 'hierarchical':
         return HierarchicalObjectStore()
 
diff --git a/lib/galaxy/tools/actions/upload_common.py b/lib/galaxy/tools/actions/upload_common.py
index b27b0a70377..b0517e13c60 100644
--- a/lib/galaxy/tools/actions/upload_common.py
+++ b/lib/galaxy/tools/actions/upload_common.py
@@ -325,7 +325,6 @@ def create_job( trans, params, tool, json_file_path, data_list, folder=None, ret
             # Create an empty file immediately
             if not dataset.dataset.external_filename:
                 trans.app.object_store.create( dataset.id )
-                print "---> Upload tool created a folder(?) %s with ID %s? %s" % (dataset.file_name, dataset.id, trans.app.object_store.exists(dataset.id))
                 # open( dataset.file_name, "w" ).close()
     else:
         for i, dataset in enumerate( data_list ):
@@ -333,7 +332,6 @@ def create_job( trans, params, tool, json_file_path, data_list, folder=None, ret
             # Create an empty file immediately
             if not dataset.dataset.external_filename:
                 trans.app.object_store.create( dataset.id )
-                print "---> Upload tool created a file %s with ID %s? %s" % (dataset.file_name, dataset.id, trans.app.object_store.exists(dataset.id))
                 # open( dataset.file_name, "w" ).close()
     job.state = job.states.NEW
     trans.sa_session.add( job )
diff --git a/scripts/set_metadata.py b/scripts/set_metadata.py
index 792f3c18b71..a972ed05cfe 100644
--- a/scripts/set_metadata.py
+++ b/scripts/set_metadata.py
@@ -27,6 +27,9 @@ galaxy.datatypes.metadata.DATABASE_CONNECTION_AVAILABLE = False #Let metadata kn
 from galaxy.util import stringify_dictionary_keys
 from galaxy.util.json import from_json_string
 from sqlalchemy.orm import clear_mappers
+from galaxy.objectstore import build_object_store_from_config
+from galaxy import config
+import ConfigParser
 
 def __main__():
     file_path = sys.argv.pop( 1 )
@@ -34,11 +37,32 @@ def __main__():
     galaxy.model.Dataset.file_path = file_path
     galaxy.datatypes.metadata.MetadataTempFile.tmp_dir = tmp_dir
     
+    # Set up reference to object store
+    # First, read in the main config file for Galaxy; this is required because
+    # the object store configuration is stored there
+    conf = ConfigParser.ConfigParser()
+    config_file_name = 'universe_wsgi.ini' # Safe assumption?
+    conf.read(config_file_name)
+    conf_dict = {}
+    for section in conf.sections():
+        for option in conf.options(section):
+            try:
+                conf_dict[option] = conf.get(section, option)
+            except ConfigParser.InterpolationMissingOptionError:
+                # Because this is not called from Paste Script, %(here)s variable
+                # is not initialized in the config file so skip those fields -
+                # just need not to use any such fields for the object store conf...
+                log.debug("Did not load option %s from %s" % (option, config_file_name))
+    # config object is required by ObjectStore class so create it now
+    universe_config = config.Configuration(**conf_dict)
+    object_store = build_object_store_from_config(universe_config)
+    galaxy.model.Dataset.object_store = object_store
+    
     # Set up datatypes registry
     config_root = sys.argv.pop( 1 )
     datatypes_config = sys.argv.pop( 1 )
     galaxy.model.set_datatypes_registry( galaxy.datatypes.registry.Registry( config_root, datatypes_config ) )
-
+    
     job_metadata = sys.argv.pop( 1 )
     ext_override = dict()
     if job_metadata != "None" and os.path.exists( job_metadata ):
@@ -83,5 +107,7 @@ def __main__():
         except Exception, e:
             simplejson.dump( ( False, str( e ) ), open( filename_results_code, 'wb+' ) ) #setting metadata has failed somehow
     clear_mappers()
+    # Shut down any additional threads that might have been created via the ObjectStore
+    object_store.shutdown()
 
-__main__()
+__main__()
\ No newline at end of file

From cdb1b47d8f17b233c514482917d624fc57a637fa Mon Sep 17 00:00:00 2001
From: John Duddy <jduddy@illumina.com>
Date: Thu, 18 Aug 2011 14:16:03 -0700
Subject: [PATCH 010/362] Allow 2 new optional parameters to workflow/run
 controller method: history_id: an encoded history id to use. Will not
 permantently switch user's             current id hide_fixed_params:
 Initially hides all workflow parameters that are not             "Set at
 Runtime" and all workflow steps that only contain them.             Intended
 to reduce clutter when launching "canned" workflows.

Also added configurable feature that governs how initial values are selected
from the history for workflow runtime input. When enabled, this feature
causes Galaxy to use each input only once until it has used them all. This
is for the paired-end scenario, to attempt to match inputs correctly by default.
---
 lib/galaxy/config.py                   |   1 +
 lib/galaxy/tools/parameters/basic.py   |  31 ++-
 lib/galaxy/web/controllers/workflow.py | 322 +++++++++++++------------
 templates/workflow/run.mako            | 102 ++++----
 universe_wsgi.ini.sample               |  17 ++
 5 files changed, 275 insertions(+), 198 deletions(-)

diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py
index 2f3c5fa7a7a..4b3c57d3484 100644
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -46,6 +46,7 @@ class Configuration( object ):
         self.enable_api = string_as_bool( kwargs.get( 'enable_api', False ) )
         self.enable_openid = string_as_bool( kwargs.get( 'enable_openid', False ) )
         self.enable_quotas = string_as_bool( kwargs.get( 'enable_quotas', False ) )
+        self.enable_unique_workflow_defaults = string_as_bool ( kwargs.get ('enable_unique_workflow_defaults', False ) )
         self.tool_path = resolve_path( kwargs.get( "tool_path", "tools" ), self.root )
         self.tool_data_path = resolve_path( kwargs.get( "tool_data_path", "tool-data" ), os.getcwd() )
         self.len_file_path = kwargs.get( "len_file_path", resolve_path(os.path.join(self.tool_data_path, 'shared','ucsc','chrom'), self.root) )
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index c02a0346edb..fd1eeba3608 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -75,6 +75,16 @@ class ToolParameter( object ):
         """
         return None
 
+    def get_initial_value_from_history_prevent_repeats( self, trans, context, already_used ):
+        """
+        Get the starting value for the parameter, but if fetching from the history, try
+        to find a value that has not yet been used. already_used is a list of objects that
+        tools must manipulate (by adding to it) to store a memento that they can use to detect
+        if a value has already been chosen from the history. This is to support the capability to
+        choose each dataset once
+        """
+        return self.get_initial_value(trans, context);
+
     def get_required_enctype( self ):
         """
         If this parameter needs the form to have a specific encoding
@@ -1385,6 +1395,9 @@ class DataToolParameter( ToolParameter ):
         return field
 
     def get_initial_value( self, trans, context ):
+        return self.get_initial_value_from_history_prevent_repeats(trans, context, None);
+
+    def get_initial_value_from_history_prevent_repeats( self, trans, context, already_used ):
         """
         NOTE: This is wasteful since dynamic options and dataset collection
               happens twice (here and when generating HTML). 
@@ -1397,7 +1410,7 @@ class DataToolParameter( ToolParameter ):
         assert history is not None, "DataToolParameter requires a history"
         if self.optional:
             return None
-        most_recent_dataset = [None]
+        most_recent_dataset = []
         filter_value = None
         if self.options:
             try:
@@ -1423,15 +1436,19 @@ class DataToolParameter( ToolParameter ):
                             data = converted_dataset
                     if not is_valid or ( self.options and self._options_filter_attribute( data ) != filter_value ):
                         continue
-                    most_recent_dataset[0] = data
+                    most_recent_dataset.append(data)
                 # Also collect children via association object
                 dataset_collector( data.children )
         dataset_collector( history.datasets )
-        most_recent_dataset = most_recent_dataset.pop()
-        if most_recent_dataset is not None:
-            return most_recent_dataset
-        else:
-            return ''
+        most_recent_dataset.reverse()
+        if already_used is not None:
+            for val in most_recent_dataset:
+                if val is not None and val not in already_used:
+                    already_used.append(val)
+                    return val
+        if len(most_recent_dataset) > 0:
+            return most_recent_dataset[0]
+        return ''
 
     def from_html( self, value, trans, other_values={} ):
         # Can't look at history in workflow mode, skip validation and such,
diff --git a/lib/galaxy/web/controllers/workflow.py b/lib/galaxy/web/controllers/workflow.py
index 497d104e806..83516f0e305 100644
--- a/lib/galaxy/web/controllers/workflow.py
+++ b/lib/galaxy/web/controllers/workflow.py
@@ -1258,7 +1258,7 @@ class WorkflowController( BaseController, Sharable, UsesStoredWorkflow, UsesAnno
             ##     % ( workflow_name, web.url_for( action='editor', id=trans.security.encode_id(stored.id) ) ) )       
         
     @web.expose
-    def run( self, trans, id, **kwargs ):
+    def run( self, trans, id, history_id=None, hide_fixed_params=False, **kwargs ):
         stored = self.get_stored_workflow( trans, id, check_ownership=False )
         user = trans.get_user()
         if stored.user != user:
@@ -1279,163 +1279,185 @@ class WorkflowController( BaseController, Sharable, UsesStoredWorkflow, UsesAnno
         errors = {}
         has_upgrade_messages = False
         has_errors = False
-        if kwargs:
-            # If kwargs were provided, the states for each step should have
-            # been POSTed
-            # Get the kwarg keys for data inputs
-            input_keys = filter(lambda a: a.endswith('|input'), kwargs)
-            # Example: prefixed='2|input'
-            # Check if one of them is a list
-            multiple_input_key = None
-            multiple_inputs = [None]
-            for input_key in input_keys:
-                if isinstance(kwargs[input_key], list):
-                    multiple_input_key = input_key
-                    multiple_inputs = kwargs[input_key]
-            # List to gather values for the template
-            invocations=[]
-            for input_number, single_input in enumerate(multiple_inputs):
-                # Example: single_input='1', single_input='2', etc...
-                # 'Fix' the kwargs, to have only the input for this iteration
-                if multiple_input_key:
-                    kwargs[multiple_input_key] = single_input
+        saved_history = None
+        if history_id is not None:
+            saved_history = trans.get_history();
+            try:
+                decoded_history_id = trans.security.decode_id( history_id )
+                history = trans.sa_session.query(trans.app.model.History).get(decoded_history_id)
+                if history.user != trans.user and not trans.user_is_admin():
+                    if trans.sa_session.query(trans.app.model.HistoryUserShareAssociation).filter_by(user=trans.user, history=history).count() == 0:
+                        error("History is not owned by or shared with current user")
+                trans.set_history(history)
+            except TypeError:
+                error("Malformed history id ( %s ) specified, unable to decode." % str( history_id ))
+            except:
+                error("That history does not exist.")
+        try: # use a try/finally block to restore the user's current history
+            if kwargs:
+                # If kwargs were provided, the states for each step should have
+                # been POSTed
+                # Get the kwarg keys for data inputs
+                input_keys = filter(lambda a: a.endswith('|input'), kwargs)
+                # Example: prefixed='2|input'
+                # Check if one of them is a list
+                multiple_input_key = None
+                multiple_inputs = [None]
+                for input_key in input_keys:
+                    if isinstance(kwargs[input_key], list):
+                        multiple_input_key = input_key
+                        multiple_inputs = kwargs[input_key]
+                # List to gather values for the template
+                invocations=[]
+                for input_number, single_input in enumerate(multiple_inputs):
+                    # Example: single_input='1', single_input='2', etc...
+                    # 'Fix' the kwargs, to have only the input for this iteration
+                    if multiple_input_key:
+                        kwargs[multiple_input_key] = single_input
+                    for step in workflow.steps:
+                        step.upgrade_messages = {}
+                        # Connections by input name
+                        step.input_connections_by_name = \
+                            dict( ( conn.input_name, conn ) for conn in step.input_connections ) 
+                        # Extract just the arguments for this step by prefix
+                        p = "%s|" % step.id
+                        l = len(p)
+                        step_args = dict( ( k[l:], v ) for ( k, v ) in kwargs.iteritems() if k.startswith( p ) )
+                        step_errors = None
+                        if step.type == 'tool' or step.type is None:
+                            module = module_factory.from_workflow_step( trans, step )
+                            # Fix any missing parameters
+                            step.upgrade_messages = module.check_and_update_state()
+                            if step.upgrade_messages:
+                                has_upgrade_messages = True
+                            # Any connected input needs to have value DummyDataset (these
+                            # are not persisted so we need to do it every time)
+                            module.add_dummy_datasets( connections=step.input_connections )    
+                            # Get the tool
+                            tool = module.tool
+                            # Get the state
+                            step.state = state = module.state
+                            # Get old errors
+                            old_errors = state.inputs.pop( "__errors__", {} )
+                            # Update the state
+                            step_errors = tool.update_state( trans, tool.inputs, step.state.inputs, step_args,
+                                                             update_only=True, old_errors=old_errors )
+                        else:
+                            # Fix this for multiple inputs
+                            module = step.module = module_factory.from_workflow_step( trans, step )
+                            state = step.state = module.decode_runtime_state( trans, step_args.pop( "tool_state" ) )
+                            step_errors = module.update_runtime_state( trans, state, step_args )
+                        if step_errors:
+                            errors[step.id] = state.inputs["__errors__"] = step_errors   
+                    if 'run_workflow' in kwargs and not errors:
+                        new_history = None
+                        if 'new_history' in kwargs:
+                            if 'new_history_name' in kwargs and kwargs['new_history_name'] != '':
+                                nh_name = kwargs['new_history_name']
+                            else:
+                                nh_name = "History from %s workflow" % workflow.name
+                            if multiple_input_key:
+                                nh_name = '%s %d' % (nh_name, input_number + 1)
+                            new_history = trans.app.model.History( user=trans.user, name=nh_name )
+                            trans.sa_session.add( new_history )
+                        # Run each step, connecting outputs to inputs
+                        workflow_invocation = model.WorkflowInvocation()
+                        workflow_invocation.workflow = workflow
+                        outputs = odict()
+                        for i, step in enumerate( workflow.steps ):
+                            # Execute module
+                            job = None
+                            if step.type == 'tool' or step.type is None:
+                                tool = trans.app.toolbox.tools_by_id[ step.tool_id ]
+                                input_values = step.state.inputs
+                                # Connect up
+                                def callback( input, value, prefixed_name, prefixed_label ):
+                                    if isinstance( input, DataToolParameter ):
+                                        if prefixed_name in step.input_connections_by_name:
+                                            conn = step.input_connections_by_name[ prefixed_name ]
+                                            return outputs[ conn.output_step.id ][ conn.output_name ]
+                                visit_input_values( tool.inputs, step.state.inputs, callback )
+                                # Execute it
+                                job, out_data = tool.execute( trans, step.state.inputs, history=new_history)
+                                outputs[ step.id ] = out_data
+                                # Create new PJA associations with the created job, to be run on completion.
+                                # PJA Parameter Replacement (only applies to immediate actions-- rename specifically, for now)
+                                # Pass along replacement dict with the execution of the PJA so we don't have to modify the object.
+                                replacement_dict = {}
+                                for k, v in kwargs.iteritems():
+                                    if k.startswith('wf_parm|'):
+                                        replacement_dict[k[8:]] = v
+                                for pja in step.post_job_actions:
+                                    if pja.action_type in ActionBox.immediate_actions:
+                                        ActionBox.execute(trans.app, trans.sa_session, pja, job, replacement_dict)
+                                    else:
+                                        job.add_post_job_action(pja)
+                            else:
+                                job, out_data = step.module.execute( trans, step.state )
+                                outputs[ step.id ] = out_data
+                            # Record invocation
+                            workflow_invocation_step = model.WorkflowInvocationStep()
+                            workflow_invocation_step.workflow_invocation = workflow_invocation
+                            workflow_invocation_step.workflow_step = step
+                            workflow_invocation_step.job = job
+                        # All jobs ran sucessfully, so we can save now
+                        trans.sa_session.add( workflow_invocation )
+                        invocations.append({'outputs': outputs,
+                                            'new_history': new_history})
+                trans.sa_session.flush()
+                return trans.fill_template( "workflow/run_complete.mako",
+                                            workflow=stored,
+                                            invocations=invocations )
+            else:
+                # Prepare each step
+                missing_tools = []
                 for step in workflow.steps:
                     step.upgrade_messages = {}
-                    # Connections by input name
-                    step.input_connections_by_name = \
-                        dict( ( conn.input_name, conn ) for conn in step.input_connections ) 
-                    # Extract just the arguments for this step by prefix
-                    p = "%s|" % step.id
-                    l = len(p)
-                    step_args = dict( ( k[l:], v ) for ( k, v ) in kwargs.iteritems() if k.startswith( p ) )
-                    step_errors = None
+                    # Contruct modules
                     if step.type == 'tool' or step.type is None:
-                        module = module_factory.from_workflow_step( trans, step )
-                        # Fix any missing parameters
-                        step.upgrade_messages = module.check_and_update_state()
+                        # Restore the tool state for the step
+                        step.module = module_factory.from_workflow_step( trans, step )
+                        if not step.module:
+                            if step.tool_id not in missing_tools:
+                                missing_tools.append(step.tool_id)
+                            continue
+                        step.upgrade_messages = step.module.check_and_update_state()
                         if step.upgrade_messages:
                             has_upgrade_messages = True
                         # Any connected input needs to have value DummyDataset (these
                         # are not persisted so we need to do it every time)
-                        module.add_dummy_datasets( connections=step.input_connections )    
-                        # Get the tool
-                        tool = module.tool
-                        # Get the state
-                        step.state = state = module.state
-                        # Get old errors
-                        old_errors = state.inputs.pop( "__errors__", {} )
-                        # Update the state
-                        step_errors = tool.update_state( trans, tool.inputs, step.state.inputs, step_args,
-                                                         update_only=True, old_errors=old_errors )
+                        step.module.add_dummy_datasets( connections=step.input_connections )                  
+                        # Store state with the step
+                        step.state = step.module.state
+                        # Error dict
+                        if step.tool_errors:
+                            has_errors = True
+                            errors[step.id] = step.tool_errors
                     else:
-                        # Fix this for multiple inputs
-                        module = step.module = module_factory.from_workflow_step( trans, step )
-                        state = step.state = module.decode_runtime_state( trans, step_args.pop( "tool_state" ) )
-                        step_errors = module.update_runtime_state( trans, state, step_args )
-                    if step_errors:
-                        errors[step.id] = state.inputs["__errors__"] = step_errors   
-                if 'run_workflow' in kwargs and not errors:
-                    new_history = None
-                    if 'new_history' in kwargs:
-                        if 'new_history_name' in kwargs and kwargs['new_history_name'] != '':
-                            nh_name = kwargs['new_history_name']
-                        else:
-                            nh_name = "History from %s workflow" % workflow.name
-                        if multiple_input_key:
-                            nh_name = '%s %d' % (nh_name, input_number + 1)
-                        new_history = trans.app.model.History( user=trans.user, name=nh_name )
-                        trans.sa_session.add( new_history )
-                    # Run each step, connecting outputs to inputs
-                    workflow_invocation = model.WorkflowInvocation()
-                    workflow_invocation.workflow = workflow
-                    outputs = odict()
-                    for i, step in enumerate( workflow.steps ):
-                        # Execute module
-                        job = None
-                        if step.type == 'tool' or step.type is None:
-                            tool = trans.app.toolbox.tools_by_id[ step.tool_id ]
-                            input_values = step.state.inputs
-                            # Connect up
-                            def callback( input, value, prefixed_name, prefixed_label ):
-                                if isinstance( input, DataToolParameter ):
-                                    if prefixed_name in step.input_connections_by_name:
-                                        conn = step.input_connections_by_name[ prefixed_name ]
-                                        return outputs[ conn.output_step.id ][ conn.output_name ]
-                            visit_input_values( tool.inputs, step.state.inputs, callback )
-                            # Execute it
-                            job, out_data = tool.execute( trans, step.state.inputs, history=new_history)
-                            outputs[ step.id ] = out_data
-                            # Create new PJA associations with the created job, to be run on completion.
-                            # PJA Parameter Replacement (only applies to immediate actions-- rename specifically, for now)
-                            # Pass along replacement dict with the execution of the PJA so we don't have to modify the object.
-                            replacement_dict = {}
-                            for k, v in kwargs.iteritems():
-                                if k.startswith('wf_parm|'):
-                                    replacement_dict[k[8:]] = v
-                            for pja in step.post_job_actions:
-                                if pja.action_type in ActionBox.immediate_actions:
-                                    ActionBox.execute(trans.app, trans.sa_session, pja, job, replacement_dict)
-                                else:
-                                    job.add_post_job_action(pja)
-                        else:
-                            job, out_data = step.module.execute( trans, step.state )
-                            outputs[ step.id ] = out_data
-                        # Record invocation
-                        workflow_invocation_step = model.WorkflowInvocationStep()
-                        workflow_invocation_step.workflow_invocation = workflow_invocation
-                        workflow_invocation_step.workflow_step = step
-                        workflow_invocation_step.job = job
-                    # All jobs ran sucessfully, so we can save now
-                    trans.sa_session.add( workflow_invocation )
-                    invocations.append({'outputs': outputs,
-                                        'new_history': new_history})
-            trans.sa_session.flush()
-            return trans.fill_template( "workflow/run_complete.mako",
-                                        workflow=stored,
-                                        invocations=invocations )
-        else:
-            # Prepare each step
-            missing_tools = []
-            for step in workflow.steps:
-                step.upgrade_messages = {}
-                # Contruct modules
-                if step.type == 'tool' or step.type is None:
-                    # Restore the tool state for the step
-                    step.module = module_factory.from_workflow_step( trans, step )
-                    if not step.module:
-                        if step.tool_id not in missing_tools:
-                            missing_tools.append(step.tool_id)
-                        continue
-                    step.upgrade_messages = step.module.check_and_update_state()
-                    if step.upgrade_messages:
-                        has_upgrade_messages = True
-                    # Any connected input needs to have value DummyDataset (these
-                    # are not persisted so we need to do it every time)
-                    step.module.add_dummy_datasets( connections=step.input_connections )                  
-                    # Store state with the step
-                    step.state = step.module.state
-                    # Error dict
-                    if step.tool_errors:
-                        has_errors = True
-                        errors[step.id] = step.tool_errors
-                else:
-                    ## Non-tool specific stuff?
-                    step.module = module_factory.from_workflow_step( trans, step )
-                    step.state = step.module.get_runtime_state()
-                # Connections by input name
-                step.input_connections_by_name = dict( ( conn.input_name, conn ) for conn in step.input_connections )
-            if missing_tools:
-                stored.annotation = self.get_item_annotation_str( trans.sa_session, trans.user, stored )
-                return trans.fill_template("workflow/run.mako", steps=[], workflow=stored, missing_tools = missing_tools)
-        # Render the form
-        stored.annotation = self.get_item_annotation_str( trans.sa_session, trans.user, stored )
-        return trans.fill_template(
-                    "workflow/run.mako", 
-                    steps=workflow.steps,
-                    workflow=stored,
-                    has_upgrade_messages=has_upgrade_messages,
-                    errors=errors,
-                    incoming=kwargs )
+                        ## Non-tool specific stuff?
+                        step.module = module_factory.from_workflow_step( trans, step )
+                        step.state = step.module.get_runtime_state()
+                    # Connections by input name
+                    step.input_connections_by_name = dict( ( conn.input_name, conn ) for conn in step.input_connections )
+                if missing_tools:
+                    stored.annotation = self.get_item_annotation_str( trans.sa_session, trans.user, stored )
+                    return trans.fill_template("workflow/run.mako", steps=[], workflow=stored, missing_tools = missing_tools)
+            # Render the form
+            stored.annotation = self.get_item_annotation_str( trans.sa_session, trans.user, stored )
+            return trans.fill_template(
+                        "workflow/run.mako", 
+                        steps=workflow.steps,
+                        workflow=stored,
+                        has_upgrade_messages=has_upgrade_messages,
+                        errors=errors,
+                        incoming=kwargs,
+                        history_id=history_id,
+                        hide_fixed_params=hide_fixed_params,
+                        enable_unique_defaults=trans.app.config.enable_unique_workflow_defaults)
+        finally:
+            # restore the active history
+            if saved_history is not None:
+                trans.set_history(saved_history) 
                     
     def get_item( self, trans, id ):
         return self.get_stored_workflow( trans, id ) 
diff --git a/templates/workflow/run.mako b/templates/workflow/run.mako
index 7d6dc5c1d4a..afe3f464122 100644
--- a/templates/workflow/run.mako
+++ b/templates/workflow/run.mako
@@ -6,8 +6,12 @@
     <script type="text/javascript">
         $( function() {
             function show_tool_body(title){
-                title.parent().css('border-bottom-width', '1px');
+                title.parent().show().css('border-bottom-width', '1px');
                 title.next().show('fast');
+                if ('${hide_fixed_params}'.toLowerCase() == 'true') {
+                    // show previously hidden parameters
+                    title.next().children(".form-row").show();
+                }
             }
             function hide_tool_body(title){
                 title.parent().css('border-bottom-width', '0px');
@@ -46,8 +50,15 @@
             $("div.toolFormTitle").click(function(){
                 toggle_tool_body($(this));
             });
-            // Collapse non-interactive run-workflow panels by default.
-            $("div.toolFormBody:not(:has(select, textarea, input[type!=hidden], .wfpspan))").hide().parent().css('border-bottom-width', '0px');
+            if ('${hide_fixed_params}'.toLowerCase() == 'true') {
+                // hide parameters that are not runtime inputs
+                $("div.form-row:not(:has(select, textarea, input[type!=hidden], .wfpspan))").hide();
+                $("div.toolForm:not(:has(select, textarea, input[type!=hidden], .wfpspan))").hide();
+            }
+            else {
+                // Collapse non-interactive run-workflow panels by default.
+                $("div.toolFormBody:not(:has(select, textarea, input[type!=hidden], .wfpspan))").hide().parent().css('border-bottom-width', '0px');
+            }
             $("#show_all_tool_body").click(function(){
                 $("div.toolFormTitle").each(function(){
                     show_tool_body($(this));
@@ -163,6 +174,8 @@ import re
 import colorsys
 import random
 
+used_accumulator = []
+
 wf_parms = {}
 for step in steps:
     for v in [ActionBox.get_short_str(pja) for pja in step.post_job_actions] + step.state.inputs.values():
@@ -178,7 +191,7 @@ if wf_parms:
         hue += hue_offset
 %>
 
-<%def name="do_inputs( inputs, values, errors, prefix, step, other_values = None )">
+<%def name="do_inputs( inputs, values, errors, prefix, step, other_values = None, already_used = None )">
   %if other_values is None:
       <% other_values = values %>
   %endif
@@ -196,7 +209,7 @@ if wf_parms:
             <div class="repeat-group-item">
             <% index = repeat_values[i]['__index__'] %>
             <div class="form-title-row"><b>${input.title} ${i + 1}</b></div>
-            ${do_inputs( input.inputs, repeat_values[ i ], rep_errors,  prefix + input.name + "_" + str(index) + "|", step, other_values )}
+            ${do_inputs( input.inputs, repeat_values[ i ], rep_errors,  prefix + input.name + "_" + str(index) + "|", step, other_values, already_used )}
             ## <div class="form-row"><input type="submit" name="${step.id}|${prefix}${input.name}_${i}_remove" value="Remove ${input.title} ${i+1}" /></div>
             </div>
           %endfor
@@ -207,15 +220,15 @@ if wf_parms:
       <% current_case = group_values['__current_case__'] %>
       <% new_prefix = prefix + input.name + "|" %>
       <% group_errors = errors.get( input.name, {} ) %>
-      ${row_for_param( input.test_param, group_values[ input.test_param.name ], other_values, group_errors, prefix, step )}
-      ${do_inputs( input.cases[ current_case ].inputs, group_values, group_errors, new_prefix, step, other_values )}
+      ${row_for_param( input.test_param, group_values[ input.test_param.name ], other_values, group_errors, prefix, step, already_used )}
+      ${do_inputs( input.cases[ current_case ].inputs, group_values, group_errors, new_prefix, step, other_values, already_used )}
     %else:
-      ${row_for_param( input, values[ input.name ], other_values, errors, prefix, step )}
+      ${row_for_param( input, values[ input.name ], other_values, errors, prefix, step, already_used )}
     %endif
   %endfor
 </%def>
 
-<%def name="row_for_param( param, value, other_values, error_dict, prefix, step )">
+<%def name="row_for_param( param, value, other_values, error_dict, prefix, step, already_used )">
     ## -- ${param.name} -- ${step.state.inputs} --
     %if error_dict.has_key( param.name ):
         <% cls = "form-row form-row-error" %>
@@ -235,7 +248,9 @@ if wf_parms:
                     ## FIXME: Initialize in the controller
                     <%
                     if value is None:
-                        value = other_values[ param.name ] = param.get_initial_value( t, other_values )
+                        value = other_values[ param.name ] = param.get_initial_value_from_history_prevent_repeats( t, other_values, already_used )
+                        if not enable_unique_defaults:
+                            del already_used[:]
                     %>
                     ${param.get_html_field( t, value, other_values ).get_html( str(step.id) + "|" + prefix )}
                     <input type="hidden" name="${step.id}|__force_update__${prefix}${param.name}" value="true" />
@@ -250,7 +265,11 @@ if wf_parms:
                 ## controller should go through the inputs on the first
                 ## load, fill in initial values where needed, and mark
                 ## all that are runtime modifiable in some way.
-                <% value = other_values[ param.name ] = param.get_initial_value( t, other_values ) %>
+                <%
+                    value = other_values[ param.name ] = param.get_initial_value_from_history_prevent_repeats( t, other_values, already_used )
+                    if not enable_unique_defaults:
+                        del already_used[:]
+                %>
                 ${param.get_html_field( t, value, other_values ).get_html( str(step.id) + "|" + prefix )}
                 <input type="hidden" name="${step.id}|__runtime__${prefix}${param.name}" value="true" />
             %else:
@@ -342,7 +361,6 @@ if wf_parms:
     });
     </script>
 %endif
-
 %for i, step in enumerate( steps ):
     %if step.type == 'tool' or step.type is None:
       <% tool = app.toolbox.tools_by_id[step.tool_id] %>
@@ -355,36 +373,36 @@ if wf_parms:
               % endif
           </div>
           <div class="toolFormBody">
-            ${do_inputs( tool.inputs, step.state.inputs, errors.get( step.id, dict() ), "", step )}
-            % if step.post_job_actions:
-                <hr/>
-                <div class='form-row'>
-                % if len(step.post_job_actions) > 1:
-                    <label>Actions:</label>
-                % else:
-                    <label>Action:</label>
+                ${do_inputs( tool.inputs, step.state.inputs, errors.get( step.id, dict() ), "", step, None, used_accumulator )}
+                % if step.post_job_actions:
+                    <hr/>
+                    <div class='form-row'>
+                    % if len(step.post_job_actions) > 1:
+                        <label>Actions:</label>
+                    % else:
+                        <label>Action:</label>
+                    % endif
+                    <%
+                    pja_ss_all = []
+                    for pja_ss in [ActionBox.get_short_str(pja) for pja in step.post_job_actions]:
+                        for rematch in re.findall('\$\{.+?\}', pja_ss):
+                            pja_ss = pja_ss.replace(rematch, '<span style="background-color:%s" class="wfpspan wf_parm__%s pja_wfp">%s</span>' % (wf_parms[rematch[2:-1]], rematch[2:-1], rematch[2:-1]))
+                        pja_ss_all.append(pja_ss)
+                    %>
+                    ${'<br/>'.join(pja_ss_all)}
+                    </div>
                 % endif
-                <%
-                pja_ss_all = []
-                for pja_ss in [ActionBox.get_short_str(pja) for pja in step.post_job_actions]:
-                    for rematch in re.findall('\$\{.+?\}', pja_ss):
-                        pja_ss = pja_ss.replace(rematch, '<span style="background-color:%s" class="wfpspan wf_parm__%s pja_wfp">%s</span>' % (wf_parms[rematch[2:-1]], rematch[2:-1], rematch[2:-1]))
-                    pja_ss_all.append(pja_ss)
-                %>
-                ${'<br/>'.join(pja_ss_all)}
-                </div>
-            % endif
+              </div>
           </div>
-      </div>
-    %else:
-    <% module = step.module %>
-      <input type="hidden" name="${step.id}|tool_state" value="${module.encode_runtime_state( t, step.state )}">
-      <div class="toolForm">
-          <div class="toolFormTitle">
-              <span class='title_ul_text'>Step ${int(step.order_index)+1}: ${module.name}</span>
-              % if step.annotations:
-                <div class="step-annotation">${step.annotations[0].annotation}</div>
-              % endif
+        %else:
+        <% module = step.module %>
+          <input type="hidden" name="${step.id}|tool_state" value="${module.encode_runtime_state( t, step.state )}">
+          <div class="toolForm">
+              <div class="toolFormTitle">
+                  <span class='title_ul_text'>Step ${int(step.order_index)+1}: ${module.name}</span>
+                  % if step.annotations:
+                    <div class="step-annotation">${step.annotations[0].annotation}</div>
+                  % endif
           </div>
           <div class="toolFormBody">
               <%
@@ -397,7 +415,7 @@ if wf_parms:
               if not type_filter:
                   type_filter = ['data']
               %>
-              ${do_inputs( module.get_runtime_inputs(type_filter), step.state.inputs, errors.get( step.id, dict() ), "", step )}
+              ${do_inputs( module.get_runtime_inputs(type_filter), step.state.inputs, errors.get( step.id, dict() ), "", step, None, used_accumulator )}
           </div>
       </div>
     %endif
@@ -411,10 +429,12 @@ if wf_parms:
     %endfor
     </ul>
 %else:
+    %if history_id is None:
 <p id='new_history_p'>
     <input type="checkbox" name='new_history' value="true" id='new_history_cbx'/><label for='new_history_cbx'>Send results to a new history </label>
     <span id="new_history_input">named: <input type='text' name='new_history_name' value='${h.to_unicode( workflow.name )}'/></span>
 </p>
+    %endif
 <input type="submit" name="run_workflow" value="Run workflow" />
 </form>
 %endif
diff --git a/universe_wsgi.ini.sample b/universe_wsgi.ini.sample
index a33f65ad01e..8dbd1002669 100644
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -444,6 +444,14 @@ use_interactive = True
 # large servers.
 #enable_tool_tags = False
 
+# Enable a feature when running workflows. When enabled, default datasets
+# are selected for "Set at Runtime" inputs from the history such that the
+# same input will not be selected twice, unless there are more inputs than
+# compatible datasets in the history.
+# When False, the most recently added compatible item in the history will
+# be used for each "Set at Runtime" input, independent of others in the Workflow
+#enable_unique_workflow_defaults = False
+
 # Enable Galaxy's "Upload via FTP" interface.  You'll need to install and
 # configure an FTP server (we've used ProFTPd since it can use Galaxy's
 # database for authentication) and set the following two options.
@@ -459,6 +467,15 @@ use_interactive = True
 # Enable enforcement of quotas.  Quotas can be set from the Admin interface.
 #enable_quotas = False
 
+# Enable a feature when running workflows. When enabled, default datasets
+# are selected for "Set at Runtime" inputs from the history such that the
+# same input will not be selected twice, unless there are more inputs than
+# compatible datasets in the history.
+# When False, the most recently added compatible item in the history will
+# be used for each "Set at Runtime" input, independent of others in the Workflow
+#enable_unique_workflow_defaults = False
+
+
 # -- Job Execution
 
 # If running multiple Galaxy processes, one can be designated as the job

From 2eeb2a14aad097d86f84106537c90f118e3641bb Mon Sep 17 00:00:00 2001
From: John Duddy <jduddy@illumina.com>
Date: Thu, 18 Aug 2011 14:38:26 -0700
Subject: [PATCH 011/362] Removed duplicate section (merge error)

---
 universe_wsgi.ini.sample | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/universe_wsgi.ini.sample b/universe_wsgi.ini.sample
index 8dbd1002669..feee5ad718b 100644
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -444,14 +444,6 @@ use_interactive = True
 # large servers.
 #enable_tool_tags = False
 
-# Enable a feature when running workflows. When enabled, default datasets
-# are selected for "Set at Runtime" inputs from the history such that the
-# same input will not be selected twice, unless there are more inputs than
-# compatible datasets in the history.
-# When False, the most recently added compatible item in the history will
-# be used for each "Set at Runtime" input, independent of others in the Workflow
-#enable_unique_workflow_defaults = False
-
 # Enable Galaxy's "Upload via FTP" interface.  You'll need to install and
 # configure an FTP server (we've used ProFTPd since it can use Galaxy's
 # database for authentication) and set the following two options.

From 4770146fad06cb17108cf465a946f1394cfac24f Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Mon, 3 Oct 2011 17:12:41 -0400
Subject: [PATCH 012/362] Fix typos.

---
 tools/ngs_rna/cufflinks_wrapper.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/ngs_rna/cufflinks_wrapper.xml b/tools/ngs_rna/cufflinks_wrapper.xml
index 9b727b96264..59c4f122ee6 100644
--- a/tools/ngs_rna/cufflinks_wrapper.xml
+++ b/tools/ngs_rna/cufflinks_wrapper.xml
@@ -61,10 +61,10 @@
             </param>
             <when value="No"></when>
             <when value="Use reference annotation">
-                <param format="gff3,gtf" name="reference_annotation_file" type="data" label="Reference Aonnotation" help="Make sure your annotation file is in GTF format and that Galaxy knows that your file is GTF--not GFF."/>
+                <param format="gff3,gtf" name="reference_annotation_file" type="data" label="Reference Annotation" help="Make sure your annotation file is in GTF format and that Galaxy knows that your file is GTF--not GFF."/>
             	</when>
 	        <when value="Use reference annotation guide">
-                <param format="gff3,gtf" name="reference_annotation_guide_file" type="data" label="Reference Aonnotation" help="Make sure your annotation file is in GTF format and that Galaxy knows that your file is GTF--not GFF."/>
+                <param format="gff3,gtf" name="reference_annotation_guide_file" type="data" label="Reference Annotation" help="Make sure your annotation file is in GTF format and that Galaxy knows that your file is GTF--not GFF."/>
                 </when>
         </conditional>
         <conditional name="bias_correction">

From f8261fe8063e7be8844fdd067dca315e33b5e596 Mon Sep 17 00:00:00 2001
From: Ross Lazarus <ross.lazarus@gmail.com>
Date: Tue, 4 Oct 2011 09:38:33 +1100
Subject: [PATCH 013/362] Increase size limit for display of html files to
 10000000 bytes - mirdeep2 creates very large html objects. Size limit for
 display should probably be configurable.

---
 lib/galaxy/web/controllers/dataset.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/lib/galaxy/web/controllers/dataset.py b/lib/galaxy/web/controllers/dataset.py
index 700823c1f66..6cb7598d369 100644
--- a/lib/galaxy/web/controllers/dataset.py
+++ b/lib/galaxy/web/controllers/dataset.py
@@ -376,6 +376,8 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesHistory, UsesHist
             raise paste.httpexceptions.HTTPNotFound( "File Not Found (%s)." % data.file_name )
         
         max_peek_size = 1000000 # 1 MB
+        if isinstance(data.datatype, datatypes.images.Html):
+            max_peek_size = 10000000 # 10 MB for html
         if not preview or isinstance(data.datatype, datatypes.images.Image) or os.stat( data.file_name ).st_size < max_peek_size:
             return open( data.file_name )
         else:

From a12ef5b45d89117691973d6a9877fd3a67b89687 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Tue, 4 Oct 2011 10:14:25 -0400
Subject: [PATCH 014/362] Fix bug in setting shared visualization's viewport.

---
 templates/visualization/display.mako | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/templates/visualization/display.mako b/templates/visualization/display.mako
index 2cf9992a1dd..a34b132f71a 100644
--- a/templates/visualization/display.mako
+++ b/templates/visualization/display.mako
@@ -92,7 +92,8 @@
                 var callback = function() { view.change_chrom( '${config['viewport']['chrom']}', ${config['viewport']['start']}, ${config['viewport']['end']} ); }
             %endif
             view = create_visualization( container_element, "${config.get('title') | h}", 
-                                         "${config.get('vis_id')}", "${config.get('dbkey')}", callback,
+                                         "${config.get('vis_id')}", "${config.get('dbkey')}",
+                                         JSON.parse('${ h.to_json_string( config.get( 'viewport', dict() ) ) }'),
                                          JSON.parse('${ h.to_json_string( config.get('tracks') ) }'),
                                          JSON.parse('${ h.to_json_string( config.get('bookmarks') ) }')
                                          );

From 362026e64e4237c655d3444a79ef39c8c4c4af58 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Tue, 4 Oct 2011 15:56:21 -0400
Subject: [PATCH 015/362] Trackster: add feature-position mapper so that a
 feature's data can be recovered using from screen position. This is the
 foundation for providing feature data on mouseover and/or click.

---
 static/scripts/packed/trackster.js |  2 +-
 static/scripts/trackster.js        | 92 ++++++++++++++++++++++++++----
 2 files changed, 82 insertions(+), 12 deletions(-)

diff --git a/static/scripts/packed/trackster.js b/static/scripts/packed/trackster.js
index a6885227861..0b6e08e398d 100644
--- a/static/scripts/packed/trackster.js
+++ b/static/scripts/packed/trackster.js
@@ -1 +1 @@
-var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var trackster_module=function(f,aa){var q=f("class").extend,t=f("slotting"),N=f("painters");var ag=function(ah,ai){this.document=ah;this.default_font=ai!==undefined?ai:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};q(ag.prototype,{load_pattern:function(ah,al){var ai=this.patterns,aj=this.dummy_context,ak=new Image();ak.src=image_path+al;ak.onload=function(){ai[ah]=aj.createPattern(ak,"repeat")}},get_pattern:function(ah){return this.patterns[ah]},new_canvas:function(){var ah=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ah)}ah.manager=this;return ah}});var o={};var m=function(ah,ai){o[ah.attr("id")]=ai};var n=function(ah,aj,al,ak){al=".group";var ai={};o[ah.attr("id")]=ak;ah.bind("drag",{handle:"."+aj,relative:true},function(au,av){var at=$(this);var ay=$(this).parent(),ap=ay.children(),ar=o[$(this).attr("id")],ao,an,aw,am,aq;an=$(this).parents(al);if(an.length!==0){aw=an.position().top;am=aw+an.outerHeight();if(av.offsetY<aw){$(this).insertBefore(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable_before(ar,ax);return}else{if(av.offsetY>am){$(this).insertAfter(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable(ar);return}}}an=null;for(aq=0;aq<ap.length;aq++){ao=$(ap.get(aq));aw=ao.position().top;am=aw+ao.outerHeight();if(ao.is(al)&&this!==ao.get(0)&&av.offsetY>=aw&&av.offsetY<=am){if(av.offsetY-aw<am-av.offsetY){ao.find(".content-div").prepend(this)}else{ao.find(".content-div").append(this)}if(ar.container){ar.container.remove_drawable(ar)}o[ao.attr("id")].add_drawable(ar);return}}for(aq=0;aq<ap.length;aq++){if(av.offsetY<$(ap.get(aq)).position().top){break}}if(aq===ap.length){if(this!==ap.get(aq-1)){ay.append(this);o[ay.attr("id")].move_drawable(ar,aq)}}else{if(this!==ap.get(aq)){$(this).insertBefore(ap.get(aq));o[ay.attr("id")].move_drawable(ar,(av.deltaY>0?aq-1:aq))}}}).bind("dragstart",function(){ai["border-top"]=ah.css("border-top");ai["border-bottom"]=ah.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ai)})};aa.moveable=n;var af=16,I=9,F=20,V=I+2,B=100,K=12000,T=200,E=5,w=10,M=5000,x=100,p="There was an error in indexing this dataset. ",L="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",u="Currently indexing... please wait",z="Tool cannot be rerun: ",a="Loading data...",ab="Ready for display",d=10,v=5,D=5;function y(ah){return Math.round(ah*1000)/1000}var c=function(ah){this.num_elements=ah;this.clear()};q(c.prototype,{get:function(ai){var ah=this.key_ary.indexOf(ai);if(ah!==-1){if(this.obj_cache[ai].stale){this.key_ary.splice(ah,1);delete this.obj_cache[ai]}else{this.move_key_to_end(ai,ah)}}return this.obj_cache[ai]},set:function(ai,aj){if(!this.obj_cache[ai]){if(this.key_ary.length>=this.num_elements){var ah=this.key_ary.shift();delete this.obj_cache[ah]}this.key_ary.push(ai)}this.obj_cache[ai]=aj;return aj},move_key_to_end:function(ai,ah){this.key_ary.splice(ah,1);this.key_ary.push(ai)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var U=function(ai,ah,aj){c.call(this,ai);this.track=ah;this.subset=(aj!==undefined?aj:true)};q(U.prototype,c.prototype,{load_data:function(aq,al,ao,ai,an){var ap=this.track.view.chrom,ak={chrom:ap,low:aq,high:al,mode:ao,resolution:ai,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ak,an);if(this.track.filters_manager){var ar=[];var ah=this.track.filters_manager.filters;for(var am=0;am<ah.length;am++){ar[ar.length]=ah[am].name}ak.filter_cols=JSON.stringify(ar)}var aj=this;return $.getJSON(this.track.data_url,ak,function(at){aj.set_data(aq,al,ao,at)})},get_data:function(ah,al,am,ai,ak){var aj=this.get_data_from_cache(ah,al,am);if(aj){return aj}aj=this.load_data(ah,al,am,ai,ak);this.set_data(ah,al,am,aj);return aj},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ap,ak,ao,aj,an,al){var aq=this.get_data_from_cache(ap,ak,ao);if(!aq){console.log("ERROR: no current data for: ",this.track,ap,ak,ao,aj,an);return}aq.stale=true;var ai=ap;if(al===this.DEEP_DATA_REQ){$.extend(an,{start_val:aq.data.length+1})}else{if(al===this.BROAD_DATA_REQ){ai=(aq.max_high?aq.max_high:aq.data[aq.data.length-1][2])+1}}var ah=this,am=this.load_data(ai,ak,ao,aj,an);new_data_available=$.Deferred();this.set_data(ap,ak,ao,new_data_available);$.when(am).then(function(ar){if(ar.data){ar.data=aq.data.concat(ar.data);if(ar.max_low){ar.max_low=aq.max_low}if(ar.message){ar.message=ar.message.replace(/[0-9]+/,ar.data.length)}}ah.set_data(ap,ak,ao,ar);new_data_available.resolve(ar)});return new_data_available},get_data_from_cache:function(ah,ai,aj){return this.get(this.gen_key(ah,ai,aj))},set_data:function(ai,aj,ak,ah){return this.set(this.gen_key(ai,aj,ak),ah)},gen_key:function(ah,aj,ak){var ai=ah+"_"+aj+"_"+ak;return ai},split_key:function(ah){return ah.split("_")}});var J=function(ai,ah,aj){U.call(this,ai,ah,aj)};q(J.prototype,U.prototype,c.prototype,{load_data:function(aj,ah,al,am,ai,ak){if(ai>1){return}return U.prototype.load_data.call(this,aj,ah,al,am,ai,ak)}});var r=function(ak,ai,ah,aj,al){this.name=ak;this.view=ai;this.container=ah;this.drag_handle_class=al;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak}],saved_values:aj,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values};q(r.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},make_name_popup_menu:function(){},set_name:function(ah){this.old_name=this.name;this.name=ah;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var A=function(al,ak,ai,ah,aj,am){r.call(this,ak,ai,ah,aj,am);this.obj_type=al;this.drawables=[]};q(A.prototype,r.prototype,{init:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah].init()}},_draw:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah]._draw()}},to_json:function(){var ai=[];for(var ah=0;ah<this.drawables.length;ah++){ai.push(this.drawables[ah].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ai}},add_drawable:function(ah){this.drawables.push(ah);ah.container=this},add_drawable_before:function(aj,ah){var ai=this.drawables.indexOf(ah);if(ai!=-1){this.drawables.splice(ai,0,aj);return true}return false},remove_drawable:function(ai){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);ai.container=null;return true}return false},move_drawable:function(ai,aj){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);this.drawables.splice(aj,0,ai);return true}return false}});var S=function(ak,ai,ah,aj){A.call(this,"DrawableGroup",ak,ai,ah,aj,"group-handle");if(!S.id_counter){S.id_counter=0}var al=S.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+al).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+al+"_content_div").appendTo(this.container_div);m(this.container_div,this);m(this.content_div,this);n(this.container_div,this.drag_handle_class,".group",this);this.make_name_popup_menu()};q(S.prototype,r.prototype,A.prototype,{make_name_popup_menu:function(){var ai=this;var ah={};ah["Edit configuration"]=function(){var al=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aj=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(am){if((am.keyCode||am.which)===27){al()}else{if((am.keyCode||am.which)===13){aj()}}};$(window).bind("keypress.check_enter_esc",ak);show_modal("Configure Group",ai.config.build_form(),{Cancel:al,OK:aj})};ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)}});var ae=function(ah,ak,aj,ai){A.call(this,"View");this.container=ah;this.chrom=null;this.vis_id=aj;this.dbkey=ai;this.title=ak;this.tracks=this.drawables;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ag(ah.get(0).ownerDocument);this.reset()};q(ae.prototype,A.prototype,{init:function(){var aj=this.container,ah=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aj);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;m(this.viewport_container,ah);this.intro_div=$("<div/>").addClass("intro");var ak=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ai=function(al){if(al.type==="focusout"||(al.keyCode||al.which)===13||(al.keyCode||al.which)===27){if((al.keyCode||al.which)!==27){ah.go_to($(this).val())}$(this).hide();$(this).val("");ah.location_span.show();ah.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ai).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ah.location_span.hide();ah.chrom_select.hide();ah.nav_input.val(ah.chrom+":"+ah.low+"-"+ah.high);ah.nav_input.css("display","inline-block");ah.nav_input.select();ah.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ah.zoom_out();ah.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.browser_content_div.click(function(al){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("<div />").css({height:ah.browser_content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,{content_div:this.top_labeltrack}));this.add_label_track(new ad(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new C(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(al,ai,an){if(!al||al==="None"){return}var ak=this;if(al==="previous"){ak.load_chroms({low:this.chrom_start_index-x});return}if(al==="next"){ak.load_chroms({low:this.chrom_start_index+x});return}var am=$.grep(ak.chrom_data,function(ap,aq){return ap.chrom===al})[0];if(am===undefined){ak.load_chroms({chrom:al},function(){ak.change_chrom(al,ai,an)});return}else{if(al!==ak.chrom){ak.chrom=al;ak.chrom_select.val(ak.chrom);ak.max_high=am.len-1;ak.reset();ak.request_redraw(true);for(var ao=0,ah=ak.tracks.length;ao<ah;ao++){var aj=ak.tracks[ao];if(aj.init){aj.init()}}}if(ai!==undefined&&an!==undefined){ak.low=Math.max(ai,0);ak.high=Math.min(an,ak.max_high)}ak.reset_overview();ak.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){A.prototype.add_drawable.call(this,ah);if(ah.init){ah.init()}this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;this.label_tracks.push(ah)},remove_drawable:function(aj,ai){A.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.tracks),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(E,Math.ceil(Math.log((this.high-this.low)/T)/Math.log(E)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){$.when(ah.get_overview_tile()).then(function(ai){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ai.canvas);view.overview_highlight.show().height(ai.canvas.height());view.overview_viewport.height(ai.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ah;ah.set_is_overview(true)});view.has_changes=true},reset_overview:function(){this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new P(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},al=this.track,aj=ai.tool_id+al.tool_region_and_parameters_str(ai.chrom,ai.low,ai.high),ah,am;if(al.container===view){var ak=new S(this.name,this.track.view,this.track.container);al.container.add_drawable(ak);al.container.remove_drawable(al);ak.add_drawable(al);al.container_div.appendTo(ak.content_div);ah=ak}else{ah=al.container}if(al instanceof e){am=new X(aj,view,ah,"hda");am.change_mode(al.mode);ah.add_drawable(am)}am.content_div.text("Starting job.");this.run(ai,am,function(an){am.dataset_id=an.dataset_id;am.content_div.text("Running job.");am.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(L)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(z+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var P=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){P.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var Y=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};q(Y.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=parseFloat(ah[this.index]);return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(ar,ay){this.track=ar;this.filters=[];for(var at=0;at<ay.length;at++){var au=ay[at],az=au.name,ah=au.type,ak=au.index,ax=au.tool_id,aw=au.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[at]=new Y(az,ak,ax,aw)}else{console.log("ERROR: unsupported filter: ",az,ah)}}var al=function(aA,aB,aC){aA.click(function(){var aD=aB.text();max=parseFloat(aC.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aC.slider("option","values")){input_size=2*input_size+1;multi_value=true}aB.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aD).appendTo(aB).focus().select().click(function(aE){aE.stopPropagation()}).blur(function(){$(this).remove();aB.text(aD)}).keyup(function(aI){if(aI.keyCode===27){$(this).trigger("blur")}else{if(aI.keyCode===13){var aG=aC.slider("option","min"),aE=aC.slider("option","max"),aH=function(aJ){return(isNaN(aJ)||aJ>aE||aJ<aG)},aF=$(this).val();if(!multi_value){aF=parseFloat(aF);if(aH(aF)){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}else{aF=aF.split("-");aF=[parseFloat(aF[0]),parseFloat(aF[1])];if(aH(aF[0])||aH(aF[1])){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}aC.slider((multi_value?"values":"value"),aF)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aA){aA.stopPropagation()}).click(function(aA){aA.stopPropagation()}).bind("dblclick",function(aA){aA.stopPropagation()}).bind("keydown",function(aA){aA.stopPropagation()});var av=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aD,aF){aF.container=$("<div/>").addClass("slider-row").appendTo(av);var aE=$("<div/>").addClass("elt-label").appendTo(aF.container);var aC=$("<span/>").addClass("slider-name").text(aF.name+"  ").appendTo(aE);var aB=$("<span/>");var aH=$("<span/>").addClass("slider-value").appendTo(aE).append("[").append(aB).append("]");var aA=$("<div/>").addClass("slider").appendTo(aF.container);aF.control_element=$("<div/>").attr("id",aF.name+"-filter-control").appendTo(aA);var aG=[0,0];aF.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aJ,aK){var aI=aK.values;aB.text(aI[0]+"-"+aI[1]);aF.low=aI[0];aF.high=aI[1];ap.track.request_draw(true,true)},change:function(aI,aJ){aF.control_element.slider("option","slide").call(aF.control_element,aI,aJ)}});aF.slider=aF.control_element;aF.slider_label=aB;al(aH,aB,aF.control_element);$("<div style='clear: both;'/>").appendTo(aF.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(av);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var aj=this;ao.click(function(){aj.run_on_dataset()})}var aq=$("<div/>").addClass("display-controls").appendTo(this.parent_div),an=$("<span/>").addClass("elt-label").text("Transparency:").appendTo(aq),ai=$("<select/>").attr("name","alpha_dropdown").appendTo(aq);this.alpha_filter=null;$("<option/>").attr("value",-1).text("== None ==").appendTo(ai);for(var at=0;at<this.filters.length;at++){$("<option/>").attr("value",at).text(this.filters[at].name).appendTo(ai)}ai.change(function(){$(this).children("option:selected").each(function(){var aA=parseInt($(this).val());ap.alpha_filter=(aA>=0?ap.filters[aA]:null);ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var Q=function(ai,ah){N.AlphaGenerator.call(this,ah);this.filter=ai};Q.prototype.gen_alpha=function(ah){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_alpha}return((parseFloat(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var H=function(ah){this.track=ah.track;this.params=ah.params;this.values={};this.restore_values((ah.saved_values?ah.saved_values:{}));this.onchange=ah.onchange};q(H.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(aj,ai,ah,ak){this.index=aj;this.low=aj*T*ai;this.high=(aj+1)*T*ai;this.resolution=ai;this.canvas=$("<div class='track-tile'/>").append(ah);this.data=ak;this.stale=false};var l=function(aj,ai,ah,ak,al){b.call(this,aj,ai,ah,ak);this.max_val=al};var R=function(aj,ai,ah,al,ak){b.call(this,aj,ai,ah,al);this.message=ak};var j=function(ak,ai,ah,aj,al,am){r.call(this,ak,ai,ah,{},"draghandle");this.data_url=(al?al:default_data_url);this.data_url_extra_params={};this.data_query_wait=(am?am:M);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.container_div=$("<div />").addClass("track").attr("id","track_"+j.id_counter++).css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof C){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Z){return"ReadTrack"}else{if(this instanceof X){return"ToolDataFeatureTrack"}else{if(this instanceof W){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var ak=ah.view.tracks.indexOf(ah);var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(L)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(G)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.make_name_popup_menu()}ah.content_div.text(ab);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}})},predraw_init:function(){},});var O=function(ao,am){var ai=this,ap=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=new ac(this,(ao!==undefined?ao:{}));this.filters_available=false;this.filters_visible=false;this.tool=(am!==undefined&&obj_length(am)>0?new s(this,am):undefined);this.is_overview=false;if(ai.hidden){return}if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(ai.display_modes!==undefined){if(ai.mode_div===undefined){ai.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ai.header_div);var aj=(ai.config&&ai.config.values.mode?ai.config.values.mode:ai.display_modes[0]);ai.mode=aj;ai.mode_div.text(aj);var ah={};for(var ak=0,an=ai.display_modes.length;ak<an;ak++){var al=ai.display_modes[ak];ah[al]=function(aq){return function(){ai.change_mode(aq)}}(al)}make_popupmenu(ai.mode_div,ah)}else{ai.mode_div.hide()}}this.make_name_popup_menu()};q(O.prototype,r.prototype,j.prototype,{to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw();return ah},make_name_popup_menu:function(){var ai=this;var ah={};ah[(this.is_overview?"Hide overview":"Set as overview")]=function(){if(ai.is_overview){ai.view.reset_overview()}else{ai.view.set_overview(ai)}};ah["Edit configuration"]=function(){var am=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},al=function(an){if((an.keyCode||an.which)===27){am()}else{if((an.keyCode||an.which)===13){ak()}}};$(window).bind("keypress.check_enter_esc",al);show_modal("Configure Track",ai.config.build_form(),{Cancel:am,OK:ak})};if(ai.filters_available>0){var aj=(ai.filters_div.is(":visible")?"Hide filters":"Show filters");ah[aj]=function(){ai.filters_visible=(ai.filters_div.is(":visible"));if(ai.filters_visible){ai.filters_manager.reset_filters()}ai.filters_div.toggle();ai.make_name_popup_menu()}}if(ai.tool){var aj=(ai.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");ah[aj]=function(){if(!ai.dynamic_tool_div.is(":visible")){ai.set_name(ai.name+ai.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ai.revert_name()}ai.dynamic_tool_div.toggle();ai.make_name_popup_menu()}}ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)},set_is_overview:function(ah){this.is_overview=ah;this.make_name_popup_menu()},get_overview_tile:function(){var ah=this;view=ah.view,resolution=Math.pow(E,Math.ceil(Math.log((view.max_high-view.max_low)/T)/Math.log(E))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ah.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ah.data_url_extra_params)).then(function(ai){var ak=ah._gen_tile_cache_key(view_width,w_scale,0),am=ah.tile_cache.get(ak);if(!am){am=ah.draw_tile(ai,"Auto",resolution,0,w_scale);ah.tile_cache.set(ak,am)}var ap=$(am.canvas.find("canvas")),al=ap.clone(),ao=ap.get(0).getContext("2d"),aj=al.get(0).getContext("2d"),an=ao.getImageData(0,0,ao.canvas.width,ao.canvas.height);aj.putImageData(an,-ah.left_offset,(am.data.dataset_type==="summary_tree"?V:0));new_tile=new b(-1,resolution,al);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof C)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/T);var ap=true;var at=[];var ah=0;while((ai*T*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",F)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*T*an,ax=ap+T*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);al.tile_cache.set(at,aq);if(aq!==undefined){al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw()});return null},show_tile:function(ao,aq,ar){var aj=this,ai=ao.canvas,an=ai;if(ao.message){var at=$("<div/>"),ap=$("<div/>").addClass("tile-message").text(ao.message).css({height:F-1,width:ao.canvas.width}).appendTo(at),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ap),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ap);at.append(ai);an=at;al.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()});ah.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()})}var am=this.view.high-this.view.low,ak=(ao.low-this.view.low)*ar;if(this.left_offset){ak-=this.left_offset}an.css({position:"absolute",top:0,left:ak,height:""});aq.append(an);aj.max_height=Math.max(aj.max_height,an.height());aj.content_div.css("height",aj.max_height+"px");aq.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*T*ai,al=T*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ai,ah){this.hidden=true;j.call(this,"label",ai,ah,{});this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var C=function(ah){this.hidden=true;j.call(this,"reference",ah,{content_div:ah.top_labeltrack},{});O.call(this);ah.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ah.dbkey};this.data_manager=new J(D,this,false);this.tile_cache=new c(v)};q(C.prototype,r.prototype,O.prototype,{draw_tile:function(ar,an,am,ai,at){var al=this,aj=T*am;if(at>this.view.canvas_manager.char_width_px){if(ar===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(am,ak,aj,an,ah,al){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,am,ak,aj,al);O.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=an;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new U(D,this);this.tile_cache=new c(v);this.left_offset=0;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:am},{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:al,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.track_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.track_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};q(k.prototype,r.prototype,O.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this,ai=ah.view.tracks.indexOf(ah);ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(aj){ah.container_div.addClass("line-track");var al=aj.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=al.min;ah.prefs.max_value=al.max;$("#track_"+ai+"_minval").val(ah.prefs.min_value);$("#track_"+ai+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=al.total_frequency;ah.container_div.find(".yaxislabel").remove();var am=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ai+"_minval").text(y(ah.prefs.min_value));var ak=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ai+"_maxval").text(y(ah.prefs.max_value));ak.css({position:"absolute",top:"24px",left:"10px"});ak.prependTo(ah.container_div);am.css({position:"absolute",bottom:"2px",left:"10px"});am.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new N.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(aj,al,ak,au.data)}});var e=function(ah,an,ai,am,ap,ao,ak,al){var aj=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];j.call(this,ah,an,ai,ao);O.call(this,ak,al);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){aj.set_name(aj.prefs.name);aj.tile_cache.clear();aj.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=am;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new U(20,this);this.left_offset=200;this.painter=N.LinkedFeaturePainter};q(e.prototype,r.prototype,O.prototype,{postdraw_actions:function(ax,ah,ay,aw){O.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.make_name_popup_menu()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",B,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aE,aI,ar,ak){var aB=this,am=aB._get_tile_bounds(aI,aE),aK=am[0],ai=am[1],ay=ai-aK,aC=Math.ceil(ay*ar),aO=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"){az="no_detail"}else{var aN=aw.data;if(this.view.high-this.view.low>K){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aC+al;aj.height=an+V;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aK,ai,200);if(aw.max){at.max=aw.max}aw=at}var aL=new N.SummaryTreePainter(aw,aK,ai,this.prefs);var aD=aj.getContext("2d");aD.translate(al,V);aL.draw(aD,aC,an);return new l(aI,aE,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aF=0,aH=aw.data.length;aF<aH;aF++){var ao=aw.data[aF];var 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A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var c=function(y,C,E,F,A){n.call(this,y,C,E,F,A);if(this.prefs.min_value===undefined){var G=Infinity;for(var z=0,B=this.data.length;z<B;z++){G=Math.min(G,this.data[z][1])}this.prefs.min_value=G}if(this.prefs.max_value===undefined){var D=-Infinity;for(var z=0,B=this.data.length;z<B;z++){D=Math.max(D,this.data[z][1])}this.prefs.max_value=D}};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var 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+var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var trackster_module=function(f,aa){var q=f("class").extend,t=f("slotting"),N=f("painters");var ag=function(ah,ai){this.document=ah;this.default_font=ai!==undefined?ai:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};q(ag.prototype,{load_pattern:function(ah,al){var ai=this.patterns,aj=this.dummy_context,ak=new Image();ak.src=image_path+al;ak.onload=function(){ai[ah]=aj.createPattern(ak,"repeat")}},get_pattern:function(ah){return this.patterns[ah]},new_canvas:function(){var ah=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ah)}ah.manager=this;return ah}});var o={};var m=function(ah,ai){o[ah.attr("id")]=ai};var n=function(ah,aj,al,ak){al=".group";var ai={};o[ah.attr("id")]=ak;ah.bind("drag",{handle:"."+aj,relative:true},function(au,av){var at=$(this);var ay=$(this).parent(),ap=ay.children(),ar=o[$(this).attr("id")],ao,an,aw,am,aq;an=$(this).parents(al);if(an.length!==0){aw=an.position().top;am=aw+an.outerHeight();if(av.offsetY<aw){$(this).insertBefore(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable_before(ar,ax);return}else{if(av.offsetY>am){$(this).insertAfter(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable(ar);return}}}an=null;for(aq=0;aq<ap.length;aq++){ao=$(ap.get(aq));aw=ao.position().top;am=aw+ao.outerHeight();if(ao.is(al)&&this!==ao.get(0)&&av.offsetY>=aw&&av.offsetY<=am){if(av.offsetY-aw<am-av.offsetY){ao.find(".content-div").prepend(this)}else{ao.find(".content-div").append(this)}if(ar.container){ar.container.remove_drawable(ar)}o[ao.attr("id")].add_drawable(ar);return}}for(aq=0;aq<ap.length;aq++){if(av.offsetY<$(ap.get(aq)).position().top){break}}if(aq===ap.length){if(this!==ap.get(aq-1)){ay.append(this);o[ay.attr("id")].move_drawable(ar,aq)}}else{if(this!==ap.get(aq)){$(this).insertBefore(ap.get(aq));o[ay.attr("id")].move_drawable(ar,(av.deltaY>0?aq-1:aq))}}}).bind("dragstart",function(){ai["border-top"]=ah.css("border-top");ai["border-bottom"]=ah.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ai)})};aa.moveable=n;var af=16,I=9,F=20,V=I+2,B=100,K=12000,T=200,E=5,w=10,M=5000,x=100,p="There was an error in indexing this dataset. ",L="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",u="Currently indexing... please wait",z="Tool cannot be rerun: ",a="Loading data...",ab="Ready for display",d=10,v=5,D=5;function y(ah){return Math.round(ah*1000)/1000}var c=function(ah){this.num_elements=ah;this.clear()};q(c.prototype,{get:function(ai){var ah=this.key_ary.indexOf(ai);if(ah!==-1){if(this.obj_cache[ai].stale){this.key_ary.splice(ah,1);delete this.obj_cache[ai]}else{this.move_key_to_end(ai,ah)}}return this.obj_cache[ai]},set:function(ai,aj){if(!this.obj_cache[ai]){if(this.key_ary.length>=this.num_elements){var ah=this.key_ary.shift();delete this.obj_cache[ah]}this.key_ary.push(ai)}this.obj_cache[ai]=aj;return aj},move_key_to_end:function(ai,ah){this.key_ary.splice(ah,1);this.key_ary.push(ai)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var U=function(ai,ah,aj){c.call(this,ai);this.track=ah;this.subset=(aj!==undefined?aj:true)};q(U.prototype,c.prototype,{load_data:function(aq,al,ao,ai,an){var ap=this.track.view.chrom,ak={chrom:ap,low:aq,high:al,mode:ao,resolution:ai,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ak,an);if(this.track.filters_manager){var ar=[];var ah=this.track.filters_manager.filters;for(var am=0;am<ah.length;am++){ar[ar.length]=ah[am].name}ak.filter_cols=JSON.stringify(ar)}var aj=this;return $.getJSON(this.track.data_url,ak,function(at){aj.set_data(aq,al,ao,at)})},get_data:function(ah,al,am,ai,ak){var aj=this.get_data_from_cache(ah,al,am);if(aj){return aj}aj=this.load_data(ah,al,am,ai,ak);this.set_data(ah,al,am,aj);return aj},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ap,ak,ao,aj,an,al){var aq=this.get_data_from_cache(ap,ak,ao);if(!aq){console.log("ERROR: no current data for: ",this.track,ap,ak,ao,aj,an);return}aq.stale=true;var ai=ap;if(al===this.DEEP_DATA_REQ){$.extend(an,{start_val:aq.data.length+1})}else{if(al===this.BROAD_DATA_REQ){ai=(aq.max_high?aq.max_high:aq.data[aq.data.length-1][2])+1}}var ah=this,am=this.load_data(ai,ak,ao,aj,an);new_data_available=$.Deferred();this.set_data(ap,ak,ao,new_data_available);$.when(am).then(function(ar){if(ar.data){ar.data=aq.data.concat(ar.data);if(ar.max_low){ar.max_low=aq.max_low}if(ar.message){ar.message=ar.message.replace(/[0-9]+/,ar.data.length)}}ah.set_data(ap,ak,ao,ar);new_data_available.resolve(ar)});return new_data_available},get_data_from_cache:function(ah,ai,aj){return this.get(this.gen_key(ah,ai,aj))},set_data:function(ai,aj,ak,ah){return this.set(this.gen_key(ai,aj,ak),ah)},gen_key:function(ah,aj,ak){var ai=ah+"_"+aj+"_"+ak;return ai},split_key:function(ah){return ah.split("_")}});var J=function(ai,ah,aj){U.call(this,ai,ah,aj)};q(J.prototype,U.prototype,c.prototype,{load_data:function(aj,ah,al,am,ai,ak){if(ai>1){return}return U.prototype.load_data.call(this,aj,ah,al,am,ai,ak)}});var r=function(ak,ai,ah,aj,al){this.name=ak;this.view=ai;this.container=ah;this.drag_handle_class=al;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak}],saved_values:aj,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values};q(r.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},make_name_popup_menu:function(){},set_name:function(ah){this.old_name=this.name;this.name=ah;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var A=function(al,ak,ai,ah,aj,am){r.call(this,ak,ai,ah,aj,am);this.obj_type=al;this.drawables=[]};q(A.prototype,r.prototype,{init:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah].init()}},_draw:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah]._draw()}},to_json:function(){var ai=[];for(var ah=0;ah<this.drawables.length;ah++){ai.push(this.drawables[ah].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ai}},add_drawable:function(ah){this.drawables.push(ah);ah.container=this},add_drawable_before:function(aj,ah){var ai=this.drawables.indexOf(ah);if(ai!=-1){this.drawables.splice(ai,0,aj);return true}return false},remove_drawable:function(ai){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);ai.container=null;return true}return false},move_drawable:function(ai,aj){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);this.drawables.splice(aj,0,ai);return true}return false}});var S=function(ak,ai,ah,aj){A.call(this,"DrawableGroup",ak,ai,ah,aj,"group-handle");if(!S.id_counter){S.id_counter=0}var al=S.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+al).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+al+"_content_div").appendTo(this.container_div);m(this.container_div,this);m(this.content_div,this);n(this.container_div,this.drag_handle_class,".group",this);this.make_name_popup_menu()};q(S.prototype,r.prototype,A.prototype,{make_name_popup_menu:function(){var ai=this;var ah={};ah["Edit configuration"]=function(){var al=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aj=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(am){if((am.keyCode||am.which)===27){al()}else{if((am.keyCode||am.which)===13){aj()}}};$(window).bind("keypress.check_enter_esc",ak);show_modal("Configure Group",ai.config.build_form(),{Cancel:al,OK:aj})};ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)}});var ae=function(ah,ak,aj,ai){A.call(this,"View");this.container=ah;this.chrom=null;this.vis_id=aj;this.dbkey=ai;this.title=ak;this.tracks=this.drawables;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ag(ah.get(0).ownerDocument);this.reset()};q(ae.prototype,A.prototype,{init:function(){var aj=this.container,ah=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aj);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;m(this.viewport_container,ah);this.intro_div=$("<div/>").addClass("intro");var ak=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ai=function(al){if(al.type==="focusout"||(al.keyCode||al.which)===13||(al.keyCode||al.which)===27){if((al.keyCode||al.which)!==27){ah.go_to($(this).val())}$(this).hide();$(this).val("");ah.location_span.show();ah.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ai).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ah.location_span.hide();ah.chrom_select.hide();ah.nav_input.val(ah.chrom+":"+ah.low+"-"+ah.high);ah.nav_input.css("display","inline-block");ah.nav_input.select();ah.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ah.zoom_out();ah.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.browser_content_div.click(function(al){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("<div />").css({height:ah.browser_content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,{content_div:this.top_labeltrack}));this.add_label_track(new ad(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new C(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(al,ai,an){if(!al||al==="None"){return}var ak=this;if(al==="previous"){ak.load_chroms({low:this.chrom_start_index-x});return}if(al==="next"){ak.load_chroms({low:this.chrom_start_index+x});return}var am=$.grep(ak.chrom_data,function(ap,aq){return ap.chrom===al})[0];if(am===undefined){ak.load_chroms({chrom:al},function(){ak.change_chrom(al,ai,an)});return}else{if(al!==ak.chrom){ak.chrom=al;ak.chrom_select.val(ak.chrom);ak.max_high=am.len-1;ak.reset();ak.request_redraw(true);for(var ao=0,ah=ak.tracks.length;ao<ah;ao++){var aj=ak.tracks[ao];if(aj.init){aj.init()}}}if(ai!==undefined&&an!==undefined){ak.low=Math.max(ai,0);ak.high=Math.min(an,ak.max_high)}ak.reset_overview();ak.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){A.prototype.add_drawable.call(this,ah);ah.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;ah.init();this.label_tracks.push(ah)},remove_drawable:function(aj,ai){A.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.tracks),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(E,Math.ceil(Math.log((this.high-this.low)/T)/Math.log(E)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){$.when(ah.get_overview_tile()).then(function(ai){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ai.canvas);view.overview_highlight.show().height(ai.canvas.height());view.overview_viewport.height(ai.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ah;ah.set_is_overview(true)});view.has_changes=true},reset_overview:function(){this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new P(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},al=this.track,aj=ai.tool_id+al.tool_region_and_parameters_str(ai.chrom,ai.low,ai.high),ah,am;if(al.container===view){var ak=new S(this.name,this.track.view,this.track.container);al.container.add_drawable(ak);al.container.remove_drawable(al);ak.add_drawable(al);al.container_div.appendTo(ak.content_div);ah=ak}else{ah=al.container}if(al instanceof e){am=new X(aj,view,ah,"hda");am.change_mode(al.mode);ah.add_drawable(am)}am.content_div.text("Starting job.");this.run(ai,am,function(an){am.dataset_id=an.dataset_id;am.content_div.text("Running job.");am.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(L)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(z+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var P=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){P.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var Y=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};q(Y.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=parseFloat(ah[this.index]);return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(ar,ay){this.track=ar;this.filters=[];for(var at=0;at<ay.length;at++){var au=ay[at],az=au.name,ah=au.type,ak=au.index,ax=au.tool_id,aw=au.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[at]=new Y(az,ak,ax,aw)}else{console.log("ERROR: unsupported filter: ",az,ah)}}var al=function(aA,aB,aC){aA.click(function(){var aD=aB.text();max=parseFloat(aC.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aC.slider("option","values")){input_size=2*input_size+1;multi_value=true}aB.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aD).appendTo(aB).focus().select().click(function(aE){aE.stopPropagation()}).blur(function(){$(this).remove();aB.text(aD)}).keyup(function(aI){if(aI.keyCode===27){$(this).trigger("blur")}else{if(aI.keyCode===13){var aG=aC.slider("option","min"),aE=aC.slider("option","max"),aH=function(aJ){return(isNaN(aJ)||aJ>aE||aJ<aG)},aF=$(this).val();if(!multi_value){aF=parseFloat(aF);if(aH(aF)){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}else{aF=aF.split("-");aF=[parseFloat(aF[0]),parseFloat(aF[1])];if(aH(aF[0])||aH(aF[1])){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}aC.slider((multi_value?"values":"value"),aF)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aA){aA.stopPropagation()}).click(function(aA){aA.stopPropagation()}).bind("dblclick",function(aA){aA.stopPropagation()}).bind("keydown",function(aA){aA.stopPropagation()});var av=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aD,aF){aF.container=$("<div/>").addClass("slider-row").appendTo(av);var aE=$("<div/>").addClass("elt-label").appendTo(aF.container);var aC=$("<span/>").addClass("slider-name").text(aF.name+"  ").appendTo(aE);var aB=$("<span/>");var aH=$("<span/>").addClass("slider-value").appendTo(aE).append("[").append(aB).append("]");var aA=$("<div/>").addClass("slider").appendTo(aF.container);aF.control_element=$("<div/>").attr("id",aF.name+"-filter-control").appendTo(aA);var aG=[0,0];aF.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aJ,aK){var aI=aK.values;aB.text(aI[0]+"-"+aI[1]);aF.low=aI[0];aF.high=aI[1];ap.track.request_draw(true,true)},change:function(aI,aJ){aF.control_element.slider("option","slide").call(aF.control_element,aI,aJ)}});aF.slider=aF.control_element;aF.slider_label=aB;al(aH,aB,aF.control_element);$("<div style='clear: both;'/>").appendTo(aF.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(av);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var aj=this;ao.click(function(){aj.run_on_dataset()})}var aq=$("<div/>").addClass("display-controls").appendTo(this.parent_div),an=$("<span/>").addClass("elt-label").text("Transparency:").appendTo(aq),ai=$("<select/>").attr("name","alpha_dropdown").appendTo(aq);this.alpha_filter=null;$("<option/>").attr("value",-1).text("== None ==").appendTo(ai);for(var at=0;at<this.filters.length;at++){$("<option/>").attr("value",at).text(this.filters[at].name).appendTo(ai)}ai.change(function(){$(this).children("option:selected").each(function(){var aA=parseInt($(this).val());ap.alpha_filter=(aA>=0?ap.filters[aA]:null);ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var Q=function(ai,ah){N.AlphaGenerator.call(this,ah);this.filter=ai};Q.prototype.gen_alpha=function(ah){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_alpha}return((parseFloat(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var H=function(ah){this.track=ah.track;this.params=ah.params;this.values={};this.restore_values((ah.saved_values?ah.saved_values:{}));this.onchange=ah.onchange};q(H.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(aj,ai,ah,ak){this.index=aj;this.low=aj*T*ai;this.high=(aj+1)*T*ai;this.resolution=ai;this.canvas=$("<div class='track-tile'/>").append(ah);this.data=ak;this.stale=false};var l=function(aj,ai,ah,ak,al){b.call(this,aj,ai,ah,ak);this.max_val=al};var R=function(ak,aj,ai,an,am,ah){b.call(this,ak,aj,ai,an);this.message=am;this.feature_mapper=ah;var al=this;$(this.canvas).mousemove(function(ap){var ao=al.feature_mapper.get_feature_data(ap.offsetX,ap.offsetY)})};var j=function(ak,ai,ah,aj,al,am){r.call(this,ak,ai,ah,{},"draghandle");this.data_url=(al?al:default_data_url);this.data_url_extra_params={};this.data_query_wait=(am?am:M);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.container_div=$("<div />").addClass("track").attr("id","track_"+j.id_counter++).css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof C){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Z){return"ReadTrack"}else{if(this instanceof X){return"ToolDataFeatureTrack"}else{if(this instanceof W){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var ak=ah.view.tracks.indexOf(ah);var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(L)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(G)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.make_name_popup_menu()}ah.content_div.text(ab);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}})},predraw_init:function(){},});var O=function(ao,am){var ai=this,ap=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=new ac(this,(ao!==undefined?ao:{}));this.filters_available=false;this.filters_visible=false;this.tool=(am!==undefined&&obj_length(am)>0?new s(this,am):undefined);this.is_overview=false;if(ai.hidden){return}if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(ai.display_modes!==undefined){if(ai.mode_div===undefined){ai.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ai.header_div);var aj=(ai.config&&ai.config.values.mode?ai.config.values.mode:ai.display_modes[0]);ai.mode=aj;ai.mode_div.text(aj);var ah={};for(var ak=0,an=ai.display_modes.length;ak<an;ak++){var al=ai.display_modes[ak];ah[al]=function(aq){return function(){ai.change_mode(aq)}}(al)}make_popupmenu(ai.mode_div,ah)}else{ai.mode_div.hide()}}this.make_name_popup_menu()};q(O.prototype,r.prototype,j.prototype,{to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw();return ah},make_name_popup_menu:function(){var ai=this;var ah={};ah[(this.is_overview?"Hide overview":"Set as overview")]=function(){if(ai.is_overview){ai.view.reset_overview()}else{ai.view.set_overview(ai)}};ah["Edit configuration"]=function(){var am=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},al=function(an){if((an.keyCode||an.which)===27){am()}else{if((an.keyCode||an.which)===13){ak()}}};$(window).bind("keypress.check_enter_esc",al);show_modal("Configure Track",ai.config.build_form(),{Cancel:am,OK:ak})};if(ai.filters_available>0){var aj=(ai.filters_div.is(":visible")?"Hide filters":"Show filters");ah[aj]=function(){ai.filters_visible=(ai.filters_div.is(":visible"));if(ai.filters_visible){ai.filters_manager.reset_filters()}ai.filters_div.toggle();ai.make_name_popup_menu()}}if(ai.tool){var aj=(ai.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");ah[aj]=function(){if(!ai.dynamic_tool_div.is(":visible")){ai.set_name(ai.name+ai.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ai.revert_name()}ai.dynamic_tool_div.toggle();ai.make_name_popup_menu()}}ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)},set_is_overview:function(ah){this.is_overview=ah;this.make_name_popup_menu()},get_overview_tile:function(){var ah=this;view=ah.view,resolution=Math.pow(E,Math.ceil(Math.log((view.max_high-view.max_low)/T)/Math.log(E))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ah.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ah.data_url_extra_params)).then(function(ai){var ak=ah._gen_tile_cache_key(view_width,w_scale,0),am=ah.tile_cache.get(ak);if(!am){am=ah.draw_tile(ai,"Auto",resolution,0,w_scale);ah.tile_cache.set(ak,am)}var ap=$(am.canvas.find("canvas")),al=ap.clone(),ao=ap.get(0).getContext("2d"),aj=al.get(0).getContext("2d"),an=ao.getImageData(0,0,ao.canvas.width,ao.canvas.height);aj.putImageData(an,-ah.left_offset,(am.data.dataset_type==="summary_tree"?V:0));new_tile=new b(-1,resolution,al);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof C)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/T);var ap=true;var at=[];var ah=0;while((ai*T*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",F)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*T*an,ax=ap+T*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);al.tile_cache.set(at,aq);if(aq!==undefined){al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw()});return null},show_tile:function(ao,aq,ar){var aj=this,ai=ao.canvas,an=ai;if(ao.message){var at=$("<div/>"),ap=$("<div/>").addClass("tile-message").text(ao.message).css({height:F-1,width:ao.canvas.width}).appendTo(at),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ap),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ap);at.append(ai);an=at;al.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()});ah.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()})}var am=this.view.high-this.view.low,ak=(ao.low-this.view.low)*ar;if(this.left_offset){ak-=this.left_offset}an.css({position:"absolute",top:0,left:ak,height:""});aq.append(an);aj.max_height=Math.max(aj.max_height,an.height());aj.content_div.css("height",aj.max_height+"px");aq.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*T*ai,al=T*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ai,ah){this.hidden=true;j.call(this,"label",ai,ah,{});this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{init:function(){this.enabled=true},_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var C=function(ah){this.hidden=true;j.call(this,"reference",ah,{content_div:ah.top_labeltrack},{});O.call(this);ah.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ah.dbkey};this.data_manager=new J(D,this,false);this.tile_cache=new c(v)};q(C.prototype,r.prototype,O.prototype,{init:function(){this.enabled=true},draw_tile:function(ar,an,am,ai,at){var al=this,aj=T*am;if(at>this.view.canvas_manager.char_width_px){if(ar===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(am,ak,aj,an,ah,al){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,am,ak,aj,al);O.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=an;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new U(D,this);this.tile_cache=new c(v);this.left_offset=0;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:am},{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:al,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.track_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.track_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};q(k.prototype,r.prototype,O.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this,ai=ah.view.tracks.indexOf(ah);ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(aj){ah.container_div.addClass("line-track");var al=aj.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=al.min;ah.prefs.max_value=al.max;$("#track_"+ai+"_minval").val(ah.prefs.min_value);$("#track_"+ai+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=al.total_frequency;ah.container_div.find(".yaxislabel").remove();var am=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ai+"_minval").text(y(ah.prefs.min_value));var ak=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ai+"_maxval").text(y(ah.prefs.max_value));ak.css({position:"absolute",top:"24px",left:"10px"});ak.prependTo(ah.container_div);am.css({position:"absolute",bottom:"2px",left:"10px"});am.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new N.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(aj,al,ak,au.data)}});var e=function(ah,an,ai,am,ap,ao,ak,al){var aj=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];j.call(this,ah,an,ai,ao);O.call(this,ak,al);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){aj.set_name(aj.prefs.name);aj.tile_cache.clear();aj.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=am;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new U(20,this);this.left_offset=200;this.painter=N.LinkedFeaturePainter};q(e.prototype,r.prototype,O.prototype,{postdraw_actions:function(ax,ah,ay,aw){O.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.make_name_popup_menu()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",B,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aE,aI,ar,ak){var aB=this,am=aB._get_tile_bounds(aI,aE),aL=am[0],ai=am[1],ay=ai-aL,aC=Math.ceil(ay*ar),aP=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"){az="no_detail"}else{var aO=aw.data;if(this.view.high-this.view.low>K){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aC+al;aj.height=an+V;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aL,ai,200);if(aw.max){at.max=aw.max}aw=at}var aM=new N.SummaryTreePainter(aw,aL,ai,this.prefs);var aD=aj.getContext("2d");aD.translate(al,V);aM.draw(aD,aC,an);return new l(aI,aE,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aF=0,aH=aw.data.length;aF<aH;aF++){var ao=aw.data[aF];var aG=false;var av;for(var aK=0,aN=au.length;aK<aN;aK++){av=au[aK];av.update_attrs(ao);if(!av.keep(ao)){aG=true;break}}if(!aG){aq.push(ao)}}}var aA=(this.filters_manager.alpha_filter?new Q(this.filters_manager.alpha_filter):null);var aM=new (this.painter)(aq,aL,ai,this.prefs,az,aA,ak);var an=Math.max(af,aM.get_required_height(ap));var aj=this.view.canvas_manager.new_canvas();var aJ=null;aj.width=aC+al;aj.height=an;var aD=aj.getContext("2d");aD.fillStyle=this.prefs.block_color;aD.font=aD.canvas.manager.default_font;aD.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aw.data){aD.translate(al,0);aJ=aM.draw(aD,aC,an,ax);aJ.translation=-al}return new R(aI,aE,aj,aw.data,aw.message,aJ)}});var W=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.painter=N.VariantPainter};q(W.prototype,r.prototype,O.prototype,e.prototype);var Z=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ak,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=N.ReadPainter;this.make_name_popup_menu()};q(Z.prototype,r.prototype,O.prototype,e.prototype);var X=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am,{});this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};q(X.prototype,r.prototype,O.prototype,e.prototype,{predraw_init:function(){var ai=this;var ah=function(){if(ai.data_manager.size()===0){setTimeout(ah,300)}else{ai.data_url=default_data_url;ai.data_query_wait=M;ai.dataset_state_url=converted_datasets_state_url;$.getJSON(ai.dataset_state_url,{dataset_id:ai.dataset_id,hda_ldda:ai.hda_ldda},function(aj){})}};ah()}});aa.View=ae;aa.DrawableGroup=S;aa.LineTrack=k;aa.FeatureTrack=e;aa.ReadTrack=Z};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(k,y){var v=k("class").extend;var q=function(J,B,H,A,G,E){if(E===undefined){E=4}var D=A-B;var C=G-H;var F=Math.floor(Math.sqrt(D*D+C*C)/E);var K=D/F;var I=C/F;var z;for(z=0;z<F;z++,B+=K,H+=I){if(z%2!==0){continue}J.fillRect(B,H,E,1)}};var r=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var g=function(z){this.default_alpha=(z?z:1)};g.prototype.gen_alpha=function(z){return this.default_alpha};var n=function(B,D,z,A,C){this.data=B;this.view_start=D;this.view_end=z;this.prefs=v({},this.default_prefs,A);this.mode=C};n.prototype.default_prefs={};var w=function(B,D,z,A,C){n.call(this,B,D,z,A,C)};w.prototype.default_prefs={show_counts:false};w.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var c=function(z,D,F,G,B){n.call(this,z,D,F,G,B);if(this.prefs.min_value===undefined){var H=Infinity;for(var A=0,C=this.data.length;A<C;A++){H=Math.min(H,this.data[A][1])}this.prefs.min_value=H}if(this.prefs.max_value===undefined){var E=-Infinity;for(var A=0,C=this.data.length;A<C;A++){E=Math.max(E,this.data[A][1])}this.prefs.max_value=E}};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var o=function(z){this.feature_positions={};this.slot_height=z;this.translation=0};o.prototype.map_feature_data=function(A,C,z,B){if(!this.feature_positions[C]){this.feature_positions[C]=[]}this.feature_positions[C].push({data:A,x_start:z,x_end:B})};o.prototype.get_feature_data=function(z,D){var C=Math.floor(D/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var p=function(C,E,z,B,D,A){n.call(this,C,E,z,B,D);this.alpha_generator=(A?A:new g())};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};v(p.prototype,{get_required_height:function(A){var z=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){z=A*y_scale}return z+Math.max(Math.round(y_scale/2),5)},draw:function(L,J,H,G){var R=this.data,E=this.view_start,N=this.view_end;L.save();L.fillStyle=this.prefs.block_color;L.textAlign="right";var I=this.view_end-this.view_start,F=J/I,M=this.get_row_height(),Q=new o(M),C;for(var O=0,P=R.length;O<P;O++){var B=R[O],D=B[0],K=B[1],z=B[2],A=(G&&G[D]!==undefined?G[D]:null);if((K<N&&z>E)&&(this.mode=="Dense"||A!==null)){C=this.draw_element(L,this.mode,B,A,E,N,F,M,J);Q.map_feature_data(B,A,C[0],C[1])}}L.restore();return Q},draw_element:function(F,B,H,D,C,E,G,A,z){console.log("WARNING: Unimplemented function.");return[0,0]}});var d=10,j=3,m=5,x=10,f=1,t=3,e=3,a=9,l=2,h="#ccc";var s=function(C,E,z,B,D,A){p.call(this,C,E,z,B,D,A)};v(s.prototype,p.prototype,{get_row_height:function(){var A=this.mode,z;if(A==="Dense"){z=d}else{if(A==="no_detail"){z=j}else{if(A==="Squish"){z=m}else{z=x}}}return z},draw_element:function(L,E,T,G,N,ae,ai,ak,z){var Q=T[0],ag=T[1],Y=T[2],O=T[3],Z=Math.floor(Math.max(0,(ag-N)*ai)),M=Math.ceil(Math.min(z,Math.max(0,(Y-N)*ai))),X=Z,aj=M,W=(E==="Dense"?0:(0+G))*ak,K,ac,P=null,al=null,C=this.prefs.block_color,ab=this.prefs.label_color;L.globalAlpha=this.alpha_generator.gen_alpha(T);if(E=="Dense"){G=1}if(E==="no_detail"){L.fillStyle=C;L.fillRect(Z,W+5,M-Z,f)}else{var J=T[4],V=T[5],aa=T[6],D=T[7];if(V&&aa){P=Math.floor(Math.max(0,(V-N)*ai));al=Math.ceil(Math.min(z,Math.max(0,(aa-N)*ai)))}var ah,R;if(E==="Squish"||E==="Dense"){ah=1;R=e}else{ah=5;R=a}if(!D){if(T.strand){if(T.strand==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand_inv")}else{if(T.strand==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand_inv")}}}else{L.fillStyle=C}L.fillRect(Z,W,M-Z,R)}else{var I,S;if(E==="Squish"||E==="Dense"){L.fillStyle=h;I=W+Math.floor(e/2)+1;S=1}else{if(J){var I=W;var S=R;if(J==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand")}else{if(J==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand")}}}else{L.fillStyle=h;I+=(e/2)+1;S=1}}L.fillRect(Z,I,M-Z,S);for(var af=0,B=D.length;af<B;af++){var F=D[af],A=Math.floor(Math.max(0,(F[0]-N)*ai)),U=Math.ceil(Math.min(z,Math.max((F[1]-N)*ai)));if(A>U){continue}L.fillStyle=C;L.fillRect(A,W+(R-ah)/2+1,U-A,ah);if(P!==undefined&&aa>V&&!(A>al||U<P)){var ad=Math.max(A,P),H=Math.min(U,al);L.fillRect(ad,W+1,H-ad,R);if(D.length==1&&E=="Pack"){if(J==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand_inv")}else{if(J==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand_inv")}}if(ad+14<H){ad+=2;H-=2}L.fillRect(ad,W+1,H-ad,R)}}}}if(E==="Pack"&&ag>N){L.fillStyle=ab;if(N===0&&Z-L.measureText(O).width<0){L.textAlign="left";L.fillText(O,M+l,W+8);aj+=L.measureText(O).width+l}else{L.textAlign="right";L.fillText(O,Z-l,W+8);X-=L.measureText(O).width+l}}}L.globalAlpha=1;return[X,aj]}});var b=function(C,E,z,B,D,A){p.call(this,C,E,z,B,D,A)};v(b.prototype,p.prototype,{draw_element:function(S,N,H,D,V,B,K,T,Q){var H=data[i],J=H[0],R=H[1],C=H[2],M=H[3],F=Math.floor(Math.max(0,(R-V)*K)),I=Math.ceil(Math.min(Q,Math.max(0,(C-V)*K))),E=(N==="Dense"?0:(0+D))*T,z,W,A=null,L=null;if(no_label){S.fillStyle=block_color;S.fillRect(F+left_offset,E+5,I-F,1)}else{var U=H[4],P=H[5],G=H[6];z=9;W=1;S.fillRect(F+left_offset,E,I-F,z);if(N!=="Dense"&&M!==undefined&&R>V){S.fillStyle=label_color;if(V===0&&F-S.measureText(M).width<0){S.textAlign="left";S.fillText(M,I+2+left_offset,E+8)}else{S.textAlign="right";S.fillText(M,F-2+left_offset,E+8)}S.fillStyle=block_color}var O=U+" / "+P;if(R>V&&S.measureText(O).width<(I-F)){S.fillStyle="white";S.textAlign="center";S.fillText(O,left_offset+F+(I-F)/2,E+8);S.fillStyle=block_color}}}});var u=function(D,F,z,C,E,A,B){p.call(this,D,F,z,C,E,A);this.ref_seq=B};u.prototype.default_prefs=v({},p.prototype.default_prefs,{show_insertions:false});v(u.prototype,p.prototype,{get_row_height:function(){var z,A=this.mode;if(A==="Dense"){z=d}else{if(A==="Squish"){z=m}else{z=x;if(this.prefs.show_insertions){z*=2}}}return z},draw_read:function(V,Q,M,aa,B,U,J,G,F){V.textAlign="center";var T=this,A=[aa,B],P=0,W=0,S=0;ref_seq=this.ref_seq,char_width_px=V.canvas.manager.char_width_px;var af=[];if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){S=Math.round(M/2)}if(!J){J=[[0,G.length]]}for(var N=0,Y=J.length;N<Y;N++){var K=J[N],C="MIDNSHP=X"[K[0]],O=K[1];if(C==="H"||C==="S"){P-=O}var H=U+P,ae=Math.floor(Math.max(0,(H-aa)*M)),I=Math.floor(Math.max(0,(H+O-aa)*M));if(ae===I){I+=1}switch(C){case"H":break;case"S":case"M":case"=":if(is_overlap([H,H+O],A)){var R=G.slice(W,W+O);if(S>0){V.fillStyle=this.prefs.block_color;V.fillRect(ae-S,F+1,I-ae,9);V.fillStyle=h;for(var ac=0,z=R.length;ac<z;ac++){if(this.prefs.show_differences&&ref_seq){var L=ref_seq[H-aa+ac];if(!L||L.toLowerCase()===R[ac].toLowerCase()){continue}}if(H+ac>=aa&&H+ac<=B){var ad=Math.floor(Math.max(0,(H+ac-aa)*M));V.fillText(R[ac],ad,F+9)}}}else{V.fillStyle=this.prefs.block_color;V.fillRect(ae,F+4,I-ae,e)}}W+=O;P+=O;break;case"N":V.fillStyle=h;V.fillRect(ae-S,F+5,I-ae,1);P+=O;break;case"D":V.fillStyle="red";V.fillRect(ae-S,F+4,I-ae,3);P+=O;break;case"P":break;case"I":var Z=ae-S;if(is_overlap([H,H+O],A)){var R=G.slice(W,W+O);if(this.prefs.show_insertions){var E=ae-(I-ae)/2;if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){V.fillStyle="yellow";V.fillRect(E-S,F-9,I-ae,9);af[af.length]={type:"triangle",data:[Z,F+4,5]};V.fillStyle=h;switch(seq_tile_overlap){case (OVERLAP_START):R=R.slice(aa-H);break;case (OVERLAP_END):R=R.slice(0,H-B);break;case (CONTAINED_BY):break;case (CONTAINS):R=R.slice(aa-H,H-B);break}for(var ac=0,z=R.length;ac<z;ac++){var ad=Math.floor(Math.max(0,(H+ac-aa)*M));V.fillText(R[ac],ad-(I-ae)/2,F)}}else{V.fillStyle="yellow";V.fillRect(E,F+(this.mode!=="Dense"?2:5),I-ae,(Q!=="Dense"?e:t))}}else{if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){af[af.length]={type:"text",data:[R.length,Z,F+9]}}else{}}}W+=O;break;case"X":W+=O;break}}V.fillStyle="yellow";var ab,D,ag;for(var X=0;X<af.length;X++){ab=af[X];D=ab.type;ag=ab.data;if(D==="text"){V.save();V.font="bold "+V.font;V.fillText(ag[0],ag[1],ag[2]);V.restore()}else{if(D=="triangle"){r(V,ag[0],ag[1],ag[2])}}}},draw_element:function(S,N,F,C,V,A,J,T,Q){var I=F[0],R=F[1],B=F[2],K=F[3],E=Math.floor(Math.max(0,(R-V)*J)),G=Math.ceil(Math.min(Q,Math.max(0,(B-V)*J))),D=(N==="Dense"?0:(0+C))*T,W=this.prefs.block_color,H=this.prefs.label_color,P=0;if((N==="Pack"||this.mode==="Auto")&&J>S.canvas.manager.char_width_px){var P=Math.round(J/2)}S.fillStyle=W;if(F[5] instanceof Array){var O=Math.floor(Math.max(0,(F[4][0]-V)*J)),M=Math.ceil(Math.min(Q,Math.max(0,(F[4][1]-V)*J))),L=Math.floor(Math.max(0,(F[5][0]-V)*J)),z=Math.ceil(Math.min(Q,Math.max(0,(F[5][1]-V)*J)));if(F[4][1]>=V&&F[4][0]<=A&&F[4][2]){this.draw_read(S,N,J,V,A,F[4][0],F[4][2],F[4][3],D)}if(F[5][1]>=V&&F[5][0]<=A&&F[5][2]){this.draw_read(S,N,J,V,A,F[5][0],F[5][2],F[5][3],D)}if(L>M){S.fillStyle=h;q(S,M-P,D+5,L-P,D+5)}}else{S.fillStyle=W;this.draw_read(S,N,J,V,A,R,F[4],F[5],D)}if(N==="Pack"&&R>V){S.fillStyle=this.prefs.label_color;var U=1;if(U===0&&E-S.measureText(K).width<0){S.textAlign="left";S.fillText(K,G+l-P,D+8)}else{S.textAlign="right";S.fillText(K,E-l-P,D+8)}S.fillStyle=W}}});y.AlphaGenerator=g;y.SummaryTreePainter=w;y.LinePainter=c;y.LinkedFeaturePainter=s;y.ReadPainter=u;y.VariantPainter=b};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window);
\ No newline at end of file
diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index f837f4d574a..c5762c320ac 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -2101,9 +2101,21 @@ var SummaryTreeTile = function(index, resolution, canvas, data, max_val) {
     this.max_val = max_val;
 };
 
-var FeatureTrackTile = function(index, resolution, canvas, data, message) {
+var FeatureTrackTile = function(index, resolution, canvas, data, message, feature_mapper) {
     Tile.call(this, index, resolution, canvas, data);
     this.message = message;
+    this.feature_mapper = feature_mapper;
+    
+    //
+    // Set up display of feature data on mouseover.
+    //
+    var tile = this;
+    $(this.canvas).mousemove(function (e) {
+        var feature_data = tile.feature_mapper.get_feature_data(e.offsetX, e.offsetY);
+        
+        // TODO: show popup with feature's information.
+    });
+
 };
 
 /**
@@ -3316,6 +3328,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
         var painter = new (this.painter)(filtered, tile_low, tile_high, this.prefs, mode, filter_alpha_generator, ref_seq);
         var required_height = Math.max(MIN_TRACK_HEIGHT, painter.get_required_height(slots_required));
         var canvas = this.view.canvas_manager.new_canvas();
+        var feature_mapper = null;
         
         canvas.width = width + left_offset;
         canvas.height = required_height;
@@ -3330,10 +3343,11 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
         if (result.data) {
             // Draw features.
             ctx.translate(left_offset, 0);
-            painter.draw(ctx, width, required_height, slots);
+            feature_mapper = painter.draw(ctx, width, required_height, slots);
+            feature_mapper.translation = -left_offset;
         }
         
-        return new FeatureTrackTile(tile_index, resolution, canvas, result.data, result.message);        
+        return new FeatureTrackTile(tile_index, resolution, canvas, result.data, result.message, feature_mapper);        
     }
 });
 
@@ -3847,7 +3861,53 @@ LinePainter.prototype.draw = function(ctx, width, height) {
     }
     
     ctx.restore();
-}
+};
+
+/**
+ * Mapper that contains information about feature locations and data.
+ */
+var FeaturePositionMapper = function(slot_height) {
+    this.feature_positions = {};
+    this.slot_height = slot_height;
+    this.translation = 0;
+};
+
+/**
+ * Map feature data to a position defined by <slot, x_start, x_end>.
+ */
+FeaturePositionMapper.prototype.map_feature_data = function(feature_data, slot, x_start, x_end) {
+    if (!this.feature_positions[slot]) {
+        this.feature_positions[slot] = [];
+    }
+    this.feature_positions[slot].push({
+        data: feature_data,
+        x_start: x_start,
+        x_end: x_end
+    });
+};
+
+/**
+ * Get feature data for position <x, y>
+ */
+FeaturePositionMapper.prototype.get_feature_data = function(x, y) {
+    // Find slot using Y.
+    var slot = Math.floor(y/this.slot_height),
+        feature_dict;
+
+    // May not be over a slot due to padding, margin, etc.
+    if (!this.feature_positions[slot]) {
+        return null;
+    }
+    
+    // Find feature using X.
+    x += this.translation;
+    for (var i = 0; i < this.feature_positions[slot].length; i++) {
+        feature_dict = this.feature_positions[slot][i];
+        if (x >= feature_dict.x_start && x <= feature_dict.x_end) {
+            return feature_dict.data;
+        }
+    }
+};
 
 /**
  * Abstract object for painting feature tracks. Subclasses must implement draw_element() for painting to work.
@@ -3855,7 +3915,7 @@ LinePainter.prototype.draw = function(ctx, width, height) {
 var FeaturePainter = function(data, view_start, view_end, prefs, mode, alpha_generator) {
     Painter.call(this, data, view_start, view_end, prefs, mode);
     this.alpha_generator = (alpha_generator ? alpha_generator : new AlphaGenerator());
-}
+};
 
 FeaturePainter.prototype.default_prefs = { block_color: "#FFF", connector_color: "#FFF" };
 
@@ -3870,9 +3930,9 @@ extend(FeaturePainter.prototype, {
         // Pad bottom by half a row, at least 5 px
         return required_height + Math.max( Math.round( y_scale / 2 ), 5 );
     },
-
     /**
-     * Draw data on ctx using slots and within the rectangle defined by width and height.
+     * Draw data on ctx using slots and within the rectangle defined by width and height. Returns
+     * a FeaturePositionMapper object with information about where features were drawn.
      */
     draw: function(ctx, width, height, slots) {
         var data = this.data, view_start = this.view_start, view_end = this.view_end;
@@ -3884,7 +3944,9 @@ extend(FeaturePainter.prototype, {
 
         var view_range = this.view_end - this.view_start,
             w_scale = width / view_range,
-            y_scale = this.get_row_height();
+            y_scale = this.get_row_height(),
+            feature_mapper = new FeaturePositionMapper(y_scale),
+            x_draw_coords;
 
         for (var i = 0, len = data.length; i < len; i++) {
             var feature = data[i],
@@ -3897,18 +3959,20 @@ extend(FeaturePainter.prototype, {
                 
             // Draw feature if there's overlap and mode is dense or feature is slotted (as it must be for all non-dense modes).
             if ( ( feature_start < view_end && feature_end > view_start ) && (this.mode == "Dense" || slot !== null) ) {
-                this.draw_element(ctx, this.mode, feature, slot, view_start, view_end, w_scale, y_scale, width);
+                x_draw_coords = this.draw_element(ctx, this.mode, feature, slot, view_start, view_end, w_scale, y_scale, width);
+                feature_mapper.map_feature_data(feature, slot, x_draw_coords[0], x_draw_coords[1]);
             }
         }
 
         ctx.restore();
+        return feature_mapper;
     },
-    
     /** 
      * Abstract function for drawing an individual feature.
      */
     draw_element: function(ctx, mode, feature, slot, tile_low, tile_high, w_scale, y_scale, width ) {
         console.log("WARNING: Unimplemented function.");
+        return [0, 0];
     }
 });
 
@@ -3952,7 +4016,7 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
     },
 
     /**
-     * Draw a feature.
+     * Draw a feature. Returns an array with feature's start and end X coordinates.
      */
     draw_element: function(ctx, mode, feature, slot, tile_low, tile_high, w_scale, y_scale, width) {
         var 
@@ -3962,6 +4026,8 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
             feature_name = feature[3],
             f_start = Math.floor( Math.max(0, (feature_start - tile_low) * w_scale) ),
             f_end   = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low) * w_scale)) ),
+            draw_start = f_start,
+            draw_end = f_end,
             y_center = (mode === "Dense" ? 0 : (0 + slot)) * y_scale,
             thickness, y_start, thick_start = null, thick_end = null,
             // TODO: is there any reason why block, label color cannot be set at the Painter level?
@@ -4096,9 +4162,11 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
                 if (tile_low === 0 && f_start - ctx.measureText(feature_name).width < 0) {
                     ctx.textAlign = "left";
                     ctx.fillText(feature_name, f_end + LABEL_SPACING, y_center + 8);
+                    draw_end += ctx.measureText(feature_name).width + LABEL_SPACING;
                 } else {
                     ctx.textAlign = "right";
                     ctx.fillText(feature_name, f_start - LABEL_SPACING, y_center + 8);
+                    draw_start -= ctx.measureText(feature_name).width + LABEL_SPACING;
                 }
                 //ctx.fillStyle = block_color;
             }
@@ -4106,6 +4174,8 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
         
         // Reset global alpha.
         ctx.globalAlpha = 1;
+        
+        return [draw_start, draw_end];
     }
 });
 

From 684fbad5bc7c8c923e8b5c3ce280a774e3bfc96e Mon Sep 17 00:00:00 2001
From: Kanwei Li <kanwei@gmail.com>
Date: Tue, 4 Oct 2011 22:25:08 -0400
Subject: [PATCH 016/362] Force octet-stream MIME only when downloading
 datasets to prevent Safari from appending MIME extension

---
 lib/galaxy/web/controllers/dataset.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/web/controllers/dataset.py b/lib/galaxy/web/controllers/dataset.py
index 6cb7598d369..32b6ed0de43 100644
--- a/lib/galaxy/web/controllers/dataset.py
+++ b/lib/galaxy/web/controllers/dataset.py
@@ -218,7 +218,7 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesHistory, UsesHist
         outfname = data.name[0:150]
         outfname = ''.join(c in valid_chars and c or '_' for c in outfname)
         if (params.do_action == None):
-     	    params.do_action = 'zip' # default
+            params.do_action = 'zip' # default
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
         if not data:
@@ -370,6 +370,7 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesHistory, UsesHist
                     to_ext = data.extension
                 valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
                 fname = ''.join(c in valid_chars and c or '_' for c in data.name)[0:150]
+                trans.response.set_content_type( "application/octet-stream" ) #force octet-stream so Safari doesn't append mime extensions to filename
                 trans.response.headers["Content-Disposition"] = "attachment; filename=Galaxy%s-[%s].%s" % (data.hid, fname, to_ext)
                 return open( data.file_name )
         if not os.path.exists( data.file_name ):

From 8ef579f7148834f123010ee4e3a02fb2b9e5fd08 Mon Sep 17 00:00:00 2001
From: Kanwei Li <kanwei@gmail.com>
Date: Tue, 4 Oct 2011 23:11:23 -0400
Subject: [PATCH 017/362] Grouping tool: make error clearer when a line doesn't
 have entry on grouped column

---
 tools/stats/grouping.py | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/tools/stats/grouping.py b/tools/stats/grouping.py
index 90f07a6093f..084d5e253b3 100644
--- a/tools/stats/grouping.py
+++ b/tools/stats/grouping.py
@@ -1,7 +1,6 @@
 #!/usr/bin/env python
 # Guruprasad Ananda
-# Refactored 2011, Kanwei Li
-# Refactored to use numpy instead of rpy
+# Refactored 2011 to use numpy instead of rpy, Kanwei Li
 """
 This tool provides the SQL "group by" functionality.
 """
@@ -83,7 +82,11 @@ def main():
     fout = open(sys.argv[1], "w")
     
     def is_new_item(line):
-        item = line.strip().split("\t")[group_col]
+        try:
+            item = line.strip().split("\t")[group_col]
+        except IndexError:
+            stop_err( "The following line didn't have %s columns: %s" % (group_col+1, line) )
+            
         if ignorecase == 1:
             return item.lower()
         return item

From fec37cd896f2354f9976a858e0619622070232d1 Mon Sep 17 00:00:00 2001
From: Kanwei Li <kanwei@gmail.com>
Date: Tue, 4 Oct 2011 23:29:08 -0400
Subject: [PATCH 018/362] Standardize {datatypes|tool}_conf.xml.sample with 2
 space indentation and newline before <label> blocks

---
 datatypes_conf.xml.sample | 698 +++++++++++++++++++-------------------
 tool_conf.xml.sample      | 442 ++++++++++++------------
 2 files changed, 582 insertions(+), 558 deletions(-)

diff --git a/datatypes_conf.xml.sample b/datatypes_conf.xml.sample
index a7d31f05a5a..053009b4905 100644
--- a/datatypes_conf.xml.sample
+++ b/datatypes_conf.xml.sample
@@ -1,352 +1,352 @@
 <?xml version="1.0"?>
 <datatypes>
-    <registration converters_path="lib/galaxy/datatypes/converters" display_path="display_applications">
-        <datatype extension="ab1" type="galaxy.datatypes.binary:Ab1" mimetype="application/octet-stream" display_in_upload="true"/>
-        <datatype extension="afg" type="galaxy.datatypes.assembly:Amos" display_in_upload="false"/>
-        <datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true"/>
-        <datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true">
-            <converter file="bam_to_bai.xml" target_datatype="bai"/>
-            <converter file="bam_to_summary_tree_converter.xml" target_datatype="summary_tree" depends_on="bai"/>
-            <display file="ucsc/bam.xml" />
-            <display file="ensembl/ensembl_bam.xml" />
-            <!-- <display file="igv/bam.xml" /> -->
-        </datatype>
-        <datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true">
-            <converter file="bed_to_gff_converter.xml" target_datatype="gff"/>
-            <converter file="interval_to_coverage.xml" target_datatype="coverage"/>
-            <converter file="bed_to_bgzip_converter.xml" target_datatype="bgzip"/>
-            <converter file="bed_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
-            <converter file="bed_to_summary_tree_converter.xml" target_datatype="summary_tree"/>
-            <!-- <display file="ucsc/interval_as_bed.xml" /> -->
-            <display file="genetrack.xml" />
-        </datatype>
-        <datatype extension="bedgraph" type="galaxy.datatypes.interval:BedGraph" display_in_upload="true" />
-        <datatype extension="bedstrict" type="galaxy.datatypes.interval:BedStrict" />
-        <datatype extension="bed6" type="galaxy.datatypes.interval:Bed6">
-            <converter file="bed_to_genetrack_converter.xml" target_datatype="genetrack"/>
-        </datatype>
-        <datatype extension="bed12" type="galaxy.datatypes.interval:Bed12" />
-        <datatype extension="len" type="galaxy.datatypes.chrominfo:ChromInfo" display_in_upload="true">
-			<converter file="len_to_linecount.xml" target_datatype="linecount" />
-        </datatype>
-        <datatype extension="bigbed" type="galaxy.datatypes.binary:BigBed" mimetype="application/octet-stream" display_in_upload="true">
-            <display file="ucsc/bigbed.xml" />
-        </datatype>
-        <datatype extension="bigwig" type="galaxy.datatypes.binary:BigWig" mimetype="application/octet-stream" display_in_upload="true">
-            <display file="ucsc/bigwig.xml" />
-        </datatype>
-        <datatype extension="coverage" type="galaxy.datatypes.coverage:LastzCoverage" display_in_upload="true">
-            <indexer file="coverage.xml" />
-        </datatype>
-        <datatype extension="coverage" type="galaxy.datatypes.coverage:LastzCoverage" display_in_upload="true">
-            <indexer file="coverage.xml" />
-        </datatype>
-        <!-- MSI added Datatypes -->
-        <datatype extension="csv" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="true" /> <!-- FIXME: csv is 'tabular'ized data, but not 'tab-delimited'; the class used here is intended for 'tab-delimited' -->
-        <!-- End MSI added Datatypes -->
-        <datatype extension="customtrack" type="galaxy.datatypes.interval:CustomTrack"/>
-        <datatype extension="bowtie_color_index" type="galaxy.datatypes.ngsindex:BowtieColorIndex" mimetype="text/html" display_in_upload="False"/>
-        <datatype extension="bowtie_base_index" type="galaxy.datatypes.ngsindex:BowtieBaseIndex" mimetype="text/html" display_in_upload="False"/>
-        <datatype extension="csfasta" type="galaxy.datatypes.sequence:csFasta" display_in_upload="true"/>
-        <datatype extension="data" type="galaxy.datatypes.data:Data" mimetype="application/octet-stream" max_optional_metadata_filesize="1048576" />
-        <datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta" display_in_upload="true">
-            <converter file="fasta_to_tabular_converter.xml" target_datatype="tabular"/>
-            <converter file="fasta_to_bowtie_base_index_converter.xml" target_datatype="bowtie_base_index"/>
-            <converter file="fasta_to_bowtie_color_index_converter.xml" target_datatype="bowtie_color_index"/>
-			<converter file="fasta_to_2bit.xml" target_datatype="twobit"/>
-			<converter file="fasta_to_len.xml" target_datatype="len"/>
-        </datatype>
-        <datatype extension="fastq" type="galaxy.datatypes.sequence:Fastq" display_in_upload="true"/>
-        <datatype extension="fastqsanger" type="galaxy.datatypes.sequence:FastqSanger" display_in_upload="true"/>
-        <datatype extension="fastqsolexa" type="galaxy.datatypes.sequence:FastqSolexa" display_in_upload="true"/>
-        <datatype extension="fastqcssanger" type="galaxy.datatypes.sequence:FastqCSSanger" display_in_upload="true"/>
-        <datatype extension="fastqillumina" type="galaxy.datatypes.sequence:FastqIllumina" display_in_upload="true"/>
-        <datatype extension="eland" type="galaxy.datatypes.tabular:Eland" display_in_upload="true"/>
-        <datatype extension="elandmulti" type="galaxy.datatypes.tabular:ElandMulti" display_in_upload="true"/>
-        <datatype extension="genetrack" type="galaxy.datatypes.tracks:GeneTrack">
-            <!-- <display file="genetrack.xml" /> -->
-        </datatype>
-        <datatype extension="gff" type="galaxy.datatypes.interval:Gff" display_in_upload="true">
-            <converter file="gff_to_bed_converter.xml" target_datatype="bed"/>
-            <converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/>
-            <converter file="gff_to_summary_tree_converter.xml" target_datatype="summary_tree"/>
-            <display file="ensembl/ensembl_gff.xml" inherit="True"/>
-            <!-- <display file="gbrowse/gbrowse_gff.xml" inherit="True" /> -->
-        </datatype>
-        <datatype extension="gff3" type="galaxy.datatypes.interval:Gff3" display_in_upload="true"/>
-        <datatype extension="gif" type="galaxy.datatypes.images:Gif" mimetype="image/gif"/>
-        <datatype extension="gmaj.zip" type="galaxy.datatypes.images:Gmaj" mimetype="application/zip"/>
-        <datatype extension="gtf" type="galaxy.datatypes.interval:Gtf" display_in_upload="true"/>
-        <datatype extension="h5" type="galaxy.datatypes.data:Data" mimetype="application/octet-stream"/>
-        <datatype extension="html" type="galaxy.datatypes.images:Html" mimetype="text/html"/>
-        <datatype extension="interval" type="galaxy.datatypes.interval:Interval" display_in_upload="true">
-            <converter file="interval_to_bed_converter.xml" target_datatype="bed"/>
-            <converter file="interval_to_bedstrict_converter.xml" target_datatype="bedstrict"/>
-            <converter file="interval_to_bed6_converter.xml" target_datatype="bed6"/>
-            <converter file="interval_to_bed12_converter.xml" target_datatype="bed12"/>
-            <indexer file="interval_awk.xml" />
-            <!-- <display file="ucsc/interval_as_bed.xml" inherit="True" /> -->
-            <display file="genetrack.xml" inherit="True"/>
-            <display file="ensembl/ensembl_interval_as_bed.xml" inherit="True"/>
-            <display file="gbrowse/gbrowse_interval_as_bed.xml" inherit="True"/>
-        </datatype>
-        <datatype extension="picard_interval_list" type="galaxy.datatypes.data:Text" subclass="True" display_in_upload="True"/>
-        <datatype extension="gatk_interval" type="galaxy.datatypes.data:Text" subclass="True" display_in_upload="True"/>
-        <datatype extension="gatk_dbsnp" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"/>
-        <datatype extension="gatk_tranche" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"/>
-        <datatype extension="gatk_recal" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"/>
-        <datatype extension="jpg" type="galaxy.datatypes.images:Jpg" mimetype="image/jpeg"/>
-        <datatype extension="tiff" type="galaxy.datatypes.images:Tiff" mimetype="image/tiff"/>
-        <datatype extension="bmp" type="galaxy.datatypes.images:Bmp" mimetype="image/bmp"/>
-        <datatype extension="im" type="galaxy.datatypes.images:Im" mimetype="image/im"/>
-        <datatype extension="pcd" type="galaxy.datatypes.images:Pcd" mimetype="image/pcd"/>
-        <datatype extension="pcx" type="galaxy.datatypes.images:Pcx" mimetype="image/pcx"/>
-        <datatype extension="ppm" type="galaxy.datatypes.images:Ppm" mimetype="image/ppm"/>
-        <datatype extension="psd" type="galaxy.datatypes.images:Psd" mimetype="image/psd"/>
-        <datatype extension="xbm" type="galaxy.datatypes.images:Xbm" mimetype="image/xbm"/>
-        <datatype extension="xpm" type="galaxy.datatypes.images:Xpm" mimetype="image/xpm"/>
-        <datatype extension="rgb" type="galaxy.datatypes.images:Rgb" mimetype="image/rgb"/>
-        <datatype extension="pbm" type="galaxy.datatypes.images:Pbm" mimetype="image/pbm"/>
-        <datatype extension="pgm" type="galaxy.datatypes.images:Pgm" mimetype="image/pgm"/>
-        <datatype extension="eps" type="galaxy.datatypes.images:Eps" mimetype="image/eps"/>
-        <datatype extension="rast" type="galaxy.datatypes.images:Rast" mimetype="image/rast"/>
-        <datatype extension="laj" type="galaxy.datatypes.images:Laj"/>
-        <datatype extension="lav" type="galaxy.datatypes.sequence:Lav" display_in_upload="true"/>
-        <datatype extension="maf" type="galaxy.datatypes.sequence:Maf" display_in_upload="true">
-            <converter file="maf_to_fasta_converter.xml" target_datatype="fasta"/>
-            <converter file="maf_to_interval_converter.xml" target_datatype="interval"/>
-        </datatype>
-        <datatype extension="mafcustomtrack" type="galaxy.datatypes.sequence:MafCustomTrack">
-            <display file="ucsc/maf_customtrack.xml" />
-        </datatype>
-        <datatype extension="pdf" type="galaxy.datatypes.images:Pdf" mimetype="application/pdf"/>
-        <datatype extension="pileup" type="galaxy.datatypes.tabular:Pileup" display_in_upload="true" />
-        <datatype extension="png" type="galaxy.datatypes.images:Png" mimetype="image/png"/>
-        <datatype extension="qual" type="galaxy.datatypes.qualityscore:QualityScore" />
-        <datatype extension="qualsolexa" type="galaxy.datatypes.qualityscore:QualityScoreSolexa" display_in_upload="true"/>
-        <datatype extension="qualillumina" type="galaxy.datatypes.qualityscore:QualityScoreIllumina" display_in_upload="true"/>
-        <datatype extension="qualsolid" type="galaxy.datatypes.qualityscore:QualityScoreSOLiD" display_in_upload="true"/>
-        <datatype extension="qual454" type="galaxy.datatypes.qualityscore:QualityScore454" display_in_upload="true"/>
-        <datatype extension="Roadmaps" type="galaxy.datatypes.assembly:Roadmaps" display_in_upload="false"/>
-        <datatype extension="sam" type="galaxy.datatypes.tabular:Sam" display_in_upload="true"/>
-        <datatype extension="scf" type="galaxy.datatypes.binary:Scf" mimetype="application/octet-stream" display_in_upload="true"/>
-        <datatype extension="Sequences" type="galaxy.datatypes.assembly:Sequences" display_in_upload="false"/>
-        <datatype extension="sff" type="galaxy.datatypes.binary:Sff" mimetype="application/octet-stream" display_in_upload="true"/>
-        <datatype extension="svg" type="galaxy.datatypes.images:Image" mimetype="image/svg+xml"/>
-        <datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/>
-        <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true"/>
-        <datatype extension="twobit" type="galaxy.datatypes.binary:TwoBit" mimetype="application/octet-stream" display_in_upload="true"/>
-        <datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true"/>
-        <datatype extension="linecount" type="galaxy.datatypes.data:LineCount" display_in_upload="false"/>
-        <datatype extension="memexml" type="galaxy.datatypes.xml:MEMEXml" mimetype="application/xml" display_in_upload="true"/>
-        <datatype extension="cisml" type="galaxy.datatypes.xml:CisML" mimetype="application/xml" display_in_upload="true"/>
-        <datatype extension="blastxml" type="galaxy.datatypes.xml:BlastXml" mimetype="application/xml" display_in_upload="true"/>
-        <datatype extension="vcf" type="galaxy.datatypes.tabular:Vcf" display_in_upload="true">
-            <converter file="vcf_to_bgzip_converter.xml" target_datatype="bgzip"/>
-            <converter file="vcf_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
-            <converter file="vcf_to_summary_tree_converter.xml" target_datatype="summary_tree"/>
-        </datatype>
-        <datatype extension="wsf" type="galaxy.datatypes.wsf:SnpFile" display_in_upload="true"/>
-        <datatype extension="velvet" type="galaxy.datatypes.assembly:Velvet" display_in_upload="false"/>
-        <datatype extension="wig" type="galaxy.datatypes.interval:Wiggle" display_in_upload="true">
-            <converter file="wig_to_bigwig_converter.xml" target_datatype="bigwig"/>
-            <converter file="wiggle_to_simple_converter.xml" target_datatype="interval"/>
-            <!-- <display file="gbrowse/gbrowse_wig.xml" /> -->
-        </datatype>
-        <datatype extension="summary_tree" type="galaxy.datatypes.data:Data" />
-        <datatype extension="interval_index" type="galaxy.datatypes.data:Data" />
-        <datatype extension="tabix" type="galaxy.datatypes.data:Data" />
-        <datatype extension="bgzip" type="galaxy.datatypes.data:Data" />
-        <!-- Start EMBOSS tools -->
-        <datatype extension="acedb" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="asn1" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="btwisted" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="cai" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="charge" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="checktrans" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="chips" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="clustal" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="codata" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="codcmp" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="coderet" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="compseq" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="cpgplot" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="cpgreport" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="cusp" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="cut" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="dan" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="dbmotif" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="diffseq" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="digest" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="dreg" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="einverted" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="embl" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="epestfind" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="equicktandem" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="est2genome" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="etandem" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="excel" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="feattable" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="fitch" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="freak" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="fuzznuc" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="fuzzpro" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="fuzztran" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="garnier" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="gcg" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="geecee" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="genbank" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="helixturnhelix" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="hennig86" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="hmoment" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="ig" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="isochore" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="jackknifer" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="jackknifernon" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="markx10" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="markx1" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="markx0" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="markx3" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="markx2" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="match" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="mega" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="meganon" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="motif" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="msf" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="nametable" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="ncbi" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="needle" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="newcpgreport" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="newcpgseek" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="nexus" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="nexusnon" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="noreturn" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="pair" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="palindrome" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="pepcoil" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="pepinfo" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="pepstats" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="phylip" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="phylipnon" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="pir" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="polydot" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="preg" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="prettyseq" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="primersearch" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="regions" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="score" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="selex" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="seqtable" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="showfeat" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="showorf" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="simple" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="sixpack" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="srs" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="srspair" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="staden" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="strider" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="supermatcher" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="swiss" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="syco" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="table" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="textsearch" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="vectorstrip" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="wobble" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="wordcount" type="galaxy.datatypes.data:Text"/>
-        <datatype extension="tagseq" type="galaxy.datatypes.data:Text"/>
-        <!-- End EMBOSS tools -->
-        <!-- Start RGenetics Datatypes -->
-        <datatype extension="affybatch" type="galaxy.datatypes.genetics:Affybatch" display_in_upload="true"/>
-        <!-- eigenstrat pedigree input file -->
-        <datatype extension="eigenstratgeno" type="galaxy.datatypes.genetics:Eigenstratgeno"/>
-        <!-- eigenstrat pca output file for adjusted eigenQTL eg -->
-        <datatype extension="eigenstratpca" type="galaxy.datatypes.genetics:Eigenstratpca"/>
-        <datatype extension="eset" type="galaxy.datatypes.genetics:Eset" display_in_upload="true" />
-        <!-- fbat/pbat format pedigree (header row of marker names) -->
-        <datatype extension="fped" type="galaxy.datatypes.genetics:Fped" display_in_upload="true"/>
-        <!-- phenotype file - fbat format -->
-        <datatype extension="fphe" type="galaxy.datatypes.genetics:Fphe" display_in_upload="true" mimetype="text/html"/>
-        <!-- genome graphs ucsc file - first col is always marker then numeric values to plot -->
-        <datatype extension="gg" type="galaxy.datatypes.genetics:GenomeGraphs"/>
-        <!-- part of linkage format pedigree -->
-        <!-- information redundancy (LD) filtered plink pbed -->
-        <datatype extension="ldindep" type="galaxy.datatypes.genetics:ldIndep" display_in_upload="true">
-        </datatype>
-        <datatype extension="malist" type="galaxy.datatypes.genetics:MAlist" display_in_upload="true"/>
-        <!-- linkage format pedigree (separate .map file) -->
-        <datatype extension="lped" type="galaxy.datatypes.genetics:Lped" display_in_upload="true">
-            <converter file="lped_to_fped_converter.xml" target_datatype="fped"/>
-            <converter file="lped_to_pbed_converter.xml" target_datatype="pbed"/>
-        </datatype>
-        <!-- plink compressed file - has bed extension unfortunately -->
-        <datatype extension="pbed" type="galaxy.datatypes.genetics:Pbed" display_in_upload="true">
-            <converter file="pbed_to_lped_converter.xml" target_datatype="lped"/>
-            <converter file="pbed_ldreduced_converter.xml" target_datatype="ldindep"/>
-        </datatype>
-        <datatype extension="pheno" type="galaxy.datatypes.genetics:Pheno"/>
-        <!-- phenotype file - plink format -->
-        <datatype extension="pphe" type="galaxy.datatypes.genetics:Pphe" display_in_upload="true" mimetype="text/html"/>
-        <datatype extension="rexpbase" type="galaxy.datatypes.genetics:RexpBase"/>
-        <datatype extension="rgenetics" type="galaxy.datatypes.genetics:Rgenetics"/>
-        <datatype extension="snptest" type="galaxy.datatypes.genetics:Snptest" display_in_upload="true"/>
-        <datatype extension="snpmatrix" type="galaxy.datatypes.genetics:SNPMatrix" display_in_upload="true"/>
-        <datatype extension="xls" type="galaxy.datatypes.tabular:Tabular"/>
-        <!-- End RGenetics Datatypes -->
-    </registration>
-    <sniffers>
-        <!--
-          The order in which Galaxy attempts to determine data types is
-          important because some formats are much more loosely defined
-          than others.  The following list should be the most rigidly
-          defined format first, followed by next-most rigidly defined,
-          and so on.
-        -->
-        <sniffer type="galaxy.datatypes.tabular:Vcf"/>
-        <sniffer type="galaxy.datatypes.binary:TwoBit"/>
-        <sniffer type="galaxy.datatypes.binary:Bam"/>
-        <sniffer type="galaxy.datatypes.binary:Sff"/>
-        <sniffer type="galaxy.datatypes.xml:BlastXml"/>
-        <sniffer type="galaxy.datatypes.sequence:Maf"/>
-        <sniffer type="galaxy.datatypes.sequence:Lav"/>
-        <sniffer type="galaxy.datatypes.sequence:csFasta"/>
-        <sniffer type="galaxy.datatypes.qualityscore:QualityScoreSOLiD"/>
-        <sniffer type="galaxy.datatypes.qualityscore:QualityScore454"/>
-        <sniffer type="galaxy.datatypes.sequence:Fasta"/>
-        <sniffer type="galaxy.datatypes.sequence:Fastq"/>
-        <sniffer type="galaxy.datatypes.interval:Wiggle"/>
-        <sniffer type="galaxy.datatypes.images:Html"/>
-        <sniffer type="galaxy.datatypes.images:Pdf"/>
-        <sniffer type="galaxy.datatypes.sequence:Axt"/>
-        <sniffer type="galaxy.datatypes.interval:Bed"/>
-        <sniffer type="galaxy.datatypes.interval:CustomTrack"/>
-        <sniffer type="galaxy.datatypes.interval:Gtf"/>
-        <sniffer type="galaxy.datatypes.interval:Gff"/>
-        <sniffer type="galaxy.datatypes.interval:Gff3"/>
-        <sniffer type="galaxy.datatypes.tabular:Pileup"/>
-        <sniffer type="galaxy.datatypes.interval:Interval"/>
-        <sniffer type="galaxy.datatypes.tabular:Sam"/>
-        <sniffer type="galaxy.datatypes.images:Jpg"/>
-        <sniffer type="galaxy.datatypes.images:Png"/>
-        <sniffer type="galaxy.datatypes.images:Tiff"/>
-        <sniffer type="galaxy.datatypes.images:Bmp"/>
-        <sniffer type="galaxy.datatypes.images:Gif"/>
-        <sniffer type="galaxy.datatypes.images:Im"/>
-        <sniffer type="galaxy.datatypes.images:Pcd"/>
-        <sniffer type="galaxy.datatypes.images:Pcx"/>
-        <sniffer type="galaxy.datatypes.images:Ppm"/>
-        <sniffer type="galaxy.datatypes.images:Psd"/>
-        <sniffer type="galaxy.datatypes.images:Xbm"/>
-        <sniffer type="galaxy.datatypes.images:Xpm"/>
-        <sniffer type="galaxy.datatypes.images:Rgb"/>
-        <sniffer type="galaxy.datatypes.images:Pbm"/>
-        <sniffer type="galaxy.datatypes.images:Pgm"/>
-        <sniffer type="galaxy.datatypes.images:Xpm"/>
-        <sniffer type="galaxy.datatypes.images:Eps"/>
-        <sniffer type="galaxy.datatypes.images:Rast"/>
-        <!--
-        Keep this commented until the sniff method in the assembly.py
-        module is fixed to not read the entire file.
-        <sniffer type="galaxy.datatypes.assembly:Amos"/>
-        -->
-    </sniffers>
+  <registration converters_path="lib/galaxy/datatypes/converters" display_path="display_applications">
+    <datatype extension="ab1" type="galaxy.datatypes.binary:Ab1" mimetype="application/octet-stream" display_in_upload="true"/>
+    <datatype extension="afg" type="galaxy.datatypes.assembly:Amos" display_in_upload="false"/>
+    <datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true"/>
+    <datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true">
+      <converter file="bam_to_bai.xml" target_datatype="bai"/>
+      <converter file="bam_to_summary_tree_converter.xml" target_datatype="summary_tree" depends_on="bai"/>
+      <display file="ucsc/bam.xml" />
+      <display file="ensembl/ensembl_bam.xml" />
+      <!-- <display file="igv/bam.xml" /> -->
+    </datatype>
+    <datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true">
+      <converter file="bed_to_gff_converter.xml" target_datatype="gff"/>
+      <converter file="interval_to_coverage.xml" target_datatype="coverage"/>
+      <converter file="bed_to_bgzip_converter.xml" target_datatype="bgzip"/>
+      <converter file="bed_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
+      <converter file="bed_to_summary_tree_converter.xml" target_datatype="summary_tree"/>
+      <!-- <display file="ucsc/interval_as_bed.xml" /> -->
+      <display file="genetrack.xml" />
+    </datatype>
+    <datatype extension="bedgraph" type="galaxy.datatypes.interval:BedGraph" display_in_upload="true" />
+    <datatype extension="bedstrict" type="galaxy.datatypes.interval:BedStrict" />
+    <datatype extension="bed6" type="galaxy.datatypes.interval:Bed6">
+      <converter file="bed_to_genetrack_converter.xml" target_datatype="genetrack"/>
+    </datatype>
+    <datatype extension="bed12" type="galaxy.datatypes.interval:Bed12" />
+    <datatype extension="len" type="galaxy.datatypes.chrominfo:ChromInfo" display_in_upload="true">
+      <converter file="len_to_linecount.xml" target_datatype="linecount" />
+    </datatype>
+    <datatype extension="bigbed" type="galaxy.datatypes.binary:BigBed" mimetype="application/octet-stream" display_in_upload="true">
+      <display file="ucsc/bigbed.xml" />
+    </datatype>
+    <datatype extension="bigwig" type="galaxy.datatypes.binary:BigWig" mimetype="application/octet-stream" display_in_upload="true">
+      <display file="ucsc/bigwig.xml" />
+    </datatype>
+    <datatype extension="coverage" type="galaxy.datatypes.coverage:LastzCoverage" display_in_upload="true">
+      <indexer file="coverage.xml" />
+    </datatype>
+    <datatype extension="coverage" type="galaxy.datatypes.coverage:LastzCoverage" display_in_upload="true">
+      <indexer file="coverage.xml" />
+    </datatype>
+    <!-- MSI added Datatypes -->
+    <datatype extension="csv" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="true" /> <!-- FIXME: csv is 'tabular'ized data, but not 'tab-delimited'; the class used here is intended for 'tab-delimited' -->
+    <!-- End MSI added Datatypes -->
+    <datatype extension="customtrack" type="galaxy.datatypes.interval:CustomTrack"/>
+    <datatype extension="bowtie_color_index" type="galaxy.datatypes.ngsindex:BowtieColorIndex" mimetype="text/html" display_in_upload="False"/>
+    <datatype extension="bowtie_base_index" type="galaxy.datatypes.ngsindex:BowtieBaseIndex" mimetype="text/html" display_in_upload="False"/>
+    <datatype extension="csfasta" type="galaxy.datatypes.sequence:csFasta" display_in_upload="true"/>
+    <datatype extension="data" type="galaxy.datatypes.data:Data" mimetype="application/octet-stream" max_optional_metadata_filesize="1048576" />
+    <datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta" display_in_upload="true">
+      <converter file="fasta_to_tabular_converter.xml" target_datatype="tabular"/>
+      <converter file="fasta_to_bowtie_base_index_converter.xml" target_datatype="bowtie_base_index"/>
+      <converter file="fasta_to_bowtie_color_index_converter.xml" target_datatype="bowtie_color_index"/>
+      <converter file="fasta_to_2bit.xml" target_datatype="twobit"/>
+      <converter file="fasta_to_len.xml" target_datatype="len"/>
+    </datatype>
+    <datatype extension="fastq" type="galaxy.datatypes.sequence:Fastq" display_in_upload="true"/>
+    <datatype extension="fastqsanger" type="galaxy.datatypes.sequence:FastqSanger" display_in_upload="true"/>
+    <datatype extension="fastqsolexa" type="galaxy.datatypes.sequence:FastqSolexa" display_in_upload="true"/>
+    <datatype extension="fastqcssanger" type="galaxy.datatypes.sequence:FastqCSSanger" display_in_upload="true"/>
+    <datatype extension="fastqillumina" type="galaxy.datatypes.sequence:FastqIllumina" display_in_upload="true"/>
+    <datatype extension="eland" type="galaxy.datatypes.tabular:Eland" display_in_upload="true"/>
+    <datatype extension="elandmulti" type="galaxy.datatypes.tabular:ElandMulti" display_in_upload="true"/>
+    <datatype extension="genetrack" type="galaxy.datatypes.tracks:GeneTrack">
+      <!-- <display file="genetrack.xml" /> -->
+    </datatype>
+    <datatype extension="gff" type="galaxy.datatypes.interval:Gff" display_in_upload="true">
+      <converter file="gff_to_bed_converter.xml" target_datatype="bed"/>
+      <converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/>
+      <converter file="gff_to_summary_tree_converter.xml" target_datatype="summary_tree"/>
+      <display file="ensembl/ensembl_gff.xml" inherit="True"/>
+      <!-- <display file="gbrowse/gbrowse_gff.xml" inherit="True" /> -->
+    </datatype>
+    <datatype extension="gff3" type="galaxy.datatypes.interval:Gff3" display_in_upload="true"/>
+    <datatype extension="gif" type="galaxy.datatypes.images:Gif" mimetype="image/gif"/>
+    <datatype extension="gmaj.zip" type="galaxy.datatypes.images:Gmaj" mimetype="application/zip"/>
+    <datatype extension="gtf" type="galaxy.datatypes.interval:Gtf" display_in_upload="true"/>
+    <datatype extension="h5" type="galaxy.datatypes.data:Data" mimetype="application/octet-stream"/>
+    <datatype extension="html" type="galaxy.datatypes.images:Html" mimetype="text/html"/>
+    <datatype extension="interval" type="galaxy.datatypes.interval:Interval" display_in_upload="true">
+      <converter file="interval_to_bed_converter.xml" target_datatype="bed"/>
+      <converter file="interval_to_bedstrict_converter.xml" target_datatype="bedstrict"/>
+      <converter file="interval_to_bed6_converter.xml" target_datatype="bed6"/>
+      <converter file="interval_to_bed12_converter.xml" target_datatype="bed12"/>
+      <indexer file="interval_awk.xml" />
+      <!-- <display file="ucsc/interval_as_bed.xml" inherit="True" /> -->
+      <display file="genetrack.xml" inherit="True"/>
+      <display file="ensembl/ensembl_interval_as_bed.xml" inherit="True"/>
+      <display file="gbrowse/gbrowse_interval_as_bed.xml" inherit="True"/>
+    </datatype>
+    <datatype extension="picard_interval_list" type="galaxy.datatypes.data:Text" subclass="True" display_in_upload="True"/>
+    <datatype extension="gatk_interval" type="galaxy.datatypes.data:Text" subclass="True" display_in_upload="True"/>
+    <datatype extension="gatk_dbsnp" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"/>
+    <datatype extension="gatk_tranche" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"/>
+    <datatype extension="gatk_recal" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"/>
+    <datatype extension="jpg" type="galaxy.datatypes.images:Jpg" mimetype="image/jpeg"/>
+    <datatype extension="tiff" type="galaxy.datatypes.images:Tiff" mimetype="image/tiff"/>
+    <datatype extension="bmp" type="galaxy.datatypes.images:Bmp" mimetype="image/bmp"/>
+    <datatype extension="im" type="galaxy.datatypes.images:Im" mimetype="image/im"/>
+    <datatype extension="pcd" type="galaxy.datatypes.images:Pcd" mimetype="image/pcd"/>
+    <datatype extension="pcx" type="galaxy.datatypes.images:Pcx" mimetype="image/pcx"/>
+    <datatype extension="ppm" type="galaxy.datatypes.images:Ppm" mimetype="image/ppm"/>
+    <datatype extension="psd" type="galaxy.datatypes.images:Psd" mimetype="image/psd"/>
+    <datatype extension="xbm" type="galaxy.datatypes.images:Xbm" mimetype="image/xbm"/>
+    <datatype extension="xpm" type="galaxy.datatypes.images:Xpm" mimetype="image/xpm"/>
+    <datatype extension="rgb" type="galaxy.datatypes.images:Rgb" mimetype="image/rgb"/>
+    <datatype extension="pbm" type="galaxy.datatypes.images:Pbm" mimetype="image/pbm"/>
+    <datatype extension="pgm" type="galaxy.datatypes.images:Pgm" mimetype="image/pgm"/>
+    <datatype extension="eps" type="galaxy.datatypes.images:Eps" mimetype="image/eps"/>
+    <datatype extension="rast" type="galaxy.datatypes.images:Rast" mimetype="image/rast"/>
+    <datatype extension="laj" type="galaxy.datatypes.images:Laj"/>
+    <datatype extension="lav" type="galaxy.datatypes.sequence:Lav" display_in_upload="true"/>
+    <datatype extension="maf" type="galaxy.datatypes.sequence:Maf" display_in_upload="true">
+      <converter file="maf_to_fasta_converter.xml" target_datatype="fasta"/>
+      <converter file="maf_to_interval_converter.xml" target_datatype="interval"/>
+    </datatype>
+    <datatype extension="mafcustomtrack" type="galaxy.datatypes.sequence:MafCustomTrack">
+      <display file="ucsc/maf_customtrack.xml" />
+    </datatype>
+    <datatype extension="pdf" type="galaxy.datatypes.images:Pdf" mimetype="application/pdf"/>
+    <datatype extension="pileup" type="galaxy.datatypes.tabular:Pileup" display_in_upload="true" />
+    <datatype extension="png" type="galaxy.datatypes.images:Png" mimetype="image/png"/>
+    <datatype extension="qual" type="galaxy.datatypes.qualityscore:QualityScore" />
+    <datatype extension="qualsolexa" type="galaxy.datatypes.qualityscore:QualityScoreSolexa" display_in_upload="true"/>
+    <datatype extension="qualillumina" type="galaxy.datatypes.qualityscore:QualityScoreIllumina" display_in_upload="true"/>
+    <datatype extension="qualsolid" type="galaxy.datatypes.qualityscore:QualityScoreSOLiD" display_in_upload="true"/>
+    <datatype extension="qual454" type="galaxy.datatypes.qualityscore:QualityScore454" display_in_upload="true"/>
+    <datatype extension="Roadmaps" type="galaxy.datatypes.assembly:Roadmaps" display_in_upload="false"/>
+    <datatype extension="sam" type="galaxy.datatypes.tabular:Sam" display_in_upload="true"/>
+    <datatype extension="scf" type="galaxy.datatypes.binary:Scf" mimetype="application/octet-stream" display_in_upload="true"/>
+    <datatype extension="Sequences" type="galaxy.datatypes.assembly:Sequences" display_in_upload="false"/>
+    <datatype extension="sff" type="galaxy.datatypes.binary:Sff" mimetype="application/octet-stream" display_in_upload="true"/>
+    <datatype extension="svg" type="galaxy.datatypes.images:Image" mimetype="image/svg+xml"/>
+    <datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/>
+    <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true"/>
+    <datatype extension="twobit" type="galaxy.datatypes.binary:TwoBit" mimetype="application/octet-stream" display_in_upload="true"/>
+    <datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true"/>
+    <datatype extension="linecount" type="galaxy.datatypes.data:LineCount" display_in_upload="false"/>
+    <datatype extension="memexml" type="galaxy.datatypes.xml:MEMEXml" mimetype="application/xml" display_in_upload="true"/>
+    <datatype extension="cisml" type="galaxy.datatypes.xml:CisML" mimetype="application/xml" display_in_upload="true"/>
+    <datatype extension="blastxml" type="galaxy.datatypes.xml:BlastXml" mimetype="application/xml" display_in_upload="true"/>
+    <datatype extension="vcf" type="galaxy.datatypes.tabular:Vcf" display_in_upload="true">
+      <converter file="vcf_to_bgzip_converter.xml" target_datatype="bgzip"/>
+      <converter file="vcf_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
+      <converter file="vcf_to_summary_tree_converter.xml" target_datatype="summary_tree"/>
+    </datatype>
+    <datatype extension="wsf" type="galaxy.datatypes.wsf:SnpFile" display_in_upload="true"/>
+    <datatype extension="velvet" type="galaxy.datatypes.assembly:Velvet" display_in_upload="false"/>
+    <datatype extension="wig" type="galaxy.datatypes.interval:Wiggle" display_in_upload="true">
+      <converter file="wig_to_bigwig_converter.xml" target_datatype="bigwig"/>
+      <converter file="wiggle_to_simple_converter.xml" target_datatype="interval"/>
+      <!-- <display file="gbrowse/gbrowse_wig.xml" /> -->
+    </datatype>
+    <datatype extension="summary_tree" type="galaxy.datatypes.data:Data" />
+    <datatype extension="interval_index" type="galaxy.datatypes.data:Data" />
+    <datatype extension="tabix" type="galaxy.datatypes.data:Data" />
+    <datatype extension="bgzip" type="galaxy.datatypes.data:Data" />
+    <!-- Start EMBOSS tools -->
+    <datatype extension="acedb" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="asn1" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="btwisted" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="cai" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="charge" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="checktrans" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="chips" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="clustal" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="codata" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="codcmp" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="coderet" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="compseq" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="cpgplot" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="cpgreport" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="cusp" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="cut" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="dan" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="dbmotif" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="diffseq" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="digest" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="dreg" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="einverted" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="embl" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="epestfind" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="equicktandem" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="est2genome" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="etandem" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="excel" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="feattable" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="fitch" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="freak" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="fuzznuc" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="fuzzpro" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="fuzztran" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="garnier" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="gcg" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="geecee" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="genbank" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="helixturnhelix" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="hennig86" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="hmoment" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="ig" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="isochore" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="jackknifer" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="jackknifernon" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="markx10" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="markx1" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="markx0" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="markx3" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="markx2" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="match" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="mega" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="meganon" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="motif" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="msf" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="nametable" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="ncbi" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="needle" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="newcpgreport" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="newcpgseek" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="nexus" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="nexusnon" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="noreturn" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="pair" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="palindrome" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="pepcoil" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="pepinfo" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="pepstats" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="phylip" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="phylipnon" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="pir" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="polydot" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="preg" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="prettyseq" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="primersearch" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="regions" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="score" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="selex" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="seqtable" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="showfeat" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="showorf" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="simple" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="sixpack" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="srs" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="srspair" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="staden" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="strider" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="supermatcher" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="swiss" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="syco" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="table" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="textsearch" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="vectorstrip" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="wobble" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="wordcount" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="tagseq" type="galaxy.datatypes.data:Text"/>
+    <!-- End EMBOSS tools -->
+    <!-- Start RGenetics Datatypes -->
+    <datatype extension="affybatch" type="galaxy.datatypes.genetics:Affybatch" display_in_upload="true"/>
+    <!-- eigenstrat pedigree input file -->
+    <datatype extension="eigenstratgeno" type="galaxy.datatypes.genetics:Eigenstratgeno"/>
+    <!-- eigenstrat pca output file for adjusted eigenQTL eg -->
+    <datatype extension="eigenstratpca" type="galaxy.datatypes.genetics:Eigenstratpca"/>
+    <datatype extension="eset" type="galaxy.datatypes.genetics:Eset" display_in_upload="true" />
+    <!-- fbat/pbat format pedigree (header row of marker names) -->
+    <datatype extension="fped" type="galaxy.datatypes.genetics:Fped" display_in_upload="true"/>
+    <!-- phenotype file - fbat format -->
+    <datatype extension="fphe" type="galaxy.datatypes.genetics:Fphe" display_in_upload="true" mimetype="text/html"/>
+    <!-- genome graphs ucsc file - first col is always marker then numeric values to plot -->
+    <datatype extension="gg" type="galaxy.datatypes.genetics:GenomeGraphs"/>
+    <!-- part of linkage format pedigree -->
+    <!-- information redundancy (LD) filtered plink pbed -->
+    <datatype extension="ldindep" type="galaxy.datatypes.genetics:ldIndep" display_in_upload="true">
+    </datatype>
+    <datatype extension="malist" type="galaxy.datatypes.genetics:MAlist" display_in_upload="true"/>
+    <!-- linkage format pedigree (separate .map file) -->
+    <datatype extension="lped" type="galaxy.datatypes.genetics:Lped" display_in_upload="true">
+      <converter file="lped_to_fped_converter.xml" target_datatype="fped"/>
+      <converter file="lped_to_pbed_converter.xml" target_datatype="pbed"/>
+    </datatype>
+    <!-- plink compressed file - has bed extension unfortunately -->
+    <datatype extension="pbed" type="galaxy.datatypes.genetics:Pbed" display_in_upload="true">
+      <converter file="pbed_to_lped_converter.xml" target_datatype="lped"/>
+      <converter file="pbed_ldreduced_converter.xml" target_datatype="ldindep"/>
+    </datatype>
+    <datatype extension="pheno" type="galaxy.datatypes.genetics:Pheno"/>
+    <!-- phenotype file - plink format -->
+    <datatype extension="pphe" type="galaxy.datatypes.genetics:Pphe" display_in_upload="true" mimetype="text/html"/>
+    <datatype extension="rexpbase" type="galaxy.datatypes.genetics:RexpBase"/>
+    <datatype extension="rgenetics" type="galaxy.datatypes.genetics:Rgenetics"/>
+    <datatype extension="snptest" type="galaxy.datatypes.genetics:Snptest" display_in_upload="true"/>
+    <datatype extension="snpmatrix" type="galaxy.datatypes.genetics:SNPMatrix" display_in_upload="true"/>
+    <datatype extension="xls" type="galaxy.datatypes.tabular:Tabular"/>
+    <!-- End RGenetics Datatypes -->
+  </registration>
+  <sniffers>
+    <!--
+    The order in which Galaxy attempts to determine data types is
+    important because some formats are much more loosely defined
+    than others.  The following list should be the most rigidly
+    defined format first, followed by next-most rigidly defined,
+    and so on.
+    -->
+    <sniffer type="galaxy.datatypes.tabular:Vcf"/>
+    <sniffer type="galaxy.datatypes.binary:TwoBit"/>
+    <sniffer type="galaxy.datatypes.binary:Bam"/>
+    <sniffer type="galaxy.datatypes.binary:Sff"/>
+    <sniffer type="galaxy.datatypes.xml:BlastXml"/>
+    <sniffer type="galaxy.datatypes.sequence:Maf"/>
+    <sniffer type="galaxy.datatypes.sequence:Lav"/>
+    <sniffer type="galaxy.datatypes.sequence:csFasta"/>
+    <sniffer type="galaxy.datatypes.qualityscore:QualityScoreSOLiD"/>
+    <sniffer type="galaxy.datatypes.qualityscore:QualityScore454"/>
+    <sniffer type="galaxy.datatypes.sequence:Fasta"/>
+    <sniffer type="galaxy.datatypes.sequence:Fastq"/>
+    <sniffer type="galaxy.datatypes.interval:Wiggle"/>
+    <sniffer type="galaxy.datatypes.images:Html"/>
+    <sniffer type="galaxy.datatypes.images:Pdf"/>
+    <sniffer type="galaxy.datatypes.sequence:Axt"/>
+    <sniffer type="galaxy.datatypes.interval:Bed"/>
+    <sniffer type="galaxy.datatypes.interval:CustomTrack"/>
+    <sniffer type="galaxy.datatypes.interval:Gtf"/>
+    <sniffer type="galaxy.datatypes.interval:Gff"/>
+    <sniffer type="galaxy.datatypes.interval:Gff3"/>
+    <sniffer type="galaxy.datatypes.tabular:Pileup"/>
+    <sniffer type="galaxy.datatypes.interval:Interval"/>
+    <sniffer type="galaxy.datatypes.tabular:Sam"/>
+    <sniffer type="galaxy.datatypes.images:Jpg"/>
+    <sniffer type="galaxy.datatypes.images:Png"/>
+    <sniffer type="galaxy.datatypes.images:Tiff"/>
+    <sniffer type="galaxy.datatypes.images:Bmp"/>
+    <sniffer type="galaxy.datatypes.images:Gif"/>
+    <sniffer type="galaxy.datatypes.images:Im"/>
+    <sniffer type="galaxy.datatypes.images:Pcd"/>
+    <sniffer type="galaxy.datatypes.images:Pcx"/>
+    <sniffer type="galaxy.datatypes.images:Ppm"/>
+    <sniffer type="galaxy.datatypes.images:Psd"/>
+    <sniffer type="galaxy.datatypes.images:Xbm"/>
+    <sniffer type="galaxy.datatypes.images:Xpm"/>
+    <sniffer type="galaxy.datatypes.images:Rgb"/>
+    <sniffer type="galaxy.datatypes.images:Pbm"/>
+    <sniffer type="galaxy.datatypes.images:Pgm"/>
+    <sniffer type="galaxy.datatypes.images:Xpm"/>
+    <sniffer type="galaxy.datatypes.images:Eps"/>
+    <sniffer type="galaxy.datatypes.images:Rast"/>
+    <!--
+    Keep this commented until the sniff method in the assembly.py
+    module is fixed to not read the entire file.
+    <sniffer type="galaxy.datatypes.assembly:Amos"/>
+    -->
+  </sniffers>
 </datatypes>
diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index 76ae18a276b..be30a5d35e9 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -64,11 +64,12 @@
     <tool file="stats/filtering.xml" />
     <tool file="filters/sorter.xml" />
     <tool file="filters/grep.xml" />
+    
     <label text="GFF" id="gff" />
-        <tool file="filters/gff/extract_GFF_Features.xml" />
-        <tool file="filters/gff/gff_filter_by_attribute.xml" />
-        <tool file="filters/gff/gff_filter_by_feature_count.xml" />
-        <tool file="filters/gff/gtf_filter_by_attribute_values_list.xml" />
+    <tool file="filters/gff/extract_GFF_Features.xml" />
+    <tool file="filters/gff/gff_filter_by_attribute.xml" />
+    <tool file="filters/gff/gff_filter_by_feature_count.xml" />
+    <tool file="filters/gff/gtf_filter_by_attribute_values_list.xml" />
   </section>
   <section name="Join, Subtract and Group" id="group">
     <tool file="filters/joiner.xml" />
@@ -144,8 +145,9 @@
     <tool file="stats/plot_from_lda.xml" />
     <tool file="regVariation/t_test_two_samples.xml" />
     <tool file="regVariation/compute_q_values.xml" />
+    
     <label text="GFF" id="gff" />
-      <tool file="stats/count_gff_features.xml" />
+    <tool file="stats/count_gff_features.xml" />
   </section>
   <section name="Wavelet Analysis" id="dwt">
     <tool file="discreteWavelet/execute_dwt_var_perFeature.xml" />
@@ -156,7 +158,7 @@
     <tool file="discreteWavelet/execute_dwt_cor_aVb_all.xml" />
     <tool file="discreteWavelet/execute_dwt_var_perClass.xml" />
     -->
- </section>
+  </section>
   <section name="Graph/Display Data" id="plots">
     <tool file="plotting/histogram2.xml" />
     <tool file="plotting/scatterplot.xml" />
@@ -200,14 +202,14 @@
     <tool file="multivariate_stats/kpca.xml" />
     <tool file="multivariate_stats/kcca.xml" />
   </section>
- <section name="Evolution" id="hyphy">
+  <section name="Evolution" id="hyphy">
     <tool file="hyphy/hyphy_branch_lengths_wrapper.xml" />
     <tool file="hyphy/hyphy_nj_tree_wrapper.xml" />
     <tool file="hyphy/hyphy_dnds_wrapper.xml" />
     <tool file="evolution/mutate_snp_codon.xml" />
     <tool file="evolution/codingSnps.xml" />
     <tool file="evolution/add_scores.xml" />
- </section>
+  </section>
   <section name="Motif Tools" id="motifs">
     <tool file="meme/meme.xml"/>
     <tool file="meme/fimo.xml"/>
@@ -216,7 +218,7 @@
   <section name="Multiple Alignments" id="clustal">
     <tool file="rgenetics/rgClustalw.xml" />
   </section>
- <section name="Metagenomic analyses" id="tax_manipulation">
+  <section name="Metagenomic analyses" id="tax_manipulation">
     <tool file="taxonomy/gi2taxonomy.xml" />
     <tool file="taxonomy/t2t_report.xml" />
     <tool file="taxonomy/t2ps_wrapper.xml" />
@@ -235,30 +237,35 @@
     <tool file="fastx_toolkit/fastx_collapser.xml" />
   </section>
   <section name="NCBI BLAST+" id="ncbi_blast_plus_tools">
-   <tool file="ncbi_blast_plus/ncbi_blastn_wrapper.xml" />
-   <tool file="ncbi_blast_plus/ncbi_blastp_wrapper.xml" />
-   <tool file="ncbi_blast_plus/ncbi_blastx_wrapper.xml" />
-   <tool file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml" />
-   <tool file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml" />
-   <tool file="ncbi_blast_plus/blastxml_to_tabular.xml" />
+    <tool file="ncbi_blast_plus/ncbi_blastn_wrapper.xml" />
+    <tool file="ncbi_blast_plus/ncbi_blastp_wrapper.xml" />
+    <tool file="ncbi_blast_plus/ncbi_blastx_wrapper.xml" />
+    <tool file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml" />
+    <tool file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml" />
+    <tool file="ncbi_blast_plus/blastxml_to_tabular.xml" />
   </section>
   <section name="NGS: QC and manipulation" id="NGS_QC">
-   <label text="FastQC: fastq/sam/bam" id="fastqcsambam" />
+    
+    <label text="FastQC: fastq/sam/bam" id="fastqcsambam" />
     <tool file="rgenetics/rgFastQC.xml" />
-   <label text="Illumina fastq" id="illumina" />
+    
+    <label text="Illumina fastq" id="illumina" />
     <tool file="fastq/fastq_groomer.xml" />
     <tool file="fastq/fastq_paired_end_splitter.xml" />
     <tool file="fastq/fastq_paired_end_joiner.xml" />
     <tool file="fastq/fastq_stats.xml" />
-   <label text="Roche-454 data" id="454" />
+    
+    <label text="Roche-454 data" id="454" />
     <tool file="metag_tools/short_reads_figure_score.xml" />
     <tool file="metag_tools/short_reads_trim_seq.xml" />
     <tool file="fastq/fastq_combiner.xml" />
-   <label text="AB-SOLiD data" id="solid" />
+    
+    <label text="AB-SOLiD data" id="solid" />
     <tool file="next_gen_conversion/solid2fastq.xml" />
     <tool file="solid_tools/solid_qual_stats.xml" />
     <tool file="solid_tools/solid_qual_boxplot.xml" />
-   <label text="Generic FASTQ manipulation" id="generic_fastq" />
+    
+    <label text="Generic FASTQ manipulation" id="generic_fastq" />
     <tool file="fastq/fastq_filter.xml" />
     <tool file="fastq/fastq_trimmer.xml" />
     <tool file="fastq/fastq_trimmer_by_quality.xml" />
@@ -269,7 +276,8 @@
     <tool file="fastq/fastq_to_fasta.xml" />
     <tool file="fastq/fastq_to_tabular.xml" />
     <tool file="fastq/tabular_to_fastq.xml" />
-   <label text="FASTX-Toolkit for FASTQ data" id="fastx_toolkit" />
+    
+    <label text="FASTX-Toolkit for FASTQ data" id="fastx_toolkit" />
     <tool file="fastx_toolkit/fastq_quality_converter.xml" />
     <tool file="fastx_toolkit/fastx_quality_statistics.xml" />
     <tool file="fastx_toolkit/fastq_quality_boxplot.xml" />
@@ -283,9 +291,10 @@
     <tool file="fastx_toolkit/fastx_collapser.xml" />
     <tool file="fastx_toolkit/fastx_renamer.xml" />
     <tool file="fastx_toolkit/fastx_reverse_complement.xml" />
-     <tool file="fastx_toolkit/fastx_trimmer.xml" />
+    <tool file="fastx_toolkit/fastx_trimmer.xml" />
   </section>
   <section name="NGS: Picard (beta)" id="picard_beta">
+    
     <label text="QC/Metrics for sam/bam" id="qcsambam"/>
     <tool file="picard/picard_BamIndexStats.xml" />
     <tool file="picard/rgPicardASMetrics.xml" />
@@ -293,7 +302,8 @@
     <tool file="picard/rgPicardLibComplexity.xml" />
     <tool file="picard/rgPicardInsertSize.xml" />
     <tool file="picard/rgPicardHsMetrics.xml" />
-  <label text="bam/sam Cleaning" id="picard-clean" />
+    
+    <label text="bam/sam Cleaning" id="picard-clean" />
     <tool file="picard/picard_AddOrReplaceReadGroups.xml" />
     <tool file="picard/picard_ReorderSam.xml" />
     <tool file="picard/picard_ReplaceSamHeader.xml" />
@@ -306,108 +316,122 @@
   included in the distribution but will not be hosted on our
   public servers for the current time.
   <section name="NGS: Assembly" id="ngs_assembly">
-        <label text="Velvet" id="velvet"/>
-        <tool file="sr_assembly/velvetg.xml" />
-        <tool file="sr_assembly/velveth.xml" />
+  <label text="Velvet" id="velvet"/>
+  <tool file="sr_assembly/velvetg.xml" />
+  <tool file="sr_assembly/velveth.xml" />
   </section>
   -->
   <section name="NGS: Mapping" id="solexa_tools">
-   <tool file="sr_mapping/lastz_wrapper.xml" />
-   <tool file="sr_mapping/lastz_paired_reads_wrapper.xml" />
-   <tool file="sr_mapping/bowtie_wrapper.xml" />
-   <tool file="sr_mapping/bowtie_color_wrapper.xml" />
-   <tool file="sr_mapping/bwa_wrapper.xml" />
-   <tool file="sr_mapping/bwa_color_wrapper.xml" />
-   <tool file="sr_mapping/bfast_wrapper.xml" />
-   <tool file="metag_tools/megablast_wrapper.xml" />
-   <tool file="metag_tools/megablast_xml_parser.xml" />
-   <tool file="sr_mapping/PerM.xml" />
-   <tool file="sr_mapping/srma_wrapper.xml" />
-   <tool file="sr_mapping/mosaik.xml"/>
+    <tool file="sr_mapping/lastz_wrapper.xml" />
+    <tool file="sr_mapping/lastz_paired_reads_wrapper.xml" />
+    <tool file="sr_mapping/bowtie_wrapper.xml" />
+    <tool file="sr_mapping/bowtie_color_wrapper.xml" />
+    <tool file="sr_mapping/bwa_wrapper.xml" />
+    <tool file="sr_mapping/bwa_color_wrapper.xml" />
+    <tool file="sr_mapping/bfast_wrapper.xml" />
+    <tool file="metag_tools/megablast_wrapper.xml" />
+    <tool file="metag_tools/megablast_xml_parser.xml" />
+    <tool file="sr_mapping/PerM.xml" />
+    <tool file="sr_mapping/srma_wrapper.xml" />
+    <tool file="sr_mapping/mosaik.xml"/>
   </section>
   <section name="NGS: Indel Analysis" id="indel_analysis">
-   <tool file="indels/sam_indel_filter.xml" />
-   <tool file="indels/indel_sam2interval.xml" />
-   <tool file="indels/indel_table.xml" />
-   <tool file="indels/indel_analysis.xml" />
+    <tool file="indels/sam_indel_filter.xml" />
+    <tool file="indels/indel_sam2interval.xml" />
+    <tool file="indels/indel_table.xml" />
+    <tool file="indels/indel_analysis.xml" />
   </section>
   <section name="NGS: RNA Analysis" id="ngs-rna-tools">
-   <label text="RNA-seq" id="rna_seq" />
-      <tool file="ngs_rna/tophat_wrapper.xml" />
-      <tool file="ngs_rna/tophat_color_wrapper.xml" />
-      <tool file="ngs_rna/cufflinks_wrapper.xml" />
-      <tool file="ngs_rna/cuffcompare_wrapper.xml" />
-      <tool file="ngs_rna/cuffdiff_wrapper.xml" />
-   <!-- Trinity is very memory-intensive and should only be enabled/run
-		on instances with sufficient resources. 
-   <label text="De novo Assembly" id="de_novo_assembly "/>
-      <tool file="ngs_rna/trinity_all.xml" />
-	-->
-   <label text="Filtering" id="filtering" />
-      <tool file="ngs_rna/filter_transcripts_via_tracking.xml" />
+    
+    <label text="RNA-seq" id="rna_seq" />
+    <tool file="ngs_rna/tophat_wrapper.xml" />
+    <tool file="ngs_rna/tophat_color_wrapper.xml" />
+    <tool file="ngs_rna/cufflinks_wrapper.xml" />
+    <tool file="ngs_rna/cuffcompare_wrapper.xml" />
+    <tool file="ngs_rna/cuffdiff_wrapper.xml" />
+    <!-- Trinity is very memory-intensive and should only be enabled/run
+    on instances with sufficient resources. 
+    <label text="De novo Assembly" id="de_novo_assembly "/>
+    <tool file="ngs_rna/trinity_all.xml" />
+    -->
+    
+    <label text="Filtering" id="filtering" />
+    <tool file="ngs_rna/filter_transcripts_via_tracking.xml" />
   </section>
   <section name="NGS: SAM Tools" id="samtools">
-   <tool file="samtools/sam_bitwise_flag_filter.xml" />
-   <tool file="samtools/sam2interval.xml" />
-   <tool file="samtools/sam_to_bam.xml" />
-   <tool file="samtools/bam_to_sam.xml" />
-   <tool file="samtools/sam_merge.xml" />
-   <tool file="samtools/sam_pileup.xml" />
-   <tool file="samtools/pileup_parser.xml" />
-   <tool file="samtools/pileup_interval.xml" />
-   <tool file="samtools/samtools_flagstat.xml" />
-   <tool file="samtools/samtools_rmdup.xml" />
+    <tool file="samtools/sam_bitwise_flag_filter.xml" />
+    <tool file="samtools/sam2interval.xml" />
+    <tool file="samtools/sam_to_bam.xml" />
+    <tool file="samtools/bam_to_sam.xml" />
+    <tool file="samtools/sam_merge.xml" />
+    <tool file="samtools/sam_pileup.xml" />
+    <tool file="samtools/pileup_parser.xml" />
+    <tool file="samtools/pileup_interval.xml" />
+    <tool file="samtools/samtools_flagstat.xml" />
+    <tool file="samtools/samtools_rmdup.xml" />
   </section>
   <section name="NGS: GATK Tools (beta)" id="gatk">
-   <label text="Realignment" id="gatk_realignment" />
-     <tool file="gatk/realigner_target_creator.xml" />
-     <tool file="gatk/indel_realigner.xml" />
-   <label text="Base Recalibration" id="gatk_recalibration" />
-     <tool file="gatk/count_covariates.xml" />
-     <tool file="gatk/table_recalibration.xml" />
-     <tool file="gatk/analyze_covariates.xml" />
-   <label text="Genotyping" id="gatk_genotyping" />
-     <tool file="gatk/unified_genotyper.xml" />
-   <label text="Annotation" id="gatk_annotation" />
-     <tool file="gatk/variant_annotator.xml" />
-   <label text="Filtration" id="gatk_filtration" />
-     <tool file="gatk/variant_filtration.xml" />
-     <tool file="gatk/variant_filtration.xml" />
-   <label text="Variant Quality Score Recalibration" id="gatk_variant_quality_score_recalibration" />
-     <tool file="gatk/variant_recalibrator.xml" />
-     <tool file="gatk/variant_apply_recalibration.xml" />
-   <label text="Variant Utilities" id="gatk_variant_utilities"/>
-     <tool file="gatk/variants_validate.xml" />
-     <tool file="gatk/variant_eval.xml" />
-     <tool file="gatk/variant_combine.xml" />
+    
+    <label text="Realignment" id="gatk_realignment" />
+    <tool file="gatk/realigner_target_creator.xml" />
+    <tool file="gatk/indel_realigner.xml" />
+    
+    <label text="Base Recalibration" id="gatk_recalibration" />
+    <tool file="gatk/count_covariates.xml" />
+    <tool file="gatk/table_recalibration.xml" />
+    <tool file="gatk/analyze_covariates.xml" />
+    
+    <label text="Genotyping" id="gatk_genotyping" />
+    <tool file="gatk/unified_genotyper.xml" />
+    
+    <label text="Annotation" id="gatk_annotation" />
+    <tool file="gatk/variant_annotator.xml" />
+    
+    <label text="Filtration" id="gatk_filtration" />
+    <tool file="gatk/variant_filtration.xml" />
+    <tool file="gatk/variant_filtration.xml" />
+    
+    <label text="Variant Quality Score Recalibration" id="gatk_variant_quality_score_recalibration" />
+    <tool file="gatk/variant_recalibrator.xml" />
+    <tool file="gatk/variant_apply_recalibration.xml" />
+    
+    <label text="Variant Utilities" id="gatk_variant_utilities"/>
+    <tool file="gatk/variants_validate.xml" />
+    <tool file="gatk/variant_eval.xml" />
+    <tool file="gatk/variant_combine.xml" />
   </section>
   <section name="NGS: Peak Calling" id="peak_calling">
-   <tool file="peak_calling/macs_wrapper.xml" />
-   <tool file="peak_calling/sicer_wrapper.xml" />
-   <tool file="peak_calling/ccat_wrapper.xml" />
-   <tool file="genetrack/genetrack_indexer.xml" />
-   <tool file="genetrack/genetrack_peak_prediction.xml" />
+    <tool file="peak_calling/macs_wrapper.xml" />
+    <tool file="peak_calling/sicer_wrapper.xml" />
+    <tool file="peak_calling/ccat_wrapper.xml" />
+    <tool file="genetrack/genetrack_indexer.xml" />
+    <tool file="genetrack/genetrack_peak_prediction.xml" />
   </section>
   <section name="NGS: Simulation" id="ngs-simulation">
     <tool file="ngs_simulation/ngs_simulation.xml" />
   </section>
   <section name="SNP/WGA: Data; Filters" id="rgdat">
-  <label text="Data: Import and upload" id="rgimport" />
+    
+    <label text="Data: Import and upload" id="rgimport" />
     <tool file="data_source/upload.xml"/>
     <tool file="data_source/access_libraries.xml" />
-  <label text="Data: Filter and Clean" id="rgfilter" />
+    
+    <label text="Data: Filter and Clean" id="rgfilter" />
     <tool file="rgenetics/rgClean.xml"/>
     <tool file="rgenetics/rgPedSub.xml"/>
     <tool file="rgenetics/rgLDIndep.xml"/>
-  <label text="Simulate" id="rgsim" />
+    
+    <label text="Simulate" id="rgsim" />
     <tool file="rgenetics/rgfakePhe.xml"/>
     <tool file="rgenetics/rgfakePed.xml"/>
   </section>
   <section name="SNP/WGA: QC; LD; Plots" id="rgqcplot">
-  <label text="QC; Eigenstrat" id="rgvisual" />
+    
+    <label text="QC; Eigenstrat" id="rgvisual" />
     <tool file="rgenetics/rgQC.xml"/>
     <tool file="rgenetics/rgEigPCA.xml"/>
-  <label text="LD; Manhattan/QQ; GRR" id="rgld" />
+    
+    <label text="LD; Manhattan/QQ; GRR" id="rgld" />
     <tool file="rgenetics/rgHaploView.xml"/>
     <tool file="rgenetics/rgManQQ.xml"/>
     <tool file="rgenetics/rgGRR.xml"/>
@@ -451,128 +475,128 @@
     <tool file="ilmn_pacbio/quake.xml"/>
     <tool file="ilmn_pacbio/quake_pe.xml"/>
     <tool file="ilmn_pacbio/soap_denovo.xml"/>
-<!--
+    <!--
     Uncomment this tool when we support the HDF5 format
     <tool file="ilmn_pacbio/smrtpipe_filter.xml"/>
--->
+    -->
     <tool file="ilmn_pacbio/smrtpipe_hybrid.xml"/>
     <tool file="ilmn_pacbio/assembly_stats.xml"/>
   </section>
-<!--
+  <!--
   TODO: uncomment the following EMBOSS section whenever
   moving to test, but comment it in .sample to eliminate
   it from buildbot functional tests since these tools
   rarely change.
--->
-<!--
+  -->
+  <!--
   <section name="EMBOSS" id="EMBOSSLite">
-    <tool file="emboss_5/emboss_antigenic.xml" />
-    <tool file="emboss_5/emboss_backtranseq.xml" />
-    <tool file="emboss_5/emboss_banana.xml" />
-    <tool file="emboss_5/emboss_biosed.xml" />
-    <tool file="emboss_5/emboss_btwisted.xml" />
-    <tool file="emboss_5/emboss_cai_custom.xml" />
-    <tool file="emboss_5/emboss_cai.xml" />
-    <tool file="emboss_5/emboss_chaos.xml" />
-    <tool file="emboss_5/emboss_charge.xml" />
-    <tool file="emboss_5/emboss_checktrans.xml" />
-    <tool file="emboss_5/emboss_chips.xml" />
-    <tool file="emboss_5/emboss_cirdna.xml" />
-    <tool file="emboss_5/emboss_codcmp.xml" />
-    <tool file="emboss_5/emboss_coderet.xml" />
-    <tool file="emboss_5/emboss_compseq.xml" />
-    <tool file="emboss_5/emboss_cpgplot.xml" />
-    <tool file="emboss_5/emboss_cpgreport.xml" />
-    <tool file="emboss_5/emboss_cusp.xml" />
-    <tool file="emboss_5/emboss_cutseq.xml" />
-    <tool file="emboss_5/emboss_dan.xml" />
-    <tool file="emboss_5/emboss_degapseq.xml" />
-    <tool file="emboss_5/emboss_descseq.xml" />
-    <tool file="emboss_5/emboss_diffseq.xml" />
-    <tool file="emboss_5/emboss_digest.xml" />
-    <tool file="emboss_5/emboss_dotmatcher.xml" />
-    <tool file="emboss_5/emboss_dotpath.xml" />
-    <tool file="emboss_5/emboss_dottup.xml" />
-    <tool file="emboss_5/emboss_dreg.xml" />
-    <tool file="emboss_5/emboss_einverted.xml" />
-    <tool file="emboss_5/emboss_epestfind.xml" />
-    <tool file="emboss_5/emboss_equicktandem.xml" />
-    <tool file="emboss_5/emboss_est2genome.xml" />
-    <tool file="emboss_5/emboss_etandem.xml" />
-    <tool file="emboss_5/emboss_extractfeat.xml" />
-    <tool file="emboss_5/emboss_extractseq.xml" />
-    <tool file="emboss_5/emboss_freak.xml" />
-    <tool file="emboss_5/emboss_fuzznuc.xml" />
-    <tool file="emboss_5/emboss_fuzzpro.xml" />
-    <tool file="emboss_5/emboss_fuzztran.xml" />
-    <tool file="emboss_5/emboss_garnier.xml" />
-    <tool file="emboss_5/emboss_geecee.xml" />
-    <tool file="emboss_5/emboss_getorf.xml" />
-    <tool file="emboss_5/emboss_helixturnhelix.xml" />
-    <tool file="emboss_5/emboss_hmoment.xml" />
-    <tool file="emboss_5/emboss_iep.xml" />
-    <tool file="emboss_5/emboss_infoseq.xml" />
-    <tool file="emboss_5/emboss_isochore.xml" />
-    <tool file="emboss_5/emboss_lindna.xml" />
-    <tool file="emboss_5/emboss_marscan.xml" />
-    <tool file="emboss_5/emboss_maskfeat.xml" />
-    <tool file="emboss_5/emboss_maskseq.xml" />
-    <tool file="emboss_5/emboss_matcher.xml" />
-    <tool file="emboss_5/emboss_megamerger.xml" />
-    <tool file="emboss_5/emboss_merger.xml" />
-    <tool file="emboss_5/emboss_msbar.xml" />
-    <tool file="emboss_5/emboss_needle.xml" />
-    <tool file="emboss_5/emboss_newcpgreport.xml" />
-    <tool file="emboss_5/emboss_newcpgseek.xml" />
-    <tool file="emboss_5/emboss_newseq.xml" />
-    <tool file="emboss_5/emboss_noreturn.xml" />
-    <tool file="emboss_5/emboss_notseq.xml" />
-    <tool file="emboss_5/emboss_nthseq.xml" />
-    <tool file="emboss_5/emboss_octanol.xml" />
-    <tool file="emboss_5/emboss_oddcomp.xml" />
-    <tool file="emboss_5/emboss_palindrome.xml" />
-    <tool file="emboss_5/emboss_pasteseq.xml" />
-    <tool file="emboss_5/emboss_patmatdb.xml" />
-    <tool file="emboss_5/emboss_pepcoil.xml" />
-    <tool file="emboss_5/emboss_pepinfo.xml" />
-    <tool file="emboss_5/emboss_pepnet.xml" />
-    <tool file="emboss_5/emboss_pepstats.xml" />
-    <tool file="emboss_5/emboss_pepwheel.xml" />
-    <tool file="emboss_5/emboss_pepwindow.xml" />
-    <tool file="emboss_5/emboss_pepwindowall.xml" />
-    <tool file="emboss_5/emboss_plotcon.xml" />
-    <tool file="emboss_5/emboss_plotorf.xml" />
-    <tool file="emboss_5/emboss_polydot.xml" />
-    <tool file="emboss_5/emboss_preg.xml" />
-    <tool file="emboss_5/emboss_prettyplot.xml" />
-    <tool file="emboss_5/emboss_prettyseq.xml" />
-    <tool file="emboss_5/emboss_primersearch.xml" />
-    <tool file="emboss_5/emboss_revseq.xml" />
-    <tool file="emboss_5/emboss_seqmatchall.xml" />
-    <tool file="emboss_5/emboss_seqret.xml" />
-    <tool file="emboss_5/emboss_showfeat.xml" />
-    <tool file="emboss_5/emboss_shuffleseq.xml" />
-    <tool file="emboss_5/emboss_sigcleave.xml" />
-    <tool file="emboss_5/emboss_sirna.xml" />
-    <tool file="emboss_5/emboss_sixpack.xml" />
-    <tool file="emboss_5/emboss_skipseq.xml" />
-    <tool file="emboss_5/emboss_splitter.xml" />
-    <tool file="emboss_5/emboss_supermatcher.xml" />
-    <tool file="emboss_5/emboss_syco.xml" />
-    <tool file="emboss_5/emboss_tcode.xml" />
-    <tool file="emboss_5/emboss_textsearch.xml" />
-    <tool file="emboss_5/emboss_tmap.xml" />
-    <tool file="emboss_5/emboss_tranalign.xml" />
-    <tool file="emboss_5/emboss_transeq.xml" />
-    <tool file="emboss_5/emboss_trimest.xml" />
-    <tool file="emboss_5/emboss_trimseq.xml" />
-    <tool file="emboss_5/emboss_twofeat.xml" />
-    <tool file="emboss_5/emboss_union.xml" />
-    <tool file="emboss_5/emboss_vectorstrip.xml" />
-    <tool file="emboss_5/emboss_water.xml" />
-    <tool file="emboss_5/emboss_wobble.xml" />
-    <tool file="emboss_5/emboss_wordcount.xml" />
-    <tool file="emboss_5/emboss_wordmatch.xml" />
+  <tool file="emboss_5/emboss_antigenic.xml" />
+  <tool file="emboss_5/emboss_backtranseq.xml" />
+  <tool file="emboss_5/emboss_banana.xml" />
+  <tool file="emboss_5/emboss_biosed.xml" />
+  <tool file="emboss_5/emboss_btwisted.xml" />
+  <tool file="emboss_5/emboss_cai_custom.xml" />
+  <tool file="emboss_5/emboss_cai.xml" />
+  <tool file="emboss_5/emboss_chaos.xml" />
+  <tool file="emboss_5/emboss_charge.xml" />
+  <tool file="emboss_5/emboss_checktrans.xml" />
+  <tool file="emboss_5/emboss_chips.xml" />
+  <tool file="emboss_5/emboss_cirdna.xml" />
+  <tool file="emboss_5/emboss_codcmp.xml" />
+  <tool file="emboss_5/emboss_coderet.xml" />
+  <tool file="emboss_5/emboss_compseq.xml" />
+  <tool file="emboss_5/emboss_cpgplot.xml" />
+  <tool file="emboss_5/emboss_cpgreport.xml" />
+  <tool file="emboss_5/emboss_cusp.xml" />
+  <tool file="emboss_5/emboss_cutseq.xml" />
+  <tool file="emboss_5/emboss_dan.xml" />
+  <tool file="emboss_5/emboss_degapseq.xml" />
+  <tool file="emboss_5/emboss_descseq.xml" />
+  <tool file="emboss_5/emboss_diffseq.xml" />
+  <tool file="emboss_5/emboss_digest.xml" />
+  <tool file="emboss_5/emboss_dotmatcher.xml" />
+  <tool file="emboss_5/emboss_dotpath.xml" />
+  <tool file="emboss_5/emboss_dottup.xml" />
+  <tool file="emboss_5/emboss_dreg.xml" />
+  <tool file="emboss_5/emboss_einverted.xml" />
+  <tool file="emboss_5/emboss_epestfind.xml" />
+  <tool file="emboss_5/emboss_equicktandem.xml" />
+  <tool file="emboss_5/emboss_est2genome.xml" />
+  <tool file="emboss_5/emboss_etandem.xml" />
+  <tool file="emboss_5/emboss_extractfeat.xml" />
+  <tool file="emboss_5/emboss_extractseq.xml" />
+  <tool file="emboss_5/emboss_freak.xml" />
+  <tool file="emboss_5/emboss_fuzznuc.xml" />
+  <tool file="emboss_5/emboss_fuzzpro.xml" />
+  <tool file="emboss_5/emboss_fuzztran.xml" />
+  <tool file="emboss_5/emboss_garnier.xml" />
+  <tool file="emboss_5/emboss_geecee.xml" />
+  <tool file="emboss_5/emboss_getorf.xml" />
+  <tool file="emboss_5/emboss_helixturnhelix.xml" />
+  <tool file="emboss_5/emboss_hmoment.xml" />
+  <tool file="emboss_5/emboss_iep.xml" />
+  <tool file="emboss_5/emboss_infoseq.xml" />
+  <tool file="emboss_5/emboss_isochore.xml" />
+  <tool file="emboss_5/emboss_lindna.xml" />
+  <tool file="emboss_5/emboss_marscan.xml" />
+  <tool file="emboss_5/emboss_maskfeat.xml" />
+  <tool file="emboss_5/emboss_maskseq.xml" />
+  <tool file="emboss_5/emboss_matcher.xml" />
+  <tool file="emboss_5/emboss_megamerger.xml" />
+  <tool file="emboss_5/emboss_merger.xml" />
+  <tool file="emboss_5/emboss_msbar.xml" />
+  <tool file="emboss_5/emboss_needle.xml" />
+  <tool file="emboss_5/emboss_newcpgreport.xml" />
+  <tool file="emboss_5/emboss_newcpgseek.xml" />
+  <tool file="emboss_5/emboss_newseq.xml" />
+  <tool file="emboss_5/emboss_noreturn.xml" />
+  <tool file="emboss_5/emboss_notseq.xml" />
+  <tool file="emboss_5/emboss_nthseq.xml" />
+  <tool file="emboss_5/emboss_octanol.xml" />
+  <tool file="emboss_5/emboss_oddcomp.xml" />
+  <tool file="emboss_5/emboss_palindrome.xml" />
+  <tool file="emboss_5/emboss_pasteseq.xml" />
+  <tool file="emboss_5/emboss_patmatdb.xml" />
+  <tool file="emboss_5/emboss_pepcoil.xml" />
+  <tool file="emboss_5/emboss_pepinfo.xml" />
+  <tool file="emboss_5/emboss_pepnet.xml" />
+  <tool file="emboss_5/emboss_pepstats.xml" />
+  <tool file="emboss_5/emboss_pepwheel.xml" />
+  <tool file="emboss_5/emboss_pepwindow.xml" />
+  <tool file="emboss_5/emboss_pepwindowall.xml" />
+  <tool file="emboss_5/emboss_plotcon.xml" />
+  <tool file="emboss_5/emboss_plotorf.xml" />
+  <tool file="emboss_5/emboss_polydot.xml" />
+  <tool file="emboss_5/emboss_preg.xml" />
+  <tool file="emboss_5/emboss_prettyplot.xml" />
+  <tool file="emboss_5/emboss_prettyseq.xml" />
+  <tool file="emboss_5/emboss_primersearch.xml" />
+  <tool file="emboss_5/emboss_revseq.xml" />
+  <tool file="emboss_5/emboss_seqmatchall.xml" />
+  <tool file="emboss_5/emboss_seqret.xml" />
+  <tool file="emboss_5/emboss_showfeat.xml" />
+  <tool file="emboss_5/emboss_shuffleseq.xml" />
+  <tool file="emboss_5/emboss_sigcleave.xml" />
+  <tool file="emboss_5/emboss_sirna.xml" />
+  <tool file="emboss_5/emboss_sixpack.xml" />
+  <tool file="emboss_5/emboss_skipseq.xml" />
+  <tool file="emboss_5/emboss_splitter.xml" />
+  <tool file="emboss_5/emboss_supermatcher.xml" />
+  <tool file="emboss_5/emboss_syco.xml" />
+  <tool file="emboss_5/emboss_tcode.xml" />
+  <tool file="emboss_5/emboss_textsearch.xml" />
+  <tool file="emboss_5/emboss_tmap.xml" />
+  <tool file="emboss_5/emboss_tranalign.xml" />
+  <tool file="emboss_5/emboss_transeq.xml" />
+  <tool file="emboss_5/emboss_trimest.xml" />
+  <tool file="emboss_5/emboss_trimseq.xml" />
+  <tool file="emboss_5/emboss_twofeat.xml" />
+  <tool file="emboss_5/emboss_union.xml" />
+  <tool file="emboss_5/emboss_vectorstrip.xml" />
+  <tool file="emboss_5/emboss_water.xml" />
+  <tool file="emboss_5/emboss_wobble.xml" />
+  <tool file="emboss_5/emboss_wordcount.xml" />
+  <tool file="emboss_5/emboss_wordmatch.xml" />
   </section>
--->
+  -->
 </toolbox>

From 433ad57c25f72c6274ecbaae1ffb9d9d83b5147f Mon Sep 17 00:00:00 2001
From: Kanwei Li <kanwei@gmail.com>
Date: Wed, 5 Oct 2011 00:15:37 -0400
Subject: [PATCH 019/362] Typo

---
 lib/galaxy/util/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/util/__init__.py b/lib/galaxy/util/__init__.py
index 1854d64b090..cad925ec778 100644
--- a/lib/galaxy/util/__init__.py
+++ b/lib/galaxy/util/__init__.py
@@ -544,7 +544,7 @@ def nice_size(size):
 
 def size_to_bytes( size ):
     """
-    Returns a number of bytes if given a reasably formatted string with the size
+    Returns a number of bytes if given a reasonably formatted string with the size
     """
     # Assume input in bytes if we can convert directly to an int
     try:

From a23fc2cfbbf473f029b1f5f1b3c5aee99ccf361b Mon Sep 17 00:00:00 2001
From: Kanwei Li <kanwei@gmail.com>
Date: Wed, 5 Oct 2011 00:18:15 -0400
Subject: [PATCH 020/362] Cache bust using unix timestamp that server started
 on to force reloading of stylesheets and javascripts whenever server restarts

---
 lib/galaxy/web/framework/helpers/__init__.py | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/web/framework/helpers/__init__.py b/lib/galaxy/web/framework/helpers/__init__.py
index 7937406d224..02441e0cbfe 100644
--- a/lib/galaxy/web/framework/helpers/__init__.py
+++ b/lib/galaxy/web/framework/helpers/__init__.py
@@ -6,9 +6,12 @@ from webhelpers import *
 from galaxy.util.json import to_json_string
 from galaxy.util import hash_util
 from datetime import datetime, timedelta
+import time
 
 from cgi import escape
 
+server_starttime = int(time.time())
+
 # If the date is more than one week ago, then display the actual date instead of in words
 def time_ago( x ):
     delta = timedelta(weeks=1)
@@ -38,20 +41,18 @@ def css( *args ):
     Take a list of stylesheet names (no extension) and return appropriate string
     of link tags.
     
-    TODO: This has a hardcoded "?v=X" to defeat caching. This should be done
-          in a better way.
+    Cache-bust with time that server started running on
     """
-    return "\n".join( [ stylesheet_link_tag( "/static/style/" + name + ".css?v=3" ) for name in args ] )
+    return "\n".join( [ stylesheet_link_tag( "/static/style/" + name + ".css?v=%s" % server_starttime ) for name in args ] )
         
 def js( *args ):
     """
     Take a list of javascript names (no extension) and return appropriate
     string of script tags.
 
-    TODO: This has a hardcoded "?v=X" to defeat caching. This should be done
-          in a better way.
+    Cache-bust with time that server started running on
     """
-    return "\n".join( [ javascript_include_tag( "/static/scripts/" + name + ".js?v=8" ) for name in args ] )
+    return "\n".join( [ javascript_include_tag( "/static/scripts/" + name + ".js?v=%s" % server_starttime ) for name in args ] )
     
 # Hashes
 

From 420f9177e18b4640dc7d9fb3c635bee7fb9fb236 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Thu, 6 Oct 2011 09:24:05 -0400
Subject: [PATCH 021/362] Fix for .wiki_url in tool_form.mako

---
 templates/tool_form.mako | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/templates/tool_form.mako b/templates/tool_form.mako
index 7e3a9daadb7..eabb338449d 100644
--- a/templates/tool_form.mako
+++ b/templates/tool_form.mako
@@ -242,7 +242,7 @@
         If you're not familiar with Galaxy, please consider visiting the
         <a href="${h.url_for( controller='root' )}" target="_top">welcome page</a>.
         To learn more about what Galaxy is and what it can do for you, please visit
-        the <a href="$add_frame.wiki_url" target="_top">Galaxy wiki</a>.
+        the <a href="${add_frame.wiki_url}" target="_top">Galaxy wiki</a>.
     </div>
     <br/>
 %endif

From 8f6c6bad42df71b1202235b73389115df58924e4 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Thu, 6 Oct 2011 09:34:51 -0400
Subject: [PATCH 022/362] Trackster: return drawing coordinates for all
 features. Pack scripts.

---
 static/scripts/packed/trackster.js | 2 +-
 static/scripts/trackster.js        | 8 +++++++-
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/static/scripts/packed/trackster.js b/static/scripts/packed/trackster.js
index 0b6e08e398d..dbde8c480cb 100644
--- a/static/scripts/packed/trackster.js
+++ b/static/scripts/packed/trackster.js
@@ -1 +1 @@
-var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var trackster_module=function(f,aa){var q=f("class").extend,t=f("slotting"),N=f("painters");var ag=function(ah,ai){this.document=ah;this.default_font=ai!==undefined?ai:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};q(ag.prototype,{load_pattern:function(ah,al){var ai=this.patterns,aj=this.dummy_context,ak=new Image();ak.src=image_path+al;ak.onload=function(){ai[ah]=aj.createPattern(ak,"repeat")}},get_pattern:function(ah){return this.patterns[ah]},new_canvas:function(){var ah=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ah)}ah.manager=this;return ah}});var o={};var m=function(ah,ai){o[ah.attr("id")]=ai};var n=function(ah,aj,al,ak){al=".group";var ai={};o[ah.attr("id")]=ak;ah.bind("drag",{handle:"."+aj,relative:true},function(au,av){var at=$(this);var ay=$(this).parent(),ap=ay.children(),ar=o[$(this).attr("id")],ao,an,aw,am,aq;an=$(this).parents(al);if(an.length!==0){aw=an.position().top;am=aw+an.outerHeight();if(av.offsetY<aw){$(this).insertBefore(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable_before(ar,ax);return}else{if(av.offsetY>am){$(this).insertAfter(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable(ar);return}}}an=null;for(aq=0;aq<ap.length;aq++){ao=$(ap.get(aq));aw=ao.position().top;am=aw+ao.outerHeight();if(ao.is(al)&&this!==ao.get(0)&&av.offsetY>=aw&&av.offsetY<=am){if(av.offsetY-aw<am-av.offsetY){ao.find(".content-div").prepend(this)}else{ao.find(".content-div").append(this)}if(ar.container){ar.container.remove_drawable(ar)}o[ao.attr("id")].add_drawable(ar);return}}for(aq=0;aq<ap.length;aq++){if(av.offsetY<$(ap.get(aq)).position().top){break}}if(aq===ap.length){if(this!==ap.get(aq-1)){ay.append(this);o[ay.attr("id")].move_drawable(ar,aq)}}else{if(this!==ap.get(aq)){$(this).insertBefore(ap.get(aq));o[ay.attr("id")].move_drawable(ar,(av.deltaY>0?aq-1:aq))}}}).bind("dragstart",function(){ai["border-top"]=ah.css("border-top");ai["border-bottom"]=ah.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ai)})};aa.moveable=n;var af=16,I=9,F=20,V=I+2,B=100,K=12000,T=200,E=5,w=10,M=5000,x=100,p="There was an error in indexing this dataset. ",L="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",u="Currently indexing... please wait",z="Tool cannot be rerun: ",a="Loading data...",ab="Ready for display",d=10,v=5,D=5;function y(ah){return Math.round(ah*1000)/1000}var c=function(ah){this.num_elements=ah;this.clear()};q(c.prototype,{get:function(ai){var ah=this.key_ary.indexOf(ai);if(ah!==-1){if(this.obj_cache[ai].stale){this.key_ary.splice(ah,1);delete this.obj_cache[ai]}else{this.move_key_to_end(ai,ah)}}return this.obj_cache[ai]},set:function(ai,aj){if(!this.obj_cache[ai]){if(this.key_ary.length>=this.num_elements){var ah=this.key_ary.shift();delete this.obj_cache[ah]}this.key_ary.push(ai)}this.obj_cache[ai]=aj;return aj},move_key_to_end:function(ai,ah){this.key_ary.splice(ah,1);this.key_ary.push(ai)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var U=function(ai,ah,aj){c.call(this,ai);this.track=ah;this.subset=(aj!==undefined?aj:true)};q(U.prototype,c.prototype,{load_data:function(aq,al,ao,ai,an){var ap=this.track.view.chrom,ak={chrom:ap,low:aq,high:al,mode:ao,resolution:ai,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ak,an);if(this.track.filters_manager){var ar=[];var ah=this.track.filters_manager.filters;for(var am=0;am<ah.length;am++){ar[ar.length]=ah[am].name}ak.filter_cols=JSON.stringify(ar)}var aj=this;return $.getJSON(this.track.data_url,ak,function(at){aj.set_data(aq,al,ao,at)})},get_data:function(ah,al,am,ai,ak){var aj=this.get_data_from_cache(ah,al,am);if(aj){return aj}aj=this.load_data(ah,al,am,ai,ak);this.set_data(ah,al,am,aj);return aj},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ap,ak,ao,aj,an,al){var aq=this.get_data_from_cache(ap,ak,ao);if(!aq){console.log("ERROR: no current data for: ",this.track,ap,ak,ao,aj,an);return}aq.stale=true;var ai=ap;if(al===this.DEEP_DATA_REQ){$.extend(an,{start_val:aq.data.length+1})}else{if(al===this.BROAD_DATA_REQ){ai=(aq.max_high?aq.max_high:aq.data[aq.data.length-1][2])+1}}var ah=this,am=this.load_data(ai,ak,ao,aj,an);new_data_available=$.Deferred();this.set_data(ap,ak,ao,new_data_available);$.when(am).then(function(ar){if(ar.data){ar.data=aq.data.concat(ar.data);if(ar.max_low){ar.max_low=aq.max_low}if(ar.message){ar.message=ar.message.replace(/[0-9]+/,ar.data.length)}}ah.set_data(ap,ak,ao,ar);new_data_available.resolve(ar)});return new_data_available},get_data_from_cache:function(ah,ai,aj){return this.get(this.gen_key(ah,ai,aj))},set_data:function(ai,aj,ak,ah){return this.set(this.gen_key(ai,aj,ak),ah)},gen_key:function(ah,aj,ak){var ai=ah+"_"+aj+"_"+ak;return ai},split_key:function(ah){return ah.split("_")}});var J=function(ai,ah,aj){U.call(this,ai,ah,aj)};q(J.prototype,U.prototype,c.prototype,{load_data:function(aj,ah,al,am,ai,ak){if(ai>1){return}return U.prototype.load_data.call(this,aj,ah,al,am,ai,ak)}});var r=function(ak,ai,ah,aj,al){this.name=ak;this.view=ai;this.container=ah;this.drag_handle_class=al;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak}],saved_values:aj,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values};q(r.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},make_name_popup_menu:function(){},set_name:function(ah){this.old_name=this.name;this.name=ah;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var A=function(al,ak,ai,ah,aj,am){r.call(this,ak,ai,ah,aj,am);this.obj_type=al;this.drawables=[]};q(A.prototype,r.prototype,{init:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah].init()}},_draw:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah]._draw()}},to_json:function(){var ai=[];for(var ah=0;ah<this.drawables.length;ah++){ai.push(this.drawables[ah].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ai}},add_drawable:function(ah){this.drawables.push(ah);ah.container=this},add_drawable_before:function(aj,ah){var ai=this.drawables.indexOf(ah);if(ai!=-1){this.drawables.splice(ai,0,aj);return true}return false},remove_drawable:function(ai){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);ai.container=null;return true}return false},move_drawable:function(ai,aj){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);this.drawables.splice(aj,0,ai);return true}return false}});var S=function(ak,ai,ah,aj){A.call(this,"DrawableGroup",ak,ai,ah,aj,"group-handle");if(!S.id_counter){S.id_counter=0}var al=S.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+al).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+al+"_content_div").appendTo(this.container_div);m(this.container_div,this);m(this.content_div,this);n(this.container_div,this.drag_handle_class,".group",this);this.make_name_popup_menu()};q(S.prototype,r.prototype,A.prototype,{make_name_popup_menu:function(){var ai=this;var ah={};ah["Edit configuration"]=function(){var al=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aj=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(am){if((am.keyCode||am.which)===27){al()}else{if((am.keyCode||am.which)===13){aj()}}};$(window).bind("keypress.check_enter_esc",ak);show_modal("Configure Group",ai.config.build_form(),{Cancel:al,OK:aj})};ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)}});var ae=function(ah,ak,aj,ai){A.call(this,"View");this.container=ah;this.chrom=null;this.vis_id=aj;this.dbkey=ai;this.title=ak;this.tracks=this.drawables;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ag(ah.get(0).ownerDocument);this.reset()};q(ae.prototype,A.prototype,{init:function(){var aj=this.container,ah=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aj);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;m(this.viewport_container,ah);this.intro_div=$("<div/>").addClass("intro");var ak=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ai=function(al){if(al.type==="focusout"||(al.keyCode||al.which)===13||(al.keyCode||al.which)===27){if((al.keyCode||al.which)!==27){ah.go_to($(this).val())}$(this).hide();$(this).val("");ah.location_span.show();ah.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ai).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ah.location_span.hide();ah.chrom_select.hide();ah.nav_input.val(ah.chrom+":"+ah.low+"-"+ah.high);ah.nav_input.css("display","inline-block");ah.nav_input.select();ah.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ah.zoom_out();ah.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.browser_content_div.click(function(al){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("<div />").css({height:ah.browser_content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,{content_div:this.top_labeltrack}));this.add_label_track(new ad(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new C(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(al,ai,an){if(!al||al==="None"){return}var ak=this;if(al==="previous"){ak.load_chroms({low:this.chrom_start_index-x});return}if(al==="next"){ak.load_chroms({low:this.chrom_start_index+x});return}var am=$.grep(ak.chrom_data,function(ap,aq){return ap.chrom===al})[0];if(am===undefined){ak.load_chroms({chrom:al},function(){ak.change_chrom(al,ai,an)});return}else{if(al!==ak.chrom){ak.chrom=al;ak.chrom_select.val(ak.chrom);ak.max_high=am.len-1;ak.reset();ak.request_redraw(true);for(var ao=0,ah=ak.tracks.length;ao<ah;ao++){var aj=ak.tracks[ao];if(aj.init){aj.init()}}}if(ai!==undefined&&an!==undefined){ak.low=Math.max(ai,0);ak.high=Math.min(an,ak.max_high)}ak.reset_overview();ak.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){A.prototype.add_drawable.call(this,ah);ah.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;ah.init();this.label_tracks.push(ah)},remove_drawable:function(aj,ai){A.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.tracks),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(E,Math.ceil(Math.log((this.high-this.low)/T)/Math.log(E)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){$.when(ah.get_overview_tile()).then(function(ai){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ai.canvas);view.overview_highlight.show().height(ai.canvas.height());view.overview_viewport.height(ai.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ah;ah.set_is_overview(true)});view.has_changes=true},reset_overview:function(){this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new P(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},al=this.track,aj=ai.tool_id+al.tool_region_and_parameters_str(ai.chrom,ai.low,ai.high),ah,am;if(al.container===view){var ak=new S(this.name,this.track.view,this.track.container);al.container.add_drawable(ak);al.container.remove_drawable(al);ak.add_drawable(al);al.container_div.appendTo(ak.content_div);ah=ak}else{ah=al.container}if(al instanceof e){am=new X(aj,view,ah,"hda");am.change_mode(al.mode);ah.add_drawable(am)}am.content_div.text("Starting job.");this.run(ai,am,function(an){am.dataset_id=an.dataset_id;am.content_div.text("Running job.");am.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(L)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(z+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var P=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){P.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var Y=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};q(Y.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=parseFloat(ah[this.index]);return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(ar,ay){this.track=ar;this.filters=[];for(var at=0;at<ay.length;at++){var au=ay[at],az=au.name,ah=au.type,ak=au.index,ax=au.tool_id,aw=au.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[at]=new Y(az,ak,ax,aw)}else{console.log("ERROR: unsupported filter: ",az,ah)}}var al=function(aA,aB,aC){aA.click(function(){var aD=aB.text();max=parseFloat(aC.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aC.slider("option","values")){input_size=2*input_size+1;multi_value=true}aB.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aD).appendTo(aB).focus().select().click(function(aE){aE.stopPropagation()}).blur(function(){$(this).remove();aB.text(aD)}).keyup(function(aI){if(aI.keyCode===27){$(this).trigger("blur")}else{if(aI.keyCode===13){var aG=aC.slider("option","min"),aE=aC.slider("option","max"),aH=function(aJ){return(isNaN(aJ)||aJ>aE||aJ<aG)},aF=$(this).val();if(!multi_value){aF=parseFloat(aF);if(aH(aF)){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}else{aF=aF.split("-");aF=[parseFloat(aF[0]),parseFloat(aF[1])];if(aH(aF[0])||aH(aF[1])){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}aC.slider((multi_value?"values":"value"),aF)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aA){aA.stopPropagation()}).click(function(aA){aA.stopPropagation()}).bind("dblclick",function(aA){aA.stopPropagation()}).bind("keydown",function(aA){aA.stopPropagation()});var av=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aD,aF){aF.container=$("<div/>").addClass("slider-row").appendTo(av);var aE=$("<div/>").addClass("elt-label").appendTo(aF.container);var aC=$("<span/>").addClass("slider-name").text(aF.name+"  ").appendTo(aE);var aB=$("<span/>");var aH=$("<span/>").addClass("slider-value").appendTo(aE).append("[").append(aB).append("]");var aA=$("<div/>").addClass("slider").appendTo(aF.container);aF.control_element=$("<div/>").attr("id",aF.name+"-filter-control").appendTo(aA);var aG=[0,0];aF.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aJ,aK){var aI=aK.values;aB.text(aI[0]+"-"+aI[1]);aF.low=aI[0];aF.high=aI[1];ap.track.request_draw(true,true)},change:function(aI,aJ){aF.control_element.slider("option","slide").call(aF.control_element,aI,aJ)}});aF.slider=aF.control_element;aF.slider_label=aB;al(aH,aB,aF.control_element);$("<div style='clear: both;'/>").appendTo(aF.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(av);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var aj=this;ao.click(function(){aj.run_on_dataset()})}var aq=$("<div/>").addClass("display-controls").appendTo(this.parent_div),an=$("<span/>").addClass("elt-label").text("Transparency:").appendTo(aq),ai=$("<select/>").attr("name","alpha_dropdown").appendTo(aq);this.alpha_filter=null;$("<option/>").attr("value",-1).text("== None ==").appendTo(ai);for(var at=0;at<this.filters.length;at++){$("<option/>").attr("value",at).text(this.filters[at].name).appendTo(ai)}ai.change(function(){$(this).children("option:selected").each(function(){var aA=parseInt($(this).val());ap.alpha_filter=(aA>=0?ap.filters[aA]:null);ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var Q=function(ai,ah){N.AlphaGenerator.call(this,ah);this.filter=ai};Q.prototype.gen_alpha=function(ah){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_alpha}return((parseFloat(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var H=function(ah){this.track=ah.track;this.params=ah.params;this.values={};this.restore_values((ah.saved_values?ah.saved_values:{}));this.onchange=ah.onchange};q(H.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(aj,ai,ah,ak){this.index=aj;this.low=aj*T*ai;this.high=(aj+1)*T*ai;this.resolution=ai;this.canvas=$("<div class='track-tile'/>").append(ah);this.data=ak;this.stale=false};var l=function(aj,ai,ah,ak,al){b.call(this,aj,ai,ah,ak);this.max_val=al};var R=function(ak,aj,ai,an,am,ah){b.call(this,ak,aj,ai,an);this.message=am;this.feature_mapper=ah;var al=this;$(this.canvas).mousemove(function(ap){var ao=al.feature_mapper.get_feature_data(ap.offsetX,ap.offsetY)})};var j=function(ak,ai,ah,aj,al,am){r.call(this,ak,ai,ah,{},"draghandle");this.data_url=(al?al:default_data_url);this.data_url_extra_params={};this.data_query_wait=(am?am:M);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.container_div=$("<div />").addClass("track").attr("id","track_"+j.id_counter++).css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof C){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Z){return"ReadTrack"}else{if(this instanceof X){return"ToolDataFeatureTrack"}else{if(this instanceof W){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var ak=ah.view.tracks.indexOf(ah);var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(L)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(G)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.make_name_popup_menu()}ah.content_div.text(ab);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}})},predraw_init:function(){},});var O=function(ao,am){var ai=this,ap=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=new ac(this,(ao!==undefined?ao:{}));this.filters_available=false;this.filters_visible=false;this.tool=(am!==undefined&&obj_length(am)>0?new s(this,am):undefined);this.is_overview=false;if(ai.hidden){return}if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(ai.display_modes!==undefined){if(ai.mode_div===undefined){ai.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ai.header_div);var aj=(ai.config&&ai.config.values.mode?ai.config.values.mode:ai.display_modes[0]);ai.mode=aj;ai.mode_div.text(aj);var ah={};for(var ak=0,an=ai.display_modes.length;ak<an;ak++){var al=ai.display_modes[ak];ah[al]=function(aq){return function(){ai.change_mode(aq)}}(al)}make_popupmenu(ai.mode_div,ah)}else{ai.mode_div.hide()}}this.make_name_popup_menu()};q(O.prototype,r.prototype,j.prototype,{to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw();return ah},make_name_popup_menu:function(){var ai=this;var ah={};ah[(this.is_overview?"Hide overview":"Set as overview")]=function(){if(ai.is_overview){ai.view.reset_overview()}else{ai.view.set_overview(ai)}};ah["Edit configuration"]=function(){var am=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},al=function(an){if((an.keyCode||an.which)===27){am()}else{if((an.keyCode||an.which)===13){ak()}}};$(window).bind("keypress.check_enter_esc",al);show_modal("Configure Track",ai.config.build_form(),{Cancel:am,OK:ak})};if(ai.filters_available>0){var aj=(ai.filters_div.is(":visible")?"Hide filters":"Show filters");ah[aj]=function(){ai.filters_visible=(ai.filters_div.is(":visible"));if(ai.filters_visible){ai.filters_manager.reset_filters()}ai.filters_div.toggle();ai.make_name_popup_menu()}}if(ai.tool){var aj=(ai.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");ah[aj]=function(){if(!ai.dynamic_tool_div.is(":visible")){ai.set_name(ai.name+ai.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ai.revert_name()}ai.dynamic_tool_div.toggle();ai.make_name_popup_menu()}}ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)},set_is_overview:function(ah){this.is_overview=ah;this.make_name_popup_menu()},get_overview_tile:function(){var ah=this;view=ah.view,resolution=Math.pow(E,Math.ceil(Math.log((view.max_high-view.max_low)/T)/Math.log(E))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ah.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ah.data_url_extra_params)).then(function(ai){var ak=ah._gen_tile_cache_key(view_width,w_scale,0),am=ah.tile_cache.get(ak);if(!am){am=ah.draw_tile(ai,"Auto",resolution,0,w_scale);ah.tile_cache.set(ak,am)}var ap=$(am.canvas.find("canvas")),al=ap.clone(),ao=ap.get(0).getContext("2d"),aj=al.get(0).getContext("2d"),an=ao.getImageData(0,0,ao.canvas.width,ao.canvas.height);aj.putImageData(an,-ah.left_offset,(am.data.dataset_type==="summary_tree"?V:0));new_tile=new b(-1,resolution,al);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof C)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/T);var ap=true;var at=[];var ah=0;while((ai*T*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",F)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*T*an,ax=ap+T*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);al.tile_cache.set(at,aq);if(aq!==undefined){al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw()});return null},show_tile:function(ao,aq,ar){var aj=this,ai=ao.canvas,an=ai;if(ao.message){var at=$("<div/>"),ap=$("<div/>").addClass("tile-message").text(ao.message).css({height:F-1,width:ao.canvas.width}).appendTo(at),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ap),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ap);at.append(ai);an=at;al.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()});ah.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()})}var am=this.view.high-this.view.low,ak=(ao.low-this.view.low)*ar;if(this.left_offset){ak-=this.left_offset}an.css({position:"absolute",top:0,left:ak,height:""});aq.append(an);aj.max_height=Math.max(aj.max_height,an.height());aj.content_div.css("height",aj.max_height+"px");aq.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*T*ai,al=T*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ai,ah){this.hidden=true;j.call(this,"label",ai,ah,{});this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{init:function(){this.enabled=true},_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var C=function(ah){this.hidden=true;j.call(this,"reference",ah,{content_div:ah.top_labeltrack},{});O.call(this);ah.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ah.dbkey};this.data_manager=new J(D,this,false);this.tile_cache=new c(v)};q(C.prototype,r.prototype,O.prototype,{init:function(){this.enabled=true},draw_tile:function(ar,an,am,ai,at){var al=this,aj=T*am;if(at>this.view.canvas_manager.char_width_px){if(ar===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(am,ak,aj,an,ah,al){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,am,ak,aj,al);O.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=an;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new U(D,this);this.tile_cache=new c(v);this.left_offset=0;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:am},{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:al,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.track_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.track_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};q(k.prototype,r.prototype,O.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this,ai=ah.view.tracks.indexOf(ah);ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(aj){ah.container_div.addClass("line-track");var al=aj.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=al.min;ah.prefs.max_value=al.max;$("#track_"+ai+"_minval").val(ah.prefs.min_value);$("#track_"+ai+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=al.total_frequency;ah.container_div.find(".yaxislabel").remove();var am=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ai+"_minval").text(y(ah.prefs.min_value));var ak=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ai+"_maxval").text(y(ah.prefs.max_value));ak.css({position:"absolute",top:"24px",left:"10px"});ak.prependTo(ah.container_div);am.css({position:"absolute",bottom:"2px",left:"10px"});am.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new N.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(aj,al,ak,au.data)}});var e=function(ah,an,ai,am,ap,ao,ak,al){var aj=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];j.call(this,ah,an,ai,ao);O.call(this,ak,al);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){aj.set_name(aj.prefs.name);aj.tile_cache.clear();aj.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=am;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new U(20,this);this.left_offset=200;this.painter=N.LinkedFeaturePainter};q(e.prototype,r.prototype,O.prototype,{postdraw_actions:function(ax,ah,ay,aw){O.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.make_name_popup_menu()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",B,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aE,aI,ar,ak){var aB=this,am=aB._get_tile_bounds(aI,aE),aL=am[0],ai=am[1],ay=ai-aL,aC=Math.ceil(ay*ar),aP=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"){az="no_detail"}else{var aO=aw.data;if(this.view.high-this.view.low>K){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aC+al;aj.height=an+V;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aL,ai,200);if(aw.max){at.max=aw.max}aw=at}var aM=new N.SummaryTreePainter(aw,aL,ai,this.prefs);var aD=aj.getContext("2d");aD.translate(al,V);aM.draw(aD,aC,an);return new l(aI,aE,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aF=0,aH=aw.data.length;aF<aH;aF++){var ao=aw.data[aF];var aG=false;var av;for(var aK=0,aN=au.length;aK<aN;aK++){av=au[aK];av.update_attrs(ao);if(!av.keep(ao)){aG=true;break}}if(!aG){aq.push(ao)}}}var aA=(this.filters_manager.alpha_filter?new Q(this.filters_manager.alpha_filter):null);var aM=new (this.painter)(aq,aL,ai,this.prefs,az,aA,ak);var an=Math.max(af,aM.get_required_height(ap));var aj=this.view.canvas_manager.new_canvas();var aJ=null;aj.width=aC+al;aj.height=an;var aD=aj.getContext("2d");aD.fillStyle=this.prefs.block_color;aD.font=aD.canvas.manager.default_font;aD.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aw.data){aD.translate(al,0);aJ=aM.draw(aD,aC,an,ax);aJ.translation=-al}return new R(aI,aE,aj,aw.data,aw.message,aJ)}});var W=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.painter=N.VariantPainter};q(W.prototype,r.prototype,O.prototype,e.prototype);var Z=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ak,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=N.ReadPainter;this.make_name_popup_menu()};q(Z.prototype,r.prototype,O.prototype,e.prototype);var X=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am,{});this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};q(X.prototype,r.prototype,O.prototype,e.prototype,{predraw_init:function(){var ai=this;var ah=function(){if(ai.data_manager.size()===0){setTimeout(ah,300)}else{ai.data_url=default_data_url;ai.data_query_wait=M;ai.dataset_state_url=converted_datasets_state_url;$.getJSON(ai.dataset_state_url,{dataset_id:ai.dataset_id,hda_ldda:ai.hda_ldda},function(aj){})}};ah()}});aa.View=ae;aa.DrawableGroup=S;aa.LineTrack=k;aa.FeatureTrack=e;aa.ReadTrack=Z};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var 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A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var c=function(z,D,F,G,B){n.call(this,z,D,F,G,B);if(this.prefs.min_value===undefined){var H=Infinity;for(var A=0,C=this.data.length;A<C;A++){H=Math.min(H,this.data[A][1])}this.prefs.min_value=H}if(this.prefs.max_value===undefined){var E=-Infinity;for(var A=0,C=this.data.length;A<C;A++){E=Math.max(E,this.data[A][1])}this.prefs.max_value=E}};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var 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b=function(C,E,z,B,D,A){p.call(this,C,E,z,B,D,A)};v(b.prototype,p.prototype,{draw_element:function(S,N,H,D,V,B,K,T,Q){var H=data[i],J=H[0],R=H[1],C=H[2],M=H[3],F=Math.floor(Math.max(0,(R-V)*K)),I=Math.ceil(Math.min(Q,Math.max(0,(C-V)*K))),E=(N==="Dense"?0:(0+D))*T,z,W,A=null,L=null;if(no_label){S.fillStyle=block_color;S.fillRect(F+left_offset,E+5,I-F,1)}else{var U=H[4],P=H[5],G=H[6];z=9;W=1;S.fillRect(F+left_offset,E,I-F,z);if(N!=="Dense"&&M!==undefined&&R>V){S.fillStyle=label_color;if(V===0&&F-S.measureText(M).width<0){S.textAlign="left";S.fillText(M,I+2+left_offset,E+8)}else{S.textAlign="right";S.fillText(M,F-2+left_offset,E+8)}S.fillStyle=block_color}var O=U+" / "+P;if(R>V&&S.measureText(O).width<(I-F)){S.fillStyle="white";S.textAlign="center";S.fillText(O,left_offset+F+(I-F)/2,E+8);S.fillStyle=block_color}}}});var 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e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window);
\ No newline at end of file
+var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var trackster_module=function(f,aa){var q=f("class").extend,t=f("slotting"),N=f("painters");var ag=function(ah,ai){this.document=ah;this.default_font=ai!==undefined?ai:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};q(ag.prototype,{load_pattern:function(ah,al){var ai=this.patterns,aj=this.dummy_context,ak=new Image();ak.src=image_path+al;ak.onload=function(){ai[ah]=aj.createPattern(ak,"repeat")}},get_pattern:function(ah){return this.patterns[ah]},new_canvas:function(){var ah=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ah)}ah.manager=this;return ah}});var o={};var m=function(ah,ai){o[ah.attr("id")]=ai};var n=function(ah,aj,al,ak){al=".group";var ai={};o[ah.attr("id")]=ak;ah.bind("drag",{handle:"."+aj,relative:true},function(au,av){var at=$(this);var ay=$(this).parent(),ap=ay.children(),ar=o[$(this).attr("id")],ao,an,aw,am,aq;an=$(this).parents(al);if(an.length!==0){aw=an.position().top;am=aw+an.outerHeight();if(av.offsetY<aw){$(this).insertBefore(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable_before(ar,ax);return}else{if(av.offsetY>am){$(this).insertAfter(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable(ar);return}}}an=null;for(aq=0;aq<ap.length;aq++){ao=$(ap.get(aq));aw=ao.position().top;am=aw+ao.outerHeight();if(ao.is(al)&&this!==ao.get(0)&&av.offsetY>=aw&&av.offsetY<=am){if(av.offsetY-aw<am-av.offsetY){ao.find(".content-div").prepend(this)}else{ao.find(".content-div").append(this)}if(ar.container){ar.container.remove_drawable(ar)}o[ao.attr("id")].add_drawable(ar);return}}for(aq=0;aq<ap.length;aq++){if(av.offsetY<$(ap.get(aq)).position().top){break}}if(aq===ap.length){if(this!==ap.get(aq-1)){ay.append(this);o[ay.attr("id")].move_drawable(ar,aq)}}else{if(this!==ap.get(aq)){$(this).insertBefore(ap.get(aq));o[ay.attr("id")].move_drawable(ar,(av.deltaY>0?aq-1:aq))}}}).bind("dragstart",function(){ai["border-top"]=ah.css("border-top");ai["border-bottom"]=ah.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ai)})};aa.moveable=n;var af=16,I=9,F=20,V=I+2,B=100,K=12000,T=200,E=5,w=10,M=5000,x=100,p="There was an error in indexing this dataset. ",L="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",u="Currently indexing... please wait",z="Tool cannot be rerun: ",a="Loading data...",ab="Ready for display",d=10,v=5,D=5;function y(ah){return Math.round(ah*1000)/1000}var c=function(ah){this.num_elements=ah;this.clear()};q(c.prototype,{get:function(ai){var ah=this.key_ary.indexOf(ai);if(ah!==-1){if(this.obj_cache[ai].stale){this.key_ary.splice(ah,1);delete this.obj_cache[ai]}else{this.move_key_to_end(ai,ah)}}return this.obj_cache[ai]},set:function(ai,aj){if(!this.obj_cache[ai]){if(this.key_ary.length>=this.num_elements){var ah=this.key_ary.shift();delete this.obj_cache[ah]}this.key_ary.push(ai)}this.obj_cache[ai]=aj;return aj},move_key_to_end:function(ai,ah){this.key_ary.splice(ah,1);this.key_ary.push(ai)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var U=function(ai,ah,aj){c.call(this,ai);this.track=ah;this.subset=(aj!==undefined?aj:true)};q(U.prototype,c.prototype,{load_data:function(aq,al,ao,ai,an){var ap=this.track.view.chrom,ak={chrom:ap,low:aq,high:al,mode:ao,resolution:ai,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ak,an);if(this.track.filters_manager){var ar=[];var ah=this.track.filters_manager.filters;for(var am=0;am<ah.length;am++){ar[ar.length]=ah[am].name}ak.filter_cols=JSON.stringify(ar)}var aj=this;return $.getJSON(this.track.data_url,ak,function(at){aj.set_data(aq,al,ao,at)})},get_data:function(ah,al,am,ai,ak){var aj=this.get_data_from_cache(ah,al,am);if(aj){return aj}aj=this.load_data(ah,al,am,ai,ak);this.set_data(ah,al,am,aj);return aj},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ap,ak,ao,aj,an,al){var aq=this.get_data_from_cache(ap,ak,ao);if(!aq){console.log("ERROR: no current data for: ",this.track,ap,ak,ao,aj,an);return}aq.stale=true;var ai=ap;if(al===this.DEEP_DATA_REQ){$.extend(an,{start_val:aq.data.length+1})}else{if(al===this.BROAD_DATA_REQ){ai=(aq.max_high?aq.max_high:aq.data[aq.data.length-1][2])+1}}var ah=this,am=this.load_data(ai,ak,ao,aj,an);new_data_available=$.Deferred();this.set_data(ap,ak,ao,new_data_available);$.when(am).then(function(ar){if(ar.data){ar.data=aq.data.concat(ar.data);if(ar.max_low){ar.max_low=aq.max_low}if(ar.message){ar.message=ar.message.replace(/[0-9]+/,ar.data.length)}}ah.set_data(ap,ak,ao,ar);new_data_available.resolve(ar)});return new_data_available},get_data_from_cache:function(ah,ai,aj){return this.get(this.gen_key(ah,ai,aj))},set_data:function(ai,aj,ak,ah){return this.set(this.gen_key(ai,aj,ak),ah)},gen_key:function(ah,aj,ak){var ai=ah+"_"+aj+"_"+ak;return ai},split_key:function(ah){return ah.split("_")}});var J=function(ai,ah,aj){U.call(this,ai,ah,aj)};q(J.prototype,U.prototype,c.prototype,{load_data:function(aj,ah,al,am,ai,ak){if(ai>1){return}return U.prototype.load_data.call(this,aj,ah,al,am,ai,ak)}});var r=function(ak,ai,ah,aj,al){this.name=ak;this.view=ai;this.container=ah;this.drag_handle_class=al;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak}],saved_values:aj,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values};q(r.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},make_name_popup_menu:function(){},set_name:function(ah){this.old_name=this.name;this.name=ah;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var A=function(al,ak,ai,ah,aj,am){r.call(this,ak,ai,ah,aj,am);this.obj_type=al;this.drawables=[]};q(A.prototype,r.prototype,{init:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah].init()}},_draw:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah]._draw()}},to_json:function(){var ai=[];for(var ah=0;ah<this.drawables.length;ah++){ai.push(this.drawables[ah].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ai}},add_drawable:function(ah){this.drawables.push(ah);ah.container=this},add_drawable_before:function(aj,ah){var ai=this.drawables.indexOf(ah);if(ai!=-1){this.drawables.splice(ai,0,aj);return true}return false},remove_drawable:function(ai){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);ai.container=null;return true}return false},move_drawable:function(ai,aj){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);this.drawables.splice(aj,0,ai);return true}return false}});var S=function(ak,ai,ah,aj){A.call(this,"DrawableGroup",ak,ai,ah,aj,"group-handle");if(!S.id_counter){S.id_counter=0}var al=S.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+al).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+al+"_content_div").appendTo(this.container_div);m(this.container_div,this);m(this.content_div,this);n(this.container_div,this.drag_handle_class,".group",this);this.make_name_popup_menu()};q(S.prototype,r.prototype,A.prototype,{make_name_popup_menu:function(){var ai=this;var ah={};ah["Edit configuration"]=function(){var al=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aj=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(am){if((am.keyCode||am.which)===27){al()}else{if((am.keyCode||am.which)===13){aj()}}};$(window).bind("keypress.check_enter_esc",ak);show_modal("Configure Group",ai.config.build_form(),{Cancel:al,OK:aj})};ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)}});var ae=function(ah,ak,aj,ai){A.call(this,"View");this.container=ah;this.chrom=null;this.vis_id=aj;this.dbkey=ai;this.title=ak;this.tracks=this.drawables;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ag(ah.get(0).ownerDocument);this.reset()};q(ae.prototype,A.prototype,{init:function(){var aj=this.container,ah=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aj);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;m(this.viewport_container,ah);this.intro_div=$("<div/>").addClass("intro");var ak=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ai=function(al){if(al.type==="focusout"||(al.keyCode||al.which)===13||(al.keyCode||al.which)===27){if((al.keyCode||al.which)!==27){ah.go_to($(this).val())}$(this).hide();$(this).val("");ah.location_span.show();ah.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ai).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ah.location_span.hide();ah.chrom_select.hide();ah.nav_input.val(ah.chrom+":"+ah.low+"-"+ah.high);ah.nav_input.css("display","inline-block");ah.nav_input.select();ah.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ah.zoom_out();ah.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.browser_content_div.click(function(al){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("<div />").css({height:ah.browser_content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,{content_div:this.top_labeltrack}));this.add_label_track(new ad(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new C(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(al,ai,an){if(!al||al==="None"){return}var ak=this;if(al==="previous"){ak.load_chroms({low:this.chrom_start_index-x});return}if(al==="next"){ak.load_chroms({low:this.chrom_start_index+x});return}var am=$.grep(ak.chrom_data,function(ap,aq){return ap.chrom===al})[0];if(am===undefined){ak.load_chroms({chrom:al},function(){ak.change_chrom(al,ai,an)});return}else{if(al!==ak.chrom){ak.chrom=al;ak.chrom_select.val(ak.chrom);ak.max_high=am.len-1;ak.reset();ak.request_redraw(true);for(var ao=0,ah=ak.tracks.length;ao<ah;ao++){var aj=ak.tracks[ao];if(aj.init){aj.init()}}}if(ai!==undefined&&an!==undefined){ak.low=Math.max(ai,0);ak.high=Math.min(an,ak.max_high)}ak.reset_overview();ak.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){A.prototype.add_drawable.call(this,ah);ah.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;ah.init();this.label_tracks.push(ah)},remove_drawable:function(aj,ai){A.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.tracks),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(E,Math.ceil(Math.log((this.high-this.low)/T)/Math.log(E)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){$.when(ah.get_overview_tile()).then(function(ai){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ai.canvas);view.overview_highlight.show().height(ai.canvas.height());view.overview_viewport.height(ai.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ah;ah.set_is_overview(true)});view.has_changes=true},reset_overview:function(){this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new P(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},al=this.track,aj=ai.tool_id+al.tool_region_and_parameters_str(ai.chrom,ai.low,ai.high),ah,am;if(al.container===view){var ak=new S(this.name,this.track.view,this.track.container);al.container.add_drawable(ak);al.container.remove_drawable(al);ak.add_drawable(al);al.container_div.appendTo(ak.content_div);ah=ak}else{ah=al.container}if(al instanceof e){am=new X(aj,view,ah,"hda");am.change_mode(al.mode);ah.add_drawable(am)}am.content_div.text("Starting job.");this.run(ai,am,function(an){am.dataset_id=an.dataset_id;am.content_div.text("Running job.");am.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(L)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(z+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var P=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){P.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var Y=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};q(Y.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=parseFloat(ah[this.index]);return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(ar,ay){this.track=ar;this.filters=[];for(var at=0;at<ay.length;at++){var au=ay[at],az=au.name,ah=au.type,ak=au.index,ax=au.tool_id,aw=au.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[at]=new Y(az,ak,ax,aw)}else{console.log("ERROR: unsupported filter: ",az,ah)}}var al=function(aA,aB,aC){aA.click(function(){var aD=aB.text();max=parseFloat(aC.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aC.slider("option","values")){input_size=2*input_size+1;multi_value=true}aB.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aD).appendTo(aB).focus().select().click(function(aE){aE.stopPropagation()}).blur(function(){$(this).remove();aB.text(aD)}).keyup(function(aI){if(aI.keyCode===27){$(this).trigger("blur")}else{if(aI.keyCode===13){var aG=aC.slider("option","min"),aE=aC.slider("option","max"),aH=function(aJ){return(isNaN(aJ)||aJ>aE||aJ<aG)},aF=$(this).val();if(!multi_value){aF=parseFloat(aF);if(aH(aF)){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}else{aF=aF.split("-");aF=[parseFloat(aF[0]),parseFloat(aF[1])];if(aH(aF[0])||aH(aF[1])){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}aC.slider((multi_value?"values":"value"),aF)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aA){aA.stopPropagation()}).click(function(aA){aA.stopPropagation()}).bind("dblclick",function(aA){aA.stopPropagation()}).bind("keydown",function(aA){aA.stopPropagation()});var av=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aD,aF){aF.container=$("<div/>").addClass("slider-row").appendTo(av);var aE=$("<div/>").addClass("elt-label").appendTo(aF.container);var aC=$("<span/>").addClass("slider-name").text(aF.name+"  ").appendTo(aE);var aB=$("<span/>");var aH=$("<span/>").addClass("slider-value").appendTo(aE).append("[").append(aB).append("]");var aA=$("<div/>").addClass("slider").appendTo(aF.container);aF.control_element=$("<div/>").attr("id",aF.name+"-filter-control").appendTo(aA);var aG=[0,0];aF.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aJ,aK){var aI=aK.values;aB.text(aI[0]+"-"+aI[1]);aF.low=aI[0];aF.high=aI[1];ap.track.request_draw(true,true)},change:function(aI,aJ){aF.control_element.slider("option","slide").call(aF.control_element,aI,aJ)}});aF.slider=aF.control_element;aF.slider_label=aB;al(aH,aB,aF.control_element);$("<div style='clear: both;'/>").appendTo(aF.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(av);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var aj=this;ao.click(function(){aj.run_on_dataset()})}var aq=$("<div/>").addClass("display-controls").appendTo(this.parent_div),an=$("<span/>").addClass("elt-label").text("Transparency:").appendTo(aq),ai=$("<select/>").attr("name","alpha_dropdown").appendTo(aq);this.alpha_filter=null;$("<option/>").attr("value",-1).text("== None ==").appendTo(ai);for(var at=0;at<this.filters.length;at++){$("<option/>").attr("value",at).text(this.filters[at].name).appendTo(ai)}ai.change(function(){$(this).children("option:selected").each(function(){var aA=parseInt($(this).val());ap.alpha_filter=(aA>=0?ap.filters[aA]:null);ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var Q=function(ai,ah){N.AlphaGenerator.call(this,ah);this.filter=ai};Q.prototype.gen_alpha=function(ah){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_alpha}return((parseFloat(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var H=function(ah){this.track=ah.track;this.params=ah.params;this.values={};this.restore_values((ah.saved_values?ah.saved_values:{}));this.onchange=ah.onchange};q(H.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(aj,ai,ah,ak){this.index=aj;this.low=aj*T*ai;this.high=(aj+1)*T*ai;this.resolution=ai;this.canvas=$("<div class='track-tile'/>").append(ah);this.data=ak;this.stale=false};var l=function(aj,ai,ah,ak,al){b.call(this,aj,ai,ah,ak);this.max_val=al};var R=function(ak,aj,ai,an,am,ah){b.call(this,ak,aj,ai,an);this.message=am;this.feature_mapper=ah;var al=this;$(this.canvas).mousemove(function(ap){var ao=al.feature_mapper.get_feature_data(ap.offsetX,ap.offsetY)})};var j=function(ak,ai,ah,aj,al,am){r.call(this,ak,ai,ah,{},"draghandle");this.data_url=(al?al:default_data_url);this.data_url_extra_params={};this.data_query_wait=(am?am:M);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.container_div=$("<div />").addClass("track").attr("id","track_"+j.id_counter++).css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof C){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Z){return"ReadTrack"}else{if(this instanceof X){return"ToolDataFeatureTrack"}else{if(this instanceof W){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var ak=ah.view.tracks.indexOf(ah);var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(L)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(G)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.make_name_popup_menu()}ah.content_div.text(ab);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}})},predraw_init:function(){},});var O=function(ao,am){var ai=this,ap=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=new ac(this,(ao!==undefined?ao:{}));this.filters_available=false;this.filters_visible=false;this.tool=(am!==undefined&&obj_length(am)>0?new s(this,am):undefined);this.is_overview=false;if(ai.hidden){return}if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(ai.display_modes!==undefined){if(ai.mode_div===undefined){ai.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ai.header_div);var aj=(ai.config&&ai.config.values.mode?ai.config.values.mode:ai.display_modes[0]);ai.mode=aj;ai.mode_div.text(aj);var ah={};for(var ak=0,an=ai.display_modes.length;ak<an;ak++){var al=ai.display_modes[ak];ah[al]=function(aq){return function(){ai.change_mode(aq)}}(al)}make_popupmenu(ai.mode_div,ah)}else{ai.mode_div.hide()}}this.make_name_popup_menu()};q(O.prototype,r.prototype,j.prototype,{to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw();return ah},make_name_popup_menu:function(){var ai=this;var ah={};ah[(this.is_overview?"Hide overview":"Set as overview")]=function(){if(ai.is_overview){ai.view.reset_overview()}else{ai.view.set_overview(ai)}};ah["Edit configuration"]=function(){var am=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},al=function(an){if((an.keyCode||an.which)===27){am()}else{if((an.keyCode||an.which)===13){ak()}}};$(window).bind("keypress.check_enter_esc",al);show_modal("Configure Track",ai.config.build_form(),{Cancel:am,OK:ak})};if(ai.filters_available>0){var aj=(ai.filters_div.is(":visible")?"Hide filters":"Show filters");ah[aj]=function(){ai.filters_visible=(ai.filters_div.is(":visible"));if(ai.filters_visible){ai.filters_manager.reset_filters()}ai.filters_div.toggle();ai.make_name_popup_menu()}}if(ai.tool){var aj=(ai.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");ah[aj]=function(){if(!ai.dynamic_tool_div.is(":visible")){ai.set_name(ai.name+ai.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ai.revert_name()}ai.dynamic_tool_div.toggle();ai.make_name_popup_menu()}}ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)},set_is_overview:function(ah){this.is_overview=ah;this.make_name_popup_menu()},get_overview_tile:function(){var ah=this;view=ah.view,resolution=Math.pow(E,Math.ceil(Math.log((view.max_high-view.max_low)/T)/Math.log(E))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ah.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ah.data_url_extra_params)).then(function(ai){var ak=ah._gen_tile_cache_key(view_width,w_scale,0),am=ah.tile_cache.get(ak);if(!am){am=ah.draw_tile(ai,"Auto",resolution,0,w_scale);ah.tile_cache.set(ak,am)}var ap=$(am.canvas.find("canvas")),al=ap.clone(),ao=ap.get(0).getContext("2d"),aj=al.get(0).getContext("2d"),an=ao.getImageData(0,0,ao.canvas.width,ao.canvas.height);aj.putImageData(an,-ah.left_offset,(am.data.dataset_type==="summary_tree"?V:0));new_tile=new b(-1,resolution,al);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof C)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/T);var ap=true;var at=[];var ah=0;while((ai*T*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",F)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*T*an,ax=ap+T*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);al.tile_cache.set(at,aq);if(aq!==undefined){al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw()});return null},show_tile:function(ao,aq,ar){var aj=this,ai=ao.canvas,an=ai;if(ao.message){var at=$("<div/>"),ap=$("<div/>").addClass("tile-message").text(ao.message).css({height:F-1,width:ao.canvas.width}).appendTo(at),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ap),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ap);at.append(ai);an=at;al.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()});ah.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()})}var am=this.view.high-this.view.low,ak=(ao.low-this.view.low)*ar;if(this.left_offset){ak-=this.left_offset}an.css({position:"absolute",top:0,left:ak,height:""});aq.append(an);aj.max_height=Math.max(aj.max_height,an.height());aj.content_div.css("height",aj.max_height+"px");aq.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*T*ai,al=T*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ai,ah){this.hidden=true;j.call(this,"label",ai,ah,{});this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{init:function(){this.enabled=true},_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var C=function(ah){this.hidden=true;j.call(this,"reference",ah,{content_div:ah.top_labeltrack},{});O.call(this);ah.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ah.dbkey};this.data_manager=new J(D,this,false);this.tile_cache=new c(v)};q(C.prototype,r.prototype,O.prototype,{init:function(){this.enabled=true},draw_tile:function(ar,an,am,ai,at){var al=this,aj=T*am;if(at>this.view.canvas_manager.char_width_px){if(ar===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(am,ak,aj,an,ah,al){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,am,ak,aj,al);O.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=an;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new U(D,this);this.tile_cache=new c(v);this.left_offset=0;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:am},{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:al,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.track_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.track_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};q(k.prototype,r.prototype,O.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this,ai=ah.view.tracks.indexOf(ah);ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(aj){ah.container_div.addClass("line-track");var al=aj.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=al.min;ah.prefs.max_value=al.max;$("#track_"+ai+"_minval").val(ah.prefs.min_value);$("#track_"+ai+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=al.total_frequency;ah.container_div.find(".yaxislabel").remove();var am=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ai+"_minval").text(y(ah.prefs.min_value));var ak=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ai+"_maxval").text(y(ah.prefs.max_value));ak.css({position:"absolute",top:"24px",left:"10px"});ak.prependTo(ah.container_div);am.css({position:"absolute",bottom:"2px",left:"10px"});am.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new N.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(aj,al,ak,au.data)}});var e=function(ah,an,ai,am,ap,ao,ak,al){var aj=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];j.call(this,ah,an,ai,ao);O.call(this,ak,al);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){aj.set_name(aj.prefs.name);aj.tile_cache.clear();aj.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=am;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new U(20,this);this.left_offset=200;this.painter=N.LinkedFeaturePainter};q(e.prototype,r.prototype,O.prototype,{postdraw_actions:function(ax,ah,ay,aw){O.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.make_name_popup_menu()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",B,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aE,aI,ar,ak){var aB=this,am=aB._get_tile_bounds(aI,aE),aL=am[0],ai=am[1],ay=ai-aL,aC=Math.ceil(ay*ar),aP=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"){az="no_detail"}else{var aO=aw.data;if(this.view.high-this.view.low>K){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aC+al;aj.height=an+V;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aL,ai,200);if(aw.max){at.max=aw.max}aw=at}var aM=new N.SummaryTreePainter(aw,aL,ai,this.prefs);var aD=aj.getContext("2d");aD.translate(al,V);aM.draw(aD,aC,an);return new l(aI,aE,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aF=0,aH=aw.data.length;aF<aH;aF++){var ao=aw.data[aF];var aG=false;var av;for(var aK=0,aN=au.length;aK<aN;aK++){av=au[aK];av.update_attrs(ao);if(!av.keep(ao)){aG=true;break}}if(!aG){aq.push(ao)}}}var aA=(this.filters_manager.alpha_filter?new Q(this.filters_manager.alpha_filter):null);var aM=new (this.painter)(aq,aL,ai,this.prefs,az,aA,ak);var an=Math.max(af,aM.get_required_height(ap));var aj=this.view.canvas_manager.new_canvas();var aJ=null;aj.width=aC+al;aj.height=an;var aD=aj.getContext("2d");aD.fillStyle=this.prefs.block_color;aD.font=aD.canvas.manager.default_font;aD.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aw.data){aD.translate(al,0);aJ=aM.draw(aD,aC,an,ax);aJ.translation=-al}return new R(aI,aE,aj,aw.data,aw.message,aJ)}});var W=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.painter=N.VariantPainter};q(W.prototype,r.prototype,O.prototype,e.prototype);var Z=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ak,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=N.ReadPainter;this.make_name_popup_menu()};q(Z.prototype,r.prototype,O.prototype,e.prototype);var X=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am,{});this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};q(X.prototype,r.prototype,O.prototype,e.prototype,{predraw_init:function(){var ai=this;var ah=function(){if(ai.data_manager.size()===0){setTimeout(ah,300)}else{ai.data_url=default_data_url;ai.data_query_wait=M;ai.dataset_state_url=converted_datasets_state_url;$.getJSON(ai.dataset_state_url,{dataset_id:ai.dataset_id,hda_ldda:ai.hda_ldda},function(aj){})}};ah()}});aa.View=ae;aa.DrawableGroup=S;aa.LineTrack=k;aa.FeatureTrack=e;aa.ReadTrack=Z};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(k,y){var v=k("class").extend;var q=function(J,B,H,A,G,E){if(E===undefined){E=4}var D=A-B;var C=G-H;var F=Math.floor(Math.sqrt(D*D+C*C)/E);var K=D/F;var I=C/F;var z;for(z=0;z<F;z++,B+=K,H+=I){if(z%2!==0){continue}J.fillRect(B,H,E,1)}};var r=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var g=function(z){this.default_alpha=(z?z:1)};g.prototype.gen_alpha=function(z){return this.default_alpha};var n=function(B,D,z,A,C){this.data=B;this.view_start=D;this.view_end=z;this.prefs=v({},this.default_prefs,A);this.mode=C};n.prototype.default_prefs={};var w=function(B,D,z,A,C){n.call(this,B,D,z,A,C)};w.prototype.default_prefs={show_counts:false};w.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var 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o=function(z){this.feature_positions={};this.slot_height=z;this.translation=0};o.prototype.map_feature_data=function(A,C,z,B){if(!this.feature_positions[C]){this.feature_positions[C]=[]}this.feature_positions[C].push({data:A,x_start:z,x_end:B})};o.prototype.get_feature_data=function(z,D){var C=Math.floor(D/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var p=function(C,E,z,B,D,A){n.call(this,C,E,z,B,D);this.alpha_generator=(A?A:new g())};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};v(p.prototype,{get_required_height:function(A){var z=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){z=A*y_scale}return z+Math.max(Math.round(y_scale/2),5)},draw:function(L,J,H,G){var R=this.data,E=this.view_start,N=this.view_end;L.save();L.fillStyle=this.prefs.block_color;L.textAlign="right";var I=this.view_end-this.view_start,F=J/I,M=this.get_row_height(),Q=new o(M),C;for(var O=0,P=R.length;O<P;O++){var B=R[O],D=B[0],K=B[1],z=B[2],A=(G&&G[D]!==undefined?G[D]:null);if((K<N&&z>E)&&(this.mode=="Dense"||A!==null)){C=this.draw_element(L,this.mode,B,A,E,N,F,M,J);Q.map_feature_data(B,A,C[0],C[1])}}L.restore();return Q},draw_element:function(F,B,H,D,C,E,G,A,z){console.log("WARNING: Unimplemented function.");return[0,0]}});var d=10,j=3,m=5,x=10,f=1,t=3,e=3,a=9,l=2,h="#ccc";var s=function(C,E,z,B,D,A){p.call(this,C,E,z,B,D,A)};v(s.prototype,p.prototype,{get_row_height:function(){var A=this.mode,z;if(A==="Dense"){z=d}else{if(A==="no_detail"){z=j}else{if(A==="Squish"){z=m}else{z=x}}}return z},draw_element:function(L,E,T,G,N,ae,ai,ak,z){var Q=T[0],ag=T[1],Y=T[2],O=T[3],Z=Math.floor(Math.max(0,(ag-N)*ai)),M=Math.ceil(Math.min(z,Math.max(0,(Y-N)*ai))),X=Z,aj=M,W=(E==="Dense"?0:(0+G))*ak,K,ac,P=null,al=null,C=this.prefs.block_color,ab=this.prefs.label_color;L.globalAlpha=this.alpha_generator.gen_alpha(T);if(E=="Dense"){G=1}if(E==="no_detail"){L.fillStyle=C;L.fillRect(Z,W+5,M-Z,f)}else{var J=T[4],V=T[5],aa=T[6],D=T[7];if(V&&aa){P=Math.floor(Math.max(0,(V-N)*ai));al=Math.ceil(Math.min(z,Math.max(0,(aa-N)*ai)))}var ah,R;if(E==="Squish"||E==="Dense"){ah=1;R=e}else{ah=5;R=a}if(!D){if(T.strand){if(T.strand==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand_inv")}else{if(T.strand==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand_inv")}}}else{L.fillStyle=C}L.fillRect(Z,W,M-Z,R)}else{var I,S;if(E==="Squish"||E==="Dense"){L.fillStyle=h;I=W+Math.floor(e/2)+1;S=1}else{if(J){var I=W;var 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b=function(C,E,z,B,D,A){p.call(this,C,E,z,B,D,A)};v(b.prototype,p.prototype,{draw_element:function(S,N,H,D,V,B,K,T,Q){var H=data[i],J=H[0],R=H[1],C=H[2],M=H[3],F=Math.floor(Math.max(0,(R-V)*K)),I=Math.ceil(Math.min(Q,Math.max(0,(C-V)*K))),E=(N==="Dense"?0:(0+D))*T,z,W,A=null,L=null;if(no_label){S.fillStyle=block_color;S.fillRect(F+left_offset,E+5,I-F,1)}else{var U=H[4],P=H[5],G=H[6];z=9;W=1;S.fillRect(F+left_offset,E,I-F,z);if(N!=="Dense"&&M!==undefined&&R>V){S.fillStyle=label_color;if(V===0&&F-S.measureText(M).width<0){S.textAlign="left";S.fillText(M,I+2+left_offset,E+8)}else{S.textAlign="right";S.fillText(M,F-2+left_offset,E+8)}S.fillStyle=block_color}var O=U+" / "+P;if(R>V&&S.measureText(O).width<(I-F)){S.fillStyle="white";S.textAlign="center";S.fillText(O,left_offset+F+(I-F)/2,E+8);S.fillStyle=block_color}}return[F,I]}});var u=function(D,F,z,C,E,A,B){p.call(this,D,F,z,C,E,A);this.ref_seq=B};u.prototype.default_prefs=v({},p.prototype.default_prefs,{show_insertions:false});v(u.prototype,p.prototype,{get_row_height:function(){var z,A=this.mode;if(A==="Dense"){z=d}else{if(A==="Squish"){z=m}else{z=x;if(this.prefs.show_insertions){z*=2}}}return z},draw_read:function(V,Q,M,aa,B,U,J,G,F){V.textAlign="center";var T=this,A=[aa,B],P=0,W=0,S=0;ref_seq=this.ref_seq,char_width_px=V.canvas.manager.char_width_px;var af=[];if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){S=Math.round(M/2)}if(!J){J=[[0,G.length]]}for(var N=0,Y=J.length;N<Y;N++){var K=J[N],C="MIDNSHP=X"[K[0]],O=K[1];if(C==="H"||C==="S"){P-=O}var H=U+P,ae=Math.floor(Math.max(0,(H-aa)*M)),I=Math.floor(Math.max(0,(H+O-aa)*M));if(ae===I){I+=1}switch(C){case"H":break;case"S":case"M":case"=":if(is_overlap([H,H+O],A)){var R=G.slice(W,W+O);if(S>0){V.fillStyle=this.prefs.block_color;V.fillRect(ae-S,F+1,I-ae,9);V.fillStyle=h;for(var ac=0,z=R.length;ac<z;ac++){if(this.prefs.show_differences&&ref_seq){var L=ref_seq[H-aa+ac];if(!L||L.toLowerCase()===R[ac].toLowerCase()){continue}}if(H+ac>=aa&&H+ac<=B){var ad=Math.floor(Math.max(0,(H+ac-aa)*M));V.fillText(R[ac],ad,F+9)}}}else{V.fillStyle=this.prefs.block_color;V.fillRect(ae,F+4,I-ae,e)}}W+=O;P+=O;break;case"N":V.fillStyle=h;V.fillRect(ae-S,F+5,I-ae,1);P+=O;break;case"D":V.fillStyle="red";V.fillRect(ae-S,F+4,I-ae,3);P+=O;break;case"P":break;case"I":var Z=ae-S;if(is_overlap([H,H+O],A)){var R=G.slice(W,W+O);if(this.prefs.show_insertions){var E=ae-(I-ae)/2;if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){V.fillStyle="yellow";V.fillRect(E-S,F-9,I-ae,9);af[af.length]={type:"triangle",data:[Z,F+4,5]};V.fillStyle=h;switch(seq_tile_overlap){case (OVERLAP_START):R=R.slice(aa-H);break;case (OVERLAP_END):R=R.slice(0,H-B);break;case (CONTAINED_BY):break;case (CONTAINS):R=R.slice(aa-H,H-B);break}for(var ac=0,z=R.length;ac<z;ac++){var ad=Math.floor(Math.max(0,(H+ac-aa)*M));V.fillText(R[ac],ad-(I-ae)/2,F)}}else{V.fillStyle="yellow";V.fillRect(E,F+(this.mode!=="Dense"?2:5),I-ae,(Q!=="Dense"?e:t))}}else{if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){af[af.length]={type:"text",data:[R.length,Z,F+9]}}else{}}}W+=O;break;case"X":W+=O;break}}V.fillStyle="yellow";var ab,D,ag;for(var X=0;X<af.length;X++){ab=af[X];D=ab.type;ag=ab.data;if(D==="text"){V.save();V.font="bold "+V.font;V.fillText(ag[0],ag[1],ag[2]);V.restore()}else{if(D=="triangle"){r(V,ag[0],ag[1],ag[2])}}}},draw_element:function(S,N,F,C,V,A,J,T,Q){var I=F[0],R=F[1],B=F[2],K=F[3],E=Math.floor(Math.max(0,(R-V)*J)),G=Math.ceil(Math.min(Q,Math.max(0,(B-V)*J))),D=(N==="Dense"?0:(0+C))*T,W=this.prefs.block_color,H=this.prefs.label_color,P=0;if((N==="Pack"||this.mode==="Auto")&&J>S.canvas.manager.char_width_px){var P=Math.round(J/2)}S.fillStyle=W;if(F[5] instanceof Array){var O=Math.floor(Math.max(0,(F[4][0]-V)*J)),M=Math.ceil(Math.min(Q,Math.max(0,(F[4][1]-V)*J))),L=Math.floor(Math.max(0,(F[5][0]-V)*J)),z=Math.ceil(Math.min(Q,Math.max(0,(F[5][1]-V)*J)));if(F[4][1]>=V&&F[4][0]<=A&&F[4][2]){this.draw_read(S,N,J,V,A,F[4][0],F[4][2],F[4][3],D)}if(F[5][1]>=V&&F[5][0]<=A&&F[5][2]){this.draw_read(S,N,J,V,A,F[5][0],F[5][2],F[5][3],D)}if(L>M){S.fillStyle=h;q(S,M-P,D+5,L-P,D+5)}}else{S.fillStyle=W;this.draw_read(S,N,J,V,A,R,F[4],F[5],D)}if(N==="Pack"&&R>V){S.fillStyle=this.prefs.label_color;var U=1;if(U===0&&E-S.measureText(K).width<0){S.textAlign="left";S.fillText(K,G+l-P,D+8)}else{S.textAlign="right";S.fillText(K,E-l-P,D+8)}S.fillStyle=W}return[0,0]}});y.AlphaGenerator=g;y.SummaryTreePainter=w;y.LinePainter=c;y.LinkedFeaturePainter=s;y.ReadPainter=u;y.VariantPainter=b};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window);
\ No newline at end of file
diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index c5762c320ac..69e810ed39f 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -4200,7 +4200,8 @@ extend(VariantPainter.prototype, FeaturePainter.prototype, {
         if (no_label) {
             ctx.fillStyle = block_color;
             ctx.fillRect(f_start + left_offset, y_center + 5, f_end - f_start, 1);
-        } else { // Show blocks, labels, etc.                        
+        } 
+        else { // Show blocks, labels, etc.                        
             // Unpack.
             var ref_base = feature[4], alt_base = feature[5], qual = feature[6];
         
@@ -4232,6 +4233,8 @@ extend(VariantPainter.prototype, FeaturePainter.prototype, {
                 ctx.fillStyle = block_color;
             }
         }
+        
+        return [f_start, f_end];
     }
 });
 
@@ -4519,6 +4522,9 @@ extend(ReadPainter.prototype, FeaturePainter.prototype, {
             }
             ctx.fillStyle = block_color;
         }
+        
+        // FIXME: provide actual coordinates for drawn read.
+        return [0,0];
     }
 });
 

From 77df47e50dd73237a3fd55c1039f28d819e54d25 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Thu, 6 Oct 2011 10:59:50 -0400
Subject: [PATCH 023/362] Add a link to allow the user to switch to the new
 history directly after cloning.

---
 lib/galaxy/web/controllers/history.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/web/controllers/history.py b/lib/galaxy/web/controllers/history.py
index 40e0fa8580e..aa7142d2c20 100644
--- a/lib/galaxy/web/controllers/history.py
+++ b/lib/galaxy/web/controllers/history.py
@@ -1214,7 +1214,7 @@ class HistoryController( BaseUIController, Sharable, UsesAnnotations, UsesItemRa
                 name += " (active items only)"
                 new_history = history.copy( name=name, target_user=user )
         if len( histories ) == 1:
-            msg = 'Clone with name "%s" is now included in your previously stored histories.' % new_history.name
+            msg = 'Clone with name "<a href="%s" target="_top">%s</a>" is now included in your previously stored histories.' % ( url_for( controller="history", action="switch_to_history", hist_id=trans.security.encode_id( new_history.id ) ) , new_history.name )
         else:
             msg = '%d cloned histories are now included in your previously stored histories.' % len( histories )
         return trans.show_ok_message( msg )

From c87682305d0bb544364afd1e747cfc16ba75f939 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Thu, 6 Oct 2011 12:16:48 -0400
Subject: [PATCH 024/362] HTML escape job stderr/stdout/info on dataset error
 page.

---
 templates/dataset/errors.mako | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/templates/dataset/errors.mako b/templates/dataset/errors.mako
index 3f4ef586ba1..3d8eaec23bc 100644
--- a/templates/dataset/errors.mako
+++ b/templates/dataset/errors.mako
@@ -24,21 +24,21 @@
             <% job = hda.creating_job_associations[0].job %>
             %if job.traceback:
                 The Galaxy framework encountered the following error while attempting to run the tool:
-                <pre>${job.traceback}</pre>
+                <pre>${job.traceback | h}</pre>
             %endif
             %if job.stderr or job.info:
                 Tool execution generated the following error message:
                 %if job.stderr:
-                    <pre>${job.stderr}</pre>
+                    <pre>${job.stderr | h}</pre>
                 %elif job.info:
-                    <pre>${job.info}</pre>
+                    <pre>${job.info | h}</pre>
                 %endif
             %else:
                 Tool execution did not generate any error messages.
             %endif
             %if job.stdout:
                 The tool produced the following additional output:
-                <pre>${job.stdout}</pre>
+                <pre>${job.stdout | h}</pre>
             %endif
         %else:
             The tool did not create any additional job / error info.

From 8fa20276b46fbaa5f3fef540873887cf5d5f7fbd Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Thu, 6 Oct 2011 12:27:48 -0400
Subject: [PATCH 025/362] Some gatk_wrapper.py tweaks.

---
 tools/gatk/gatk_wrapper.py | 18 ++++++++----------
 1 file changed, 8 insertions(+), 10 deletions(-)

diff --git a/tools/gatk/gatk_wrapper.py b/tools/gatk/gatk_wrapper.py
index affc85b7a1a..a395ad806e0 100644
--- a/tools/gatk/gatk_wrapper.py
+++ b/tools/gatk/gatk_wrapper.py
@@ -8,7 +8,7 @@ A wrapper script for running the GenomeAnalysisTK.jar commands.
 import sys, optparse, os, tempfile, subprocess, shutil
 from string import Template
 
-GALAXY_EXT_TO_GATK_EXT = { 'gatk_interval':'intervals', 'bam_index':'bam.bai', 'gatk_dbsnp':'dbsnp', 'picard_interval_list':'interval_list' } #items not listed here, will use the galaxy extension as-is
+GALAXY_EXT_TO_GATK_EXT = { 'gatk_interval':'intervals', 'bam_index':'bam.bai', 'gatk_dbsnp':'dbSNP', 'picard_interval_list':'interval_list' } #items not listed here will use the galaxy extension as-is
 GALAXY_EXT_TO_GATK_FILE_TYPE = GALAXY_EXT_TO_GATK_EXT #for now, these are the same, but could be different if needed
 DEFAULT_GATK_PREFIX = "gatk_file"
 CHUNK_SIZE = 2**20 #1mb
@@ -48,21 +48,21 @@ def __main__():
     parser.add_option( '-p', '--pass_through', dest='pass_through_options', action='append', type="string", help='These options are passed through directly to GATK, without any modification.' )
     parser.add_option( '-d', '--dataset', dest='datasets', action='append', type="string", nargs=4, help='"-argument" "original_filename" "galaxy_filetype" "name_prefix"' )
     parser.add_option( '', '--max_jvm_heap', dest='max_jvm_heap', action='store', type="string", default=None, help='If specified, the maximum java virtual machine heap size will be set to the provide value.' )
-    parser.add_option( '', '--max_jvm_heap_fraction', dest='max_jvm_heap_fraction', action='store', type="int", default=0, help='If specified, the maximum java virtual machine heap size will be set to the provide value as a fraction of total physical memory.' )
+    parser.add_option( '', '--max_jvm_heap_fraction', dest='max_jvm_heap_fraction', action='store', type="int", default=None, help='If specified, the maximum java virtual machine heap size will be set to the provide value as a fraction of total physical memory.' )
     parser.add_option( '', '--stdout', dest='stdout', action='store', type="string", default=None, help='If specified, the output of stdout will be written to this file.' )
     parser.add_option( '', '--stderr', dest='stderr', action='store', type="string", default=None, help='If specified, the output of stderr will be written to this file.' )
     parser.add_option( '', '--html_report_from_directory', dest='html_report_from_directory', action='append', type="string", nargs=2, help='"Target HTML File" "Directory"')
     (options, args) = parser.parse_args()
     
-    tmp_dir = tempfile.mkdtemp()
+    tmp_dir = tempfile.mkdtemp( prefix='tmp-gatk-' )
     if options.pass_through_options:
         cmd = ' '.join( options.pass_through_options )
     else:
         cmd = ''
-    if options.max_jvm_heap:
-        cmd.replace( 'java ', 'java -Xmx%s ' % ( options.max_jvm_heap ), 1 )
-    elif options.max_jvm_heap_fraction:
-        cmd.replace( 'java ', 'java -XX:DefaultMaxRAMFraction=%s  -XX:+UseParallelGC ' % ( options.max_jvm_heap_fraction ), 1 )
+    if options.max_jvm_heap is not None:
+        cmd = cmd.replace( 'java ', 'java -Xmx%s ' % ( options.max_jvm_heap ), 1 )
+    elif options.max_jvm_heap_fraction is not None:
+        cmd = cmd.replace( 'java ', 'java -XX:DefaultMaxRAMFraction=%s  -XX:+UseParallelGC ' % ( options.max_jvm_heap_fraction ), 1 )
     if options.datasets:
         for ( dataset_arg, filename, galaxy_ext, prefix ) in options.datasets:
             gatk_filename = gatk_filename_from_galaxy( filename, galaxy_ext, target_dir = tmp_dir, prefix = prefix )
@@ -73,9 +73,7 @@ def __main__():
     stderr = open_file_from_option( options.stderr, mode = 'wb' )
     #if no stderr file is specified, we'll use our own
     if stderr is None:
-        stderr = tempfile.NamedTemporaryFile( dir=tmp_dir )
-        stderr.close()
-        stderr = open( stderr.name, 'w+b' )
+        stderr = tempfile.NamedTemporaryFile( prefix="gatk-stderr-", dir=tmp_dir )
     
     proc = subprocess.Popen( args=cmd, stdout=stdout, stderr=stderr, shell=True, cwd=tmp_dir )
     return_code = proc.wait()

From 3ac6f3c26dc238a6dde8a227bb8c8335aec96ea1 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Thu, 6 Oct 2011 13:41:27 -0400
Subject: [PATCH 026/362] A much more efficient query for calculating a
 history's disk usage.

---
 lib/galaxy/model/__init__.py | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 264fab91b9e..48d4d9c4442 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -17,6 +17,7 @@ from galaxy.util.hash_util import *
 from galaxy.web.form_builder import *
 from galaxy.model.item_attrs import UsesAnnotations, APIItem
 from sqlalchemy.orm import object_session
+from sqlalchemy.sql.expression import func
 import os.path, os, errno, codecs, operator, socket, pexpect, logging, time, shutil
 
 if sys.version_info[:2] < ( 2, 5 ):
@@ -468,7 +469,12 @@ class History( object, UsesAnnotations ):
         return self.get_disk_size( nice_size=False )
     def get_disk_size( self, nice_size=False ):
         # unique datasets only
-        rval = sum( [ d.get_total_size() for d in list( set( [ hda.dataset for hda in self.datasets if not hda.purged ] ) ) if not d.purged ] )
+        db_session = object_session( self )
+        rval = db_session.query( func.sum( db_session.query( HistoryDatasetAssociation.dataset_id, Dataset.total_size ).join( Dataset )
+                                                     .filter( HistoryDatasetAssociation.table.c.history_id == self.id )
+                                                     .distinct().subquery().c.total_size ) ).first()[0]
+        if rval is None:
+            rval = 0
         if nice_size:
             rval = galaxy.datatypes.data.nice_size( rval )
         return rval

From e8d8d8e7c3bdc5bd62e6240fa8a69950fcc485a0 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Thu, 6 Oct 2011 13:55:25 -0400
Subject: [PATCH 027/362] Add test/development GenomeSpace file importer
 datasource tool.

---
 tool_conf.xml.sample                          |   1 +
 tools/data_source/genomespace_file_browser.py | 157 ++++++++++++++++++
 .../genomespace_file_browser_dev.xml          |  15 ++
 3 files changed, 173 insertions(+)
 create mode 100644 tools/data_source/genomespace_file_browser.py
 create mode 100644 tools/data_source/genomespace_file_browser_dev.xml

diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index be30a5d35e9..3f02ba7cbd3 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -26,6 +26,7 @@
     <tool file="data_source/epigraph_import.xml" />
     <tool file="data_source/epigraph_import_test.xml" />
     <tool file="data_source/hbvar.xml" />
+    <tool file="data_source/genomespace_file_browser_dev.xml" />
     <tool file="validation/fix_errors.xml" />
   </section>
   <section name="Send Data" id="send">
diff --git a/tools/data_source/genomespace_file_browser.py b/tools/data_source/genomespace_file_browser.py
new file mode 100644
index 00000000000..a476a444b3f
--- /dev/null
+++ b/tools/data_source/genomespace_file_browser.py
@@ -0,0 +1,157 @@
+#Dan Blankenberg
+
+import optparse, os, urllib2, cookielib
+
+from galaxy import eggs
+import pkg_resources
+
+pkg_resources.require( "simplejson" )
+import simplejson
+
+CHUNK_SIZE = 2**20 #1mb
+
+DEFAULT_GALAXY_EXT = "data"
+
+#genomespace format identifier is the URL
+GENOMESPACE_FORMAT_IDENTIFIER_TO_GENOMESPACE_EXT = { 'http://www.genomespace.org/datamanager/dataformat/res/0.0.0': 'res', 
+                                               'http://www.genomespace.org/datamanager/dataformat/cbs/0.0.0': 'CBS', 
+                                               'http://www.genomespace.org/datamanager/dataformat/lowercasetxt/0.0.0': 'lowercasetxt', 
+                                               'http://www.genomespace.org/datamanager/dataformat/gff/0.0.0': 'GFF', 
+                                               'http://www.genomespace.org/datamanager/dataformat/reversedtxt/0.0.0': 'reversedtxt', 
+                                               'http://www.genomespace.org/datamanager/dataformat/gxp/0.0.0': 'gxp', 
+                                               'http://www.genomespace.org/datamanager/dataformat/unknown/0.0.0': 'unknown', 
+                                               'http://www.genomespace.org/datamanager/dataformat/gtf/0.0.0': 'GTF', 
+                                               'http://www.genomespace.org/datamanager/dataformat/cn/0.0.0': 'cn', 
+                                               'http://www.genomespace.org/datamanager/dataformat/gct/0.0.0': 'gct', 
+                                               'http://www.genomespace.org/datamanager/dataformat/nowhitespace/0.0.0': 'nowhitespace', 
+                                               'http://www.genomespace.org/datamanager/dataformat/gistic/0.0.0': 'GISTIC', 
+                                               'http://www.genomespace.org/datamanager/dataformat/rifles/0.0.0': 'rifles', 
+                                               'http://www.genomespace.org/datamanager/dataformat/bed/0.0.0': 'bed', 
+                                               'http://www.genomespace.org/datamanager/dataformat/txt/0.0.0': 'txt', 
+                                               'http://www.genomespace.org/datamanager/dataformat/uppercasetxt/0.0.0': 'uppercasetxt', 
+                                               'http://www.genomespace.org/datamanager/dataformat/xcn/0.0.0': 'xcn', 
+                                               'http://www.genomespace.org/datamanager/dataformat/gmt/0.0.0': 'gmt', 
+                                               'http://www.genomespace.org/datamanager/dataformat/genomicatab/0.0.0': 'genomicatab', 
+                                               'http://www.genomespace.org/datamanager/dataformat/lifes/0.0.0': 'lifes' }
+
+GENOMESPACE_EXT_TO_GALAXY_EXT = {'rifles': 'rifles', 
+                                 'lifes': 'lifes', 
+                                 'cn': 'cn', 
+                                 'GTF': 'gtf', 
+                                 'res': 'res', 
+                                 'xcn': 'xcn', 
+                                 'lowercasetxt': 'lowercasetxt', 
+                                 'bed': 'bed', 
+                                 'CBS': 'cbs', 
+                                 'genomicatab': 'genomicatab', 
+                                 'gxp': 'gxp', 
+                                 'reversedtxt': 'reversedtxt', 
+                                 'nowhitespace': 'nowhitespace', 
+                                 'unknown': 'unknown', 
+                                 'txt': 'txt', 'uppercasetxt': 
+                                 'uppercasetxt', 
+                                 'GISTIC': 'gistic', 
+                                 'GFF': 'gff', 
+                                 'gmt': 'gmt', 
+                                 'gct': 'gct'}
+
+'''
+https://dmdev.genomespace.org:8444/datamanager/dataformat/list
+from galaxy import eggs
+import pkg_resources
+pkg_resources.require( "simplejson" )
+import simplejson
+formats = simplejson.loads( '[{"name":"GISTIC","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/gistic\/0.0.0","fileExtension":"gistic"},{"name":"GFF","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/gff\/0.0.0","fileExtension":"seg"},{"name":"gct","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/gct\/0.0.0","fileExtension":"gct"},{"name":"lifes","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/lifes\/0.0.0","fileExtension":"lifes"},{"name":"GTF","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/gtf\/0.0.0","fileExtension":"gtf"},{"name":"rifles","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/rifles\/0.0.0","fileExtension":"rifles"},{"name":"CBS","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/cbs\/0.0.0","fileExtension":"cbs"},{"name":"unknown","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/unknown\/0.0.0"},{"name":"reversedtxt","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/reversedtxt\/0.0.0","fileExtension":"reversedtxt"},{"name":"res","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/res\/0.0.0","fileExtension":"res"},{"name":"cn","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/cn\/0.0.0","fileExtension":"cn"},{"name":"gmt","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/gmt\/0.0.0","fileExtension":"gmt"},{"name":"bed","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/bed\/0.0.0","fileExtension":"bed"},{"name":"gxp","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/gxp\/0.0.0","fileExtension":"gxp"},{"name":"uppercasetxt","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/uppercasetxt\/0.0.0","fileExtension":"uppertxt"},{"name":"lowercasetxt","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/lowercasetxt\/0.0.0","fileExtension":"lowertxt"},{"name":"genomicatab","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/genomicatab\/0.0.0","fileExtension":"tab"},{"name":"nowhitespace","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/nowhitespace\/0.0.0","fileExtension":"nowhitespace"},{"name":"xcn","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/xcn\/0.0.0","fileExtension":"xcn"},{"name":"txt","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/txt\/0.0.0","fileExtension":"txt"}]' )
+formats = [{"name":"GISTIC","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/gistic\/0.0.0","fileExtension":"gistic"},{"name":"GFF","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/gff\/0.0.0","fileExtension":"seg"},{"name":"gct","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/gct\/0.0.0","fileExtension":"gct"},{"name":"lifes","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/lifes\/0.0.0","fileExtension":"lifes"},{"name":"GTF","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/gtf\/0.0.0","fileExtension":"gtf"},{"name":"rifles","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/rifles\/0.0.0","fileExtension":"rifles"},{"name":"CBS","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/cbs\/0.0.0","fileExtension":"cbs"},{"name":"unknown","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/unknown\/0.0.0"},{"name":"reversedtxt","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/reversedtxt\/0.0.0","fileExtension":"reversedtxt"},{"name":"res","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/res\/0.0.0","fileExtension":"res"},{"name":"cn","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/cn\/0.0.0","fileExtension":"cn"},{"name":"gmt","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/gmt\/0.0.0","fileExtension":"gmt"},{"name":"bed","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/bed\/0.0.0","fileExtension":"bed"},{"name":"gxp","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/gxp\/0.0.0","fileExtension":"gxp"},{"name":"uppercasetxt","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/uppercasetxt\/0.0.0","fileExtension":"uppertxt"},{"name":"lowercasetxt","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/lowercasetxt\/0.0.0","fileExtension":"lowertxt"},{"name":"genomicatab","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/genomicatab\/0.0.0","fileExtension":"tab"},{"name":"nowhitespace","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/nowhitespace\/0.0.0","fileExtension":"nowhitespace"},{"name":"xcn","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/xcn\/0.0.0","fileExtension":"xcn"},{"name":"txt","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/txt\/0.0.0","fileExtension":"txt"}]
+GENOMESPACE_FORMAT_IDENTIFIER_TO_GALAXY_EXT = {}
+for format in formats:
+    GENOMESPACE_FORMAT_IDENTIFIER_TO_GALAXY_EXT[ format[ 'url' ] ] = format['name']
+
+print GENOMESPACE_FORMAT_IDENTIFIER_TO_GALAXY_EXT
+#do manual change to galaxy exts
+'''
+
+
+def chunk_write( source_stream, target_stream, source_method = "read", target_method="write" ):
+    source_method = getattr( source_stream, source_method )
+    target_method = getattr( target_stream, target_method )
+    while True:
+        chunk = source_method( CHUNK_SIZE )
+        if chunk:
+            target_method( chunk )
+        else:
+            break
+
+def get_cookie_opener( gs_username, gs_token  ):
+    """ Create a GenomeSpace cookie opener """
+    cj = cookielib.CookieJar()
+    for cookie_name, cookie_value in [ ( 'gs-token', gs_token ), ( 'gs-username', gs_username ) ]:
+        #create a super-cookie, valid for all domains
+        cookie = cookielib.Cookie(version=0, name=cookie_name, value=cookie_value, port=None, port_specified=False, domain='', domain_specified=False, domain_initial_dot=False, path='/', path_specified=True, secure=False, expires=None, discard=True, comment=None, comment_url=None, rest={'HttpOnly': None}, rfc2109=False )
+        cj.set_cookie( cookie )
+    cookie_opener = urllib2.build_opener( urllib2.HTTPCookieProcessor( cj ) )
+    return cookie_opener
+
+def get_galaxy_ext_from_genomespace_format_url( url_opener, file_format_url ):
+    ext = GENOMESPACE_FORMAT_IDENTIFIER_TO_GENOMESPACE_EXT.get( file_format_url, None )
+    if ext is not None:
+        ext = GENOMESPACE_EXT_TO_GALAXY_EXT.get( ext, None )
+    if ext is None:
+        #could check content type, etc here
+        ext = DEFAULT_GALAXY_EXT
+    return ext
+
+def download_from_genomespace_file_browser( json_parameter_file ):
+    json_params = simplejson.loads( open( json_parameter_file, 'r' ).read() )
+    datasource_params = json_params.get( 'param_dict' )
+    username = datasource_params.get( "gs-username", None )
+    token = datasource_params.get( "gs-token", None )
+    assert None not in [ username, token ], "Missing GenomeSpace username or token."
+    output_filename = datasource_params.get( "output", None )
+    dataset_id = json_params['output_data'][0]['dataset_id']
+    url_opener = get_cookie_opener( username, token )
+    file_count = 1
+    file_url_prefix = "fileUrl"
+    file_type_prefix = "fileFormat"
+    metadata_parameter_file = open( json_params['job_config']['TOOL_PROVIDED_JOB_METADATA_FILE'], 'wb' )
+    file_numbers = []
+    for name in datasource_params.keys():
+        if name.startswith( file_url_prefix ):
+            name = name[len( file_url_prefix ):]
+            file_numbers.append( int( name ) )
+    file_numbers.sort()
+    print 'file_numbers', file_numbers
+    #print 'datasource_params', datasource_params
+    for file_num in file_numbers:
+        url_key = "%s%i" % ( file_url_prefix, file_num )
+        download_url = datasource_params.get( url_key, None )
+        if download_url is None:
+            print 'wtf none', file_num
+            break
+        filetype_key = "%s%i" % ( file_type_prefix, file_num )
+        filetype_url = datasource_params.get( filetype_key, None )
+        galaxy_ext = get_galaxy_ext_from_genomespace_format_url( url_opener, filetype_url )
+        if output_filename is None:
+            output_filename = os.path.join( datasource_params['__new_file_path__'],  'primary_%i_output%i_visible_%s' % ( dataset_id, file_count, galaxy_ext ) )
+        else:
+            if dataset_id is not None:
+               metadata_parameter_file.write( "%s\n" % simplejson.dumps( dict( type = 'dataset',
+                                     dataset_id = dataset_id,
+                                     ext = galaxy_ext ) ) )
+        output_file = open( output_filename, 'wb' )
+        new_file_request = urllib2.Request( download_url )
+        new_file_request.get_method = lambda: 'GET'
+        target_download_url = url_opener.open( new_file_request )
+        chunk_write( target_download_url, output_file )
+        output_file.close()
+        output_filename = None #only have one filename available
+    metadata_parameter_file.close()
+    return True
+
+if __name__ == '__main__':
+    #Parse Command Line
+    parser = optparse.OptionParser()
+    parser.add_option( '-p', '--json_parameter_file', dest='json_parameter_file', action='store', type="string", default=None, help='json_parameter_file' )
+    (options, args) = parser.parse_args()
+    
+    download_from_genomespace_file_browser( options.json_parameter_file )
diff --git a/tools/data_source/genomespace_file_browser_dev.xml b/tools/data_source/genomespace_file_browser_dev.xml
new file mode 100644
index 00000000000..584f1603c66
--- /dev/null
+++ b/tools/data_source/genomespace_file_browser_dev.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0"?>
+<tool name="GenomeSpace import" id="genomespace_file_browser_dev" tool_type="data_source" add_galaxy_url="False" force_history_refresh="True" version="0.0.1">
+    <description>from file browser</description>
+    <command interpreter="python">genomespace_file_browser.py --json_parameter_file "${output}"</command>
+    <inputs action="https://dmdev.genomespace.org:8444/datamanager/defaultdirectory" check_values="False" method="post"> 
+        <display>go to GenomeSpace Data Manager </display>
+        <param name="appCallbackUrl" type="baseurl" value="/tool_runner?tool_id=genomespace_file_browser_dev&amp;runtool_btn=Execute" />
+        <param name="appName" type="hidden" value="Galaxy" />
+    </inputs>
+    <uihints minwidth="800"/>
+    <outputs>
+        <data name="output" format="auto" />
+    </outputs>
+    <options sanitize="False" refresh="True"/>
+</tool>

From 68f2b7656b6a9c8d7bcf2b5416f7d69af4aee7dd Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Thu, 6 Oct 2011 14:22:59 -0400
Subject: [PATCH 028/362] Some genomespace_file_browser tweaks.

---
 lib/galaxy/tools/__init__.py                  | 1 +
 tools/data_source/genomespace_file_browser.py | 7 ++-----
 2 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index db2368b02a5..784c306ad24 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -2028,6 +2028,7 @@ class DataSourceTool( Tool ):
             data_dict = dict( out_data_name = out_name,
                               ext = data.ext,
                               dataset_id = data.dataset.id,
+                              hda_id = data.id,
                               file_name = file_name,
                               extra_files_path = extra_files_path )
             
diff --git a/tools/data_source/genomespace_file_browser.py b/tools/data_source/genomespace_file_browser.py
index a476a444b3f..ba46af26117 100644
--- a/tools/data_source/genomespace_file_browser.py
+++ b/tools/data_source/genomespace_file_browser.py
@@ -109,8 +109,8 @@ def download_from_genomespace_file_browser( json_parameter_file ):
     assert None not in [ username, token ], "Missing GenomeSpace username or token."
     output_filename = datasource_params.get( "output", None )
     dataset_id = json_params['output_data'][0]['dataset_id']
+    hda_id = json_params['output_data'][0]['hda_id']
     url_opener = get_cookie_opener( username, token )
-    file_count = 1
     file_url_prefix = "fileUrl"
     file_type_prefix = "fileFormat"
     metadata_parameter_file = open( json_params['job_config']['TOOL_PROVIDED_JOB_METADATA_FILE'], 'wb' )
@@ -120,19 +120,16 @@ def download_from_genomespace_file_browser( json_parameter_file ):
             name = name[len( file_url_prefix ):]
             file_numbers.append( int( name ) )
     file_numbers.sort()
-    print 'file_numbers', file_numbers
-    #print 'datasource_params', datasource_params
     for file_num in file_numbers:
         url_key = "%s%i" % ( file_url_prefix, file_num )
         download_url = datasource_params.get( url_key, None )
         if download_url is None:
-            print 'wtf none', file_num
             break
         filetype_key = "%s%i" % ( file_type_prefix, file_num )
         filetype_url = datasource_params.get( filetype_key, None )
         galaxy_ext = get_galaxy_ext_from_genomespace_format_url( url_opener, filetype_url )
         if output_filename is None:
-            output_filename = os.path.join( datasource_params['__new_file_path__'],  'primary_%i_output%i_visible_%s' % ( dataset_id, file_count, galaxy_ext ) )
+            output_filename = os.path.join( datasource_params['__new_file_path__'],  'primary_%i_output%i_visible_%s' % ( hda_id, file_num, galaxy_ext ) )
         else:
             if dataset_id is not None:
                metadata_parameter_file.write( "%s\n" % simplejson.dumps( dict( type = 'dataset',

From e3003750a92cda27d8b239c41d12b16d98c15f23 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Thu, 6 Oct 2011 16:30:46 -0400
Subject: [PATCH 029/362] Add get info/parameter button to empty datasets in
 history item view.

---
 templates/root/history_common.mako | 1 +
 1 file changed, 1 insertion(+)

diff --git a/templates/root/history_common.mako b/templates/root/history_common.mako
index 245b9758881..6f4064e0cf1 100644
--- a/templates/root/history_common.mako
+++ b/templates/root/history_common.mako
@@ -263,6 +263,7 @@
                         <br />
                     %endfor
                 %elif for_editing:
+                    <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title="View Details" class="icon-button information tooltip"></a>
                     <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title="Run this job again" class="icon-button arrow-circle tooltip"></a>
                 %endif
     

From 3f82cfad20c722215cf498eeabc0db57e6f067f7 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Thu, 6 Oct 2011 17:10:34 -0400
Subject: [PATCH 030/362] UI enhancements for purging histories and deleted
 datasets in a history.

---
 lib/galaxy/web/controllers/history.py | 52 ++++++++++++++++++++++++---
 templates/history/grid.mako           |  8 +++++
 templates/root/index.mako             | 10 ++++++
 3 files changed, 66 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/web/controllers/history.py b/lib/galaxy/web/controllers/history.py
index aa7142d2c20..7e2f27f637b 100644
--- a/lib/galaxy/web/controllers/history.py
+++ b/lib/galaxy/web/controllers/history.py
@@ -88,7 +88,7 @@ class HistoryListGrid( grids.Grid ):
         grids.GridOperation( "Share or Publish", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ),
         grids.GridOperation( "Rename", condition=( lambda item: not item.deleted ), async_compatible=False  ),
         grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), async_compatible=True ),
-        grids.GridOperation( "Delete and remove datasets from disk", condition=( lambda item: not item.deleted ), async_compatible=True ),
+        grids.GridOperation( "Delete Permanently", confirm="History contents will be removed from disk, this cannot be undone.  Continue?", async_compatible=True ),
         grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ), async_compatible=True ),
     ]
     standard_filters = [
@@ -240,8 +240,8 @@ class HistoryController( BaseUIController, Sharable, UsesAnnotations, UsesItemRa
                         return trans.response.send_redirect( url_for( "/" ) )
                     else:
                         trans.template_context['refresh_frames'] = ['history']
-                elif operation in ( "delete", "delete and remove datasets from disk" ):
-                    if operation == "delete and remove datasets from disk":
+                elif operation in ( "delete", "delete permanently" ):
+                    if operation == "delete permanently":
                         status, message = self._list_delete( trans, histories, purge=True )
                     else:
                         status, message = self._list_delete( trans, histories )
@@ -303,6 +303,9 @@ class HistoryController( BaseUIController, Sharable, UsesAnnotations, UsesItemRa
                             trans.sa_session.add( hda.dataset )
                         except:
                             log.exception( 'Unable to purge dataset (%s) on purge of hda (%s):' % ( hda.dataset.id, hda.id ) )
+                history.purged = True
+                self.sa_session.add( history )
+                self.sa_session.flush()
         trans.sa_session.flush()
         if n_deleted:
             part = "Deleted %d %s" % ( n_deleted, iff( n_deleted != 1, "histories", "history" ) )
@@ -467,7 +470,30 @@ class HistoryController( BaseUIController, Sharable, UsesAnnotations, UsesItemRa
         return trans.fill_template( "history/display_structured.mako", items=items )
 
     @web.expose
-    def delete_current( self, trans ):
+    def purge_deleted_datasets( self, trans ):
+        count = 0
+        if trans.app.config.allow_user_dataset_purge:
+            for hda in trans.history.datasets:
+                if not hda.deleted or hda.purged:
+                    continue
+                if trans.user:
+                    trans.user.total_disk_usage -= hda.quota_amount( trans.user )
+                hda.purged = True
+                trans.sa_session.add( hda )
+                trans.log_event( "HDA id %s has been purged" % hda.id )
+                trans.sa_session.flush()
+                if hda.dataset.user_can_purge:
+                    try:
+                        hda.dataset.full_delete()
+                        trans.log_event( "Dataset id %s has been purged upon the the purge of HDA id %s" % ( hda.dataset.id, hda.id ) ) 
+                        trans.sa_session.add( hda.dataset )
+                    except:
+                        log.exception( 'Unable to purge dataset (%s) on purge of hda (%s):' % ( hda.dataset.id, hda.id ) )
+                count += 1
+        return trans.show_ok_message( "%d datasets have been deleted permanently" % count, refresh_frames=['history'] )
+
+    @web.expose
+    def delete_current( self, trans, purge=False ):
         """Delete just the active history -- this does not require a logged in user."""
         history = trans.get_history()
         if history.users_shared_with:
@@ -477,6 +503,24 @@ class HistoryController( BaseUIController, Sharable, UsesAnnotations, UsesItemRa
             trans.sa_session.add( history )
             trans.sa_session.flush()
             trans.log_event( "History id %d marked as deleted" % history.id )
+        if purge and trans.app.config.allow_user_dataset_purge:
+            for hda in history.datasets:
+                if trans.user:
+                    trans.user.total_disk_usage -= hda.quota_amount( trans.user )
+                hda.purged = True
+                trans.sa_session.add( hda )
+                trans.log_event( "HDA id %s has been purged" % hda.id )
+                trans.sa_session.flush()
+                if hda.dataset.user_can_purge:
+                    try:
+                        hda.dataset.full_delete()
+                        trans.log_event( "Dataset id %s has been purged upon the the purge of HDA id %s" % ( hda.dataset.id, hda.id ) )
+                        trans.sa_session.add( hda.dataset )
+                    except:
+                        log.exception( 'Unable to purge dataset (%s) on purge of hda (%s):' % ( hda.dataset.id, hda.id ) )
+            history.purged = True
+            self.sa_session.add( history )
+            self.sa_session.flush()
         # Regardless of whether it was previously deleted, we make a new history active
         trans.new_history()
         return trans.show_ok_message( "History deleted, a new history is active", refresh_frames=['history'] )
diff --git a/templates/history/grid.mako b/templates/history/grid.mako
index 0cca2140029..9171d735d90 100644
--- a/templates/history/grid.mako
+++ b/templates/history/grid.mako
@@ -15,3 +15,11 @@
         %endif
     </script>
 </%def>
+
+<%def name="grid_body( grid )">
+    ${self.make_grid( grid )}
+    <br/>
+    <div class="toolParamHelp" style="clear: both;">
+        Histories that have been deleted for more than a time period specified by the Galaxy administrator(s) may be permanently deleted.
+    </div>
+</%def>
diff --git a/templates/root/index.mako b/templates/root/index.mako
index 8cbd99b103a..e6f28509b79 100644
--- a/templates/root/index.mako
+++ b/templates/root/index.mako
@@ -43,6 +43,11 @@
             "Show Hidden Datasets": function() {
                 galaxy_history.location = "${h.url_for( controller='root', action='history', show_hidden=True)}";
             },
+            "Purge Deleted Datasets": function() {
+                if ( confirm( "Really delete all deleted datasets permanently? This cannot be undone." ) ) {
+                    galaxy_main.location = "${h.url_for( controller='history', action='purge_deleted_datasets' )}";
+                }
+            },
             "Show Structure": function() {
                 galaxy_main.location = "${h.url_for( controller='history', action='display_structured' )}";
             },
@@ -54,6 +59,11 @@
                     galaxy_main.location = "${h.url_for( controller='history', action='delete_current' )}";
                 }
             },
+            "Delete Permanently": function() {
+                if ( confirm( "Really delete the current history permanently? This cannot be undone." ) ) {
+                    galaxy_main.location = "${h.url_for( controller='history', action='delete_current', purge=True )}";
+                }
+            },
             "Other Actions": null,
             "Import from File": function() {
                 galaxy_main.location = "${h.url_for( controller='history', action='import_archive' )}";

From 05b79d357ac6ecbcbed4ad731a27152fb152b789 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Fri, 7 Oct 2011 11:47:00 -0400
Subject: [PATCH 031/362] Grid UI fixes: (a) make operation buttons work after
 refresh and (b) show message each time.

---
 templates/grid_base.mako | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/templates/grid_base.mako b/templates/grid_base.mako
index 7ea91674f0d..48668e61c4c 100644
--- a/templates/grid_base.mako
+++ b/templates/grid_base.mako
@@ -116,8 +116,8 @@
             async_ops['${operation.label.lower()}'] = "True";
         %endfor
         
-        // Initialize grid controls
-        function init_grid_controls() {
+        // Init operation buttons.
+        var init_operation_buttons = function() {
             // Initialize operation buttons.
             $('input[name=operation]:submit').each(function() {
                 $(this).click( function() {
@@ -132,6 +132,11 @@
                    do_operation(webapp, operation_name, item_ids); 
                 });
             });
+        };
+        
+        // Initialize grid controls
+        function init_grid_controls() {
+            init_operation_buttons();    
             
             // Initialize submit image elements.
             $('.submit-image').each( function() {
@@ -569,6 +574,7 @@
                     
                     // Init grid.
                     init_grid_elements();
+                    init_operation_buttons();
                     make_popup_menus();
                     
                     // Hide loading overlay.
@@ -577,7 +583,7 @@
                     // Show message if there is one.
                     var message = $.trim( parsed_response_text[2] );
                     if (message != "") {
-                        $('#grid-message').html( message );
+                        $('#grid-message').html( message ).show();
                         setTimeout( function() { $('#grid-message').hide(); }, 5000);
                     }
                 }

From 7efc30c01e4d94089c658318ea8a088490b9041b Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Fri, 7 Oct 2011 15:24:27 -0400
Subject: [PATCH 032/362] Bug fixes: (a) trackster: don't cache tile if
 undefined and (b) define init_operation_buttons differently to prevent
 ordering issue. Pack scripts.

---
 static/scripts/packed/trackster.js | 2 +-
 static/scripts/trackster.js        | 8 ++++----
 templates/grid_base.mako           | 2 +-
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/static/scripts/packed/trackster.js b/static/scripts/packed/trackster.js
index dbde8c480cb..07737a929f9 100644
--- a/static/scripts/packed/trackster.js
+++ b/static/scripts/packed/trackster.js
@@ -1 +1 @@
-var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var trackster_module=function(f,aa){var q=f("class").extend,t=f("slotting"),N=f("painters");var ag=function(ah,ai){this.document=ah;this.default_font=ai!==undefined?ai:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};q(ag.prototype,{load_pattern:function(ah,al){var ai=this.patterns,aj=this.dummy_context,ak=new Image();ak.src=image_path+al;ak.onload=function(){ai[ah]=aj.createPattern(ak,"repeat")}},get_pattern:function(ah){return this.patterns[ah]},new_canvas:function(){var ah=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ah)}ah.manager=this;return ah}});var o={};var m=function(ah,ai){o[ah.attr("id")]=ai};var n=function(ah,aj,al,ak){al=".group";var ai={};o[ah.attr("id")]=ak;ah.bind("drag",{handle:"."+aj,relative:true},function(au,av){var at=$(this);var ay=$(this).parent(),ap=ay.children(),ar=o[$(this).attr("id")],ao,an,aw,am,aq;an=$(this).parents(al);if(an.length!==0){aw=an.position().top;am=aw+an.outerHeight();if(av.offsetY<aw){$(this).insertBefore(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable_before(ar,ax);return}else{if(av.offsetY>am){$(this).insertAfter(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable(ar);return}}}an=null;for(aq=0;aq<ap.length;aq++){ao=$(ap.get(aq));aw=ao.position().top;am=aw+ao.outerHeight();if(ao.is(al)&&this!==ao.get(0)&&av.offsetY>=aw&&av.offsetY<=am){if(av.offsetY-aw<am-av.offsetY){ao.find(".content-div").prepend(this)}else{ao.find(".content-div").append(this)}if(ar.container){ar.container.remove_drawable(ar)}o[ao.attr("id")].add_drawable(ar);return}}for(aq=0;aq<ap.length;aq++){if(av.offsetY<$(ap.get(aq)).position().top){break}}if(aq===ap.length){if(this!==ap.get(aq-1)){ay.append(this);o[ay.attr("id")].move_drawable(ar,aq)}}else{if(this!==ap.get(aq)){$(this).insertBefore(ap.get(aq));o[ay.attr("id")].move_drawable(ar,(av.deltaY>0?aq-1:aq))}}}).bind("dragstart",function(){ai["border-top"]=ah.css("border-top");ai["border-bottom"]=ah.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ai)})};aa.moveable=n;var af=16,I=9,F=20,V=I+2,B=100,K=12000,T=200,E=5,w=10,M=5000,x=100,p="There was an error in indexing this dataset. ",L="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",u="Currently indexing... please wait",z="Tool cannot be rerun: ",a="Loading data...",ab="Ready for display",d=10,v=5,D=5;function y(ah){return Math.round(ah*1000)/1000}var c=function(ah){this.num_elements=ah;this.clear()};q(c.prototype,{get:function(ai){var ah=this.key_ary.indexOf(ai);if(ah!==-1){if(this.obj_cache[ai].stale){this.key_ary.splice(ah,1);delete this.obj_cache[ai]}else{this.move_key_to_end(ai,ah)}}return this.obj_cache[ai]},set:function(ai,aj){if(!this.obj_cache[ai]){if(this.key_ary.length>=this.num_elements){var ah=this.key_ary.shift();delete this.obj_cache[ah]}this.key_ary.push(ai)}this.obj_cache[ai]=aj;return aj},move_key_to_end:function(ai,ah){this.key_ary.splice(ah,1);this.key_ary.push(ai)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var U=function(ai,ah,aj){c.call(this,ai);this.track=ah;this.subset=(aj!==undefined?aj:true)};q(U.prototype,c.prototype,{load_data:function(aq,al,ao,ai,an){var ap=this.track.view.chrom,ak={chrom:ap,low:aq,high:al,mode:ao,resolution:ai,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ak,an);if(this.track.filters_manager){var ar=[];var ah=this.track.filters_manager.filters;for(var am=0;am<ah.length;am++){ar[ar.length]=ah[am].name}ak.filter_cols=JSON.stringify(ar)}var aj=this;return $.getJSON(this.track.data_url,ak,function(at){aj.set_data(aq,al,ao,at)})},get_data:function(ah,al,am,ai,ak){var aj=this.get_data_from_cache(ah,al,am);if(aj){return aj}aj=this.load_data(ah,al,am,ai,ak);this.set_data(ah,al,am,aj);return aj},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ap,ak,ao,aj,an,al){var aq=this.get_data_from_cache(ap,ak,ao);if(!aq){console.log("ERROR: no current data for: ",this.track,ap,ak,ao,aj,an);return}aq.stale=true;var ai=ap;if(al===this.DEEP_DATA_REQ){$.extend(an,{start_val:aq.data.length+1})}else{if(al===this.BROAD_DATA_REQ){ai=(aq.max_high?aq.max_high:aq.data[aq.data.length-1][2])+1}}var ah=this,am=this.load_data(ai,ak,ao,aj,an);new_data_available=$.Deferred();this.set_data(ap,ak,ao,new_data_available);$.when(am).then(function(ar){if(ar.data){ar.data=aq.data.concat(ar.data);if(ar.max_low){ar.max_low=aq.max_low}if(ar.message){ar.message=ar.message.replace(/[0-9]+/,ar.data.length)}}ah.set_data(ap,ak,ao,ar);new_data_available.resolve(ar)});return new_data_available},get_data_from_cache:function(ah,ai,aj){return this.get(this.gen_key(ah,ai,aj))},set_data:function(ai,aj,ak,ah){return this.set(this.gen_key(ai,aj,ak),ah)},gen_key:function(ah,aj,ak){var ai=ah+"_"+aj+"_"+ak;return ai},split_key:function(ah){return ah.split("_")}});var J=function(ai,ah,aj){U.call(this,ai,ah,aj)};q(J.prototype,U.prototype,c.prototype,{load_data:function(aj,ah,al,am,ai,ak){if(ai>1){return}return 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ah=0;ah<this.drawables.length;ah++){this.drawables[ah].init()}},_draw:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah]._draw()}},to_json:function(){var ai=[];for(var ah=0;ah<this.drawables.length;ah++){ai.push(this.drawables[ah].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ai}},add_drawable:function(ah){this.drawables.push(ah);ah.container=this},add_drawable_before:function(aj,ah){var ai=this.drawables.indexOf(ah);if(ai!=-1){this.drawables.splice(ai,0,aj);return true}return false},remove_drawable:function(ai){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);ai.container=null;return true}return false},move_drawable:function(ai,aj){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);this.drawables.splice(aj,0,ai);return true}return false}});var S=function(ak,ai,ah,aj){A.call(this,"DrawableGroup",ak,ai,ah,aj,"group-handle");if(!S.id_counter){S.id_counter=0}var al=S.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+al).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+al+"_content_div").appendTo(this.container_div);m(this.container_div,this);m(this.content_div,this);n(this.container_div,this.drag_handle_class,".group",this);this.make_name_popup_menu()};q(S.prototype,r.prototype,A.prototype,{make_name_popup_menu:function(){var ai=this;var ah={};ah["Edit configuration"]=function(){var al=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aj=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(am){if((am.keyCode||am.which)===27){al()}else{if((am.keyCode||am.which)===13){aj()}}};$(window).bind("keypress.check_enter_esc",ak);show_modal("Configure Group",ai.config.build_form(),{Cancel:al,OK:aj})};ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)}});var ae=function(ah,ak,aj,ai){A.call(this,"View");this.container=ah;this.chrom=null;this.vis_id=aj;this.dbkey=ai;this.title=ak;this.tracks=this.drawables;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ag(ah.get(0).ownerDocument);this.reset()};q(ae.prototype,A.prototype,{init:function(){var aj=this.container,ah=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aj);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;m(this.viewport_container,ah);this.intro_div=$("<div/>").addClass("intro");var ak=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ai=function(al){if(al.type==="focusout"||(al.keyCode||al.which)===13||(al.keyCode||al.which)===27){if((al.keyCode||al.which)!==27){ah.go_to($(this).val())}$(this).hide();$(this).val("");ah.location_span.show();ah.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ai).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ah.location_span.hide();ah.chrom_select.hide();ah.nav_input.val(ah.chrom+":"+ah.low+"-"+ah.high);ah.nav_input.css("display","inline-block");ah.nav_input.select();ah.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ah.zoom_out();ah.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.browser_content_div.click(function(al){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("<div />").css({height:ah.browser_content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,{content_div:this.top_labeltrack}));this.add_label_track(new ad(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new C(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(al,ai,an){if(!al||al==="None"){return}var ak=this;if(al==="previous"){ak.load_chroms({low:this.chrom_start_index-x});return}if(al==="next"){ak.load_chroms({low:this.chrom_start_index+x});return}var am=$.grep(ak.chrom_data,function(ap,aq){return ap.chrom===al})[0];if(am===undefined){ak.load_chroms({chrom:al},function(){ak.change_chrom(al,ai,an)});return}else{if(al!==ak.chrom){ak.chrom=al;ak.chrom_select.val(ak.chrom);ak.max_high=am.len-1;ak.reset();ak.request_redraw(true);for(var ao=0,ah=ak.tracks.length;ao<ah;ao++){var aj=ak.tracks[ao];if(aj.init){aj.init()}}}if(ai!==undefined&&an!==undefined){ak.low=Math.max(ai,0);ak.high=Math.min(an,ak.max_high)}ak.reset_overview();ak.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){A.prototype.add_drawable.call(this,ah);ah.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;ah.init();this.label_tracks.push(ah)},remove_drawable:function(aj,ai){A.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.tracks),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(E,Math.ceil(Math.log((this.high-this.low)/T)/Math.log(E)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){$.when(ah.get_overview_tile()).then(function(ai){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ai.canvas);view.overview_highlight.show().height(ai.canvas.height());view.overview_viewport.height(ai.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ah;ah.set_is_overview(true)});view.has_changes=true},reset_overview:function(){this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new P(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},al=this.track,aj=ai.tool_id+al.tool_region_and_parameters_str(ai.chrom,ai.low,ai.high),ah,am;if(al.container===view){var ak=new S(this.name,this.track.view,this.track.container);al.container.add_drawable(ak);al.container.remove_drawable(al);ak.add_drawable(al);al.container_div.appendTo(ak.content_div);ah=ak}else{ah=al.container}if(al instanceof e){am=new X(aj,view,ah,"hda");am.change_mode(al.mode);ah.add_drawable(am)}am.content_div.text("Starting job.");this.run(ai,am,function(an){am.dataset_id=an.dataset_id;am.content_div.text("Running job.");am.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(L)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(z+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var P=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){P.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var Y=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};q(Y.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=parseFloat(ah[this.index]);return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(ar,ay){this.track=ar;this.filters=[];for(var at=0;at<ay.length;at++){var au=ay[at],az=au.name,ah=au.type,ak=au.index,ax=au.tool_id,aw=au.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[at]=new Y(az,ak,ax,aw)}else{console.log("ERROR: unsupported filter: ",az,ah)}}var al=function(aA,aB,aC){aA.click(function(){var aD=aB.text();max=parseFloat(aC.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aC.slider("option","values")){input_size=2*input_size+1;multi_value=true}aB.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aD).appendTo(aB).focus().select().click(function(aE){aE.stopPropagation()}).blur(function(){$(this).remove();aB.text(aD)}).keyup(function(aI){if(aI.keyCode===27){$(this).trigger("blur")}else{if(aI.keyCode===13){var aG=aC.slider("option","min"),aE=aC.slider("option","max"),aH=function(aJ){return(isNaN(aJ)||aJ>aE||aJ<aG)},aF=$(this).val();if(!multi_value){aF=parseFloat(aF);if(aH(aF)){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}else{aF=aF.split("-");aF=[parseFloat(aF[0]),parseFloat(aF[1])];if(aH(aF[0])||aH(aF[1])){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}aC.slider((multi_value?"values":"value"),aF)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aA){aA.stopPropagation()}).click(function(aA){aA.stopPropagation()}).bind("dblclick",function(aA){aA.stopPropagation()}).bind("keydown",function(aA){aA.stopPropagation()});var av=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aD,aF){aF.container=$("<div/>").addClass("slider-row").appendTo(av);var aE=$("<div/>").addClass("elt-label").appendTo(aF.container);var aC=$("<span/>").addClass("slider-name").text(aF.name+"  ").appendTo(aE);var aB=$("<span/>");var aH=$("<span/>").addClass("slider-value").appendTo(aE).append("[").append(aB).append("]");var aA=$("<div/>").addClass("slider").appendTo(aF.container);aF.control_element=$("<div/>").attr("id",aF.name+"-filter-control").appendTo(aA);var aG=[0,0];aF.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aJ,aK){var aI=aK.values;aB.text(aI[0]+"-"+aI[1]);aF.low=aI[0];aF.high=aI[1];ap.track.request_draw(true,true)},change:function(aI,aJ){aF.control_element.slider("option","slide").call(aF.control_element,aI,aJ)}});aF.slider=aF.control_element;aF.slider_label=aB;al(aH,aB,aF.control_element);$("<div style='clear: both;'/>").appendTo(aF.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(av);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var aj=this;ao.click(function(){aj.run_on_dataset()})}var aq=$("<div/>").addClass("display-controls").appendTo(this.parent_div),an=$("<span/>").addClass("elt-label").text("Transparency:").appendTo(aq),ai=$("<select/>").attr("name","alpha_dropdown").appendTo(aq);this.alpha_filter=null;$("<option/>").attr("value",-1).text("== None ==").appendTo(ai);for(var at=0;at<this.filters.length;at++){$("<option/>").attr("value",at).text(this.filters[at].name).appendTo(ai)}ai.change(function(){$(this).children("option:selected").each(function(){var aA=parseInt($(this).val());ap.alpha_filter=(aA>=0?ap.filters[aA]:null);ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var Q=function(ai,ah){N.AlphaGenerator.call(this,ah);this.filter=ai};Q.prototype.gen_alpha=function(ah){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_alpha}return((parseFloat(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var H=function(ah){this.track=ah.track;this.params=ah.params;this.values={};this.restore_values((ah.saved_values?ah.saved_values:{}));this.onchange=ah.onchange};q(H.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(aj,ai,ah,ak){this.index=aj;this.low=aj*T*ai;this.high=(aj+1)*T*ai;this.resolution=ai;this.canvas=$("<div class='track-tile'/>").append(ah);this.data=ak;this.stale=false};var l=function(aj,ai,ah,ak,al){b.call(this,aj,ai,ah,ak);this.max_val=al};var R=function(ak,aj,ai,an,am,ah){b.call(this,ak,aj,ai,an);this.message=am;this.feature_mapper=ah;var al=this;$(this.canvas).mousemove(function(ap){var ao=al.feature_mapper.get_feature_data(ap.offsetX,ap.offsetY)})};var j=function(ak,ai,ah,aj,al,am){r.call(this,ak,ai,ah,{},"draghandle");this.data_url=(al?al:default_data_url);this.data_url_extra_params={};this.data_query_wait=(am?am:M);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.container_div=$("<div />").addClass("track").attr("id","track_"+j.id_counter++).css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof C){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Z){return"ReadTrack"}else{if(this instanceof X){return"ToolDataFeatureTrack"}else{if(this instanceof W){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var ak=ah.view.tracks.indexOf(ah);var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(L)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(G)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.make_name_popup_menu()}ah.content_div.text(ab);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}})},predraw_init:function(){},});var O=function(ao,am){var ai=this,ap=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=new ac(this,(ao!==undefined?ao:{}));this.filters_available=false;this.filters_visible=false;this.tool=(am!==undefined&&obj_length(am)>0?new s(this,am):undefined);this.is_overview=false;if(ai.hidden){return}if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(ai.display_modes!==undefined){if(ai.mode_div===undefined){ai.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ai.header_div);var aj=(ai.config&&ai.config.values.mode?ai.config.values.mode:ai.display_modes[0]);ai.mode=aj;ai.mode_div.text(aj);var ah={};for(var ak=0,an=ai.display_modes.length;ak<an;ak++){var al=ai.display_modes[ak];ah[al]=function(aq){return function(){ai.change_mode(aq)}}(al)}make_popupmenu(ai.mode_div,ah)}else{ai.mode_div.hide()}}this.make_name_popup_menu()};q(O.prototype,r.prototype,j.prototype,{to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw();return ah},make_name_popup_menu:function(){var ai=this;var ah={};ah[(this.is_overview?"Hide overview":"Set as overview")]=function(){if(ai.is_overview){ai.view.reset_overview()}else{ai.view.set_overview(ai)}};ah["Edit configuration"]=function(){var am=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},al=function(an){if((an.keyCode||an.which)===27){am()}else{if((an.keyCode||an.which)===13){ak()}}};$(window).bind("keypress.check_enter_esc",al);show_modal("Configure Track",ai.config.build_form(),{Cancel:am,OK:ak})};if(ai.filters_available>0){var aj=(ai.filters_div.is(":visible")?"Hide filters":"Show filters");ah[aj]=function(){ai.filters_visible=(ai.filters_div.is(":visible"));if(ai.filters_visible){ai.filters_manager.reset_filters()}ai.filters_div.toggle();ai.make_name_popup_menu()}}if(ai.tool){var aj=(ai.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");ah[aj]=function(){if(!ai.dynamic_tool_div.is(":visible")){ai.set_name(ai.name+ai.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ai.revert_name()}ai.dynamic_tool_div.toggle();ai.make_name_popup_menu()}}ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)},set_is_overview:function(ah){this.is_overview=ah;this.make_name_popup_menu()},get_overview_tile:function(){var ah=this;view=ah.view,resolution=Math.pow(E,Math.ceil(Math.log((view.max_high-view.max_low)/T)/Math.log(E))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ah.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ah.data_url_extra_params)).then(function(ai){var ak=ah._gen_tile_cache_key(view_width,w_scale,0),am=ah.tile_cache.get(ak);if(!am){am=ah.draw_tile(ai,"Auto",resolution,0,w_scale);ah.tile_cache.set(ak,am)}var ap=$(am.canvas.find("canvas")),al=ap.clone(),ao=ap.get(0).getContext("2d"),aj=al.get(0).getContext("2d"),an=ao.getImageData(0,0,ao.canvas.width,ao.canvas.height);aj.putImageData(an,-ah.left_offset,(am.data.dataset_type==="summary_tree"?V:0));new_tile=new b(-1,resolution,al);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof C)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/T);var ap=true;var at=[];var ah=0;while((ai*T*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",F)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*T*an,ax=ap+T*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);al.tile_cache.set(at,aq);if(aq!==undefined){al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw()});return null},show_tile:function(ao,aq,ar){var aj=this,ai=ao.canvas,an=ai;if(ao.message){var at=$("<div/>"),ap=$("<div/>").addClass("tile-message").text(ao.message).css({height:F-1,width:ao.canvas.width}).appendTo(at),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ap),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ap);at.append(ai);an=at;al.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()});ah.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()})}var am=this.view.high-this.view.low,ak=(ao.low-this.view.low)*ar;if(this.left_offset){ak-=this.left_offset}an.css({position:"absolute",top:0,left:ak,height:""});aq.append(an);aj.max_height=Math.max(aj.max_height,an.height());aj.content_div.css("height",aj.max_height+"px");aq.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*T*ai,al=T*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ai,ah){this.hidden=true;j.call(this,"label",ai,ah,{});this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{init:function(){this.enabled=true},_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var C=function(ah){this.hidden=true;j.call(this,"reference",ah,{content_div:ah.top_labeltrack},{});O.call(this);ah.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ah.dbkey};this.data_manager=new J(D,this,false);this.tile_cache=new c(v)};q(C.prototype,r.prototype,O.prototype,{init:function(){this.enabled=true},draw_tile:function(ar,an,am,ai,at){var al=this,aj=T*am;if(at>this.view.canvas_manager.char_width_px){if(ar===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(am,ak,aj,an,ah,al){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,am,ak,aj,al);O.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=an;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new U(D,this);this.tile_cache=new c(v);this.left_offset=0;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:am},{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:al,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.track_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.track_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};q(k.prototype,r.prototype,O.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this,ai=ah.view.tracks.indexOf(ah);ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(aj){ah.container_div.addClass("line-track");var al=aj.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=al.min;ah.prefs.max_value=al.max;$("#track_"+ai+"_minval").val(ah.prefs.min_value);$("#track_"+ai+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=al.total_frequency;ah.container_div.find(".yaxislabel").remove();var am=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ai+"_minval").text(y(ah.prefs.min_value));var ak=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ai+"_maxval").text(y(ah.prefs.max_value));ak.css({position:"absolute",top:"24px",left:"10px"});ak.prependTo(ah.container_div);am.css({position:"absolute",bottom:"2px",left:"10px"});am.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new N.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(aj,al,ak,au.data)}});var e=function(ah,an,ai,am,ap,ao,ak,al){var aj=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];j.call(this,ah,an,ai,ao);O.call(this,ak,al);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){aj.set_name(aj.prefs.name);aj.tile_cache.clear();aj.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=am;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new U(20,this);this.left_offset=200;this.painter=N.LinkedFeaturePainter};q(e.prototype,r.prototype,O.prototype,{postdraw_actions:function(ax,ah,ay,aw){O.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.make_name_popup_menu()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",B,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aE,aI,ar,ak){var aB=this,am=aB._get_tile_bounds(aI,aE),aL=am[0],ai=am[1],ay=ai-aL,aC=Math.ceil(ay*ar),aP=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"){az="no_detail"}else{var aO=aw.data;if(this.view.high-this.view.low>K){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aC+al;aj.height=an+V;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aL,ai,200);if(aw.max){at.max=aw.max}aw=at}var aM=new N.SummaryTreePainter(aw,aL,ai,this.prefs);var aD=aj.getContext("2d");aD.translate(al,V);aM.draw(aD,aC,an);return new l(aI,aE,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aF=0,aH=aw.data.length;aF<aH;aF++){var ao=aw.data[aF];var aG=false;var av;for(var aK=0,aN=au.length;aK<aN;aK++){av=au[aK];av.update_attrs(ao);if(!av.keep(ao)){aG=true;break}}if(!aG){aq.push(ao)}}}var aA=(this.filters_manager.alpha_filter?new Q(this.filters_manager.alpha_filter):null);var aM=new (this.painter)(aq,aL,ai,this.prefs,az,aA,ak);var an=Math.max(af,aM.get_required_height(ap));var aj=this.view.canvas_manager.new_canvas();var aJ=null;aj.width=aC+al;aj.height=an;var aD=aj.getContext("2d");aD.fillStyle=this.prefs.block_color;aD.font=aD.canvas.manager.default_font;aD.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aw.data){aD.translate(al,0);aJ=aM.draw(aD,aC,an,ax);aJ.translation=-al}return new R(aI,aE,aj,aw.data,aw.message,aJ)}});var W=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.painter=N.VariantPainter};q(W.prototype,r.prototype,O.prototype,e.prototype);var Z=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ak,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=N.ReadPainter;this.make_name_popup_menu()};q(Z.prototype,r.prototype,O.prototype,e.prototype);var X=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am,{});this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};q(X.prototype,r.prototype,O.prototype,e.prototype,{predraw_init:function(){var ai=this;var ah=function(){if(ai.data_manager.size()===0){setTimeout(ah,300)}else{ai.data_url=default_data_url;ai.data_query_wait=M;ai.dataset_state_url=converted_datasets_state_url;$.getJSON(ai.dataset_state_url,{dataset_id:ai.dataset_id,hda_ldda:ai.hda_ldda},function(aj){})}};ah()}});aa.View=ae;aa.DrawableGroup=S;aa.LineTrack=k;aa.FeatureTrack=e;aa.ReadTrack=Z};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(k,y){var v=k("class").extend;var q=function(J,B,H,A,G,E){if(E===undefined){E=4}var D=A-B;var C=G-H;var F=Math.floor(Math.sqrt(D*D+C*C)/E);var K=D/F;var I=C/F;var z;for(z=0;z<F;z++,B+=K,H+=I){if(z%2!==0){continue}J.fillRect(B,H,E,1)}};var r=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var g=function(z){this.default_alpha=(z?z:1)};g.prototype.gen_alpha=function(z){return this.default_alpha};var n=function(B,D,z,A,C){this.data=B;this.view_start=D;this.view_end=z;this.prefs=v({},this.default_prefs,A);this.mode=C};n.prototype.default_prefs={};var w=function(B,D,z,A,C){n.call(this,B,D,z,A,C)};w.prototype.default_prefs={show_counts:false};w.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var c=function(z,D,F,G,B){n.call(this,z,D,F,G,B);if(this.prefs.min_value===undefined){var H=Infinity;for(var A=0,C=this.data.length;A<C;A++){H=Math.min(H,this.data[A][1])}this.prefs.min_value=H}if(this.prefs.max_value===undefined){var E=-Infinity;for(var A=0,C=this.data.length;A<C;A++){E=Math.max(E,this.data[A][1])}this.prefs.max_value=E}};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var o=function(z){this.feature_positions={};this.slot_height=z;this.translation=0};o.prototype.map_feature_data=function(A,C,z,B){if(!this.feature_positions[C]){this.feature_positions[C]=[]}this.feature_positions[C].push({data:A,x_start:z,x_end:B})};o.prototype.get_feature_data=function(z,D){var C=Math.floor(D/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var p=function(C,E,z,B,D,A){n.call(this,C,E,z,B,D);this.alpha_generator=(A?A:new g())};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};v(p.prototype,{get_required_height:function(A){var z=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){z=A*y_scale}return z+Math.max(Math.round(y_scale/2),5)},draw:function(L,J,H,G){var R=this.data,E=this.view_start,N=this.view_end;L.save();L.fillStyle=this.prefs.block_color;L.textAlign="right";var I=this.view_end-this.view_start,F=J/I,M=this.get_row_height(),Q=new o(M),C;for(var O=0,P=R.length;O<P;O++){var B=R[O],D=B[0],K=B[1],z=B[2],A=(G&&G[D]!==undefined?G[D]:null);if((K<N&&z>E)&&(this.mode=="Dense"||A!==null)){C=this.draw_element(L,this.mode,B,A,E,N,F,M,J);Q.map_feature_data(B,A,C[0],C[1])}}L.restore();return Q},draw_element:function(F,B,H,D,C,E,G,A,z){console.log("WARNING: Unimplemented function.");return[0,0]}});var d=10,j=3,m=5,x=10,f=1,t=3,e=3,a=9,l=2,h="#ccc";var s=function(C,E,z,B,D,A){p.call(this,C,E,z,B,D,A)};v(s.prototype,p.prototype,{get_row_height:function(){var A=this.mode,z;if(A==="Dense"){z=d}else{if(A==="no_detail"){z=j}else{if(A==="Squish"){z=m}else{z=x}}}return z},draw_element:function(L,E,T,G,N,ae,ai,ak,z){var Q=T[0],ag=T[1],Y=T[2],O=T[3],Z=Math.floor(Math.max(0,(ag-N)*ai)),M=Math.ceil(Math.min(z,Math.max(0,(Y-N)*ai))),X=Z,aj=M,W=(E==="Dense"?0:(0+G))*ak,K,ac,P=null,al=null,C=this.prefs.block_color,ab=this.prefs.label_color;L.globalAlpha=this.alpha_generator.gen_alpha(T);if(E=="Dense"){G=1}if(E==="no_detail"){L.fillStyle=C;L.fillRect(Z,W+5,M-Z,f)}else{var J=T[4],V=T[5],aa=T[6],D=T[7];if(V&&aa){P=Math.floor(Math.max(0,(V-N)*ai));al=Math.ceil(Math.min(z,Math.max(0,(aa-N)*ai)))}var ah,R;if(E==="Squish"||E==="Dense"){ah=1;R=e}else{ah=5;R=a}if(!D){if(T.strand){if(T.strand==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand_inv")}else{if(T.strand==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand_inv")}}}else{L.fillStyle=C}L.fillRect(Z,W,M-Z,R)}else{var I,S;if(E==="Squish"||E==="Dense"){L.fillStyle=h;I=W+Math.floor(e/2)+1;S=1}else{if(J){var I=W;var S=R;if(J==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand")}else{if(J==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand")}}}else{L.fillStyle=h;I+=(e/2)+1;S=1}}L.fillRect(Z,I,M-Z,S);for(var af=0,B=D.length;af<B;af++){var F=D[af],A=Math.floor(Math.max(0,(F[0]-N)*ai)),U=Math.ceil(Math.min(z,Math.max((F[1]-N)*ai)));if(A>U){continue}L.fillStyle=C;L.fillRect(A,W+(R-ah)/2+1,U-A,ah);if(P!==undefined&&aa>V&&!(A>al||U<P)){var ad=Math.max(A,P),H=Math.min(U,al);L.fillRect(ad,W+1,H-ad,R);if(D.length==1&&E=="Pack"){if(J==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand_inv")}else{if(J==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand_inv")}}if(ad+14<H){ad+=2;H-=2}L.fillRect(ad,W+1,H-ad,R)}}}}if(E==="Pack"&&ag>N){L.fillStyle=ab;if(N===0&&Z-L.measureText(O).width<0){L.textAlign="left";L.fillText(O,M+l,W+8);aj+=L.measureText(O).width+l}else{L.textAlign="right";L.fillText(O,Z-l,W+8);X-=L.measureText(O).width+l}}}L.globalAlpha=1;return[X,aj]}});var b=function(C,E,z,B,D,A){p.call(this,C,E,z,B,D,A)};v(b.prototype,p.prototype,{draw_element:function(S,N,H,D,V,B,K,T,Q){var H=data[i],J=H[0],R=H[1],C=H[2],M=H[3],F=Math.floor(Math.max(0,(R-V)*K)),I=Math.ceil(Math.min(Q,Math.max(0,(C-V)*K))),E=(N==="Dense"?0:(0+D))*T,z,W,A=null,L=null;if(no_label){S.fillStyle=block_color;S.fillRect(F+left_offset,E+5,I-F,1)}else{var U=H[4],P=H[5],G=H[6];z=9;W=1;S.fillRect(F+left_offset,E,I-F,z);if(N!=="Dense"&&M!==undefined&&R>V){S.fillStyle=label_color;if(V===0&&F-S.measureText(M).width<0){S.textAlign="left";S.fillText(M,I+2+left_offset,E+8)}else{S.textAlign="right";S.fillText(M,F-2+left_offset,E+8)}S.fillStyle=block_color}var O=U+" / "+P;if(R>V&&S.measureText(O).width<(I-F)){S.fillStyle="white";S.textAlign="center";S.fillText(O,left_offset+F+(I-F)/2,E+8);S.fillStyle=block_color}}return[F,I]}});var u=function(D,F,z,C,E,A,B){p.call(this,D,F,z,C,E,A);this.ref_seq=B};u.prototype.default_prefs=v({},p.prototype.default_prefs,{show_insertions:false});v(u.prototype,p.prototype,{get_row_height:function(){var z,A=this.mode;if(A==="Dense"){z=d}else{if(A==="Squish"){z=m}else{z=x;if(this.prefs.show_insertions){z*=2}}}return z},draw_read:function(V,Q,M,aa,B,U,J,G,F){V.textAlign="center";var T=this,A=[aa,B],P=0,W=0,S=0;ref_seq=this.ref_seq,char_width_px=V.canvas.manager.char_width_px;var af=[];if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){S=Math.round(M/2)}if(!J){J=[[0,G.length]]}for(var N=0,Y=J.length;N<Y;N++){var K=J[N],C="MIDNSHP=X"[K[0]],O=K[1];if(C==="H"||C==="S"){P-=O}var H=U+P,ae=Math.floor(Math.max(0,(H-aa)*M)),I=Math.floor(Math.max(0,(H+O-aa)*M));if(ae===I){I+=1}switch(C){case"H":break;case"S":case"M":case"=":if(is_overlap([H,H+O],A)){var R=G.slice(W,W+O);if(S>0){V.fillStyle=this.prefs.block_color;V.fillRect(ae-S,F+1,I-ae,9);V.fillStyle=h;for(var ac=0,z=R.length;ac<z;ac++){if(this.prefs.show_differences&&ref_seq){var L=ref_seq[H-aa+ac];if(!L||L.toLowerCase()===R[ac].toLowerCase()){continue}}if(H+ac>=aa&&H+ac<=B){var ad=Math.floor(Math.max(0,(H+ac-aa)*M));V.fillText(R[ac],ad,F+9)}}}else{V.fillStyle=this.prefs.block_color;V.fillRect(ae,F+4,I-ae,e)}}W+=O;P+=O;break;case"N":V.fillStyle=h;V.fillRect(ae-S,F+5,I-ae,1);P+=O;break;case"D":V.fillStyle="red";V.fillRect(ae-S,F+4,I-ae,3);P+=O;break;case"P":break;case"I":var Z=ae-S;if(is_overlap([H,H+O],A)){var R=G.slice(W,W+O);if(this.prefs.show_insertions){var E=ae-(I-ae)/2;if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){V.fillStyle="yellow";V.fillRect(E-S,F-9,I-ae,9);af[af.length]={type:"triangle",data:[Z,F+4,5]};V.fillStyle=h;switch(seq_tile_overlap){case (OVERLAP_START):R=R.slice(aa-H);break;case (OVERLAP_END):R=R.slice(0,H-B);break;case (CONTAINED_BY):break;case (CONTAINS):R=R.slice(aa-H,H-B);break}for(var ac=0,z=R.length;ac<z;ac++){var ad=Math.floor(Math.max(0,(H+ac-aa)*M));V.fillText(R[ac],ad-(I-ae)/2,F)}}else{V.fillStyle="yellow";V.fillRect(E,F+(this.mode!=="Dense"?2:5),I-ae,(Q!=="Dense"?e:t))}}else{if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){af[af.length]={type:"text",data:[R.length,Z,F+9]}}else{}}}W+=O;break;case"X":W+=O;break}}V.fillStyle="yellow";var ab,D,ag;for(var X=0;X<af.length;X++){ab=af[X];D=ab.type;ag=ab.data;if(D==="text"){V.save();V.font="bold "+V.font;V.fillText(ag[0],ag[1],ag[2]);V.restore()}else{if(D=="triangle"){r(V,ag[0],ag[1],ag[2])}}}},draw_element:function(S,N,F,C,V,A,J,T,Q){var I=F[0],R=F[1],B=F[2],K=F[3],E=Math.floor(Math.max(0,(R-V)*J)),G=Math.ceil(Math.min(Q,Math.max(0,(B-V)*J))),D=(N==="Dense"?0:(0+C))*T,W=this.prefs.block_color,H=this.prefs.label_color,P=0;if((N==="Pack"||this.mode==="Auto")&&J>S.canvas.manager.char_width_px){var P=Math.round(J/2)}S.fillStyle=W;if(F[5] instanceof Array){var O=Math.floor(Math.max(0,(F[4][0]-V)*J)),M=Math.ceil(Math.min(Q,Math.max(0,(F[4][1]-V)*J))),L=Math.floor(Math.max(0,(F[5][0]-V)*J)),z=Math.ceil(Math.min(Q,Math.max(0,(F[5][1]-V)*J)));if(F[4][1]>=V&&F[4][0]<=A&&F[4][2]){this.draw_read(S,N,J,V,A,F[4][0],F[4][2],F[4][3],D)}if(F[5][1]>=V&&F[5][0]<=A&&F[5][2]){this.draw_read(S,N,J,V,A,F[5][0],F[5][2],F[5][3],D)}if(L>M){S.fillStyle=h;q(S,M-P,D+5,L-P,D+5)}}else{S.fillStyle=W;this.draw_read(S,N,J,V,A,R,F[4],F[5],D)}if(N==="Pack"&&R>V){S.fillStyle=this.prefs.label_color;var U=1;if(U===0&&E-S.measureText(K).width<0){S.textAlign="left";S.fillText(K,G+l-P,D+8)}else{S.textAlign="right";S.fillText(K,E-l-P,D+8)}S.fillStyle=W}return[0,0]}});y.AlphaGenerator=g;y.SummaryTreePainter=w;y.LinePainter=c;y.LinkedFeaturePainter=s;y.ReadPainter=u;y.VariantPainter=b};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window);
\ No newline at end of file
+var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var trackster_module=function(f,aa){var q=f("class").extend,t=f("slotting"),N=f("painters");var ag=function(ah,ai){this.document=ah;this.default_font=ai!==undefined?ai:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};q(ag.prototype,{load_pattern:function(ah,al){var ai=this.patterns,aj=this.dummy_context,ak=new Image();ak.src=image_path+al;ak.onload=function(){ai[ah]=aj.createPattern(ak,"repeat")}},get_pattern:function(ah){return this.patterns[ah]},new_canvas:function(){var ah=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ah)}ah.manager=this;return ah}});var o={};var m=function(ah,ai){o[ah.attr("id")]=ai};var n=function(ah,aj,al,ak){al=".group";var ai={};o[ah.attr("id")]=ak;ah.bind("drag",{handle:"."+aj,relative:true},function(au,av){var at=$(this);var ay=$(this).parent(),ap=ay.children(),ar=o[$(this).attr("id")],ao,an,aw,am,aq;an=$(this).parents(al);if(an.length!==0){aw=an.position().top;am=aw+an.outerHeight();if(av.offsetY<aw){$(this).insertBefore(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable_before(ar,ax);return}else{if(av.offsetY>am){$(this).insertAfter(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable(ar);return}}}an=null;for(aq=0;aq<ap.length;aq++){ao=$(ap.get(aq));aw=ao.position().top;am=aw+ao.outerHeight();if(ao.is(al)&&this!==ao.get(0)&&av.offsetY>=aw&&av.offsetY<=am){if(av.offsetY-aw<am-av.offsetY){ao.find(".content-div").prepend(this)}else{ao.find(".content-div").append(this)}if(ar.container){ar.container.remove_drawable(ar)}o[ao.attr("id")].add_drawable(ar);return}}for(aq=0;aq<ap.length;aq++){if(av.offsetY<$(ap.get(aq)).position().top){break}}if(aq===ap.length){if(this!==ap.get(aq-1)){ay.append(this);o[ay.attr("id")].move_drawable(ar,aq)}}else{if(this!==ap.get(aq)){$(this).insertBefore(ap.get(aq));o[ay.attr("id")].move_drawable(ar,(av.deltaY>0?aq-1:aq))}}}).bind("dragstart",function(){ai["border-top"]=ah.css("border-top");ai["border-bottom"]=ah.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ai)})};aa.moveable=n;var af=16,I=9,F=20,V=I+2,B=100,K=12000,T=200,E=5,w=10,M=5000,x=100,p="There was an error in indexing this dataset. ",L="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",u="Currently indexing... please wait",z="Tool cannot be rerun: ",a="Loading data...",ab="Ready for display",d=10,v=5,D=5;function y(ah){return Math.round(ah*1000)/1000}var c=function(ah){this.num_elements=ah;this.clear()};q(c.prototype,{get:function(ai){var ah=this.key_ary.indexOf(ai);if(ah!==-1){if(this.obj_cache[ai].stale){this.key_ary.splice(ah,1);delete this.obj_cache[ai]}else{this.move_key_to_end(ai,ah)}}return this.obj_cache[ai]},set:function(ai,aj){if(!this.obj_cache[ai]){if(this.key_ary.length>=this.num_elements){var ah=this.key_ary.shift();delete this.obj_cache[ah]}this.key_ary.push(ai)}this.obj_cache[ai]=aj;return aj},move_key_to_end:function(ai,ah){this.key_ary.splice(ah,1);this.key_ary.push(ai)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var U=function(ai,ah,aj){c.call(this,ai);this.track=ah;this.subset=(aj!==undefined?aj:true)};q(U.prototype,c.prototype,{load_data:function(aq,al,ao,ai,an){var ap=this.track.view.chrom,ak={chrom:ap,low:aq,high:al,mode:ao,resolution:ai,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ak,an);if(this.track.filters_manager){var ar=[];var ah=this.track.filters_manager.filters;for(var am=0;am<ah.length;am++){ar[ar.length]=ah[am].name}ak.filter_cols=JSON.stringify(ar)}var aj=this;return $.getJSON(this.track.data_url,ak,function(at){aj.set_data(aq,al,ao,at)})},get_data:function(ah,al,am,ai,ak){var aj=this.get_data_from_cache(ah,al,am);if(aj){return aj}aj=this.load_data(ah,al,am,ai,ak);this.set_data(ah,al,am,aj);return aj},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ap,ak,ao,aj,an,al){var aq=this.get_data_from_cache(ap,ak,ao);if(!aq){console.log("ERROR: no current data for: ",this.track,ap,ak,ao,aj,an);return}aq.stale=true;var ai=ap;if(al===this.DEEP_DATA_REQ){$.extend(an,{start_val:aq.data.length+1})}else{if(al===this.BROAD_DATA_REQ){ai=(aq.max_high?aq.max_high:aq.data[aq.data.length-1][2])+1}}var ah=this,am=this.load_data(ai,ak,ao,aj,an);new_data_available=$.Deferred();this.set_data(ap,ak,ao,new_data_available);$.when(am).then(function(ar){if(ar.data){ar.data=aq.data.concat(ar.data);if(ar.max_low){ar.max_low=aq.max_low}if(ar.message){ar.message=ar.message.replace(/[0-9]+/,ar.data.length)}}ah.set_data(ap,ak,ao,ar);new_data_available.resolve(ar)});return new_data_available},get_data_from_cache:function(ah,ai,aj){return this.get(this.gen_key(ah,ai,aj))},set_data:function(ai,aj,ak,ah){return this.set(this.gen_key(ai,aj,ak),ah)},gen_key:function(ah,aj,ak){var ai=ah+"_"+aj+"_"+ak;return ai},split_key:function(ah){return ah.split("_")}});var J=function(ai,ah,aj){U.call(this,ai,ah,aj)};q(J.prototype,U.prototype,c.prototype,{load_data:function(aj,ah,al,am,ai,ak){if(ai>1){return}return U.prototype.load_data.call(this,aj,ah,al,am,ai,ak)}});var r=function(ak,ai,ah,aj,al){this.name=ak;this.view=ai;this.container=ah;this.drag_handle_class=al;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak}],saved_values:aj,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values};q(r.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},make_name_popup_menu:function(){},set_name:function(ah){this.old_name=this.name;this.name=ah;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var A=function(al,ak,ai,ah,aj,am){r.call(this,ak,ai,ah,aj,am);this.obj_type=al;this.drawables=[]};q(A.prototype,r.prototype,{init:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah].init()}},_draw:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah]._draw()}},to_json:function(){var ai=[];for(var ah=0;ah<this.drawables.length;ah++){ai.push(this.drawables[ah].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ai}},add_drawable:function(ah){this.drawables.push(ah);ah.container=this},add_drawable_before:function(aj,ah){var ai=this.drawables.indexOf(ah);if(ai!=-1){this.drawables.splice(ai,0,aj);return true}return false},remove_drawable:function(ai){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);ai.container=null;return true}return false},move_drawable:function(ai,aj){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);this.drawables.splice(aj,0,ai);return true}return false}});var S=function(ak,ai,ah,aj){A.call(this,"DrawableGroup",ak,ai,ah,aj,"group-handle");if(!S.id_counter){S.id_counter=0}var al=S.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+al).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+al+"_content_div").appendTo(this.container_div);m(this.container_div,this);m(this.content_div,this);n(this.container_div,this.drag_handle_class,".group",this);this.make_name_popup_menu()};q(S.prototype,r.prototype,A.prototype,{make_name_popup_menu:function(){var ai=this;var ah={};ah["Edit configuration"]=function(){var al=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aj=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(am){if((am.keyCode||am.which)===27){al()}else{if((am.keyCode||am.which)===13){aj()}}};$(window).bind("keypress.check_enter_esc",ak);show_modal("Configure Group",ai.config.build_form(),{Cancel:al,OK:aj})};ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)}});var ae=function(ah,ak,aj,ai){A.call(this,"View");this.container=ah;this.chrom=null;this.vis_id=aj;this.dbkey=ai;this.title=ak;this.tracks=this.drawables;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ag(ah.get(0).ownerDocument);this.reset()};q(ae.prototype,A.prototype,{init:function(){var aj=this.container,ah=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aj);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;m(this.viewport_container,ah);this.intro_div=$("<div/>").addClass("intro");var ak=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ai=function(al){if(al.type==="focusout"||(al.keyCode||al.which)===13||(al.keyCode||al.which)===27){if((al.keyCode||al.which)!==27){ah.go_to($(this).val())}$(this).hide();$(this).val("");ah.location_span.show();ah.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ai).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ah.location_span.hide();ah.chrom_select.hide();ah.nav_input.val(ah.chrom+":"+ah.low+"-"+ah.high);ah.nav_input.css("display","inline-block");ah.nav_input.select();ah.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ah.zoom_out();ah.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.browser_content_div.click(function(al){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("<div />").css({height:ah.browser_content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,{content_div:this.top_labeltrack}));this.add_label_track(new ad(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new C(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(al,ai,an){if(!al||al==="None"){return}var ak=this;if(al==="previous"){ak.load_chroms({low:this.chrom_start_index-x});return}if(al==="next"){ak.load_chroms({low:this.chrom_start_index+x});return}var am=$.grep(ak.chrom_data,function(ap,aq){return ap.chrom===al})[0];if(am===undefined){ak.load_chroms({chrom:al},function(){ak.change_chrom(al,ai,an)});return}else{if(al!==ak.chrom){ak.chrom=al;ak.chrom_select.val(ak.chrom);ak.max_high=am.len-1;ak.reset();ak.request_redraw(true);for(var ao=0,ah=ak.tracks.length;ao<ah;ao++){var aj=ak.tracks[ao];if(aj.init){aj.init()}}}if(ai!==undefined&&an!==undefined){ak.low=Math.max(ai,0);ak.high=Math.min(an,ak.max_high)}ak.reset_overview();ak.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){A.prototype.add_drawable.call(this,ah);ah.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;ah.init();this.label_tracks.push(ah)},remove_drawable:function(aj,ai){A.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.tracks),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(E,Math.ceil(Math.log((this.high-this.low)/T)/Math.log(E)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){$.when(ah.get_overview_tile()).then(function(ai){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ai.canvas);view.overview_highlight.show().height(ai.canvas.height());view.overview_viewport.height(ai.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ah;ah.set_is_overview(true)});view.has_changes=true},reset_overview:function(){this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new P(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},al=this.track,aj=ai.tool_id+al.tool_region_and_parameters_str(ai.chrom,ai.low,ai.high),ah,am;if(al.container===view){var ak=new S(this.name,this.track.view,this.track.container);al.container.add_drawable(ak);al.container.remove_drawable(al);ak.add_drawable(al);al.container_div.appendTo(ak.content_div);ah=ak}else{ah=al.container}if(al instanceof e){am=new X(aj,view,ah,"hda");am.change_mode(al.mode);ah.add_drawable(am)}am.content_div.text("Starting job.");this.run(ai,am,function(an){am.dataset_id=an.dataset_id;am.content_div.text("Running job.");am.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(L)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(z+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var P=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){P.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var Y=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};q(Y.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=parseFloat(ah[this.index]);return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(ar,ay){this.track=ar;this.filters=[];for(var at=0;at<ay.length;at++){var au=ay[at],az=au.name,ah=au.type,ak=au.index,ax=au.tool_id,aw=au.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[at]=new Y(az,ak,ax,aw)}else{console.log("ERROR: unsupported filter: ",az,ah)}}var al=function(aA,aB,aC){aA.click(function(){var aD=aB.text();max=parseFloat(aC.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aC.slider("option","values")){input_size=2*input_size+1;multi_value=true}aB.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aD).appendTo(aB).focus().select().click(function(aE){aE.stopPropagation()}).blur(function(){$(this).remove();aB.text(aD)}).keyup(function(aI){if(aI.keyCode===27){$(this).trigger("blur")}else{if(aI.keyCode===13){var aG=aC.slider("option","min"),aE=aC.slider("option","max"),aH=function(aJ){return(isNaN(aJ)||aJ>aE||aJ<aG)},aF=$(this).val();if(!multi_value){aF=parseFloat(aF);if(aH(aF)){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}else{aF=aF.split("-");aF=[parseFloat(aF[0]),parseFloat(aF[1])];if(aH(aF[0])||aH(aF[1])){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}aC.slider((multi_value?"values":"value"),aF)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aA){aA.stopPropagation()}).click(function(aA){aA.stopPropagation()}).bind("dblclick",function(aA){aA.stopPropagation()}).bind("keydown",function(aA){aA.stopPropagation()});var av=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aD,aF){aF.container=$("<div/>").addClass("slider-row").appendTo(av);var aE=$("<div/>").addClass("elt-label").appendTo(aF.container);var aC=$("<span/>").addClass("slider-name").text(aF.name+"  ").appendTo(aE);var aB=$("<span/>");var aH=$("<span/>").addClass("slider-value").appendTo(aE).append("[").append(aB).append("]");var aA=$("<div/>").addClass("slider").appendTo(aF.container);aF.control_element=$("<div/>").attr("id",aF.name+"-filter-control").appendTo(aA);var aG=[0,0];aF.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aJ,aK){var aI=aK.values;aB.text(aI[0]+"-"+aI[1]);aF.low=aI[0];aF.high=aI[1];ap.track.request_draw(true,true)},change:function(aI,aJ){aF.control_element.slider("option","slide").call(aF.control_element,aI,aJ)}});aF.slider=aF.control_element;aF.slider_label=aB;al(aH,aB,aF.control_element);$("<div style='clear: both;'/>").appendTo(aF.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(av);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var aj=this;ao.click(function(){aj.run_on_dataset()})}var aq=$("<div/>").addClass("display-controls").appendTo(this.parent_div),an=$("<span/>").addClass("elt-label").text("Transparency:").appendTo(aq),ai=$("<select/>").attr("name","alpha_dropdown").appendTo(aq);this.alpha_filter=null;$("<option/>").attr("value",-1).text("== None ==").appendTo(ai);for(var at=0;at<this.filters.length;at++){$("<option/>").attr("value",at).text(this.filters[at].name).appendTo(ai)}ai.change(function(){$(this).children("option:selected").each(function(){var aA=parseInt($(this).val());ap.alpha_filter=(aA>=0?ap.filters[aA]:null);ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var Q=function(ai,ah){N.AlphaGenerator.call(this,ah);this.filter=ai};Q.prototype.gen_alpha=function(ah){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_alpha}return((parseFloat(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var H=function(ah){this.track=ah.track;this.params=ah.params;this.values={};this.restore_values((ah.saved_values?ah.saved_values:{}));this.onchange=ah.onchange};q(H.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(aj,ai,ah,ak){this.index=aj;this.low=aj*T*ai;this.high=(aj+1)*T*ai;this.resolution=ai;this.canvas=$("<div class='track-tile'/>").append(ah);this.data=ak;this.stale=false};var l=function(aj,ai,ah,ak,al){b.call(this,aj,ai,ah,ak);this.max_val=al};var R=function(ak,aj,ai,an,am,ah){b.call(this,ak,aj,ai,an);this.message=am;this.feature_mapper=ah;var al=this;$(this.canvas).mousemove(function(ap){var ao=al.feature_mapper.get_feature_data(ap.offsetX,ap.offsetY)})};var j=function(ak,ai,ah,aj,al,am){r.call(this,ak,ai,ah,{},"draghandle");this.data_url=(al?al:default_data_url);this.data_url_extra_params={};this.data_query_wait=(am?am:M);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.container_div=$("<div />").addClass("track").attr("id","track_"+j.id_counter++).css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof C){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Z){return"ReadTrack"}else{if(this instanceof X){return"ToolDataFeatureTrack"}else{if(this instanceof W){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var ak=ah.view.tracks.indexOf(ah);var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(L)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(G)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.make_name_popup_menu()}ah.content_div.text(ab);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}})},predraw_init:function(){},});var O=function(ao,am){var ai=this,ap=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=new ac(this,(ao!==undefined?ao:{}));this.filters_available=false;this.filters_visible=false;this.tool=(am!==undefined&&obj_length(am)>0?new s(this,am):undefined);this.is_overview=false;if(ai.hidden){return}if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(ai.display_modes!==undefined){if(ai.mode_div===undefined){ai.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ai.header_div);var aj=(ai.config&&ai.config.values.mode?ai.config.values.mode:ai.display_modes[0]);ai.mode=aj;ai.mode_div.text(aj);var ah={};for(var ak=0,an=ai.display_modes.length;ak<an;ak++){var al=ai.display_modes[ak];ah[al]=function(aq){return function(){ai.change_mode(aq)}}(al)}make_popupmenu(ai.mode_div,ah)}else{ai.mode_div.hide()}}this.make_name_popup_menu()};q(O.prototype,r.prototype,j.prototype,{to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw();return ah},make_name_popup_menu:function(){var ai=this;var ah={};ah[(this.is_overview?"Hide overview":"Set as overview")]=function(){if(ai.is_overview){ai.view.reset_overview()}else{ai.view.set_overview(ai)}};ah["Edit configuration"]=function(){var am=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},al=function(an){if((an.keyCode||an.which)===27){am()}else{if((an.keyCode||an.which)===13){ak()}}};$(window).bind("keypress.check_enter_esc",al);show_modal("Configure Track",ai.config.build_form(),{Cancel:am,OK:ak})};if(ai.filters_available>0){var aj=(ai.filters_div.is(":visible")?"Hide filters":"Show filters");ah[aj]=function(){ai.filters_visible=(ai.filters_div.is(":visible"));if(ai.filters_visible){ai.filters_manager.reset_filters()}ai.filters_div.toggle();ai.make_name_popup_menu()}}if(ai.tool){var aj=(ai.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");ah[aj]=function(){if(!ai.dynamic_tool_div.is(":visible")){ai.set_name(ai.name+ai.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ai.revert_name()}ai.dynamic_tool_div.toggle();ai.make_name_popup_menu()}}ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)},set_is_overview:function(ah){this.is_overview=ah;this.make_name_popup_menu()},get_overview_tile:function(){var ah=this;view=ah.view,resolution=Math.pow(E,Math.ceil(Math.log((view.max_high-view.max_low)/T)/Math.log(E))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ah.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ah.data_url_extra_params)).then(function(ai){var ak=ah._gen_tile_cache_key(view_width,w_scale,0),am=ah.tile_cache.get(ak);if(!am){am=ah.draw_tile(ai,"Auto",resolution,0,w_scale);ah.tile_cache.set(ak,am)}var ap=$(am.canvas.find("canvas")),al=ap.clone(),ao=ap.get(0).getContext("2d"),aj=al.get(0).getContext("2d"),an=ao.getImageData(0,0,ao.canvas.width,ao.canvas.height);aj.putImageData(an,-ah.left_offset,(am.data.dataset_type==="summary_tree"?V:0));new_tile=new b(-1,resolution,al);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof C)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/T);var ap=true;var at=[];var ah=0;while((ai*T*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",F)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*T*an,ax=ap+T*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);if(aq!==undefined){al.tile_cache.set(at,aq);al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw()});return null},show_tile:function(ao,aq,ar){var aj=this,ai=ao.canvas,an=ai;if(ao.message){var at=$("<div/>"),ap=$("<div/>").addClass("tile-message").text(ao.message).css({height:F-1,width:ao.canvas.width}).appendTo(at),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ap),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ap);at.append(ai);an=at;al.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()});ah.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()})}var am=this.view.high-this.view.low,ak=(ao.low-this.view.low)*ar;if(this.left_offset){ak-=this.left_offset}an.css({position:"absolute",top:0,left:ak,height:""});aq.append(an);aj.max_height=Math.max(aj.max_height,an.height());aj.content_div.css("height",aj.max_height+"px");aq.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*T*ai,al=T*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ai,ah){this.hidden=true;j.call(this,"label",ai,ah,{});this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{init:function(){this.enabled=true},_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var C=function(ah){this.hidden=true;j.call(this,"reference",ah,{content_div:ah.top_labeltrack},{});O.call(this);ah.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ah.dbkey};this.data_manager=new J(D,this,false);this.tile_cache=new c(v)};q(C.prototype,r.prototype,O.prototype,{init:function(){this.enabled=true},draw_tile:function(ar,an,am,ai,at){var al=this,aj=T*am;if(at>this.view.canvas_manager.char_width_px){if(ar===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(am,ak,aj,an,ah,al){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,am,ak,aj,al);O.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=an;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new U(D,this);this.tile_cache=new c(v);this.left_offset=0;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:am},{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:al,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.track_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.track_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};q(k.prototype,r.prototype,O.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this,ai=ah.view.tracks.indexOf(ah);ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(aj){ah.container_div.addClass("line-track");var al=aj.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=al.min;ah.prefs.max_value=al.max;$("#track_"+ai+"_minval").val(ah.prefs.min_value);$("#track_"+ai+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=al.total_frequency;ah.container_div.find(".yaxislabel").remove();var am=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ai+"_minval").text(y(ah.prefs.min_value));var ak=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ai+"_maxval").text(y(ah.prefs.max_value));ak.css({position:"absolute",top:"24px",left:"10px"});ak.prependTo(ah.container_div);am.css({position:"absolute",bottom:"2px",left:"10px"});am.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new N.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(aj,al,ak,au.data)}});var e=function(ah,an,ai,am,ap,ao,ak,al){var aj=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];j.call(this,ah,an,ai,ao);O.call(this,ak,al);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){aj.set_name(aj.prefs.name);aj.tile_cache.clear();aj.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=am;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new U(20,this);this.left_offset=200;this.painter=N.LinkedFeaturePainter};q(e.prototype,r.prototype,O.prototype,{postdraw_actions:function(ax,ah,ay,aw){O.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.make_name_popup_menu()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",B,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aE,aI,ar,ak){var aB=this,am=aB._get_tile_bounds(aI,aE),aL=am[0],ai=am[1],ay=ai-aL,aC=Math.ceil(ay*ar),aP=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"){az="no_detail"}else{var aO=aw.data;if(this.view.high-this.view.low>K){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aC+al;aj.height=an+V;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aL,ai,200);if(aw.max){at.max=aw.max}aw=at}var aM=new N.SummaryTreePainter(aw,aL,ai,this.prefs);var aD=aj.getContext("2d");aD.translate(al,V);aM.draw(aD,aC,an);return new l(aI,aE,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aF=0,aH=aw.data.length;aF<aH;aF++){var ao=aw.data[aF];var 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D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var g=function(z){this.default_alpha=(z?z:1)};g.prototype.gen_alpha=function(z){return this.default_alpha};var n=function(B,D,z,A,C){this.data=B;this.view_start=D;this.view_end=z;this.prefs=v({},this.default_prefs,A);this.mode=C};n.prototype.default_prefs={};var w=function(B,D,z,A,C){n.call(this,B,D,z,A,C)};w.prototype.default_prefs={show_counts:false};w.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var c=function(z,D,F,G,B){n.call(this,z,D,F,G,B);if(this.prefs.min_value===undefined){var H=Infinity;for(var A=0,C=this.data.length;A<C;A++){H=Math.min(H,this.data[A][1])}this.prefs.min_value=H}if(this.prefs.max_value===undefined){var E=-Infinity;for(var A=0,C=this.data.length;A<C;A++){E=Math.max(E,this.data[A][1])}this.prefs.max_value=E}};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var o=function(z){this.feature_positions={};this.slot_height=z;this.translation=0};o.prototype.map_feature_data=function(A,C,z,B){if(!this.feature_positions[C]){this.feature_positions[C]=[]}this.feature_positions[C].push({data:A,x_start:z,x_end:B})};o.prototype.get_feature_data=function(z,D){var C=Math.floor(D/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var p=function(C,E,z,B,D,A){n.call(this,C,E,z,B,D);this.alpha_generator=(A?A:new g())};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};v(p.prototype,{get_required_height:function(A){var z=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){z=A*y_scale}return z+Math.max(Math.round(y_scale/2),5)},draw:function(L,J,H,G){var R=this.data,E=this.view_start,N=this.view_end;L.save();L.fillStyle=this.prefs.block_color;L.textAlign="right";var I=this.view_end-this.view_start,F=J/I,M=this.get_row_height(),Q=new o(M),C;for(var O=0,P=R.length;O<P;O++){var B=R[O],D=B[0],K=B[1],z=B[2],A=(G&&G[D]!==undefined?G[D]:null);if((K<N&&z>E)&&(this.mode=="Dense"||A!==null)){C=this.draw_element(L,this.mode,B,A,E,N,F,M,J);Q.map_feature_data(B,A,C[0],C[1])}}L.restore();return Q},draw_element:function(F,B,H,D,C,E,G,A,z){console.log("WARNING: Unimplemented function.");return[0,0]}});var d=10,j=3,m=5,x=10,f=1,t=3,e=3,a=9,l=2,h="#ccc";var s=function(C,E,z,B,D,A){p.call(this,C,E,z,B,D,A)};v(s.prototype,p.prototype,{get_row_height:function(){var A=this.mode,z;if(A==="Dense"){z=d}else{if(A==="no_detail"){z=j}else{if(A==="Squish"){z=m}else{z=x}}}return z},draw_element:function(L,E,T,G,N,ae,ai,ak,z){var Q=T[0],ag=T[1],Y=T[2],O=T[3],Z=Math.floor(Math.max(0,(ag-N)*ai)),M=Math.ceil(Math.min(z,Math.max(0,(Y-N)*ai))),X=Z,aj=M,W=(E==="Dense"?0:(0+G))*ak,K,ac,P=null,al=null,C=this.prefs.block_color,ab=this.prefs.label_color;L.globalAlpha=this.alpha_generator.gen_alpha(T);if(E=="Dense"){G=1}if(E==="no_detail"){L.fillStyle=C;L.fillRect(Z,W+5,M-Z,f)}else{var J=T[4],V=T[5],aa=T[6],D=T[7];if(V&&aa){P=Math.floor(Math.max(0,(V-N)*ai));al=Math.ceil(Math.min(z,Math.max(0,(aa-N)*ai)))}var ah,R;if(E==="Squish"||E==="Dense"){ah=1;R=e}else{ah=5;R=a}if(!D){if(T.strand){if(T.strand==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand_inv")}else{if(T.strand==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand_inv")}}}else{L.fillStyle=C}L.fillRect(Z,W,M-Z,R)}else{var I,S;if(E==="Squish"||E==="Dense"){L.fillStyle=h;I=W+Math.floor(e/2)+1;S=1}else{if(J){var I=W;var 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b=function(C,E,z,B,D,A){p.call(this,C,E,z,B,D,A)};v(b.prototype,p.prototype,{draw_element:function(S,N,H,D,V,B,K,T,Q){var H=data[i],J=H[0],R=H[1],C=H[2],M=H[3],F=Math.floor(Math.max(0,(R-V)*K)),I=Math.ceil(Math.min(Q,Math.max(0,(C-V)*K))),E=(N==="Dense"?0:(0+D))*T,z,W,A=null,L=null;if(no_label){S.fillStyle=block_color;S.fillRect(F+left_offset,E+5,I-F,1)}else{var U=H[4],P=H[5],G=H[6];z=9;W=1;S.fillRect(F+left_offset,E,I-F,z);if(N!=="Dense"&&M!==undefined&&R>V){S.fillStyle=label_color;if(V===0&&F-S.measureText(M).width<0){S.textAlign="left";S.fillText(M,I+2+left_offset,E+8)}else{S.textAlign="right";S.fillText(M,F-2+left_offset,E+8)}S.fillStyle=block_color}var O=U+" / "+P;if(R>V&&S.measureText(O).width<(I-F)){S.fillStyle="white";S.textAlign="center";S.fillText(O,left_offset+F+(I-F)/2,E+8);S.fillStyle=block_color}}return[F,I]}});var 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O=Math.floor(Math.max(0,(F[4][0]-V)*J)),M=Math.ceil(Math.min(Q,Math.max(0,(F[4][1]-V)*J))),L=Math.floor(Math.max(0,(F[5][0]-V)*J)),z=Math.ceil(Math.min(Q,Math.max(0,(F[5][1]-V)*J)));if(F[4][1]>=V&&F[4][0]<=A&&F[4][2]){this.draw_read(S,N,J,V,A,F[4][0],F[4][2],F[4][3],D)}if(F[5][1]>=V&&F[5][0]<=A&&F[5][2]){this.draw_read(S,N,J,V,A,F[5][0],F[5][2],F[5][3],D)}if(L>M){S.fillStyle=h;q(S,M-P,D+5,L-P,D+5)}}else{S.fillStyle=W;this.draw_read(S,N,J,V,A,R,F[4],F[5],D)}if(N==="Pack"&&R>V){S.fillStyle=this.prefs.label_color;var U=1;if(U===0&&E-S.measureText(K).width<0){S.textAlign="left";S.fillText(K,G+l-P,D+8)}else{S.textAlign="right";S.fillText(K,E-l-P,D+8)}S.fillStyle=W}return[0,0]}});y.AlphaGenerator=g;y.SummaryTreePainter=w;y.LinePainter=c;y.LinkedFeaturePainter=s;y.ReadPainter=u;y.VariantPainter=b};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window);
\ No newline at end of file
diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index 69e810ed39f..ddd64af9353 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -2627,16 +2627,16 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
             }
         }
                 
-        // If we can draw now, do so
+        // If we can draw now, do so.
         if ( can_draw_now ) {
             extend( tile_data, more_tile_data );
             var tile = track.draw_tile(tile_data, track.mode, resolution, tile_index, w_scale, seq_data);
-            track.tile_cache.set(key, tile);
-            // Don't show if no tile
+            // Don't cache, show if no tile.
             if (tile !== undefined) {
+                track.tile_cache.set(key, tile);
                 track.show_tile(tile, parent_element, w_scale);
             }
-            return tile
+            return tile;
         }
          
         // Can't draw now, so trigger another redraw when the data is ready
diff --git a/templates/grid_base.mako b/templates/grid_base.mako
index 48668e61c4c..4121d115023 100644
--- a/templates/grid_base.mako
+++ b/templates/grid_base.mako
@@ -117,7 +117,7 @@
         %endfor
         
         // Init operation buttons.
-        var init_operation_buttons = function() {
+        function init_operation_buttons() {
             // Initialize operation buttons.
             $('input[name=operation]:submit').each(function() {
                 $(this).click( function() {

From c279ecd33bb9dfdceda6a17e289faa85b1ba01e7 Mon Sep 17 00:00:00 2001
From: John Duddy <jduddy@illumina.com>
Date: Fri, 7 Oct 2011 14:12:40 -0700
Subject: [PATCH 033/362] Upgrade of splitting code to do splitting in the
 tasks versus in the Galaxy process

---
 extract_dataset_parts.sh                      |   8 +
 lib/galaxy/datatypes/data.py                  |  14 +-
 lib/galaxy/datatypes/sequence.py              | 397 ++++++++++++------
 lib/galaxy/jobs/__init__.py                   | 111 ++---
 lib/galaxy/jobs/runners/__init__.py           |   6 +-
 lib/galaxy/jobs/runners/lwr.py                |   6 +
 lib/galaxy/jobs/splitters/multi.py            |  87 ++--
 lib/galaxy/model/__init__.py                  |  27 +-
 lib/galaxy/model/mapping.py                   |  11 +-
 .../0083_add_prepare_files_to_task.py         |  63 +++
 lib/galaxy/util/__init__.py                   |   3 +
 scripts/extract_dataset_part.py               |  48 +++
 12 files changed, 540 insertions(+), 241 deletions(-)
 create mode 100644 extract_dataset_parts.sh
 create mode 100644 lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py
 create mode 100644 scripts/extract_dataset_part.py

diff --git a/extract_dataset_parts.sh b/extract_dataset_parts.sh
new file mode 100644
index 00000000000..26f915c0c3d
--- /dev/null
+++ b/extract_dataset_parts.sh
@@ -0,0 +1,8 @@
+#!/bin/sh
+
+cd `dirname $0`
+for file in $1/split_info*.json
+do
+    # echo processing $file
+    python ./scripts/extract_dataset_part.py $file
+done
diff --git a/lib/galaxy/datatypes/data.py b/lib/galaxy/datatypes/data.py
index b26670c41a0..6172713a54a 100644
--- a/lib/galaxy/datatypes/data.py
+++ b/lib/galaxy/datatypes/data.py
@@ -360,9 +360,12 @@ class Data( object ):
         but might be brittle. Need to revisit this.
         """
         if len(split_files) == 1:
-            os.system( 'mv -f %s %s' % ( split_files[0], output_file ) )
+            cmd = 'mv -f %s %s' % ( split_files[0], output_file ) 
         else:
-            os.system( 'cat %s > %s' % ( ' '.join(split_files), output_file ) )
+            cmd = 'cat %s > %s' % ( ' '.join(split_files), output_file ) 
+        result = os.system(cmd)
+        if result != 0:
+            raise Exception('Result %s from %s' % (result, cmd))
     merge = staticmethod(merge)
 
 class Text( Data ):
@@ -533,6 +536,13 @@ class Text( Data ):
         f.close()
     split = staticmethod(split)
 
+class LineCount( Text ):
+    """
+    Dataset contains a single line with a single integer that denotes the
+    line count for a related dataset. Used for custom builds.
+    """
+    pass
+
 class Newick( Text ):
     pass
 
diff --git a/lib/galaxy/datatypes/sequence.py b/lib/galaxy/datatypes/sequence.py
index 80e1324965e..feedebeeaa3 100644
--- a/lib/galaxy/datatypes/sequence.py
+++ b/lib/galaxy/datatypes/sequence.py
@@ -7,6 +7,7 @@ import data
 import logging
 import re
 import string
+import os
 from cgi import escape
 from galaxy.datatypes.metadata import MetadataElement
 from galaxy.datatypes import metadata
@@ -14,8 +15,52 @@ import galaxy.model
 from galaxy import util
 from sniff import *
 
+import pkg_resources
+pkg_resources.require("simplejson")
+import simplejson
+
 log = logging.getLogger(__name__)
 
+class SequenceSplitLocations( data.Text ):
+    """
+    Class storing information about a sequence file composed of multiple gzip files concatenated as
+    one OR an uncompressed file. In the GZIP case, each sub-file's location is stored in start and end. 
+    The format of the file is JSON:
+    { "sections" : [
+            { "start" : "x", "end" : "y", "clusters" : "z" },
+            ...
+    ]}
+    """
+    def set_peek( self, dataset, is_multi_byte=False ):
+        if not dataset.dataset.purged:
+            try:
+                parsed_data = simplejson.load(open(dataset.file_name))
+                # dataset.peek = simplejson.dumps(data, sort_keys=True, indent=4)
+                dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
+                dataset.blurb = '%d sections' % len(parsed_data['sections'])
+            except Exception, e:
+                dataset.peek = 'Not FQTOC file'
+                dataset.blurb = 'Not FQTOC file'
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+
+    file_ext = "fqtoc"
+
+    def sniff( self, filename ):
+        if os.path.getsize(filename) < 50000:
+            try:
+                data = simplejson.load(open(filename))
+                sections = data['sections']
+                for section in sections:
+                    if 'start' not in section or 'end' not in section or 'clusters' not in section:
+                        return False
+                return True
+            except:
+                pass
+        return False
+
+
 class Sequence( data.Text ):
     """Class describing a sequence"""
 
@@ -50,143 +95,237 @@ class Sequence( data.Text ):
         else:
             dataset.peek = 'file does not exist'
             dataset.blurb = 'file purged from disk'
+
+    def get_sequences_per_file(total_clusters, split_params):
+        if split_params['split_mode'] == 'number_of_parts':
+            # legacy basic mode - split into a specified number of parts
+            parts = int(split_params['split_size'])
+            sequences_per_file = [total_clusters/parts for i in range(parts)]
+            for i in range(total_clusters % parts):
+                sequences_per_file[i] += 1
+        elif split_params['split_mode'] == 'to_size':
+            # loop through the sections and calculate the number of clusters
+            chunk_size = long(split_params['split_size'])
+
+            chunks = total_clusters / chunk_size
+            rem = total_clusters % chunk_size
+            sequences_per_file = [chunk_size for i in range(total_clusters / chunk_size)]
+            # TODO: Should we invest the time in a better way to handle small remainders?
+            if rem > 0:
+                sequences_per_file.append(rem)
+        else:
+            raise Exception('Unsupported split mode %s' % split_params['split_mode'])
+        return sequences_per_file
+    get_sequences_per_file = staticmethod(get_sequences_per_file)
+
+    def do_slow_split( cls, input_datasets, subdir_generator_function, split_params):
+        # count the clusters so we can split
+        # TODO: if metadata is present, take the number of lines / 4
+        if input_datasets[0].metadata is not None and input_datasets[0].metadata.sequences is not None:
+            total_clusters = input_datasets[0].metadata.sequences
+        else:
+            input_file = input_datasets[0].file_name
+            compress = is_gzip(input_file)
+            if compress:
+                # gzip is really slow before python 2.7!
+                in_file = gzip.GzipFile(input_file, 'r')
+            else:
+                # TODO
+                # if a file is not compressed, seek locations can be calculated and stored
+                # ideally, this would be done in metadata
+                # TODO
+                # Add BufferedReader if python 2.7?
+                in_file = open(input_file, 'rt')
+            total_clusters = long(0)
+            for i, line in enumerate(in_file):
+                total_clusters += 1
+            in_file.close()
+            total_clusters /= 4
+
+        sequences_per_file = cls.get_sequences_per_file(total_clusters, split_params)
+        return cls.write_split_files(input_datasets, None, subdir_generator_function, sequences_per_file)
+    do_slow_split = classmethod(do_slow_split)
+
+    def do_fast_split( cls, input_datasets, toc_file_datasets, subdir_generator_function, split_params):
+        data = simplejson.load(open(toc_file_datasets[0].file_name))
+        sections = data['sections']
+        total_clusters = long(0)
+        for section in sections:
+            total_clusters += long(section['clusters'])
+        sequences_per_file = cls.get_sequences_per_file(total_clusters, split_params)
+        return cls.write_split_files(input_datasets, toc_file_datasets, subdir_generator_function, sequences_per_file)
+    do_fast_split = classmethod(do_fast_split)
+
+    def write_split_files(cls, input_datasets, toc_file_datasets, subdir_generator_function, sequences_per_file):
+        directories = []
+        def get_subdir(idx):
+            if idx < len(directories):
+                return directories[idx]
+            dir = subdir_generator_function()
+            directories.append(dir)
+            return dir
+
+        # we know how many splits and how many clusters in each. What remains is to write out instructions for the 
+        # splitting of all the input files. To decouple the format of those instructions from this code, the exact format of
+        # those instructions is delegated to scripts
+        start_sequence=0
+        for part_no in range(len(sequences_per_file)):
+            dir = get_subdir(part_no)
+            for ds_no in range(len(input_datasets)):
+                ds = input_datasets[ds_no]
+                base_name = os.path.basename(ds.file_name)
+                part_path = os.path.join(dir, base_name)
+                split_data = dict(class_name='%s.%s' % (cls.__module__, cls.__name__),
+                                  output_name=part_path,
+                                  input_name=ds.file_name,
+                                  args=dict(start_sequence=start_sequence, num_sequences=sequences_per_file[part_no]))
+                if toc_file_datasets is not None:
+                    toc = toc_file_datasets[ds_no]
+                    split_data['args']['toc_file'] = toc.file_name
+                f = open(os.path.join(dir, 'split_info_%s.json' % base_name), 'w')
+                simplejson.dump(split_data, f)
+                f.close()
+            start_sequence += sequences_per_file[part_no]
+        return directories
+    write_split_files = classmethod(write_split_files)
     
-    def split( input_files, subdir_generator_function, split_params):
+    def split( cls, input_datasets, subdir_generator_function, split_params):
         """
         FASTQ files are split on cluster boundaries, in increments of 4 lines
         """
         if split_params is None:
-            return
-        
-        def split_calculate_clusters( input_file, get_dir, default_clusters):
-            """
-            Split the 0th file into even sized chunks, and return the number of clusters in each
-            """
-            compress = is_gzip(input_file)
-            if compress:
-# TODO: Python 2.4, 2.5 don't have io.BufferedReader!!!
-# add a buffered reader because gzip is really slow before python 2.7
-                in_file = gzip.GzipFile(input_file, 'r')
-            else:
-                in_file = open(input_file, 'rt')
-            part_file = None
-            part = 0
-            local_clusters_per_file = []
-            for i, line in enumerate(in_file):
-                cluster_number,  line_in_cluster = divmod(i, 4)
-                current_part, remainder = divmod(cluster_number, default_clusters)
-                
-                if (current_part != part or part_file is None):
-                    if (part_file):
-                        part_file.close()
-                    part = current_part
-                    part_dir = get_dir()
-                    part_path = os.path.join(part_dir, os.path.basename(input_file))
-# TODO: If the input was compressed, compress the output?
-                    part_file = open(part_path, 'w')
-                    local_clusters_per_file.append(default_clusters)
-                part_file.write(line)
-            if (part_file):
-                part_file.close()
-            in_file.close()
-            local_clusters_per_file[part] = remainder + 1
-            return local_clusters_per_file
-    
-        def split_to_size(input_file, get_dir, clusters_per_file):
-            """
-            Split the files beyond the 0th to the same number of clusters as the 0th.
-            This is used to split in a variety of ways, so these are both legal for
-            clusters_per_file:
-                [ 10000, 10000, 10000, 10000, 2 ] # to_size=10000, 40002 total
-                [ 10001, 10001, 10000, 10000 ] # number_of_parts = 4, 40002 total
+            return None
 
-            """
-            compress = is_gzip(input_file)
-            if compress:
-# TODO: Python 2.4, 2.5 don't have io.BufferedReader!!!
-# add a buffered reader because gzip is really slow before python 2.7
-                in_file = gzip.GzipFile(input_file, 'r')
-            else:
-                in_file = open(input_file, 'rt')
-            part_file = None
-            part = 0
-            clusters_this_part = 0
-            for i, line in enumerate(in_file):
-                cluster_number,  line_in_cluster = divmod(i, 4)
-                if clusters_this_part  == clusters_per_file[part]:
-                    current_part = part + 1
-                else:
-                    current_part = part
-                
-                if (current_part != part or part_file is None):
-                    if (part_file):
-                        part_file.close()
-                    part = current_part
-                    clusters_this_part = 0
-                    part_dir = get_dir()
-                    part_path = os.path.join(part_dir, os.path.basename(input_file))
-# TODO: If the input was compressed, compress the output?
-                    part_file = open(part_path, 'w')
-                    if clusters_per_file is None and part > 0:
-                        local_clusters_per_file.append(default_clusters)
-                part_file.write(line)
-                if line_in_cluster == 3:
-                    clusters_this_part += 1
-            if (part_file):
-                part_file.close()
-            in_file.close()
+        # first, see if there are any associated FQTOC files that will give us the split locations
+        # if so, we don't need to read the files to do the splitting
+        toc_file_datasets = []
+        for ds in input_datasets:
+            tmp_ds = ds
+            fqtoc_file = None
+            while fqtoc_file is None and tmp_ds is not None:
+                fqtoc_file = tmp_ds.get_converted_files_by_type('fqtoc')
+                tmp_ds = tmp_ds.copied_from_library_dataset_dataset_association
 
-        directories = []
-        def create_subdir():
-            dir = subdir_generator_function()
-            directories.append(dir)
-            return dir
+            if fqtoc_file is not None:
+                toc_file_datasets.append(fqtoc_file)
+
+        if len(toc_file_datasets) == len(input_datasets):
+            return cls.do_fast_split(input_datasets, toc_file_datasets, subdir_generator_function, split_params)
+        return cls.do_slow_split(input_datasets, subdir_generator_function, split_params)
+    split = classmethod(split)
+
+    def process_split_file(data):
+        """
+        This is called in the context of an external process launched by a Task (possibly not on the Galaxy machine)
+        to create the input files for the Task. The parameters:
+        data - a dict containing the contents of the split file
+        """
+        args = data['args']
+        input_name = data['input_name']
+        output_name = data['output_name']
+        start_sequence = long(args['start_sequence'])
+        sequence_count = long(args['num_sequences'])
         
-        clusters_per_file = None
-        if split_params['split_mode'] == 'number_of_parts':
-            # legacy splitting. To keep things simple, just scan the 0th file and count the clusters,
-            # then split it
-            clusters_per_file = []
-            in_file = open(input_files[0], 'rt')
-            for i, line in enumerate(in_file):
-                pass
-            in_file.close()
-            length = (i+1)/4
-            
-            if length <= 0:
-                raise Exception('Invalid sequence file %s' % input_files[0])
-            parts = int(split_params['split_size'])
-            if length < parts:
-                parts = length
-            len_each, remainder = divmod(length, parts)
-            while length > 0:
-                chunk = len_each
-                if remainder > 0:
-                    chunk += 1
-                clusters_per_file.append(chunk)
-                remainder=- 1
-                length -= chunk
-            split_to_size(input_files[0],  create_subdir,  clusters_per_file)
-        elif split_params['split_mode'] == 'to_size':
-            # split one file and see what the cluster sizes turn out to be
-            clusters_per_file = split_calculate_clusters(input_files[0],  create_subdir,  
-                int(split_params['split_size']))
+        if 'toc_file' in args:
+            toc_file = simplejson.load(open(args['toc_file'], 'r'))
+            commands = Sequence.get_split_commands_with_toc(input_name, output_name, toc_file, start_sequence, sequence_count)
         else:
-            raise Exception('Unsupported split mode %s' % split_params['split_mode'])
+            commands = Sequence.get_split_commands_sequential(is_gzip(input_name), input_name, output_name, start_sequence, sequence_count)
+        for cmd in commands:
+            if 0 != os.system(cmd):
+                raise Exception("Executing '%s' failed" % cmd)
+        return True
+    process_split_file = staticmethod(process_split_file)
+    
+    def get_split_commands_with_toc(input_name, output_name, toc_file, start_sequence, sequence_count):
+        """
+        Uses a Table of Contents dict, parsed from an FQTOC file, to come up with a set of
+        shell commands that will extract the parts necessary
+        >>> three_sections=[dict(start=0, end=74, clusters=10), dict(start=74, end=148, clusters=10), dict(start=148, end=148+76, clusters=10)]
+        >>> Sequence.get_split_commands_with_toc('./input.gz', './output.gz', dict(sections=three_sections), start_sequence=0, sequence_count=10)
+        ['dd bs=1 skip=0 count=74 if=./input.gz 2> /dev/null >> ./output.gz']
+        >>> Sequence.get_split_commands_with_toc('./input.gz', './output.gz', dict(sections=three_sections), start_sequence=1, sequence_count=5)
+        ['(dd bs=1 skip=0 count=74 if=./input.gz 2> /dev/null )| zcat | ( tail -n +5 2> /dev/null) | head -20 | gzip -c >> ./output.gz']
+        >>> Sequence.get_split_commands_with_toc('./input.gz', './output.gz', dict(sections=three_sections), start_sequence=0, sequence_count=20)
+        ['dd bs=1 skip=0 count=148 if=./input.gz 2> /dev/null >> ./output.gz']
+        >>> Sequence.get_split_commands_with_toc('./input.gz', './output.gz', dict(sections=three_sections), start_sequence=5, sequence_count=10)
+        ['(dd bs=1 skip=0 count=74 if=./input.gz 2> /dev/null )| zcat | ( tail -n +21 2> /dev/null) | head -20 | gzip -c >> ./output.gz', '(dd bs=1 skip=74 count=74 if=./input.gz 2> /dev/null )| zcat | ( tail -n +1 2> /dev/null) | head -20 | gzip -c >> ./output.gz']
+        >>> Sequence.get_split_commands_with_toc('./input.gz', './output.gz', dict(sections=three_sections), start_sequence=10, sequence_count=10)
+        ['dd bs=1 skip=74 count=74 if=./input.gz 2> /dev/null >> ./output.gz']
+        >>> Sequence.get_split_commands_with_toc('./input.gz', './output.gz', dict(sections=three_sections), start_sequence=5, sequence_count=20)
+        ['(dd bs=1 skip=0 count=74 if=./input.gz 2> /dev/null )| zcat | ( tail -n +21 2> /dev/null) | head -20 | gzip -c >> ./output.gz', 'dd bs=1 skip=74 count=74 if=./input.gz 2> /dev/null >> ./output.gz', '(dd bs=1 skip=148 count=76 if=./input.gz 2> /dev/null )| zcat | ( tail -n +1 2> /dev/null) | head -20 | gzip -c >> ./output.gz']
+        """
+        sections = toc_file['sections']
+        result = []
+
+        current_sequence = long(0)
+        i=0
+        # skip to the section that contains my starting sequence
+        while i < len(sections) and start_sequence >= current_sequence + long(sections[i]['clusters']):
+            current_sequence += long(sections[i]['clusters'])
+            i += 1
+        if i == len(sections): # bad input data!
+            raise Exception('No FQTOC section contains starting sequence %s' % start_sequence)
+    
+        # These two variables act as an accumulator for consecutive entire blocks that
+        # can be copied verbatim (without decompressing)
+        start_chunk = long(-1)
+        end_chunk = long(-1)
+        copy_chunk_cmd = 'dd bs=1 skip=%s count=%s if=%s 2> /dev/null >> %s'
         
-        # split the rest, using the same number of clusters for each file
-        current_dir_idx = [0] # use a list to get around Python 2.x lame closure support
-        def get_subdir():
-            if len(directories) <= current_dir_idx[0]:
-                raise Exception('FASTQ files do not have the same number of clusters - splitting failed')
-            result = directories[current_dir_idx[0]]
-            current_dir_idx[0] = current_dir_idx[0] + 1
-            return result
-            
-        for i in range(1,  len(input_files)):
-            current_dir_idx[0] = 0
-            split_to_size(input_files[i],  get_subdir,  clusters_per_file)
-    split = staticmethod(split)
+        while sequence_count > 0 and i < len(sections):
+            # we need to extract partial data. So, find the byte offsets of the chunks that contain the data we need
+            # use a combination of dd (to pull just the right sections out) tail (to skip lines) and head (to get the 
+            # right number of lines
+            sequences = long(sections[i]['clusters'])
+            skip_sequences = start_sequence-current_sequence
+            sequences_to_extract = min(sequence_count, sequences-skip_sequences)
+            start_copy = long(sections[i]['start'])
+            end_copy = long(sections[i]['end'])
+            if sequences_to_extract < sequences:
+                if start_chunk > -1:
+                    result.append(copy_chunk_cmd % (start_chunk, end_chunk-start_chunk, input_name, output_name))
+                    start_chunk = -1
+                # extract, unzip, trim, recompress
+                result.append('(dd bs=1 skip=%s count=%s if=%s 2> /dev/null )| zcat | ( tail -n +%s 2> /dev/null) | head -%s | gzip -c >> %s' % 
+                    (start_copy, end_copy-start_copy, input_name, skip_sequences*4+1, sequences_to_extract*4, output_name))
+            else: # whole section - add it to the start_chunk/end_chunk accumulator
+                if start_chunk == -1:
+                    start_chunk = start_copy
+                end_chunk = end_copy
+            sequence_count -= sequences_to_extract
+            start_sequence += sequences_to_extract
+            current_sequence += sequences
+            i += 1
+        if start_chunk > -1:
+            result.append(copy_chunk_cmd % (start_chunk, end_chunk-start_chunk, input_name, output_name))
+                
+        if sequence_count > 0:
+            raise Exception('%s sequences not found in file' % sequence_count)
+             
+        return result
+    get_split_commands_with_toc = staticmethod(get_split_commands_with_toc)
+
+
+    def get_split_commands_sequential(is_compressed, input_name, output_name, start_sequence, sequence_count):
+        """
+        Does a brain-dead sequential scan & extract of certain sequences
+        >>> Sequence.get_split_commands_sequential(True, './input.gz', './output.gz', start_sequence=0, sequence_count=10)
+        ['zcat "./input.gz" | ( tail -n +1 2> /dev/null) | head -40 | gzip -c > "./output.gz"']
+        >>> Sequence.get_split_commands_sequential(False, './input.fastq', './output.fastq', start_sequence=10, sequence_count=10)
+        ['tail -n +41 "./input.fastq" 2> /dev/null | head -40 > "./output.fastq"']
+        """
+        start_line = start_sequence * 4
+        line_count = sequence_count * 4
+        # TODO: verify that tail can handle 64-bit numbers
+        if is_compressed:
+            cmd = 'zcat "%s" | ( tail -n +%s 2> /dev/null) | head -%s | gzip -c' % (input_name, start_line+1, line_count)
+        else:
+            cmd = 'tail -n +%s "%s" 2> /dev/null | head -%s'  % (start_line+1, input_name, line_count)
+        cmd += ' > "%s"' % output_name
+        
+        return [cmd]
+    get_split_commands_sequential = staticmethod(get_split_commands_sequential)
 
 
 
@@ -690,3 +829,7 @@ class Lav( data.Text ):
                 return False
         except:
             return False
+
+if __name__ == '__main__':
+    import doctest, sys
+    doctest.testmod(sys.modules[__name__])
\ No newline at end of file
diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 65283dcf132..ca97c24c7d7 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -32,9 +32,9 @@ TOOL_PROVIDED_JOB_METADATA_FILE = 'galaxy.json'
 class JobManager( object ):
     """
     Highest level interface to job management.
-
+    
     TODO: Currently the app accesses "job_queue" and "job_stop_queue" directly.
-          This should be decoupled.
+          This should be decoupled. 
     """
     def __init__( self, app ):
         self.app = app
@@ -71,7 +71,7 @@ class Sleeper( object ):
 
 class JobQueue( object ):
     """
-    Job manager, waits for jobs to be runnable and then dispatches to
+    Job manager, waits for jobs to be runnable and then dispatches to 
     a JobRunner.
     """
     STOP_SIGNAL = object()
@@ -95,7 +95,7 @@ class JobQueue( object ):
         self.running = True
         self.dispatcher = dispatcher
         self.monitor_thread = threading.Thread( target=self.__monitor )
-        self.monitor_thread.start()
+        self.monitor_thread.start()        
         log.info( "job manager started" )
         if app.config.get_bool( 'enable_job_recovery', True ):
             self.__check_jobs_at_startup()
@@ -132,7 +132,7 @@ class JobQueue( object ):
 
     def __monitor( self ):
         """
-        Continually iterate the waiting jobs, checking is each is ready to
+        Continually iterate the waiting jobs, checking is each is ready to 
         run and dispatching if so.
         """
         # HACK: Delay until after forking, we need a way to do post fork notification!!!
@@ -180,12 +180,12 @@ class JobQueue( object ):
                     jobs_to_check.append( self.sa_session.query( model.Job ).get( job_id ) )
             except Empty:
                 pass
-        # Iterate over new and waiting jobs and look for any that are
+        # Iterate over new and waiting jobs and look for any that are 
         # ready to run
         new_waiting_jobs = []
         for job in jobs_to_check:
             try:
-                # Check the job's dependencies, requeue if they're not done
+                # Check the job's dependencies, requeue if they're not done                    
                 job_state = self.__check_if_ready_to_run( job )
                 if job_state == JOB_WAIT:
                     if not self.track_jobs_in_database:
@@ -216,7 +216,7 @@ class JobQueue( object ):
         self.waiting_jobs = new_waiting_jobs
         # Done with the session
         self.sa_session.remove()
-
+        
     def __check_if_ready_to_run( self, job ):
         """
         Check if a job is ready to run by verifying that each of its input
@@ -281,13 +281,13 @@ class JobQueue( object ):
         if len( user_jobs ) >= self.app.config.user_job_limit:
             return JOB_WAIT
         return JOB_READY
-
+            
     def put( self, job_id, tool ):
         """Add a job to the queue (by job identifier)"""
         if not self.track_jobs_in_database:
             self.queue.put( ( job_id, tool.id ) )
             self.sleeper.wake()
-
+    
     def shutdown( self ):
         """Attempts to gracefully shut down the worker thread"""
         if self.parent_pid != os.getpid():
@@ -304,7 +304,7 @@ class JobQueue( object ):
 
 class JobWrapper( object ):
     """
-    Wraps a 'model.Job' with convenience methods for running processes and
+    Wraps a 'model.Job' with convenience methods for running processes and 
     state management.
     """
     def __init__( self, job, queue ):
@@ -330,15 +330,15 @@ class JobWrapper( object ):
         self.output_dataset_paths = None
         self.tool_provided_job_metadata = None
         # Wrapper holding the info required to restore and clean up from files used for setting metadata externally
-        self.external_output_metadata = metadata.JobExternalOutputMetadataWrapper( job )
-
+        self.external_output_metadata = metadata.JobExternalOutputMetadataWrapper( job )        
+    
     def get_job( self ):
         return self.sa_session.query( model.Job ).get( self.job_id )
-
+    
     def get_id_tag(self):
         # For compatability with drmaa, which uses job_id right now, and TaskWrapper
         return str(self.job_id)
-
+    
     def get_param_dict( self ):
         """
         Restore the dictionary of parameters from the database.
@@ -347,10 +347,10 @@ class JobWrapper( object ):
         param_dict = dict( [ ( p.name, p.value ) for p in job.parameters ] )
         param_dict = self.tool.params_from_strings( param_dict, self.app )
         return param_dict
-
+        
     def get_version_string_path( self ):
         return os.path.abspath(os.path.join(self.app.config.new_file_path, "GALAXY_VERSION_STRING_%s" % self.job_id))
-
+        
     def prepare( self ):
         """
         Prepare the job to run by creating the working directory and the
@@ -372,9 +372,9 @@ class JobWrapper( object ):
         out_data = dict( [ ( da.name, da.dataset ) for da in job.output_datasets ] )
         inp_data.update( [ ( da.name, da.dataset ) for da in job.input_library_datasets ] )
         out_data.update( [ ( da.name, da.dataset ) for da in job.output_library_datasets ] )
-
-        # Set up output dataset association for export history jobs. Because job
-        # uses a Dataset rather than an HDA or LDA, it's necessary to set up a
+        
+        # Set up output dataset association for export history jobs. Because job 
+        # uses a Dataset rather than an HDA or LDA, it's necessary to set up a 
         # fake dataset association that provides the needed attributes for
         # preparing a job.
         class FakeDatasetAssociation ( object ):
@@ -401,7 +401,7 @@ class JobWrapper( object ):
         # ( this used to be performed in the "exec_before_job" hook, but hooks are deprecated ).
         self.tool.exec_before_job( self.queue.app, inp_data, out_data, param_dict )
         # Run the before queue ("exec_before_job") hook
-        self.tool.call_hook( 'exec_before_job', self.queue.app, inp_data=inp_data,
+        self.tool.call_hook( 'exec_before_job', self.queue.app, inp_data=inp_data, 
                              out_data=out_data, tool=self.tool, param_dict=incoming)
         self.sa_session.flush()
         # Build any required config files
@@ -434,7 +434,7 @@ class JobWrapper( object ):
 
     def fail( self, message, exception=False ):
         """
-        Indicate job failure by setting state and message on all output
+        Indicate job failure by setting state and message on all output 
         datasets.
         """
         job = self.get_job()
@@ -480,7 +480,7 @@ class JobWrapper( object ):
         if self.tool:
             self.tool.job_failed( self, message, exception )
         self.cleanup()
-
+        
     def change_state( self, state, info = False ):
         job = self.get_job()
         self.sa_session.refresh( job )
@@ -510,12 +510,12 @@ class JobWrapper( object ):
         job.job_runner_external_id = external_id
         self.sa_session.add( job )
         self.sa_session.flush()
-
+        
     def finish( self, stdout, stderr ):
         """
-        Called to indicate that the associated command has been run. Updates
+        Called to indicate that the associated command has been run. Updates 
         the output datasets based on stderr and stdout from the command, and
-        the contents of the output files.
+        the contents of the output files. 
         """
         # default post job setup
         self.sa_session.expunge_all()
@@ -537,7 +537,7 @@ class JobWrapper( object ):
             if os.path.exists(version_filename):
                 self.version_string = open(version_filename).read()
                 os.unlink(version_filename)
-
+            
         if self.app.config.outputs_to_working_directory:
             for dataset_path in self.get_output_fnames():
                 try:
@@ -585,7 +585,7 @@ class JobWrapper( object ):
                             else:
                                 # Security violation.
                                 log.exception( "from_work_dir specified a location not in the working directory: %s, %s" % ( source_file, self.working_directory ) )
-
+            
                 dataset.blurb = 'done'
                 dataset.peek  = 'no peek'
                 dataset.info  = context['stdout'] + context['stderr']
@@ -600,7 +600,7 @@ class JobWrapper( object ):
                         dataset.init_meta( copy_from=dataset )
                     #if a dataset was copied, it won't appear in our dictionary:
                     #either use the metadata from originating output dataset, or call set_meta on the copies
-                    #it would be quicker to just copy the metadata from the originating output dataset,
+                    #it would be quicker to just copy the metadata from the originating output dataset, 
                     #but somewhat trickier (need to recurse up the copied_from tree), for now we'll call set_meta()
                     if not self.app.config.set_metadata_externally or \
                      ( not self.external_output_metadata.external_metadata_set_successfully( dataset, self.sa_session ) \
@@ -612,7 +612,7 @@ class JobWrapper( object ):
                         #load metadata from file
                         #we need to no longer allow metadata to be edited while the job is still running,
                         #since if it is edited, the metadata changed on the running output will no longer match
-                        #the metadata that was stored to disk for use via the external process,
+                        #the metadata that was stored to disk for use via the external process, 
                         #and the changes made by the user will be lost, without warning or notice
                         dataset.metadata.from_JSON_dict( self.external_output_metadata.get_output_filenames_by_dataset( dataset, self.sa_session ).filename_out )
                     try:
@@ -653,13 +653,13 @@ class JobWrapper( object ):
         # Flush all the dataset and job changes above.  Dataset state changes
         # will now be seen by the user.
         self.sa_session.flush()
-        # Save stdout and stderr
+        # Save stdout and stderr    
         if len( stdout ) > 32768:
             log.error( "stdout for job %d is greater than 32K, only first part will be logged to database" % job.id )
         job.stdout = stdout[:32768]
         if len( stderr ) > 32768:
             log.error( "stderr for job %d is greater than 32K, only first part will be logged to database" % job.id )
-        job.stderr = stderr[:32768]
+        job.stderr = stderr[:32768]  
         # custom post process setup
         inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] )
         out_data = dict( [ ( da.name, da.dataset ) for da in job.output_datasets ] )
@@ -676,8 +676,8 @@ class JobWrapper( object ):
         # ( this used to be performed in the "exec_after_process" hook, but hooks are deprecated ).
         self.tool.exec_after_process( self.queue.app, inp_data, out_data, param_dict, job = job )
         # Call 'exec_after_process' hook
-        self.tool.call_hook( 'exec_after_process', self.queue.app, inp_data=inp_data,
-                             out_data=out_data, param_dict=param_dict,
+        self.tool.call_hook( 'exec_after_process', self.queue.app, inp_data=inp_data, 
+                             out_data=out_data, param_dict=param_dict, 
                              tool=self.tool, stdout=stdout, stderr=stderr )
         job.command_line = self.command_line
 
@@ -696,7 +696,7 @@ class JobWrapper( object ):
         self.sa_session.flush()
         log.debug( 'job %d ended' % self.job_id )
         self.cleanup()
-
+        
     def cleanup( self ):
         # remove temporary files
         try:
@@ -710,10 +710,10 @@ class JobWrapper( object ):
             galaxy.tools.imp_exp.JobImportHistoryArchiveWrapper( self.job_id ).cleanup_after_job( self.sa_session )
         except:
             log.exception( "Unable to cleanup job %d" % self.job_id )
-
+        
     def get_command_line( self ):
         return self.command_line
-
+    
     def get_session_id( self ):
         return self.session_id
 
@@ -884,13 +884,17 @@ class TaskWrapper(JobWrapper):
     Should be refactored into a generalized executable unit wrapper parent, then jobs and tasks.
     """
     # Abstract this to be more useful for running tasks that *don't* necessarily compose a job.
-
+    
     def __init__(self, task, queue):
         super(TaskWrapper, self).__init__(task.job, queue)
         self.task_id = task.id
         self.working_directory = task.working_directory
+        if task.prepare_input_files_cmd is not None:
+            self.prepare_input_files_cmds = [ task.prepare_input_files_cmd ]
+        else:
+            self.prepare_input_files_cmds = None
         self.status = task.states.NEW
-
+       
     def get_job( self ):
         if self.job_id:
             return self.sa_session.query( model.Job ).get( self.job_id )
@@ -953,7 +957,7 @@ class TaskWrapper(JobWrapper):
         # ( this used to be performed in the "exec_before_job" hook, but hooks are deprecated ).
         self.tool.exec_before_job( self.queue.app, inp_data, out_data, param_dict )
         # Run the before queue ("exec_before_job") hook
-        self.tool.call_hook( 'exec_before_job', self.queue.app, inp_data=inp_data,
+        self.tool.call_hook( 'exec_before_job', self.queue.app, inp_data=inp_data, 
                              out_data=out_data, tool=self.tool, param_dict=incoming)
         self.sa_session.flush()
         # Build any required config files
@@ -1000,12 +1004,12 @@ class TaskWrapper(JobWrapper):
         task.state = state
         self.sa_session.add( task )
         self.sa_session.flush()
-
+            
     def get_state( self ):
         task = self.get_task()
         self.sa_session.refresh( task )
         return task.state
-
+        
     def set_runner( self, runner_url, external_id ):
         task = self.get_task()
         self.sa_session.refresh( task )
@@ -1014,15 +1018,15 @@ class TaskWrapper(JobWrapper):
         # DBTODO Check task job_runner_stuff
         self.sa_session.add( task )
         self.sa_session.flush()
-
+        
     def finish( self, stdout, stderr ):
         # DBTODO integrate previous finish logic.
         # Simple finish for tasks.  Just set the flag OK.
         log.debug( 'task %s for job %d ended' % (self.task_id, self.job_id) )
         """
-        Called to indicate that the associated command has been run. Updates
+        Called to indicate that the associated command has been run. Updates 
         the output datasets based on stderr and stdout from the command, and
-        the contents of the output files.
+        the contents of the output files. 
         """
         # default post job setup_external_metadata
         self.sa_session.expunge_all()
@@ -1039,7 +1043,7 @@ class TaskWrapper(JobWrapper):
             task.state = task.states.ERROR
         else:
             task.state = task.states.OK
-        # Save stdout and stderr
+        # Save stdout and stderr    
         if len( stdout ) > 32768:
             log.error( "stdout for task %d is greater than 32K, only first part will be logged to database" % task.id )
         task.stdout = stdout[:32768]
@@ -1053,7 +1057,7 @@ class TaskWrapper(JobWrapper):
     def cleanup( self ):
         # There is no task cleanup.  The job cleans up for all tasks.
         pass
-
+        
     def get_command_line( self ):
         return self.command_line
 
@@ -1063,7 +1067,7 @@ class TaskWrapper(JobWrapper):
     def get_output_file_id( self, file ):
         # There is no permanent output file for tasks.
         return None
-
+        
     def get_tool_provided_job_metadata( self ):
         # DBTODO Handle this as applicable for tasks.
         return None
@@ -1085,7 +1089,7 @@ class TaskWrapper(JobWrapper):
     def setup_external_metadata( self, exec_dir = None, tmp_dir = None, dataset_files_path = None, config_root = None, datatypes_config = None, set_extension = True, **kwds ):
         # There is no metadata setting for tasks.  This is handled after the merge, at the job level.
         return ""
-
+        
 class DefaultJobDispatcher( object ):
     def __init__( self, app ):
         self.app = app
@@ -1115,7 +1119,7 @@ class DefaultJobDispatcher( object ):
             runner = getattr( module, obj )
             self.job_runners[name] = runner( self.app )
             log.debug( 'Loaded job runner: %s' % display_name )
-
+            
     def put( self, job_wrapper ):
         try:
             if self.app.config.use_tasked_jobs and job_wrapper.tool.parallelism is not None:
@@ -1126,8 +1130,8 @@ class DefaultJobDispatcher( object ):
                     self.job_runners[runner_name].put( job_wrapper )
                 else:
                     runner_name = "tasks"
-                    log.debug( "dispatching job %d to %s runner" %( job_wrapper.job_id, runner_name ) )
-                    self.job_runners[runner_name].put( job_wrapper )
+                log.debug( "dispatching job %d to %s runner" %( job_wrapper.job_id, runner_name ) )
+                self.job_runners[runner_name].put( job_wrapper )
             else:
                 runner_name = ( job_wrapper.tool.job_runner.split(":", 1) )[0]
                 log.debug( "dispatching job %d to %s runner" %( job_wrapper.job_id, runner_name ) )
@@ -1183,7 +1187,7 @@ class JobStopQueue( object ):
         self.sleeper = Sleeper()
         self.running = True
         self.monitor_thread = threading.Thread( target=self.monitor )
-        self.monitor_thread.start()
+        self.monitor_thread.start()        
         log.info( "job stopper started" )
 
     def monitor( self ):
@@ -1263,4 +1267,3 @@ class NoopQueue( object ):
         return
     def shutdown( self ):
         return
-
diff --git a/lib/galaxy/jobs/runners/__init__.py b/lib/galaxy/jobs/runners/__init__.py
index 597d517309f..51d714b1296 100644
--- a/lib/galaxy/jobs/runners/__init__.py
+++ b/lib/galaxy/jobs/runners/__init__.py
@@ -6,6 +6,7 @@ class BaseJobRunner( object ):
         Compose the sequence of commands necessary to execute a job. This will
         currently include:
             - environment settings corresponding to any requirement tags
+            - preparing input files
             - command line taken from job wrapper
             - commands to set metadata (if include_metadata is True)
         """
@@ -17,10 +18,13 @@ class BaseJobRunner( object ):
         # Prepend version string
         if job_wrapper.version_string_cmd:
             commands = "%s &> %s; " % ( job_wrapper.version_string_cmd, job_wrapper.get_version_string_path() ) + commands
+        # prepend getting input files (if defined)
+        if hasattr(job_wrapper, 'prepare_input_files_cmds') and job_wrapper.prepare_input_files_cmds is not None:
+            commands = "; ".join( job_wrapper.prepare_input_files_cmds + [ commands ] ) 
         # Prepend dependency injection
         if job_wrapper.dependency_shell_commands:
             commands = "; ".join( job_wrapper.dependency_shell_commands + [ commands ] ) 
-        
+
         # Append metadata setting commands, we don't want to overwrite metadata
         # that was copied over in init_meta(), as per established behavior
         if include_metadata and self.app.config.set_metadata_externally:
diff --git a/lib/galaxy/jobs/runners/lwr.py b/lib/galaxy/jobs/runners/lwr.py
index 56d099b505c..465f92ba6f6 100644
--- a/lib/galaxy/jobs/runners/lwr.py
+++ b/lib/galaxy/jobs/runners/lwr.py
@@ -249,6 +249,12 @@ class LwrJobRunner( BaseJobRunner ):
 
         try:
             job_wrapper.prepare()
+            if hasattr(job_wrapper, 'prepare_input_files_cmds') and job_wrapper.prepare_input_files_cmds is not None:
+                for cmd in job_wrapper.prepare_input_file_cmds: # run the commands to stage the input files
+                    #log.debug( 'executing: %s' % cmd )
+                    if 0 != os.system(cmd):
+                        raise Exception('Error running file staging command: %s' % cmd)
+                job_wrapper.prepare_input_files_cmds = None # prevent them from being used in-line
             command_line = self.build_command_line( job_wrapper, include_metadata=False )
         except:
             job_wrapper.fail( "failure preparing job", exception=True )
diff --git a/lib/galaxy/jobs/splitters/multi.py b/lib/galaxy/jobs/splitters/multi.py
index 71df3058e76..dac31b06264 100644
--- a/lib/galaxy/jobs/splitters/multi.py
+++ b/lib/galaxy/jobs/splitters/multi.py
@@ -1,5 +1,6 @@
 import os, logging,  shutil
-from galaxy import model
+from galaxy import model, util
+
 
 log = logging.getLogger( __name__ )
     
@@ -54,7 +55,7 @@ def do_split (job_wrapper):
         raise Exception(log_error)
     
     # split the first one to build up the task directories
-    input_files = []
+    input_datasets = []
     for input in parent_job.input_datasets:
         if input.name in split_inputs:
             this_input_files = job_wrapper.get_input_dataset_fnames(input.dataset)
@@ -62,13 +63,13 @@ def do_split (job_wrapper):
                 log_error = "The input '%s' is composed of multiple files - splitting is not allowed" % str(input.name)
                 log.error(log_error)
                 raise Exception(log_error)
-            input_files.extend(this_input_files)    
+            input_datasets.append(input.dataset)
     
     input_type = type_to_input_map.keys()[0]
     # DBTODO execute an external task to do the splitting, this should happen at refactor.
     # If the number of tasks is sufficiently high, we can use it to calculate job completion % and give a running status.
     try:
-        input_type.split(input_files, get_new_working_directory_name, parallel_settings)
+        input_type.split(input_datasets, get_new_working_directory_name, parallel_settings)
     except AttributeError:
         log_error = "The type '%s' does not define a method for splitting files" % str(input_type)
         log.error(log_error)
@@ -82,8 +83,9 @@ def do_split (job_wrapper):
                 for file in names:
                     os.symlink(file, os.path.join(dir,  os.path.basename(file)))
     tasks = []
+    prepare_files = os.path.join(util.galaxy_directory(), 'extract_dataset_parts.sh') + ' %s'
     for dir in task_dirs:
-        task = model.Task(parent_job, dir)
+        task = model.Task(parent_job, dir, prepare_files % dir)
         tasks.append(task)
     return tasks
                                
@@ -106,44 +108,51 @@ def do_merge( job_wrapper,  task_wrappers):
     
     illegal_outputs = [x for x in merge_outputs if x in pickone_outputs]
     if len(illegal_outputs) > 0:
-        raise Exception("Outputs have conflicting parallelism attributes: %s" % str( illegal_outputs ))
-
+        return ('Tool file error', 'Outputs have conflicting parallelism attributes: %s' % str( illegal_outputs ))
     
-    working_directory = job_wrapper.working_directory
-    task_dirs = [os.path.join(working_directory, x) for x in os.listdir(working_directory) if x.startswith('task_')]
-    # TODO: Output datasets can be very complex. This doesn't handle metadata files
-    outputs = job_wrapper.get_output_datasets_and_fnames()
-    pickone_done = []
-    task_dirs = [os.path.join(working_directory, x) for x in os.listdir(working_directory) if x.startswith('task_')]
-    for output in outputs:
-        output_file_name = str(outputs[output][1])
-        base_output_name = os.path.basename(output_file_name)
-        if output in merge_outputs:
-            output_type = outputs[output][0].datatype
-            output_files = [os.path.join(dir,base_output_name) for dir in task_dirs]
-            log.debug('files %s ' % output_files)
-            output_type.merge(output_files, output_file_name)
-            log.debug('merge finished: %s' % output_file_name)
-            pass # TODO: merge all the files
-        elif output in pickone_outputs:
-            # just pick one of them
-            if output not in pickone_done:
-                task_file_name = os.path.join(task_dirs[0], base_output_name)
-                shutil.move( task_file_name,  output_file_name )
-                pickone_done.append(output)
-        else:
-            log_error = "The output '%s' does not define a method for implementing parallelism" % output
-            log.error(log_error)
-            raise Exception(log_error)
-
     stdout = ''
-    stderr=''
+    stderr = ''
+    
+    try:
+        working_directory = job_wrapper.working_directory
+        task_dirs = [os.path.join(working_directory, x) for x in os.listdir(working_directory) if x.startswith('task_')]
+        # TODO: Output datasets can be very complex. This doesn't handle metadata files
+        outputs = job_wrapper.get_output_datasets_and_fnames()
+        pickone_done = []
+        task_dirs = [os.path.join(working_directory, x) for x in os.listdir(working_directory) if x.startswith('task_')]
+        for output in outputs:
+            output_file_name = str(outputs[output][1])
+            base_output_name = os.path.basename(output_file_name)
+            if output in merge_outputs:
+                output_type = outputs[output][0].datatype
+                output_files = [os.path.join(dir,base_output_name) for dir in task_dirs]
+                log.debug('files %s ' % output_files)
+                output_type.merge(output_files, output_file_name)
+                log.debug('merge finished: %s' % output_file_name)
+                pass # TODO: merge all the files
+            elif output in pickone_outputs:
+                # just pick one of them
+                if output not in pickone_done:
+                    task_file_name = os.path.join(task_dirs[0], base_output_name)
+                    shutil.move( task_file_name,  output_file_name )
+                    pickone_done.append(output)
+            else:
+                log_error = "The output '%s' does not define a method for implementing parallelism" % output
+                log.error(log_error)
+                raise Exception(log_error)
+    except Exception, e:
+        stdout = 'Error merging files';
+        stderr = str(e)
+        
+
     for tw in task_wrappers:
         # Prevent repetitive output, e.g. "Sequence File Aligned"x20
         # Eventually do a reduce for jobs that output "N reads mapped", combining all N for tasks.
-        if stdout.strip() != tw.get_task().stdout.strip():
-            stdout += tw.get_task().stdout
-        if stderr.strip() != tw.get_task().stderr.strip():                        
-            stderr += tw.get_task().stderr
+        out = tw.get_task().stdout.strip()
+        err = tw.get_task().stderr.strip()
+        if len(out) > 0:
+            stdout += tw.working_directory + ':\n' + out
+        if len(err) > 0:
+            stderr += tw.working_directory + ':\n' + err
     return (stdout,  stderr)
     
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 0b887c5137d..c87a94e3d88 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -204,29 +204,19 @@ class Task( object ):
                     ERROR = 'error',
                     DELETED = 'deleted' )
 
-    def __init__( self, job, part_file = None ):
+    def __init__( self, job, working_directory, prepare_files_cmd ):
         self.command_line = None
         self.parameters = []
         self.state = Task.states.NEW
         self.info = None
-        # TODO: Rename this to working_directory
-        # Does this necessitate a DB migration step?
-        self.part_file = part_file
+        self.working_directory = working_directory
         self.task_runner_name = None
         self.task_runner_external_id = None
         self.job = job
         self.stdout = None
         self.stderr = None
+        self.prepare_input_files_cmd = prepare_files_cmd
     
-    @property
-    def working_directory(self):
-        if self.part_file is not None:
-            if not os.path.isdir(self.part_file):
-                return os.path.dirname(self.part_file)
-            else:
-                return self.part_file
-        return None
-
     def set_state( self, state ):
         self.state = state
 
@@ -907,7 +897,9 @@ class DatasetInstance( object ):
     def get_converted_files_by_type( self, file_type ):
         for assoc in self.implicitly_converted_datasets:
             if not assoc.deleted and assoc.type == file_type:
-                return assoc.dataset
+                if assoc.dataset:
+                    return assoc.dataset
+                return assoc.dataset_ldda
         return None
     def get_converted_dataset_deps(self, trans, target_ext):
         """
@@ -1599,7 +1591,12 @@ class DatasetToValidationErrorAssociation( object ):
 class ImplicitlyConvertedDatasetAssociation( object ):
     def __init__( self, id = None, parent = None, dataset = None, file_type = None, deleted = False, purged = False, metadata_safe = True ):
         self.id = id
-        self.dataset = dataset
+        if isinstance(dataset, HistoryDatasetAssociation):
+            self.dataset = dataset
+        elif isinstance(dataset, LibraryDatasetDatasetAssociation):
+            self.dataset_ldda = dataset
+        else:
+            raise AttributeError, 'Unknown dataset type provided for dataset: %s' % type( dataset )
         if isinstance(parent, HistoryDatasetAssociation):
             self.parent_hda = parent
         elif isinstance(parent, LibraryDatasetDatasetAssociation):
diff --git a/lib/galaxy/model/mapping.py b/lib/galaxy/model/mapping.py
index f013186a978..6187af2e9ed 100644
--- a/lib/galaxy/model/mapping.py
+++ b/lib/galaxy/model/mapping.py
@@ -148,6 +148,7 @@ ImplicitlyConvertedDatasetAssociation.table = Table( "implicitly_converted_datas
     Column( "create_time", DateTime, default=now ),
     Column( "update_time", DateTime, default=now, onupdate=now ),
     Column( "hda_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True, nullable=True ),
+    Column( "ldda_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), index=True, nullable=True ),
     Column( "hda_parent_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ),
     Column( "ldda_parent_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), index=True ),
     Column( "deleted", Boolean, index=True, default=False ),
@@ -469,9 +470,10 @@ Task.table = Table( "task", metadata,
     Column( "stderr", TEXT ),
     Column( "traceback", TEXT ),
     Column( "job_id", Integer, ForeignKey( "job.id" ), index=True, nullable=False ),
-    Column( "part_file", String(1024)),
+    Column( "working_directory", String(1024)),
     Column( "task_runner_name", String( 255 ) ),
-    Column( "task_runner_external_id", String( 255 ) ) )
+    Column( "task_runner_external_id", String( 255 ) ),
+    Column( "prepare_input_files_cmd", TEXT ) )
 
 PostJobAction.table = Table("post_job_action", metadata,
     Column("id", Integer, primary_key=True),
@@ -1211,6 +1213,9 @@ assign_mapper( context, ImplicitlyConvertedDatasetAssociation, ImplicitlyConvert
                         LibraryDatasetDatasetAssociation, 
                         primaryjoin=( ImplicitlyConvertedDatasetAssociation.table.c.ldda_parent_id == LibraryDatasetDatasetAssociation.table.c.id ) ),
                      
+                     dataset_ldda=relation( 
+                        LibraryDatasetDatasetAssociation, 
+                        primaryjoin=( ImplicitlyConvertedDatasetAssociation.table.c.ldda_id == LibraryDatasetDatasetAssociation.table.c.id ) ),
                      dataset=relation( 
                         HistoryDatasetAssociation, 
                         primaryjoin=( ImplicitlyConvertedDatasetAssociation.table.c.hda_id == HistoryDatasetAssociation.table.c.id ) ) ) )
@@ -1594,7 +1599,7 @@ assign_mapper( context, Page, Page.table,
                      annotations=relation( PageAnnotationAssociation, order_by=PageAnnotationAssociation.table.c.id, backref="pages" ),
                      ratings=relation( PageRatingAssociation, order_by=PageRatingAssociation.table.c.id, backref="pages" )  
                    ) )
-
+                   
 assign_mapper( context, ToolShedRepository, ToolShedRepository.table )
 
 # Set up proxy so that 
diff --git a/lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py b/lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py
new file mode 100644
index 00000000000..b2431c85710
--- /dev/null
+++ b/lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py
@@ -0,0 +1,63 @@
+"""
+Migration script to add 'prepare_input_files_cmd' column to the task table and to rename a column.
+"""
+
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+from migrate.changeset import *
+
+import logging
+log = logging.getLogger( __name__ )
+
+metadata = MetaData( migrate_engine )
+db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) )
+
+def upgrade():
+    print __doc__
+    metadata.reflect()
+    try:
+        task_table = Table( "task", metadata, autoload=True )
+        c = Column( "prepare_input_files_cmd", TEXT, nullable=True )
+        c.create( task_table )
+        assert c is task_table.c.prepare_input_files_cmd
+    except Exception, e:
+        print "Adding prepare_input_files_cmd column to task table failed: %s" % str( e )
+        log.debug( "Adding prepare_input_files_cmd column to task table failed: %s" % str( e ) )
+    try:
+        task_table = Table( "task", metadata, autoload=True )
+        c = Column( "working_directory", String ( 1024 ), nullable=True )
+        c.create( task_table )
+        assert c is task_table.c.working_directory
+    except Exception, e:
+        print "Adding working_directory column to task table failed: %s" % str( e )
+        log.debug( "Adding working_directory column to task table failed: %s" % str( e ) )
+
+    # remove the 'part_file' column - nobody used tasks before this, so no data needs to be migrated
+    try:
+        task_table.c.part_file.drop()
+    except Exception, e:
+        log.debug( "Deleting column 'part_file' from the 'task' table failed: %s" % ( str( e ) ) )
+
+def downgrade():
+    metadata.reflect()
+    try:
+        task_table = Table( "task", metadata, autoload=True )
+        task_table.c.prepare_input_files_cmd.drop()
+    except Exception, e:
+        print "Dropping prepare_input_files_cmd column from task table failed: %s" % str( e )
+        log.debug( "Dropping prepare_input_files_cmd column from task table failed: %s" % str( e ) )
+    try:
+        task_table = Table( "task", metadata, autoload=True )
+        task_table.c.working_directory.drop()
+    except Exception, e:
+        print "Dropping working_directory column from task table failed: %s" % str( e )
+        log.debug( "Dropping working_directory column from task table failed: %s" % str( e ) )
+    try:
+        task_table = Table( "task", metadata, autoload=True )
+        c = Column( "part_file", String ( 1024 ), nullable=True )
+        c.create( task_table )
+        assert c is task_table.c.part_file
+    except Exception, e:
+        print "Adding part_file column to task table failed: %s" % str( e )
+        log.debug( "Adding part_file column to task table failed: %s" % str( e ) )
diff --git a/lib/galaxy/util/__init__.py b/lib/galaxy/util/__init__.py
index cad925ec778..76655450295 100644
--- a/lib/galaxy/util/__init__.py
+++ b/lib/galaxy/util/__init__.py
@@ -623,6 +623,9 @@ ucsc_build_sites = read_build_sites( os.path.join( galaxy_root_path, "tool-data"
 gbrowse_build_sites = read_build_sites( os.path.join( galaxy_root_path, "tool-data", "shared", "gbrowse", "gbrowse_build_sites.txt" ) )
 genetrack_sites = read_build_sites( os.path.join( galaxy_root_path, "tool-data", "shared", "genetrack", "genetrack_sites.txt" ), check_builds=False )
 
+def galaxy_directory():
+    return os.path.abspath(galaxy_root_path)
+
 if __name__ == '__main__':
     import doctest, sys
     doctest.testmod(sys.modules[__name__], verbose=False)
diff --git a/scripts/extract_dataset_part.py b/scripts/extract_dataset_part.py
new file mode 100644
index 00000000000..99fb3583595
--- /dev/null
+++ b/scripts/extract_dataset_part.py
@@ -0,0 +1,48 @@
+"""
+Reads a JSON file and uses it to call into a datatype class to extract
+a subset of a dataset for processing.
+
+Used by jobs that split large files into pieces to be processed concurrently
+on a gid in a scatter-gather mode. This does part of the scatter.
+
+"""
+import os
+import sys
+import logging
+logging.basicConfig()
+log = logging.getLogger( __name__ )
+
+new_path = [ os.path.join( os.getcwd(), "lib" ) ]
+new_path.extend( sys.path[1:] ) # remove scripts/ from the path
+sys.path = new_path
+
+from galaxy import eggs
+import pkg_resources
+pkg_resources.require("simplejson")
+import simplejson
+
+# This junk is here to prevent loading errors
+import galaxy.model.mapping #need to load this before we unpickle, in order to setup properties assigned by the mappers
+galaxy.model.Job() #this looks REAL stupid, but it is REQUIRED in order for SA to insert parameters into the classes defined by the mappers --> it appears that instantiating ANY mapper'ed class would suffice here
+galaxy.datatypes.metadata.DATABASE_CONNECTION_AVAILABLE = False #Let metadata know that there is no database connection, and to just assume object ids are valid
+
+def __main__():
+    """
+    Argument: a JSON file
+    """
+    file_path = sys.argv.pop( 1 )
+    data = simplejson.load(open(file_path, 'r'))
+    try:
+        class_name_parts = data['class_name'].split('.')
+        module_name = '.'.join(class_name_parts[:-1])
+        class_name = class_name_parts[-1]
+        mod = __import__(module_name, globals(),  locals(),  [class_name])
+        cls = getattr(mod,  class_name)
+        if not cls.process_split_file(data):
+            sys.stderr.write('Writing split file failed\n')
+            sys.exit(1)
+    except Exception, e:
+        sys.stderr.write(str(e))
+        sys.exit(1)
+        
+__main__()

From a9870b2cd8a46357ab2da0b555c532d3755bc2be Mon Sep 17 00:00:00 2001
From: John Duddy <jduddy@illumina.com>
Date: Mon, 10 Oct 2011 12:07:19 -0700
Subject: [PATCH 034/362] Fix missing columns for Task, add migration to add
 ldda for associated types

---
 lib/galaxy/model/mapping.py                   |  1 +
 ...dd_ldda_id_to_implicit_conversion_table.py | 35 +++++++++++++++++++
 .../migrate/versions/0085_add_task_info.py    | 35 +++++++++++++++++++
 3 files changed, 71 insertions(+)
 create mode 100644 lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py
 create mode 100644 lib/galaxy/model/migrate/versions/0085_add_task_info.py

diff --git a/lib/galaxy/model/mapping.py b/lib/galaxy/model/mapping.py
index 6187af2e9ed..3ae5ac2f476 100644
--- a/lib/galaxy/model/mapping.py
+++ b/lib/galaxy/model/mapping.py
@@ -468,6 +468,7 @@ Task.table = Table( "task", metadata,
     Column( "runner_name", String( 255 ) ),
     Column( "stdout", TEXT ),
     Column( "stderr", TEXT ),
+    Column( "info", TrimmedString ( 255 ) ),
     Column( "traceback", TEXT ),
     Column( "job_id", Integer, ForeignKey( "job.id" ), index=True, nullable=False ),
     Column( "working_directory", String(1024)),
diff --git a/lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py b/lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py
new file mode 100644
index 00000000000..a10caee2f05
--- /dev/null
+++ b/lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py
@@ -0,0 +1,35 @@
+"""
+Migration script to add 'ldda_id' column to the implicitly_converted_dataset_association table.
+"""
+
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+from migrate.changeset import *
+
+import logging
+log = logging.getLogger( __name__ )
+
+metadata = MetaData( migrate_engine )
+db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) )
+
+def upgrade():
+    print __doc__
+    metadata.reflect()
+    try:
+        Implicitly_converted_table = Table( "implicitly_converted_dataset_association", metadata, autoload=True )
+        c = Column( "ldda_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), index=True, nullable=True )
+        c.create( Implicitly_converted_table )
+        assert c is Implicitly_converted_table.c.ldda_id
+    except Exception, e:
+        print "Adding ldda_id column to implicitly_converted_dataset_association table failed: %s" % str( e )
+        log.debug( "Adding ldda_id column to implicitly_converted_dataset_association table failed: %s" % str( e ) )
+
+def downgrade():
+    metadata.reflect()
+    try:
+        Implicitly_converted_table = Table( "implicitly_converted_dataset_association", metadata, autoload=True )
+        Implicitly_converted_table.c.ldda_id.drop()
+    except Exception, e:
+        print "Dropping ldda_id column from implicitly_converted_dataset_association table failed: %s" % str( e )
+        log.debug( "Dropping ldda_id column from implicitly_converted_dataset_association table failed: %s" % str( e ) )
diff --git a/lib/galaxy/model/migrate/versions/0085_add_task_info.py b/lib/galaxy/model/migrate/versions/0085_add_task_info.py
new file mode 100644
index 00000000000..368a91a0c2c
--- /dev/null
+++ b/lib/galaxy/model/migrate/versions/0085_add_task_info.py
@@ -0,0 +1,35 @@
+"""
+Migration script to add 'info' column to the task table.
+"""
+
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+from migrate.changeset import *
+
+import logging
+log = logging.getLogger( __name__ )
+
+metadata = MetaData( migrate_engine )
+db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) )
+
+def upgrade():
+    print __doc__
+    metadata.reflect()
+    try:
+        task_table = Table( "task", metadata, autoload=True )
+        c = Column( "info", TrimmedString (255) , nullable=True )
+        c.create( task_table )
+        assert c is task_table.c.info
+    except Exception, e:
+        print "Adding info column to table table failed: %s" % str( e )
+        log.debug( "Adding info column to task table failed: %s" % str( e ) )
+
+def downgrade():
+    metadata.reflect()
+    try:
+        task_table = Table( "task", metadata, autoload=True )
+        task_table.c.info.drop()
+    except Exception, e:
+        print "Dropping info column from task table failed: %s" % str( e )
+        log.debug( "Dropping info column from task table failed: %s" % str( e ) )

From 642688263c22bf9ce10070a3860deb0b7ad8c1ec Mon Sep 17 00:00:00 2001
From: John Duddy <jduddy@illumina.com>
Date: Mon, 10 Oct 2011 12:17:57 -0700
Subject: [PATCH 035/362] add FQTOC datatype to drive file splitting

---
 datatypes_conf.xml.sample                     | 21 ++++++--
 .../datatypes/converters/fastq_to_fqtoc.py    | 46 ++++++++++++++++++
 .../datatypes/converters/fastq_to_fqtoc.xml   | 13 +++++
 lib/galaxy/datatypes/sequence.py              | 48 +++++++++----------
 4 files changed, 99 insertions(+), 29 deletions(-)
 create mode 100644 lib/galaxy/datatypes/converters/fastq_to_fqtoc.py
 create mode 100644 lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml

diff --git a/datatypes_conf.xml.sample b/datatypes_conf.xml.sample
index 053009b4905..029903fc08c 100644
--- a/datatypes_conf.xml.sample
+++ b/datatypes_conf.xml.sample
@@ -56,11 +56,22 @@
       <converter file="fasta_to_2bit.xml" target_datatype="twobit"/>
       <converter file="fasta_to_len.xml" target_datatype="len"/>
     </datatype>
-    <datatype extension="fastq" type="galaxy.datatypes.sequence:Fastq" display_in_upload="true"/>
-    <datatype extension="fastqsanger" type="galaxy.datatypes.sequence:FastqSanger" display_in_upload="true"/>
-    <datatype extension="fastqsolexa" type="galaxy.datatypes.sequence:FastqSolexa" display_in_upload="true"/>
-    <datatype extension="fastqcssanger" type="galaxy.datatypes.sequence:FastqCSSanger" display_in_upload="true"/>
-    <datatype extension="fastqillumina" type="galaxy.datatypes.sequence:FastqIllumina" display_in_upload="true"/>
+    <datatype extension="fastq" type="galaxy.datatypes.sequence:Fastq" display_in_upload="true">
+        <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/>
+    </datatype>
+    <datatype extension="fastqsanger" type="galaxy.datatypes.sequence:FastqSanger" display_in_upload="true">
+        <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/>
+    </datatype>
+    <datatype extension="fastqsolexa" type="galaxy.datatypes.sequence:FastqSolexa" display_in_upload="true">
+        <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/>
+    </datatype>
+    <datatype extension="fastqcssanger" type="galaxy.datatypes.sequence:FastqCSSanger" display_in_upload="true">
+        <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/>
+    </datatype>
+    <datatype extension="fastqillumina" type="galaxy.datatypes.sequence:FastqIllumina" display_in_upload="true">
+        <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/>
+    </datatype>
+    <datatype extension="fqtoc" type="galaxy.datatypes.sequence:SequenceSplitLocations" display_in_upload="true"/>
     <datatype extension="eland" type="galaxy.datatypes.tabular:Eland" display_in_upload="true"/>
     <datatype extension="elandmulti" type="galaxy.datatypes.tabular:ElandMulti" display_in_upload="true"/>
     <datatype extension="genetrack" type="galaxy.datatypes.tracks:GeneTrack">
diff --git a/lib/galaxy/datatypes/converters/fastq_to_fqtoc.py b/lib/galaxy/datatypes/converters/fastq_to_fqtoc.py
new file mode 100644
index 00000000000..a4e3b6a8f70
--- /dev/null
+++ b/lib/galaxy/datatypes/converters/fastq_to_fqtoc.py
@@ -0,0 +1,46 @@
+#!/usr/bin/env python
+
+import sys, os, gzip
+from galaxy.datatypes.checkers import is_gzip
+
+
+def main():
+    """
+    The format of the file is JSON:
+    { "sections" : [
+            { "start" : "x", "end" : "y", "sequences" : "z" },
+            ...
+    ]}
+    This works only for UNCOMPRESSED fastq files. The Python GzipFile does not provide seekable
+    offsets via tell(), so clients just have to split the slow way
+    """
+    input_fname = sys.argv[1]
+    if is_gzip(input_fname):
+        print 'Conversion is only possible for uncompressed files'
+        sys.exit(1)
+
+    out_file = open(sys.argv[2], 'w')
+
+    current_line = 0
+    sequences=1000000
+    lines_per_chunk = 4*sequences
+    chunk_begin = 0
+
+    in_file = open(input_name)
+
+    out_file.write('{"sections" : [');
+
+    for line in in_file:
+        current_line += 1
+        if 0 == current_line % lines_per_chunk:
+            chunk_end = in_file.tell()
+            out_file.write('{"start":"%s","end":"%s","sequences":"%s"},' % (chunk_begin, chunk_end, sequences))
+            chunk_begin = chunk_end
+        
+    chunk_end = in_file.tell()
+    out_file.write('{"start":"%s","end":"%s","sequences":"%s"}' % (chunk_begin, chunk_end, (current_line % lines_per_chunk) / 4))
+    out_file.write(']}\n')
+    
+
+if __name__ == "__main__": 
+    main()
diff --git a/lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml b/lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml
new file mode 100644
index 00000000000..cf1d2f3ad11
--- /dev/null
+++ b/lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml
@@ -0,0 +1,13 @@
+<tool id="CONVERTER_fastq_to_fqtoc0" name="Convert FASTQ files to seek locations" version="1.0.0" hidden="true">
+  <command interpreter="python">fastq_to_fqtoc.py $input1 $output1</command>
+  <inputs>
+    <page>
+        <param format="fastq" name="input1" type="data" label="Choose FASTQ file"/>
+    </page>
+   </inputs>
+  <outputs>
+    <data format="fqtoc" name="output1"/>
+  </outputs>
+  <help>
+  </help>
+</tool>
diff --git a/lib/galaxy/datatypes/sequence.py b/lib/galaxy/datatypes/sequence.py
index feedebeeaa3..445c55fba8e 100644
--- a/lib/galaxy/datatypes/sequence.py
+++ b/lib/galaxy/datatypes/sequence.py
@@ -27,7 +27,7 @@ class SequenceSplitLocations( data.Text ):
     one OR an uncompressed file. In the GZIP case, each sub-file's location is stored in start and end. 
     The format of the file is JSON:
     { "sections" : [
-            { "start" : "x", "end" : "y", "clusters" : "z" },
+            { "start" : "x", "end" : "y", "sequences" : "z" },
             ...
     ]}
     """
@@ -53,7 +53,7 @@ class SequenceSplitLocations( data.Text ):
                 data = simplejson.load(open(filename))
                 sections = data['sections']
                 for section in sections:
-                    if 'start' not in section or 'end' not in section or 'clusters' not in section:
+                    if 'start' not in section or 'end' not in section or 'sequences' not in section:
                         return False
                 return True
             except:
@@ -96,20 +96,20 @@ class Sequence( data.Text ):
             dataset.peek = 'file does not exist'
             dataset.blurb = 'file purged from disk'
 
-    def get_sequences_per_file(total_clusters, split_params):
+    def get_sequences_per_file(total_sequences, split_params):
         if split_params['split_mode'] == 'number_of_parts':
             # legacy basic mode - split into a specified number of parts
             parts = int(split_params['split_size'])
-            sequences_per_file = [total_clusters/parts for i in range(parts)]
-            for i in range(total_clusters % parts):
+            sequences_per_file = [total_sequences/parts for i in range(parts)]
+            for i in range(total_sequences % parts):
                 sequences_per_file[i] += 1
         elif split_params['split_mode'] == 'to_size':
-            # loop through the sections and calculate the number of clusters
+            # loop through the sections and calculate the number of sequences
             chunk_size = long(split_params['split_size'])
 
-            chunks = total_clusters / chunk_size
-            rem = total_clusters % chunk_size
-            sequences_per_file = [chunk_size for i in range(total_clusters / chunk_size)]
+            chunks = total_sequences / chunk_size
+            rem = total_sequences % chunk_size
+            sequences_per_file = [chunk_size for i in range(total_sequences / chunk_size)]
             # TODO: Should we invest the time in a better way to handle small remainders?
             if rem > 0:
                 sequences_per_file.append(rem)
@@ -119,10 +119,10 @@ class Sequence( data.Text ):
     get_sequences_per_file = staticmethod(get_sequences_per_file)
 
     def do_slow_split( cls, input_datasets, subdir_generator_function, split_params):
-        # count the clusters so we can split
+        # count the sequences so we can split
         # TODO: if metadata is present, take the number of lines / 4
         if input_datasets[0].metadata is not None and input_datasets[0].metadata.sequences is not None:
-            total_clusters = input_datasets[0].metadata.sequences
+            total_sequences = input_datasets[0].metadata.sequences
         else:
             input_file = input_datasets[0].file_name
             compress = is_gzip(input_file)
@@ -136,23 +136,23 @@ class Sequence( data.Text ):
                 # TODO
                 # Add BufferedReader if python 2.7?
                 in_file = open(input_file, 'rt')
-            total_clusters = long(0)
+            total_sequences = long(0)
             for i, line in enumerate(in_file):
-                total_clusters += 1
+                total_sequences += 1
             in_file.close()
-            total_clusters /= 4
+            total_sequences /= 4
 
-        sequences_per_file = cls.get_sequences_per_file(total_clusters, split_params)
+        sequences_per_file = cls.get_sequences_per_file(total_sequences, split_params)
         return cls.write_split_files(input_datasets, None, subdir_generator_function, sequences_per_file)
     do_slow_split = classmethod(do_slow_split)
 
     def do_fast_split( cls, input_datasets, toc_file_datasets, subdir_generator_function, split_params):
         data = simplejson.load(open(toc_file_datasets[0].file_name))
         sections = data['sections']
-        total_clusters = long(0)
+        total_sequences = long(0)
         for section in sections:
-            total_clusters += long(section['clusters'])
-        sequences_per_file = cls.get_sequences_per_file(total_clusters, split_params)
+            total_sequences += long(section['sequences'])
+        sequences_per_file = cls.get_sequences_per_file(total_sequences, split_params)
         return cls.write_split_files(input_datasets, toc_file_datasets, subdir_generator_function, sequences_per_file)
     do_fast_split = classmethod(do_fast_split)
 
@@ -165,7 +165,7 @@ class Sequence( data.Text ):
             directories.append(dir)
             return dir
 
-        # we know how many splits and how many clusters in each. What remains is to write out instructions for the 
+        # we know how many splits and how many sequences in each. What remains is to write out instructions for the 
         # splitting of all the input files. To decouple the format of those instructions from this code, the exact format of
         # those instructions is delegated to scripts
         start_sequence=0
@@ -241,7 +241,7 @@ class Sequence( data.Text ):
         """
         Uses a Table of Contents dict, parsed from an FQTOC file, to come up with a set of
         shell commands that will extract the parts necessary
-        >>> three_sections=[dict(start=0, end=74, clusters=10), dict(start=74, end=148, clusters=10), dict(start=148, end=148+76, clusters=10)]
+        >>> three_sections=[dict(start=0, end=74, sequences=10), dict(start=74, end=148, sequences=10), dict(start=148, end=148+76, sequences=10)]
         >>> Sequence.get_split_commands_with_toc('./input.gz', './output.gz', dict(sections=three_sections), start_sequence=0, sequence_count=10)
         ['dd bs=1 skip=0 count=74 if=./input.gz 2> /dev/null >> ./output.gz']
         >>> Sequence.get_split_commands_with_toc('./input.gz', './output.gz', dict(sections=three_sections), start_sequence=1, sequence_count=5)
@@ -261,8 +261,8 @@ class Sequence( data.Text ):
         current_sequence = long(0)
         i=0
         # skip to the section that contains my starting sequence
-        while i < len(sections) and start_sequence >= current_sequence + long(sections[i]['clusters']):
-            current_sequence += long(sections[i]['clusters'])
+        while i < len(sections) and start_sequence >= current_sequence + long(sections[i]['sequences']):
+            current_sequence += long(sections[i]['sequences'])
             i += 1
         if i == len(sections): # bad input data!
             raise Exception('No FQTOC section contains starting sequence %s' % start_sequence)
@@ -277,7 +277,7 @@ class Sequence( data.Text ):
             # we need to extract partial data. So, find the byte offsets of the chunks that contain the data we need
             # use a combination of dd (to pull just the right sections out) tail (to skip lines) and head (to get the 
             # right number of lines
-            sequences = long(sections[i]['clusters'])
+            sequences = long(sections[i]['sequences'])
             skip_sequences = start_sequence-current_sequence
             sequences_to_extract = min(sequence_count, sequences-skip_sequences)
             start_copy = long(sections[i]['start'])
@@ -832,4 +832,4 @@ class Lav( data.Text ):
 
 if __name__ == '__main__':
     import doctest, sys
-    doctest.testmod(sys.modules[__name__])
\ No newline at end of file
+    doctest.testmod(sys.modules[__name__])

From 491959bb527070cb9fbb077b78fa1c18df89c063 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Mon, 10 Oct 2011 15:45:31 -0400
Subject: [PATCH 036/362] Make purged histories visible in the history list
 grid, make any history viewable from the grid.

---
 lib/galaxy/web/controllers/history.py | 43 ++++++++++++++++++++++-----
 templates/display_common.mako         |  2 +-
 templates/history/view.mako           | 28 ++++++++++++-----
 3 files changed, 58 insertions(+), 15 deletions(-)

diff --git a/lib/galaxy/web/controllers/history.py b/lib/galaxy/web/controllers/history.py
index 7e2f27f637b..9ee28edf66b 100644
--- a/lib/galaxy/web/controllers/history.py
+++ b/lib/galaxy/web/controllers/history.py
@@ -59,6 +59,21 @@ class HistoryListGrid( grids.Grid ):
             if not history.deleted:
                 link = dict( operation="Switch", id=history.id, use_panels=grid.use_panels )
             return link
+    class DeletedColumn( grids.DeletedColumn ):
+        def get_value( self, trans, grid, history ):
+            if history == trans.history:
+                return "<strong>current history</strong>"
+            if history.purged:
+                return "deleted permanently"
+            elif history.deleted:
+                return "deleted"
+            return ""
+        def sort( self, trans, query, ascending, column_name=None ):
+            if ascending:
+                query = query.order_by( self.model_class.table.c.purged.asc(), self.model_class.table.c.update_time.desc() )
+            else:
+                query = query.order_by( self.model_class.table.c.purged.desc(), self.model_class.table.c.update_time.desc() )
+            return query
 
     # Grid definition
     title = "Saved Histories"
@@ -74,8 +89,7 @@ class HistoryListGrid( grids.Grid ):
         grids.GridColumn( "Size on Disk", key="get_disk_size_bytes", format=nice_size, sortable=False ),
         grids.GridColumn( "Created", key="create_time", format=time_ago ),
         grids.GridColumn( "Last Updated", key="update_time", format=time_ago ),
-        # Columns that are valid for filtering but are not visible.
-        grids.DeletedColumn( "Status", key="deleted", visible=False, filterable="advanced" )
+        DeletedColumn( "Status", key="deleted", filterable="advanced" )
     ]
     columns.append(
         grids.MulticolFilterColumn(
@@ -85,11 +99,12 @@ class HistoryListGrid( grids.Grid ):
                 )
     operations = [
         grids.GridOperation( "Switch", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ),
+        grids.GridOperation( "View", allow_multiple=False ),
         grids.GridOperation( "Share or Publish", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ),
         grids.GridOperation( "Rename", condition=( lambda item: not item.deleted ), async_compatible=False  ),
         grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), async_compatible=True ),
-        grids.GridOperation( "Delete Permanently", confirm="History contents will be removed from disk, this cannot be undone.  Continue?", async_compatible=True ),
-        grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ), async_compatible=True ),
+        grids.GridOperation( "Delete Permanently", condition=( lambda item: not item.purged ), confirm="History contents will be removed from disk, this cannot be undone.  Continue?", async_compatible=True ),
+        grids.GridOperation( "Undelete", condition=( lambda item: item.deleted and not item.purged ), async_compatible=True ),
     ]
     standard_filters = [
         grids.GridColumnFilter( "Active", args=dict( deleted=False ) ),
@@ -104,7 +119,7 @@ class HistoryListGrid( grids.Grid ):
     def get_current_item( self, trans, **kwargs ):
         return trans.get_history()
     def apply_query_filter( self, trans, query, **kwargs ):
-        return query.filter_by( user=trans.user, purged=False, importing=False )
+        return query.filter_by( user=trans.user, importing=False )
 
 class SharedHistoryListGrid( grids.Grid ):
     # Custom column types
@@ -212,6 +227,15 @@ class HistoryController( BaseUIController, Sharable, UsesAnnotations, UsesItemRa
                 if 'name' in kwargs:
                     del kwargs['name'] # Remove ajax name param that rename method uses
                 return self.rename( trans, **kwargs )
+            if operation == "view":
+                history = self.get_history( trans, kwargs.get( 'id', None ) )
+                if history:
+                    return trans.response.send_redirect( url_for( controller='history',
+                                                                  action='view',
+                                                                  id=kwargs['id'],
+                                                                  show_deleted=history.deleted,
+                                                                  use_panels=False ) )
+                    #return self.view( trans, id=kwargs['id'], show_deleted=history.deleted, use_panels=False )
             history_ids = util.listify( kwargs.get( 'id', [] ) )
             # Display no message by default
             status, message = None, None
@@ -793,7 +817,7 @@ class HistoryController( BaseUIController, Sharable, UsesAnnotations, UsesItemRa
             """ % ( web.url_for( id=id, confirm=True, referer=trans.request.referer ), referer_message ), use_panels=True )
 
     @web.expose
-    def view( self, trans, id=None, show_deleted=False ):
+    def view( self, trans, id=None, show_deleted=False, use_panels=True ):
         """View a history. If a history is importable, then it is viewable by any user."""
         # Get history to view.
         if not id:
@@ -808,10 +832,15 @@ class HistoryController( BaseUIController, Sharable, UsesAnnotations, UsesItemRa
         # View history.
         show_deleted = util.string_as_bool( show_deleted )
         datasets = self.get_history_datasets( trans, history_to_view, show_deleted=show_deleted )
+        try:
+            use_panels = util.string_as_bool( use_panels )
+        except:
+            pass # already a bool
         return trans.stream_template_mako( "history/view.mako",
                                            history = history_to_view,
                                            datasets = datasets,
-                                           show_deleted = show_deleted )
+                                           show_deleted = show_deleted,
+                                           use_panels = use_panels )
 
     @web.expose
     def display_by_username_and_slug( self, trans, username, slug ):
diff --git a/templates/display_common.mako b/templates/display_common.mako
index 937fec95b85..c8aef4f7271 100644
--- a/templates/display_common.mako
+++ b/templates/display_common.mako
@@ -138,7 +138,7 @@
     %if history.slug and history.user.username:
         <% return h.url_for( controller='/history', action='display_by_username_and_slug', username=history.user.username, slug=history.slug, qualified=qualify ) %>
     %else:
-        <% return h.url_for( controller='/history', action='view', id=trans.security.encode_id( history.id ), qualified=qualify ) %>
+        <% return h.url_for( controller='/history', action='view', id=trans.security.encode_id( history.id ), qualified=qualify, use_panels=context.get('use_panels', True) ) %>
     %endif
 </%def>
 
diff --git a/templates/history/view.mako b/templates/history/view.mako
index fc8fc8d2856..fdef5575a9f 100644
--- a/templates/history/view.mako
+++ b/templates/history/view.mako
@@ -1,8 +1,16 @@
-<%inherit file="/webapps/galaxy/base_panels.mako"/>
 <%namespace file="/display_common.mako" import="get_history_link, get_controller_name" />
 <%namespace file="/root/history_common.mako" import="render_dataset" />
 <%namespace file="/tagging_common.mako" import="render_individual_tagging_element, render_community_tagging_element" />
 
+<%!
+    def inherit(context):
+        if context.get('use_panels'):
+            return '/webapps/galaxy/base_panels.mako'
+        else:
+            return '/base.mako'
+%>
+<%inherit file="${inherit(context)}"/>
+
 <%def name="javascripts()">
     ${parent.javascripts()}
     ${h.js( "galaxy.base", "jquery", "json2", "jstorage" )}
@@ -63,6 +71,10 @@
 %>
 </%def>
 
+<%def name="body()">
+    ${center_panel()}
+</%def>
+
 <%def name="center_panel()">
     ## Get URL to other histories owned by user that owns this history.
     <%
@@ -81,14 +93,16 @@
         <div style="overflow: auto; height: 100%;">
             ## Render view of history.
             <div id="top-links" class="historyLinks" style="padding: 0px 0px 5px 0px">
+                %if not history.purged:
                     <a href="${h.url_for( action='imp', id=trans.security.encode_id(history.id) )}">import and start using history</a> |
-                <a href="${get_history_link( history )}">${_('refresh')}</a> 
-                %if show_deleted:
-                | <a href="${h.url_for( id=trans.security.encode_id(history.id), show_deleted=False )}">${_('hide deleted')}</a> 
-                %else:
-                | <a href="${h.url_for( id=trans.security.encode_id(history.id), show_deleted=True )}">${_('show deleted')}</a> 
+                    <a href="${get_history_link( history )}">${_('refresh')}</a> |
                 %endif
-                | <a href="#" class="toggle">collapse all</a>
+                %if show_deleted:
+                    <a href="${h.url_for( id=trans.security.encode_id(history.id), show_deleted=False, use_panels=use_panels )}">${_('hide deleted')}</a> |
+                %else:
+                    <a href="${h.url_for( id=trans.security.encode_id(history.id), show_deleted=True, use_panels=use_panels )}">${_('show deleted')}</a> |
+                %endif
+                <a href="#" class="toggle">collapse all</a>
             </div>
 
             <div id="history-name-area" class="historyLinks" style="color: gray; font-weight: bold; padding: 0px 0px 5px 0px">

From d14faced7a90b698ff662d6fccdd083eabf34eef Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Mon, 10 Oct 2011 15:51:43 -0400
Subject: [PATCH 037/362] Miscellaneous enhancements for the tool shed: 1.
 Enable the same behavior for the config settings named "tool_config_file" and
 "tool_config_files" since this config setting can now be a comma-separated
 list of file names.

2. Display an error message if a user attempts to install a Galaxy tool shed repository but they do not have a shed tool config file named in the "tool_config_file" setting in universe_wsgi.ini.

3. If tool search using whoosh is enabled, re-index the tool box when new tools are installed from a tool shed.
---
 lib/galaxy/config.py                |  8 +++++++-
 lib/galaxy/web/controllers/admin.py | 13 +++++++++++++
 universe_wsgi.ini.sample            |  4 ++--
 3 files changed, 22 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py
index e556555a23a..a5369a3256a 100644
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -52,7 +52,13 @@ class Configuration( object ):
         self.tool_data_path = resolve_path( kwargs.get( "tool_data_path", "tool-data" ), os.getcwd() )
         self.len_file_path = kwargs.get( "len_file_path", resolve_path(os.path.join(self.tool_data_path, 'shared','ucsc','chrom'), self.root) )
         self.test_conf = resolve_path( kwargs.get( "test_conf", "" ), self.root )
-        self.tool_configs = [ resolve_path( p, self.root ) for p in listify( kwargs.get( 'tool_config_file', 'tool_conf.xml' ) ) ]    
+        if 'tool_config_file' in kwargs:
+            tcf = kwargs[ 'tool_config_file' ]
+        elif 'tool_config_files' in kwargs:
+            tcf = kwargs[ 'tool_config_files' ]
+        else:
+            tcf = 'tool_conf.xml'
+        self.tool_configs = [ resolve_path( p, self.root ) for p in listify( tcf ) ] 
         self.tool_data_table_config_path = resolve_path( kwargs.get( 'tool_data_table_config_path', 'tool_data_table_conf.xml' ), self.root )
         self.tool_secret = kwargs.get( "tool_secret", "" )
         self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" )
diff --git a/lib/galaxy/web/controllers/admin.py b/lib/galaxy/web/controllers/admin.py
index 6ca4cb6e328..c6e6bd583c5 100644
--- a/lib/galaxy/web/controllers/admin.py
+++ b/lib/galaxy/web/controllers/admin.py
@@ -2,6 +2,7 @@ from galaxy.web.base.controller import *
 from galaxy import model
 from galaxy.model.orm import *
 from galaxy.web.framework.helpers import time_ago, iff, grids
+from galaxy.tools.search import ToolBoxSearch
 import logging
 log = logging.getLogger( __name__ )
 
@@ -693,6 +694,15 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
     @web.expose
     @web.require_admin
     def install_tool_shed_repository( self, trans, **kwd ):
+        if not trans.app.toolbox.shed_tool_confs:
+            message = 'The <b>tool_config_file</b> setting in <b>universe_wsgi.ini</b> must include at least one shed tool configuration file name with a '
+            message += '<b>&lt;toolbox&gt;</b> tag that includes a <b>tool_path</b> attribute value which is a directory relative to the Galaxy installation '
+            message += 'directory in order to automatically install tools from a Galaxy tool shed (e.g., the file name <b>shed_tool_conf.xml</b> whose '
+            message += '<b>&lt;toolbox&gt;</b> tag is <b>&lt;toolbox tool_path="../shed_tools"&gt;</b>).<p/>See the '
+            message += '<a href="http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance" '
+            message += 'target=_blank">Automatic installation of Galaxy tool shed repository tools into a local Galaxy instance</a> section of the '
+            message += '<a href="http://wiki.g2.bx.psu.edu/Tool%20Shed" target="_blank">Galaxy tool shed wiki</a> for all of the details.'
+            return trans.show_error_message( message )
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
@@ -782,6 +792,9 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
                                     pass
                                 # Append the new section to the shed_tool_config file.
                                 self.__add_shed_tool_conf_entry( trans, shed_tool_conf, new_tool_section )
+                                if trans.app.toolbox_search.enabled:
+                                    # If search support for tools is enabled, index the new installed tools.
+                                    trans.app.toolbox_search = ToolBoxSearch( trans.app.toolbox )
                             message = 'Revision <b>%s</b> of repository <b>%s</b> has been installed in tool panel section <b>%s</b>.' % \
                                 ( changeset_revision, name, tool_section.name )
                             return trans.show_ok_message( message )
diff --git a/universe_wsgi.ini.sample b/universe_wsgi.ini.sample
index 9ff6d4fed97..1cadd24543b 100644
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -124,8 +124,8 @@ paste.app_factory = galaxy.web.buildapp:app_factory
 #new_file_path = database/tmp
 
 # Tool config files, defines what tools are available in Galaxy.
-# Tools can be locally developed or installed from tool sheds.
-#tool_config_file = tool_conf.xml
+# Tools can be locally developed or installed from Galaxy tool sheds.
+#tool_config_file = tool_conf.xml,shed_tool_conf.xml
 
 # Default path to the directory containing the tools defined in tool_conf.xml.
 # Other tool config files must include the tool_path as an attribute in the <toolbox> tag.

From a1d4bb9babe3d255bc7f5aff9df3a925cfb89f66 Mon Sep 17 00:00:00 2001
From: Jennifer Jackson <jen@bx.psu.edu>
Date: Mon, 10 Oct 2011 18:33:48 -0400
Subject: [PATCH 038/362] Other genome description: revised all, corrected
 canonical male

---
 tools/sr_mapping/bowtie_color_wrapper.xml | 2 +-
 tools/sr_mapping/bowtie_wrapper.xml       | 2 +-
 tools/sr_mapping/bwa_color_wrapper.xml    | 2 +-
 tools/sr_mapping/bwa_wrapper.xml          | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/tools/sr_mapping/bowtie_color_wrapper.xml b/tools/sr_mapping/bowtie_color_wrapper.xml
index af2d465dc43..2c94a618597 100644
--- a/tools/sr_mapping/bowtie_color_wrapper.xml
+++ b/tools/sr_mapping/bowtie_color_wrapper.xml
@@ -566,7 +566,7 @@ Bowtie accepts files in Sanger FASTQ format. Use the FASTQ Groomer to prepare yo
 
 **A Note on Built-in Reference Genomes**
 
-Some genomes have multiple variants. If only one "type" of genome is listed, it is the Full version, which means that everything that came in the original genome data download (possibly with mitochondrial and plasmid DNA added if it wasn't already included). The Full version is available for every genome. Some genomes also come in the Canonical variant, which contains only the "canonical" (well-defined) chromosomes or segments, such as chr1-chr22, chrX, chrY, and chrM for human. Other variations include gender. These will come in the canonical form only, so the general Canonical variant is actually Canonical Female and the other is Canonical Male (identical to female excluding chrX).
+The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped and other plasmid segments. When only one version of a genome is available in this tool, it represents the default "Full" variant. Some genomes will have more than one variant available. The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY.
 
 ------
 
diff --git a/tools/sr_mapping/bowtie_wrapper.xml b/tools/sr_mapping/bowtie_wrapper.xml
index d743677e532..420511c4d2c 100644
--- a/tools/sr_mapping/bowtie_wrapper.xml
+++ b/tools/sr_mapping/bowtie_wrapper.xml
@@ -687,7 +687,7 @@ Bowtie accepts files in Sanger FASTQ format. Use the FASTQ Groomer to prepare yo
 
 **A Note on Built-in Reference Genomes**
 
-Some genomes have multiple variants. If only one "type" of genome is listed, it is the Full version, which means that everything that came in the original genome data download (possibly with mitochondrial and plasmid DNA added if it wasn't already included). The Full version is available for every genome. Some genomes also come in the Canonical variant, which contains only the "canonical" (well-defined) chromosomes or segments, such as chr1-chr22, chrX, chrY, and chrM for human. Other variations include gender. These will come in the canonical form only, so the general Canonical variant is actually Canonical Female and the other is Canonical Male (identical to female excluding chrX).
+The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped and other plasmid segments. When only one version of a genome is available in this tool, it represents the default "Full" variant. Some genomes will have more than one variant available. The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY.
 
 ------
 
diff --git a/tools/sr_mapping/bwa_color_wrapper.xml b/tools/sr_mapping/bwa_color_wrapper.xml
index 36ccec9d352..b09aa3ee86b 100644
--- a/tools/sr_mapping/bwa_color_wrapper.xml
+++ b/tools/sr_mapping/bwa_color_wrapper.xml
@@ -342,7 +342,7 @@ If you have Color Space Sanger, it must be converted to nucleotide-space first.
 
 **A Note on Built-in Reference Genomes**
 
-Some genomes have multiple variants. If only one "type" of genome is listed, it is the Full version, which means that everything that came in the original genome data download (possibly with mitochondrial and plasmid DNA added if it wasn't already included). The Full version is available for every genome. Some genomes also come in the Canonical variant, which contains only the "canonical" (well-defined) chromosomes or segments, such as chr1-chr22, chrX, chrY, and chrM for human. Other variations include gender. These will come in the canonical form only, so the general Canonical variant is actually Canonical Female and the other is Canonical Male (identical to female excluding chrX).
+The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped and other plasmid segments. When only one version of a genome is available in this tool, it represents the default "Full" variant. Some genomes will have more than one variant available. The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY.
 
 ------
 
diff --git a/tools/sr_mapping/bwa_wrapper.xml b/tools/sr_mapping/bwa_wrapper.xml
index 5344a0a7f44..0a232a8dfe6 100644
--- a/tools/sr_mapping/bwa_wrapper.xml
+++ b/tools/sr_mapping/bwa_wrapper.xml
@@ -334,7 +334,7 @@ BWA accepts files in either Sanger FASTQ format (galaxy type *fastqsanger*) or I
 
 **A Note on Built-in Reference Genomes**
 
-Some genomes have multiple variants. If only one "type" of genome is listed, it is the Full version, which means that everything that came in the original genome data download (possibly with mitochondrial and plasmid DNA added if it wasn't already included). The Full version is available for every genome. Some genomes also come in the Canonical variant, which contains only the "canonical" (well-defined) chromosomes or segments, such as chr1-chr22, chrX, chrY, and chrM for human. Other variations include gender. These will come in the canonical form only, so the general Canonical variant is actually Canonical Female and the other is Canonical Male (identical to female excluding chrX).
+The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped and other plasmid segments. When only one version of a genome is available in this tool, it represents the default "Full" variant. Some genomes will have more than one variant available. The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY.
 
 ------
 

From 2ff5dcfb33ce47fe984384866fd9ce9693ff6835 Mon Sep 17 00:00:00 2001
From: Jennifer Jackson <jen@bx.psu.edu>
Date: Mon, 10 Oct 2011 18:42:31 -0400
Subject: [PATCH 039/362] Other genome description: corrected typo.

---
 tools/sr_mapping/bowtie_color_wrapper.xml | 2 +-
 tools/sr_mapping/bowtie_wrapper.xml       | 2 +-
 tools/sr_mapping/bwa_color_wrapper.xml    | 2 +-
 tools/sr_mapping/bwa_wrapper.xml          | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/tools/sr_mapping/bowtie_color_wrapper.xml b/tools/sr_mapping/bowtie_color_wrapper.xml
index 2c94a618597..04e2e79f52d 100644
--- a/tools/sr_mapping/bowtie_color_wrapper.xml
+++ b/tools/sr_mapping/bowtie_color_wrapper.xml
@@ -566,7 +566,7 @@ Bowtie accepts files in Sanger FASTQ format. Use the FASTQ Groomer to prepare yo
 
 **A Note on Built-in Reference Genomes**
 
-The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped and other plasmid segments. When only one version of a genome is available in this tool, it represents the default "Full" variant. Some genomes will have more than one variant available. The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY.
+The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped, plasmid, and other segments. When only one version of a genome is available in this tool, it represents the default "Full" variant. Some genomes will have more than one variant available. The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY.
 
 ------
 
diff --git a/tools/sr_mapping/bowtie_wrapper.xml b/tools/sr_mapping/bowtie_wrapper.xml
index 420511c4d2c..8bd57c3d6ee 100644
--- a/tools/sr_mapping/bowtie_wrapper.xml
+++ b/tools/sr_mapping/bowtie_wrapper.xml
@@ -687,7 +687,7 @@ Bowtie accepts files in Sanger FASTQ format. Use the FASTQ Groomer to prepare yo
 
 **A Note on Built-in Reference Genomes**
 
-The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped and other plasmid segments. When only one version of a genome is available in this tool, it represents the default "Full" variant. Some genomes will have more than one variant available. The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY.
+The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped, plasmid, and other segments. When only one version of a genome is available in this tool, it represents the default "Full" variant. Some genomes will have more than one variant available. The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY.
 
 ------
 
diff --git a/tools/sr_mapping/bwa_color_wrapper.xml b/tools/sr_mapping/bwa_color_wrapper.xml
index b09aa3ee86b..1a6040dde82 100644
--- a/tools/sr_mapping/bwa_color_wrapper.xml
+++ b/tools/sr_mapping/bwa_color_wrapper.xml
@@ -342,7 +342,7 @@ If you have Color Space Sanger, it must be converted to nucleotide-space first.
 
 **A Note on Built-in Reference Genomes**
 
-The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped and other plasmid segments. When only one version of a genome is available in this tool, it represents the default "Full" variant. Some genomes will have more than one variant available. The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY.
+The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped, plasmid, and other segments. When only one version of a genome is available in this tool, it represents the default "Full" variant. Some genomes will have more than one variant available. The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY.
 
 ------
 
diff --git a/tools/sr_mapping/bwa_wrapper.xml b/tools/sr_mapping/bwa_wrapper.xml
index 0a232a8dfe6..bd27181746d 100644
--- a/tools/sr_mapping/bwa_wrapper.xml
+++ b/tools/sr_mapping/bwa_wrapper.xml
@@ -334,7 +334,7 @@ BWA accepts files in either Sanger FASTQ format (galaxy type *fastqsanger*) or I
 
 **A Note on Built-in Reference Genomes**
 
-The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped and other plasmid segments. When only one version of a genome is available in this tool, it represents the default "Full" variant. Some genomes will have more than one variant available. The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY.
+The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped, plasmid, and other segments. When only one version of a genome is available in this tool, it represents the default "Full" variant. Some genomes will have more than one variant available. The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY.
 
 ------
 

From 9b98a68127bbc9b839b88be98ab3d22eacdb2290 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Tue, 11 Oct 2011 10:09:32 -0400
Subject: [PATCH 040/362] Add Secure Hash/Message Digest tool to
 tool_conf.xml.main.

---
 tool_conf.xml.main | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tool_conf.xml.main b/tool_conf.xml.main
index 80af7fe1b34..34f94f96206 100644
--- a/tool_conf.xml.main
+++ b/tool_conf.xml.main
@@ -45,6 +45,7 @@
     <tool file="filters/tailWrapper.xml" />
     <tool file="filters/trimmer.xml" />
     <tool file="filters/wc_gnu.xml" />
+    <tool file="filters/secure_hash_message_digest.xml" />
   </section>
   <section name="Convert Formats" id="convert">
     <tool file="filters/bed2gff.xml" />

From 9d70c02ccbdcdb71fa92f736f2991b3a59d78c68 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 11 Oct 2011 09:42:05 -0500
Subject: [PATCH 041/362] Small refactoring to the code used by job runners and
 job wrapper to access the job runner url and compute the job runner name.
 Should not change functionality at all, just tighten some abstractions and
 reduce code duplication.

---
 lib/galaxy/jobs/__init__.py      | 27 +++++++++++++++------------
 lib/galaxy/jobs/runners/drmaa.py |  4 ++--
 lib/galaxy/jobs/runners/lwr.py   |  4 ++--
 lib/galaxy/jobs/runners/pbs.py   |  4 ++--
 lib/galaxy/jobs/runners/sge.py   |  4 ++--
 5 files changed, 23 insertions(+), 20 deletions(-)

diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 4998dfb7e61..966bb661d5a 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -331,6 +331,9 @@ class JobWrapper( object ):
         # Wrapper holding the info required to restore and clean up from files used for setting metadata externally
         self.external_output_metadata = metadata.JobExternalOutputMetadataWrapper( job )
 
+    def get_job_runner( self ):
+        return self.tool.job_runner
+
     def get_job( self ):
         return self.sa_session.query( model.Job ).get( self.job_id )
 
@@ -1102,22 +1105,22 @@ class DefaultJobDispatcher( object ):
             self.job_runners[name] = runner( self.app )
             log.debug( 'Loaded job runner: %s' % display_name )
 
+    def __get_runner_name( self, job_wrapper ):
+        if self.app.config.use_tasked_jobs and job_wrapper.tool.parallelism is not None and not isinstance(job_wrapper, TaskWrapper):
+            runnner_name = "tasks"
+        else:
+            runner_name = ( job_wrapper.get_job_runner().split(":", 1) )[0]
+        return runner_name
+
     def put( self, job_wrapper ):
         try:
-            if self.app.config.use_tasked_jobs and job_wrapper.tool.parallelism is not None:
-                if isinstance(job_wrapper, TaskWrapper):
-                    #DBTODO Refactor
-                    runner_name = ( job_wrapper.tool.job_runner.split(":", 1) )[0]
-                    log.debug( "dispatching task %s, of job %d, to %s runner" %( job_wrapper.task_id, job_wrapper.job_id, runner_name ) )
-                    self.job_runners[runner_name].put( job_wrapper )
-                else:
-                    runner_name = "tasks"
-                    log.debug( "dispatching job %d to %s runner" %( job_wrapper.job_id, runner_name ) )
-                    self.job_runners[runner_name].put( job_wrapper )
+            runner_name = self.__get_runner_name( job_wrapper )
+            if self.app.config.use_tasked_jobs and job_wrapper.tool.parallelism is not None and isinstance(job_wrapper, TaskWrapper):
+                #DBTODO Refactor
+                log.debug( "dispatching task %s, of job %d, to %s runner" %( job_wrapper.task_id, job_wrapper.job_id, runner_name ) )
             else:
-                runner_name = ( job_wrapper.tool.job_runner.split(":", 1) )[0]
                 log.debug( "dispatching job %d to %s runner" %( job_wrapper.job_id, runner_name ) )
-                self.job_runners[runner_name].put( job_wrapper )
+            self.job_runners[runner_name].put( job_wrapper )
         except KeyError:
             log.error( 'put(): (%s) Invalid job runner: %s' % ( job_wrapper.job_id, runner_name ) )
             job_wrapper.fail( 'Unable to run job due to a misconfiguration of the Galaxy job running system.  Please contact a site administrator.' )
diff --git a/lib/galaxy/jobs/runners/drmaa.py b/lib/galaxy/jobs/runners/drmaa.py
index 440851e74eb..805d5d771ce 100644
--- a/lib/galaxy/jobs/runners/drmaa.py
+++ b/lib/galaxy/jobs/runners/drmaa.py
@@ -128,7 +128,7 @@ class DRMAAJobRunner( BaseJobRunner ):
             log.exception("failure running job %s" % job_wrapper.get_id_tag())
             return
 
-        runner_url = job_wrapper.tool.job_runner
+        runner_url = job_wrapper.get_job_runner()
         
         # This is silly, why would we queue a job with no command line?
         if not command_line:
@@ -336,7 +336,7 @@ class DRMAAJobRunner( BaseJobRunner ):
         drm_job_state.efile = "%s/database/pbs/%s.e" % (os.getcwd(), job.id)
         drm_job_state.job_file = "%s/database/pbs/galaxy_%s.sh" % (os.getcwd(), job.id)
         drm_job_state.job_id = str( job.job_runner_external_id )
-        drm_job_state.runner_url = job_wrapper.tool.job_runner
+        drm_job_state.runner_url = job_wrapper.get_job_runner()
         job_wrapper.command_line = job.command_line
         drm_job_state.job_wrapper = job_wrapper
         if job.state == model.Job.states.RUNNING:
diff --git a/lib/galaxy/jobs/runners/lwr.py b/lib/galaxy/jobs/runners/lwr.py
index 56d099b505c..9e04a5ace37 100644
--- a/lib/galaxy/jobs/runners/lwr.py
+++ b/lib/galaxy/jobs/runners/lwr.py
@@ -236,7 +236,7 @@ class LwrJobRunner( BaseJobRunner ):
         return  lwr_url 
 
     def get_client_from_wrapper(self, job_wrapper):
-        return self.get_client( job_wrapper.tool.job_runner, job_wrapper.job_id )
+        return self.get_client( job_wrapper.get_job_runner(), job_wrapper.job_id )
 
     def get_client(self, job_runner, job_id):
         lwr_url = self.determine_lwr_url( job_runner )
@@ -245,7 +245,7 @@ class LwrJobRunner( BaseJobRunner ):
     def run_job( self, job_wrapper ):
         stderr = stdout = command_line = ''
 
-        runner_url = job_wrapper.tool.job_runner
+        runner_url = job_wrapper.get_job_runner()
 
         try:
             job_wrapper.prepare()
diff --git a/lib/galaxy/jobs/runners/pbs.py b/lib/galaxy/jobs/runners/pbs.py
index 11c4925a2c5..d92b1aff9d4 100644
--- a/lib/galaxy/jobs/runners/pbs.py
+++ b/lib/galaxy/jobs/runners/pbs.py
@@ -204,7 +204,7 @@ class PBSJobRunner( BaseJobRunner ):
             log.exception("failure running job %d" % job_wrapper.job_id)
             return
 
-        runner_url = job_wrapper.tool.job_runner
+        runner_url = job_wrapper.get_job_runner()
         
         # This is silly, why would we queue a job with no command line?
         if not command_line:
@@ -581,7 +581,7 @@ class PBSJobRunner( BaseJobRunner ):
         pbs_job_state.efile = "%s/%s.e" % (self.app.config.cluster_files_directory, job.id)
         pbs_job_state.job_file = "%s/%s.sh" % (self.app.config.cluster_files_directory, job.id)
         pbs_job_state.job_id = str( job.job_runner_external_id )
-        pbs_job_state.runner_url = job_wrapper.tool.job_runner
+        pbs_job_state.runner_url = job_wrapper.get_job_runner()
         job_wrapper.command_line = job.command_line
         pbs_job_state.job_wrapper = job_wrapper
         if job.state == model.Job.states.RUNNING:
diff --git a/lib/galaxy/jobs/runners/sge.py b/lib/galaxy/jobs/runners/sge.py
index c7b9f3f60ae..7db3777d339 100644
--- a/lib/galaxy/jobs/runners/sge.py
+++ b/lib/galaxy/jobs/runners/sge.py
@@ -164,7 +164,7 @@ class SGEJobRunner( BaseJobRunner ):
             log.exception("failure running job %d" % job_wrapper.job_id)
             return
 
-        runner_url = job_wrapper.tool.job_runner
+        runner_url = job_wrapper.get_job_runner()
         
         # This is silly, why would we queue a job with no command line?
         if not command_line:
@@ -377,7 +377,7 @@ class SGEJobRunner( BaseJobRunner ):
         sge_job_state.efile = "%s/database/pbs/%s.e" % (os.getcwd(), job.id)
         sge_job_state.job_file = "%s/database/pbs/galaxy_%s.sh" % (os.getcwd(), job.id)
         sge_job_state.job_id = str( job.job_runner_external_id )
-        sge_job_state.runner_url = job_wrapper.tool.job_runner
+        sge_job_state.runner_url = job_wrapper.get_job_runner()
         job_wrapper.command_line = job.command_line
         sge_job_state.job_wrapper = job_wrapper
         if job.state == model.Job.states.RUNNING:

From 31569d239671be59398baae6df27b9f49bfe51ff Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Tue, 11 Oct 2011 14:05:08 -0400
Subject: [PATCH 042/362] Trackster: in pack mode for feature tracks, show
 feature details on mouseover. Also: (a) provide general method for rounding
 numbers; (b) return numerical filter values as floats rather than strings;
 and (c) pack scripts.

---
 .../visualization/tracks/data_providers.py    |  10 +-
 static/june_2007_style/blue/trackster.css     |   3 +-
 static/june_2007_style/trackster.css.tmpl     |   7 +-
 static/scripts/packed/trackster.js            |   2 +-
 static/scripts/trackster.js                   | 154 +++++++++++++++---
 5 files changed, 142 insertions(+), 34 deletions(-)

diff --git a/lib/galaxy/visualization/tracks/data_providers.py b/lib/galaxy/visualization/tracks/data_providers.py
index 787b4ad32e8..437870e547c 100644
--- a/lib/galaxy/visualization/tracks/data_providers.py
+++ b/lib/galaxy/visualization/tracks/data_providers.py
@@ -804,7 +804,7 @@ def package_gff_feature( feature, no_detail=False, filter_cols=[] ):
     # Return full feature.
     payload = [ feature.start, 
                 feature.end, 
-                feature.name(), 
+                feature.name(),
                 feature.strand,
                 # No notion of thick start, end in GFF, so make everything
                 # thick.
@@ -828,9 +828,13 @@ def package_gff_feature( feature, no_detail=False, filter_cols=[] ):
     # Add filter data to payload.
     for col in filter_cols:
         if col == "Score":
-            payload.append( feature.score )
+            payload.append( float( feature.score ) )
         elif col in feature.attributes:
-            payload.append( feature.attributes[col] )
+            try:
+                payload.append( float( feature.attributes[col] ) )
+            except:
+                # Feature is not a float.
+                payload.append( feature.attributes[col] )
         else:
             # Dummy value.
             payload.append( "na" )
diff --git a/static/june_2007_style/blue/trackster.css b/static/june_2007_style/blue/trackster.css
index 240576b1da7..0c37f05b0a9 100644
--- a/static/june_2007_style/blue/trackster.css
+++ b/static/june_2007_style/blue/trackster.css
@@ -24,7 +24,7 @@
 .track{background:white;}
 .track-header{text-align:left;padding:4px 0px;color:#666;}
 .track-header .menubutton{margin-left:0px;}
-.track-content{overflow:hidden;text-align:center;border-top:1px solid #eee;border-bottom:2px solid #eee;background:#eee url('/static/images/tracks/diag_bg.gif');min-height:16px;}
+.track-content{text-align:center;border-top:1px solid #eee;border-bottom:2px solid #eee;background:#eee url('/static/images/tracks/diag_bg.gif');min-height:16px;}
 .label-track .track-content{background:white;}
 .track-tile{background:white;}
 .track-tile canvas{position:relative;z-index:100;}
@@ -62,3 +62,4 @@ input{font:10px verdana;}
 .icon.more-across{background:url('../images/fugue/arrow-transition-bw.png') no-repeat 0px 0px;}
 .intro{padding:1em;}
 .intro > .action-button{background-color:#CCC;padding:1em;}
+.feature-popup{background-color:#DDD;position:absolute;z-index:1000}
diff --git a/static/june_2007_style/trackster.css.tmpl b/static/june_2007_style/trackster.css.tmpl
index 2b58db5bb43..f5012db8c14 100644
--- a/static/june_2007_style/trackster.css.tmpl
+++ b/static/june_2007_style/trackster.css.tmpl
@@ -156,7 +156,6 @@
 }
 
 .track-content {
-    overflow: hidden;
     text-align: center;
     border-top: 1px solid #eee;
     border-bottom: 2px solid #eee;
@@ -335,4 +334,8 @@ input {
     background-color: #CCC;
     padding: 1em;
 }
-
+.feature-popup{ 
+    background-color: #DDD;
+    position: absolute;
+    z-index: 1000
+}
diff --git a/static/scripts/packed/trackster.js b/static/scripts/packed/trackster.js
index 07737a929f9..eab64c3be2b 100644
--- a/static/scripts/packed/trackster.js
+++ b/static/scripts/packed/trackster.js
@@ -1 +1 @@
-var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var trackster_module=function(f,aa){var q=f("class").extend,t=f("slotting"),N=f("painters");var ag=function(ah,ai){this.document=ah;this.default_font=ai!==undefined?ai:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};q(ag.prototype,{load_pattern:function(ah,al){var ai=this.patterns,aj=this.dummy_context,ak=new Image();ak.src=image_path+al;ak.onload=function(){ai[ah]=aj.createPattern(ak,"repeat")}},get_pattern:function(ah){return this.patterns[ah]},new_canvas:function(){var ah=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ah)}ah.manager=this;return ah}});var o={};var m=function(ah,ai){o[ah.attr("id")]=ai};var n=function(ah,aj,al,ak){al=".group";var ai={};o[ah.attr("id")]=ak;ah.bind("drag",{handle:"."+aj,relative:true},function(au,av){var at=$(this);var ay=$(this).parent(),ap=ay.children(),ar=o[$(this).attr("id")],ao,an,aw,am,aq;an=$(this).parents(al);if(an.length!==0){aw=an.position().top;am=aw+an.outerHeight();if(av.offsetY<aw){$(this).insertBefore(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable_before(ar,ax);return}else{if(av.offsetY>am){$(this).insertAfter(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable(ar);return}}}an=null;for(aq=0;aq<ap.length;aq++){ao=$(ap.get(aq));aw=ao.position().top;am=aw+ao.outerHeight();if(ao.is(al)&&this!==ao.get(0)&&av.offsetY>=aw&&av.offsetY<=am){if(av.offsetY-aw<am-av.offsetY){ao.find(".content-div").prepend(this)}else{ao.find(".content-div").append(this)}if(ar.container){ar.container.remove_drawable(ar)}o[ao.attr("id")].add_drawable(ar);return}}for(aq=0;aq<ap.length;aq++){if(av.offsetY<$(ap.get(aq)).position().top){break}}if(aq===ap.length){if(this!==ap.get(aq-1)){ay.append(this);o[ay.attr("id")].move_drawable(ar,aq)}}else{if(this!==ap.get(aq)){$(this).insertBefore(ap.get(aq));o[ay.attr("id")].move_drawable(ar,(av.deltaY>0?aq-1:aq))}}}).bind("dragstart",function(){ai["border-top"]=ah.css("border-top");ai["border-bottom"]=ah.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ai)})};aa.moveable=n;var af=16,I=9,F=20,V=I+2,B=100,K=12000,T=200,E=5,w=10,M=5000,x=100,p="There was an error in indexing this dataset. ",L="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",u="Currently indexing... please wait",z="Tool cannot be rerun: ",a="Loading data...",ab="Ready for display",d=10,v=5,D=5;function y(ah){return Math.round(ah*1000)/1000}var c=function(ah){this.num_elements=ah;this.clear()};q(c.prototype,{get:function(ai){var ah=this.key_ary.indexOf(ai);if(ah!==-1){if(this.obj_cache[ai].stale){this.key_ary.splice(ah,1);delete this.obj_cache[ai]}else{this.move_key_to_end(ai,ah)}}return this.obj_cache[ai]},set:function(ai,aj){if(!this.obj_cache[ai]){if(this.key_ary.length>=this.num_elements){var ah=this.key_ary.shift();delete this.obj_cache[ah]}this.key_ary.push(ai)}this.obj_cache[ai]=aj;return aj},move_key_to_end:function(ai,ah){this.key_ary.splice(ah,1);this.key_ary.push(ai)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var U=function(ai,ah,aj){c.call(this,ai);this.track=ah;this.subset=(aj!==undefined?aj:true)};q(U.prototype,c.prototype,{load_data:function(aq,al,ao,ai,an){var ap=this.track.view.chrom,ak={chrom:ap,low:aq,high:al,mode:ao,resolution:ai,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ak,an);if(this.track.filters_manager){var ar=[];var ah=this.track.filters_manager.filters;for(var am=0;am<ah.length;am++){ar[ar.length]=ah[am].name}ak.filter_cols=JSON.stringify(ar)}var aj=this;return $.getJSON(this.track.data_url,ak,function(at){aj.set_data(aq,al,ao,at)})},get_data:function(ah,al,am,ai,ak){var aj=this.get_data_from_cache(ah,al,am);if(aj){return aj}aj=this.load_data(ah,al,am,ai,ak);this.set_data(ah,al,am,aj);return aj},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ap,ak,ao,aj,an,al){var aq=this.get_data_from_cache(ap,ak,ao);if(!aq){console.log("ERROR: no current data for: ",this.track,ap,ak,ao,aj,an);return}aq.stale=true;var ai=ap;if(al===this.DEEP_DATA_REQ){$.extend(an,{start_val:aq.data.length+1})}else{if(al===this.BROAD_DATA_REQ){ai=(aq.max_high?aq.max_high:aq.data[aq.data.length-1][2])+1}}var ah=this,am=this.load_data(ai,ak,ao,aj,an);new_data_available=$.Deferred();this.set_data(ap,ak,ao,new_data_available);$.when(am).then(function(ar){if(ar.data){ar.data=aq.data.concat(ar.data);if(ar.max_low){ar.max_low=aq.max_low}if(ar.message){ar.message=ar.message.replace(/[0-9]+/,ar.data.length)}}ah.set_data(ap,ak,ao,ar);new_data_available.resolve(ar)});return new_data_available},get_data_from_cache:function(ah,ai,aj){return this.get(this.gen_key(ah,ai,aj))},set_data:function(ai,aj,ak,ah){return this.set(this.gen_key(ai,aj,ak),ah)},gen_key:function(ah,aj,ak){var ai=ah+"_"+aj+"_"+ak;return ai},split_key:function(ah){return ah.split("_")}});var J=function(ai,ah,aj){U.call(this,ai,ah,aj)};q(J.prototype,U.prototype,c.prototype,{load_data:function(aj,ah,al,am,ai,ak){if(ai>1){return}return U.prototype.load_data.call(this,aj,ah,al,am,ai,ak)}});var r=function(ak,ai,ah,aj,al){this.name=ak;this.view=ai;this.container=ah;this.drag_handle_class=al;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak}],saved_values:aj,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values};q(r.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},make_name_popup_menu:function(){},set_name:function(ah){this.old_name=this.name;this.name=ah;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var A=function(al,ak,ai,ah,aj,am){r.call(this,ak,ai,ah,aj,am);this.obj_type=al;this.drawables=[]};q(A.prototype,r.prototype,{init:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah].init()}},_draw:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah]._draw()}},to_json:function(){var ai=[];for(var ah=0;ah<this.drawables.length;ah++){ai.push(this.drawables[ah].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ai}},add_drawable:function(ah){this.drawables.push(ah);ah.container=this},add_drawable_before:function(aj,ah){var ai=this.drawables.indexOf(ah);if(ai!=-1){this.drawables.splice(ai,0,aj);return true}return false},remove_drawable:function(ai){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);ai.container=null;return true}return false},move_drawable:function(ai,aj){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);this.drawables.splice(aj,0,ai);return true}return false}});var S=function(ak,ai,ah,aj){A.call(this,"DrawableGroup",ak,ai,ah,aj,"group-handle");if(!S.id_counter){S.id_counter=0}var al=S.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+al).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+al+"_content_div").appendTo(this.container_div);m(this.container_div,this);m(this.content_div,this);n(this.container_div,this.drag_handle_class,".group",this);this.make_name_popup_menu()};q(S.prototype,r.prototype,A.prototype,{make_name_popup_menu:function(){var ai=this;var ah={};ah["Edit configuration"]=function(){var al=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aj=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(am){if((am.keyCode||am.which)===27){al()}else{if((am.keyCode||am.which)===13){aj()}}};$(window).bind("keypress.check_enter_esc",ak);show_modal("Configure Group",ai.config.build_form(),{Cancel:al,OK:aj})};ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)}});var ae=function(ah,ak,aj,ai){A.call(this,"View");this.container=ah;this.chrom=null;this.vis_id=aj;this.dbkey=ai;this.title=ak;this.tracks=this.drawables;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ag(ah.get(0).ownerDocument);this.reset()};q(ae.prototype,A.prototype,{init:function(){var aj=this.container,ah=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aj);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;m(this.viewport_container,ah);this.intro_div=$("<div/>").addClass("intro");var ak=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ai=function(al){if(al.type==="focusout"||(al.keyCode||al.which)===13||(al.keyCode||al.which)===27){if((al.keyCode||al.which)!==27){ah.go_to($(this).val())}$(this).hide();$(this).val("");ah.location_span.show();ah.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ai).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ah.location_span.hide();ah.chrom_select.hide();ah.nav_input.val(ah.chrom+":"+ah.low+"-"+ah.high);ah.nav_input.css("display","inline-block");ah.nav_input.select();ah.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ah.zoom_out();ah.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.browser_content_div.click(function(al){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("<div />").css({height:ah.browser_content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,{content_div:this.top_labeltrack}));this.add_label_track(new ad(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new C(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(al,ai,an){if(!al||al==="None"){return}var ak=this;if(al==="previous"){ak.load_chroms({low:this.chrom_start_index-x});return}if(al==="next"){ak.load_chroms({low:this.chrom_start_index+x});return}var am=$.grep(ak.chrom_data,function(ap,aq){return ap.chrom===al})[0];if(am===undefined){ak.load_chroms({chrom:al},function(){ak.change_chrom(al,ai,an)});return}else{if(al!==ak.chrom){ak.chrom=al;ak.chrom_select.val(ak.chrom);ak.max_high=am.len-1;ak.reset();ak.request_redraw(true);for(var ao=0,ah=ak.tracks.length;ao<ah;ao++){var aj=ak.tracks[ao];if(aj.init){aj.init()}}}if(ai!==undefined&&an!==undefined){ak.low=Math.max(ai,0);ak.high=Math.min(an,ak.max_high)}ak.reset_overview();ak.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){A.prototype.add_drawable.call(this,ah);ah.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;ah.init();this.label_tracks.push(ah)},remove_drawable:function(aj,ai){A.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.tracks),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(E,Math.ceil(Math.log((this.high-this.low)/T)/Math.log(E)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){$.when(ah.get_overview_tile()).then(function(ai){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ai.canvas);view.overview_highlight.show().height(ai.canvas.height());view.overview_viewport.height(ai.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ah;ah.set_is_overview(true)});view.has_changes=true},reset_overview:function(){this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new P(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},al=this.track,aj=ai.tool_id+al.tool_region_and_parameters_str(ai.chrom,ai.low,ai.high),ah,am;if(al.container===view){var ak=new S(this.name,this.track.view,this.track.container);al.container.add_drawable(ak);al.container.remove_drawable(al);ak.add_drawable(al);al.container_div.appendTo(ak.content_div);ah=ak}else{ah=al.container}if(al instanceof e){am=new X(aj,view,ah,"hda");am.change_mode(al.mode);ah.add_drawable(am)}am.content_div.text("Starting job.");this.run(ai,am,function(an){am.dataset_id=an.dataset_id;am.content_div.text("Running job.");am.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(L)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(z+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var P=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){P.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var Y=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};q(Y.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=parseFloat(ah[this.index]);return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(ar,ay){this.track=ar;this.filters=[];for(var at=0;at<ay.length;at++){var au=ay[at],az=au.name,ah=au.type,ak=au.index,ax=au.tool_id,aw=au.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[at]=new Y(az,ak,ax,aw)}else{console.log("ERROR: unsupported filter: ",az,ah)}}var al=function(aA,aB,aC){aA.click(function(){var aD=aB.text();max=parseFloat(aC.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aC.slider("option","values")){input_size=2*input_size+1;multi_value=true}aB.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aD).appendTo(aB).focus().select().click(function(aE){aE.stopPropagation()}).blur(function(){$(this).remove();aB.text(aD)}).keyup(function(aI){if(aI.keyCode===27){$(this).trigger("blur")}else{if(aI.keyCode===13){var aG=aC.slider("option","min"),aE=aC.slider("option","max"),aH=function(aJ){return(isNaN(aJ)||aJ>aE||aJ<aG)},aF=$(this).val();if(!multi_value){aF=parseFloat(aF);if(aH(aF)){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}else{aF=aF.split("-");aF=[parseFloat(aF[0]),parseFloat(aF[1])];if(aH(aF[0])||aH(aF[1])){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}aC.slider((multi_value?"values":"value"),aF)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aA){aA.stopPropagation()}).click(function(aA){aA.stopPropagation()}).bind("dblclick",function(aA){aA.stopPropagation()}).bind("keydown",function(aA){aA.stopPropagation()});var av=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aD,aF){aF.container=$("<div/>").addClass("slider-row").appendTo(av);var aE=$("<div/>").addClass("elt-label").appendTo(aF.container);var aC=$("<span/>").addClass("slider-name").text(aF.name+"  ").appendTo(aE);var aB=$("<span/>");var aH=$("<span/>").addClass("slider-value").appendTo(aE).append("[").append(aB).append("]");var aA=$("<div/>").addClass("slider").appendTo(aF.container);aF.control_element=$("<div/>").attr("id",aF.name+"-filter-control").appendTo(aA);var aG=[0,0];aF.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aJ,aK){var aI=aK.values;aB.text(aI[0]+"-"+aI[1]);aF.low=aI[0];aF.high=aI[1];ap.track.request_draw(true,true)},change:function(aI,aJ){aF.control_element.slider("option","slide").call(aF.control_element,aI,aJ)}});aF.slider=aF.control_element;aF.slider_label=aB;al(aH,aB,aF.control_element);$("<div style='clear: both;'/>").appendTo(aF.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(av);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var aj=this;ao.click(function(){aj.run_on_dataset()})}var aq=$("<div/>").addClass("display-controls").appendTo(this.parent_div),an=$("<span/>").addClass("elt-label").text("Transparency:").appendTo(aq),ai=$("<select/>").attr("name","alpha_dropdown").appendTo(aq);this.alpha_filter=null;$("<option/>").attr("value",-1).text("== None ==").appendTo(ai);for(var at=0;at<this.filters.length;at++){$("<option/>").attr("value",at).text(this.filters[at].name).appendTo(ai)}ai.change(function(){$(this).children("option:selected").each(function(){var aA=parseInt($(this).val());ap.alpha_filter=(aA>=0?ap.filters[aA]:null);ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var Q=function(ai,ah){N.AlphaGenerator.call(this,ah);this.filter=ai};Q.prototype.gen_alpha=function(ah){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_alpha}return((parseFloat(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var H=function(ah){this.track=ah.track;this.params=ah.params;this.values={};this.restore_values((ah.saved_values?ah.saved_values:{}));this.onchange=ah.onchange};q(H.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(aj,ai,ah,ak){this.index=aj;this.low=aj*T*ai;this.high=(aj+1)*T*ai;this.resolution=ai;this.canvas=$("<div class='track-tile'/>").append(ah);this.data=ak;this.stale=false};var l=function(aj,ai,ah,ak,al){b.call(this,aj,ai,ah,ak);this.max_val=al};var R=function(ak,aj,ai,an,am,ah){b.call(this,ak,aj,ai,an);this.message=am;this.feature_mapper=ah;var al=this;$(this.canvas).mousemove(function(ap){var ao=al.feature_mapper.get_feature_data(ap.offsetX,ap.offsetY)})};var j=function(ak,ai,ah,aj,al,am){r.call(this,ak,ai,ah,{},"draghandle");this.data_url=(al?al:default_data_url);this.data_url_extra_params={};this.data_query_wait=(am?am:M);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.container_div=$("<div />").addClass("track").attr("id","track_"+j.id_counter++).css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof C){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Z){return"ReadTrack"}else{if(this instanceof X){return"ToolDataFeatureTrack"}else{if(this instanceof W){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var ak=ah.view.tracks.indexOf(ah);var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(L)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(G)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.make_name_popup_menu()}ah.content_div.text(ab);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}})},predraw_init:function(){},});var O=function(ao,am){var ai=this,ap=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=new ac(this,(ao!==undefined?ao:{}));this.filters_available=false;this.filters_visible=false;this.tool=(am!==undefined&&obj_length(am)>0?new s(this,am):undefined);this.is_overview=false;if(ai.hidden){return}if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(ai.display_modes!==undefined){if(ai.mode_div===undefined){ai.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ai.header_div);var aj=(ai.config&&ai.config.values.mode?ai.config.values.mode:ai.display_modes[0]);ai.mode=aj;ai.mode_div.text(aj);var ah={};for(var ak=0,an=ai.display_modes.length;ak<an;ak++){var al=ai.display_modes[ak];ah[al]=function(aq){return function(){ai.change_mode(aq)}}(al)}make_popupmenu(ai.mode_div,ah)}else{ai.mode_div.hide()}}this.make_name_popup_menu()};q(O.prototype,r.prototype,j.prototype,{to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw();return ah},make_name_popup_menu:function(){var ai=this;var ah={};ah[(this.is_overview?"Hide overview":"Set as overview")]=function(){if(ai.is_overview){ai.view.reset_overview()}else{ai.view.set_overview(ai)}};ah["Edit configuration"]=function(){var am=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},al=function(an){if((an.keyCode||an.which)===27){am()}else{if((an.keyCode||an.which)===13){ak()}}};$(window).bind("keypress.check_enter_esc",al);show_modal("Configure Track",ai.config.build_form(),{Cancel:am,OK:ak})};if(ai.filters_available>0){var aj=(ai.filters_div.is(":visible")?"Hide filters":"Show filters");ah[aj]=function(){ai.filters_visible=(ai.filters_div.is(":visible"));if(ai.filters_visible){ai.filters_manager.reset_filters()}ai.filters_div.toggle();ai.make_name_popup_menu()}}if(ai.tool){var aj=(ai.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");ah[aj]=function(){if(!ai.dynamic_tool_div.is(":visible")){ai.set_name(ai.name+ai.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ai.revert_name()}ai.dynamic_tool_div.toggle();ai.make_name_popup_menu()}}ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)},set_is_overview:function(ah){this.is_overview=ah;this.make_name_popup_menu()},get_overview_tile:function(){var ah=this;view=ah.view,resolution=Math.pow(E,Math.ceil(Math.log((view.max_high-view.max_low)/T)/Math.log(E))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ah.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ah.data_url_extra_params)).then(function(ai){var ak=ah._gen_tile_cache_key(view_width,w_scale,0),am=ah.tile_cache.get(ak);if(!am){am=ah.draw_tile(ai,"Auto",resolution,0,w_scale);ah.tile_cache.set(ak,am)}var ap=$(am.canvas.find("canvas")),al=ap.clone(),ao=ap.get(0).getContext("2d"),aj=al.get(0).getContext("2d"),an=ao.getImageData(0,0,ao.canvas.width,ao.canvas.height);aj.putImageData(an,-ah.left_offset,(am.data.dataset_type==="summary_tree"?V:0));new_tile=new b(-1,resolution,al);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof C)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/T);var ap=true;var at=[];var ah=0;while((ai*T*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",F)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*T*an,ax=ap+T*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);if(aq!==undefined){al.tile_cache.set(at,aq);al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw()});return null},show_tile:function(ao,aq,ar){var aj=this,ai=ao.canvas,an=ai;if(ao.message){var at=$("<div/>"),ap=$("<div/>").addClass("tile-message").text(ao.message).css({height:F-1,width:ao.canvas.width}).appendTo(at),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ap),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ap);at.append(ai);an=at;al.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()});ah.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()})}var am=this.view.high-this.view.low,ak=(ao.low-this.view.low)*ar;if(this.left_offset){ak-=this.left_offset}an.css({position:"absolute",top:0,left:ak,height:""});aq.append(an);aj.max_height=Math.max(aj.max_height,an.height());aj.content_div.css("height",aj.max_height+"px");aq.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*T*ai,al=T*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ai,ah){this.hidden=true;j.call(this,"label",ai,ah,{});this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{init:function(){this.enabled=true},_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var C=function(ah){this.hidden=true;j.call(this,"reference",ah,{content_div:ah.top_labeltrack},{});O.call(this);ah.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ah.dbkey};this.data_manager=new J(D,this,false);this.tile_cache=new c(v)};q(C.prototype,r.prototype,O.prototype,{init:function(){this.enabled=true},draw_tile:function(ar,an,am,ai,at){var al=this,aj=T*am;if(at>this.view.canvas_manager.char_width_px){if(ar===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(am,ak,aj,an,ah,al){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,am,ak,aj,al);O.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=an;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new U(D,this);this.tile_cache=new c(v);this.left_offset=0;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:am},{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:al,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.track_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.track_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};q(k.prototype,r.prototype,O.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this,ai=ah.view.tracks.indexOf(ah);ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(aj){ah.container_div.addClass("line-track");var al=aj.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=al.min;ah.prefs.max_value=al.max;$("#track_"+ai+"_minval").val(ah.prefs.min_value);$("#track_"+ai+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=al.total_frequency;ah.container_div.find(".yaxislabel").remove();var am=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ai+"_minval").text(y(ah.prefs.min_value));var ak=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ai+"_maxval").text(y(ah.prefs.max_value));ak.css({position:"absolute",top:"24px",left:"10px"});ak.prependTo(ah.container_div);am.css({position:"absolute",bottom:"2px",left:"10px"});am.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new N.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(aj,al,ak,au.data)}});var e=function(ah,an,ai,am,ap,ao,ak,al){var aj=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];j.call(this,ah,an,ai,ao);O.call(this,ak,al);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){aj.set_name(aj.prefs.name);aj.tile_cache.clear();aj.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=am;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new U(20,this);this.left_offset=200;this.painter=N.LinkedFeaturePainter};q(e.prototype,r.prototype,O.prototype,{postdraw_actions:function(ax,ah,ay,aw){O.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.make_name_popup_menu()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",B,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aE,aI,ar,ak){var aB=this,am=aB._get_tile_bounds(aI,aE),aL=am[0],ai=am[1],ay=ai-aL,aC=Math.ceil(ay*ar),aP=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"){az="no_detail"}else{var aO=aw.data;if(this.view.high-this.view.low>K){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aC+al;aj.height=an+V;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aL,ai,200);if(aw.max){at.max=aw.max}aw=at}var aM=new N.SummaryTreePainter(aw,aL,ai,this.prefs);var aD=aj.getContext("2d");aD.translate(al,V);aM.draw(aD,aC,an);return new l(aI,aE,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aF=0,aH=aw.data.length;aF<aH;aF++){var ao=aw.data[aF];var aG=false;var av;for(var aK=0,aN=au.length;aK<aN;aK++){av=au[aK];av.update_attrs(ao);if(!av.keep(ao)){aG=true;break}}if(!aG){aq.push(ao)}}}var aA=(this.filters_manager.alpha_filter?new Q(this.filters_manager.alpha_filter):null);var aM=new (this.painter)(aq,aL,ai,this.prefs,az,aA,ak);var an=Math.max(af,aM.get_required_height(ap));var aj=this.view.canvas_manager.new_canvas();var aJ=null;aj.width=aC+al;aj.height=an;var aD=aj.getContext("2d");aD.fillStyle=this.prefs.block_color;aD.font=aD.canvas.manager.default_font;aD.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aw.data){aD.translate(al,0);aJ=aM.draw(aD,aC,an,ax);aJ.translation=-al}return new R(aI,aE,aj,aw.data,aw.message,aJ)}});var W=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.painter=N.VariantPainter};q(W.prototype,r.prototype,O.prototype,e.prototype);var Z=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ak,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=N.ReadPainter;this.make_name_popup_menu()};q(Z.prototype,r.prototype,O.prototype,e.prototype);var X=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am,{});this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};q(X.prototype,r.prototype,O.prototype,e.prototype,{predraw_init:function(){var ai=this;var ah=function(){if(ai.data_manager.size()===0){setTimeout(ah,300)}else{ai.data_url=default_data_url;ai.data_query_wait=M;ai.dataset_state_url=converted_datasets_state_url;$.getJSON(ai.dataset_state_url,{dataset_id:ai.dataset_id,hda_ldda:ai.hda_ldda},function(aj){})}};ah()}});aa.View=ae;aa.DrawableGroup=S;aa.LineTrack=k;aa.FeatureTrack=e;aa.ReadTrack=Z};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(k,y){var v=k("class").extend;var q=function(J,B,H,A,G,E){if(E===undefined){E=4}var D=A-B;var C=G-H;var F=Math.floor(Math.sqrt(D*D+C*C)/E);var K=D/F;var I=C/F;var z;for(z=0;z<F;z++,B+=K,H+=I){if(z%2!==0){continue}J.fillRect(B,H,E,1)}};var r=function(B,A,z,E){var 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+var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var trackster_module=function(f,Z){var q=f("class").extend,t=f("slotting"),M=f("painters");var ag=function(ah,ai){this.document=ah;this.default_font=ai!==undefined?ai:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};q(ag.prototype,{load_pattern:function(ah,al){var ai=this.patterns,aj=this.dummy_context,ak=new Image();ak.src=image_path+al;ak.onload=function(){ai[ah]=aj.createPattern(ak,"repeat")}},get_pattern:function(ah){return this.patterns[ah]},new_canvas:function(){var ah=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ah)}ah.manager=this;return ah}});var o={};var m=function(ah,ai){o[ah.attr("id")]=ai};var n=function(ah,aj,al,ak){al=".group";var ai={};o[ah.attr("id")]=ak;ah.bind("drag",{handle:"."+aj,relative:true},function(au,av){var at=$(this);var ay=$(this).parent(),ap=ay.children(),ar=o[$(this).attr("id")],ao,an,aw,am,aq;an=$(this).parents(al);if(an.length!==0){aw=an.position().top;am=aw+an.outerHeight();if(av.offsetY<aw){$(this).insertBefore(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable_before(ar,ax);return}else{if(av.offsetY>am){$(this).insertAfter(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable(ar);return}}}an=null;for(aq=0;aq<ap.length;aq++){ao=$(ap.get(aq));aw=ao.position().top;am=aw+ao.outerHeight();if(ao.is(al)&&this!==ao.get(0)&&av.offsetY>=aw&&av.offsetY<=am){if(av.offsetY-aw<am-av.offsetY){ao.find(".content-div").prepend(this)}else{ao.find(".content-div").append(this)}if(ar.container){ar.container.remove_drawable(ar)}o[ao.attr("id")].add_drawable(ar);return}}for(aq=0;aq<ap.length;aq++){if(av.offsetY<$(ap.get(aq)).position().top){break}}if(aq===ap.length){if(this!==ap.get(aq-1)){ay.append(this);o[ay.attr("id")].move_drawable(ar,aq)}}else{if(this!==ap.get(aq)){$(this).insertBefore(ap.get(aq));o[ay.attr("id")].move_drawable(ar,(av.deltaY>0?aq-1:aq))}}}).bind("dragstart",function(){ai["border-top"]=ah.css("border-top");ai["border-bottom"]=ah.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ai)})};Z.moveable=n;var af=16,H=9,E=20,U=H+2,A=100,J=12000,S=200,D=5,w=10,L=5000,x=100,p="There was an error in indexing this dataset. ",K="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",F="No data for this chrom/contig.",u="Currently indexing... please wait",y="Tool cannot be rerun: ",a="Loading data...",aa="Ready for display",d=10,v=5,C=5;function ab(ai,ah){if(!ah){ah=0}var aj=Math.pow(10,ah);return Math.round(ai*aj)/aj}var c=function(ah){this.num_elements=ah;this.clear()};q(c.prototype,{get:function(ai){var ah=this.key_ary.indexOf(ai);if(ah!==-1){if(this.obj_cache[ai].stale){this.key_ary.splice(ah,1);delete this.obj_cache[ai]}else{this.move_key_to_end(ai,ah)}}return this.obj_cache[ai]},set:function(ai,aj){if(!this.obj_cache[ai]){if(this.key_ary.length>=this.num_elements){var ah=this.key_ary.shift();delete this.obj_cache[ah]}this.key_ary.push(ai)}this.obj_cache[ai]=aj;return aj},move_key_to_end:function(ai,ah){this.key_ary.splice(ah,1);this.key_ary.push(ai)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var T=function(ai,ah,aj){c.call(this,ai);this.track=ah;this.subset=(aj!==undefined?aj:true)};q(T.prototype,c.prototype,{load_data:function(aq,al,ao,ai,an){var ap=this.track.view.chrom,ak={chrom:ap,low:aq,high:al,mode:ao,resolution:ai,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ak,an);if(this.track.filters_manager){var ar=[];var ah=this.track.filters_manager.filters;for(var am=0;am<ah.length;am++){ar[ar.length]=ah[am].name}ak.filter_cols=JSON.stringify(ar)}var aj=this;return $.getJSON(this.track.data_url,ak,function(at){aj.set_data(aq,al,ao,at)})},get_data:function(ah,al,am,ai,ak){var aj=this.get_data_from_cache(ah,al,am);if(aj){return aj}aj=this.load_data(ah,al,am,ai,ak);this.set_data(ah,al,am,aj);return aj},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ap,ak,ao,aj,an,al){var aq=this.get_data_from_cache(ap,ak,ao);if(!aq){console.log("ERROR: no current data for: ",this.track,ap,ak,ao,aj,an);return}aq.stale=true;var ai=ap;if(al===this.DEEP_DATA_REQ){$.extend(an,{start_val:aq.data.length+1})}else{if(al===this.BROAD_DATA_REQ){ai=(aq.max_high?aq.max_high:aq.data[aq.data.length-1][2])+1}}var ah=this,am=this.load_data(ai,ak,ao,aj,an);new_data_available=$.Deferred();this.set_data(ap,ak,ao,new_data_available);$.when(am).then(function(ar){if(ar.data){ar.data=aq.data.concat(ar.data);if(ar.max_low){ar.max_low=aq.max_low}if(ar.message){ar.message=ar.message.replace(/[0-9]+/,ar.data.length)}}ah.set_data(ap,ak,ao,ar);new_data_available.resolve(ar)});return new_data_available},get_data_from_cache:function(ah,ai,aj){return this.get(this.gen_key(ah,ai,aj))},set_data:function(ai,aj,ak,ah){return this.set(this.gen_key(ai,aj,ak),ah)},gen_key:function(ah,aj,ak){var ai=ah+"_"+aj+"_"+ak;return ai},split_key:function(ah){return ah.split("_")}});var I=function(ai,ah,aj){T.call(this,ai,ah,aj)};q(I.prototype,T.prototype,c.prototype,{load_data:function(aj,ah,al,am,ai,ak){if(ai>1){return}return T.prototype.load_data.call(this,aj,ah,al,am,ai,ak)}});var r=function(ak,ai,ah,aj,al){this.name=ak;this.view=ai;this.container=ah;this.drag_handle_class=al;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak}],saved_values:aj,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values};q(r.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},make_name_popup_menu:function(){},set_name:function(ah){this.old_name=this.name;this.name=ah;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var z=function(al,ak,ai,ah,aj,am){r.call(this,ak,ai,ah,aj,am);this.obj_type=al;this.drawables=[]};q(z.prototype,r.prototype,{init:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah].init()}},_draw:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah]._draw()}},to_json:function(){var ai=[];for(var ah=0;ah<this.drawables.length;ah++){ai.push(this.drawables[ah].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ai}},add_drawable:function(ah){this.drawables.push(ah);ah.container=this},add_drawable_before:function(aj,ah){var ai=this.drawables.indexOf(ah);if(ai!=-1){this.drawables.splice(ai,0,aj);return true}return false},remove_drawable:function(ai){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);ai.container=null;return true}return false},move_drawable:function(ai,aj){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);this.drawables.splice(aj,0,ai);return true}return false}});var R=function(ak,ai,ah,aj){z.call(this,"DrawableGroup",ak,ai,ah,aj,"group-handle");if(!R.id_counter){R.id_counter=0}var al=R.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+al).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+al+"_content_div").appendTo(this.container_div);m(this.container_div,this);m(this.content_div,this);n(this.container_div,this.drag_handle_class,".group",this);this.make_name_popup_menu()};q(R.prototype,r.prototype,z.prototype,{make_name_popup_menu:function(){var ai=this;var ah={};ah["Edit configuration"]=function(){var al=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aj=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(am){if((am.keyCode||am.which)===27){al()}else{if((am.keyCode||am.which)===13){aj()}}};$(window).bind("keypress.check_enter_esc",ak);show_modal("Configure Group",ai.config.build_form(),{Cancel:al,OK:aj})};ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)}});var ae=function(ah,ak,aj,ai){z.call(this,"View");this.container=ah;this.chrom=null;this.vis_id=aj;this.dbkey=ai;this.title=ak;this.tracks=this.drawables;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ag(ah.get(0).ownerDocument);this.reset()};q(ae.prototype,z.prototype,{init:function(){var aj=this.container,ah=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aj);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;m(this.viewport_container,ah);this.intro_div=$("<div/>").addClass("intro");var ak=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ai=function(al){if(al.type==="focusout"||(al.keyCode||al.which)===13||(al.keyCode||al.which)===27){if((al.keyCode||al.which)!==27){ah.go_to($(this).val())}$(this).hide();$(this).val("");ah.location_span.show();ah.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ai).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ah.location_span.hide();ah.chrom_select.hide();ah.nav_input.val(ah.chrom+":"+ah.low+"-"+ah.high);ah.nav_input.css("display","inline-block");ah.nav_input.select();ah.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ah.zoom_out();ah.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.browser_content_div.click(function(al){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("<div />").css({height:ah.browser_content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,{content_div:this.top_labeltrack}));this.add_label_track(new ad(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new B(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(al,ai,an){if(!al||al==="None"){return}var ak=this;if(al==="previous"){ak.load_chroms({low:this.chrom_start_index-x});return}if(al==="next"){ak.load_chroms({low:this.chrom_start_index+x});return}var am=$.grep(ak.chrom_data,function(ap,aq){return ap.chrom===al})[0];if(am===undefined){ak.load_chroms({chrom:al},function(){ak.change_chrom(al,ai,an)});return}else{if(al!==ak.chrom){ak.chrom=al;ak.chrom_select.val(ak.chrom);ak.max_high=am.len-1;ak.reset();ak.request_redraw(true);for(var ao=0,ah=ak.tracks.length;ao<ah;ao++){var aj=ak.tracks[ao];if(aj.init){aj.init()}}}if(ai!==undefined&&an!==undefined){ak.low=Math.max(ai,0);ak.high=Math.min(an,ak.max_high)}ak.reset_overview();ak.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){z.prototype.add_drawable.call(this,ah);ah.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;ah.init();this.label_tracks.push(ah)},remove_drawable:function(aj,ai){z.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.tracks),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(D,Math.ceil(Math.log((this.high-this.low)/S)/Math.log(D)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){$.when(ah.get_overview_tile()).then(function(ai){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ai.canvas);view.overview_highlight.show().height(ai.canvas.height());view.overview_viewport.height(ai.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ah;ah.set_is_overview(true)});view.has_changes=true},reset_overview:function(){this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new O(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},al=this.track,aj=ai.tool_id+al.tool_region_and_parameters_str(ai.chrom,ai.low,ai.high),ah,am;if(al.container===view){var ak=new R(this.name,this.track.view,this.track.container);al.container.add_drawable(ak);al.container.remove_drawable(al);ak.add_drawable(al);al.container_div.appendTo(ak.content_div);ah=ak}else{ah=al.container}if(al instanceof e){am=new W(aj,view,ah,"hda");am.change_mode(al.mode);ah.add_drawable(am)}am.content_div.text("Starting job.");this.run(ai,am,function(an){am.dataset_id=an.dataset_id;am.content_div.text("Running job.");am.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(K)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(y+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var O=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){O.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var X=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};q(X.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=parseFloat(ah[this.index]);return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(ar,ay){this.track=ar;this.filters=[];for(var at=0;at<ay.length;at++){var au=ay[at],az=au.name,ah=au.type,ak=au.index,ax=au.tool_id,aw=au.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[at]=new X(az,ak,ax,aw)}else{console.log("ERROR: unsupported filter: ",az,ah)}}var al=function(aA,aB,aC){aA.click(function(){var aD=aB.text();max=parseFloat(aC.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aC.slider("option","values")){input_size=2*input_size+1;multi_value=true}aB.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aD).appendTo(aB).focus().select().click(function(aE){aE.stopPropagation()}).blur(function(){$(this).remove();aB.text(aD)}).keyup(function(aI){if(aI.keyCode===27){$(this).trigger("blur")}else{if(aI.keyCode===13){var aG=aC.slider("option","min"),aE=aC.slider("option","max"),aH=function(aJ){return(isNaN(aJ)||aJ>aE||aJ<aG)},aF=$(this).val();if(!multi_value){aF=parseFloat(aF);if(aH(aF)){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}else{aF=aF.split("-");aF=[parseFloat(aF[0]),parseFloat(aF[1])];if(aH(aF[0])||aH(aF[1])){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}aC.slider((multi_value?"values":"value"),aF)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aA){aA.stopPropagation()}).click(function(aA){aA.stopPropagation()}).bind("dblclick",function(aA){aA.stopPropagation()}).bind("keydown",function(aA){aA.stopPropagation()});var av=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aD,aF){aF.container=$("<div/>").addClass("slider-row").appendTo(av);var aE=$("<div/>").addClass("elt-label").appendTo(aF.container);var aC=$("<span/>").addClass("slider-name").text(aF.name+"  ").appendTo(aE);var aB=$("<span/>");var aH=$("<span/>").addClass("slider-value").appendTo(aE).append("[").append(aB).append("]");var aA=$("<div/>").addClass("slider").appendTo(aF.container);aF.control_element=$("<div/>").attr("id",aF.name+"-filter-control").appendTo(aA);var aG=[0,0];aF.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aJ,aK){var aI=aK.values;aB.text(aI[0]+"-"+aI[1]);aF.low=aI[0];aF.high=aI[1];ap.track.request_draw(true,true)},change:function(aI,aJ){aF.control_element.slider("option","slide").call(aF.control_element,aI,aJ)}});aF.slider=aF.control_element;aF.slider_label=aB;al(aH,aB,aF.control_element);$("<div style='clear: both;'/>").appendTo(aF.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(av);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var aj=this;ao.click(function(){aj.run_on_dataset()})}var aq=$("<div/>").addClass("display-controls").appendTo(this.parent_div),an=$("<span/>").addClass("elt-label").text("Transparency:").appendTo(aq),ai=$("<select/>").attr("name","alpha_dropdown").appendTo(aq);this.alpha_filter=null;$("<option/>").attr("value",-1).text("== None ==").appendTo(ai);for(var at=0;at<this.filters.length;at++){$("<option/>").attr("value",at).text(this.filters[at].name).appendTo(ai)}ai.change(function(){$(this).children("option:selected").each(function(){var aA=parseInt($(this).val());ap.alpha_filter=(aA>=0?ap.filters[aA]:null);ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var P=function(ai,ah){M.AlphaGenerator.call(this,ah);this.filter=ai};P.prototype.gen_alpha=function(ah){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_alpha}return((parseFloat(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var G=function(ah){this.track=ah.track;this.params=ah.params;this.values={};this.restore_values((ah.saved_values?ah.saved_values:{}));this.onchange=ah.onchange};q(G.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(ah,ak,aj,ai,al){this.track=ah;this.index=ak;this.low=ak*S*aj;this.high=(ak+1)*S*aj;this.resolution=aj;this.canvas=$("<div class='track-tile'/>").append(ai);this.data=al;this.stale=false};b.prototype.predisplay_actions=function(){};var l=function(ah,ak,aj,ai,al,am){b.call(this,ah,ak,aj,ai,al);this.max_val=am};q(l.prototype,b.prototype);var Q=function(ah,al,ak,aj,an,ao,am,ai){b.call(this,ah,al,ak,aj,an);this.mode=ao;this.message=am;this.feature_mapper=ai};q(Q.prototype,b.prototype);Q.prototype.predisplay_actions=function(){var ai=this,ah={};if(ai.mode!=="Pack"){return}$(this.canvas).mousemove(function(au){var ao=$(this).offset(),at=au.pageX-ao.left,ar=au.pageY-ao.top,ay=ai.feature_mapper.get_feature_data(at,ar),ap=(ay?ay[0]:null);$(this).siblings(".feature-popup").each(function(){if(!ap||$(this).attr("id")!==ap.toString()){$(this).remove()}});if(ay){var ak=ah[ap];if(!ak){var ap=ay[0],av={name:ay[3],start:ay[1],end:ay[2],strand:ay[4]},an=ai.track.filters_manager.filters,am;for(var aq=0;aq<an.length;aq++){am=an[aq];av[am.name]=ay[am.index]}var ak=$("<div/>").attr("id",ap).addClass("feature-popup"),ax,aw,az=$("<table/>").appendTo(ak),aA;for(ax in av){aw=av[ax];aA=$("<tr/>").appendTo(az);$("<th/>").appendTo(aA).text(ax);$("<td/>").attr("align","left").appendTo(aA).text(typeof(aw)=="number"?ab(aw,2):aw)}ah[ap]=ak}ak.appendTo($(ai.canvas).parent());var al=at+parseInt(ai.canvas.css("left"))+7,aj=ar+parseInt(ai.canvas.css("top"))+7;ak.css("left",al+"px").css("top",aj+"px")}else{if(!au.isPropagationStopped()){au.stopPropagation();$(this).siblings().each(function(){$(this).trigger(au)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var j=function(ak,ai,ah,aj,al,am){r.call(this,ak,ai,ah,{},"draghandle");this.data_url=(al?al:default_data_url);this.data_url_extra_params={};this.data_query_wait=(am?am:L);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.container_div=$("<div />").addClass("track").attr("id","track_"+j.id_counter++).css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Y){return"ReadTrack"}else{if(this instanceof W){return"ToolDataFeatureTrack"}else{if(this instanceof V){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var ak=ah.view.tracks.indexOf(ah);var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(K)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(F)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.make_name_popup_menu()}ah.content_div.text(aa);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}})},predraw_init:function(){},});var N=function(ao,am){var ai=this,ap=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=new ac(this,(ao!==undefined?ao:{}));this.filters_available=false;this.filters_visible=false;this.tool=(am!==undefined&&obj_length(am)>0?new s(this,am):undefined);this.is_overview=false;if(ai.hidden){return}if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(ai.display_modes!==undefined){if(ai.mode_div===undefined){ai.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ai.header_div);var aj=(ai.config&&ai.config.values.mode?ai.config.values.mode:ai.display_modes[0]);ai.mode=aj;ai.mode_div.text(aj);var ah={};for(var ak=0,an=ai.display_modes.length;ak<an;ak++){var al=ai.display_modes[ak];ah[al]=function(aq){return function(){ai.change_mode(aq)}}(al)}make_popupmenu(ai.mode_div,ah)}else{ai.mode_div.hide()}}this.make_name_popup_menu()};q(N.prototype,r.prototype,j.prototype,{to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw();return ah},make_name_popup_menu:function(){var ai=this;var ah={};ah[(this.is_overview?"Hide overview":"Set as overview")]=function(){if(ai.is_overview){ai.view.reset_overview()}else{ai.view.set_overview(ai)}};ah["Edit configuration"]=function(){var am=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},al=function(an){if((an.keyCode||an.which)===27){am()}else{if((an.keyCode||an.which)===13){ak()}}};$(window).bind("keypress.check_enter_esc",al);show_modal("Configure Track",ai.config.build_form(),{Cancel:am,OK:ak})};if(ai.filters_available>0){var aj=(ai.filters_div.is(":visible")?"Hide filters":"Show filters");ah[aj]=function(){ai.filters_visible=(ai.filters_div.is(":visible"));if(ai.filters_visible){ai.filters_manager.reset_filters()}ai.filters_div.toggle();ai.make_name_popup_menu()}}if(ai.tool){var aj=(ai.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");ah[aj]=function(){if(!ai.dynamic_tool_div.is(":visible")){ai.set_name(ai.name+ai.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ai.revert_name()}ai.dynamic_tool_div.toggle();ai.make_name_popup_menu()}}ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)},set_is_overview:function(ah){this.is_overview=ah;this.make_name_popup_menu()},get_overview_tile:function(){var ah=this;view=ah.view,resolution=Math.pow(D,Math.ceil(Math.log((view.max_high-view.max_low)/S)/Math.log(D))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ah.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ah.data_url_extra_params)).then(function(ai){var ak=ah._gen_tile_cache_key(view_width,w_scale,0),am=ah.tile_cache.get(ak);if(!am){am=ah.draw_tile(ai,"Auto",resolution,0,w_scale);ah.tile_cache.set(ak,am)}var ap=$(am.canvas.find("canvas")),al=ap.clone(),ao=ap.get(0).getContext("2d"),aj=al.get(0).getContext("2d"),an=ao.getImageData(0,0,ao.canvas.width,ao.canvas.height);aj.putImageData(an,-ah.left_offset,(am.data.dataset_type==="summary_tree"?U:0));new_tile=new b(ah,-1,resolution,al);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof B)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/S);var ap=true;var at=[];var ah=0;while((ai*S*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",E)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*S*an,ax=ap+S*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);if(aq!==undefined){al.tile_cache.set(at,aq);al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw()});return null},show_tile:function(ao,aq,ar){var aj=this,ai=ao.canvas,an=ai;if(ao.message){var at=$("<div/>"),ap=$("<div/>").addClass("tile-message").text(ao.message).css({height:E-1,width:ao.canvas.width}).appendTo(at),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ap),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ap);at.append(ai);an=at;al.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()});ah.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()})}ao.predisplay_actions();var am=this.view.high-this.view.low,ak=(ao.low-this.view.low)*ar;if(this.left_offset){ak-=this.left_offset}an.css({position:"absolute",top:0,left:ak,height:""});aq.append(an);aj.max_height=Math.max(aj.max_height,an.height());aj.content_div.css("height",aj.max_height+"px");aq.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*S*ai,al=S*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ai,ah){this.hidden=true;j.call(this,"label",ai,ah,{});this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{init:function(){this.enabled=true},_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var B=function(ah){this.hidden=true;j.call(this,"reference",ah,{content_div:ah.top_labeltrack},{});N.call(this);ah.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ah.dbkey};this.data_manager=new I(C,this,false);this.tile_cache=new c(v)};q(B.prototype,r.prototype,N.prototype,{init:function(){this.enabled=true},draw_tile:function(ar,an,am,ai,at){var al=this,aj=S*am;if(at>this.view.canvas_manager.char_width_px){if(ar===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(al,ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(am,ak,aj,an,ah,al){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,am,ak,aj,al);N.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=an;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new T(C,this);this.tile_cache=new c(v);this.left_offset=0;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:am},{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:al,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.track_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.track_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};q(k.prototype,r.prototype,N.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this,ai=ah.view.tracks.indexOf(ah);ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(aj){ah.container_div.addClass("line-track");var al=aj.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=al.min;ah.prefs.max_value=al.max;$("#track_"+ai+"_minval").val(ah.prefs.min_value);$("#track_"+ai+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=al.total_frequency;ah.container_div.find(".yaxislabel").remove();var am=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ai+"_minval").text(ab(ah.prefs.min_value,3));var ak=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ai+"_maxval").text(ab(ah.prefs.max_value,3));ak.css({position:"absolute",top:"24px",left:"10px"});ak.prependTo(ah.container_div);am.css({position:"absolute",bottom:"2px",left:"10px"});am.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new M.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(this.track,aj,al,ak,au.data)}});var e=function(ah,an,ai,am,ap,ao,ak,al){var aj=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];j.call(this,ah,an,ai,ao);N.call(this,ak,al);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){aj.set_name(aj.prefs.name);aj.tile_cache.clear();aj.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=am;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new T(20,this);this.left_offset=200;this.painter=M.LinkedFeaturePainter};q(e.prototype,r.prototype,N.prototype,{postdraw_actions:function(ax,ah,ay,aw){N.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.make_name_popup_menu()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",A,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aE,aI,ar,ak){var aB=this,am=aB._get_tile_bounds(aI,aE),aL=am[0],ai=am[1],ay=ai-aL,aC=Math.ceil(ay*ar),aP=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"){az="no_detail"}else{var aO=aw.data;if(this.view.high-this.view.low>J){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aC+al;aj.height=an+U;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aL,ai,200);if(aw.max){at.max=aw.max}aw=at}var aM=new M.SummaryTreePainter(aw,aL,ai,this.prefs);var aD=aj.getContext("2d");aD.translate(al,U);aM.draw(aD,aC,an);return new l(aB,aI,aE,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aF=0,aH=aw.data.length;aF<aH;aF++){var ao=aw.data[aF];var aG=false;var av;for(var aK=0,aN=au.length;aK<aN;aK++){av=au[aK];av.update_attrs(ao);if(!av.keep(ao)){aG=true;break}}if(!aG){aq.push(ao)}}}var aA=(this.filters_manager.alpha_filter?new P(this.filters_manager.alpha_filter):null);var aM=new (this.painter)(aq,aL,ai,this.prefs,az,aA,ak);var an=Math.max(af,aM.get_required_height(ap));var aj=this.view.canvas_manager.new_canvas();var aJ=null;aj.width=aC+al;aj.height=an;var aD=aj.getContext("2d");aD.fillStyle=this.prefs.block_color;aD.font=aD.canvas.manager.default_font;aD.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aw.data){aD.translate(al,0);aJ=aM.draw(aD,aC,an,ax);aJ.translation=-al}return new Q(aB,aI,aE,aj,aw.data,az,aw.message,aJ)}});var V=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.painter=M.VariantPainter};q(V.prototype,r.prototype,N.prototype,e.prototype);var Y=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ak,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter;this.make_name_popup_menu()};q(Y.prototype,r.prototype,N.prototype,e.prototype);var W=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am,{});this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};q(W.prototype,r.prototype,N.prototype,e.prototype,{predraw_init:function(){var ai=this;var ah=function(){if(ai.data_manager.size()===0){setTimeout(ah,300)}else{ai.data_url=default_data_url;ai.data_query_wait=L;ai.dataset_state_url=converted_datasets_state_url;$.getJSON(ai.dataset_state_url,{dataset_id:ai.dataset_id,hda_ldda:ai.hda_ldda},function(aj){})}};ah()}});Z.View=ae;Z.DrawableGroup=R;Z.LineTrack=k;Z.FeatureTrack=e;Z.ReadTrack=Y};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(k,y){var v=k("class").extend;var q=function(J,B,H,A,G,E){if(E===undefined){E=4}var D=A-B;var C=G-H;var F=Math.floor(Math.sqrt(D*D+C*C)/E);var K=D/F;var I=C/F;var z;for(z=0;z<F;z++,B+=K,H+=I){if(z%2!==0){continue}J.fillRect(B,H,E,1)}};var r=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var g=function(z){this.default_alpha=(z?z:1)};g.prototype.gen_alpha=function(z){return this.default_alpha};var n=function(B,D,z,A,C){this.data=B;this.view_start=D;this.view_end=z;this.prefs=v({},this.default_prefs,A);this.mode=C};n.prototype.default_prefs={};var w=function(B,D,z,A,C){n.call(this,B,D,z,A,C)};w.prototype.default_prefs={show_counts:false};w.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var c=function(z,D,F,G,B){n.call(this,z,D,F,G,B);if(this.prefs.min_value===undefined){var H=Infinity;for(var A=0,C=this.data.length;A<C;A++){H=Math.min(H,this.data[A][1])}this.prefs.min_value=H}if(this.prefs.max_value===undefined){var E=-Infinity;for(var A=0,C=this.data.length;A<C;A++){E=Math.max(E,this.data[A][1])}this.prefs.max_value=E}};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var o=function(z){this.feature_positions={};this.slot_height=z;this.translation=0};o.prototype.map_feature_data=function(A,C,z,B){if(!this.feature_positions[C]){this.feature_positions[C]=[]}this.feature_positions[C].push({data:A,x_start:z,x_end:B})};o.prototype.get_feature_data=function(z,D){var C=Math.floor(D/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var p=function(C,E,z,B,D,A){n.call(this,C,E,z,B,D);this.alpha_generator=(A?A:new g())};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};v(p.prototype,{get_required_height:function(A){var z=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){z=A*y_scale}return z+Math.max(Math.round(y_scale/2),5)},draw:function(L,J,H,G){var R=this.data,E=this.view_start,N=this.view_end;L.save();L.fillStyle=this.prefs.block_color;L.textAlign="right";var I=this.view_end-this.view_start,F=J/I,M=this.get_row_height(),Q=new o(M),C;for(var O=0,P=R.length;O<P;O++){var B=R[O],D=B[0],K=B[1],z=B[2],A=(G&&G[D]!==undefined?G[D]:null);if((K<N&&z>E)&&(this.mode=="Dense"||A!==null)){C=this.draw_element(L,this.mode,B,A,E,N,F,M,J);Q.map_feature_data(B,A,C[0],C[1])}}L.restore();return Q},draw_element:function(F,B,H,D,C,E,G,A,z){console.log("WARNING: Unimplemented function.");return[0,0]}});var d=10,j=3,m=5,x=10,f=1,t=3,e=3,a=9,l=2,h="#ccc";var s=function(C,E,z,B,D,A){p.call(this,C,E,z,B,D,A)};v(s.prototype,p.prototype,{get_row_height:function(){var A=this.mode,z;if(A==="Dense"){z=d}else{if(A==="no_detail"){z=j}else{if(A==="Squish"){z=m}else{z=x}}}return z},draw_element:function(L,E,T,G,N,ae,ai,ak,z){var Q=T[0],ag=T[1],Y=T[2],O=T[3],Z=Math.floor(Math.max(0,(ag-N)*ai)),M=Math.ceil(Math.min(z,Math.max(0,(Y-N)*ai))),X=Z,aj=M,W=(E==="Dense"?0:(0+G))*ak,K,ac,P=null,al=null,C=this.prefs.block_color,ab=this.prefs.label_color;L.globalAlpha=this.alpha_generator.gen_alpha(T);if(E=="Dense"){G=1}if(E==="no_detail"){L.fillStyle=C;L.fillRect(Z,W+5,M-Z,f)}else{var J=T[4],V=T[5],aa=T[6],D=T[7];if(V&&aa){P=Math.floor(Math.max(0,(V-N)*ai));al=Math.ceil(Math.min(z,Math.max(0,(aa-N)*ai)))}var ah,R;if(E==="Squish"||E==="Dense"){ah=1;R=e}else{ah=5;R=a}if(!D){if(T.strand){if(T.strand==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand_inv")}else{if(T.strand==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand_inv")}}}else{L.fillStyle=C}L.fillRect(Z,W,M-Z,R)}else{var I,S;if(E==="Squish"||E==="Dense"){L.fillStyle=h;I=W+Math.floor(e/2)+1;S=1}else{if(J){var I=W;var S=R;if(J==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand")}else{if(J==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand")}}}else{L.fillStyle=h;I+=(e/2)+1;S=1}}L.fillRect(Z,I,M-Z,S);for(var af=0,B=D.length;af<B;af++){var F=D[af],A=Math.floor(Math.max(0,(F[0]-N)*ai)),U=Math.ceil(Math.min(z,Math.max((F[1]-N)*ai)));if(A>U){continue}L.fillStyle=C;L.fillRect(A,W+(R-ah)/2+1,U-A,ah);if(P!==undefined&&aa>V&&!(A>al||U<P)){var ad=Math.max(A,P),H=Math.min(U,al);L.fillRect(ad,W+1,H-ad,R);if(D.length==1&&E=="Pack"){if(J==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand_inv")}else{if(J==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand_inv")}}if(ad+14<H){ad+=2;H-=2}L.fillRect(ad,W+1,H-ad,R)}}}}if(E==="Pack"&&ag>N){L.fillStyle=ab;if(N===0&&Z-L.measureText(O).width<0){L.textAlign="left";L.fillText(O,M+l,W+8);aj+=L.measureText(O).width+l}else{L.textAlign="right";L.fillText(O,Z-l,W+8);X-=L.measureText(O).width+l}}}L.globalAlpha=1;return[X,aj]}});var b=function(C,E,z,B,D,A){p.call(this,C,E,z,B,D,A)};v(b.prototype,p.prototype,{draw_element:function(S,N,H,D,V,B,K,T,Q){var H=data[i],J=H[0],R=H[1],C=H[2],M=H[3],F=Math.floor(Math.max(0,(R-V)*K)),I=Math.ceil(Math.min(Q,Math.max(0,(C-V)*K))),E=(N==="Dense"?0:(0+D))*T,z,W,A=null,L=null;if(no_label){S.fillStyle=block_color;S.fillRect(F+left_offset,E+5,I-F,1)}else{var U=H[4],P=H[5],G=H[6];z=9;W=1;S.fillRect(F+left_offset,E,I-F,z);if(N!=="Dense"&&M!==undefined&&R>V){S.fillStyle=label_color;if(V===0&&F-S.measureText(M).width<0){S.textAlign="left";S.fillText(M,I+2+left_offset,E+8)}else{S.textAlign="right";S.fillText(M,F-2+left_offset,E+8)}S.fillStyle=block_color}var O=U+" / "+P;if(R>V&&S.measureText(O).width<(I-F)){S.fillStyle="white";S.textAlign="center";S.fillText(O,left_offset+F+(I-F)/2,E+8);S.fillStyle=block_color}}return[F,I]}});var u=function(D,F,z,C,E,A,B){p.call(this,D,F,z,C,E,A);this.ref_seq=B};u.prototype.default_prefs=v({},p.prototype.default_prefs,{show_insertions:false});v(u.prototype,p.prototype,{get_row_height:function(){var z,A=this.mode;if(A==="Dense"){z=d}else{if(A==="Squish"){z=m}else{z=x;if(this.prefs.show_insertions){z*=2}}}return z},draw_read:function(V,Q,M,aa,B,U,J,G,F){V.textAlign="center";var T=this,A=[aa,B],P=0,W=0,S=0;ref_seq=this.ref_seq,char_width_px=V.canvas.manager.char_width_px;var af=[];if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){S=Math.round(M/2)}if(!J){J=[[0,G.length]]}for(var N=0,Y=J.length;N<Y;N++){var K=J[N],C="MIDNSHP=X"[K[0]],O=K[1];if(C==="H"||C==="S"){P-=O}var H=U+P,ae=Math.floor(Math.max(0,(H-aa)*M)),I=Math.floor(Math.max(0,(H+O-aa)*M));if(ae===I){I+=1}switch(C){case"H":break;case"S":case"M":case"=":if(is_overlap([H,H+O],A)){var R=G.slice(W,W+O);if(S>0){V.fillStyle=this.prefs.block_color;V.fillRect(ae-S,F+1,I-ae,9);V.fillStyle=h;for(var ac=0,z=R.length;ac<z;ac++){if(this.prefs.show_differences&&ref_seq){var L=ref_seq[H-aa+ac];if(!L||L.toLowerCase()===R[ac].toLowerCase()){continue}}if(H+ac>=aa&&H+ac<=B){var ad=Math.floor(Math.max(0,(H+ac-aa)*M));V.fillText(R[ac],ad,F+9)}}}else{V.fillStyle=this.prefs.block_color;V.fillRect(ae,F+4,I-ae,e)}}W+=O;P+=O;break;case"N":V.fillStyle=h;V.fillRect(ae-S,F+5,I-ae,1);P+=O;break;case"D":V.fillStyle="red";V.fillRect(ae-S,F+4,I-ae,3);P+=O;break;case"P":break;case"I":var Z=ae-S;if(is_overlap([H,H+O],A)){var R=G.slice(W,W+O);if(this.prefs.show_insertions){var E=ae-(I-ae)/2;if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){V.fillStyle="yellow";V.fillRect(E-S,F-9,I-ae,9);af[af.length]={type:"triangle",data:[Z,F+4,5]};V.fillStyle=h;switch(seq_tile_overlap){case (OVERLAP_START):R=R.slice(aa-H);break;case (OVERLAP_END):R=R.slice(0,H-B);break;case (CONTAINED_BY):break;case (CONTAINS):R=R.slice(aa-H,H-B);break}for(var ac=0,z=R.length;ac<z;ac++){var ad=Math.floor(Math.max(0,(H+ac-aa)*M));V.fillText(R[ac],ad-(I-ae)/2,F)}}else{V.fillStyle="yellow";V.fillRect(E,F+(this.mode!=="Dense"?2:5),I-ae,(Q!=="Dense"?e:t))}}else{if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){af[af.length]={type:"text",data:[R.length,Z,F+9]}}else{}}}W+=O;break;case"X":W+=O;break}}V.fillStyle="yellow";var ab,D,ag;for(var X=0;X<af.length;X++){ab=af[X];D=ab.type;ag=ab.data;if(D==="text"){V.save();V.font="bold "+V.font;V.fillText(ag[0],ag[1],ag[2]);V.restore()}else{if(D=="triangle"){r(V,ag[0],ag[1],ag[2])}}}},draw_element:function(S,N,F,C,V,A,J,T,Q){var I=F[0],R=F[1],B=F[2],K=F[3],E=Math.floor(Math.max(0,(R-V)*J)),G=Math.ceil(Math.min(Q,Math.max(0,(B-V)*J))),D=(N==="Dense"?0:(0+C))*T,W=this.prefs.block_color,H=this.prefs.label_color,P=0;if((N==="Pack"||this.mode==="Auto")&&J>S.canvas.manager.char_width_px){var P=Math.round(J/2)}S.fillStyle=W;if(F[5] instanceof Array){var O=Math.floor(Math.max(0,(F[4][0]-V)*J)),M=Math.ceil(Math.min(Q,Math.max(0,(F[4][1]-V)*J))),L=Math.floor(Math.max(0,(F[5][0]-V)*J)),z=Math.ceil(Math.min(Q,Math.max(0,(F[5][1]-V)*J)));if(F[4][1]>=V&&F[4][0]<=A&&F[4][2]){this.draw_read(S,N,J,V,A,F[4][0],F[4][2],F[4][3],D)}if(F[5][1]>=V&&F[5][0]<=A&&F[5][2]){this.draw_read(S,N,J,V,A,F[5][0],F[5][2],F[5][3],D)}if(L>M){S.fillStyle=h;q(S,M-P,D+5,L-P,D+5)}}else{S.fillStyle=W;this.draw_read(S,N,J,V,A,R,F[4],F[5],D)}if(N==="Pack"&&R>V){S.fillStyle=this.prefs.label_color;var U=1;if(U===0&&E-S.measureText(K).width<0){S.textAlign="left";S.fillText(K,G+l-P,D+8)}else{S.textAlign="right";S.fillText(K,E-l-P,D+8)}S.fillStyle=W}return[0,0]}});y.AlphaGenerator=g;y.SummaryTreePainter=w;y.LinePainter=c;y.LinkedFeaturePainter=s;y.ReadPainter=u;y.VariantPainter=b};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window);
\ No newline at end of file
diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index ddd64af9353..98cacf84f01 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -309,10 +309,19 @@ var
     CACHED_TILES_FEATURE = 10,
     CACHED_TILES_LINE = 5,
     CACHED_DATA = 5;
-
-function round_1000(num) {
-    return Math.round(num * 1000) / 1000;    
-};
+    
+/**
+ * Round a number to a given number of decimal places.
+ */
+function round(num, places) {
+    // Default rounding is to integer.
+    if (!places) {
+        places = 0;
+    }
+    
+    var val = Math.pow(10, places);
+    return Math.round(num * val) / val;
+}
 
 /**
  * Generic cache that handles key/value pairs.
@@ -2085,7 +2094,8 @@ extend(DrawableConfig.prototype, {
 /**
  * Tiles drawn by tracks.
  */
-var Tile = function(index, resolution, canvas, data) {
+var Tile = function(track, index, resolution, canvas, data) {
+    this.track = track;
     this.index = index;
     this.low = index * DENSITY * resolution;
     this.high = (index + 1) * DENSITY * resolution;
@@ -2096,26 +2106,114 @@ var Tile = function(index, resolution, canvas, data) {
     this.stale = false;
 };
 
-var SummaryTreeTile = function(index, resolution, canvas, data, max_val) {
-    Tile.call(this, index, resolution, canvas, data);
+/**
+ * Perform pre-display actions.
+ */
+Tile.prototype.predisplay_actions = function() {};
+
+var SummaryTreeTile = function(track, index, resolution, canvas, data, max_val) {
+    Tile.call(this, track, index, resolution, canvas, data);
     this.max_val = max_val;
 };
+extend(SummaryTreeTile.prototype, Tile.prototype);
 
-var FeatureTrackTile = function(index, resolution, canvas, data, message, feature_mapper) {
-    Tile.call(this, index, resolution, canvas, data);
+var FeatureTrackTile = function(track, index, resolution, canvas, data, mode, message, feature_mapper) {
+    Tile.call(this, track, index, resolution, canvas, data);
+    this.mode = mode;
     this.message = message;
     this.feature_mapper = feature_mapper;
-    
-    //
-    // Set up display of feature data on mouseover.
-    //
-    var tile = this;
-    $(this.canvas).mousemove(function (e) {
-        var feature_data = tile.feature_mapper.get_feature_data(e.offsetX, e.offsetY);
-        
-        // TODO: show popup with feature's information.
-    });
+};
+extend(FeatureTrackTile.prototype, Tile.prototype);
 
+/**
+ * Sets up support for popups.
+ */
+FeatureTrackTile.prototype.predisplay_actions = function() {
+    //
+    // Add support for popups.
+    //
+    var tile = this,
+        popups = {};
+        
+    // Only show popups in Pack mode.
+    if (tile.mode !== "Pack") { return; }
+    
+    $(this.canvas).mousemove(function (e) {
+        // Get feature data for position.
+        var 
+            this_offset = $(this).offset(),
+            offsetX = e.pageX - this_offset.left,
+            offsetY = e.pageY - this_offset.top,
+            feature_data = tile.feature_mapper.get_feature_data(offsetX, offsetY),
+            feature_uid = (feature_data ? feature_data[0] : null);
+        // Hide visible popup if not over a feature or over a different feature.
+        $(this).siblings(".feature-popup").each(function() {
+            if ( !feature_uid || 
+                 $(this).attr("id") !== feature_uid.toString() ) {
+                $(this).remove();
+            }
+        });
+            
+        if (feature_data) {
+            // Get or create popup.
+            var popup = popups[feature_uid];
+            if (!popup) {
+                // Create feature's popup element.            
+                var 
+                    feature_uid = feature_data[0],
+                    feature_dict = {
+                        name: feature_data[3],
+                        start: feature_data[1],
+                        end: feature_data[2],
+                        strand: feature_data[4]
+                    },
+                    filters = tile.track.filters_manager.filters,
+                    filter;
+                
+                // Add filter values to feature dict.   
+                for (var i = 0; i < filters.length; i++) {
+                    filter = filters[i];
+                    feature_dict[filter.name] = feature_data[filter.index];
+                }
+                
+                // Build popup.
+                
+                var popup = $("<div/>").attr("id", feature_uid).addClass("feature-popup"),
+                    key, value, 
+                    table = $("<table/>").appendTo(popup), row;
+                for (key in feature_dict) {
+                    value = feature_dict[key];
+                    row = $("<tr/>").appendTo(table);
+                    $("<th/>").appendTo(row).text(key);
+                    $("<td/>").attr("align", "left").appendTo(row)
+                              .text(typeof(value) == 'number' ? round(value, 2) : value);
+                }
+                popups[feature_uid] = popup;
+            }
+            
+            // Attach popup to canvas's parent.
+            popup.appendTo($(tile.canvas).parent());
+            
+            // Offsets are within canvas, but popup must be positioned relative to parent element.
+            // parseInt strips "px" from left, top measurements. +7 so that mouse pointer does not
+            // overlap popup.
+            var 
+                popupX = offsetX + parseInt( tile.canvas.css("left") ) + 7,
+                popupY = offsetY + parseInt( tile.canvas.css("top") ) + 7;
+            popup.css("left", popupX + "px").css("top", popupY + "px")
+        }
+        else if (!e.isPropagationStopped()) {
+            // Propogate event to other tiles because overlapping tiles prevent mousemove from being 
+            // called on tiles under this tile.
+            e.stopPropagation();
+            $(this).siblings().each(function() {
+                $(this).trigger(e);
+            });
+        }
+    })
+    .mouseleave(function() {
+        $(this).siblings(".feature-popup").remove();
+    });
 };
 
 /**
@@ -2492,7 +2590,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
                 data = src_ctx.getImageData(0, 0, src_ctx.canvas.width, src_ctx.canvas.height);
             // Need to undo offsets when placing image data.
             tgt_ctx.putImageData(data, -track.left_offset, (tile.data.dataset_type === "summary_tree" ? SUMMARY_TREE_TOP_PADDING : 0));
-            new_tile = new Tile(-1, resolution, new_canvas);
+            new_tile = new Tile(track, -1, resolution, new_canvas);
             overview_tile.resolve(new_tile);
         });
         
@@ -2697,6 +2795,8 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
         //
         // Show tile element.
         //
+        
+        tile.predisplay_actions();
       
         // Position tile element, recalculate left position at display time
         var range = this.view.high - this.view.low,
@@ -2812,7 +2912,7 @@ extend(ReferenceTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
                 var c_start = Math.round(c * w_scale);
                 ctx.fillText(seq[c], c_start + track.left_offset, 10);
             }
-            return new Tile(tile_index, resolution, canvas, seq);
+            return new Tile(track, tile_index, resolution, canvas, seq);
         }
         this.content_div.css("height", "0px");
     }
@@ -2920,8 +3020,8 @@ extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
             // Draw y-axis labels if necessary
             track.container_div.find(".yaxislabel").remove();
             
-            var min_label = $("<div />").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_minval').text(round_1000(track.prefs.min_value));
-            var max_label = $("<div />").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_maxval').text(round_1000(track.prefs.max_value));
+            var min_label = $("<div />").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_minval').text(round(track.prefs.min_value, 3));
+            var max_label = $("<div />").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_maxval').text(round(track.prefs.max_value, 3));
             
             max_label.css({ position: "absolute", top: "24px", left: "10px" });
             max_label.prependTo(track.container_div);
@@ -2955,7 +3055,7 @@ extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
         var painter = new painters.LinePainter(result.data, tile_low, tile_high, this.prefs, mode);
         painter.draw(ctx, width, height);
         
-        return new Tile(tile_index, resolution, canvas, result.data);
+        return new Tile(this.track, tile_index, resolution, canvas, result.data);
     } 
 });
 
@@ -3288,7 +3388,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
             // Deal with left_offset by translating.
             ctx.translate(left_offset, SUMMARY_TREE_TOP_PADDING);
             painter.draw(ctx, width, required_height);
-            return new SummaryTreeTile(tile_index, resolution, canvas, result.data, result.max);
+            return new SummaryTreeTile(track, tile_index, resolution, canvas, result.data, result.max);
         }
 
         // Start dealing with row-by-row tracks
@@ -3347,7 +3447,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
             feature_mapper.translation = -left_offset;
         }
         
-        return new FeatureTrackTile(tile_index, resolution, canvas, result.data, result.message, feature_mapper);        
+        return new FeatureTrackTile(track, tile_index, resolution, canvas, result.data, mode, result.message, feature_mapper);        
     }
 });
 
@@ -3891,7 +3991,7 @@ FeaturePositionMapper.prototype.map_feature_data = function(feature_data, slot,
  */
 FeaturePositionMapper.prototype.get_feature_data = function(x, y) {
     // Find slot using Y.
-    var slot = Math.floor(y/this.slot_height),
+    var slot = Math.floor( y/this.slot_height ),
         feature_dict;
 
     // May not be over a slot due to padding, margin, etc.

From 879e25886cf5d74c276c4fdba86093d45c880ea0 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Tue, 11 Oct 2011 14:14:06 -0400
Subject: [PATCH 043/362] Trackster: no need to parse floats because data
 providers now return floats rather than strings.

---
 static/scripts/trackster.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index 98cacf84f01..951bac957d4 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -1638,7 +1638,7 @@ extend(NumberFilter.prototype, {
             // No element to filter on.
             return true;
         }
-        var val = parseFloat(element[this.index]);
+        var val = element[this.index];
         return (isNaN(val) || (val >= this.low && val <= this.high));
     },
     /**

From a053ecac5739d3ae89a0c91622da7967a9c03f9b Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Tue, 11 Oct 2011 14:47:34 -0400
Subject: [PATCH 044/362] Trackster: refactoring to remove (a) references to
 view.tracks because view can hold any drawable option and (b) track ids
 because they are no longer used.

---
 static/scripts/packed/trackster.js    |  2 +-
 static/scripts/packed/trackster_ui.js |  2 +-
 static/scripts/trackster.js           | 28 ++++++++++++---------------
 static/scripts/trackster_ui.js        |  6 +++---
 4 files changed, 17 insertions(+), 21 deletions(-)

diff --git a/static/scripts/packed/trackster.js b/static/scripts/packed/trackster.js
index eab64c3be2b..1cf9953e992 100644
--- a/static/scripts/packed/trackster.js
+++ b/static/scripts/packed/trackster.js
@@ -1 +1 @@
-var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var trackster_module=function(f,Z){var q=f("class").extend,t=f("slotting"),M=f("painters");var ag=function(ah,ai){this.document=ah;this.default_font=ai!==undefined?ai:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};q(ag.prototype,{load_pattern:function(ah,al){var ai=this.patterns,aj=this.dummy_context,ak=new Image();ak.src=image_path+al;ak.onload=function(){ai[ah]=aj.createPattern(ak,"repeat")}},get_pattern:function(ah){return this.patterns[ah]},new_canvas:function(){var ah=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ah)}ah.manager=this;return ah}});var o={};var m=function(ah,ai){o[ah.attr("id")]=ai};var n=function(ah,aj,al,ak){al=".group";var ai={};o[ah.attr("id")]=ak;ah.bind("drag",{handle:"."+aj,relative:true},function(au,av){var at=$(this);var ay=$(this).parent(),ap=ay.children(),ar=o[$(this).attr("id")],ao,an,aw,am,aq;an=$(this).parents(al);if(an.length!==0){aw=an.position().top;am=aw+an.outerHeight();if(av.offsetY<aw){$(this).insertBefore(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable_before(ar,ax);return}else{if(av.offsetY>am){$(this).insertAfter(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable(ar);return}}}an=null;for(aq=0;aq<ap.length;aq++){ao=$(ap.get(aq));aw=ao.position().top;am=aw+ao.outerHeight();if(ao.is(al)&&this!==ao.get(0)&&av.offsetY>=aw&&av.offsetY<=am){if(av.offsetY-aw<am-av.offsetY){ao.find(".content-div").prepend(this)}else{ao.find(".content-div").append(this)}if(ar.container){ar.container.remove_drawable(ar)}o[ao.attr("id")].add_drawable(ar);return}}for(aq=0;aq<ap.length;aq++){if(av.offsetY<$(ap.get(aq)).position().top){break}}if(aq===ap.length){if(this!==ap.get(aq-1)){ay.append(this);o[ay.attr("id")].move_drawable(ar,aq)}}else{if(this!==ap.get(aq)){$(this).insertBefore(ap.get(aq));o[ay.attr("id")].move_drawable(ar,(av.deltaY>0?aq-1:aq))}}}).bind("dragstart",function(){ai["border-top"]=ah.css("border-top");ai["border-bottom"]=ah.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ai)})};Z.moveable=n;var af=16,H=9,E=20,U=H+2,A=100,J=12000,S=200,D=5,w=10,L=5000,x=100,p="There was an error in indexing this dataset. ",K="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",F="No data for this chrom/contig.",u="Currently indexing... please wait",y="Tool cannot be rerun: ",a="Loading data...",aa="Ready for display",d=10,v=5,C=5;function ab(ai,ah){if(!ah){ah=0}var aj=Math.pow(10,ah);return Math.round(ai*aj)/aj}var c=function(ah){this.num_elements=ah;this.clear()};q(c.prototype,{get:function(ai){var ah=this.key_ary.indexOf(ai);if(ah!==-1){if(this.obj_cache[ai].stale){this.key_ary.splice(ah,1);delete this.obj_cache[ai]}else{this.move_key_to_end(ai,ah)}}return this.obj_cache[ai]},set:function(ai,aj){if(!this.obj_cache[ai]){if(this.key_ary.length>=this.num_elements){var ah=this.key_ary.shift();delete this.obj_cache[ah]}this.key_ary.push(ai)}this.obj_cache[ai]=aj;return aj},move_key_to_end:function(ai,ah){this.key_ary.splice(ah,1);this.key_ary.push(ai)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var T=function(ai,ah,aj){c.call(this,ai);this.track=ah;this.subset=(aj!==undefined?aj:true)};q(T.prototype,c.prototype,{load_data:function(aq,al,ao,ai,an){var ap=this.track.view.chrom,ak={chrom:ap,low:aq,high:al,mode:ao,resolution:ai,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ak,an);if(this.track.filters_manager){var ar=[];var ah=this.track.filters_manager.filters;for(var am=0;am<ah.length;am++){ar[ar.length]=ah[am].name}ak.filter_cols=JSON.stringify(ar)}var aj=this;return $.getJSON(this.track.data_url,ak,function(at){aj.set_data(aq,al,ao,at)})},get_data:function(ah,al,am,ai,ak){var aj=this.get_data_from_cache(ah,al,am);if(aj){return aj}aj=this.load_data(ah,al,am,ai,ak);this.set_data(ah,al,am,aj);return aj},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ap,ak,ao,aj,an,al){var aq=this.get_data_from_cache(ap,ak,ao);if(!aq){console.log("ERROR: no current data for: ",this.track,ap,ak,ao,aj,an);return}aq.stale=true;var ai=ap;if(al===this.DEEP_DATA_REQ){$.extend(an,{start_val:aq.data.length+1})}else{if(al===this.BROAD_DATA_REQ){ai=(aq.max_high?aq.max_high:aq.data[aq.data.length-1][2])+1}}var ah=this,am=this.load_data(ai,ak,ao,aj,an);new_data_available=$.Deferred();this.set_data(ap,ak,ao,new_data_available);$.when(am).then(function(ar){if(ar.data){ar.data=aq.data.concat(ar.data);if(ar.max_low){ar.max_low=aq.max_low}if(ar.message){ar.message=ar.message.replace(/[0-9]+/,ar.data.length)}}ah.set_data(ap,ak,ao,ar);new_data_available.resolve(ar)});return new_data_available},get_data_from_cache:function(ah,ai,aj){return this.get(this.gen_key(ah,ai,aj))},set_data:function(ai,aj,ak,ah){return this.set(this.gen_key(ai,aj,ak),ah)},gen_key:function(ah,aj,ak){var ai=ah+"_"+aj+"_"+ak;return ai},split_key:function(ah){return ah.split("_")}});var I=function(ai,ah,aj){T.call(this,ai,ah,aj)};q(I.prototype,T.prototype,c.prototype,{load_data:function(aj,ah,al,am,ai,ak){if(ai>1){return}return T.prototype.load_data.call(this,aj,ah,al,am,ai,ak)}});var r=function(ak,ai,ah,aj,al){this.name=ak;this.view=ai;this.container=ah;this.drag_handle_class=al;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak}],saved_values:aj,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values};q(r.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},make_name_popup_menu:function(){},set_name:function(ah){this.old_name=this.name;this.name=ah;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var z=function(al,ak,ai,ah,aj,am){r.call(this,ak,ai,ah,aj,am);this.obj_type=al;this.drawables=[]};q(z.prototype,r.prototype,{init:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah].init()}},_draw:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah]._draw()}},to_json:function(){var ai=[];for(var ah=0;ah<this.drawables.length;ah++){ai.push(this.drawables[ah].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ai}},add_drawable:function(ah){this.drawables.push(ah);ah.container=this},add_drawable_before:function(aj,ah){var ai=this.drawables.indexOf(ah);if(ai!=-1){this.drawables.splice(ai,0,aj);return true}return false},remove_drawable:function(ai){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);ai.container=null;return true}return false},move_drawable:function(ai,aj){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);this.drawables.splice(aj,0,ai);return true}return false}});var R=function(ak,ai,ah,aj){z.call(this,"DrawableGroup",ak,ai,ah,aj,"group-handle");if(!R.id_counter){R.id_counter=0}var al=R.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+al).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+al+"_content_div").appendTo(this.container_div);m(this.container_div,this);m(this.content_div,this);n(this.container_div,this.drag_handle_class,".group",this);this.make_name_popup_menu()};q(R.prototype,r.prototype,z.prototype,{make_name_popup_menu:function(){var ai=this;var ah={};ah["Edit configuration"]=function(){var al=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aj=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(am){if((am.keyCode||am.which)===27){al()}else{if((am.keyCode||am.which)===13){aj()}}};$(window).bind("keypress.check_enter_esc",ak);show_modal("Configure Group",ai.config.build_form(),{Cancel:al,OK:aj})};ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)}});var ae=function(ah,ak,aj,ai){z.call(this,"View");this.container=ah;this.chrom=null;this.vis_id=aj;this.dbkey=ai;this.title=ak;this.tracks=this.drawables;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ag(ah.get(0).ownerDocument);this.reset()};q(ae.prototype,z.prototype,{init:function(){var aj=this.container,ah=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aj);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;m(this.viewport_container,ah);this.intro_div=$("<div/>").addClass("intro");var ak=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ai=function(al){if(al.type==="focusout"||(al.keyCode||al.which)===13||(al.keyCode||al.which)===27){if((al.keyCode||al.which)!==27){ah.go_to($(this).val())}$(this).hide();$(this).val("");ah.location_span.show();ah.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ai).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ah.location_span.hide();ah.chrom_select.hide();ah.nav_input.val(ah.chrom+":"+ah.low+"-"+ah.high);ah.nav_input.css("display","inline-block");ah.nav_input.select();ah.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ah.zoom_out();ah.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.browser_content_div.click(function(al){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("<div />").css({height:ah.browser_content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,{content_div:this.top_labeltrack}));this.add_label_track(new ad(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new B(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(al,ai,an){if(!al||al==="None"){return}var ak=this;if(al==="previous"){ak.load_chroms({low:this.chrom_start_index-x});return}if(al==="next"){ak.load_chroms({low:this.chrom_start_index+x});return}var am=$.grep(ak.chrom_data,function(ap,aq){return ap.chrom===al})[0];if(am===undefined){ak.load_chroms({chrom:al},function(){ak.change_chrom(al,ai,an)});return}else{if(al!==ak.chrom){ak.chrom=al;ak.chrom_select.val(ak.chrom);ak.max_high=am.len-1;ak.reset();ak.request_redraw(true);for(var ao=0,ah=ak.tracks.length;ao<ah;ao++){var aj=ak.tracks[ao];if(aj.init){aj.init()}}}if(ai!==undefined&&an!==undefined){ak.low=Math.max(ai,0);ak.high=Math.min(an,ak.max_high)}ak.reset_overview();ak.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){z.prototype.add_drawable.call(this,ah);ah.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;ah.init();this.label_tracks.push(ah)},remove_drawable:function(aj,ai){z.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.tracks),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(D,Math.ceil(Math.log((this.high-this.low)/S)/Math.log(D)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){$.when(ah.get_overview_tile()).then(function(ai){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ai.canvas);view.overview_highlight.show().height(ai.canvas.height());view.overview_viewport.height(ai.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ah;ah.set_is_overview(true)});view.has_changes=true},reset_overview:function(){this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new O(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},al=this.track,aj=ai.tool_id+al.tool_region_and_parameters_str(ai.chrom,ai.low,ai.high),ah,am;if(al.container===view){var ak=new R(this.name,this.track.view,this.track.container);al.container.add_drawable(ak);al.container.remove_drawable(al);ak.add_drawable(al);al.container_div.appendTo(ak.content_div);ah=ak}else{ah=al.container}if(al instanceof e){am=new W(aj,view,ah,"hda");am.change_mode(al.mode);ah.add_drawable(am)}am.content_div.text("Starting job.");this.run(ai,am,function(an){am.dataset_id=an.dataset_id;am.content_div.text("Running job.");am.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no 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ai=parseFloat(ah[this.index]);return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(ar,ay){this.track=ar;this.filters=[];for(var at=0;at<ay.length;at++){var au=ay[at],az=au.name,ah=au.type,ak=au.index,ax=au.tool_id,aw=au.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[at]=new X(az,ak,ax,aw)}else{console.log("ERROR: unsupported filter: ",az,ah)}}var al=function(aA,aB,aC){aA.click(function(){var aD=aB.text();max=parseFloat(aC.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aC.slider("option","values")){input_size=2*input_size+1;multi_value=true}aB.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aD).appendTo(aB).focus().select().click(function(aE){aE.stopPropagation()}).blur(function(){$(this).remove();aB.text(aD)}).keyup(function(aI){if(aI.keyCode===27){$(this).trigger("blur")}else{if(aI.keyCode===13){var aG=aC.slider("option","min"),aE=aC.slider("option","max"),aH=function(aJ){return(isNaN(aJ)||aJ>aE||aJ<aG)},aF=$(this).val();if(!multi_value){aF=parseFloat(aF);if(aH(aF)){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}else{aF=aF.split("-");aF=[parseFloat(aF[0]),parseFloat(aF[1])];if(aH(aF[0])||aH(aF[1])){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}aC.slider((multi_value?"values":"value"),aF)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aA){aA.stopPropagation()}).click(function(aA){aA.stopPropagation()}).bind("dblclick",function(aA){aA.stopPropagation()}).bind("keydown",function(aA){aA.stopPropagation()});var av=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aD,aF){aF.container=$("<div/>").addClass("slider-row").appendTo(av);var aE=$("<div/>").addClass("elt-label").appendTo(aF.container);var aC=$("<span/>").addClass("slider-name").text(aF.name+"  ").appendTo(aE);var aB=$("<span/>");var aH=$("<span/>").addClass("slider-value").appendTo(aE).append("[").append(aB).append("]");var aA=$("<div/>").addClass("slider").appendTo(aF.container);aF.control_element=$("<div/>").attr("id",aF.name+"-filter-control").appendTo(aA);var aG=[0,0];aF.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aJ,aK){var aI=aK.values;aB.text(aI[0]+"-"+aI[1]);aF.low=aI[0];aF.high=aI[1];ap.track.request_draw(true,true)},change:function(aI,aJ){aF.control_element.slider("option","slide").call(aF.control_element,aI,aJ)}});aF.slider=aF.control_element;aF.slider_label=aB;al(aH,aB,aF.control_element);$("<div style='clear: both;'/>").appendTo(aF.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(av);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var aj=this;ao.click(function(){aj.run_on_dataset()})}var aq=$("<div/>").addClass("display-controls").appendTo(this.parent_div),an=$("<span/>").addClass("elt-label").text("Transparency:").appendTo(aq),ai=$("<select/>").attr("name","alpha_dropdown").appendTo(aq);this.alpha_filter=null;$("<option/>").attr("value",-1).text("== None ==").appendTo(ai);for(var at=0;at<this.filters.length;at++){$("<option/>").attr("value",at).text(this.filters[at].name).appendTo(ai)}ai.change(function(){$(this).children("option:selected").each(function(){var aA=parseInt($(this).val());ap.alpha_filter=(aA>=0?ap.filters[aA]:null);ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var P=function(ai,ah){M.AlphaGenerator.call(this,ah);this.filter=ai};P.prototype.gen_alpha=function(ah){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_alpha}return((parseFloat(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var G=function(ah){this.track=ah.track;this.params=ah.params;this.values={};this.restore_values((ah.saved_values?ah.saved_values:{}));this.onchange=ah.onchange};q(G.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(ah,ak,aj,ai,al){this.track=ah;this.index=ak;this.low=ak*S*aj;this.high=(ak+1)*S*aj;this.resolution=aj;this.canvas=$("<div class='track-tile'/>").append(ai);this.data=al;this.stale=false};b.prototype.predisplay_actions=function(){};var l=function(ah,ak,aj,ai,al,am){b.call(this,ah,ak,aj,ai,al);this.max_val=am};q(l.prototype,b.prototype);var Q=function(ah,al,ak,aj,an,ao,am,ai){b.call(this,ah,al,ak,aj,an);this.mode=ao;this.message=am;this.feature_mapper=ai};q(Q.prototype,b.prototype);Q.prototype.predisplay_actions=function(){var ai=this,ah={};if(ai.mode!=="Pack"){return}$(this.canvas).mousemove(function(au){var ao=$(this).offset(),at=au.pageX-ao.left,ar=au.pageY-ao.top,ay=ai.feature_mapper.get_feature_data(at,ar),ap=(ay?ay[0]:null);$(this).siblings(".feature-popup").each(function(){if(!ap||$(this).attr("id")!==ap.toString()){$(this).remove()}});if(ay){var ak=ah[ap];if(!ak){var ap=ay[0],av={name:ay[3],start:ay[1],end:ay[2],strand:ay[4]},an=ai.track.filters_manager.filters,am;for(var aq=0;aq<an.length;aq++){am=an[aq];av[am.name]=ay[am.index]}var ak=$("<div/>").attr("id",ap).addClass("feature-popup"),ax,aw,az=$("<table/>").appendTo(ak),aA;for(ax in av){aw=av[ax];aA=$("<tr/>").appendTo(az);$("<th/>").appendTo(aA).text(ax);$("<td/>").attr("align","left").appendTo(aA).text(typeof(aw)=="number"?ab(aw,2):aw)}ah[ap]=ak}ak.appendTo($(ai.canvas).parent());var al=at+parseInt(ai.canvas.css("left"))+7,aj=ar+parseInt(ai.canvas.css("top"))+7;ak.css("left",al+"px").css("top",aj+"px")}else{if(!au.isPropagationStopped()){au.stopPropagation();$(this).siblings().each(function(){$(this).trigger(au)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var j=function(ak,ai,ah,aj,al,am){r.call(this,ak,ai,ah,{},"draghandle");this.data_url=(al?al:default_data_url);this.data_url_extra_params={};this.data_query_wait=(am?am:L);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.container_div=$("<div />").addClass("track").attr("id","track_"+j.id_counter++).css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Y){return"ReadTrack"}else{if(this instanceof W){return"ToolDataFeatureTrack"}else{if(this instanceof V){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var ak=ah.view.tracks.indexOf(ah);var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(K)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(F)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.make_name_popup_menu()}ah.content_div.text(aa);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}})},predraw_init:function(){},});var N=function(ao,am){var ai=this,ap=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=new ac(this,(ao!==undefined?ao:{}));this.filters_available=false;this.filters_visible=false;this.tool=(am!==undefined&&obj_length(am)>0?new s(this,am):undefined);this.is_overview=false;if(ai.hidden){return}if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(ai.display_modes!==undefined){if(ai.mode_div===undefined){ai.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ai.header_div);var aj=(ai.config&&ai.config.values.mode?ai.config.values.mode:ai.display_modes[0]);ai.mode=aj;ai.mode_div.text(aj);var ah={};for(var ak=0,an=ai.display_modes.length;ak<an;ak++){var al=ai.display_modes[ak];ah[al]=function(aq){return function(){ai.change_mode(aq)}}(al)}make_popupmenu(ai.mode_div,ah)}else{ai.mode_div.hide()}}this.make_name_popup_menu()};q(N.prototype,r.prototype,j.prototype,{to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw();return ah},make_name_popup_menu:function(){var ai=this;var ah={};ah[(this.is_overview?"Hide overview":"Set as overview")]=function(){if(ai.is_overview){ai.view.reset_overview()}else{ai.view.set_overview(ai)}};ah["Edit configuration"]=function(){var am=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},al=function(an){if((an.keyCode||an.which)===27){am()}else{if((an.keyCode||an.which)===13){ak()}}};$(window).bind("keypress.check_enter_esc",al);show_modal("Configure Track",ai.config.build_form(),{Cancel:am,OK:ak})};if(ai.filters_available>0){var aj=(ai.filters_div.is(":visible")?"Hide filters":"Show filters");ah[aj]=function(){ai.filters_visible=(ai.filters_div.is(":visible"));if(ai.filters_visible){ai.filters_manager.reset_filters()}ai.filters_div.toggle();ai.make_name_popup_menu()}}if(ai.tool){var aj=(ai.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");ah[aj]=function(){if(!ai.dynamic_tool_div.is(":visible")){ai.set_name(ai.name+ai.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ai.revert_name()}ai.dynamic_tool_div.toggle();ai.make_name_popup_menu()}}ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)},set_is_overview:function(ah){this.is_overview=ah;this.make_name_popup_menu()},get_overview_tile:function(){var ah=this;view=ah.view,resolution=Math.pow(D,Math.ceil(Math.log((view.max_high-view.max_low)/S)/Math.log(D))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ah.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ah.data_url_extra_params)).then(function(ai){var ak=ah._gen_tile_cache_key(view_width,w_scale,0),am=ah.tile_cache.get(ak);if(!am){am=ah.draw_tile(ai,"Auto",resolution,0,w_scale);ah.tile_cache.set(ak,am)}var ap=$(am.canvas.find("canvas")),al=ap.clone(),ao=ap.get(0).getContext("2d"),aj=al.get(0).getContext("2d"),an=ao.getImageData(0,0,ao.canvas.width,ao.canvas.height);aj.putImageData(an,-ah.left_offset,(am.data.dataset_type==="summary_tree"?U:0));new_tile=new b(ah,-1,resolution,al);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof B)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/S);var ap=true;var at=[];var ah=0;while((ai*S*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",E)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*S*an,ax=ap+S*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);if(aq!==undefined){al.tile_cache.set(at,aq);al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw()});return null},show_tile:function(ao,aq,ar){var aj=this,ai=ao.canvas,an=ai;if(ao.message){var at=$("<div/>"),ap=$("<div/>").addClass("tile-message").text(ao.message).css({height:E-1,width:ao.canvas.width}).appendTo(at),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ap),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ap);at.append(ai);an=at;al.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()});ah.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()})}ao.predisplay_actions();var am=this.view.high-this.view.low,ak=(ao.low-this.view.low)*ar;if(this.left_offset){ak-=this.left_offset}an.css({position:"absolute",top:0,left:ak,height:""});aq.append(an);aj.max_height=Math.max(aj.max_height,an.height());aj.content_div.css("height",aj.max_height+"px");aq.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*S*ai,al=S*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ai,ah){this.hidden=true;j.call(this,"label",ai,ah,{});this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{init:function(){this.enabled=true},_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var B=function(ah){this.hidden=true;j.call(this,"reference",ah,{content_div:ah.top_labeltrack},{});N.call(this);ah.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ah.dbkey};this.data_manager=new I(C,this,false);this.tile_cache=new c(v)};q(B.prototype,r.prototype,N.prototype,{init:function(){this.enabled=true},draw_tile:function(ar,an,am,ai,at){var al=this,aj=S*am;if(at>this.view.canvas_manager.char_width_px){if(ar===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(al,ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(am,ak,aj,an,ah,al){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,am,ak,aj,al);N.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=an;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new T(C,this);this.tile_cache=new c(v);this.left_offset=0;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:am},{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:al,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.track_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.track_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};q(k.prototype,r.prototype,N.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this,ai=ah.view.tracks.indexOf(ah);ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(aj){ah.container_div.addClass("line-track");var al=aj.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=al.min;ah.prefs.max_value=al.max;$("#track_"+ai+"_minval").val(ah.prefs.min_value);$("#track_"+ai+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=al.total_frequency;ah.container_div.find(".yaxislabel").remove();var am=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ai+"_minval").text(ab(ah.prefs.min_value,3));var ak=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ai+"_maxval").text(ab(ah.prefs.max_value,3));ak.css({position:"absolute",top:"24px",left:"10px"});ak.prependTo(ah.container_div);am.css({position:"absolute",bottom:"2px",left:"10px"});am.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new M.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(this.track,aj,al,ak,au.data)}});var e=function(ah,an,ai,am,ap,ao,ak,al){var aj=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];j.call(this,ah,an,ai,ao);N.call(this,ak,al);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){aj.set_name(aj.prefs.name);aj.tile_cache.clear();aj.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=am;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new T(20,this);this.left_offset=200;this.painter=M.LinkedFeaturePainter};q(e.prototype,r.prototype,N.prototype,{postdraw_actions:function(ax,ah,ay,aw){N.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.make_name_popup_menu()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",A,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aE,aI,ar,ak){var aB=this,am=aB._get_tile_bounds(aI,aE),aL=am[0],ai=am[1],ay=ai-aL,aC=Math.ceil(ay*ar),aP=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"){az="no_detail"}else{var aO=aw.data;if(this.view.high-this.view.low>J){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aC+al;aj.height=an+U;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aL,ai,200);if(aw.max){at.max=aw.max}aw=at}var aM=new M.SummaryTreePainter(aw,aL,ai,this.prefs);var aD=aj.getContext("2d");aD.translate(al,U);aM.draw(aD,aC,an);return new l(aB,aI,aE,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aF=0,aH=aw.data.length;aF<aH;aF++){var ao=aw.data[aF];var aG=false;var av;for(var aK=0,aN=au.length;aK<aN;aK++){av=au[aK];av.update_attrs(ao);if(!av.keep(ao)){aG=true;break}}if(!aG){aq.push(ao)}}}var aA=(this.filters_manager.alpha_filter?new P(this.filters_manager.alpha_filter):null);var aM=new (this.painter)(aq,aL,ai,this.prefs,az,aA,ak);var an=Math.max(af,aM.get_required_height(ap));var aj=this.view.canvas_manager.new_canvas();var aJ=null;aj.width=aC+al;aj.height=an;var aD=aj.getContext("2d");aD.fillStyle=this.prefs.block_color;aD.font=aD.canvas.manager.default_font;aD.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aw.data){aD.translate(al,0);aJ=aM.draw(aD,aC,an,ax);aJ.translation=-al}return new Q(aB,aI,aE,aj,aw.data,az,aw.message,aJ)}});var V=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.painter=M.VariantPainter};q(V.prototype,r.prototype,N.prototype,e.prototype);var Y=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ak,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter;this.make_name_popup_menu()};q(Y.prototype,r.prototype,N.prototype,e.prototype);var W=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am,{});this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};q(W.prototype,r.prototype,N.prototype,e.prototype,{predraw_init:function(){var ai=this;var ah=function(){if(ai.data_manager.size()===0){setTimeout(ah,300)}else{ai.data_url=default_data_url;ai.data_query_wait=L;ai.dataset_state_url=converted_datasets_state_url;$.getJSON(ai.dataset_state_url,{dataset_id:ai.dataset_id,hda_ldda:ai.hda_ldda},function(aj){})}};ah()}});Z.View=ae;Z.DrawableGroup=R;Z.LineTrack=k;Z.FeatureTrack=e;Z.ReadTrack=Y};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(k,y){var v=k("class").extend;var q=function(J,B,H,A,G,E){if(E===undefined){E=4}var D=A-B;var C=G-H;var F=Math.floor(Math.sqrt(D*D+C*C)/E);var K=D/F;var I=C/F;var z;for(z=0;z<F;z++,B+=K,H+=I){if(z%2!==0){continue}J.fillRect(B,H,E,1)}};var r=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var g=function(z){this.default_alpha=(z?z:1)};g.prototype.gen_alpha=function(z){return this.default_alpha};var n=function(B,D,z,A,C){this.data=B;this.view_start=D;this.view_end=z;this.prefs=v({},this.default_prefs,A);this.mode=C};n.prototype.default_prefs={};var w=function(B,D,z,A,C){n.call(this,B,D,z,A,C)};w.prototype.default_prefs={show_counts:false};w.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var c=function(z,D,F,G,B){n.call(this,z,D,F,G,B);if(this.prefs.min_value===undefined){var H=Infinity;for(var A=0,C=this.data.length;A<C;A++){H=Math.min(H,this.data[A][1])}this.prefs.min_value=H}if(this.prefs.max_value===undefined){var E=-Infinity;for(var A=0,C=this.data.length;A<C;A++){E=Math.max(E,this.data[A][1])}this.prefs.max_value=E}};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var o=function(z){this.feature_positions={};this.slot_height=z;this.translation=0};o.prototype.map_feature_data=function(A,C,z,B){if(!this.feature_positions[C]){this.feature_positions[C]=[]}this.feature_positions[C].push({data:A,x_start:z,x_end:B})};o.prototype.get_feature_data=function(z,D){var C=Math.floor(D/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var p=function(C,E,z,B,D,A){n.call(this,C,E,z,B,D);this.alpha_generator=(A?A:new g())};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};v(p.prototype,{get_required_height:function(A){var z=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){z=A*y_scale}return z+Math.max(Math.round(y_scale/2),5)},draw:function(L,J,H,G){var R=this.data,E=this.view_start,N=this.view_end;L.save();L.fillStyle=this.prefs.block_color;L.textAlign="right";var I=this.view_end-this.view_start,F=J/I,M=this.get_row_height(),Q=new o(M),C;for(var O=0,P=R.length;O<P;O++){var B=R[O],D=B[0],K=B[1],z=B[2],A=(G&&G[D]!==undefined?G[D]:null);if((K<N&&z>E)&&(this.mode=="Dense"||A!==null)){C=this.draw_element(L,this.mode,B,A,E,N,F,M,J);Q.map_feature_data(B,A,C[0],C[1])}}L.restore();return Q},draw_element:function(F,B,H,D,C,E,G,A,z){console.log("WARNING: Unimplemented function.");return[0,0]}});var d=10,j=3,m=5,x=10,f=1,t=3,e=3,a=9,l=2,h="#ccc";var s=function(C,E,z,B,D,A){p.call(this,C,E,z,B,D,A)};v(s.prototype,p.prototype,{get_row_height:function(){var A=this.mode,z;if(A==="Dense"){z=d}else{if(A==="no_detail"){z=j}else{if(A==="Squish"){z=m}else{z=x}}}return z},draw_element:function(L,E,T,G,N,ae,ai,ak,z){var Q=T[0],ag=T[1],Y=T[2],O=T[3],Z=Math.floor(Math.max(0,(ag-N)*ai)),M=Math.ceil(Math.min(z,Math.max(0,(Y-N)*ai))),X=Z,aj=M,W=(E==="Dense"?0:(0+G))*ak,K,ac,P=null,al=null,C=this.prefs.block_color,ab=this.prefs.label_color;L.globalAlpha=this.alpha_generator.gen_alpha(T);if(E=="Dense"){G=1}if(E==="no_detail"){L.fillStyle=C;L.fillRect(Z,W+5,M-Z,f)}else{var J=T[4],V=T[5],aa=T[6],D=T[7];if(V&&aa){P=Math.floor(Math.max(0,(V-N)*ai));al=Math.ceil(Math.min(z,Math.max(0,(aa-N)*ai)))}var ah,R;if(E==="Squish"||E==="Dense"){ah=1;R=e}else{ah=5;R=a}if(!D){if(T.strand){if(T.strand==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand_inv")}else{if(T.strand==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand_inv")}}}else{L.fillStyle=C}L.fillRect(Z,W,M-Z,R)}else{var I,S;if(E==="Squish"||E==="Dense"){L.fillStyle=h;I=W+Math.floor(e/2)+1;S=1}else{if(J){var I=W;var S=R;if(J==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand")}else{if(J==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand")}}}else{L.fillStyle=h;I+=(e/2)+1;S=1}}L.fillRect(Z,I,M-Z,S);for(var af=0,B=D.length;af<B;af++){var F=D[af],A=Math.floor(Math.max(0,(F[0]-N)*ai)),U=Math.ceil(Math.min(z,Math.max((F[1]-N)*ai)));if(A>U){continue}L.fillStyle=C;L.fillRect(A,W+(R-ah)/2+1,U-A,ah);if(P!==undefined&&aa>V&&!(A>al||U<P)){var ad=Math.max(A,P),H=Math.min(U,al);L.fillRect(ad,W+1,H-ad,R);if(D.length==1&&E=="Pack"){if(J==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand_inv")}else{if(J==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand_inv")}}if(ad+14<H){ad+=2;H-=2}L.fillRect(ad,W+1,H-ad,R)}}}}if(E==="Pack"&&ag>N){L.fillStyle=ab;if(N===0&&Z-L.measureText(O).width<0){L.textAlign="left";L.fillText(O,M+l,W+8);aj+=L.measureText(O).width+l}else{L.textAlign="right";L.fillText(O,Z-l,W+8);X-=L.measureText(O).width+l}}}L.globalAlpha=1;return[X,aj]}});var b=function(C,E,z,B,D,A){p.call(this,C,E,z,B,D,A)};v(b.prototype,p.prototype,{draw_element:function(S,N,H,D,V,B,K,T,Q){var H=data[i],J=H[0],R=H[1],C=H[2],M=H[3],F=Math.floor(Math.max(0,(R-V)*K)),I=Math.ceil(Math.min(Q,Math.max(0,(C-V)*K))),E=(N==="Dense"?0:(0+D))*T,z,W,A=null,L=null;if(no_label){S.fillStyle=block_color;S.fillRect(F+left_offset,E+5,I-F,1)}else{var U=H[4],P=H[5],G=H[6];z=9;W=1;S.fillRect(F+left_offset,E,I-F,z);if(N!=="Dense"&&M!==undefined&&R>V){S.fillStyle=label_color;if(V===0&&F-S.measureText(M).width<0){S.textAlign="left";S.fillText(M,I+2+left_offset,E+8)}else{S.textAlign="right";S.fillText(M,F-2+left_offset,E+8)}S.fillStyle=block_color}var O=U+" / "+P;if(R>V&&S.measureText(O).width<(I-F)){S.fillStyle="white";S.textAlign="center";S.fillText(O,left_offset+F+(I-F)/2,E+8);S.fillStyle=block_color}}return[F,I]}});var u=function(D,F,z,C,E,A,B){p.call(this,D,F,z,C,E,A);this.ref_seq=B};u.prototype.default_prefs=v({},p.prototype.default_prefs,{show_insertions:false});v(u.prototype,p.prototype,{get_row_height:function(){var z,A=this.mode;if(A==="Dense"){z=d}else{if(A==="Squish"){z=m}else{z=x;if(this.prefs.show_insertions){z*=2}}}return z},draw_read:function(V,Q,M,aa,B,U,J,G,F){V.textAlign="center";var T=this,A=[aa,B],P=0,W=0,S=0;ref_seq=this.ref_seq,char_width_px=V.canvas.manager.char_width_px;var af=[];if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){S=Math.round(M/2)}if(!J){J=[[0,G.length]]}for(var N=0,Y=J.length;N<Y;N++){var K=J[N],C="MIDNSHP=X"[K[0]],O=K[1];if(C==="H"||C==="S"){P-=O}var H=U+P,ae=Math.floor(Math.max(0,(H-aa)*M)),I=Math.floor(Math.max(0,(H+O-aa)*M));if(ae===I){I+=1}switch(C){case"H":break;case"S":case"M":case"=":if(is_overlap([H,H+O],A)){var R=G.slice(W,W+O);if(S>0){V.fillStyle=this.prefs.block_color;V.fillRect(ae-S,F+1,I-ae,9);V.fillStyle=h;for(var ac=0,z=R.length;ac<z;ac++){if(this.prefs.show_differences&&ref_seq){var L=ref_seq[H-aa+ac];if(!L||L.toLowerCase()===R[ac].toLowerCase()){continue}}if(H+ac>=aa&&H+ac<=B){var ad=Math.floor(Math.max(0,(H+ac-aa)*M));V.fillText(R[ac],ad,F+9)}}}else{V.fillStyle=this.prefs.block_color;V.fillRect(ae,F+4,I-ae,e)}}W+=O;P+=O;break;case"N":V.fillStyle=h;V.fillRect(ae-S,F+5,I-ae,1);P+=O;break;case"D":V.fillStyle="red";V.fillRect(ae-S,F+4,I-ae,3);P+=O;break;case"P":break;case"I":var Z=ae-S;if(is_overlap([H,H+O],A)){var R=G.slice(W,W+O);if(this.prefs.show_insertions){var E=ae-(I-ae)/2;if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){V.fillStyle="yellow";V.fillRect(E-S,F-9,I-ae,9);af[af.length]={type:"triangle",data:[Z,F+4,5]};V.fillStyle=h;switch(seq_tile_overlap){case (OVERLAP_START):R=R.slice(aa-H);break;case (OVERLAP_END):R=R.slice(0,H-B);break;case (CONTAINED_BY):break;case (CONTAINS):R=R.slice(aa-H,H-B);break}for(var ac=0,z=R.length;ac<z;ac++){var ad=Math.floor(Math.max(0,(H+ac-aa)*M));V.fillText(R[ac],ad-(I-ae)/2,F)}}else{V.fillStyle="yellow";V.fillRect(E,F+(this.mode!=="Dense"?2:5),I-ae,(Q!=="Dense"?e:t))}}else{if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){af[af.length]={type:"text",data:[R.length,Z,F+9]}}else{}}}W+=O;break;case"X":W+=O;break}}V.fillStyle="yellow";var ab,D,ag;for(var X=0;X<af.length;X++){ab=af[X];D=ab.type;ag=ab.data;if(D==="text"){V.save();V.font="bold "+V.font;V.fillText(ag[0],ag[1],ag[2]);V.restore()}else{if(D=="triangle"){r(V,ag[0],ag[1],ag[2])}}}},draw_element:function(S,N,F,C,V,A,J,T,Q){var I=F[0],R=F[1],B=F[2],K=F[3],E=Math.floor(Math.max(0,(R-V)*J)),G=Math.ceil(Math.min(Q,Math.max(0,(B-V)*J))),D=(N==="Dense"?0:(0+C))*T,W=this.prefs.block_color,H=this.prefs.label_color,P=0;if((N==="Pack"||this.mode==="Auto")&&J>S.canvas.manager.char_width_px){var P=Math.round(J/2)}S.fillStyle=W;if(F[5] instanceof Array){var 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",K="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",F="No data for this chrom/contig.",u="Currently indexing... please wait",y="Tool cannot be rerun: ",a="Loading data...",aa="Ready for display",d=10,v=5,C=5;function ab(ai,ah){if(!ah){ah=0}var aj=Math.pow(10,ah);return Math.round(ai*aj)/aj}var c=function(ah){this.num_elements=ah;this.clear()};q(c.prototype,{get:function(ai){var ah=this.key_ary.indexOf(ai);if(ah!==-1){if(this.obj_cache[ai].stale){this.key_ary.splice(ah,1);delete this.obj_cache[ai]}else{this.move_key_to_end(ai,ah)}}return this.obj_cache[ai]},set:function(ai,aj){if(!this.obj_cache[ai]){if(this.key_ary.length>=this.num_elements){var ah=this.key_ary.shift();delete this.obj_cache[ah]}this.key_ary.push(ai)}this.obj_cache[ai]=aj;return aj},move_key_to_end:function(ai,ah){this.key_ary.splice(ah,1);this.key_ary.push(ai)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var 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al=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aj=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(am){if((am.keyCode||am.which)===27){al()}else{if((am.keyCode||am.which)===13){aj()}}};$(window).bind("keypress.check_enter_esc",ak);show_modal("Configure Group",ai.config.build_form(),{Cancel:al,OK:aj})};ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)}});var ae=function(ah,ak,aj,ai){z.call(this,"View");this.container=ah;this.chrom=null;this.vis_id=aj;this.dbkey=ai;this.title=ak;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ag(ah.get(0).ownerDocument);this.reset()};q(ae.prototype,z.prototype,{init:function(){var aj=this.container,ah=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aj);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;m(this.viewport_container,ah);this.intro_div=$("<div/>").addClass("intro");var ak=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ai=function(al){if(al.type==="focusout"||(al.keyCode||al.which)===13||(al.keyCode||al.which)===27){if((al.keyCode||al.which)!==27){ah.go_to($(this).val())}$(this).hide();$(this).val("");ah.location_span.show();ah.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ai).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ah.location_span.hide();ah.chrom_select.hide();ah.nav_input.val(ah.chrom+":"+ah.low+"-"+ah.high);ah.nav_input.css("display","inline-block");ah.nav_input.select();ah.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ah.zoom_out();ah.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.browser_content_div.click(function(al){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("<div />").css({height:ah.browser_content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,{content_div:this.top_labeltrack}));this.add_label_track(new ad(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new B(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(am,ai,ao){if(!am||am==="None"){return}var aj=this;if(am==="previous"){aj.load_chroms({low:this.chrom_start_index-x});return}if(am==="next"){aj.load_chroms({low:this.chrom_start_index+x});return}var an=$.grep(aj.chrom_data,function(ap,aq){return ap.chrom===am})[0];if(an===undefined){aj.load_chroms({chrom:am},function(){aj.change_chrom(am,ai,ao)});return}else{if(am!==aj.chrom){aj.chrom=am;aj.chrom_select.val(aj.chrom);aj.max_high=an.len-1;aj.reset();aj.request_redraw(true);for(var al=0,ah=aj.drawables.length;al<ah;al++){var ak=aj.drawables[al];if(ak.init){ak.init()}}}if(ai!==undefined&&ao!==undefined){aj.low=Math.max(ai,0);aj.high=Math.min(ao,aj.max_high)}aj.reset_overview();aj.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){z.prototype.add_drawable.call(this,ah);ah.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;ah.init();this.label_tracks.push(ah)},remove_drawable:function(aj,ai){z.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.drawables),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(D,Math.ceil(Math.log((this.high-this.low)/S)/Math.log(D)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){$.when(ah.get_overview_tile()).then(function(ai){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ai.canvas);view.overview_highlight.show().height(ai.canvas.height());view.overview_viewport.height(ai.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ah;ah.set_is_overview(true)});view.has_changes=true},reset_overview:function(){this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new O(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},al=this.track,aj=ai.tool_id+al.tool_region_and_parameters_str(ai.chrom,ai.low,ai.high),ah,am;if(al.container===view){var ak=new R(this.name,this.track.view,this.track.container);al.container.add_drawable(ak);al.container.remove_drawable(al);ak.add_drawable(al);al.container_div.appendTo(ak.content_div);ah=ak}else{ah=al.container}if(al instanceof e){am=new W(aj,view,ah,"hda");am.change_mode(al.mode);ah.add_drawable(am)}am.content_div.text("Starting job.");this.run(ai,am,function(an){am.dataset_id=an.dataset_id;am.content_div.text("Running job.");am.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(K)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(y+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var O=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){O.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var X=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};q(X.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=ah[this.index];return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(ar,ay){this.track=ar;this.filters=[];for(var at=0;at<ay.length;at++){var au=ay[at],az=au.name,ah=au.type,ak=au.index,ax=au.tool_id,aw=au.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[at]=new X(az,ak,ax,aw)}else{console.log("ERROR: unsupported filter: ",az,ah)}}var al=function(aA,aB,aC){aA.click(function(){var aD=aB.text();max=parseFloat(aC.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aC.slider("option","values")){input_size=2*input_size+1;multi_value=true}aB.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aD).appendTo(aB).focus().select().click(function(aE){aE.stopPropagation()}).blur(function(){$(this).remove();aB.text(aD)}).keyup(function(aI){if(aI.keyCode===27){$(this).trigger("blur")}else{if(aI.keyCode===13){var aG=aC.slider("option","min"),aE=aC.slider("option","max"),aH=function(aJ){return(isNaN(aJ)||aJ>aE||aJ<aG)},aF=$(this).val();if(!multi_value){aF=parseFloat(aF);if(aH(aF)){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}else{aF=aF.split("-");aF=[parseFloat(aF[0]),parseFloat(aF[1])];if(aH(aF[0])||aH(aF[1])){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}aC.slider((multi_value?"values":"value"),aF)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aA){aA.stopPropagation()}).click(function(aA){aA.stopPropagation()}).bind("dblclick",function(aA){aA.stopPropagation()}).bind("keydown",function(aA){aA.stopPropagation()});var av=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aD,aF){aF.container=$("<div/>").addClass("slider-row").appendTo(av);var aE=$("<div/>").addClass("elt-label").appendTo(aF.container);var aC=$("<span/>").addClass("slider-name").text(aF.name+"  ").appendTo(aE);var aB=$("<span/>");var aH=$("<span/>").addClass("slider-value").appendTo(aE).append("[").append(aB).append("]");var aA=$("<div/>").addClass("slider").appendTo(aF.container);aF.control_element=$("<div/>").attr("id",aF.name+"-filter-control").appendTo(aA);var aG=[0,0];aF.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aJ,aK){var aI=aK.values;aB.text(aI[0]+"-"+aI[1]);aF.low=aI[0];aF.high=aI[1];ap.track.request_draw(true,true)},change:function(aI,aJ){aF.control_element.slider("option","slide").call(aF.control_element,aI,aJ)}});aF.slider=aF.control_element;aF.slider_label=aB;al(aH,aB,aF.control_element);$("<div style='clear: both;'/>").appendTo(aF.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(av);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var aj=this;ao.click(function(){aj.run_on_dataset()})}var aq=$("<div/>").addClass("display-controls").appendTo(this.parent_div),an=$("<span/>").addClass("elt-label").text("Transparency:").appendTo(aq),ai=$("<select/>").attr("name","alpha_dropdown").appendTo(aq);this.alpha_filter=null;$("<option/>").attr("value",-1).text("== None ==").appendTo(ai);for(var at=0;at<this.filters.length;at++){$("<option/>").attr("value",at).text(this.filters[at].name).appendTo(ai)}ai.change(function(){$(this).children("option:selected").each(function(){var aA=parseInt($(this).val());ap.alpha_filter=(aA>=0?ap.filters[aA]:null);ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var P=function(ai,ah){M.AlphaGenerator.call(this,ah);this.filter=ai};P.prototype.gen_alpha=function(ah){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_alpha}return((parseFloat(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var G=function(ah){this.track=ah.track;this.params=ah.params;this.values={};this.restore_values((ah.saved_values?ah.saved_values:{}));this.onchange=ah.onchange};q(G.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(ah,ak,aj,ai,al){this.track=ah;this.index=ak;this.low=ak*S*aj;this.high=(ak+1)*S*aj;this.resolution=aj;this.canvas=$("<div class='track-tile'/>").append(ai);this.data=al;this.stale=false};b.prototype.predisplay_actions=function(){};var l=function(ah,ak,aj,ai,al,am){b.call(this,ah,ak,aj,ai,al);this.max_val=am};q(l.prototype,b.prototype);var Q=function(ah,al,ak,aj,an,ao,am,ai){b.call(this,ah,al,ak,aj,an);this.mode=ao;this.message=am;this.feature_mapper=ai};q(Q.prototype,b.prototype);Q.prototype.predisplay_actions=function(){var ai=this,ah={};if(ai.mode!=="Pack"){return}$(this.canvas).mousemove(function(au){var ao=$(this).offset(),at=au.pageX-ao.left,ar=au.pageY-ao.top,ay=ai.feature_mapper.get_feature_data(at,ar),ap=(ay?ay[0]:null);$(this).siblings(".feature-popup").each(function(){if(!ap||$(this).attr("id")!==ap.toString()){$(this).remove()}});if(ay){var ak=ah[ap];if(!ak){var ap=ay[0],av={name:ay[3],start:ay[1],end:ay[2],strand:ay[4]},an=ai.track.filters_manager.filters,am;for(var aq=0;aq<an.length;aq++){am=an[aq];av[am.name]=ay[am.index]}var ak=$("<div/>").attr("id",ap).addClass("feature-popup"),ax,aw,az=$("<table/>").appendTo(ak),aA;for(ax in av){aw=av[ax];aA=$("<tr/>").appendTo(az);$("<th/>").appendTo(aA).text(ax);$("<td/>").attr("align","left").appendTo(aA).text(typeof(aw)=="number"?ab(aw,2):aw)}ah[ap]=ak}ak.appendTo($(ai.canvas).parent());var al=at+parseInt(ai.canvas.css("left"))+7,aj=ar+parseInt(ai.canvas.css("top"))+7;ak.css("left",al+"px").css("top",aj+"px")}else{if(!au.isPropagationStopped()){au.stopPropagation();$(this).siblings().each(function(){$(this).trigger(au)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var j=function(ak,ai,ah,aj,al,am){r.call(this,ak,ai,ah,{},"draghandle");this.data_url=(al?al:default_data_url);this.data_url_extra_params={};this.data_query_wait=(am?am:L);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.container_div=$("<div />").addClass("track").attr("id","track_"+j.id_counter++).css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Y){return"ReadTrack"}else{if(this instanceof W){return"ToolDataFeatureTrack"}else{if(this instanceof V){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(K)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(F)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.make_name_popup_menu()}ah.content_div.text(aa);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}})},predraw_init:function(){},});var N=function(ao,am){var ai=this,ap=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=new ac(this,(ao!==undefined?ao:{}));this.filters_available=false;this.filters_visible=false;this.tool=(am!==undefined&&obj_length(am)>0?new s(this,am):undefined);this.is_overview=false;if(ai.hidden){return}if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(ai.display_modes!==undefined){if(ai.mode_div===undefined){ai.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ai.header_div);var aj=(ai.config&&ai.config.values.mode?ai.config.values.mode:ai.display_modes[0]);ai.mode=aj;ai.mode_div.text(aj);var ah={};for(var ak=0,an=ai.display_modes.length;ak<an;ak++){var al=ai.display_modes[ak];ah[al]=function(aq){return function(){ai.change_mode(aq)}}(al)}make_popupmenu(ai.mode_div,ah)}else{ai.mode_div.hide()}}this.make_name_popup_menu()};q(N.prototype,r.prototype,j.prototype,{to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw();return ah},make_name_popup_menu:function(){var ai=this;var ah={};ah[(this.is_overview?"Hide overview":"Set as overview")]=function(){if(ai.is_overview){ai.view.reset_overview()}else{ai.view.set_overview(ai)}};ah["Edit configuration"]=function(){var am=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},al=function(an){if((an.keyCode||an.which)===27){am()}else{if((an.keyCode||an.which)===13){ak()}}};$(window).bind("keypress.check_enter_esc",al);show_modal("Configure Track",ai.config.build_form(),{Cancel:am,OK:ak})};if(ai.filters_available>0){var aj=(ai.filters_div.is(":visible")?"Hide filters":"Show filters");ah[aj]=function(){ai.filters_visible=(ai.filters_div.is(":visible"));if(ai.filters_visible){ai.filters_manager.reset_filters()}ai.filters_div.toggle();ai.make_name_popup_menu()}}if(ai.tool){var aj=(ai.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");ah[aj]=function(){if(!ai.dynamic_tool_div.is(":visible")){ai.set_name(ai.name+ai.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ai.revert_name()}ai.dynamic_tool_div.toggle();ai.make_name_popup_menu()}}ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)},set_is_overview:function(ah){this.is_overview=ah;this.make_name_popup_menu()},get_overview_tile:function(){var ah=this;view=ah.view,resolution=Math.pow(D,Math.ceil(Math.log((view.max_high-view.max_low)/S)/Math.log(D))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ah.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ah.data_url_extra_params)).then(function(ai){var ak=ah._gen_tile_cache_key(view_width,w_scale,0),am=ah.tile_cache.get(ak);if(!am){am=ah.draw_tile(ai,"Auto",resolution,0,w_scale);ah.tile_cache.set(ak,am)}var ap=$(am.canvas.find("canvas")),al=ap.clone(),ao=ap.get(0).getContext("2d"),aj=al.get(0).getContext("2d"),an=ao.getImageData(0,0,ao.canvas.width,ao.canvas.height);aj.putImageData(an,-ah.left_offset,(am.data.dataset_type==="summary_tree"?U:0));new_tile=new b(ah,-1,resolution,al);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof B)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/S);var ap=true;var at=[];var ah=0;while((ai*S*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",E)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*S*an,ax=ap+S*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);if(aq!==undefined){al.tile_cache.set(at,aq);al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw()});return null},show_tile:function(ao,aq,ar){var aj=this,ai=ao.canvas,an=ai;if(ao.message){var at=$("<div/>"),ap=$("<div/>").addClass("tile-message").text(ao.message).css({height:E-1,width:ao.canvas.width}).appendTo(at),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ap),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ap);at.append(ai);an=at;al.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()});ah.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()})}ao.predisplay_actions();var am=this.view.high-this.view.low,ak=(ao.low-this.view.low)*ar;if(this.left_offset){ak-=this.left_offset}an.css({position:"absolute",top:0,left:ak,height:""});aq.append(an);aj.max_height=Math.max(aj.max_height,an.height());aj.content_div.css("height",aj.max_height+"px");aq.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*S*ai,al=S*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ai,ah){this.hidden=true;j.call(this,"label",ai,ah,{});this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{init:function(){this.enabled=true},_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var B=function(ah){this.hidden=true;j.call(this,"reference",ah,{content_div:ah.top_labeltrack},{});N.call(this);ah.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ah.dbkey};this.data_manager=new I(C,this,false);this.tile_cache=new c(v)};q(B.prototype,r.prototype,N.prototype,{init:function(){this.enabled=true},draw_tile:function(ar,an,am,ai,at){var al=this,aj=S*am;if(at>this.view.canvas_manager.char_width_px){if(ar===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(al,ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(am,ak,aj,an,ah,al){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,am,ak,aj,al);N.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=an;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new T(C,this);this.tile_cache=new c(v);this.left_offset=0;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:am},{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:al,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.dataset_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.dataset_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};q(k.prototype,r.prototype,N.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this;ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(ai){ah.container_div.addClass("line-track");var ak=ai.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=ak.min;ah.prefs.max_value=ak.max;$("#track_"+ah.dataset_id+"_minval").val(ah.prefs.min_value);$("#track_"+ah.dataset_id+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=ak.total_frequency;ah.container_div.find(".yaxislabel").remove();var al=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_minval").text(ab(ah.prefs.min_value,3));var aj=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_maxval").text(ab(ah.prefs.max_value,3));aj.css({position:"absolute",top:"24px",left:"10px"});aj.prependTo(ah.container_div);al.css({position:"absolute",bottom:"2px",left:"10px"});al.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new M.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(this.track,aj,al,ak,au.data)}});var e=function(ah,an,ai,am,ap,ao,ak,al){var aj=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];j.call(this,ah,an,ai,ao);N.call(this,ak,al);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){aj.set_name(aj.prefs.name);aj.tile_cache.clear();aj.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=am;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new T(20,this);this.left_offset=200;this.painter=M.LinkedFeaturePainter};q(e.prototype,r.prototype,N.prototype,{postdraw_actions:function(ax,ah,ay,aw){N.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.make_name_popup_menu()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",A,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aE,aI,ar,ak){var aB=this,am=aB._get_tile_bounds(aI,aE),aL=am[0],ai=am[1],ay=ai-aL,aC=Math.ceil(ay*ar),aP=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"){az="no_detail"}else{var aO=aw.data;if(this.view.high-this.view.low>J){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aC+al;aj.height=an+U;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aL,ai,200);if(aw.max){at.max=aw.max}aw=at}var aM=new M.SummaryTreePainter(aw,aL,ai,this.prefs);var aD=aj.getContext("2d");aD.translate(al,U);aM.draw(aD,aC,an);return new l(aB,aI,aE,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aF=0,aH=aw.data.length;aF<aH;aF++){var ao=aw.data[aF];var aG=false;var av;for(var aK=0,aN=au.length;aK<aN;aK++){av=au[aK];av.update_attrs(ao);if(!av.keep(ao)){aG=true;break}}if(!aG){aq.push(ao)}}}var aA=(this.filters_manager.alpha_filter?new P(this.filters_manager.alpha_filter):null);var aM=new (this.painter)(aq,aL,ai,this.prefs,az,aA,ak);var an=Math.max(af,aM.get_required_height(ap));var aj=this.view.canvas_manager.new_canvas();var aJ=null;aj.width=aC+al;aj.height=an;var aD=aj.getContext("2d");aD.fillStyle=this.prefs.block_color;aD.font=aD.canvas.manager.default_font;aD.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aw.data){aD.translate(al,0);aJ=aM.draw(aD,aC,an,ax);aJ.translation=-al}return new Q(aB,aI,aE,aj,aw.data,az,aw.message,aJ)}});var V=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.painter=M.VariantPainter};q(V.prototype,r.prototype,N.prototype,e.prototype);var Y=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ak,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter;this.make_name_popup_menu()};q(Y.prototype,r.prototype,N.prototype,e.prototype);var W=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am,{});this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};q(W.prototype,r.prototype,N.prototype,e.prototype,{predraw_init:function(){var ai=this;var ah=function(){if(ai.data_manager.size()===0){setTimeout(ah,300)}else{ai.data_url=default_data_url;ai.data_query_wait=L;ai.dataset_state_url=converted_datasets_state_url;$.getJSON(ai.dataset_state_url,{dataset_id:ai.dataset_id,hda_ldda:ai.hda_ldda},function(aj){})}};ah()}});Z.View=ae;Z.DrawableGroup=R;Z.LineTrack=k;Z.FeatureTrack=e;Z.ReadTrack=Y};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(k,y){var v=k("class").extend;var q=function(J,B,H,A,G,E){if(E===undefined){E=4}var D=A-B;var C=G-H;var F=Math.floor(Math.sqrt(D*D+C*C)/E);var K=D/F;var I=C/F;var z;for(z=0;z<F;z++,B+=K,H+=I){if(z%2!==0){continue}J.fillRect(B,H,E,1)}};var r=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var g=function(z){this.default_alpha=(z?z:1)};g.prototype.gen_alpha=function(z){return this.default_alpha};var n=function(B,D,z,A,C){this.data=B;this.view_start=D;this.view_end=z;this.prefs=v({},this.default_prefs,A);this.mode=C};n.prototype.default_prefs={};var w=function(B,D,z,A,C){n.call(this,B,D,z,A,C)};w.prototype.default_prefs={show_counts:false};w.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var c=function(z,D,F,G,B){n.call(this,z,D,F,G,B);if(this.prefs.min_value===undefined){var H=Infinity;for(var A=0,C=this.data.length;A<C;A++){H=Math.min(H,this.data[A][1])}this.prefs.min_value=H}if(this.prefs.max_value===undefined){var E=-Infinity;for(var A=0,C=this.data.length;A<C;A++){E=Math.max(E,this.data[A][1])}this.prefs.max_value=E}};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var o=function(z){this.feature_positions={};this.slot_height=z;this.translation=0};o.prototype.map_feature_data=function(A,C,z,B){if(!this.feature_positions[C]){this.feature_positions[C]=[]}this.feature_positions[C].push({data:A,x_start:z,x_end:B})};o.prototype.get_feature_data=function(z,D){var C=Math.floor(D/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var p=function(C,E,z,B,D,A){n.call(this,C,E,z,B,D);this.alpha_generator=(A?A:new g())};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};v(p.prototype,{get_required_height:function(A){var z=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){z=A*y_scale}return z+Math.max(Math.round(y_scale/2),5)},draw:function(L,J,H,G){var R=this.data,E=this.view_start,N=this.view_end;L.save();L.fillStyle=this.prefs.block_color;L.textAlign="right";var I=this.view_end-this.view_start,F=J/I,M=this.get_row_height(),Q=new o(M),C;for(var O=0,P=R.length;O<P;O++){var B=R[O],D=B[0],K=B[1],z=B[2],A=(G&&G[D]!==undefined?G[D]:null);if((K<N&&z>E)&&(this.mode=="Dense"||A!==null)){C=this.draw_element(L,this.mode,B,A,E,N,F,M,J);Q.map_feature_data(B,A,C[0],C[1])}}L.restore();return Q},draw_element:function(F,B,H,D,C,E,G,A,z){console.log("WARNING: Unimplemented function.");return[0,0]}});var d=10,j=3,m=5,x=10,f=1,t=3,e=3,a=9,l=2,h="#ccc";var s=function(C,E,z,B,D,A){p.call(this,C,E,z,B,D,A)};v(s.prototype,p.prototype,{get_row_height:function(){var A=this.mode,z;if(A==="Dense"){z=d}else{if(A==="no_detail"){z=j}else{if(A==="Squish"){z=m}else{z=x}}}return z},draw_element:function(L,E,T,G,N,ae,ai,ak,z){var Q=T[0],ag=T[1],Y=T[2],O=T[3],Z=Math.floor(Math.max(0,(ag-N)*ai)),M=Math.ceil(Math.min(z,Math.max(0,(Y-N)*ai))),X=Z,aj=M,W=(E==="Dense"?0:(0+G))*ak,K,ac,P=null,al=null,C=this.prefs.block_color,ab=this.prefs.label_color;L.globalAlpha=this.alpha_generator.gen_alpha(T);if(E=="Dense"){G=1}if(E==="no_detail"){L.fillStyle=C;L.fillRect(Z,W+5,M-Z,f)}else{var J=T[4],V=T[5],aa=T[6],D=T[7];if(V&&aa){P=Math.floor(Math.max(0,(V-N)*ai));al=Math.ceil(Math.min(z,Math.max(0,(aa-N)*ai)))}var ah,R;if(E==="Squish"||E==="Dense"){ah=1;R=e}else{ah=5;R=a}if(!D){if(T.strand){if(T.strand==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand_inv")}else{if(T.strand==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand_inv")}}}else{L.fillStyle=C}L.fillRect(Z,W,M-Z,R)}else{var I,S;if(E==="Squish"||E==="Dense"){L.fillStyle=h;I=W+Math.floor(e/2)+1;S=1}else{if(J){var I=W;var S=R;if(J==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand")}else{if(J==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand")}}}else{L.fillStyle=h;I+=(e/2)+1;S=1}}L.fillRect(Z,I,M-Z,S);for(var af=0,B=D.length;af<B;af++){var F=D[af],A=Math.floor(Math.max(0,(F[0]-N)*ai)),U=Math.ceil(Math.min(z,Math.max((F[1]-N)*ai)));if(A>U){continue}L.fillStyle=C;L.fillRect(A,W+(R-ah)/2+1,U-A,ah);if(P!==undefined&&aa>V&&!(A>al||U<P)){var ad=Math.max(A,P),H=Math.min(U,al);L.fillRect(ad,W+1,H-ad,R);if(D.length==1&&E=="Pack"){if(J==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand_inv")}else{if(J==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand_inv")}}if(ad+14<H){ad+=2;H-=2}L.fillRect(ad,W+1,H-ad,R)}}}}if(E==="Pack"&&ag>N){L.fillStyle=ab;if(N===0&&Z-L.measureText(O).width<0){L.textAlign="left";L.fillText(O,M+l,W+8);aj+=L.measureText(O).width+l}else{L.textAlign="right";L.fillText(O,Z-l,W+8);X-=L.measureText(O).width+l}}}L.globalAlpha=1;return[X,aj]}});var b=function(C,E,z,B,D,A){p.call(this,C,E,z,B,D,A)};v(b.prototype,p.prototype,{draw_element:function(S,N,H,D,V,B,K,T,Q){var H=data[i],J=H[0],R=H[1],C=H[2],M=H[3],F=Math.floor(Math.max(0,(R-V)*K)),I=Math.ceil(Math.min(Q,Math.max(0,(C-V)*K))),E=(N==="Dense"?0:(0+D))*T,z,W,A=null,L=null;if(no_label){S.fillStyle=block_color;S.fillRect(F+left_offset,E+5,I-F,1)}else{var U=H[4],P=H[5],G=H[6];z=9;W=1;S.fillRect(F+left_offset,E,I-F,z);if(N!=="Dense"&&M!==undefined&&R>V){S.fillStyle=label_color;if(V===0&&F-S.measureText(M).width<0){S.textAlign="left";S.fillText(M,I+2+left_offset,E+8)}else{S.textAlign="right";S.fillText(M,F-2+left_offset,E+8)}S.fillStyle=block_color}var O=U+" / "+P;if(R>V&&S.measureText(O).width<(I-F)){S.fillStyle="white";S.textAlign="center";S.fillText(O,left_offset+F+(I-F)/2,E+8);S.fillStyle=block_color}}return[F,I]}});var u=function(D,F,z,C,E,A,B){p.call(this,D,F,z,C,E,A);this.ref_seq=B};u.prototype.default_prefs=v({},p.prototype.default_prefs,{show_insertions:false});v(u.prototype,p.prototype,{get_row_height:function(){var z,A=this.mode;if(A==="Dense"){z=d}else{if(A==="Squish"){z=m}else{z=x;if(this.prefs.show_insertions){z*=2}}}return z},draw_read:function(V,Q,M,aa,B,U,J,G,F){V.textAlign="center";var T=this,A=[aa,B],P=0,W=0,S=0;ref_seq=this.ref_seq,char_width_px=V.canvas.manager.char_width_px;var af=[];if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){S=Math.round(M/2)}if(!J){J=[[0,G.length]]}for(var N=0,Y=J.length;N<Y;N++){var K=J[N],C="MIDNSHP=X"[K[0]],O=K[1];if(C==="H"||C==="S"){P-=O}var H=U+P,ae=Math.floor(Math.max(0,(H-aa)*M)),I=Math.floor(Math.max(0,(H+O-aa)*M));if(ae===I){I+=1}switch(C){case"H":break;case"S":case"M":case"=":if(is_overlap([H,H+O],A)){var R=G.slice(W,W+O);if(S>0){V.fillStyle=this.prefs.block_color;V.fillRect(ae-S,F+1,I-ae,9);V.fillStyle=h;for(var ac=0,z=R.length;ac<z;ac++){if(this.prefs.show_differences&&ref_seq){var L=ref_seq[H-aa+ac];if(!L||L.toLowerCase()===R[ac].toLowerCase()){continue}}if(H+ac>=aa&&H+ac<=B){var ad=Math.floor(Math.max(0,(H+ac-aa)*M));V.fillText(R[ac],ad,F+9)}}}else{V.fillStyle=this.prefs.block_color;V.fillRect(ae,F+4,I-ae,e)}}W+=O;P+=O;break;case"N":V.fillStyle=h;V.fillRect(ae-S,F+5,I-ae,1);P+=O;break;case"D":V.fillStyle="red";V.fillRect(ae-S,F+4,I-ae,3);P+=O;break;case"P":break;case"I":var Z=ae-S;if(is_overlap([H,H+O],A)){var R=G.slice(W,W+O);if(this.prefs.show_insertions){var E=ae-(I-ae)/2;if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){V.fillStyle="yellow";V.fillRect(E-S,F-9,I-ae,9);af[af.length]={type:"triangle",data:[Z,F+4,5]};V.fillStyle=h;switch(seq_tile_overlap){case (OVERLAP_START):R=R.slice(aa-H);break;case (OVERLAP_END):R=R.slice(0,H-B);break;case (CONTAINED_BY):break;case (CONTAINS):R=R.slice(aa-H,H-B);break}for(var ac=0,z=R.length;ac<z;ac++){var ad=Math.floor(Math.max(0,(H+ac-aa)*M));V.fillText(R[ac],ad-(I-ae)/2,F)}}else{V.fillStyle="yellow";V.fillRect(E,F+(this.mode!=="Dense"?2:5),I-ae,(Q!=="Dense"?e:t))}}else{if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){af[af.length]={type:"text",data:[R.length,Z,F+9]}}else{}}}W+=O;break;case"X":W+=O;break}}V.fillStyle="yellow";var ab,D,ag;for(var X=0;X<af.length;X++){ab=af[X];D=ab.type;ag=ab.data;if(D==="text"){V.save();V.font="bold "+V.font;V.fillText(ag[0],ag[1],ag[2]);V.restore()}else{if(D=="triangle"){r(V,ag[0],ag[1],ag[2])}}}},draw_element:function(S,N,F,C,V,A,J,T,Q){var I=F[0],R=F[1],B=F[2],K=F[3],E=Math.floor(Math.max(0,(R-V)*J)),G=Math.ceil(Math.min(Q,Math.max(0,(B-V)*J))),D=(N==="Dense"?0:(0+C))*T,W=this.prefs.block_color,H=this.prefs.label_color,P=0;if((N==="Pack"||this.mode==="Auto")&&J>S.canvas.manager.char_width_px){var P=Math.round(J/2)}S.fillStyle=W;if(F[5] instanceof Array){var O=Math.floor(Math.max(0,(F[4][0]-V)*J)),M=Math.ceil(Math.min(Q,Math.max(0,(F[4][1]-V)*J))),L=Math.floor(Math.max(0,(F[5][0]-V)*J)),z=Math.ceil(Math.min(Q,Math.max(0,(F[5][1]-V)*J)));if(F[4][1]>=V&&F[4][0]<=A&&F[4][2]){this.draw_read(S,N,J,V,A,F[4][0],F[4][2],F[4][3],D)}if(F[5][1]>=V&&F[5][0]<=A&&F[5][2]){this.draw_read(S,N,J,V,A,F[5][0],F[5][2],F[5][3],D)}if(L>M){S.fillStyle=h;q(S,M-P,D+5,L-P,D+5)}}else{S.fillStyle=W;this.draw_read(S,N,J,V,A,R,F[4],F[5],D)}if(N==="Pack"&&R>V){S.fillStyle=this.prefs.label_color;var U=1;if(U===0&&E-S.measureText(K).width<0){S.textAlign="left";S.fillText(K,G+l-P,D+8)}else{S.textAlign="right";S.fillText(K,E-l-P,D+8)}S.fillStyle=W}return[0,0]}});y.AlphaGenerator=g;y.SummaryTreePainter=w;y.LinePainter=c;y.LinkedFeaturePainter=s;y.ReadPainter=u;y.VariantPainter=b};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window);
\ No newline at end of file
diff --git a/static/scripts/packed/trackster_ui.js b/static/scripts/packed/trackster_ui.js
index 0dd3b73f91e..67fef91ff89 100644
--- a/static/scripts/packed/trackster_ui.js
+++ b/static/scripts/packed/trackster_ui.js
@@ -1 +1 @@
-var add_bookmark=function(b,a){var g=$("#bookmarks-container"),d=$("<div/>").addClass("bookmark").appendTo(g),c=$("<div/>").addClass("delete-icon-container").appendTo(d).click(function(){d.slideUp("fast");d.remove();view.has_changes=true;return false}),e=$("<a href=''/>").addClass("icon-button delete").appendTo(c),f=$("<div/>").addClass("position").appendTo(d),h=$("<a href=''/>").text(b).appendTo(f).click(function(){view.go_to(b);return false});annotation_div=get_editable_text_elt(a,true).addClass("annotation").appendTo(d);view.has_changes=true;return d};var addable_objects={LineTrack:LineTrack,FeatureTrack:FeatureTrack,ReadTrack:ReadTrack,DrawableGroup:DrawableGroup};var track_from_dict=function(c,b){var a=new addable_objects[c.track_type](c.name,view,b,c.hda_ldda,c.dataset_id,c.prefs,c.filters,c.tool);if(c.mode){a.change_mode(c.mode)}return a};var drawable_collection_from_dict=function(f,a){var e=new addable_objects[f.obj_type](f.name,view,a,f.prefs,view.viewport_container,view);for(var d=0;d<f.drawables.length;d++){var b=f.drawables[d],c;if(b.track_type){c=track_from_dict(b,e)}else{c=drawable_collection_from_dict(b)}e.add_drawable(c);e.content_div.append(c.container_div)}return e};var drawable_from_dict=function(b,a){return(b.track_type?track_from_dict(b,a):drawable_collection_from_dict(b,a))};var create_visualization=function(b,e,g,c,a,d,f){view=new View(b,e,g,c);view.editor=true;$.when(view.load_chroms_deferred).then(function(){if(a){var k=a.chrom,p=a.start,h=a.end,m=a.overview;if(k&&(p!==undefined)&&h){view.change_chrom(k,p,h)}}if(d){var o;for(var j=0;j<d.length;j++){o=d[j];view.add_drawable(drawable_from_dict(o,view))}}var n;for(var j=0;j<view.tracks.length;j++){if(view.tracks[j].name==m){view.set_overview(view.tracks[j]);break}}if(f){var l;for(var j=0;j<f.length;j++){l=f[j];add_bookmark(l.position,l.annotation)}}view.has_changes=false});return view};var init_keyboard_nav=function(a){$(document).keydown(function(b){if($(b.srcElement).is(":input")){return}switch(b.which){case 37:a.move_fraction(0.25);break;case 38:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("-="+c+"px");break;case 39:a.move_fraction(-0.25);break;case 40:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("+="+c+"px");break}})};
\ No newline at end of file
+var add_bookmark=function(b,a){var g=$("#bookmarks-container"),d=$("<div/>").addClass("bookmark").appendTo(g),c=$("<div/>").addClass("delete-icon-container").appendTo(d).click(function(){d.slideUp("fast");d.remove();view.has_changes=true;return false}),e=$("<a href=''/>").addClass("icon-button delete").appendTo(c),f=$("<div/>").addClass("position").appendTo(d),h=$("<a href=''/>").text(b).appendTo(f).click(function(){view.go_to(b);return false});annotation_div=get_editable_text_elt(a,true).addClass("annotation").appendTo(d);view.has_changes=true;return d};var addable_objects={LineTrack:LineTrack,FeatureTrack:FeatureTrack,ReadTrack:ReadTrack,DrawableGroup:DrawableGroup};var track_from_dict=function(c,b){var a=new addable_objects[c.track_type](c.name,view,b,c.hda_ldda,c.dataset_id,c.prefs,c.filters,c.tool);if(c.mode){a.change_mode(c.mode)}return a};var drawable_collection_from_dict=function(f,a){var e=new addable_objects[f.obj_type](f.name,view,a,f.prefs,view.viewport_container,view);for(var d=0;d<f.drawables.length;d++){var b=f.drawables[d],c;if(b.track_type){c=track_from_dict(b,e)}else{c=drawable_collection_from_dict(b)}e.add_drawable(c);e.content_div.append(c.container_div)}return e};var drawable_from_dict=function(b,a){return(b.track_type?track_from_dict(b,a):drawable_collection_from_dict(b,a))};var create_visualization=function(b,e,g,c,a,d,f){view=new View(b,e,g,c);view.editor=true;$.when(view.load_chroms_deferred).then(function(){if(a){var k=a.chrom,p=a.start,h=a.end,m=a.overview;if(k&&(p!==undefined)&&h){view.change_chrom(k,p,h)}}if(d){var o;for(var j=0;j<d.length;j++){o=d[j];view.add_drawable(drawable_from_dict(o,view))}}var n;for(var j=0;j<view.drawables.length;j++){if(view.drawables[j].name==m){view.set_overview(view.drawables[j]);break}}if(f){var l;for(var j=0;j<f.length;j++){l=f[j];add_bookmark(l.position,l.annotation)}}view.has_changes=false});return view};var init_keyboard_nav=function(a){$(document).keydown(function(b){if($(b.srcElement).is(":input")){return}switch(b.which){case 37:a.move_fraction(0.25);break;case 38:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("-="+c+"px");break;case 39:a.move_fraction(-0.25);break;case 40:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("+="+c+"px");break}})};
\ No newline at end of file
diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index 951bac957d4..757a8ed018a 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -808,8 +808,6 @@ var View = function(container, title, vis_id, dbkey) {
     this.vis_id = vis_id;
     this.dbkey = dbkey;
     this.title = title;
-    // Alias tracks to point at drawables. TODO: changes tracks to 'drawables' or something similar.
-    this.tracks = this.drawables;
     this.label_tracks = [];
     this.tracks_to_be_redrawn = [];
     this.max_low = 0;
@@ -1106,10 +1104,10 @@ extend( View.prototype, DrawableCollection.prototype, {
                 view.reset();
                 view.request_redraw(true);
 
-                for (var track_id = 0, len = view.tracks.length; track_id < len; track_id++) {
-                    var track = view.tracks[track_id];
-                    if (track.init) {
-                        track.init();
+                for (var i = 0, len = view.drawables.length; i < len; i++) {
+                    var drawable = view.drawables[i];
+                    if (drawable.init) {
+                        drawable.init();
                     }
                 }
             }
@@ -1201,7 +1199,7 @@ extend( View.prototype, DrawableCollection.prototype, {
         var 
             view = this,
             // Either redrawing a single track or all view's tracks.
-            track_list = (track ? [track] : view.tracks),
+            track_list = (track ? [track] : view.drawables),
             track_index;
         
         // Add/update tracks in track list to redraw list.
@@ -2321,7 +2319,6 @@ extend(Track.prototype, Drawable.prototype, {
                 track.container_div.addClass("error");
                 track.content_div.text(DATA_ERROR);
                 if (result.message) {
-                    var track_id = track.view.tracks.indexOf(track);
                     var error_link = $(" <a href='javascript:void(0);'></a>").text("View error").click(function() {
                         show_modal( "Trackster Error", "<pre>" + result.message + "</pre>", { "Close" : hide_modal } );
                     });
@@ -2951,8 +2948,8 @@ var LineTrack = function (name, view, container, hda_ldda, dataset_id, prefs) {
             track.set_name(track.prefs.name);
             track.vertical_range = track.prefs.max_value - track.prefs.min_value;
             // Update the y-axis
-            $('#linetrack_' + track.track_id + '_minval').text(track.prefs.min_value);
-            $('#linetrack_' + track.track_id + '_maxval').text(track.prefs.max_value);
+            $('#linetrack_' + track.dataset_id + '_minval').text(track.prefs.min_value);
+            $('#linetrack_' + track.dataset_id + '_maxval').text(track.prefs.max_value);
             track.tile_cache.clear();
             track.request_draw();
         }
@@ -2999,8 +2996,7 @@ extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
         }).appendTo(track.container_div);
     },
     predraw_init: function() {
-        var track = this,
-            track_id = track.view.tracks.indexOf(track);
+        var track = this;
         
         track.vertical_range = undefined;
         return $.getJSON( track.data_url, {  stats: true, chrom: track.view.chrom, low: null, high: null,
@@ -3011,8 +3007,8 @@ extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
                 track.prefs.min_value = data.min;
                 track.prefs.max_value = data.max;
                 // Update the config
-                $('#track_' + track_id + '_minval').val(track.prefs.min_value);
-                $('#track_' + track_id + '_maxval').val(track.prefs.max_value);
+                $('#track_' + track.dataset_id + '_minval').val(track.prefs.min_value);
+                $('#track_' + track.dataset_id + '_maxval').val(track.prefs.max_value);
             }
             track.vertical_range = track.prefs.max_value - track.prefs.min_value;
             track.total_frequency = data.total_frequency;
@@ -3020,8 +3016,8 @@ extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
             // Draw y-axis labels if necessary
             track.container_div.find(".yaxislabel").remove();
             
-            var min_label = $("<div />").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_minval').text(round(track.prefs.min_value, 3));
-            var max_label = $("<div />").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_maxval').text(round(track.prefs.max_value, 3));
+            var min_label = $("<div />").addClass('yaxislabel').attr("id", 'linetrack_' + track.dataset_id + '_minval').text(round(track.prefs.min_value, 3));
+            var max_label = $("<div />").addClass('yaxislabel').attr("id", 'linetrack_' + track.dataset_id + '_maxval').text(round(track.prefs.max_value, 3));
             
             max_label.css({ position: "absolute", top: "24px", left: "10px" });
             max_label.prependTo(track.container_div);
diff --git a/static/scripts/trackster_ui.js b/static/scripts/trackster_ui.js
index 691c2ac385a..900dfc6a929 100644
--- a/static/scripts/trackster_ui.js
+++ b/static/scripts/trackster_ui.js
@@ -113,9 +113,9 @@ var create_visualization = function(parent_elt, title, id, dbkey, viewport_confi
         
         // Set overview.
         var overview_track;
-        for (var i = 0; i < view.tracks.length; i++) {
-            if (view.tracks[i].name == overview_track_name) {
-                view.set_overview(view.tracks[i]);
+        for (var i = 0; i < view.drawables.length; i++) {
+            if (view.drawables[i].name == overview_track_name) {
+                view.set_overview(view.drawables[i]);
                 break;
             }
         }

From 027c76f6130cbe91432903130a063540db4c37a5 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Tue, 11 Oct 2011 16:00:04 -0400
Subject: [PATCH 045/362] When copying datasets, provide links to target
 histories.

---
 lib/galaxy/web/controllers/dataset.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/web/controllers/dataset.py b/lib/galaxy/web/controllers/dataset.py
index 32b6ed0de43..d16e97ba00d 100644
--- a/lib/galaxy/web/controllers/dataset.py
+++ b/lib/galaxy/web/controllers/dataset.py
@@ -1134,7 +1134,10 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesHistory, UsesHist
                 if history in target_histories:
                     refresh_frames = ['history']
                 trans.sa_session.flush()
-                hist_names_str = ", ".join( [ hist.name for hist in target_histories ] )
+                hist_names_str = ", ".join( ['<a href="%s" target="_top">%s</a>' % 
+                                            ( url_for( controller="history", action="switch_to_history", \
+                                                        hist_id=trans.security.encode_id( hist.id ) ), hist.name ) \
+                                                        for hist in target_histories ] )
                 num_source = len( source_dataset_ids ) - invalid_datasets
                 num_target = len(target_histories)
                 done_msg = "%i %s copied to %i %s: %s." % (num_source, inflector.cond_plural(num_source, "dataset"), num_target, inflector.cond_plural(num_target, "history"), hist_names_str )

From b51582c25f152ed9ab70a1c641d0436254918c6a Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Tue, 11 Oct 2011 16:53:21 -0400
Subject: [PATCH 046/362] Handle scores with value '.' in data providers.

---
 lib/galaxy/visualization/tracks/data_providers.py | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/visualization/tracks/data_providers.py b/lib/galaxy/visualization/tracks/data_providers.py
index 437870e547c..eb561b62f74 100644
--- a/lib/galaxy/visualization/tracks/data_providers.py
+++ b/lib/galaxy/visualization/tracks/data_providers.py
@@ -205,7 +205,10 @@ class BedDataProvider( TracksDataProvider ):
 
             # Score (filter data)    
             if length >= 5 and filter_cols and filter_cols[0] == "Score":
-                payload.append( float(feature[4]) )
+                try:
+                    payload.append( float( feature[4] ) )
+                except:
+                    payload.append( feature[4] )
 
             rval.append( payload )
 
@@ -828,7 +831,10 @@ def package_gff_feature( feature, no_detail=False, filter_cols=[] ):
     # Add filter data to payload.
     for col in filter_cols:
         if col == "Score":
-            payload.append( float( feature.score ) )
+            try: 
+                payload.append( float( feature.score ) )
+            except:
+                payload.append( feature.score )
         elif col in feature.attributes:
             try:
                 payload.append( float( feature.attributes[col] ) )

From 938a60fc87b25927c99c9f542d926f8089784374 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Wed, 12 Oct 2011 09:52:30 -0400
Subject: [PATCH 047/362] Remove duplicate history links in copy datasets done
 message.

---
 lib/galaxy/web/controllers/dataset.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/lib/galaxy/web/controllers/dataset.py b/lib/galaxy/web/controllers/dataset.py
index d16e97ba00d..214da8948a4 100644
--- a/lib/galaxy/web/controllers/dataset.py
+++ b/lib/galaxy/web/controllers/dataset.py
@@ -1141,9 +1141,6 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesHistory, UsesHist
                 num_source = len( source_dataset_ids ) - invalid_datasets
                 num_target = len(target_histories)
                 done_msg = "%i %s copied to %i %s: %s." % (num_source, inflector.cond_plural(num_source, "dataset"), num_target, inflector.cond_plural(num_target, "history"), hist_names_str )
-                if new_history is not None:
-                    done_msg += " <a href=\"%s\" target=\"_top\">Switch to the new history.</a>" % url_for( 
-                        controller="history", action="switch_to_history", hist_id=trans.security.encode_id( new_history.id ) )
                 trans.sa_session.refresh( history )
         source_datasets = history.visible_datasets
         target_histories = [history]

From ce9884843019f2afdc5565b3cdedd052366aac91 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Wed, 12 Oct 2011 15:50:02 -0400
Subject: [PATCH 048/362] Force absolute path when creating temporary directory
 used when importing histories. Fixes #667

---
 lib/galaxy/tools/actions/history_imp_exp.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/tools/actions/history_imp_exp.py b/lib/galaxy/tools/actions/history_imp_exp.py
index 0725d728fd7..f1b6927f7cf 100644
--- a/lib/galaxy/tools/actions/history_imp_exp.py
+++ b/lib/galaxy/tools/actions/history_imp_exp.py
@@ -28,7 +28,10 @@ class ImportHistoryToolAction( ToolAction ):
         #
         
         # Add association for keeping track of job, history relationship.
-        archive_dir = tempfile.mkdtemp()
+        
+        # Use abspath because mkdtemp() does not, contrary to the documentation, 
+        # always return an absolute path.
+        archive_dir = os.path.abspath( tempfile.mkdtemp() )
         jiha = trans.app.model.JobImportHistoryArchive( job=job, archive_dir=archive_dir )
         trans.sa_session.add( jiha )
         job_wrapper = JobImportHistoryArchiveWrapper( job )

From 25eff8c31eea7ba444edec53b4fe0056a818cbf5 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Thu, 13 Oct 2011 10:59:14 -0400
Subject: [PATCH 049/362] Make implicit dataset conversion work with changes in
 1827729ed37e.

---
 lib/galaxy/model/__init__.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index c87a94e3d88..40d4695fd55 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -948,12 +948,11 @@ class DatasetInstance( object ):
             raise NoConverterException("A dependency (%s) is missing a converter." % dependency)
         except KeyError:
             pass # No deps
-        assoc = ImplicitlyConvertedDatasetAssociation( parent=self, file_type=target_ext, metadata_safe=False )
         new_dataset = self.datatype.convert_dataset( trans, self, target_ext, return_output=True, visible=False, deps=deps, set_output_history=False ).values()[0]
         new_dataset.name = self.name
+        assoc = ImplicitlyConvertedDatasetAssociation( parent=self, file_type=target_ext, dataset=new_dataset, metadata_safe=False )
         session = trans.sa_session
         session.add( new_dataset )
-        assoc.dataset = new_dataset
         session.add( assoc )
         session.flush()
         return None

From db5ac05169dd045477ce2eb1f66ab0846ac7928c Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Thu, 13 Oct 2011 14:47:13 -0400
Subject: [PATCH 050/362] Add the ability to search for tools within tool shed
 repositories by any combination of tool id, name and version (exact or
 partial matches).

---
 .../community/controllers/repository.py       | 139 +++++++++++++++++-
 templates/webapps/community/admin/center.mako |   6 +
 templates/webapps/community/index.mako        |   3 +
 .../community/repository/find_tools.mako      |  53 +++++++
 4 files changed, 200 insertions(+), 1 deletion(-)
 create mode 100644 templates/webapps/community/repository/find_tools.mako

diff --git a/lib/galaxy/webapps/community/controllers/repository.py b/lib/galaxy/webapps/community/controllers/repository.py
index 1a377dcc450..bd1a3e4475d 100644
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -189,7 +189,7 @@ class DownloadableRepositoryListGrid( RepositoryListGrid ):
         def get_value( self, trans, grid, repository ):
             """
             Display a SelectField whose options are the changeset_revision
-            strings of all downloadable_revisions of this repository.
+            strings of all download-able revisions of this repository.
             """
             select_field = build_changeset_revision_select_field( trans, repository )
             if len( select_field.options ) > 1:
@@ -220,8 +220,75 @@ class DownloadableRepositoryListGrid( RepositoryListGrid ):
                                .join( model.RepositoryMetadata.table ) \
                                .join( model.User.table )
 
+class MatchedRepositoryListGrid( grids.Grid ):
+    class NameColumn( grids.TextColumn ):
+        def get_value( self, trans, grid, repository_metadata ):
+            return repository_metadata.repository.name
+    class DescriptionColumn( grids.TextColumn ):
+        def get_value( self, trans, grid, repository_metadata ):
+            return repository_metadata.repository.description
+    class RevisionColumn( grids.TextColumn ):
+        def get_value( self, trans, grid, repository_metadata ):
+            return repository_metadata.changeset_revision
+    class UserColumn( grids.TextColumn ):
+        def get_value( self, trans, grid, repository_metadata ):
+            if repository_metadata.repository.user:
+                return repository_metadata.repository.user.username
+            return 'no user'
+    # Grid definition
+    title = "Matched repositories"
+    model_class = model.RepositoryMetadata
+    template='/webapps/community/repository/grid.mako'
+    default_sort_key = "name"
+    columns = [
+        NameColumn( "Name",
+                    key="name",
+                    link=( lambda item: dict( operation="view_or_manage_repository",
+                                              id=item.repository.id,
+                                              webapp="community" ) ),
+                    attach_popup=True ),
+        DescriptionColumn( "Synopsis",
+                           key="description",
+                           attach_popup=False ),
+        RevisionColumn( "Revision" ),
+        UserColumn( "Owner",
+                     model_class=model.User,
+                     attach_popup=False,
+                     key="User.username" )
+    ]
+    operations = []
+    standard_filters = []
+    default_filter = {}
+    num_rows_per_page = 50
+    preserve_state = False
+    use_paging = True
+    def build_initial_query( self, trans, **kwd ):
+        match_tuples = kwd.get( 'match_tuples', [] )
+        clause_list = []
+        if match_tuples:
+            for match_tuple in match_tuples:
+                repository_id, changeset_revision = match_tuple
+                clause_list.append( "%s=%d and %s='%s'" % ( self.model_class.table.c.repository_id,
+                                                            int( repository_id ),
+                                                            self.model_class.table.c.changeset_revision,
+                                                            changeset_revision ) )
+            q = trans.sa_session.query( self.model_class ) \
+                                .join( model.Repository ) \
+                                .join( model.User.table ) \
+                                .filter( or_( *clause_list ) )
+            return trans.sa_session.query( self.model_class ) \
+                                   .join( model.Repository ) \
+                                   .join( model.User.table ) \
+                                   .filter( or_( *clause_list ) )
+        # Return an empty query
+        return trans.sa_session.query( self.model_class ) \
+                               .join( model.Repository ) \
+                               .join( model.User.table ) \
+                               .filter( self.model_class.table.c.repository_id == 0 )
+
 class RepositoryController( BaseUIController, ItemRatings ):
 
+    matched_repository_list_grid = MatchedRepositoryListGrid()
     downloadable_repository_list_grid = DownloadableRepositoryListGrid()
     repository_list_grid = RepositoryListGrid()
     category_list_grid = CategoryListGrid()
@@ -304,6 +371,76 @@ class RepositoryController( BaseUIController, ItemRatings ):
         # Render the list view
         return self.downloadable_repository_list_grid( trans, **kwd )
     @web.expose
+    def find_tools( self, trans, **kwd ):
+        if 'operation' in kwd:
+            operation = kwd['operation'].lower()
+            if operation == "view_or_manage_repository":
+                return trans.response.send_redirect( web.url_for( controller='repository',
+                                                                  action='browse_repositories',
+                                                                  **kwd ) )
+        params = util.Params( kwd )
+        message = util.restore_text( params.get( 'message', '' ) )
+        status = params.get( 'status', 'done' )
+        # Set the toolshedgalaxyurl cookie so we can get back
+        # to the calling local Galaxy instance.
+        galaxy_url = kwd.get( 'galaxy_url', None )
+        if galaxy_url:
+            trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' )
+        tool_id = kwd.get( 'tool_id', '' ).lower()
+        tool_name = kwd.get( 'tool_name', '' ).lower()
+        tool_version = kwd.get( 'tool_version', '' ).lower()
+        exact_matches = params.get( 'exact_matches', '' )
+        exact_matches_checked = CheckboxField.is_checked( exact_matches )
+        match_tuples = []
+        if tool_id or tool_name or tool_version:
+            for repository_metadata in trans.sa_session.query( model.RepositoryMetadata.table ).all():
+                metadata = repository_metadata.metadata
+                tools = metadata[ 'tools' ]
+                found = False
+                for tool_dict in tools:
+                    if tool_id and not tool_name and not tool_version:
+                        tool_dict_tool_id = tool_dict[ 'id' ].lower()
+                        found = ( tool_id == tool_dict_tool_id ) or \
+                                ( not exact_matches_checked and tool_dict_tool_id.find( tool_id ) >= 0 )
+                    elif tool_name and not tool_id and not tool_version:
+                        tool_dict_tool_name = tool_dict[ 'name' ].lower()
+                        found = ( tool_name == tool_dict_tool_name ) or \
+                                ( not exact_matches_checked and tool_dict_tool_name.find( tool_name ) >= 0 )
+                    elif tool_version and not tool_id and not tool_name:
+                        tool_dict_tool_version = tool_dict[ 'version' ].lower()
+                        found = ( tool_version == tool_dict_tool_version ) or \
+                                ( not exact_matches_checked and tool_dict_tool_version.find( tool_version ) >= 0 )
+                    elif tool_id and tool_name and not tool_version:
+                        tool_dict_tool_id = tool_dict[ 'id' ].lower()
+                        tool_dict_tool_name = tool_dict[ 'name' ].lower()
+                        found = ( tool_id == tool_dict_tool_id and tool_name == tool_dict_tool_name ) or \
+                                ( not exact_matches_checked and tool_dict_tool_id.find( tool_id ) >= 0 and tool_dict_tool_name.find( tool_name ) >= 0 )
+                    elif tool_id and tool_version and not tool_name:
+                        tool_dict_tool_id = tool_dict[ 'id' ].lower()
+                        tool_dict_tool_version = tool_dict[ 'version' ].lower()
+                        found = ( tool_id == tool_dict_tool_id and tool_version == tool_dict_tool_version ) or \
+                                ( not exact_matches_checked and tool_dict_tool_id.find( tool_id ) >= 0 and tool_dict_tool_version.find( tool_version ) >= 0 )
+                    elif tool_version and tool_name and not tool_id:
+                        tool_dict_tool_version = tool_dict[ 'version' ].lower()
+                        tool_dict_tool_name = tool_dict[ 'name' ].lower()
+                        found = ( tool_version == tool_dict_tool_version and tool_name == tool_dict_tool_name ) or \
+                                ( not exact_matches_checked and tool_dict_tool_version.find( tool_version ) >= 0 and tool_dict_tool_name.find( tool_name ) >= 0 )
+                if found:
+                    match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
+            kwd[ 'match_tuples' ] = match_tuples
+            kwd[ 'message' ] = "tool id: <b>%s</b><br/>tool name: <b>%s</b><br/>tool version: <b>%s</b><br/>exact matches only: <b>%s</b>" % \
+                ( tool_id, tool_name, tool_version, str( exact_matches_checked ) )
+            # Render the list view
+            return self.matched_repository_list_grid( trans, **kwd )
+        exact_matches_check_box = CheckboxField( 'exact_matches', checked=exact_matches_checked )
+        return trans.fill_template( '/webapps/community/repository/find_tools.mako',
+                                    tool_id=tool_id,
+                                    tool_name=tool_name,
+                                    tool_version=tool_version,
+                                    exact_matches_check_box=exact_matches_check_box,
+                                    message=message,
+                                    status=status )
+    @web.expose
     def preview_tools_in_changeset( self, trans, repository_id, **kwd ):
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', '' ) )
diff --git a/templates/webapps/community/admin/center.mako b/templates/webapps/community/admin/center.mako
index 4726edffada..038281f0e63 100644
--- a/templates/webapps/community/admin/center.mako
+++ b/templates/webapps/community/admin/center.mako
@@ -1,7 +1,13 @@
 <%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
 
 <%def name="title()">Galaxy Administration</%def>
 
+%if message:
+    ${render_msg( message, status )}
+%endif
+
 <h2>Administration</h2>
 
 <p>The menu on the left provides the following features</p>
diff --git a/templates/webapps/community/index.mako b/templates/webapps/community/index.mako
index 4ccc02d490f..fc9d93b5ffe 100644
--- a/templates/webapps/community/index.mako
+++ b/templates/webapps/community/index.mako
@@ -61,6 +61,9 @@
                                 <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='my_repositories', webapp='community' )}">Browse my repositories</a>
                             </div>
                         %endif
+                        <div class="toolTitle">
+                            <a target="galaxy_main" href="${h.url_for( controller='repository', action='find_tools', webapp='community' )}">Search for tools</a>
+                        </div>
                     </div>
                 </div>
                 <div class="toolSectionBody">
diff --git a/templates/webapps/community/repository/find_tools.mako b/templates/webapps/community/repository/find_tools.mako
new file mode 100644
index 00000000000..5acc6099f85
--- /dev/null
+++ b/templates/webapps/community/repository/find_tools.mako
@@ -0,0 +1,53 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+<%!
+   def inherit(context):
+       if context.get('use_panels'):
+           return '/webapps/community/base_panels.mako'
+       else:
+           return '/base.mako'
+%>
+<%inherit file="${inherit(context)}"/>
+
+%if message:
+    ${render_msg( message, status )}
+%endif
+
+<div class="toolForm">
+    <div class="toolFormTitle">Search repositories for tools</div>
+    <div class="toolFormBody">
+        <div class="form-row">
+            Enter any combination of the following tool attributes to locate matching tools.
+        </div>
+        <div style="clear: both"></div>
+        <form name="find_tools" id="find_tools" action="${h.url_for( controller='repository', action='find_tools' )}" method="post" >
+            <div class="form-row">
+                <label>Tool id:</label>
+                <input name="tool_id" type="textfield" value="${tool_id}" size="40"/>
+            </div>
+            <div style="clear: both"></div>
+            <div class="form-row">
+                <label>Tool name:</label>
+                <input name="tool_name" type="textfield" value="${tool_name}" size="40"/>
+            </div>
+            <div style="clear: both"></div>
+            <div class="form-row">
+                <label>Tool version:</label>
+                <input name="tool_version" type="textfield" value="${tool_version}" size="40"/>
+            </div>
+            <div style="clear: both"></div>
+            <div class="form-row">
+                <label>Exact matches only:</label>
+                ${exact_matches_check_box.get_html()}
+                <div class="toolParamHelp" style="clear: both;">
+                    Check the box to match text exactly (text case doesn't matter as all strings are forced to lower case).
+                </div>
+            </div>
+            <div style="clear: both"></div>
+            <div class="form-row">
+                <input type="submit" value="Search repositories"/>
+            </div>
+        </form>
+    </div>
+</div>

From cc21447a786e10ac072b2da83752fbe103640058 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Thu, 13 Oct 2011 15:21:18 -0400
Subject: [PATCH 051/362] Keep track ot the changeset revision when viewing
 tool shed repositories retrieved from tool searches.

---
 .../community/controllers/repository.py       | 22 ++++++++++++++-----
 1 file changed, 17 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/webapps/community/controllers/repository.py b/lib/galaxy/webapps/community/controllers/repository.py
index bd1a3e4475d..bf4c592a399 100644
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -244,7 +244,7 @@ class MatchedRepositoryListGrid( grids.Grid ):
         NameColumn( "Name",
                     key="name",
                     link=( lambda item: dict( operation="view_or_manage_repository",
-                                              id=item.repository.id,
+                                              id=item.id,
                                               webapp="community" ) ),
                     attach_popup=True ),
         DescriptionColumn( "Synopsis",
@@ -373,11 +373,23 @@ class RepositoryController( BaseUIController, ItemRatings ):
     @web.expose
     def find_tools( self, trans, **kwd ):
         if 'operation' in kwd:
-            operation = kwd['operation'].lower()
+            operation = kwd[ 'operation' ].lower()
             if operation == "view_or_manage_repository":
-                return trans.response.send_redirect( web.url_for( controller='repository',
-                                                                  action='browse_repositories',
-                                                                  **kwd ) )
+                repository_metadata = get_repository_metadata_by_id( trans, kwd[ 'id' ] )
+                repository_id = trans.security.encode_id( repository_metadata.repository.id )
+                repository = get_repository( trans, repository_id )
+                is_admin = trans.user_is_admin()
+                # The received id is a RepositoryMetadata.id, so we have to get the repository id.
+                kwd[ 'id' ] = repository_id
+                kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision
+                if is_admin or repository.user == trans.user:
+                    return trans.response.send_redirect( web.url_for( controller='repository',
+                                                                      action='manage_repository',
+                                                                      **kwd ) )
+                else:
+                    return trans.response.send_redirect( web.url_for( controller='repository',
+                                                                      action='view_repository',
+                                                                      **kwd ) )
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', '' ) )
         status = params.get( 'status', 'done' )

From f967649dfeb7313cd59c691ed27c6770d75c63b6 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Thu, 13 Oct 2011 15:35:45 -0400
Subject: [PATCH 052/362] Sort the list of tool shed repositories by name when
 populating the grid for matching tools, but eliminate all grid column
 sorting.

---
 .../webapps/community/controllers/repository.py       | 11 +++--------
 1 file changed, 3 insertions(+), 8 deletions(-)

diff --git a/lib/galaxy/webapps/community/controllers/repository.py b/lib/galaxy/webapps/community/controllers/repository.py
index bf4c592a399..16de6f5f117 100644
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -239,16 +239,14 @@ class MatchedRepositoryListGrid( grids.Grid ):
     title = "Matched repositories"
     model_class = model.RepositoryMetadata
     template='/webapps/community/repository/grid.mako'
-    default_sort_key = "name"
+    default_sort_key = "Repository.name"
     columns = [
         NameColumn( "Name",
-                    key="name",
                     link=( lambda item: dict( operation="view_or_manage_repository",
                                               id=item.id,
                                               webapp="community" ) ),
                     attach_popup=True ),
         DescriptionColumn( "Synopsis",
-                           key="description",
                            attach_popup=False ),
         RevisionColumn( "Revision" ),
         UserColumn( "Owner",
@@ -272,14 +270,11 @@ class MatchedRepositoryListGrid( grids.Grid ):
                                                             int( repository_id ),
                                                             self.model_class.table.c.changeset_revision,
                                                             changeset_revision ) )
-            q = trans.sa_session.query( self.model_class ) \
-                                .join( model.Repository ) \
-                                .join( model.User.table ) \
-                                .filter( or_( *clause_list ) )
             return trans.sa_session.query( self.model_class ) \
                                    .join( model.Repository ) \
                                    .join( model.User.table ) \
-                                   .filter( or_( *clause_list ) )
+                                   .filter( or_( *clause_list ) ) \
+                                   .order_by( model.Repository.name )
         # Return an empty query
         return trans.sa_session.query( self.model_class ) \
                                .join( model.Repository ) \

From 2b9ed3a9868eb479a74c9e4640aa6632c2fe56ce Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Thu, 13 Oct 2011 16:09:28 -0400
Subject: [PATCH 053/362] Clarify tool searches in the tool shed.  Searches are
 retricted to only tools that properly load in Galaxy.

---
 lib/galaxy/webapps/community/controllers/repository.py | 9 +++++++--
 templates/webapps/community/index.mako                 | 8 +++++---
 templates/webapps/community/repository/find_tools.mako | 4 ++--
 3 files changed, 14 insertions(+), 7 deletions(-)

diff --git a/lib/galaxy/webapps/community/controllers/repository.py b/lib/galaxy/webapps/community/controllers/repository.py
index 16de6f5f117..8d3e75a677c 100644
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -293,7 +293,12 @@ class RepositoryController( BaseUIController, ItemRatings ):
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
-        return trans.fill_template( '/webapps/community/index.mako', message=message, status=status )
+        # See if there are any RepositoryMetadata records since menu items require them.
+        repository_metadata = trans.sa_session.query( model.RepositoryMetadata ).first()
+        return trans.fill_template( '/webapps/community/index.mako',
+                                    repository_metadata=repository_metadata,
+                                    message=message,
+                                    status=status )
     @web.expose
     def browse_categories( self, trans, **kwd ):
         if 'f-free-text-search' in kwd:
@@ -400,7 +405,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
         exact_matches_checked = CheckboxField.is_checked( exact_matches )
         match_tuples = []
         if tool_id or tool_name or tool_version:
-            for repository_metadata in trans.sa_session.query( model.RepositoryMetadata.table ).all():
+            for repository_metadata in trans.sa_session.query( model.RepositoryMetadata ):
                 metadata = repository_metadata.metadata
                 tools = metadata[ 'tools' ]
                 found = False
diff --git a/templates/webapps/community/index.mako b/templates/webapps/community/index.mako
index fc9d93b5ffe..f29208c2a01 100644
--- a/templates/webapps/community/index.mako
+++ b/templates/webapps/community/index.mako
@@ -61,9 +61,11 @@
                                 <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='my_repositories', webapp='community' )}">Browse my repositories</a>
                             </div>
                         %endif
-                        <div class="toolTitle">
-                            <a target="galaxy_main" href="${h.url_for( controller='repository', action='find_tools', webapp='community' )}">Search for tools</a>
-                        </div>
+                        %if repository_metadata:
+                            <div class="toolTitle">
+                                <a target="galaxy_main" href="${h.url_for( controller='repository', action='find_tools', webapp='community' )}">Search for valid tools</a>
+                            </div>
+                        %endif
                     </div>
                 </div>
                 <div class="toolSectionBody">
diff --git a/templates/webapps/community/repository/find_tools.mako b/templates/webapps/community/repository/find_tools.mako
index 5acc6099f85..95ad1dba210 100644
--- a/templates/webapps/community/repository/find_tools.mako
+++ b/templates/webapps/community/repository/find_tools.mako
@@ -15,10 +15,10 @@
 %endif
 
 <div class="toolForm">
-    <div class="toolFormTitle">Search repositories for tools</div>
+    <div class="toolFormTitle">Search repositories for valid tools</div>
     <div class="toolFormBody">
         <div class="form-row">
-            Enter any combination of the following tool attributes to locate matching tools.
+            Valid tools are those that properly load in Galaxy.  Enter any combination of the following tool attributes to locate matching valid tools.
         </div>
         <div style="clear: both"></div>
         <form name="find_tools" id="find_tools" action="${h.url_for( controller='repository', action='find_tools' )}" method="post" >

From 0a70d50c72eb99aa2933dd1cc9d8a10b631c86c0 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Fri, 14 Oct 2011 09:58:59 -0400
Subject: [PATCH 054/362] Remove incorrect #-S /bin/bash (SGE shell override)
 from drmaa job runner.  If you were depending on this to get jobs to run on
 your SGE cluster under bash, please add '-S /bin/bash' to your Galaxy user's
 ~/.sge_request.

---
 lib/galaxy/jobs/runners/drmaa.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/lib/galaxy/jobs/runners/drmaa.py b/lib/galaxy/jobs/runners/drmaa.py
index 440851e74eb..6667885de0f 100644
--- a/lib/galaxy/jobs/runners/drmaa.py
+++ b/lib/galaxy/jobs/runners/drmaa.py
@@ -33,7 +33,6 @@ drmaa_state = {
 }
 
 drm_template = """#!/bin/sh
-#$ -S /bin/sh
 GALAXY_LIB="%s"
 if [ "$GALAXY_LIB" != "None" ]; then
     if [ -n "$PYTHONPATH" ]; then

From d29caaf93674a820a82f36737ba5d7e01e3a6f85 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Fri, 14 Oct 2011 12:14:54 -0400
Subject: [PATCH 055/362] Add the ability to upload exported Galaxy workflow
 files.  Makew a first pass at fixing bugs when importing a workflow into a
 Galaxy instance that does not have all of the required tools.   This code is
 still full of bugs.

---
 lib/galaxy/web/base/controller.py             |  15 +-
 lib/galaxy/web/controllers/workflow.py        | 160 +++++---
 .../community/controllers/repository.py       |   3 +-
 lib/galaxy/workflow/modules.py                |  57 +--
 templates/webapps/galaxy/admin/center.mako    | 351 +++++++++---------
 templates/webapps/galaxy/admin/index.mako     |   3 +-
 templates/workflow/import.mako                |  56 +++
 templates/workflow/list.mako                  |  26 +-
 8 files changed, 397 insertions(+), 274 deletions(-)
 create mode 100644 templates/workflow/import.mako

diff --git a/lib/galaxy/web/base/controller.py b/lib/galaxy/web/base/controller.py
index b51157fe197..530706451a8 100644
--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -1299,9 +1299,8 @@ class Admin( object ):
     @web.require_admin
     def index( self, trans, **kwd ):
         webapp = kwd.get( 'webapp', 'galaxy' )
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        status = params.get( 'status', 'done' )
+        message = kwd.get( 'message', ''  )
+        status = kwd.get( 'status', 'done' )
         if webapp == 'galaxy':
             cloned_repositories = trans.sa_session.query( trans.model.ToolShedRepository ) \
                                                   .filter( trans.model.ToolShedRepository.deleted == False ) \
@@ -1320,10 +1319,16 @@ class Admin( object ):
     @web.require_admin
     def center( self, trans, **kwd ):
         webapp = kwd.get( 'webapp', 'galaxy' )
+        message = kwd.get( 'message', ''  )
+        status = kwd.get( 'status', 'done' )
         if webapp == 'galaxy':
-            return trans.fill_template( '/webapps/galaxy/admin/center.mako' )
+            return trans.fill_template( '/webapps/galaxy/admin/center.mako',
+                                        message=message,
+                                        status=status )
         else:
-            return trans.fill_template( '/webapps/community/admin/center.mako' )
+            return trans.fill_template( '/webapps/community/admin/center.mako',
+                                        message=message,
+                                        status=status )
     @web.expose
     @web.require_admin
     def reload_tool( self, trans, **kwd ):
diff --git a/lib/galaxy/web/controllers/workflow.py b/lib/galaxy/web/controllers/workflow.py
index d9112d17fea..580fb42179f 100644
--- a/lib/galaxy/web/controllers/workflow.py
+++ b/lib/galaxy/web/controllers/workflow.py
@@ -792,10 +792,10 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
                     'data_outputs': [],
                     'form_html': invalid_tool_form_html,
                     'annotation' : annotation_str,
+                    'input_connections' : {},
                     'post_job_actions' : {},
                     'workflow_outputs' : []
                 }
-                step_dict['input_connections'] = input_conn_dict
                 # Position
                 step_dict['position'] = step.position
                 # Add to return value
@@ -958,19 +958,13 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
         """
         stored = self.get_stored_workflow( trans, id, check_ownership=False, check_accessible=True )
         return trans.fill_template( "/workflow/export.mako", item=stored, use_panels=True )
-        
-        
     @web.expose
     @web.require_login( "use workflows" )
     def import_from_myexp( self, trans, myexp_id, myexp_username=None, myexp_password=None ):
         """
         Imports a workflow from the myExperiment website.
         """
-        
-        #
         # Get workflow XML.
-        #
-        
         # Get workflow content.
         conn = httplib.HTTPConnection( self.__myexp_url )
         # NOTE: blocks web thread.
@@ -985,17 +979,16 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
         parser = SingleTagContentsParser( "content" )
         parser.feed( workflow_xml )
         workflow_content = base64.b64decode( parser.tag_content )
-        
-        #
         # Process workflow XML and create workflow.
-        #
         parser = SingleTagContentsParser( "galaxy_json" )
         parser.feed( workflow_content )
         workflow_dict = from_json_string( parser.tag_content )
-        
         # Create workflow.
-        workflow = self._workflow_from_dict( trans, workflow_dict, source="myExperiment" ).latest_workflow
-        
+        workflow, missing_tool_tups = self._workflow_from_dict( trans, workflow_dict, source="myExperiment" ).latest_workflow
+        if missing_tool_tups:
+            # TODO: handle the case where the imported workflow requires tools that are not available in
+            # the local Galaxy instance.
+            pass
         # Provide user feedback.
         if workflow.has_errors:
             return trans.show_warn_message( "Imported, but some steps in this workflow have validation errors" )
@@ -1003,7 +996,6 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
             return trans.show_warn_message( "Imported, but this workflow contains cycles" )
         else:
             return trans.show_message( "Workflow '%s' imported" % workflow.name )
-         
     @web.expose
     @web.require_login( "use workflows" )
     def export_to_myexp( self, trans, id, myexp_username, myexp_password ):
@@ -1102,40 +1094,91 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
         return stored_dict
 
     @web.expose
-    def import_workflow( self, trans, workflow_text=None, url=None ):
-        if workflow_text is None and url is None:
-            return form( url_for(), "Import Workflow", submit_text="Import", use_panels=True ) \
-                    .add_text( "url", "Workflow URL", "" ) \
-                    .add_input( "textarea", "Encoded workflow (as generated by export workflow)", "workflow_text", "" )
-        if url:
-            # Load workflow from external URL
-            # NOTE: blocks the web thread. 
-            try:
-                workflow_data = urllib2.urlopen( url ).read()
-            except Exception, e:
-                return trans.show_error_message( "Failed to open URL %s<br><br>Message: %s" % ( url, str( e ) ) )
-        else:
-            workflow_data = workflow_text
-        # Convert incoming workflow data from json
-        try:
-            data = simplejson.loads( workflow_data )
-        except Exception, e:
-            return trans.show_error_message( "Data at '%s' does not appear to be a Galaxy workflow<br><br>Message: %s" % ( url, str( e ) ) )
-            
-        # Create workflow.
-        workflow = self._workflow_from_dict( trans, data, source="uploaded file" ).latest_workflow
-        
-        # Provide user feedback and show workflow list.
-        if workflow.has_errors:
-            trans.set_message( "Imported, but some steps in this workflow have validation errors", 
-                                type="warning" )
-        if workflow.has_cycles:
-            trans.set_message( "Imported, but this workflow contains cycles",
-                                type="warning" )
-        else:
-            trans.set_message( "Workflow '%s' imported" % workflow.name )
-        return self.list( trans )
-        
+    def import_workflow( self, trans, **kwd ):
+        url = kwd.get( 'url', '' )
+        message = kwd.get( 'message', '' )
+        status = kwd.get( 'status', 'done' )
+        if kwd.get( 'import_button', False ):
+            workflow_data = None
+            if url:
+                # Load workflow from external URL
+                # NOTE: blocks the web thread. 
+                try:
+                    workflow_data = urllib2.urlopen( url ).read()
+                except Exception, e:
+                    message = "Failed to open URL: <b>%s</b><br>Exception: %s" % ( url, str( e ) )
+                    status = 'error'
+            else:
+                # Load workflow from browsed file.
+                file_data = kwd.get( 'file_data', '' )
+                if file_data in ( '', None ):
+                    message = 'No exported Galaxy workflow files were selected.'
+                    status = 'error'
+                else:
+                    uploaded_file = file_data.file
+                    uploaded_file_name = uploaded_file.name
+                    uploaded_file_filename = file_data.filename
+                    if os.path.getsize( os.path.abspath( uploaded_file_name ) ) > 0:
+                        # We're reading the file as text so we can re-use the existing code below.
+                        # This may not be ideal...
+                        workflow_data = uploaded_file.read()
+                    else:
+                        message= 'You attempted to upload an empty file.'
+                        status = 'error'
+            if workflow_data:
+                # Convert incoming workflow data from json
+                try:
+                    data = simplejson.loads( workflow_data )
+                except Exception, e:
+                    data = None
+                    message = "The data content does not appear to be a Galaxy workflow.<br/>Exception: %s" % str( e )
+                    status = 'error'
+                if data:
+                    # Create workflow if possible.  If a required tool is not available in the local
+                    # Galaxy instance, the tool information will be available in the step_dict.
+                    workflow, missing_tool_tups = self._workflow_from_dict( trans, data, source="uploaded file" )
+                    workflow = workflow.latest_workflow
+                    # Provide user feedback and show workflow list.
+                    if workflow.has_errors:
+                        message += "Imported, but some steps in this workflow have validation errors. "
+                        status = "error"
+                    if workflow.has_cycles:
+                        message += "Imported, but this workflow contains cycles.  "
+                        status = "error"
+                    else:
+                        message += "Workflow '%s' imported successfully.  " % workflow.name
+                    if missing_tool_tups:
+                        if trans.user_is_admin():
+                            # A required tool is not available in the local Galaxy instance.
+                            # TODO: It would sure be nice to be able to redirec to a mako tempalte here that displays a nice
+                            # page including the links to the configured tool shed instead of this stupd message, but trying
+                            # to get the panels back is a nightmare since workflow eliminates the Galaxy panels.  Someone 
+                            #involved in workflow development needs to figure out what it will take to get the Galaxy panels back...
+                            galaxy_url = trans.request.host
+                            message += "The workflow requires the following tools that are not available in this Galaxy instance."
+                            message += "You can likely install the required tools from one of the Galaxy tool sheds listed below.<br/><br/>"
+                            for missing_tool_tup in missing_tool_tups:
+                                missing_tool_id = missing_tool_tup[0]
+                                for tool_shed_name, tool_shed_url in trans.app.tool_shed_registry.tool_sheds.items():
+                                    if tool_shed_url.endswith( '/' ):
+                                        tool_shed_url = tool_shed_url.rstrip( '/' )
+                                        url = '%s/repository/find_tools?tool_id=%s&galaxy_url=%s&webapp=community' % ( tool_shed_url, missing_tool_id, galaxy_url )
+                                    message += '<a href="%s">%s</a><br/>' % ( url, tool_shed_name )
+                                    status = 'error'
+                            return trans.response.send_redirect( web.url_for( controller='admin',
+                                                                              action='index',
+                                                                              webapp='galaxy',
+                                                                              message=message,
+                                                                              status=status ) )
+                        else:
+                            # TODO: Figure out what to do here...
+                            pass
+                    return self.list( trans )
+        return trans.fill_template( "workflow/import.mako",
+                                    url=url,
+                                    message=message,
+                                    status=status,
+                                    use_panels=True )
     @web.json
     def get_datatypes( self, trans ):
         ext_to_class_name = dict()
@@ -1605,8 +1648,7 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
             step_annotation = self.get_item_annotation_obj(trans.sa_session, trans.user, step )
             annotation_str = ""
             if step_annotation:
-                annotation_str = step_annotation.annotation
-                        
+                annotation_str = step_annotation.annotation     
             # Step info
             step_dict = {
                 'id': step.order_index,
@@ -1620,7 +1662,6 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
                 ## 'data_outputs': module.get_data_outputs(),
                 'annotation' : annotation_str
             }
-            
             # Add post-job actions to step dict.
             if module.type == 'tool':
                 pja_dict = {}
@@ -1629,7 +1670,6 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
                                                                       output_name = pja.output_name,
                                                                       action_arguments = pja.action_arguments )
                 step_dict[ 'post_job_actions' ] = pja_dict
-
             # Data inputs
             step_dict['inputs'] = []
             if module.type == "data_input":
@@ -1647,7 +1687,6 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
                         for partname, partval in val.items():
                             if type( partval ) == RuntimeValue:
                                 step_dict['inputs'].append( { "name" : name, "description" : "runtime parameter for tool %s" % module.get_name() } )
-
             # User outputs
             step_dict['user_outputs'] = []
             """
@@ -1668,7 +1707,6 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
             if type( module ) is ToolModule:
                 for output in module.get_data_outputs():
                     step_dict['outputs'].append( { 'name' : output['name'], 'type' : output['extensions'][0] } )
-        
             # Connections
             input_connections = step.input_connections
             if step.type is None or step.type == 'tool':
@@ -1692,7 +1730,6 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
             # Add to return value
             data['steps'][step.order_index] = step_dict
         return data
-        
     def _workflow_from_dict( self, trans, data, source=None ):
         """
         Creates a workflow from a dict. Created workflow is stored in the database and returned.
@@ -1714,8 +1751,12 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
         # The editor will provide ids for each step that we don't need to save,
         # but do need to use to make connections
         steps_by_external_id = {}
+        # Keep track of tools required by the workflow that are not available in
+        # the local Galaxy instance.  Each tuple in the list of missing_tool_tups
+        # will be ( tool_id, tool_name, tool_version ).
+        missing_tool_tups = []
         # First pass to build step objects and populate basic values
-        for key, step_dict in data['steps'].iteritems():
+        for key, step_dict in data[ 'steps' ].iteritems():
             # Create the model class for the step
             step = model.WorkflowStep()
             steps.append( step )
@@ -1723,6 +1764,11 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
             # FIXME: Position should be handled inside module
             step.position = step_dict['position']
             module = module_factory.from_dict( trans, step_dict, secure=False )
+            if module.tool is None:
+                # A required tool is not available in the local Galaxy instance.
+                missing_tool_tup = ( step_dict[ 'tool_id' ], step_dict[ 'name' ], step_dict[ 'tool_version' ] )
+                if missing_tool_tup not in missing_tool_tups:
+                    missing_tool_tups.append( missing_tool_tup )
             module.save_to_step( step )
             if step.tool_errors:
                 workflow.has_errors = True
@@ -1761,7 +1807,7 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
         # Persist
         trans.sa_session.add( stored )
         trans.sa_session.flush()
-        return stored
+        return stored, missing_tool_tups
     
 ## ---- Utility methods -------------------------------------------------------
 
diff --git a/lib/galaxy/webapps/community/controllers/repository.py b/lib/galaxy/webapps/community/controllers/repository.py
index 8d3e75a677c..b2247738bbc 100644
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -251,8 +251,7 @@ class MatchedRepositoryListGrid( grids.Grid ):
         RevisionColumn( "Revision" ),
         UserColumn( "Owner",
                      model_class=model.User,
-                     attach_popup=False,
-                     key="User.username" )
+                     attach_popup=False )
     ]
     operations = []
     standard_filters = []
diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
index e57fd0b864b..d3df8a450be 100644
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -8,6 +8,9 @@ from galaxy.util.bunch import Bunch
 from galaxy.util.json import from_json_string, to_json_string
 from galaxy.jobs.actions.post import ActionBox
 from galaxy.model import PostJobAction
+import logging
+
+log = logging.getLogger( __name__ )
 
 class WorkflowModule( object ):
     
@@ -163,29 +166,46 @@ class ToolModule( WorkflowModule ):
     def __init__( self, trans, tool_id ):
         self.trans = trans
         self.tool_id = tool_id
-        self.tool = trans.app.toolbox.tools_by_id[ tool_id ]
+        try:
+            self.tool = trans.app.toolbox.tools_by_id[ tool_id ]
+        except KeyError, e:
+            # Handle the case where the workflow requires a tool not available in the local Galaxy instance.
+            self.tool = None
+            # TODO: Instead of parsing the guid, get the tool_id and version from the shed_tool_conf.xml,
+            # which requires enhancements to the tool loading process.
+            for available_tool_id, available_tool in trans.app.toolbox.tools_by_id.items():
+                if available_tool_id.find( tool_id ) >=0:
+                    # We're attempting to match tool id against a tool guid.
+                    # TODO: match by tool_id (and version if we attempt that, but 
+                    # workflows will break) is not good enough because
+                    # 2 tools installed from a tool shed could both match this.  We
+                    # need to present a select list here.
+                    self.tool = available_tool
+                    break
         self.post_job_actions = {}
         self.workflow_outputs = []
         self.state = None
-        self.errors = None
-
+        if self.tool:
+            self.errors = None
+        else:
+            self.errors = {}
+            self.errors[ tool_id ] = 'Tool unavailable'
     @classmethod
     def new( Class, trans, tool_id=None ):
         module = Class( trans, tool_id )
         module.state = module.tool.new_state( trans, all_pages=True )
         return module
-        
     @classmethod
     def from_dict( Class, trans, d, secure=True ):
-        tool_id = d['tool_id']
+        tool_id = d[ 'tool_id' ]
         module = Class( trans, tool_id )
         module.state = DefaultToolState()
-        module.state.decode( d["tool_state"], module.tool, module.trans.app, secure=secure )
+        if module.tool is not None:
+            module.state.decode( d[ "tool_state" ], module.tool, module.trans.app, secure=secure )
         module.errors = d.get( "tool_errors", None )
-        module.post_job_actions = d.get("post_job_actions", {})
-        module.workflow_outputs = d.get("workflow_outputs", [])
+        module.post_job_actions = d.get( "post_job_actions", {} )
+        module.workflow_outputs = d.get( "workflow_outputs", [] )
         return module
-        
     @classmethod
     def from_workflow_step( Class, trans, step ):
         tool_id = step.tool_id
@@ -203,12 +223,15 @@ class ToolModule( WorkflowModule ):
                 pjadict[pja.action_type] = pja
             module.post_job_actions = pjadict
             return module
-
     def save_to_step( self, step ):
         step.type = self.type
         step.tool_id = self.tool_id
-        step.tool_version = self.get_tool_version()
-        step.tool_inputs = self.tool.params_to_strings( self.state.inputs, self.trans.app )
+        if self.tool:
+            step.tool_version = self.get_tool_version()
+            step.tool_inputs = self.tool.params_to_strings( self.state.inputs, self.trans.app )
+        else:
+            step.tool_version = None
+            step.tool_inputs = None
         step.tool_errors = self.errors
         for k, v in self.post_job_actions.iteritems():
             # Must have action_type, step.  output and a_args are optional.
@@ -221,7 +244,6 @@ class ToolModule( WorkflowModule ):
             else:
                 action_arguments = None
             n_p = PostJobAction(v['action_type'], step, output_name, action_arguments)
-
     def get_name( self ):
         return self.tool.name
     def get_tool_id( self ):
@@ -234,7 +256,6 @@ class ToolModule( WorkflowModule ):
         return self.errors
     def get_tooltip( self ):
         return self.tool.help
-        
     def get_data_inputs( self ):
         data_inputs = []
         def callback( input, value, prefixed_name, prefixed_label ):
@@ -268,15 +289,12 @@ class ToolModule( WorkflowModule ):
                         formats.append( format )
             data_outputs.append( dict( name=name, extensions=formats ) )
         return data_outputs
-    
     def get_post_job_actions( self ):
         return self.post_job_actions
-        
     def get_config_form( self ):
         self.add_dummy_datasets()
         return self.trans.fill_template( "workflow/editor_tool_form.mako", 
             tool=self.tool, values=self.state.inputs, errors=( self.errors or {} ) )
-
     def update_state( self, incoming ):       
         # Build a callback that handles setting an input to be required at
         # runtime. We still process all other parameters the user might have
@@ -306,10 +324,8 @@ class ToolModule( WorkflowModule ):
         # Update state using incoming values
         errors = self.tool.update_state( self.trans, self.tool.inputs, self.state.inputs, incoming, item_callback=item_callback )
         self.errors = errors or None
-        
     def check_and_update_state( self ):
         return self.tool.check_and_update_param_values( self.state.inputs, self.trans )
-        
     def add_dummy_datasets( self, connections=None):
         if connections:
             # Store onnections by input name
@@ -324,8 +340,7 @@ class ToolModule( WorkflowModule ):
                 if connections is None or prefixed_name in input_connections_by_name:
                     return DummyDataset()
         visit_input_values( self.tool.inputs, self.state.inputs, callback ) 
-    
-    
+
 class WorkflowModuleFactory( object ):
     def __init__( self, module_types ):
         self.module_types = module_types
diff --git a/templates/webapps/galaxy/admin/center.mako b/templates/webapps/galaxy/admin/center.mako
index c84a1741c08..a2b446d1dbb 100644
--- a/templates/webapps/galaxy/admin/center.mako
+++ b/templates/webapps/galaxy/admin/center.mako
@@ -1,187 +1,192 @@
 <%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
 
 <%def name="title()">Galaxy Administration</%def>
 
 <h2>Administration</h2>
 
-<p>The menu on the left provides the following features</p>
-<ul>
-    <li><strong>Security</strong> - see the <strong>Data Security and Data Libraries</strong> section below for details
+%if message:
+    ${render_msg( message, status )}
+%else:
+    <p>The menu on the left provides the following features</p>
+    <ul>
+        <li><strong>Security</strong> - see the <strong>Data Security and Data Libraries</strong> section below for details
+            <p/>
+            <ul>
+                <li>
+                    <strong>Manage users</strong> - provides a view of the registered users and all groups and non-private roles associated 
+                    with each user.  
+                </li>
+                <p/>
+                <li>
+                    <strong>Manage groups</strong> - provides a view of all groups along with the members of the group and the roles associated with
+                    each group (both private and non-private roles).  The group names include a link to a page that allows you to manage the users and 
+                    roles that are associated with the group.
+                </li>
+                <p/>
+                <li>
+                    <strong>Manage roles</strong> - provides a view of all non-private roles along with the role type, and the users and groups that
+                    are associated with the role.  The role names include a link to a page that allows you to manage the users and groups that are associated 
+                    with the role.  The page also includes a view of the data library datasets that are associated with the role and the permissions applied 
+                    to each dataset.
+                </li>
+            </ul>
+        </li>
         <p/>
-        <ul>
-            <li>
-                <strong>Manage users</strong> - provides a view of the registered users and all groups and non-private roles associated 
-                with each user.  
-            </li>
+        <li><strong>Data</strong>
             <p/>
-            <li>
-                <strong>Manage groups</strong> - provides a view of all groups along with the members of the group and the roles associated with
-                each group (both private and non-private roles).  The group names include a link to a page that allows you to manage the users and 
-                roles that are associated with the group.
-            </li>
-            <p/>
-            <li>
-                <strong>Manage roles</strong> - provides a view of all non-private roles along with the role type, and the users and groups that
-                are associated with the role.  The role names include a link to a page that allows you to manage the users and groups that are associated 
-                with the role.  The page also includes a view of the data library datasets that are associated with the role and the permissions applied 
-                to each dataset.
-            </li>
-        </ul>
-    </li>
-    <p/>
-    <li><strong>Data</strong>
+            <ul>
+                <li>
+                    <strong>Manage data libraries</strong> - Data libraries enable a Galaxy administrator to upload datasets into a data library.  Currently,
+                    only administrators can create data libraries.
+                    <p/>
+                    When a data library is first created, it is considered "public" since it will be displayed in the "Data Libraries" view for any user, even 
+                    those that are not logged in.  The Galaxy administrator can restrict access to a data library by associating roles with the data library's 
+                    "access library" permission.  This permission will conservatively override the [dataset] "access" permission for the data library's contained 
+                    datasets.
+                    <p/>
+                    For example, if a data library's "access library" permission is associated with Role1 and the data library contains "public" datasets, the 
+                    data library will still only be displayed to those users that have Role1.  However, if the data library's "access library" permission is 
+                    associated with both Role1 and Role2 and the data library contains datasets whose [dataset] "access" permission is associated with only Role1, 
+                    then users that have Role2 will be able to access the library, but will not see those contained datasets whose [dataset] "access" permission 
+                    is associated with only Role1.
+                    <p/>
+                    In addition to the "access library" permission, permission to perform the following functions on the data library (and it's contents) can 
+                    be granted to users (a library item is one of: a data library, a library folder, a library dataset).
+                    <p/>
+                    <ul>
+                        <li><strong>add library item</strong> - Users that have the role can add library items to this data library or folder</li>
+                        <li><strong>modify library item</strong> - Users that have the role can modify this library item</li>
+                        <li><strong>manage library permissions</strong> - Users that have the role can manage permissions applied to this library item</li>
+                    </ul>
+                    <p/>
+                    The default behavior is for no permissions to be applied to a data library item, but applied permissions are inherited downward (with the exception
+                    of the "access library" permission, which is only available on the data library itself).  Because of this, it is important to set desired permissions 
+                    on a new data library when it is created.  When this is done, new folders and datasets added to the data library will automatically inherit those 
+                    permissions.  In the same way, permissions can be applied to a folder, which will be automatically inherited by all contained datasets and sub-folders.
+                    <p/>
+                    The "Data Libraries" menu item allows users to access the datasets in a data library as long as they are not restricted from accessing them.
+                    Importing a library dataset into a history will not make a copy of the dataset, but will be a "pointer" to the dataset on disk.  This
+                    approach allows for multiple users to use a single (possibly very large) dataset file.
+                </li>
+            </ul>
+        </li>
         <p/>
-        <ul>
-            <li>
-                <strong>Manage data libraries</strong> - Data libraries enable a Galaxy administrator to upload datasets into a data library.  Currently,
-                only administrators can create data libraries.
+        <li><strong>Server</strong>
+            <p/>
+            <ul>
+                <li>
+                    <strong>Reload a tool's configuration</strong> - allows a new version of a tool to be loaded while the server is running
+                </li>
                 <p/>
-                When a data library is first created, it is considered "public" since it will be displayed in the "Data Libraries" view for any user, even 
-                those that are not logged in.  The Galaxy administrator can restrict access to a data library by associating roles with the data library's 
-                "access library" permission.  This permission will conservatively override the [dataset] "access" permission for the data library's contained 
-                datasets.
+                <li>
+                    <strong>Profile memory usage</strong> - measures system memory used for certain Galaxy functions
+                </li>
                 <p/>
-                For example, if a data library's "access library" permission is associated with Role1 and the data library contains "public" datasets, the 
-                data library will still only be displayed to those users that have Role1.  However, if the data library's "access library" permission is 
-                associated with both Role1 and Role2 and the data library contains datasets whose [dataset] "access" permission is associated with only Role1, 
-                then users that have Role2 will be able to access the library, but will not see those contained datasets whose [dataset] "access" permission 
-                is associated with only Role1.
-                <p/>
-                In addition to the "access library" permission, permission to perform the following functions on the data library (and it's contents) can 
-                be granted to users (a library item is one of: a data library, a library folder, a library dataset).
-                <p/>
-                <ul>
-                    <li><strong>add library item</strong> - Users that have the role can add library items to this data library or folder</li>
-                    <li><strong>modify library item</strong> - Users that have the role can modify this library item</li>
-                    <li><strong>manage library permissions</strong> - Users that have the role can manage permissions applied to this library item</li>
-                </ul>
-                <p/>
-                The default behavior is for no permissions to be applied to a data library item, but applied permissions are inherited downward (with the exception
-                of the "access library" permission, which is only available on the data library itself).  Because of this, it is important to set desired permissions 
-                on a new data library when it is created.  When this is done, new folders and datasets added to the data library will automatically inherit those 
-                permissions.  In the same way, permissions can be applied to a folder, which will be automatically inherited by all contained datasets and sub-folders.
-                <p/>
-                The "Data Libraries" menu item allows users to access the datasets in a data library as long as they are not restricted from accessing them.
-                Importing a library dataset into a history will not make a copy of the dataset, but will be a "pointer" to the dataset on disk.  This
-                approach allows for multiple users to use a single (possibly very large) dataset file.
-            </li>
-        </ul>
-    </li>
-    <p/>
-    <li><strong>Server</strong>
+                <li>
+                    <strong>Manage jobs</strong> - displays all jobs that are currently not finished (i.e., their state is new, waiting, queued, or
+                    running).  Administrators are able to cleanly stop long-running jobs. 
+                </li>
+            </ul>
+        </li>
         <p/>
-        <ul>
-            <li>
-                <strong>Reload a tool's configuration</strong> - allows a new version of a tool to be loaded while the server is running
-            </li>
-            <p/>
-            <li>
-                <strong>Profile memory usage</strong> - measures system memory used for certain Galaxy functions
-            </li>
-            <p/>
-            <li>
-                <strong>Manage jobs</strong> - displays all jobs that are currently not finished (i.e., their state is new, waiting, queued, or
-                running).  Administrators are able to cleanly stop long-running jobs. 
-            </li>
-        </ul>
-    </li>
+        <li><strong>Forms</strong>
+            <p/>To be completed
+        </li>
+        <p/>
+        <li><strong>Sequencing Requests</strong>
+            <p/>To be completed
+        </li>
+        <p/>
+        <li><strong>Cloud</strong>
+            <p/>To be completed
+        </li>
+    </ul>
     <p/>
-    <li><strong>Forms</strong>
-        <p/>To be completed
-    </li>
+    <p><strong>Data Security and Data Libraries</strong></p>
     <p/>
-    <li><strong>Sequencing Requests</strong>
-        <p/>To be completed
-    </li>
-    <p/>
-    <li><strong>Cloud</strong>
-        <p/>To be completed
-    </li>
-</ul>
-<p/>
-<p><strong>Data Security and Data Libraries</strong></p>
-<p/>
-<strong>Security</strong> - Data security in Galaxy is a new feature, so familiarize yourself with the details which can be found 
-here or in our <a href="http://g2.trac.bx.psu.edu/wiki/SecurityFeatures" target="_blank">data security page</a>.  The data security 
-process incorporates users, groups and roles, and enables the application of certain permissions on datasets, specifically "access"
-and "manage permissions".  By default, the "manage permissions" permission is associated with the dataset owner's private role, and
-the "access" permission is not set, making the dataset public.  With these default permissions, users should not see any difference
-in the way Galaxy has behaved in the past.
-<ul>
-    <li>
-        <strong>Users</strong> - registered Galaxy users that have created a Galaxy account.  Users can belong to groups and can
-        be associated with 1 or more roles.  If a user is not authenticated during a Galaxy session, they will not have access to any 
-        of the security features, and datasets they create during that session will have no permissions applied to them (i.e., they
-        will be considered "public", and no one will be allowed to change permissions on them).
-    </li>
-    <p/>
-    <li>
-        <strong>Groups</strong> - a set of 0 or more users which are considered members of the group.  Groups can be associated with 0
-        or more roles, simplifying the process of applying permissions to the data between a select group of users.
-    </li>
-    <p/>
-    <li>
-        <strong>Roles</strong> - associate users and groups with specific permissions on datasets.  For example, users in groups A and B 
-        can be associated with role C which gives them the "access" permission on datasets D, E and F.  Roles have a type which is currently
-        one of the following:
-        <ul>
-            <li>
-                <strong>private</strong> - every user is associated automatically with their own private role.  Administrators cannot 
-                manage private roles.
-            </li>
-            <li>
-                <strong>user</strong> - this is currently not used, but eventually any registered user will be able to create a new role
-                and this will be it's type.
-            </li>
-            <li>
-                <strong>sharing</strong> - a role created automatically during a Galaxy session that enables a user to share data with 
-                another user.  This can generally be considered a temporary role.
-            </li>
-            <li><strong>admin</strong> - a role created by a Galaxy administrator.</li>
-        </ul>
-    </li>
-    <p/>
-    <li>
-        <strong>Dataset Permissions</strong> - applying the following permissions will to a dataset will result in the behavior described.
-        <ul>
-            <li>
-                <strong>access</strong> - users associated with the role can import this dataset into their history for analysis.
-                <p>
-                    If no roles with the "access" permission are associated with a dataset, the dataset is "public" and may be accessed by anyone 
-                    that can access the data library in which it is contained.  See the <strong>Manage data libraries</strong> section above for 
-                    details.  Public datasets contained in public data libraries will be accessible to all users (as well as anyone not logged in 
-                    during a Galaxy session) from the list of data libraries displayed when the "Data Libraries" menu item is selected.
-                </p>
-                <p>
-                    Associating a dataset with a role that includes the "access" permission restricts the set of users that can access it.  
-                    For example, if 'Role A' includes the "access" permission and 'Role A' is associated with the dataset, only those users
-                    and groups who are associated with 'Role A' may access the dataset.
-                </p>
-                <p>
-                    If multiple roles that include the "access" permission are associated with a dataset, access to the dataset is derived
-                    from the intersection of the users associated with the roles.  For example, if 'Role A' and 'Role B' are associated with
-                    a dataset, only those users and groups who are associated with both 'Role A' AND 'Role B' may access the dataset.  When
-                    the "access" permission is applied to a dataset, Galaxy checks to make sure that at least 1 user belongs to all groups and
-                    roles associated with the "access" permission (otherwise the dataset would be restricted from everyone).
-                </p>
-                <p>
-                    In order for a user to make a dataset private (i.e., only they can access it), they should associate the dataset with
-                    their private role (the role identical to their Galaxy user name / email address).  Associating additional roles that
-                    include the "access" permission is not possible, since it would render the dataset inaccessible to everyone.
-                <p>
-                    To make a dataset private to themselves and one or more other users, the user can create a new role and associate the dataset 
-                    with that role, not their "private role".  Galaxy makes this easy by telling the user they are about to share a private dataset 
-                    and giving them the option of doing so.  If they respond positively, the sharing role is automatically created for them.
-                </p>
-                <p>
-                    Private data (data associated with roles that include the "access" permission) must be made public in order to be used
-                    with external applications like the "view at UCSC" link, or the "Perform genome analysis and prediction with EpiGRAPH" 
-                    tool.  Being made publically accessible means removing the association of all roles that include the "access" permission
-                    from the dataset.
-                <p>
-            </li>
-            <li><strong>manage permissions</strong> - Role members can manage the permissions applied to this dataset</li>
-        </ul>
-    </li>
-</ul>
-<br/>
+    <strong>Security</strong> - Data security in Galaxy is a new feature, so familiarize yourself with the details which can be found 
+    here or in our <a href="http://g2.trac.bx.psu.edu/wiki/SecurityFeatures" target="_blank">data security page</a>.  The data security 
+    process incorporates users, groups and roles, and enables the application of certain permissions on datasets, specifically "access"
+    and "manage permissions".  By default, the "manage permissions" permission is associated with the dataset owner's private role, and
+    the "access" permission is not set, making the dataset public.  With these default permissions, users should not see any difference
+    in the way Galaxy has behaved in the past.
+    <ul>
+        <li>
+            <strong>Users</strong> - registered Galaxy users that have created a Galaxy account.  Users can belong to groups and can
+            be associated with 1 or more roles.  If a user is not authenticated during a Galaxy session, they will not have access to any 
+            of the security features, and datasets they create during that session will have no permissions applied to them (i.e., they
+            will be considered "public", and no one will be allowed to change permissions on them).
+        </li>
+        <p/>
+        <li>
+            <strong>Groups</strong> - a set of 0 or more users which are considered members of the group.  Groups can be associated with 0
+            or more roles, simplifying the process of applying permissions to the data between a select group of users.
+        </li>
+        <p/>
+        <li>
+            <strong>Roles</strong> - associate users and groups with specific permissions on datasets.  For example, users in groups A and B 
+            can be associated with role C which gives them the "access" permission on datasets D, E and F.  Roles have a type which is currently
+            one of the following:
+            <ul>
+                <li>
+                    <strong>private</strong> - every user is associated automatically with their own private role.  Administrators cannot 
+                    manage private roles.
+                </li>
+                <li>
+                    <strong>user</strong> - this is currently not used, but eventually any registered user will be able to create a new role
+                    and this will be it's type.
+                </li>
+                <li>
+                    <strong>sharing</strong> - a role created automatically during a Galaxy session that enables a user to share data with 
+                    another user.  This can generally be considered a temporary role.
+                </li>
+                <li><strong>admin</strong> - a role created by a Galaxy administrator.</li>
+            </ul>
+        </li>
+        <p/>
+        <li>
+            <strong>Dataset Permissions</strong> - applying the following permissions will to a dataset will result in the behavior described.
+            <ul>
+                <li>
+                    <strong>access</strong> - users associated with the role can import this dataset into their history for analysis.
+                    <p>
+                        If no roles with the "access" permission are associated with a dataset, the dataset is "public" and may be accessed by anyone 
+                        that can access the data library in which it is contained.  See the <strong>Manage data libraries</strong> section above for 
+                        details.  Public datasets contained in public data libraries will be accessible to all users (as well as anyone not logged in 
+                        during a Galaxy session) from the list of data libraries displayed when the "Data Libraries" menu item is selected.
+                    </p>
+                    <p>
+                        Associating a dataset with a role that includes the "access" permission restricts the set of users that can access it.  
+                        For example, if 'Role A' includes the "access" permission and 'Role A' is associated with the dataset, only those users
+                        and groups who are associated with 'Role A' may access the dataset.
+                    </p>
+                    <p>
+                        If multiple roles that include the "access" permission are associated with a dataset, access to the dataset is derived
+                        from the intersection of the users associated with the roles.  For example, if 'Role A' and 'Role B' are associated with
+                        a dataset, only those users and groups who are associated with both 'Role A' AND 'Role B' may access the dataset.  When
+                        the "access" permission is applied to a dataset, Galaxy checks to make sure that at least 1 user belongs to all groups and
+                        roles associated with the "access" permission (otherwise the dataset would be restricted from everyone).
+                    </p>
+                    <p>
+                        In order for a user to make a dataset private (i.e., only they can access it), they should associate the dataset with
+                        their private role (the role identical to their Galaxy user name / email address).  Associating additional roles that
+                        include the "access" permission is not possible, since it would render the dataset inaccessible to everyone.
+                    <p>
+                        To make a dataset private to themselves and one or more other users, the user can create a new role and associate the dataset 
+                        with that role, not their "private role".  Galaxy makes this easy by telling the user they are about to share a private dataset 
+                        and giving them the option of doing so.  If they respond positively, the sharing role is automatically created for them.
+                    </p>
+                    <p>
+                        Private data (data associated with roles that include the "access" permission) must be made public in order to be used
+                        with external applications like the "view at UCSC" link, or the "Perform genome analysis and prediction with EpiGRAPH" 
+                        tool.  Being made publically accessible means removing the association of all roles that include the "access" permission
+                        from the dataset.
+                    <p>
+                </li>
+                <li><strong>manage permissions</strong> - Role members can manage the permissions applied to this dataset</li>
+            </ul>
+        </li>
+    </ul>
+    <br/>
+%endif
diff --git a/templates/webapps/galaxy/admin/index.mako b/templates/webapps/galaxy/admin/index.mako
index 4a2538d7eba..9c2edd7f498 100644
--- a/templates/webapps/galaxy/admin/index.mako
+++ b/templates/webapps/galaxy/admin/index.mako
@@ -1,4 +1,5 @@
 <%inherit file="/webapps/galaxy/base_panels.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
 
 ## Default title
 <%def name="title()">Galaxy Administration</%def>
@@ -102,6 +103,6 @@
 </%def>
 
 <%def name="center_panel()">
-    <% center_url = h.url_for( action='center', webapp='galaxy' ) %>
+    <% center_url = h.url_for( controller='admin', action='center', webapp='galaxy', message=message, status=status ) %>
     <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"> </iframe>
 </%def>
diff --git a/templates/workflow/import.mako b/templates/workflow/import.mako
new file mode 100644
index 00000000000..39b2923bdad
--- /dev/null
+++ b/templates/workflow/import.mako
@@ -0,0 +1,56 @@
+<%inherit file="/webapps/galaxy/base_panels.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+<%def name="stylesheets()">
+    ${parent.stylesheets()}
+    ${h.css( "workflow" )}
+</%def>
+
+<%def name="javascripts()">
+    ${parent.javascripts()}
+</%def>
+
+<%def name="init()">
+<%
+    self.has_left_panel=False
+    self.has_right_panel=False
+    self.active_view="workflow"
+    self.message_box_visible=False
+%>
+</%def>
+
+<%def name="title()">Import Galaxy workflow</%def>
+
+<%def name="center_panel()">
+    %if message:
+        ${render_msg( message, status )}
+    %endif
+    <div class="toolForm"> 
+        <div class="toolFormTitle">Import an exported Galaxy workflow file</div>
+        <div class="toolFormBody">
+            <form name="import_workflow" id="import_workflow" action="${h.url_for( controller='workflow', action='import_workflow' )}" enctype="multipart/form-data" method="POST">
+                <div class="form-row">
+                    <label>URL for exported Galaxy workflow:</label> 
+                    <input type="text" name="url" value="${url}" size="40">
+                    <div class="toolParamHelp" style="clear: both;">
+                        If the workflow is accessible via an URL, enter the URL above and click the <b>Import</b> button.
+                    </div>
+                    <div style="clear: both"></div>
+                </div>
+                <div class="form-row">
+                    <label>Exported Galaxy workflow file:</label>
+                    <div class="form-row-input">
+                        <input type="file" name="file_data"/>
+                    </div>
+                    <div class="toolParamHelp" style="clear: both;">
+                        If the workflow is stored locally in a file, browse and select it and then click the <b>Import</b> button.
+                    </div>
+                    <div style="clear: both"></div>
+                </div>
+                <div class="form-row">
+                    <input type="submit" class="primary-button" name="import_button" value="Import">
+                </div>
+            </form>
+        </div>
+    </div>
+</%def>
diff --git a/templates/workflow/list.mako b/templates/workflow/list.mako
index 414028b59c4..6217ef40536 100644
--- a/templates/workflow/list.mako
+++ b/templates/workflow/list.mako
@@ -37,7 +37,7 @@
                     </a>
                 </li>
                 <li>
-                    <a class="action-button" href="${h.url_for( action='import_workflow' )}">
+                    <a class="action-button" href="${h.url_for( controller='workflow', action='import_workflow' )}">
                         <img src="${h.url_for('/static/images/fugue/arrow-090.png')}" />
                         <span>Upload or import workflow</span>
                     </a>
@@ -63,22 +63,20 @@
                             ## <td>${str(workflow.update_time)[:19]}</td>
                             <td>
                                 <div popupmenu="wf-${i}-popup">
-                                <a class="action-button" href="${h.url_for( action='editor', id=trans.security.encode_id(workflow.id) )}" target="_parent">Edit</a>
-                                <a class="action-button" href="${h.url_for( controller='root', action='index', workflow_id=trans.security.encode_id(workflow.id) )}" target="_parent">Run</a>
-                                <a class="action-button" href="${h.url_for( action='sharing', id=trans.security.encode_id(workflow.id) )}">Share or Publish</a>
-                                <a class="action-button" href="${h.url_for( action='export', id=trans.security.encode_id(workflow.id) )}">Download or Export</a>
-                                <a class="action-button" href="${h.url_for( action='clone', id=trans.security.encode_id(workflow.id) )}">Clone</a>
-                                <a class="action-button" href="${h.url_for( action='rename', id=trans.security.encode_id(workflow.id) )}">Rename</a>
-                                <a class="action-button" confirm="Are you sure you want to delete workflow '${h.to_unicode( workflow.name ) | h}'?" href="${h.url_for( action='delete', id=trans.security.encode_id(workflow.id) )}">Delete</a>
+                                <a class="action-button" href="${h.url_for( controller='workflow', action='editor', id=trans.security.encode_id( workflow.id ) )}" target="_parent">Edit</a>
+                                <a class="action-button" href="${h.url_for( controller='root', action='index', workflow_id=trans.security.encode_id( workflow.id ) )}" target="_parent">Run</a>
+                                <a class="action-button" href="${h.url_for( controller='workflow', action='sharing', id=trans.security.encode_id( workflow.id ) )}">Share or Publish</a>
+                                <a class="action-button" href="${h.url_for( controller='workflow', action='export', id=trans.security.encode_id( workflow.id ) )}">Download or Export</a>
+                                <a class="action-button" href="${h.url_for( controller='workflow', action='clone', id=trans.security.encode_id( workflow.id ) )}">Clone</a>
+                                <a class="action-button" href="${h.url_for( controller='workflow', action='rename', id=trans.security.encode_id( workflow.id ) )}">Rename</a>
+                                <a class="action-button" confirm="Are you sure you want to delete workflow '${h.to_unicode( workflow.name ) | h}'?" href="${h.url_for( controller='workflow', action='delete', id=trans.security.encode_id( workflow.id ) )}">Delete</a>
                                 </div>
                             </td>
                         </tr>
                     %endfor
                 </table>
             %else:
-
                 You have no workflows.
-
             %endif
 
             <h2>Workflows shared with you by others</h2>
@@ -101,18 +99,16 @@
                             <td>${len(workflow.latest_workflow.steps)}</td>
                             <td>
                                 <div popupmenu="shared-${i}-popup">
-                                    <a class="action-button" href="${h.url_for( action='display_by_username_and_slug', username=workflow.user.username, slug=workflow.slug)}" target="_top">View</a>
-                                    <a class="action-button" href="${h.url_for( action='run', id=trans.security.encode_id(workflow.id) )}">Run</a>
-                                    <a class="action-button" href="${h.url_for( action='clone', id=trans.security.encode_id(workflow.id) )}">Clone</a>
+                                    <a class="action-button" href="${h.url_for( controller='workflow', action='display_by_username_and_slug', username=workflow.user.username, slug=workflow.slug )}" target="_top">View</a>
+                                    <a class="action-button" href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id( workflow.id ) )}">Run</a>
+                                    <a class="action-button" href="${h.url_for( controller='workflow', action='clone', id=trans.security.encode_id( workflow.id ) )}">Clone</a>
                                 </div>
                             </td>
                         </tr>
                     %endfor
                 </table>
             %else:
-
                 No workflows have been shared with you.
-
             %endif
 
             <h2>Other options</h2>

From 43db2faaa16dfd2e5c1eda9672cda70eefaff340 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Fri, 14 Oct 2011 14:21:07 -0400
Subject: [PATCH 056/362] Workflows:  Fix for 5cfec3f4f17c to accommodate
 workflows with 'input dataset' steps.

---
 lib/galaxy/web/controllers/workflow.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/web/controllers/workflow.py b/lib/galaxy/web/controllers/workflow.py
index 580fb42179f..75ecd68271f 100644
--- a/lib/galaxy/web/controllers/workflow.py
+++ b/lib/galaxy/web/controllers/workflow.py
@@ -1764,7 +1764,7 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
             # FIXME: Position should be handled inside module
             step.position = step_dict['position']
             module = module_factory.from_dict( trans, step_dict, secure=False )
-            if module.tool is None:
+            if module.type == 'tool' and module.tool is None:
                 # A required tool is not available in the local Galaxy instance.
                 missing_tool_tup = ( step_dict[ 'tool_id' ], step_dict[ 'name' ], step_dict[ 'tool_version' ] )
                 if missing_tool_tup not in missing_tool_tups:

From 0684e524b8396017eda584bf8d8eddaecd88870e Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Fri, 14 Oct 2011 15:20:12 -0400
Subject: [PATCH 057/362] Enhance tool searching in tool shed repositories to
 enable multiple values in any of tool_id, tool_name, tool_version.  In the
 tool shed search form, taking advantage of this feature requires
 comma-separated lists to be entered in the form fields.

---
 lib/galaxy/web/controllers/workflow.py        |  17 +-
 .../community/controllers/repository.py       | 180 +++++++++++++-----
 .../community/repository/find_tools.mako      |   2 +
 3 files changed, 143 insertions(+), 56 deletions(-)

diff --git a/lib/galaxy/web/controllers/workflow.py b/lib/galaxy/web/controllers/workflow.py
index 75ecd68271f..e1724ef5c49 100644
--- a/lib/galaxy/web/controllers/workflow.py
+++ b/lib/galaxy/web/controllers/workflow.py
@@ -1157,14 +1157,15 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
                             galaxy_url = trans.request.host
                             message += "The workflow requires the following tools that are not available in this Galaxy instance."
                             message += "You can likely install the required tools from one of the Galaxy tool sheds listed below.<br/><br/>"
-                            for missing_tool_tup in missing_tool_tups:
-                                missing_tool_id = missing_tool_tup[0]
-                                for tool_shed_name, tool_shed_url in trans.app.tool_shed_registry.tool_sheds.items():
-                                    if tool_shed_url.endswith( '/' ):
-                                        tool_shed_url = tool_shed_url.rstrip( '/' )
-                                        url = '%s/repository/find_tools?tool_id=%s&galaxy_url=%s&webapp=community' % ( tool_shed_url, missing_tool_id, galaxy_url )
-                                    message += '<a href="%s">%s</a><br/>' % ( url, tool_shed_name )
-                                    status = 'error'
+                            for tool_shed_name, tool_shed_url in trans.app.tool_shed_registry.tool_sheds.items():
+                                if tool_shed_url.endswith( '/' ):
+                                    tool_shed_url = tool_shed_url.rstrip( '/' )
+                                    url = '%s/repository/find_tools?galaxy_url=%s&webapp=community' % ( tool_shed_url, galaxy_url )
+                                    for missing_tool_tup in missing_tool_tups:
+                                        missing_tool_id = missing_tool_tup[0]
+                                        url += '&tool_id=%s' % missing_tool_id
+                                message += '<a href="%s">%s</a><br/>' % ( url, tool_shed_name )
+                                status = 'error'
                             return trans.response.send_redirect( web.url_for( controller='admin',
                                                                               action='index',
                                                                               webapp='galaxy',
diff --git a/lib/galaxy/webapps/community/controllers/repository.py b/lib/galaxy/webapps/community/controllers/repository.py
index b2247738bbc..25ddd14a238 100644
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -280,8 +280,18 @@ class MatchedRepositoryListGrid( grids.Grid ):
                                .join( model.User.table ) \
                                .filter( self.model_class.table.c.repository_id == 0 )
 
+class InstallMatchedRepositoryListGrid( MatchedRepositoryListGrid ):
+    # Grid definition
+    title = "Repositories with required tools"
+    operations = [ grids.GridOperation( "Preview and install tools",
+                                        url_args = dict( action='find_tools',
+                                                         operation='install_tools' ),
+                                        allow_multiple=True,
+                                        async_compatible=False ) ]
+
 class RepositoryController( BaseUIController, ItemRatings ):
 
+    install_matched_repository_list_grid = InstallMatchedRepositoryListGrid()
     matched_repository_list_grid = MatchedRepositoryListGrid()
     downloadable_repository_list_grid = DownloadableRepositoryListGrid()
     repository_list_grid = RepositoryListGrid()
@@ -366,11 +376,18 @@ class RepositoryController( BaseUIController, ItemRatings ):
                                                                                    url_args=url_args,
                                                                                    allow_multiple=False,
                                                                                    async_compatible=False ) ]
-
         # Render the list view
         return self.downloadable_repository_list_grid( trans, **kwd )
     @web.expose
     def find_tools( self, trans, **kwd ):
+        params = util.Params( kwd )
+        message = util.restore_text( params.get( 'message', '' ) )
+        status = params.get( 'status', 'done' )
+        # Set the toolshedgalaxyurl cookie so we can get back
+        # to the calling local Galaxy instance.
+        galaxy_url = kwd.get( 'galaxy_url', None )
+        if galaxy_url:
+            trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' )
         if 'operation' in kwd:
             operation = kwd[ 'operation' ].lower()
             if operation == "view_or_manage_repository":
@@ -389,61 +406,98 @@ class RepositoryController( BaseUIController, ItemRatings ):
                     return trans.response.send_redirect( web.url_for( controller='repository',
                                                                       action='view_repository',
                                                                       **kwd ) )
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', '' ) )
-        status = params.get( 'status', 'done' )
-        # Set the toolshedgalaxyurl cookie so we can get back
-        # to the calling local Galaxy instance.
-        galaxy_url = kwd.get( 'galaxy_url', None )
-        if galaxy_url:
-            trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' )
-        tool_id = kwd.get( 'tool_id', '' ).lower()
-        tool_name = kwd.get( 'tool_name', '' ).lower()
-        tool_version = kwd.get( 'tool_version', '' ).lower()
+            if operation == "preview and install tools":
+                pass
+        tool_ids = [ tid.lower() for tid in util.listify( kwd.get( 'tool_id', '' ) ) ]
+        tool_names = [ tn.lower() for tn in util.listify( kwd.get( 'tool_name', '' ) ) ]
+        tool_versions = [ tv.lower() for tv in util.listify( kwd.get( 'tool_version', '' ) ) ]
         exact_matches = params.get( 'exact_matches', '' )
         exact_matches_checked = CheckboxField.is_checked( exact_matches )
         match_tuples = []
-        if tool_id or tool_name or tool_version:
+        ok = True
+        if tool_ids or tool_names or tool_versions:
             for repository_metadata in trans.sa_session.query( model.RepositoryMetadata ):
                 metadata = repository_metadata.metadata
                 tools = metadata[ 'tools' ]
-                found = False
                 for tool_dict in tools:
-                    if tool_id and not tool_name and not tool_version:
-                        tool_dict_tool_id = tool_dict[ 'id' ].lower()
-                        found = ( tool_id == tool_dict_tool_id ) or \
-                                ( not exact_matches_checked and tool_dict_tool_id.find( tool_id ) >= 0 )
-                    elif tool_name and not tool_id and not tool_version:
-                        tool_dict_tool_name = tool_dict[ 'name' ].lower()
-                        found = ( tool_name == tool_dict_tool_name ) or \
-                                ( not exact_matches_checked and tool_dict_tool_name.find( tool_name ) >= 0 )
-                    elif tool_version and not tool_id and not tool_name:
-                        tool_dict_tool_version = tool_dict[ 'version' ].lower()
-                        found = ( tool_version == tool_dict_tool_version ) or \
-                                ( not exact_matches_checked and tool_dict_tool_version.find( tool_version ) >= 0 )
-                    elif tool_id and tool_name and not tool_version:
-                        tool_dict_tool_id = tool_dict[ 'id' ].lower()
-                        tool_dict_tool_name = tool_dict[ 'name' ].lower()
-                        found = ( tool_id == tool_dict_tool_id and tool_name == tool_dict_tool_name ) or \
-                                ( not exact_matches_checked and tool_dict_tool_id.find( tool_id ) >= 0 and tool_dict_tool_name.find( tool_name ) >= 0 )
-                    elif tool_id and tool_version and not tool_name:
-                        tool_dict_tool_id = tool_dict[ 'id' ].lower()
-                        tool_dict_tool_version = tool_dict[ 'version' ].lower()
-                        found = ( tool_id == tool_dict_tool_id and tool_version == tool_dict_tool_version ) or \
-                                ( not exact_matches_checked and tool_dict_tool_id.find( tool_id ) >= 0 and tool_dict_tool_version.find( tool_version ) >= 0 )
-                    elif tool_version and tool_name and not tool_id:
-                        tool_dict_tool_version = tool_dict[ 'version' ].lower()
-                        tool_dict_tool_name = tool_dict[ 'name' ].lower()
-                        found = ( tool_version == tool_dict_tool_version and tool_name == tool_dict_tool_name ) or \
-                                ( not exact_matches_checked and tool_dict_tool_version.find( tool_version ) >= 0 and tool_dict_tool_name.find( tool_name ) >= 0 )
-                if found:
-                    match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
-            kwd[ 'match_tuples' ] = match_tuples
-            kwd[ 'message' ] = "tool id: <b>%s</b><br/>tool name: <b>%s</b><br/>tool version: <b>%s</b><br/>exact matches only: <b>%s</b>" % \
-                ( tool_id, tool_name, tool_version, str( exact_matches_checked ) )
-            # Render the list view
-            return self.matched_repository_list_grid( trans, **kwd )
+                    if tool_ids and not tool_names and not tool_versions:
+                        for tool_id in tool_ids:
+                            if self._in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id ):
+                                match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
+                    elif tool_names and not tool_ids and not tool_versions:
+                        for tool_name in tool_names:
+                            if self._in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name ):
+                                match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
+                    elif tool_versions and not tool_ids and not tool_names:
+                        for tool_version in tool_versions:
+                            if self._in_tool_dict( tool_dict, exact_matches_checked, tool_version=tool_version ):
+                                match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
+                    elif tool_ids and tool_names and not tool_versions:
+                        if len( tool_ids ) == len( tool_names ):
+                            for i, tool_id in enumerate( tool_ids ):
+                                tool_name = tool_names[ i ]
+                                if self._in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name ):
+                                    match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
+                        else:
+                            message = "No search performed - each field must contain the same number of comma-separated items."
+                            status = "error"
+                            ok = False
+                    elif tool_ids and tool_versions and not tool_names:
+                        if len( tool_ids )  == len( tool_versions ):
+                            for i, tool_id in enumerate( tool_ids ):
+                                tool_version = tool_versions[ i ]
+                                if self._in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_version=tool_version ):
+                                    match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
+                        else:
+                            message = "No search performed - each field must contain the same number of comma-separated items."
+                            status = "error"
+                            ok = False
+                    elif tool_versions and tool_names and not tool_ids:
+                        if len( tool_versions ) == len( tool_names ):
+                            for i, tool_version in enumerate( tool_versions ):
+                                tool_name = tool_names[ i ]
+                                if self._in_tool_dict( tool_dict, exact_matches_checked, tool_version=tool_version, tool_name=tool_name ):
+                                    match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
+                        else:
+                            message = "No search performed - each field must contain the same number of comma-separated items."
+                            status = "error"
+                            ok = False
+            if ok:
+                kwd[ 'match_tuples' ] = match_tuples
+                # Render the list view
+                if galaxy_url:
+                    # Our request originated from a Galaxy instance, so we're listing tools
+                    # that have been found for a workflow in Galaxy.
+                    return self.install_matched_repository_list_grid( trans, **kwd )
+                else:
+                    if tool_ids:
+                        tool_id_str = ','.join( tool_ids )
+                    else:
+                        tool_id_str = ''
+                    if tool_names:
+                        tool_name_str = ','.join( tool_names )
+                    else:
+                        tool_name_str = ''
+                    if tool_versions:
+                        tool_version_str = ','.join( tool_versions )
+                    else:
+                        tool_version_str = ''
+                    kwd[ 'message' ] = "tool id: <b>%s</b><br/>tool name: <b>%s</b><br/>tool version: <b>%s</b><br/>exact matches only: <b>%s</b>" % \
+                        ( tool_id_str, tool_name_str, tool_version_str, str( exact_matches_checked ) )
+                    return self.matched_repository_list_grid( trans, **kwd )
         exact_matches_check_box = CheckboxField( 'exact_matches', checked=exact_matches_checked )
+        if tool_ids:
+            tool_id = ','.join( tool_ids )
+        else:
+            tool_id = ''
+        if tool_names:
+            tool_name = ','.join( tool_names )
+        else:
+            tool_name = ''
+        if tool_versions:
+            tool_version = ','.join( tool_versions )
+        else:
+            tool_version = ''
         return trans.fill_template( '/webapps/community/repository/find_tools.mako',
                                     tool_id=tool_id,
                                     tool_name=tool_name,
@@ -451,6 +505,36 @@ class RepositoryController( BaseUIController, ItemRatings ):
                                     exact_matches_check_box=exact_matches_check_box,
                                     message=message,
                                     status=status )
+    def _in_tool_dict( self, tool_dict, exact_matches_checked, tool_id=None, tool_name=None, tool_version=None ):
+        found = False
+        if tool_id and not tool_name and not tool_version:
+            tool_dict_tool_id = tool_dict[ 'id' ].lower()
+            found = ( tool_id == tool_dict_tool_id ) or \
+                    ( not exact_matches_checked and tool_dict_tool_id.find( tool_id ) >= 0 )
+        elif tool_name and not tool_id and not tool_version:
+            tool_dict_tool_name = tool_dict[ 'name' ].lower()
+            found = ( tool_name == tool_dict_tool_name ) or \
+                    ( not exact_matches_checked and tool_dict_tool_name.find( tool_name ) >= 0 )
+        elif tool_version and not tool_id and not tool_name:
+            tool_dict_tool_version = tool_dict[ 'version' ].lower()
+            found = ( tool_version == tool_dict_tool_version ) or \
+                    ( not exact_matches_checked and tool_dict_tool_version.find( tool_version ) >= 0 )
+        elif tool_id and tool_name and not tool_version:
+            tool_dict_tool_id = tool_dict[ 'id' ].lower()
+            tool_dict_tool_name = tool_dict[ 'name' ].lower()
+            found = ( tool_id == tool_dict_tool_id and tool_name == tool_dict_tool_name ) or \
+                    ( not exact_matches_checked and tool_dict_tool_id.find( tool_id ) >= 0 and tool_dict_tool_name.find( tool_name ) >= 0 )
+        elif tool_id and tool_version and not tool_name:
+            tool_dict_tool_id = tool_dict[ 'id' ].lower()
+            tool_dict_tool_version = tool_dict[ 'version' ].lower()
+            found = ( tool_id == tool_dict_tool_id and tool_version == tool_dict_tool_version ) or \
+                    ( not exact_matches_checked and tool_dict_tool_id.find( tool_id ) >= 0 and tool_dict_tool_version.find( tool_version ) >= 0 )
+        elif tool_version and tool_name and not tool_id:
+            tool_dict_tool_version = tool_dict[ 'version' ].lower()
+            tool_dict_tool_name = tool_dict[ 'name' ].lower()
+            found = ( tool_version == tool_dict_tool_version and tool_name == tool_dict_tool_name ) or \
+                    ( not exact_matches_checked and tool_dict_tool_version.find( tool_version ) >= 0 and tool_dict_tool_name.find( tool_name ) >= 0 )
+        return found
     @web.expose
     def preview_tools_in_changeset( self, trans, repository_id, **kwd ):
         params = util.Params( kwd )
diff --git a/templates/webapps/community/repository/find_tools.mako b/templates/webapps/community/repository/find_tools.mako
index 95ad1dba210..9fa0906feba 100644
--- a/templates/webapps/community/repository/find_tools.mako
+++ b/templates/webapps/community/repository/find_tools.mako
@@ -19,6 +19,8 @@
     <div class="toolFormBody">
         <div class="form-row">
             Valid tools are those that properly load in Galaxy.  Enter any combination of the following tool attributes to locate matching valid tools.
+            Comma-separated strings may be entered in each field to expand search criteria.  Each field must contain the same number of comma-separated
+            strings if these types of strings are entered in more than one field.
         </div>
         <div style="clear: both"></div>
         <form name="find_tools" id="find_tools" action="${h.url_for( controller='repository', action='find_tools' )}" method="post" >

From 38d26e946e6b0e2438ffc25e09923938860b5b35 Mon Sep 17 00:00:00 2001
From: John Duddy <jduddy@illumina.com>
Date: Fri, 14 Oct 2011 14:03:56 -0700
Subject: [PATCH 058/362] Fix API code errors, add ability to set ldda
 associations, fixed misc error in util

---
 lib/galaxy/util/__init__.py            |  2 ++
 lib/galaxy/web/api/histories.py        |  3 ++-
 lib/galaxy/web/api/history_contents.py |  4 ++--
 lib/galaxy/web/api/library_contents.py | 24 +++++++++++++++++++++---
 4 files changed, 27 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/util/__init__.py b/lib/galaxy/util/__init__.py
index 76655450295..893e9bcc408 100644
--- a/lib/galaxy/util/__init__.py
+++ b/lib/galaxy/util/__init__.py
@@ -133,6 +133,8 @@ mapped_chars = { '>' :'__gt__',
 
 def restore_text(text):
     """Restores sanitized text"""
+    if not text:
+        return text
     for key, value in mapped_chars.items():
         text = text.replace(value, key)
     return text
diff --git a/lib/galaxy/web/api/histories.py b/lib/galaxy/web/api/histories.py
index cf028201392..319d64efc92 100644
--- a/lib/galaxy/web/api/histories.py
+++ b/lib/galaxy/web/api/histories.py
@@ -88,9 +88,10 @@ class HistoriesController( BaseAPIController, UsesHistory ):
                     state = states.QUEUED
                 elif summary[states.OK] == num_sets:
                     state = states.OK                       
+				item['state_details'] = summary
             item['contents_url'] = url_for( 'history_contents', history_id=history_id )
+              
             item['state'] = state
-            item['state_details'] = summary
         except Exception, e:
             item = "Error in history API at showing history detail"
             log.error(item + ": %s" % str(e))
diff --git a/lib/galaxy/web/api/history_contents.py b/lib/galaxy/web/api/history_contents.py
index 0115079afc6..7c4808fd78e 100644
--- a/lib/galaxy/web/api/history_contents.py
+++ b/lib/galaxy/web/api/history_contents.py
@@ -14,7 +14,7 @@ import routes
 
 log = logging.getLogger( __name__ )
 
-class HistoryContentsController( BaseAPIController, UsesHistoryDatasetAssociation, UsesHistory ):
+class HistoryContentsController( BaseAPIController, UsesHistoryDatasetAssociation, UsesHistory, UsesLibrary, UsesLibraryItems ):
 
     @web.expose_api
     def index( self, trans, history_id, **kwd ):
@@ -85,7 +85,7 @@ class HistoryContentsController( BaseAPIController, UsesHistoryDatasetAssociatio
 
         if from_ld_id:
             try:
-                ld = get_library_content_for_access( trans, from_ld_id )
+                ld = self.get_library_dataset( trans, from_ld_id, check_ownership=False, check_accessible=False )
                 assert type( ld ) is trans.app.model.LibraryDataset, "Library content id ( %s ) is not a dataset" % from_ld_id
             except AssertionError, e:
                 trans.response.status = 400
diff --git a/lib/galaxy/web/api/library_contents.py b/lib/galaxy/web/api/library_contents.py
index 4d493a066ff..c49a63dd11c 100644
--- a/lib/galaxy/web/api/library_contents.py
+++ b/lib/galaxy/web/api/library_contents.py
@@ -75,9 +75,9 @@ class LibraryContentsController( BaseAPIController, UsesLibrary, UsesLibraryItem
         """
         class_name, content_id = self.__decode_library_content_id( trans, id )
         if class_name == 'LibraryFolder':
-            content = self.get_library_folder( trans, content_id, check_ownership=False, check_accessibility=True )
+            content = self.get_library_folder( trans, content_id, check_ownership=False, check_accessible=True )
         else:
-            content = self.get_library_dataset( trans, content_id, check_ownership=False, check_accessibility=True )
+            content = self.get_library_dataset( trans, content_id, check_ownership=False, check_accessible=True )
         return self.encode_all_ids( trans, content.get_api_value( view='element' ) )
 
     @web.expose_api
@@ -100,9 +100,10 @@ class LibraryContentsController( BaseAPIController, UsesLibrary, UsesLibraryItem
             return "Missing requred 'folder_id' parameter."
         else:
             folder_id = payload.pop( 'folder_id' )
+            class_name, folder_id = self.__decode_library_content_id( trans, folder_id )
         try:
             # security is checked in the downstream controller
-            parent = self.get_library_folder( trans, folder_id, check_ownership=False, check_accessibility=False )
+            parent = self.get_library_folder( trans, folder_id, check_ownership=False, check_accessible=False )
         except Exception, e:
             return str( e )
         # The rest of the security happens in the library_common controller.
@@ -128,6 +129,23 @@ class LibraryContentsController( BaseAPIController, UsesLibrary, UsesLibraryItem
                                    url = url_for( 'library_content', library_id=library_id, id=encoded_id ) ) )
             return rval
 
+    @web.expose_api
+    def update( self, trans, id,  library_id, payload, **kwd ):
+        """
+        PUT /api/libraries/{encoded_library_id}/contents/{encoded_content_type_and_id}
+        Sets relationships among items
+        """
+        if 'converted_dataset_id' in payload:
+            converted_id = payload.pop( 'converted_dataset_id' )
+            content = self.get_library_dataset( trans, id, check_ownership=False, check_accessible=False )
+            content_conv = self.get_library_dataset( trans, converted_id, check_ownership=False, check_accessible=False )
+            assoc = trans.app.model.ImplicitlyConvertedDatasetAssociation( parent = content.library_dataset_dataset_association,
+                dataset = content_conv.library_dataset_dataset_association,
+                file_type = content_conv.library_dataset_dataset_association.extension,
+                metadata_safe = True )
+            trans.sa_session.add( assoc )
+            trans.sa_session.flush()
+
     def __decode_library_content_id( self, trans, content_id ):
         if ( len( content_id ) % 16 == 0 ):
             return 'LibraryDataset', content_id

From e671ee67ce996bf7b1ef12644e79a0203fa2479c Mon Sep 17 00:00:00 2001
From: John Duddy <jduddy@illumina.com>
Date: Fri, 14 Oct 2011 14:05:15 -0700
Subject: [PATCH 059/362] Correct indentation, only access summary if it is
 set!

---
 lib/galaxy/web/api/histories.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/lib/galaxy/web/api/histories.py b/lib/galaxy/web/api/histories.py
index 319d64efc92..e3ba32f97f4 100644
--- a/lib/galaxy/web/api/histories.py
+++ b/lib/galaxy/web/api/histories.py
@@ -88,9 +88,8 @@ class HistoriesController( BaseAPIController, UsesHistory ):
                     state = states.QUEUED
                 elif summary[states.OK] == num_sets:
                     state = states.OK                       
-				item['state_details'] = summary
+                item['state_details'] = summary
             item['contents_url'] = url_for( 'history_contents', history_id=history_id )
-              
             item['state'] = state
         except Exception, e:
             item = "Error in history API at showing history detail"

From fcc8d306d8c671934a91c442822747e34e56c241 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Mon, 17 Oct 2011 12:22:27 -0400
Subject: [PATCH 060/362] Enhance automatic tool shed repository installation
 to enable installation of multiple repositories using a multi-select frid
 layout instead of installing just a single repository at a time.

---
 lib/galaxy/web/controllers/admin.py           | 182 +++++++++---------
 lib/galaxy/web/controllers/workflow.py        |  11 +-
 .../community/controllers/repository.py       |  44 +++--
 .../admin/select_tool_panel_section.mako      |   4 +-
 .../community/repository/find_tools.mako      |   2 +-
 5 files changed, 134 insertions(+), 109 deletions(-)

diff --git a/lib/galaxy/web/controllers/admin.py b/lib/galaxy/web/controllers/admin.py
index c6e6bd583c5..dd60f6d30c3 100644
--- a/lib/galaxy/web/controllers/admin.py
+++ b/lib/galaxy/web/controllers/admin.py
@@ -688,8 +688,8 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
     @web.require_admin
     def browse_tool_shed( self, trans, **kwd ):
         tool_shed_url = kwd[ 'tool_shed_url' ]
-        galaxy_url = trans.request.host
-        url = '%s/repository/browse_downloadable_repositories?galaxy_url=%s&webapp=community' % ( tool_shed_url, galaxy_url )
+        trans.set_cookie( trans.request.host, name='toolshedgalaxyurl' )
+        url = '%s/repository/browse_downloadable_repositories?webapp=galaxy' % tool_shed_url
         return trans.response.send_redirect( url )
     @web.expose
     @web.require_admin
@@ -706,11 +706,7 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
-        tool_shed_url = kwd[ 'tool_shed_url' ]
-        name = kwd[ 'name' ]
-        description = kwd[ 'description' ]
-        changeset_revision = kwd[ 'changeset_revision' ]
-        repository_clone_url = kwd[ 'repository_clone_url' ]
+        tool_shed_url = trans.get_cookie( name='galaxytoolshedurl' )
         if kwd.get( 'select_tool_panel_section_button', False ):
             shed_tool_conf = kwd[ 'shed_tool_conf' ]
             # Get the tool path.
@@ -720,94 +716,104 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
             if 'tool_panel_section' in kwd:
                 section_key = 'section_%s' % kwd[ 'tool_panel_section' ]
                 tool_section = trans.app.toolbox.tool_panel[ section_key ]
+                # Get the number of repositories to clone from a cookie.
+                num_repos_to_clone = int( trans.get_cookie( name='numrepostoclone' ) )
                 # Clone the repository to the configured location.
                 current_working_dir = os.getcwd()
-                clone_dir = os.path.join( tool_path, self.__generate_tool_path( repository_clone_url, changeset_revision ) )
-                if os.path.exists( clone_dir ):
-                    # Repository and revision has already been cloned.
-                    # TODO: implement the ability to re-install or revert an existing repository.
-                    message = 'Revision <b>%s</b> of repository <b>%s</b> has already been installed.  Updating an existing repository is not yet supported.' % \
-                    ( changeset_revision, name )
-                    status = 'error'
-                else:
-                    os.makedirs( clone_dir )
-                    log.debug( 'Cloning %s...' % repository_clone_url )
-                    cmd = 'hg clone %s' % repository_clone_url
-                    tmp_name = tempfile.NamedTemporaryFile().name
-                    tmp_stderr = open( tmp_name, 'wb' )
-                    os.chdir( clone_dir )
-                    proc = subprocess.Popen( args=cmd, shell=True, stderr=tmp_stderr.fileno() )
-                    returncode = proc.wait()
-                    os.chdir( current_working_dir )
-                    tmp_stderr.close()
-                    if returncode == 0:
-                        # Add a new record to the tool_shed_repository table.
-                        tool_shed_repository = self.__create_tool_shed_repository( trans,
-                                                                                   name,
-                                                                                   description,
-                                                                                   changeset_revision,
-                                                                                   repository_clone_url )
-                        # Update the cloned repository to changeset_revision.
-                        repo_files_dir = os.path.join( clone_dir, name )
-                        log.debug( 'Updating cloned repository to revision "%s"...' % changeset_revision )
-                        cmd = 'hg update -r %s' % changeset_revision
+                for index in range( 0, num_repos_to_clone ):
+                    cookie_name = 'toolshedrepository%i' % index
+                    clone_repo_info_str = trans.get_cookie( name=cookie_name )
+                    clone_repo_info_items = clone_repo_info_str.split( '&' )
+                    name = clone_repo_info_items[ 0 ]
+                    description = clone_repo_info_items[ 1 ]
+                    repository_clone_url = clone_repo_info_items[ 2 ]
+                    changeset_revision = clone_repo_info_items[ 3 ]
+                    clone_dir = os.path.join( tool_path, self.__generate_tool_path( repository_clone_url, changeset_revision ) )
+                    if os.path.exists( clone_dir ):
+                        # Repository and revision has already been cloned.
+                        # TODO: implement the ability to re-install or revert an existing repository.
+                        message += 'Revision <b>%s</b> of repository <b>%s</b> has already been installed.  Updating an existing repository is not yet supported.<br/>' % \
+                        ( changeset_revision, name )
+                        status = 'error'
+                    else:
+                        os.makedirs( clone_dir )
+                        log.debug( 'Cloning %s...' % repository_clone_url )
+                        cmd = 'hg clone %s' % repository_clone_url
                         tmp_name = tempfile.NamedTemporaryFile().name
                         tmp_stderr = open( tmp_name, 'wb' )
-                        os.chdir( repo_files_dir )
-                        proc = subprocess.Popen( cmd, shell=True, stderr=tmp_stderr.fileno() )
+                        os.chdir( clone_dir )
+                        proc = subprocess.Popen( args=cmd, shell=True, stderr=tmp_stderr.fileno() )
                         returncode = proc.wait()
                         os.chdir( current_working_dir )
                         tmp_stderr.close()
                         if returncode == 0:
-                            sample_files, repository_tools_tups = self.__get_repository_tools_and_sample_files( trans, tool_path, repo_files_dir )
-                            if repository_tools_tups:
-                                # Handle missing data table entries for tool parameters that are dynamically generated select lists.
-                                repository_tools_tups = self.__handle_missing_data_table_entry( trans, tool_path, sample_files, repository_tools_tups )
-                                # Handle missing index files for tool parameters that are dynamically generated select lists.
-                                repository_tools_tups = self.__handle_missing_index_file( trans, tool_path, sample_files, repository_tools_tups )
-                                # Handle tools that use fabric scripts to install dependencies.
-                                self.__handle_tool_dependencies( current_working_dir, repo_files_dir, repository_tools_tups )
-                                # Generate an in-memory tool conf section that includes the new tools.
-                                new_tool_section = self.__generate_tool_panel_section( name,
-                                                                                       repository_clone_url,
+                            # Add a new record to the tool_shed_repository table.
+                            tool_shed_repository = self.__create_tool_shed_repository( trans,
+                                                                                       name,
+                                                                                       description,
                                                                                        changeset_revision,
-                                                                                       tool_section,
-                                                                                       repository_tools_tups )
-                                # Create a temporary file to persist the in-memory tool section
-                                # TODO: Figure out how to do this in-memory using xml.etree.
-                                tmp_name = tempfile.NamedTemporaryFile().name
-                                persisted_new_tool_section = open( tmp_name, 'wb' )
-                                persisted_new_tool_section.write( new_tool_section )
-                                persisted_new_tool_section.close()
-                                # Parse the persisted tool panel section
-                                tree = ElementTree.parse( tmp_name )
-                                root = tree.getroot()
-                                ElementInclude.include( root )
-                                # Load the tools in the section into the tool panel.
-                                trans.app.toolbox.load_section_tag_set( root, trans.app.toolbox.tool_panel, tool_path )
-                                # Remove the temporary file
-                                try:
-                                    os.unlink( tmp_name )
-                                except:
-                                    pass
-                                # Append the new section to the shed_tool_config file.
-                                self.__add_shed_tool_conf_entry( trans, shed_tool_conf, new_tool_section )
-                                if trans.app.toolbox_search.enabled:
-                                    # If search support for tools is enabled, index the new installed tools.
-                                    trans.app.toolbox_search = ToolBoxSearch( trans.app.toolbox )
-                            message = 'Revision <b>%s</b> of repository <b>%s</b> has been installed in tool panel section <b>%s</b>.' % \
-                                ( changeset_revision, name, tool_section.name )
-                            return trans.show_ok_message( message )
+                                                                                       repository_clone_url )
+                            # Update the cloned repository to changeset_revision.
+                            repo_files_dir = os.path.join( clone_dir, name )
+                            log.debug( 'Updating cloned repository to revision "%s"...' % changeset_revision )
+                            cmd = 'hg update -r %s' % changeset_revision
+                            tmp_name = tempfile.NamedTemporaryFile().name
+                            tmp_stderr = open( tmp_name, 'wb' )
+                            os.chdir( repo_files_dir )
+                            proc = subprocess.Popen( cmd, shell=True, stderr=tmp_stderr.fileno() )
+                            returncode = proc.wait()
+                            os.chdir( current_working_dir )
+                            tmp_stderr.close()
+                            if returncode == 0:
+                                sample_files, repository_tools_tups = self.__get_repository_tools_and_sample_files( trans, tool_path, repo_files_dir )
+                                if repository_tools_tups:
+                                    # Handle missing data table entries for tool parameters that are dynamically generated select lists.
+                                    repository_tools_tups = self.__handle_missing_data_table_entry( trans, tool_path, sample_files, repository_tools_tups )
+                                    # Handle missing index files for tool parameters that are dynamically generated select lists.
+                                    repository_tools_tups = self.__handle_missing_index_file( trans, tool_path, sample_files, repository_tools_tups )
+                                    # Handle tools that use fabric scripts to install dependencies.
+                                    self.__handle_tool_dependencies( current_working_dir, repo_files_dir, repository_tools_tups )
+                                    # Generate an in-memory tool conf section that includes the new tools.
+                                    new_tool_section = self.__generate_tool_panel_section( name,
+                                                                                           repository_clone_url,
+                                                                                           changeset_revision,
+                                                                                           tool_section,
+                                                                                           repository_tools_tups )
+                                    # Create a temporary file to persist the in-memory tool section
+                                    # TODO: Figure out how to do this in-memory using xml.etree.
+                                    tmp_name = tempfile.NamedTemporaryFile().name
+                                    persisted_new_tool_section = open( tmp_name, 'wb' )
+                                    persisted_new_tool_section.write( new_tool_section )
+                                    persisted_new_tool_section.close()
+                                    # Parse the persisted tool panel section
+                                    tree = ElementTree.parse( tmp_name )
+                                    root = tree.getroot()
+                                    ElementInclude.include( root )
+                                    # Load the tools in the section into the tool panel.
+                                    trans.app.toolbox.load_section_tag_set( root, trans.app.toolbox.tool_panel, tool_path )
+                                    # Remove the temporary file
+                                    try:
+                                        os.unlink( tmp_name )
+                                    except:
+                                        pass
+                                    # Append the new section to the shed_tool_config file.
+                                    self.__add_shed_tool_conf_entry( trans, shed_tool_conf, new_tool_section )
+                                    if trans.app.toolbox_search.enabled:
+                                        # If search support for tools is enabled, index the new installed tools.
+                                        trans.app.toolbox_search = ToolBoxSearch( trans.app.toolbox )
+                                message += 'Revision <b>%s</b> of repository <b>%s</b> has been loaded into tool panel section <b>%s</b>.<br/>' % \
+                                    ( changeset_revision, name, tool_section.name )
+                                #return trans.show_ok_message( message )
+                            else:
+                                tmp_stderr = open( tmp_name, 'rb' )
+                                message += '%s<br/>' % tmp_stderr.read()
+                                tmp_stderr.close()
+                                status = 'error'
                         else:
                             tmp_stderr = open( tmp_name, 'rb' )
-                            message = tmp_stderr.read()
+                            message += '%s<br/>' % tmp_stderr.read()
                             tmp_stderr.close()
                             status = 'error'
-                    else:
-                        tmp_stderr = open( tmp_name, 'rb' )
-                        message = tmp_stderr.read()
-                        tmp_stderr.close()
-                        status = 'error'
             else:
                 message = 'Choose the section in your tool panel to contain the installed tools.'
                 status = 'error'
@@ -819,11 +825,6 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
             shed_tool_conf_select_field = None
         tool_panel_section_select_field = build_tool_panel_section_select_field( trans )
         return trans.fill_template( '/admin/select_tool_panel_section.mako',
-                                    tool_shed_url=tool_shed_url,
-                                    name=name,
-                                    description=description,
-                                    changeset_revision=changeset_revision,
-                                    repository_clone_url=repository_clone_url,
                                     shed_tool_conf=shed_tool_conf,
                                     shed_tool_conf_select_field=shed_tool_conf_select_field,
                                     tool_panel_section_select_field=tool_panel_section_select_field,
@@ -835,11 +836,12 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
         params = util.Params( kwd )
         repository_id = params.get( 'id', None )
         repository = get_repository( trans, repository_id )
-        galaxy_url = trans.request.host
+        trans.set_cookie( trans.request.host, name='toolshedgalaxyurl' )
         # Send a request to the relevant tool shed to see if there are any updates.
         # TODO: support https in the following url.
-        url = 'http://%s/repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=community' % \
-            ( repository.tool_shed, galaxy_url, repository.name, repository.owner, repository.changeset_revision )
+        # TODO: Set cookies for name, owner, changeset-revision instead of sending in request
+        url = 'http://%s/repository/check_for_updates?name=%s&owner=%s&changeset_revision=%s&webapp=community' % \
+            ( repository.tool_shed, repository.name, repository.owner, repository.changeset_revision )
         return trans.response.send_redirect( url )
     @web.expose
     @web.require_admin
diff --git a/lib/galaxy/web/controllers/workflow.py b/lib/galaxy/web/controllers/workflow.py
index e1724ef5c49..3ee7a50d07f 100644
--- a/lib/galaxy/web/controllers/workflow.py
+++ b/lib/galaxy/web/controllers/workflow.py
@@ -1150,17 +1150,20 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
                     if missing_tool_tups:
                         if trans.user_is_admin():
                             # A required tool is not available in the local Galaxy instance.
-                            # TODO: It would sure be nice to be able to redirec to a mako tempalte here that displays a nice
-                            # page including the links to the configured tool shed instead of this stupd message, but trying
+                            # TODO: It would sure be nice to be able to redirect to a mako template here that displays a nice
+                            # page including the links to the configured tool sheds instead of this message, but trying
                             # to get the panels back is a nightmare since workflow eliminates the Galaxy panels.  Someone 
-                            #involved in workflow development needs to figure out what it will take to get the Galaxy panels back...
+                            # involved in workflow development needs to figure out what it will take to be able to switch
+                            # back and forth between Galaxy (with panels ) and the workflow view (without panels ), having 
+                            # the Galaxy panels displayed whenever in Galaxy.
+                            trans.set_cookie( trans.request.host, name='toolshedgalaxyurl' )
                             galaxy_url = trans.request.host
                             message += "The workflow requires the following tools that are not available in this Galaxy instance."
                             message += "You can likely install the required tools from one of the Galaxy tool sheds listed below.<br/><br/>"
                             for tool_shed_name, tool_shed_url in trans.app.tool_shed_registry.tool_sheds.items():
                                 if tool_shed_url.endswith( '/' ):
                                     tool_shed_url = tool_shed_url.rstrip( '/' )
-                                    url = '%s/repository/find_tools?galaxy_url=%s&webapp=community' % ( tool_shed_url, galaxy_url )
+                                    url = '%s/repository/find_tools?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, galaxy_url )
                                     for missing_tool_tup in missing_tool_tups:
                                         missing_tool_id = missing_tool_tup[0]
                                         url += '&tool_id=%s' % missing_tool_id
diff --git a/lib/galaxy/webapps/community/controllers/repository.py b/lib/galaxy/webapps/community/controllers/repository.py
index 25ddd14a238..288b8a58823 100644
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -284,8 +284,9 @@ class InstallMatchedRepositoryListGrid( MatchedRepositoryListGrid ):
     # Grid definition
     title = "Repositories with required tools"
     operations = [ grids.GridOperation( "Preview and install tools",
-                                        url_args = dict( action='find_tools',
-                                                         operation='install_tools' ),
+                                        url_args = dict( controller='repository',
+                                                         action='find_tools',
+                                                         webapp='community' ),
                                         allow_multiple=True,
                                         async_compatible=False ) ]
 
@@ -383,6 +384,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', '' ) )
         status = params.get( 'status', 'done' )
+        webapp = params.get( 'webapp', 'galaxy' )
         # Set the toolshedgalaxyurl cookie so we can get back
         # to the calling local Galaxy instance.
         galaxy_url = kwd.get( 'galaxy_url', None )
@@ -390,11 +392,11 @@ class RepositoryController( BaseUIController, ItemRatings ):
             trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' )
         if 'operation' in kwd:
             operation = kwd[ 'operation' ].lower()
+            is_admin = trans.user_is_admin()
             if operation == "view_or_manage_repository":
                 repository_metadata = get_repository_metadata_by_id( trans, kwd[ 'id' ] )
                 repository_id = trans.security.encode_id( repository_metadata.repository.id )
                 repository = get_repository( trans, repository_id )
-                is_admin = trans.user_is_admin()
                 # The received id is a RepositoryMetadata.id, so we have to get the repository id.
                 kwd[ 'id' ] = repository_id
                 kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision
@@ -407,7 +409,17 @@ class RepositoryController( BaseUIController, ItemRatings ):
                                                                       action='view_repository',
                                                                       **kwd ) )
             if operation == "preview and install tools":
-                pass
+                galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' )
+                trans.set_cookie( trans.request.host, name='galaxytoolshedurl' )
+                # TODO: support https in the following url.
+                url = 'http://%s/admin/install_tool_shed_repository' % ( galaxy_url )
+                repos_to_clone = util.listify( kwd[ 'id' ] )
+                num_repos_to_clone = len( repos_to_clone )
+                trans.set_cookie( num_repos_to_clone, name='numrepostoclone' )
+                for index in range( 0, num_repos_to_clone ):
+                    repository_metadata_id = repos_to_clone[ index ]
+                    self._set_clone_repository_cookie( trans, index, repository_metadata_id )
+                return trans.response.send_redirect( url )
         tool_ids = [ tid.lower() for tid in util.listify( kwd.get( 'tool_id', '' ) ) ]
         tool_names = [ tn.lower() for tn in util.listify( kwd.get( 'tool_name', '' ) ) ]
         tool_versions = [ tv.lower() for tv in util.listify( kwd.get( 'tool_version', '' ) ) ]
@@ -499,6 +511,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
         else:
             tool_version = ''
         return trans.fill_template( '/webapps/community/repository/find_tools.mako',
+                                    webapp=webapp,
                                     tool_id=tool_id,
                                     tool_name=tool_name,
                                     tool_version=tool_version,
@@ -535,6 +548,16 @@ class RepositoryController( BaseUIController, ItemRatings ):
             found = ( tool_version == tool_dict_tool_version and tool_name == tool_dict_tool_name ) or \
                     ( not exact_matches_checked and tool_dict_tool_version.find( tool_version ) >= 0 and tool_dict_tool_name.find( tool_name ) >= 0 )
         return found
+    def _set_clone_repository_cookie( self, trans, index, repository_metadata_id ):
+        cookie_name = 'toolshedrepository%i' % index
+        repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id )
+        repository = get_repository( trans, trans.security.encode_id( repository_metadata.repository_id ) )
+        repository_id = trans.security.encode_id( repository.id )
+        changeset_revision = repository_metadata.changeset_revision
+        # Redirect back to local Galaxy to perform install.
+        repository_clone_url = generate_clone_url( trans, repository_id )
+        cookie_value = '%s&%s&%s&%s' % ( repository.name, repository.description, repository_clone_url, changeset_revision )
+        trans.set_cookie( cookie_value, name=cookie_name )
     @web.expose
     def preview_tools_in_changeset( self, trans, repository_id, **kwd ):
         params = util.Params( kwd )
@@ -570,11 +593,11 @@ class RepositoryController( BaseUIController, ItemRatings ):
         repository = get_repository( trans, repository_id )
         changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) )
         # Redirect back to local Galaxy to perform install.
-        tool_shed_url = trans.request.host
+        trans.set_cookie( trans.request.host, name='galaxytoolshedurl' )
         repository_clone_url = generate_clone_url( trans, repository_id )
         # TODO: support https in the following url.
-        url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s&name=%s&description=%s&repository_clone_url=%s&changeset_revision=%s' % \
-            ( galaxy_url, tool_shed_url, repository.name, repository.description, repository_clone_url, changeset_revision )
+        url = 'http://%s/admin/install_tool_shed_repository?name=%s&description=%s&repository_clone_url=%s&changeset_revision=%s' % \
+            ( galaxy_url, repository.name, repository.description, repository_clone_url, changeset_revision )
         return trans.response.send_redirect( url )
     @web.expose
     def check_for_updates( self, trans, **kwd ):
@@ -588,14 +611,11 @@ class RepositoryController( BaseUIController, ItemRatings ):
         owner = params.get( 'owner', None )
         changeset_revision = params.get( 'changeset_revision', None )
         webapp = params.get( 'webapp', None )
-        tool_shed_url = trans.request.host
+        trans.set_cookie( trans.request.host, name='galaxytoolshedurl' )
         # Start building up the url to redirect back to the calling Galaxy instance.
         # TODO: support https in the following url.
-        url = 'http://%s/admin/update_to_changeset_revision?tool_shed_url=%s' % ( galaxy_url, tool_shed_url )
+        url = 'http://%s/admin/update_to_changeset_revision' % galaxy_url
         repository = get_repository_by_name_and_owner( trans, name, owner )
-        #if error:
-        #    url += '&message=%s&status=error' % message
-        #else:
         url += '&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % \
             ( repository.name, repository.user.username, changeset_revision )
         if changeset_revision == repository.tip:
diff --git a/templates/admin/select_tool_panel_section.mako b/templates/admin/select_tool_panel_section.mako
index 125e32f323d..bd618db12b0 100644
--- a/templates/admin/select_tool_panel_section.mako
+++ b/templates/admin/select_tool_panel_section.mako
@@ -23,9 +23,9 @@
 <br/>
 
 <div class="toolForm">
-    <div class="toolFormTitle">Install tools from repository '${name}'</div>
+    <div class="toolFormTitle">Load tools into tool panel</div>
     <div class="toolFormBody">
-    <form name="select_tool_panel_section" id="select_tool_panel_section" action="${h.url_for( controller='admin', action='install_tool_shed_repository', tool_shed_url=tool_shed_url, name=name, description=description, changeset_revision=changeset_revision, repository_clone_url=repository_clone_url )}" method="post" >
+    <form name="select_tool_panel_section" id="select_tool_panel_section" action="${h.url_for( controller='admin', action='install_tool_shed_repository' )}" method="post" >
         %if shed_tool_conf_select_field:
             <div class="form-row">
                 <label>Shed tool configuration file:</label>
diff --git a/templates/webapps/community/repository/find_tools.mako b/templates/webapps/community/repository/find_tools.mako
index 9fa0906feba..ef1fb01f8f5 100644
--- a/templates/webapps/community/repository/find_tools.mako
+++ b/templates/webapps/community/repository/find_tools.mako
@@ -23,7 +23,7 @@
             strings if these types of strings are entered in more than one field.
         </div>
         <div style="clear: both"></div>
-        <form name="find_tools" id="find_tools" action="${h.url_for( controller='repository', action='find_tools' )}" method="post" >
+        <form name="find_tools" id="find_tools" action="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}" method="post" >
             <div class="form-row">
                 <label>Tool id:</label>
                 <input name="tool_id" type="textfield" value="${tool_id}" size="40"/>

From 8afea7bb9b1dfca0a5d7744bccfc9ecb1d8ce256 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Mon, 17 Oct 2011 13:49:06 -0400
Subject: [PATCH 061/362] Fix for loading a workflow that contains tools whose
 tools ids are the old version of tools ids, but whose available tools use the
 new tool guids as the tool id because the tools were installed from a Galaxy
 tool shed.

---
 lib/galaxy/workflow/modules.py | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
index d3df8a450be..2ab95083370 100644
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -209,9 +209,18 @@ class ToolModule( WorkflowModule ):
     @classmethod
     def from_workflow_step( Class, trans, step ):
         tool_id = step.tool_id
+        install_tool_id = None
         if tool_id not in trans.app.toolbox.tools_by_id:
-            return None
-        else:
+            for available_tool_id, available_tool in trans.app.toolbox.tools_by_id.items():
+                if available_tool_id.find( tool_id ) >=0:
+                    # We're attempting to match tool id against a tool guid.
+                    # TODO: match by tool_id (and version if we attempt that, but 
+                    # workflows will break) is not good enough because
+                    # 2 tools installed from a tool shed could both match this.  We
+                    # need to present a select list here.
+                    install_tool_id = available_tool_id
+                    break
+        if tool_id in trans.app.toolbox.tools_by_id or install_tool_id:
             module = Class( trans, tool_id )
             module.state = DefaultToolState()
             module.state.inputs = module.tool.params_from_strings( step.tool_inputs, trans.app, ignore_errors=True )
@@ -223,6 +232,7 @@ class ToolModule( WorkflowModule ):
                 pjadict[pja.action_type] = pja
             module.post_job_actions = pjadict
             return module
+        return None
     def save_to_step( self, step ):
         step.type = self.type
         step.tool_id = self.tool_id

From ac371e59c4ea9e65380cb1a79f526f594fcd24c2 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Mon, 17 Oct 2011 14:19:34 -0400
Subject: [PATCH 062/362] PBS cluster error user messages now suggest retrying
 the job.

---
 lib/galaxy/jobs/runners/pbs.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/jobs/runners/pbs.py b/lib/galaxy/jobs/runners/pbs.py
index d92b1aff9d4..67c88e86442 100644
--- a/lib/galaxy/jobs/runners/pbs.py
+++ b/lib/galaxy/jobs/runners/pbs.py
@@ -292,7 +292,7 @@ class PBSJobRunner( BaseJobRunner ):
         if not job_id:
             errno, text = pbs.error()
             log.debug( "(%s) pbs_submit failed, PBS error %d: %s" % (galaxy_job_id, errno, text) )
-            job_wrapper.fail( "Unable to run this job due to a cluster error" )
+            job_wrapper.fail( "Unable to run this job due to a cluster error, please retry it later" )
             return
 
         if pbs_queue_name is None:
@@ -419,7 +419,7 @@ class PBSJobRunner( BaseJobRunner ):
                     assert int( status.exit_status ) == 0
                     log.debug("(%s/%s) PBS job has completed successfully" % ( galaxy_job_id, job_id ) )
                 except AssertionError:
-                    pbs_job_state.fail_message = 'Job cannot be completed due to a cluster error.  Please retry or'
+                    pbs_job_state.fail_message = 'Job cannot be completed due to a cluster error, please retry it later'
                     log.error( '(%s/%s) PBS job failed: %s' % ( galaxy_job_id, job_id, JOB_EXIT_STATUS.get( int( status.exit_status ), 'Unknown error: %s' % status.exit_status ) ) )
                     self.work_queue.put( ( 'fail', pbs_job_state ) )
                     continue

From 15861f9d7af9e02af0c4a8ecca0c47dc704e99a7 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Mon, 17 Oct 2011 15:50:10 -0400
Subject: [PATCH 063/362] Improvements to Trackster filters: (a) scaler
 framework replaces generator framework; (b) addition of height scaler to set
 feature height based on attributes; and (c) no transparency for feature
 labels.

---
 static/june_2007_style/blue/trackster.css |   3 +-
 static/june_2007_style/trackster.css.tmpl |   6 +-
 static/scripts/packed/trackster.js        |   2 +-
 static/scripts/trackster.js               | 139 ++++++++++++++--------
 4 files changed, 96 insertions(+), 54 deletions(-)

diff --git a/static/june_2007_style/blue/trackster.css b/static/june_2007_style/blue/trackster.css
index 0c37f05b0a9..0c758a277d8 100644
--- a/static/june_2007_style/blue/trackster.css
+++ b/static/june_2007_style/blue/trackster.css
@@ -46,7 +46,8 @@ input{font:10px verdana;}
 .filters>.sliders,.display-controls{float:left;margin:1em;}
 .sliders{width:410px;}
 .display-controls{border-left:solid 2px #DDDDDD;padding-left:1em}
-.slider-row{margin-top:0.4em;margin-left:1em;}
+.filter-row{margin-top:0.4em;}
+.slider-row{margin-left:1em;}
 .elt-label{float:left;font-weight:bold;margin-right:1em;}
 .slider{float:right;width:200px;position:relative;}
 .tool-name{font-size:110%;font-weight:bold;}
diff --git a/static/june_2007_style/trackster.css.tmpl b/static/june_2007_style/trackster.css.tmpl
index f5012db8c14..11419a08032 100644
--- a/static/june_2007_style/trackster.css.tmpl
+++ b/static/june_2007_style/trackster.css.tmpl
@@ -255,12 +255,14 @@ input {
 .sliders{
     width: 410px;
 }
-.display-controls{
+.display-controls {
     border-left: solid 2px #DDDDDD;
     padding-left: 1em
 }
+.filter-row {
+    margin-top:0.4em;
+}
 .slider-row {
-    margin-top: 0.4em;
     margin-left: 1em;
 }
 .elt-label {
diff --git a/static/scripts/packed/trackster.js b/static/scripts/packed/trackster.js
index 1cf9953e992..1c3e0409caf 100644
--- a/static/scripts/packed/trackster.js
+++ b/static/scripts/packed/trackster.js
@@ -1 +1 @@
-var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var trackster_module=function(f,Z){var q=f("class").extend,t=f("slotting"),M=f("painters");var ag=function(ah,ai){this.document=ah;this.default_font=ai!==undefined?ai:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};q(ag.prototype,{load_pattern:function(ah,al){var ai=this.patterns,aj=this.dummy_context,ak=new Image();ak.src=image_path+al;ak.onload=function(){ai[ah]=aj.createPattern(ak,"repeat")}},get_pattern:function(ah){return this.patterns[ah]},new_canvas:function(){var ah=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ah)}ah.manager=this;return ah}});var o={};var m=function(ah,ai){o[ah.attr("id")]=ai};var n=function(ah,aj,al,ak){al=".group";var ai={};o[ah.attr("id")]=ak;ah.bind("drag",{handle:"."+aj,relative:true},function(au,av){var at=$(this);var ay=$(this).parent(),ap=ay.children(),ar=o[$(this).attr("id")],ao,an,aw,am,aq;an=$(this).parents(al);if(an.length!==0){aw=an.position().top;am=aw+an.outerHeight();if(av.offsetY<aw){$(this).insertBefore(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable_before(ar,ax);return}else{if(av.offsetY>am){$(this).insertAfter(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable(ar);return}}}an=null;for(aq=0;aq<ap.length;aq++){ao=$(ap.get(aq));aw=ao.position().top;am=aw+ao.outerHeight();if(ao.is(al)&&this!==ao.get(0)&&av.offsetY>=aw&&av.offsetY<=am){if(av.offsetY-aw<am-av.offsetY){ao.find(".content-div").prepend(this)}else{ao.find(".content-div").append(this)}if(ar.container){ar.container.remove_drawable(ar)}o[ao.attr("id")].add_drawable(ar);return}}for(aq=0;aq<ap.length;aq++){if(av.offsetY<$(ap.get(aq)).position().top){break}}if(aq===ap.length){if(this!==ap.get(aq-1)){ay.append(this);o[ay.attr("id")].move_drawable(ar,aq)}}else{if(this!==ap.get(aq)){$(this).insertBefore(ap.get(aq));o[ay.attr("id")].move_drawable(ar,(av.deltaY>0?aq-1:aq))}}}).bind("dragstart",function(){ai["border-top"]=ah.css("border-top");ai["border-bottom"]=ah.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ai)})};Z.moveable=n;var af=16,H=9,E=20,U=H+2,A=100,J=12000,S=200,D=5,w=10,L=5000,x=100,p="There was an error in indexing this dataset. ",K="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",F="No data for this chrom/contig.",u="Currently indexing... please wait",y="Tool cannot be rerun: ",a="Loading data...",aa="Ready for display",d=10,v=5,C=5;function ab(ai,ah){if(!ah){ah=0}var aj=Math.pow(10,ah);return Math.round(ai*aj)/aj}var c=function(ah){this.num_elements=ah;this.clear()};q(c.prototype,{get:function(ai){var ah=this.key_ary.indexOf(ai);if(ah!==-1){if(this.obj_cache[ai].stale){this.key_ary.splice(ah,1);delete this.obj_cache[ai]}else{this.move_key_to_end(ai,ah)}}return this.obj_cache[ai]},set:function(ai,aj){if(!this.obj_cache[ai]){if(this.key_ary.length>=this.num_elements){var ah=this.key_ary.shift();delete this.obj_cache[ah]}this.key_ary.push(ai)}this.obj_cache[ai]=aj;return aj},move_key_to_end:function(ai,ah){this.key_ary.splice(ah,1);this.key_ary.push(ai)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var T=function(ai,ah,aj){c.call(this,ai);this.track=ah;this.subset=(aj!==undefined?aj:true)};q(T.prototype,c.prototype,{load_data:function(aq,al,ao,ai,an){var ap=this.track.view.chrom,ak={chrom:ap,low:aq,high:al,mode:ao,resolution:ai,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ak,an);if(this.track.filters_manager){var ar=[];var ah=this.track.filters_manager.filters;for(var am=0;am<ah.length;am++){ar[ar.length]=ah[am].name}ak.filter_cols=JSON.stringify(ar)}var aj=this;return $.getJSON(this.track.data_url,ak,function(at){aj.set_data(aq,al,ao,at)})},get_data:function(ah,al,am,ai,ak){var aj=this.get_data_from_cache(ah,al,am);if(aj){return aj}aj=this.load_data(ah,al,am,ai,ak);this.set_data(ah,al,am,aj);return aj},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ap,ak,ao,aj,an,al){var aq=this.get_data_from_cache(ap,ak,ao);if(!aq){console.log("ERROR: no current data for: ",this.track,ap,ak,ao,aj,an);return}aq.stale=true;var ai=ap;if(al===this.DEEP_DATA_REQ){$.extend(an,{start_val:aq.data.length+1})}else{if(al===this.BROAD_DATA_REQ){ai=(aq.max_high?aq.max_high:aq.data[aq.data.length-1][2])+1}}var ah=this,am=this.load_data(ai,ak,ao,aj,an);new_data_available=$.Deferred();this.set_data(ap,ak,ao,new_data_available);$.when(am).then(function(ar){if(ar.data){ar.data=aq.data.concat(ar.data);if(ar.max_low){ar.max_low=aq.max_low}if(ar.message){ar.message=ar.message.replace(/[0-9]+/,ar.data.length)}}ah.set_data(ap,ak,ao,ar);new_data_available.resolve(ar)});return new_data_available},get_data_from_cache:function(ah,ai,aj){return this.get(this.gen_key(ah,ai,aj))},set_data:function(ai,aj,ak,ah){return this.set(this.gen_key(ai,aj,ak),ah)},gen_key:function(ah,aj,ak){var ai=ah+"_"+aj+"_"+ak;return ai},split_key:function(ah){return ah.split("_")}});var I=function(ai,ah,aj){T.call(this,ai,ah,aj)};q(I.prototype,T.prototype,c.prototype,{load_data:function(aj,ah,al,am,ai,ak){if(ai>1){return}return T.prototype.load_data.call(this,aj,ah,al,am,ai,ak)}});var r=function(ak,ai,ah,aj,al){this.name=ak;this.view=ai;this.container=ah;this.drag_handle_class=al;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak}],saved_values:aj,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values};q(r.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},make_name_popup_menu:function(){},set_name:function(ah){this.old_name=this.name;this.name=ah;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var z=function(al,ak,ai,ah,aj,am){r.call(this,ak,ai,ah,aj,am);this.obj_type=al;this.drawables=[]};q(z.prototype,r.prototype,{init:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah].init()}},_draw:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah]._draw()}},to_json:function(){var ai=[];for(var ah=0;ah<this.drawables.length;ah++){ai.push(this.drawables[ah].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ai}},add_drawable:function(ah){this.drawables.push(ah);ah.container=this},add_drawable_before:function(aj,ah){var ai=this.drawables.indexOf(ah);if(ai!=-1){this.drawables.splice(ai,0,aj);return true}return false},remove_drawable:function(ai){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);ai.container=null;return true}return false},move_drawable:function(ai,aj){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);this.drawables.splice(aj,0,ai);return true}return false}});var R=function(ak,ai,ah,aj){z.call(this,"DrawableGroup",ak,ai,ah,aj,"group-handle");if(!R.id_counter){R.id_counter=0}var al=R.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+al).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+al+"_content_div").appendTo(this.container_div);m(this.container_div,this);m(this.content_div,this);n(this.container_div,this.drag_handle_class,".group",this);this.make_name_popup_menu()};q(R.prototype,r.prototype,z.prototype,{make_name_popup_menu:function(){var ai=this;var ah={};ah["Edit configuration"]=function(){var al=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aj=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(am){if((am.keyCode||am.which)===27){al()}else{if((am.keyCode||am.which)===13){aj()}}};$(window).bind("keypress.check_enter_esc",ak);show_modal("Configure Group",ai.config.build_form(),{Cancel:al,OK:aj})};ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)}});var ae=function(ah,ak,aj,ai){z.call(this,"View");this.container=ah;this.chrom=null;this.vis_id=aj;this.dbkey=ai;this.title=ak;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ag(ah.get(0).ownerDocument);this.reset()};q(ae.prototype,z.prototype,{init:function(){var aj=this.container,ah=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aj);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;m(this.viewport_container,ah);this.intro_div=$("<div/>").addClass("intro");var ak=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ai=function(al){if(al.type==="focusout"||(al.keyCode||al.which)===13||(al.keyCode||al.which)===27){if((al.keyCode||al.which)!==27){ah.go_to($(this).val())}$(this).hide();$(this).val("");ah.location_span.show();ah.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ai).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ah.location_span.hide();ah.chrom_select.hide();ah.nav_input.val(ah.chrom+":"+ah.low+"-"+ah.high);ah.nav_input.css("display","inline-block");ah.nav_input.select();ah.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ah.zoom_out();ah.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.browser_content_div.click(function(al){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("<div />").css({height:ah.browser_content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,{content_div:this.top_labeltrack}));this.add_label_track(new ad(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new B(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(am,ai,ao){if(!am||am==="None"){return}var aj=this;if(am==="previous"){aj.load_chroms({low:this.chrom_start_index-x});return}if(am==="next"){aj.load_chroms({low:this.chrom_start_index+x});return}var an=$.grep(aj.chrom_data,function(ap,aq){return ap.chrom===am})[0];if(an===undefined){aj.load_chroms({chrom:am},function(){aj.change_chrom(am,ai,ao)});return}else{if(am!==aj.chrom){aj.chrom=am;aj.chrom_select.val(aj.chrom);aj.max_high=an.len-1;aj.reset();aj.request_redraw(true);for(var al=0,ah=aj.drawables.length;al<ah;al++){var ak=aj.drawables[al];if(ak.init){ak.init()}}}if(ai!==undefined&&ao!==undefined){aj.low=Math.max(ai,0);aj.high=Math.min(ao,aj.max_high)}aj.reset_overview();aj.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){z.prototype.add_drawable.call(this,ah);ah.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;ah.init();this.label_tracks.push(ah)},remove_drawable:function(aj,ai){z.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.drawables),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(D,Math.ceil(Math.log((this.high-this.low)/S)/Math.log(D)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){$.when(ah.get_overview_tile()).then(function(ai){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ai.canvas);view.overview_highlight.show().height(ai.canvas.height());view.overview_viewport.height(ai.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ah;ah.set_is_overview(true)});view.has_changes=true},reset_overview:function(){this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new O(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},al=this.track,aj=ai.tool_id+al.tool_region_and_parameters_str(ai.chrom,ai.low,ai.high),ah,am;if(al.container===view){var ak=new R(this.name,this.track.view,this.track.container);al.container.add_drawable(ak);al.container.remove_drawable(al);ak.add_drawable(al);al.container_div.appendTo(ak.content_div);ah=ak}else{ah=al.container}if(al instanceof e){am=new W(aj,view,ah,"hda");am.change_mode(al.mode);ah.add_drawable(am)}am.content_div.text("Starting job.");this.run(ai,am,function(an){am.dataset_id=an.dataset_id;am.content_div.text("Running job.");am.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(K)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(y+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var O=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){O.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var X=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};q(X.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=ah[this.index];return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(ar,ay){this.track=ar;this.filters=[];for(var at=0;at<ay.length;at++){var au=ay[at],az=au.name,ah=au.type,ak=au.index,ax=au.tool_id,aw=au.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[at]=new X(az,ak,ax,aw)}else{console.log("ERROR: unsupported filter: ",az,ah)}}var al=function(aA,aB,aC){aA.click(function(){var aD=aB.text();max=parseFloat(aC.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aC.slider("option","values")){input_size=2*input_size+1;multi_value=true}aB.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aD).appendTo(aB).focus().select().click(function(aE){aE.stopPropagation()}).blur(function(){$(this).remove();aB.text(aD)}).keyup(function(aI){if(aI.keyCode===27){$(this).trigger("blur")}else{if(aI.keyCode===13){var aG=aC.slider("option","min"),aE=aC.slider("option","max"),aH=function(aJ){return(isNaN(aJ)||aJ>aE||aJ<aG)},aF=$(this).val();if(!multi_value){aF=parseFloat(aF);if(aH(aF)){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}else{aF=aF.split("-");aF=[parseFloat(aF[0]),parseFloat(aF[1])];if(aH(aF[0])||aH(aF[1])){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}aC.slider((multi_value?"values":"value"),aF)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aA){aA.stopPropagation()}).click(function(aA){aA.stopPropagation()}).bind("dblclick",function(aA){aA.stopPropagation()}).bind("keydown",function(aA){aA.stopPropagation()});var av=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aD,aF){aF.container=$("<div/>").addClass("slider-row").appendTo(av);var aE=$("<div/>").addClass("elt-label").appendTo(aF.container);var aC=$("<span/>").addClass("slider-name").text(aF.name+"  ").appendTo(aE);var aB=$("<span/>");var aH=$("<span/>").addClass("slider-value").appendTo(aE).append("[").append(aB).append("]");var aA=$("<div/>").addClass("slider").appendTo(aF.container);aF.control_element=$("<div/>").attr("id",aF.name+"-filter-control").appendTo(aA);var aG=[0,0];aF.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aJ,aK){var aI=aK.values;aB.text(aI[0]+"-"+aI[1]);aF.low=aI[0];aF.high=aI[1];ap.track.request_draw(true,true)},change:function(aI,aJ){aF.control_element.slider("option","slide").call(aF.control_element,aI,aJ)}});aF.slider=aF.control_element;aF.slider_label=aB;al(aH,aB,aF.control_element);$("<div style='clear: both;'/>").appendTo(aF.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(av);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var aj=this;ao.click(function(){aj.run_on_dataset()})}var aq=$("<div/>").addClass("display-controls").appendTo(this.parent_div),an=$("<span/>").addClass("elt-label").text("Transparency:").appendTo(aq),ai=$("<select/>").attr("name","alpha_dropdown").appendTo(aq);this.alpha_filter=null;$("<option/>").attr("value",-1).text("== None ==").appendTo(ai);for(var at=0;at<this.filters.length;at++){$("<option/>").attr("value",at).text(this.filters[at].name).appendTo(ai)}ai.change(function(){$(this).children("option:selected").each(function(){var aA=parseInt($(this).val());ap.alpha_filter=(aA>=0?ap.filters[aA]:null);ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var P=function(ai,ah){M.AlphaGenerator.call(this,ah);this.filter=ai};P.prototype.gen_alpha=function(ah){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_alpha}return((parseFloat(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var G=function(ah){this.track=ah.track;this.params=ah.params;this.values={};this.restore_values((ah.saved_values?ah.saved_values:{}));this.onchange=ah.onchange};q(G.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(ah,ak,aj,ai,al){this.track=ah;this.index=ak;this.low=ak*S*aj;this.high=(ak+1)*S*aj;this.resolution=aj;this.canvas=$("<div class='track-tile'/>").append(ai);this.data=al;this.stale=false};b.prototype.predisplay_actions=function(){};var l=function(ah,ak,aj,ai,al,am){b.call(this,ah,ak,aj,ai,al);this.max_val=am};q(l.prototype,b.prototype);var Q=function(ah,al,ak,aj,an,ao,am,ai){b.call(this,ah,al,ak,aj,an);this.mode=ao;this.message=am;this.feature_mapper=ai};q(Q.prototype,b.prototype);Q.prototype.predisplay_actions=function(){var ai=this,ah={};if(ai.mode!=="Pack"){return}$(this.canvas).mousemove(function(au){var ao=$(this).offset(),at=au.pageX-ao.left,ar=au.pageY-ao.top,ay=ai.feature_mapper.get_feature_data(at,ar),ap=(ay?ay[0]:null);$(this).siblings(".feature-popup").each(function(){if(!ap||$(this).attr("id")!==ap.toString()){$(this).remove()}});if(ay){var ak=ah[ap];if(!ak){var ap=ay[0],av={name:ay[3],start:ay[1],end:ay[2],strand:ay[4]},an=ai.track.filters_manager.filters,am;for(var aq=0;aq<an.length;aq++){am=an[aq];av[am.name]=ay[am.index]}var ak=$("<div/>").attr("id",ap).addClass("feature-popup"),ax,aw,az=$("<table/>").appendTo(ak),aA;for(ax in av){aw=av[ax];aA=$("<tr/>").appendTo(az);$("<th/>").appendTo(aA).text(ax);$("<td/>").attr("align","left").appendTo(aA).text(typeof(aw)=="number"?ab(aw,2):aw)}ah[ap]=ak}ak.appendTo($(ai.canvas).parent());var al=at+parseInt(ai.canvas.css("left"))+7,aj=ar+parseInt(ai.canvas.css("top"))+7;ak.css("left",al+"px").css("top",aj+"px")}else{if(!au.isPropagationStopped()){au.stopPropagation();$(this).siblings().each(function(){$(this).trigger(au)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var j=function(ak,ai,ah,aj,al,am){r.call(this,ak,ai,ah,{},"draghandle");this.data_url=(al?al:default_data_url);this.data_url_extra_params={};this.data_query_wait=(am?am:L);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.container_div=$("<div />").addClass("track").attr("id","track_"+j.id_counter++).css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Y){return"ReadTrack"}else{if(this instanceof W){return"ToolDataFeatureTrack"}else{if(this instanceof V){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(K)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(F)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.make_name_popup_menu()}ah.content_div.text(aa);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}})},predraw_init:function(){},});var N=function(ao,am){var ai=this,ap=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=new ac(this,(ao!==undefined?ao:{}));this.filters_available=false;this.filters_visible=false;this.tool=(am!==undefined&&obj_length(am)>0?new s(this,am):undefined);this.is_overview=false;if(ai.hidden){return}if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(ai.display_modes!==undefined){if(ai.mode_div===undefined){ai.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ai.header_div);var aj=(ai.config&&ai.config.values.mode?ai.config.values.mode:ai.display_modes[0]);ai.mode=aj;ai.mode_div.text(aj);var ah={};for(var ak=0,an=ai.display_modes.length;ak<an;ak++){var al=ai.display_modes[ak];ah[al]=function(aq){return function(){ai.change_mode(aq)}}(al)}make_popupmenu(ai.mode_div,ah)}else{ai.mode_div.hide()}}this.make_name_popup_menu()};q(N.prototype,r.prototype,j.prototype,{to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw();return ah},make_name_popup_menu:function(){var ai=this;var ah={};ah[(this.is_overview?"Hide overview":"Set as overview")]=function(){if(ai.is_overview){ai.view.reset_overview()}else{ai.view.set_overview(ai)}};ah["Edit configuration"]=function(){var am=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},al=function(an){if((an.keyCode||an.which)===27){am()}else{if((an.keyCode||an.which)===13){ak()}}};$(window).bind("keypress.check_enter_esc",al);show_modal("Configure Track",ai.config.build_form(),{Cancel:am,OK:ak})};if(ai.filters_available>0){var aj=(ai.filters_div.is(":visible")?"Hide filters":"Show filters");ah[aj]=function(){ai.filters_visible=(ai.filters_div.is(":visible"));if(ai.filters_visible){ai.filters_manager.reset_filters()}ai.filters_div.toggle();ai.make_name_popup_menu()}}if(ai.tool){var aj=(ai.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");ah[aj]=function(){if(!ai.dynamic_tool_div.is(":visible")){ai.set_name(ai.name+ai.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ai.revert_name()}ai.dynamic_tool_div.toggle();ai.make_name_popup_menu()}}ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)},set_is_overview:function(ah){this.is_overview=ah;this.make_name_popup_menu()},get_overview_tile:function(){var ah=this;view=ah.view,resolution=Math.pow(D,Math.ceil(Math.log((view.max_high-view.max_low)/S)/Math.log(D))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ah.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ah.data_url_extra_params)).then(function(ai){var ak=ah._gen_tile_cache_key(view_width,w_scale,0),am=ah.tile_cache.get(ak);if(!am){am=ah.draw_tile(ai,"Auto",resolution,0,w_scale);ah.tile_cache.set(ak,am)}var ap=$(am.canvas.find("canvas")),al=ap.clone(),ao=ap.get(0).getContext("2d"),aj=al.get(0).getContext("2d"),an=ao.getImageData(0,0,ao.canvas.width,ao.canvas.height);aj.putImageData(an,-ah.left_offset,(am.data.dataset_type==="summary_tree"?U:0));new_tile=new b(ah,-1,resolution,al);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof B)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/S);var ap=true;var at=[];var ah=0;while((ai*S*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",E)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*S*an,ax=ap+S*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);if(aq!==undefined){al.tile_cache.set(at,aq);al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw()});return null},show_tile:function(ao,aq,ar){var aj=this,ai=ao.canvas,an=ai;if(ao.message){var at=$("<div/>"),ap=$("<div/>").addClass("tile-message").text(ao.message).css({height:E-1,width:ao.canvas.width}).appendTo(at),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ap),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ap);at.append(ai);an=at;al.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()});ah.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()})}ao.predisplay_actions();var am=this.view.high-this.view.low,ak=(ao.low-this.view.low)*ar;if(this.left_offset){ak-=this.left_offset}an.css({position:"absolute",top:0,left:ak,height:""});aq.append(an);aj.max_height=Math.max(aj.max_height,an.height());aj.content_div.css("height",aj.max_height+"px");aq.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*S*ai,al=S*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ai,ah){this.hidden=true;j.call(this,"label",ai,ah,{});this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{init:function(){this.enabled=true},_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var B=function(ah){this.hidden=true;j.call(this,"reference",ah,{content_div:ah.top_labeltrack},{});N.call(this);ah.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ah.dbkey};this.data_manager=new I(C,this,false);this.tile_cache=new c(v)};q(B.prototype,r.prototype,N.prototype,{init:function(){this.enabled=true},draw_tile:function(ar,an,am,ai,at){var al=this,aj=S*am;if(at>this.view.canvas_manager.char_width_px){if(ar===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(al,ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(am,ak,aj,an,ah,al){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,am,ak,aj,al);N.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=an;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new T(C,this);this.tile_cache=new c(v);this.left_offset=0;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:am},{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:al,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.dataset_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.dataset_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};q(k.prototype,r.prototype,N.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this;ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(ai){ah.container_div.addClass("line-track");var ak=ai.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=ak.min;ah.prefs.max_value=ak.max;$("#track_"+ah.dataset_id+"_minval").val(ah.prefs.min_value);$("#track_"+ah.dataset_id+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=ak.total_frequency;ah.container_div.find(".yaxislabel").remove();var al=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_minval").text(ab(ah.prefs.min_value,3));var aj=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_maxval").text(ab(ah.prefs.max_value,3));aj.css({position:"absolute",top:"24px",left:"10px"});aj.prependTo(ah.container_div);al.css({position:"absolute",bottom:"2px",left:"10px"});al.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new M.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(this.track,aj,al,ak,au.data)}});var e=function(ah,an,ai,am,ap,ao,ak,al){var aj=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];j.call(this,ah,an,ai,ao);N.call(this,ak,al);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){aj.set_name(aj.prefs.name);aj.tile_cache.clear();aj.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=am;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new T(20,this);this.left_offset=200;this.painter=M.LinkedFeaturePainter};q(e.prototype,r.prototype,N.prototype,{postdraw_actions:function(ax,ah,ay,aw){N.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.make_name_popup_menu()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",A,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aE,aI,ar,ak){var aB=this,am=aB._get_tile_bounds(aI,aE),aL=am[0],ai=am[1],ay=ai-aL,aC=Math.ceil(ay*ar),aP=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"){az="no_detail"}else{var aO=aw.data;if(this.view.high-this.view.low>J){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aC+al;aj.height=an+U;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aL,ai,200);if(aw.max){at.max=aw.max}aw=at}var aM=new M.SummaryTreePainter(aw,aL,ai,this.prefs);var aD=aj.getContext("2d");aD.translate(al,U);aM.draw(aD,aC,an);return new l(aB,aI,aE,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aF=0,aH=aw.data.length;aF<aH;aF++){var ao=aw.data[aF];var aG=false;var av;for(var aK=0,aN=au.length;aK<aN;aK++){av=au[aK];av.update_attrs(ao);if(!av.keep(ao)){aG=true;break}}if(!aG){aq.push(ao)}}}var aA=(this.filters_manager.alpha_filter?new P(this.filters_manager.alpha_filter):null);var aM=new (this.painter)(aq,aL,ai,this.prefs,az,aA,ak);var an=Math.max(af,aM.get_required_height(ap));var aj=this.view.canvas_manager.new_canvas();var aJ=null;aj.width=aC+al;aj.height=an;var aD=aj.getContext("2d");aD.fillStyle=this.prefs.block_color;aD.font=aD.canvas.manager.default_font;aD.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aw.data){aD.translate(al,0);aJ=aM.draw(aD,aC,an,ax);aJ.translation=-al}return new Q(aB,aI,aE,aj,aw.data,az,aw.message,aJ)}});var V=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.painter=M.VariantPainter};q(V.prototype,r.prototype,N.prototype,e.prototype);var Y=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ak,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter;this.make_name_popup_menu()};q(Y.prototype,r.prototype,N.prototype,e.prototype);var W=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am,{});this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};q(W.prototype,r.prototype,N.prototype,e.prototype,{predraw_init:function(){var ai=this;var ah=function(){if(ai.data_manager.size()===0){setTimeout(ah,300)}else{ai.data_url=default_data_url;ai.data_query_wait=L;ai.dataset_state_url=converted_datasets_state_url;$.getJSON(ai.dataset_state_url,{dataset_id:ai.dataset_id,hda_ldda:ai.hda_ldda},function(aj){})}};ah()}});Z.View=ae;Z.DrawableGroup=R;Z.LineTrack=k;Z.FeatureTrack=e;Z.ReadTrack=Y};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(k,y){var v=k("class").extend;var q=function(J,B,H,A,G,E){if(E===undefined){E=4}var D=A-B;var C=G-H;var F=Math.floor(Math.sqrt(D*D+C*C)/E);var K=D/F;var I=C/F;var z;for(z=0;z<F;z++,B+=K,H+=I){if(z%2!==0){continue}J.fillRect(B,H,E,1)}};var r=function(B,A,z,E){var 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+var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var trackster_module=function(f,Z){var q=f("class").extend,t=f("slotting"),N=f("painters");var ag=function(ah,ai){this.document=ah;this.default_font=ai!==undefined?ai:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};q(ag.prototype,{load_pattern:function(ah,al){var ai=this.patterns,aj=this.dummy_context,ak=new Image();ak.src=image_path+al;ak.onload=function(){ai[ah]=aj.createPattern(ak,"repeat")}},get_pattern:function(ah){return this.patterns[ah]},new_canvas:function(){var ah=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ah)}ah.manager=this;return ah}});var o={};var m=function(ah,ai){o[ah.attr("id")]=ai};var n=function(ah,aj,al,ak){al=".group";var ai={};o[ah.attr("id")]=ak;ah.bind("drag",{handle:"."+aj,relative:true},function(au,av){var at=$(this);var ay=$(this).parent(),ap=ay.children(),ar=o[$(this).attr("id")],ao,an,aw,am,aq;an=$(this).parents(al);if(an.length!==0){aw=an.position().top;am=aw+an.outerHeight();if(av.offsetY<aw){$(this).insertBefore(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable_before(ar,ax);return}else{if(av.offsetY>am){$(this).insertAfter(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable(ar);return}}}an=null;for(aq=0;aq<ap.length;aq++){ao=$(ap.get(aq));aw=ao.position().top;am=aw+ao.outerHeight();if(ao.is(al)&&this!==ao.get(0)&&av.offsetY>=aw&&av.offsetY<=am){if(av.offsetY-aw<am-av.offsetY){ao.find(".content-div").prepend(this)}else{ao.find(".content-div").append(this)}if(ar.container){ar.container.remove_drawable(ar)}o[ao.attr("id")].add_drawable(ar);return}}for(aq=0;aq<ap.length;aq++){if(av.offsetY<$(ap.get(aq)).position().top){break}}if(aq===ap.length){if(this!==ap.get(aq-1)){ay.append(this);o[ay.attr("id")].move_drawable(ar,aq)}}else{if(this!==ap.get(aq)){$(this).insertBefore(ap.get(aq));o[ay.attr("id")].move_drawable(ar,(av.deltaY>0?aq-1:aq))}}}).bind("dragstart",function(){ai["border-top"]=ah.css("border-top");ai["border-bottom"]=ah.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ai)})};Z.moveable=n;var af=16,I=9,F=20,U=I+2,A=100,K=12000,S=200,D=5,w=10,M=5000,x=100,p="There was an error in indexing this dataset. ",L="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",u="Currently indexing... please wait",y="Tool cannot be rerun: ",a="Loading data...",aa="Ready for display",d=10,v=5,C=5;function ab(ai,ah){if(!ah){ah=0}var aj=Math.pow(10,ah);return Math.round(ai*aj)/aj}var c=function(ah){this.num_elements=ah;this.clear()};q(c.prototype,{get:function(ai){var ah=this.key_ary.indexOf(ai);if(ah!==-1){if(this.obj_cache[ai].stale){this.key_ary.splice(ah,1);delete this.obj_cache[ai]}else{this.move_key_to_end(ai,ah)}}return this.obj_cache[ai]},set:function(ai,aj){if(!this.obj_cache[ai]){if(this.key_ary.length>=this.num_elements){var ah=this.key_ary.shift();delete this.obj_cache[ah]}this.key_ary.push(ai)}this.obj_cache[ai]=aj;return aj},move_key_to_end:function(ai,ah){this.key_ary.splice(ah,1);this.key_ary.push(ai)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var T=function(ai,ah,aj){c.call(this,ai);this.track=ah;this.subset=(aj!==undefined?aj:true)};q(T.prototype,c.prototype,{load_data:function(aq,al,ao,ai,an){var ap=this.track.view.chrom,ak={chrom:ap,low:aq,high:al,mode:ao,resolution:ai,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ak,an);if(this.track.filters_manager){var ar=[];var ah=this.track.filters_manager.filters;for(var am=0;am<ah.length;am++){ar[ar.length]=ah[am].name}ak.filter_cols=JSON.stringify(ar)}var aj=this;return $.getJSON(this.track.data_url,ak,function(at){aj.set_data(aq,al,ao,at)})},get_data:function(ah,al,am,ai,ak){var aj=this.get_data_from_cache(ah,al,am);if(aj){return aj}aj=this.load_data(ah,al,am,ai,ak);this.set_data(ah,al,am,aj);return aj},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ap,ak,ao,aj,an,al){var aq=this.get_data_from_cache(ap,ak,ao);if(!aq){console.log("ERROR: no current data for: ",this.track,ap,ak,ao,aj,an);return}aq.stale=true;var ai=ap;if(al===this.DEEP_DATA_REQ){$.extend(an,{start_val:aq.data.length+1})}else{if(al===this.BROAD_DATA_REQ){ai=(aq.max_high?aq.max_high:aq.data[aq.data.length-1][2])+1}}var ah=this,am=this.load_data(ai,ak,ao,aj,an);new_data_available=$.Deferred();this.set_data(ap,ak,ao,new_data_available);$.when(am).then(function(ar){if(ar.data){ar.data=aq.data.concat(ar.data);if(ar.max_low){ar.max_low=aq.max_low}if(ar.message){ar.message=ar.message.replace(/[0-9]+/,ar.data.length)}}ah.set_data(ap,ak,ao,ar);new_data_available.resolve(ar)});return new_data_available},get_data_from_cache:function(ah,ai,aj){return this.get(this.gen_key(ah,ai,aj))},set_data:function(ai,aj,ak,ah){return this.set(this.gen_key(ai,aj,ak),ah)},gen_key:function(ah,aj,ak){var ai=ah+"_"+aj+"_"+ak;return ai},split_key:function(ah){return ah.split("_")}});var J=function(ai,ah,aj){T.call(this,ai,ah,aj)};q(J.prototype,T.prototype,c.prototype,{load_data:function(aj,ah,al,am,ai,ak){if(ai>1){return}return T.prototype.load_data.call(this,aj,ah,al,am,ai,ak)}});var r=function(ak,ai,ah,aj,al){this.name=ak;this.view=ai;this.container=ah;this.drag_handle_class=al;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak}],saved_values:aj,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values};q(r.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},make_name_popup_menu:function(){},set_name:function(ah){this.old_name=this.name;this.name=ah;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var z=function(al,ak,ai,ah,aj,am){r.call(this,ak,ai,ah,aj,am);this.obj_type=al;this.drawables=[]};q(z.prototype,r.prototype,{init:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah].init()}},_draw:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah]._draw()}},to_json:function(){var ai=[];for(var ah=0;ah<this.drawables.length;ah++){ai.push(this.drawables[ah].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ai}},add_drawable:function(ah){this.drawables.push(ah);ah.container=this},add_drawable_before:function(aj,ah){var ai=this.drawables.indexOf(ah);if(ai!=-1){this.drawables.splice(ai,0,aj);return true}return false},remove_drawable:function(ai){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);ai.container=null;return true}return false},move_drawable:function(ai,aj){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);this.drawables.splice(aj,0,ai);return true}return false}});var R=function(ak,ai,ah,aj){z.call(this,"DrawableGroup",ak,ai,ah,aj,"group-handle");if(!R.id_counter){R.id_counter=0}var al=R.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+al).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+al+"_content_div").appendTo(this.container_div);m(this.container_div,this);m(this.content_div,this);n(this.container_div,this.drag_handle_class,".group",this);this.make_name_popup_menu()};q(R.prototype,r.prototype,z.prototype,{make_name_popup_menu:function(){var ai=this;var ah={};ah["Edit configuration"]=function(){var al=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aj=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(am){if((am.keyCode||am.which)===27){al()}else{if((am.keyCode||am.which)===13){aj()}}};$(window).bind("keypress.check_enter_esc",ak);show_modal("Configure Group",ai.config.build_form(),{Cancel:al,OK:aj})};ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)}});var ae=function(ah,ak,aj,ai){z.call(this,"View");this.container=ah;this.chrom=null;this.vis_id=aj;this.dbkey=ai;this.title=ak;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ag(ah.get(0).ownerDocument);this.reset()};q(ae.prototype,z.prototype,{init:function(){var aj=this.container,ah=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aj);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;m(this.viewport_container,ah);this.intro_div=$("<div/>").addClass("intro");var ak=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ai=function(al){if(al.type==="focusout"||(al.keyCode||al.which)===13||(al.keyCode||al.which)===27){if((al.keyCode||al.which)!==27){ah.go_to($(this).val())}$(this).hide();$(this).val("");ah.location_span.show();ah.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ai).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ah.location_span.hide();ah.chrom_select.hide();ah.nav_input.val(ah.chrom+":"+ah.low+"-"+ah.high);ah.nav_input.css("display","inline-block");ah.nav_input.select();ah.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ah.zoom_out();ah.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.browser_content_div.click(function(al){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("<div />").css({height:ah.browser_content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,{content_div:this.top_labeltrack}));this.add_label_track(new ad(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new B(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(am,ai,ao){if(!am||am==="None"){return}var aj=this;if(am==="previous"){aj.load_chroms({low:this.chrom_start_index-x});return}if(am==="next"){aj.load_chroms({low:this.chrom_start_index+x});return}var an=$.grep(aj.chrom_data,function(ap,aq){return ap.chrom===am})[0];if(an===undefined){aj.load_chroms({chrom:am},function(){aj.change_chrom(am,ai,ao)});return}else{if(am!==aj.chrom){aj.chrom=am;aj.chrom_select.val(aj.chrom);aj.max_high=an.len-1;aj.reset();aj.request_redraw(true);for(var al=0,ah=aj.drawables.length;al<ah;al++){var ak=aj.drawables[al];if(ak.init){ak.init()}}}if(ai!==undefined&&ao!==undefined){aj.low=Math.max(ai,0);aj.high=Math.min(ao,aj.max_high)}aj.reset_overview();aj.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){z.prototype.add_drawable.call(this,ah);ah.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;ah.init();this.label_tracks.push(ah)},remove_drawable:function(aj,ai){z.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.drawables),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(D,Math.ceil(Math.log((this.high-this.low)/S)/Math.log(D)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){$.when(ah.get_overview_tile()).then(function(ai){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ai.canvas);view.overview_highlight.show().height(ai.canvas.height());view.overview_viewport.height(ai.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ah;ah.set_is_overview(true)});view.has_changes=true},reset_overview:function(){this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new P(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},al=this.track,aj=ai.tool_id+al.tool_region_and_parameters_str(ai.chrom,ai.low,ai.high),ah,am;if(al.container===view){var ak=new R(this.name,this.track.view,this.track.container);al.container.add_drawable(ak);al.container.remove_drawable(al);ak.add_drawable(al);al.container_div.appendTo(ak.content_div);ah=ak}else{ah=al.container}if(al instanceof e){am=new W(aj,view,ah,"hda");am.change_mode(al.mode);ah.add_drawable(am)}am.content_div.text("Starting job.");this.run(ai,am,function(an){am.dataset_id=an.dataset_id;am.content_div.text("Running job.");am.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(L)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(y+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var P=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){P.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var X=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};q(X.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=ah[this.index];return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(at,aA){this.track=at;this.filters=[];for(var av=0;av<aA.length;av++){var aw=aA[av],aB=aw.name,ah=aw.type,aj=aw.index,az=aw.tool_id,ay=aw.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[av]=new X(aB,aj,az,ay)}else{console.log("ERROR: unsupported filter: ",aB,ah)}}var ak=function(aC,aD,aE){aC.click(function(){var aF=aD.text();max=parseFloat(aE.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aE.slider("option","values")){input_size=2*input_size+1;multi_value=true}aD.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aF).appendTo(aD).focus().select().click(function(aG){aG.stopPropagation()}).blur(function(){$(this).remove();aD.text(aF)}).keyup(function(aK){if(aK.keyCode===27){$(this).trigger("blur")}else{if(aK.keyCode===13){var aI=aE.slider("option","min"),aG=aE.slider("option","max"),aJ=function(aL){return(isNaN(aL)||aL>aG||aL<aI)},aH=$(this).val();if(!multi_value){aH=parseFloat(aH);if(aJ(aH)){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}else{aH=aH.split("-");aH=[parseFloat(aH[0]),parseFloat(aH[1])];if(aJ(aH[0])||aJ(aH[1])){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}aE.slider((multi_value?"values":"value"),aH)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aC){aC.stopPropagation()}).click(function(aC){aC.stopPropagation()}).bind("dblclick",function(aC){aC.stopPropagation()}).bind("keydown",function(aC){aC.stopPropagation()});var ax=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aF,aH){aH.container=$("<div/>").addClass("filter-row slider-row").appendTo(ax);var aG=$("<div/>").addClass("elt-label").appendTo(aH.container);var aE=$("<span/>").addClass("slider-name").text(aH.name+"  ").appendTo(aG);var aD=$("<span/>");var aJ=$("<span/>").addClass("slider-value").appendTo(aG).append("[").append(aD).append("]");var aC=$("<div/>").addClass("slider").appendTo(aH.container);aH.control_element=$("<div/>").attr("id",aH.name+"-filter-control").appendTo(aC);var aI=[0,0];aH.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aL,aM){var aK=aM.values;aD.text(aK[0]+"-"+aK[1]);aH.low=aK[0];aH.high=aK[1];ap.track.request_draw(true,true)},change:function(aK,aL){aH.control_element.slider("option","slide").call(aH.control_element,aK,aL)}});aH.slider=aH.control_element;aH.slider_label=aD;ak(aJ,aD,aH.control_element);$("<div style='clear: both;'/>").appendTo(aH.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(ax);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var ai=this;ao.click(function(){ai.run_on_dataset()})}var ar=$("<div/>").addClass("display-controls").appendTo(this.parent_div),au,an,aq,al={Transparency:function(aC){ap.alpha_filter=aC},Height:function(aC){ap.height_filter=aC}};$.each(al,function(aE,aD){au=$("<div/>").addClass("filter-row").appendTo(ar),an=$("<span/>").addClass("elt-label").text(aE+":").appendTo(au),aq=$("<select/>").attr("name",aE+"_dropdown").css("float","right").appendTo(au);$("<option/>").attr("value",-1).text("== None ==").appendTo(aq);for(var aC=0;aC<ap.filters.length;aC++){$("<option/>").attr("value",aC).text(ap.filters[aC].name).appendTo(aq)}aq.change(function(){$(this).children("option:selected").each(function(){var aF=parseInt($(this).val());al[aE]((aF>=0?ap.filters[aF]:null));ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(au)});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var E=function(ah,ai){N.Scaler.call(this,ai);this.filter=ah};E.prototype.gen_val=function(ah){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var H=function(ah){this.track=ah.track;this.params=ah.params;this.values={};this.restore_values((ah.saved_values?ah.saved_values:{}));this.onchange=ah.onchange};q(H.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(ah,ak,aj,ai,al){this.track=ah;this.index=ak;this.low=ak*S*aj;this.high=(ak+1)*S*aj;this.resolution=aj;this.canvas=$("<div class='track-tile'/>").append(ai);this.data=al;this.stale=false};b.prototype.predisplay_actions=function(){};var l=function(ah,ak,aj,ai,al,am){b.call(this,ah,ak,aj,ai,al);this.max_val=am};q(l.prototype,b.prototype);var Q=function(ah,al,ak,aj,an,ao,am,ai){b.call(this,ah,al,ak,aj,an);this.mode=ao;this.message=am;this.feature_mapper=ai};q(Q.prototype,b.prototype);Q.prototype.predisplay_actions=function(){var ai=this,ah={};if(ai.mode!=="Pack"){return}$(this.canvas).mousemove(function(au){var ao=$(this).offset(),at=au.pageX-ao.left,ar=au.pageY-ao.top,ay=ai.feature_mapper.get_feature_data(at,ar),ap=(ay?ay[0]:null);$(this).siblings(".feature-popup").each(function(){if(!ap||$(this).attr("id")!==ap.toString()){$(this).remove()}});if(ay){var ak=ah[ap];if(!ak){var ap=ay[0],av={name:ay[3],start:ay[1],end:ay[2],strand:ay[4]},an=ai.track.filters_manager.filters,am;for(var aq=0;aq<an.length;aq++){am=an[aq];av[am.name]=ay[am.index]}var ak=$("<div/>").attr("id",ap).addClass("feature-popup"),ax,aw,az=$("<table/>").appendTo(ak),aA;for(ax in av){aw=av[ax];aA=$("<tr/>").appendTo(az);$("<th/>").appendTo(aA).text(ax);$("<td/>").attr("align","left").appendTo(aA).text(typeof(aw)=="number"?ab(aw,2):aw)}ah[ap]=ak}ak.appendTo($(ai.canvas).parent());var al=at+parseInt(ai.canvas.css("left"))+7,aj=ar+parseInt(ai.canvas.css("top"))+7;ak.css("left",al+"px").css("top",aj+"px")}else{if(!au.isPropagationStopped()){au.stopPropagation();$(this).siblings().each(function(){$(this).trigger(au)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var j=function(ak,ai,ah,aj,al,am){r.call(this,ak,ai,ah,{},"draghandle");this.data_url=(al?al:default_data_url);this.data_url_extra_params={};this.data_query_wait=(am?am:M);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.container_div=$("<div />").addClass("track").attr("id","track_"+j.id_counter++).css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Y){return"ReadTrack"}else{if(this instanceof W){return"ToolDataFeatureTrack"}else{if(this instanceof V){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(L)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(G)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.make_name_popup_menu()}ah.content_div.text(aa);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}})},predraw_init:function(){},});var O=function(ao,am){var ai=this,ap=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=new ac(this,(ao!==undefined?ao:{}));this.filters_available=false;this.filters_visible=false;this.tool=(am!==undefined&&obj_length(am)>0?new s(this,am):undefined);this.is_overview=false;if(ai.hidden){return}if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(ai.display_modes!==undefined){if(ai.mode_div===undefined){ai.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ai.header_div);var aj=(ai.config&&ai.config.values.mode?ai.config.values.mode:ai.display_modes[0]);ai.mode=aj;ai.mode_div.text(aj);var ah={};for(var ak=0,an=ai.display_modes.length;ak<an;ak++){var al=ai.display_modes[ak];ah[al]=function(aq){return function(){ai.change_mode(aq)}}(al)}make_popupmenu(ai.mode_div,ah)}else{ai.mode_div.hide()}}this.make_name_popup_menu()};q(O.prototype,r.prototype,j.prototype,{to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw();return ah},make_name_popup_menu:function(){var ai=this;var ah={};ah[(this.is_overview?"Hide overview":"Set as overview")]=function(){if(ai.is_overview){ai.view.reset_overview()}else{ai.view.set_overview(ai)}};ah["Edit configuration"]=function(){var am=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},al=function(an){if((an.keyCode||an.which)===27){am()}else{if((an.keyCode||an.which)===13){ak()}}};$(window).bind("keypress.check_enter_esc",al);show_modal("Configure Track",ai.config.build_form(),{Cancel:am,OK:ak})};if(ai.filters_available>0){var aj=(ai.filters_div.is(":visible")?"Hide filters":"Show filters");ah[aj]=function(){ai.filters_visible=(ai.filters_div.is(":visible"));if(ai.filters_visible){ai.filters_manager.reset_filters()}ai.filters_div.toggle();ai.make_name_popup_menu()}}if(ai.tool){var aj=(ai.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");ah[aj]=function(){if(!ai.dynamic_tool_div.is(":visible")){ai.set_name(ai.name+ai.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ai.revert_name()}ai.dynamic_tool_div.toggle();ai.make_name_popup_menu()}}ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)},set_is_overview:function(ah){this.is_overview=ah;this.make_name_popup_menu()},get_overview_tile:function(){var ah=this;view=ah.view,resolution=Math.pow(D,Math.ceil(Math.log((view.max_high-view.max_low)/S)/Math.log(D))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ah.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ah.data_url_extra_params)).then(function(ai){var ak=ah._gen_tile_cache_key(view_width,w_scale,0),am=ah.tile_cache.get(ak);if(!am){am=ah.draw_tile(ai,"Auto",resolution,0,w_scale);ah.tile_cache.set(ak,am)}var ap=$(am.canvas.find("canvas")),al=ap.clone(),ao=ap.get(0).getContext("2d"),aj=al.get(0).getContext("2d"),an=ao.getImageData(0,0,ao.canvas.width,ao.canvas.height);aj.putImageData(an,-ah.left_offset,(am.data.dataset_type==="summary_tree"?U:0));new_tile=new b(ah,-1,resolution,al);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof B)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/S);var ap=true;var at=[];var ah=0;while((ai*S*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",F)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*S*an,ax=ap+S*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);if(aq!==undefined){al.tile_cache.set(at,aq);al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw()});return null},show_tile:function(ao,aq,ar){var aj=this,ai=ao.canvas,an=ai;if(ao.message){var at=$("<div/>"),ap=$("<div/>").addClass("tile-message").text(ao.message).css({height:F-1,width:ao.canvas.width}).appendTo(at),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ap),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ap);at.append(ai);an=at;al.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()});ah.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()})}ao.predisplay_actions();var am=this.view.high-this.view.low,ak=(ao.low-this.view.low)*ar;if(this.left_offset){ak-=this.left_offset}an.css({position:"absolute",top:0,left:ak,height:""});aq.append(an);aj.max_height=Math.max(aj.max_height,an.height());aj.content_div.css("height",aj.max_height+"px");aq.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*S*ai,al=S*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ai,ah){this.hidden=true;j.call(this,"label",ai,ah,{});this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{init:function(){this.enabled=true},_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var B=function(ah){this.hidden=true;j.call(this,"reference",ah,{content_div:ah.top_labeltrack},{});O.call(this);ah.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ah.dbkey};this.data_manager=new J(C,this,false);this.tile_cache=new c(v)};q(B.prototype,r.prototype,O.prototype,{init:function(){this.enabled=true},draw_tile:function(ar,an,am,ai,at){var al=this,aj=S*am;if(at>this.view.canvas_manager.char_width_px){if(ar===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(al,ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(am,ak,aj,an,ah,al){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,am,ak,aj,al);O.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=an;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new T(C,this);this.tile_cache=new c(v);this.left_offset=0;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:am},{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:al,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.dataset_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.dataset_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};q(k.prototype,r.prototype,O.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this;ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(ai){ah.container_div.addClass("line-track");var ak=ai.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=ak.min;ah.prefs.max_value=ak.max;$("#track_"+ah.dataset_id+"_minval").val(ah.prefs.min_value);$("#track_"+ah.dataset_id+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=ak.total_frequency;ah.container_div.find(".yaxislabel").remove();var al=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_minval").text(ab(ah.prefs.min_value,3));var aj=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_maxval").text(ab(ah.prefs.max_value,3));aj.css({position:"absolute",top:"24px",left:"10px"});aj.prependTo(ah.container_div);al.css({position:"absolute",bottom:"2px",left:"10px"});al.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new N.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(this.track,aj,al,ak,au.data)}});var e=function(ah,an,ai,am,ap,ao,ak,al){var aj=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];j.call(this,ah,an,ai,ao);O.call(this,ak,al);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){aj.set_name(aj.prefs.name);aj.tile_cache.clear();aj.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=am;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new T(20,this);this.left_offset=200;this.painter=N.LinkedFeaturePainter};q(e.prototype,r.prototype,O.prototype,{postdraw_actions:function(ax,ah,ay,aw){O.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.make_name_popup_menu()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",A,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aD,aH,ar,ak){var aA=this,am=aA._get_tile_bounds(aH,aD),aK=am[0],ai=am[1],ay=ai-aK,aB=Math.ceil(ay*ar),aQ=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"){az="no_detail"}else{var aP=aw.data;if(this.view.high-this.view.low>K){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aB+al;aj.height=an+U;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aK,ai,200);if(aw.max){at.max=aw.max}aw=at}var aM=new N.SummaryTreePainter(aw,aK,ai,this.prefs);var aC=aj.getContext("2d");aC.translate(al,U);aM.draw(aC,aB,an);return new l(aA,aH,aD,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aE=0,aG=aw.data.length;aE<aG;aE++){var ao=aw.data[aE];var aF=false;var av;for(var aJ=0,aO=au.length;aJ<aO;aJ++){av=au[aJ];av.update_attrs(ao);if(!av.keep(ao)){aF=true;break}}if(!aF){aq.push(ao)}}}var aN=(this.filters_manager.alpha_filter?new E(this.filters_manager.alpha_filter):null);var aL=(this.filters_manager.height_filter?new E(this.filters_manager.height_filter):null);var aM=new (this.painter)(aq,aK,ai,this.prefs,az,aN,aL,ak);var an=Math.max(af,aM.get_required_height(ap));var aj=this.view.canvas_manager.new_canvas();var aI=null;aj.width=aB+al;aj.height=an;var aC=aj.getContext("2d");aC.fillStyle=this.prefs.block_color;aC.font=aC.canvas.manager.default_font;aC.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aw.data){aC.translate(al,0);aI=aM.draw(aC,aB,an,ax);aI.translation=-al}return new Q(aA,aH,aD,aj,aw.data,az,aw.message,aI)}});var V=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.painter=N.VariantPainter};q(V.prototype,r.prototype,O.prototype,e.prototype);var Y=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ak,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=N.ReadPainter;this.make_name_popup_menu()};q(Y.prototype,r.prototype,O.prototype,e.prototype);var W=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am,{});this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};q(W.prototype,r.prototype,O.prototype,e.prototype,{predraw_init:function(){var ai=this;var ah=function(){if(ai.data_manager.size()===0){setTimeout(ah,300)}else{ai.data_url=default_data_url;ai.data_query_wait=M;ai.dataset_state_url=converted_datasets_state_url;$.getJSON(ai.dataset_state_url,{dataset_id:ai.dataset_id,hda_ldda:ai.hda_ldda},function(aj){})}};ah()}});Z.View=ae;Z.DrawableGroup=R;Z.LineTrack=k;Z.FeatureTrack=e;Z.ReadTrack=Y};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(k,y){var v=k("class").extend;var q=function(J,B,H,A,G,E){if(E===undefined){E=4}var D=A-B;var C=G-H;var F=Math.floor(Math.sqrt(D*D+C*C)/E);var K=D/F;var I=C/F;var z;for(z=0;z<F;z++,B+=K,H+=I){if(z%2!==0){continue}J.fillRect(B,H,E,1)}};var r=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var e=function(z){this.default_val=(z?z:1)};e.prototype.gen_val=function(z){return this.default_val};var n=function(B,D,z,A,C){this.data=B;this.view_start=D;this.view_end=z;this.prefs=v({},this.default_prefs,A);this.mode=C};n.prototype.default_prefs={};var w=function(B,D,z,A,C){n.call(this,B,D,z,A,C)};w.prototype.default_prefs={show_counts:false};w.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var c=function(z,D,F,G,B){n.call(this,z,D,F,G,B);if(this.prefs.min_value===undefined){var H=Infinity;for(var A=0,C=this.data.length;A<C;A++){H=Math.min(H,this.data[A][1])}this.prefs.min_value=H}if(this.prefs.max_value===undefined){var E=-Infinity;for(var A=0,C=this.data.length;A<C;A++){E=Math.max(E,this.data[A][1])}this.prefs.max_value=E}};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var o=function(z){this.feature_positions={};this.slot_height=z;this.translation=0};o.prototype.map_feature_data=function(A,C,z,B){if(!this.feature_positions[C]){this.feature_positions[C]=[]}this.feature_positions[C].push({data:A,x_start:z,x_end:B})};o.prototype.get_feature_data=function(z,D){var C=Math.floor(D/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var p=function(B,E,z,A,D,F,C){n.call(this,B,E,z,A,D);this.alpha_scaler=(F?F:new e());this.height_scaler=(C?C:new e())};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};v(p.prototype,{get_required_height:function(A){var z=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){z=A*y_scale}return z+Math.max(Math.round(y_scale/2),5)},draw:function(L,J,H,G){var R=this.data,E=this.view_start,N=this.view_end;L.save();L.fillStyle=this.prefs.block_color;L.textAlign="right";var I=this.view_end-this.view_start,F=J/I,M=this.get_row_height(),Q=new o(M),C;for(var O=0,P=R.length;O<P;O++){var B=R[O],D=B[0],K=B[1],z=B[2],A=(G&&G[D]!==undefined?G[D]:null);if((K<N&&z>E)&&(this.mode=="Dense"||A!==null)){C=this.draw_element(L,this.mode,B,A,E,N,F,M,J);Q.map_feature_data(B,A,C[0],C[1])}}L.restore();return Q},draw_element:function(F,B,H,D,C,E,G,A,z){console.log("WARNING: Unimplemented function.");return[0,0]}});var d=10,j=3,m=5,x=10,g=1,t=3,f=3,a=9,l=2,h="#ccc";var s=function(B,E,z,A,D,F,C){p.call(this,B,E,z,A,D,F,C)};v(s.prototype,p.prototype,{get_row_height:function(){var A=this.mode,z;if(A==="Dense"){z=d}else{if(A==="no_detail"){z=j}else{if(A==="Squish"){z=m}else{z=x}}}return z},draw_element:function(N,E,W,I,P,ah,al,an,z){var T=W[0],aj=W[1],ab=W[2],R=W[3],ac=Math.floor(Math.max(0,(aj-P)*al)),O=Math.ceil(Math.min(z,Math.max(0,(ab-P)*al))),aa=ac,am=O,Z=(E==="Dense"?0:(0+I))*an,M,af,S=null,ap=null,C=this.prefs.block_color,ae=this.prefs.label_color;N.globalAlpha=this.alpha_scaler.gen_val(W);if(E=="Dense"){I=1}if(E==="no_detail"){N.fillStyle=C;N.fillRect(ac,Z+5,O-ac,g)}else{var L=W[4],Y=W[5],ad=W[6],D=W[7];if(Y&&ad){S=Math.floor(Math.max(0,(Y-P)*al));ap=Math.ceil(Math.min(z,Math.max(0,(ad-P)*al)))}var ak,U;if(E==="Squish"||E==="Dense"){ak=1;U=f}else{ak=5;U=a}if(!D){if(W.strand){if(W.strand==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand_inv")}else{if(W.strand==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand_inv")}}}else{N.fillStyle=C}N.fillRect(ac,Z,O-ac,U)}else{var K,V;if(E==="Squish"||E==="Dense"){N.fillStyle=h;K=Z+Math.floor(f/2)+1;V=1}else{if(L){var K=Z;var V=U;if(L==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand")}else{if(L==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand")}}}else{N.fillStyle=h;K+=(f/2)+1;V=1}}N.fillRect(ac,K,O-ac,V);var F;for(var ai=0,B=D.length;ai<B;ai++){var G=D[ai],A=Math.floor(Math.max(0,(G[0]-P)*al)),X=Math.ceil(Math.min(z,Math.max((G[1]-P)*al)));if(A>X){continue}N.fillStyle=C;N.fillRect(A,Z+(U-ak)/2+1,X-A,ak);if(S!==undefined&&ad>Y&&!(A>ap||X<S)){var ag=Math.max(A,S),J=Math.min(X,ap);N.fillRect(ag,Z+1,J-ag,U);if(D.length==1&&E=="Pack"){if(L==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand_inv")}else{if(L==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand_inv")}}if(ag+14<J){ag+=2;J-=2}N.fillRect(ag,Z+1,J-ag,U)}}}if(E==="Pack"){N.globalAlpha=1;N.fillStyle="white";var H=this.height_scaler.gen_val(W),Q=Math.ceil(U*H),ao=Math.round((U-Q)/2);if(H!==1){N.fillRect(ac,K+1,O-ac,ao);N.fillRect(ac,K+U-ao+1,O-ac,ao)}}}N.globalAlpha=1;if(E==="Pack"&&aj>P){N.fillStyle=ae;if(P===0&&ac-N.measureText(R).width<0){N.textAlign="left";N.fillText(R,O+l,Z+8);am+=N.measureText(R).width+l}else{N.textAlign="right";N.fillText(R,ac-l,Z+8);aa-=N.measureText(R).width+l}}}N.globalAlpha=1;return[aa,am]}});var b=function(B,E,z,A,D,F,C){p.call(this,B,E,z,A,D,F,C)};v(b.prototype,p.prototype,{draw_element:function(S,N,H,D,V,B,K,T,Q){var H=data[i],J=H[0],R=H[1],C=H[2],M=H[3],F=Math.floor(Math.max(0,(R-V)*K)),I=Math.ceil(Math.min(Q,Math.max(0,(C-V)*K))),E=(N==="Dense"?0:(0+D))*T,z,W,A=null,L=null;if(no_label){S.fillStyle=block_color;S.fillRect(F+left_offset,E+5,I-F,1)}else{var U=H[4],P=H[5],G=H[6];z=9;W=1;S.fillRect(F+left_offset,E,I-F,z);if(N!=="Dense"&&M!==undefined&&R>V){S.fillStyle=label_color;if(V===0&&F-S.measureText(M).width<0){S.textAlign="left";S.fillText(M,I+2+left_offset,E+8)}else{S.textAlign="right";S.fillText(M,F-2+left_offset,E+8)}S.fillStyle=block_color}var O=U+" / "+P;if(R>V&&S.measureText(O).width<(I-F)){S.fillStyle="white";S.textAlign="center";S.fillText(O,left_offset+F+(I-F)/2,E+8);S.fillStyle=block_color}}return[F,I]}});var u=function(C,F,z,B,E,G,D,A){p.call(this,C,F,z,B,E,G,D);this.ref_seq=A};u.prototype.default_prefs=v({},p.prototype.default_prefs,{show_insertions:false});v(u.prototype,p.prototype,{get_row_height:function(){var z,A=this.mode;if(A==="Dense"){z=d}else{if(A==="Squish"){z=m}else{z=x;if(this.prefs.show_insertions){z*=2}}}return z},draw_read:function(V,Q,M,aa,B,U,J,G,F){V.textAlign="center";var T=this,A=[aa,B],P=0,W=0,S=0;ref_seq=this.ref_seq,char_width_px=V.canvas.manager.char_width_px;var af=[];if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){S=Math.round(M/2)}if(!J){J=[[0,G.length]]}for(var N=0,Y=J.length;N<Y;N++){var K=J[N],C="MIDNSHP=X"[K[0]],O=K[1];if(C==="H"||C==="S"){P-=O}var H=U+P,ae=Math.floor(Math.max(0,(H-aa)*M)),I=Math.floor(Math.max(0,(H+O-aa)*M));if(ae===I){I+=1}switch(C){case"H":break;case"S":case"M":case"=":if(is_overlap([H,H+O],A)){var R=G.slice(W,W+O);if(S>0){V.fillStyle=this.prefs.block_color;V.fillRect(ae-S,F+1,I-ae,9);V.fillStyle=h;for(var ac=0,z=R.length;ac<z;ac++){if(this.prefs.show_differences&&ref_seq){var L=ref_seq[H-aa+ac];if(!L||L.toLowerCase()===R[ac].toLowerCase()){continue}}if(H+ac>=aa&&H+ac<=B){var ad=Math.floor(Math.max(0,(H+ac-aa)*M));V.fillText(R[ac],ad,F+9)}}}else{V.fillStyle=this.prefs.block_color;V.fillRect(ae,F+4,I-ae,f)}}W+=O;P+=O;break;case"N":V.fillStyle=h;V.fillRect(ae-S,F+5,I-ae,1);P+=O;break;case"D":V.fillStyle="red";V.fillRect(ae-S,F+4,I-ae,3);P+=O;break;case"P":break;case"I":var Z=ae-S;if(is_overlap([H,H+O],A)){var R=G.slice(W,W+O);if(this.prefs.show_insertions){var E=ae-(I-ae)/2;if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){V.fillStyle="yellow";V.fillRect(E-S,F-9,I-ae,9);af[af.length]={type:"triangle",data:[Z,F+4,5]};V.fillStyle=h;switch(seq_tile_overlap){case (OVERLAP_START):R=R.slice(aa-H);break;case (OVERLAP_END):R=R.slice(0,H-B);break;case (CONTAINED_BY):break;case (CONTAINS):R=R.slice(aa-H,H-B);break}for(var ac=0,z=R.length;ac<z;ac++){var ad=Math.floor(Math.max(0,(H+ac-aa)*M));V.fillText(R[ac],ad-(I-ae)/2,F)}}else{V.fillStyle="yellow";V.fillRect(E,F+(this.mode!=="Dense"?2:5),I-ae,(Q!=="Dense"?f:t))}}else{if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){af[af.length]={type:"text",data:[R.length,Z,F+9]}}else{}}}W+=O;break;case"X":W+=O;break}}V.fillStyle="yellow";var ab,D,ag;for(var X=0;X<af.length;X++){ab=af[X];D=ab.type;ag=ab.data;if(D==="text"){V.save();V.font="bold "+V.font;V.fillText(ag[0],ag[1],ag[2]);V.restore()}else{if(D=="triangle"){r(V,ag[0],ag[1],ag[2])}}}},draw_element:function(S,N,F,C,V,A,J,T,Q){var I=F[0],R=F[1],B=F[2],K=F[3],E=Math.floor(Math.max(0,(R-V)*J)),G=Math.ceil(Math.min(Q,Math.max(0,(B-V)*J))),D=(N==="Dense"?0:(0+C))*T,W=this.prefs.block_color,H=this.prefs.label_color,P=0;if((N==="Pack"||this.mode==="Auto")&&J>S.canvas.manager.char_width_px){var P=Math.round(J/2)}S.fillStyle=W;if(F[5] instanceof Array){var O=Math.floor(Math.max(0,(F[4][0]-V)*J)),M=Math.ceil(Math.min(Q,Math.max(0,(F[4][1]-V)*J))),L=Math.floor(Math.max(0,(F[5][0]-V)*J)),z=Math.ceil(Math.min(Q,Math.max(0,(F[5][1]-V)*J)));if(F[4][1]>=V&&F[4][0]<=A&&F[4][2]){this.draw_read(S,N,J,V,A,F[4][0],F[4][2],F[4][3],D)}if(F[5][1]>=V&&F[5][0]<=A&&F[5][2]){this.draw_read(S,N,J,V,A,F[5][0],F[5][2],F[5][3],D)}if(L>M){S.fillStyle=h;q(S,M-P,D+5,L-P,D+5)}}else{S.fillStyle=W;this.draw_read(S,N,J,V,A,R,F[4],F[5],D)}if(N==="Pack"&&R>V){S.fillStyle=this.prefs.label_color;var U=1;if(U===0&&E-S.measureText(K).width<0){S.textAlign="left";S.fillText(K,G+l-P,D+8)}else{S.textAlign="right";S.fillText(K,E-l-P,D+8)}S.fillStyle=W}return[0,0]}});y.Scaler=e;y.SummaryTreePainter=w;y.LinePainter=c;y.LinkedFeaturePainter=s;y.ReadPainter=u;y.VariantPainter=b};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window);
\ No newline at end of file
diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index 757a8ed018a..5eac12b6dc5 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -1804,7 +1804,7 @@ var FiltersManager = function(track, filters_list) {
     var sliders_div = $("<div/>").addClass("sliders").appendTo(this.parent_div);
     var manager = this;
     $.each(this.filters, function(index, filter) {
-        filter.container = $("<div/>").addClass("slider-row").appendTo(sliders_div);
+        filter.container = $("<div/>").addClass("filter-row slider-row").appendTo(sliders_div);
         
         // Set up filter label (name, values).
         var filter_label = $("<div/>").addClass("elt-label").appendTo(filter.container)
@@ -1860,25 +1860,39 @@ var FiltersManager = function(track, filters_list) {
     //
     var 
         display_controls_div = $("<div/>").addClass("display-controls").appendTo(this.parent_div),
-        header_text = $("<span/>").addClass("elt-label").text("Transparency:").appendTo(display_controls_div),
-        alpha_select = $("<select/>").attr("name", "alpha_dropdown").appendTo(display_controls_div);
-    
-    // Dropdown for selecting attribute to use for alpha channel manipulation.
-    this.alpha_filter = null;
-    $("<option/>").attr("value", -1).text("== None ==").appendTo(alpha_select);
-    for (var i = 0; i < this.filters.length; i++) {
-        $("<option/>").attr("value", i).text(this.filters[i].name).appendTo(alpha_select);
-    }
-    alpha_select.change(function() {
-        $(this).children("option:selected").each(function() {
-            var filterIndex = parseInt($(this).val());
-            manager.alpha_filter = (filterIndex >= 0 ? manager.filters[filterIndex] : null);
-            manager.track.request_draw(true, true);
-        })
+        formatting_div,
+        header_text,
+        select,
+        // TODO: find better way to specify and change control filters.
+        filter_controls_dict = { 
+            "Transparency": function(new_filter) { manager.alpha_filter = new_filter; },
+            "Height" : function(new_filter) { manager.height_filter = new_filter; }
+        };
+        
+    $.each(filter_controls_dict, function(control_name, filter) {
+        // Display name and select option.
+        formatting_div = $("<div/>").addClass("filter-row").appendTo(display_controls_div),
+        header_text = $("<span/>").addClass("elt-label").text(control_name + ":").appendTo(formatting_div),
+        select = $("<select/>").attr("name", control_name + "_dropdown").css("float", "right").appendTo(formatting_div);
+
+        // Dropdown for selecting filter.
+        $("<option/>").attr("value", -1).text("== None ==").appendTo(select);
+        for (var i = 0; i < manager.filters.length; i++) {
+            $("<option/>").attr("value", i).text(manager.filters[i].name).appendTo(select);
+        }
+        select.change(function() {
+            $(this).children("option:selected").each(function() {
+                var filterIndex = parseInt($(this).val());
+                filter_controls_dict[control_name]( (filterIndex >= 0 ? manager.filters[filterIndex] : null) );
+                manager.track.request_draw(true, true);
+            })
+        });
+        
+        // Clear floating.
+        $("<div style='clear: both;'/>").appendTo(formatting_div);
     });
     
     // Clear floating.
-    // Add to clear floating layout.
     $("<div style='clear: both;'/>").appendTo(this.parent_div);
 };
 
@@ -1892,6 +1906,7 @@ extend(FiltersManager.prototype, {
             filter.slider.slider("option", "values", [filter.min, filter.max]);
         }
         this.alpha_filter = null;
+        this.height_filter = null;
     },
     run_on_dataset: function() {
         // Get or create dictionary item.
@@ -1979,20 +1994,20 @@ extend(FiltersManager.prototype, {
 });
 
 /**
- * Generates alpha values based on filter and feature's value for filter.
+ * Generates scale values based on filter and feature's value for filter.
  */
-var FilterAlphaGenerator = function(filter, default_alpha) {
-    painters.AlphaGenerator.call(this, default_alpha);
+var FilterScaler = function(filter, default_val) {
+    painters.Scaler.call(this, default_val);
     this.filter = filter;
 };
 
-FilterAlphaGenerator.prototype.gen_alpha = function(feature_data) {
-    // If filter is not initalized yet, return default alpha.
+FilterScaler.prototype.gen_val = function(feature_data) {
+    // If filter is not initalized yet, return default val.
     if (this.filter.high === Number.MAX_VALUE || this.filter.low === -Number.MAX_VALUE || this.filter.low === this.filter.high) {
-        return this.default_alpha;
+        return this.default_val;
     }
     
-    // Alpha value is ratio of (filter's value compared to low) to (complete filter range).
+    // Scaling value is ratio of (filter's value compared to low) to (complete filter range).
     return ( ( parseFloat(feature_data[this.filter.index]) - this.filter.low ) / ( this.filter.high - this.filter.low ) );
 };
 
@@ -3419,9 +3434,10 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
         }        
         
         // Create painter, and canvas of sufficient size to contain all features.
-        var filter_alpha_generator = (this.filters_manager.alpha_filter ? new FilterAlphaGenerator(this.filters_manager.alpha_filter) : null);
+        var filter_alpha_scaler = (this.filters_manager.alpha_filter ? new FilterScaler(this.filters_manager.alpha_filter) : null);
+        var filter_height_scaler = (this.filters_manager.height_filter ? new FilterScaler(this.filters_manager.height_filter) : null);
         // HACK: ref_seq will only be defined for ReadTracks, and only the ReadPainter accepts that argument
-        var painter = new (this.painter)(filtered, tile_low, tile_high, this.prefs, mode, filter_alpha_generator, ref_seq);
+        var painter = new (this.painter)(filtered, tile_low, tile_high, this.prefs, mode, filter_alpha_scaler, filter_height_scaler, ref_seq);
         var required_height = Math.max(MIN_TRACK_HEIGHT, painter.get_required_height(slots_required));
         var canvas = this.view.canvas_manager.new_canvas();
         var feature_mapper = null;
@@ -3755,17 +3771,17 @@ var drawDownwardEquilateralTriangle = function(ctx, down_vertex_x, down_vertex_y
 };
 
 /**
- * Base class for all alpha generators.
+ * Base class for all scalers. Scalers produce values that are used to change (scale) drawing attributes.
  */
-var AlphaGenerator = function(default_alpha) {
-    this.default_alpha = (default_alpha ? default_alpha : 1);
+var Scaler = function(default_val) {
+    this.default_val = (default_val ? default_val : 1);
 };
 
 /**
- * Base method for generating an alpha channel value; returns default alpha  if not implemented.
+ * Produce a scaling value.
  */
-AlphaGenerator.prototype.gen_alpha = function(data) {
-    return this.default_alpha;  
+Scaler.prototype.gen_val = function(input) {
+    return this.default_val;
 };
 
 /**
@@ -4008,9 +4024,10 @@ FeaturePositionMapper.prototype.get_feature_data = function(x, y) {
 /**
  * Abstract object for painting feature tracks. Subclasses must implement draw_element() for painting to work.
  */
-var FeaturePainter = function(data, view_start, view_end, prefs, mode, alpha_generator) {
+var FeaturePainter = function(data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler) {
     Painter.call(this, data, view_start, view_end, prefs, mode);
-    this.alpha_generator = (alpha_generator ? alpha_generator : new AlphaGenerator());
+    this.alpha_scaler = (alpha_scaler ? alpha_scaler : new Scaler());
+    this.height_scaler = (height_scaler ? height_scaler : new Scaler());
 };
 
 FeaturePainter.prototype.default_prefs = { block_color: "#FFF", connector_color: "#FFF" };
@@ -4085,8 +4102,8 @@ var DENSE_TRACK_HEIGHT = 10,
     LABEL_SPACING = 2,
     CONNECTOR_COLOR = "#ccc";
 
-var LinkedFeaturePainter = function(data, view_start, view_end, prefs, mode, alpha_generator) {
-    FeaturePainter.call(this, data, view_start, view_end, prefs, mode, alpha_generator);
+var LinkedFeaturePainter = function(data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler) {
+    FeaturePainter.call(this, data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler);
 };
 
 extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
@@ -4131,8 +4148,8 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
             label_color = this.prefs.label_color;
         
         // Set global alpha.
-        ctx.globalAlpha = this.alpha_generator.gen_alpha(feature);
-
+        ctx.globalAlpha = this.alpha_scaler.gen_val(feature);
+        
         // In dense mode, put all data in top slot.
         if (mode == "Dense") {
             slot = 1;
@@ -4141,7 +4158,6 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
         if (mode === "no_detail") {
             // No details for feature, so only one way to display.
             ctx.fillStyle = block_color;
-            // TODO: what should width be here?
             ctx.fillRect(f_start, y_center + 5, f_end - f_start, NO_DETAIL_FEATURE_HEIGHT);
         } 
         else { // Mode is either Squish or Pack:
@@ -4181,6 +4197,7 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
                 }                            
                 ctx.fillRect(f_start, y_center, f_end - f_start, thick_height);
             } else { 
+                //
                 // There are feature blocks and mode is either Squish or Pack.
                 //
                 // Approach: (a) draw whole feature as connector/intron and (b) draw blocks as 
@@ -4213,6 +4230,8 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
                 }
                 ctx.fillRect(f_start, cur_y_center, f_end - f_start, cur_height);
                 
+                // Draw blocks.
+                var start_and_height;
                 for (var k = 0, k_len = feature_blocks.length; k < k_len; k++) {
                     var block = feature_blocks[k],
                         block_start = Math.floor( Math.max(0, (block[0] - tile_low) * w_scale) ),
@@ -4223,17 +4242,16 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
 
                     // Draw thin block.
                     ctx.fillStyle = block_color;
-                    ctx.fillRect(block_start, y_center + (thick_height-thin_height)/2 + 1, 
-                                 block_end - block_start, thin_height);
+                    ctx.fillRect(block_start, y_center + (thick_height-thin_height)/2 + 1, block_end - block_start, thin_height );
 
                     // If block intersects with thick region, draw block as thick.
                     // - No thick is sometimes encoded as thick_start == thick_end, so don't draw in that case
                     if (thick_start !== undefined && feature_te > feature_ts && !(block_start > thick_end || block_end < thick_start) ) {
                         var block_thick_start = Math.max(block_start, thick_start),
-                            block_thick_end = Math.min(block_end, thick_end); 
-                        ctx.fillRect(block_thick_start, y_center + 1, block_thick_end - block_thick_start, thick_height);
+                            block_thick_end = Math.min(block_end, thick_end);
+                        ctx.fillRect(block_thick_start, y_center + 1, block_thick_end - block_thick_start, thick_height );
                         if ( feature_blocks.length == 1 && mode == "Pack") {
-                            // Exactly one block  means we have no introns, but do have a distinct "thick" region,
+                            // Exactly one block means we have no introns, but do have a distinct "thick" region,
                             // draw arrows over it if in pack mode
                             if (feature_strand === "+") {
                                 ctx.fillStyle = ctx.canvas.manager.get_pattern( 'right_strand_inv' );
@@ -4245,12 +4263,33 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
                                 block_thick_start += 2;
                                 block_thick_end -= 2;
                             }
-                            ctx.fillRect(block_thick_start, y_center + 1, block_thick_end - block_thick_start, thick_height);
+                            ctx.fillRect(block_thick_start, y_center + 1, block_thick_end - block_thick_start, thick_height );
                         }   
                     }
                 }
+                                
+                // FIXME: Height scaling only works in Pack mode right now.
+                if (mode === "Pack") {
+                    // Reset alpha so height scaling is not impacted by alpha scaling.
+                    ctx.globalAlpha = 1;
+                    
+                    // Height scaling: draw white lines to reduce height according to height scale factor.
+                    ctx.fillStyle = "white"; // TODO: set this to background color.
+                    var 
+                        hscale_factor = this.height_scaler.gen_val(feature),
+                        // Ceil ensures that min height is >= 1.
+                        new_height = Math.ceil(thick_height * hscale_factor),
+                        ws_height = Math.round( (thick_height-new_height)/2 );
+                    if (hscale_factor !== 1) {
+                        ctx.fillRect(f_start, cur_y_center + 1, f_end - f_start, ws_height);
+                        ctx.fillRect(f_start, cur_y_center + thick_height - ws_height + 1, f_end - f_start, ws_height);
+                    }   
+                }                
             }
             
+            // Reset alpha so that label is not transparent.
+            ctx.globalAlpha = 1;
+                        
             // Draw label for Pack mode.
             if (mode === "Pack" && feature_start > tile_low) {
                 ctx.fillStyle = label_color;
@@ -4276,8 +4315,8 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
 });
 
 
-var VariantPainter = function(data, view_start, view_end, prefs, mode, alpha_generator) {
-    FeaturePainter.call(this, data, view_start, view_end, prefs, mode, alpha_generator);
+var VariantPainter = function(data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler) {
+    FeaturePainter.call(this, data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler);
 }
 
 extend(VariantPainter.prototype, FeaturePainter.prototype, {
@@ -4334,8 +4373,8 @@ extend(VariantPainter.prototype, FeaturePainter.prototype, {
     }
 });
 
-var ReadPainter = function(data, view_start, view_end, prefs, mode, alpha_generator, ref_seq) {
-    FeaturePainter.call(this, data, view_start, view_end, prefs, mode, alpha_generator);
+var ReadPainter = function(data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler, ref_seq) {
+    FeaturePainter.call(this, data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler);
     this.ref_seq = ref_seq;
 };
 
@@ -4624,7 +4663,7 @@ extend(ReadPainter.prototype, FeaturePainter.prototype, {
     }
 });
 
-exports.AlphaGenerator = AlphaGenerator;
+exports.Scaler = Scaler;
 exports.SummaryTreePainter = SummaryTreePainter;
 exports.LinePainter = LinePainter;
 exports.LinkedFeaturePainter = LinkedFeaturePainter;

From a2eb4594c81316d0c48643e954233e2156927c75 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Mon, 17 Oct 2011 16:03:47 -0400
Subject: [PATCH 064/362] Fix Trackster bug that prevented differences from
 being displayed in mapped reads.

---
 static/scripts/packed/trackster.js | 2 +-
 static/scripts/trackster.js        | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/static/scripts/packed/trackster.js b/static/scripts/packed/trackster.js
index 1c3e0409caf..d759f8f88cf 100644
--- a/static/scripts/packed/trackster.js
+++ b/static/scripts/packed/trackster.js
@@ -1 +1 @@
-var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var trackster_module=function(f,Z){var q=f("class").extend,t=f("slotting"),N=f("painters");var ag=function(ah,ai){this.document=ah;this.default_font=ai!==undefined?ai:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};q(ag.prototype,{load_pattern:function(ah,al){var ai=this.patterns,aj=this.dummy_context,ak=new Image();ak.src=image_path+al;ak.onload=function(){ai[ah]=aj.createPattern(ak,"repeat")}},get_pattern:function(ah){return this.patterns[ah]},new_canvas:function(){var ah=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ah)}ah.manager=this;return ah}});var o={};var m=function(ah,ai){o[ah.attr("id")]=ai};var n=function(ah,aj,al,ak){al=".group";var ai={};o[ah.attr("id")]=ak;ah.bind("drag",{handle:"."+aj,relative:true},function(au,av){var at=$(this);var ay=$(this).parent(),ap=ay.children(),ar=o[$(this).attr("id")],ao,an,aw,am,aq;an=$(this).parents(al);if(an.length!==0){aw=an.position().top;am=aw+an.outerHeight();if(av.offsetY<aw){$(this).insertBefore(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable_before(ar,ax);return}else{if(av.offsetY>am){$(this).insertAfter(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable(ar);return}}}an=null;for(aq=0;aq<ap.length;aq++){ao=$(ap.get(aq));aw=ao.position().top;am=aw+ao.outerHeight();if(ao.is(al)&&this!==ao.get(0)&&av.offsetY>=aw&&av.offsetY<=am){if(av.offsetY-aw<am-av.offsetY){ao.find(".content-div").prepend(this)}else{ao.find(".content-div").append(this)}if(ar.container){ar.container.remove_drawable(ar)}o[ao.attr("id")].add_drawable(ar);return}}for(aq=0;aq<ap.length;aq++){if(av.offsetY<$(ap.get(aq)).position().top){break}}if(aq===ap.length){if(this!==ap.get(aq-1)){ay.append(this);o[ay.attr("id")].move_drawable(ar,aq)}}else{if(this!==ap.get(aq)){$(this).insertBefore(ap.get(aq));o[ay.attr("id")].move_drawable(ar,(av.deltaY>0?aq-1:aq))}}}).bind("dragstart",function(){ai["border-top"]=ah.css("border-top");ai["border-bottom"]=ah.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ai)})};Z.moveable=n;var af=16,I=9,F=20,U=I+2,A=100,K=12000,S=200,D=5,w=10,M=5000,x=100,p="There was an error in indexing this dataset. ",L="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",u="Currently indexing... please wait",y="Tool cannot be rerun: ",a="Loading data...",aa="Ready for display",d=10,v=5,C=5;function ab(ai,ah){if(!ah){ah=0}var aj=Math.pow(10,ah);return Math.round(ai*aj)/aj}var c=function(ah){this.num_elements=ah;this.clear()};q(c.prototype,{get:function(ai){var ah=this.key_ary.indexOf(ai);if(ah!==-1){if(this.obj_cache[ai].stale){this.key_ary.splice(ah,1);delete this.obj_cache[ai]}else{this.move_key_to_end(ai,ah)}}return this.obj_cache[ai]},set:function(ai,aj){if(!this.obj_cache[ai]){if(this.key_ary.length>=this.num_elements){var ah=this.key_ary.shift();delete this.obj_cache[ah]}this.key_ary.push(ai)}this.obj_cache[ai]=aj;return aj},move_key_to_end:function(ai,ah){this.key_ary.splice(ah,1);this.key_ary.push(ai)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var T=function(ai,ah,aj){c.call(this,ai);this.track=ah;this.subset=(aj!==undefined?aj:true)};q(T.prototype,c.prototype,{load_data:function(aq,al,ao,ai,an){var ap=this.track.view.chrom,ak={chrom:ap,low:aq,high:al,mode:ao,resolution:ai,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ak,an);if(this.track.filters_manager){var ar=[];var ah=this.track.filters_manager.filters;for(var am=0;am<ah.length;am++){ar[ar.length]=ah[am].name}ak.filter_cols=JSON.stringify(ar)}var aj=this;return $.getJSON(this.track.data_url,ak,function(at){aj.set_data(aq,al,ao,at)})},get_data:function(ah,al,am,ai,ak){var aj=this.get_data_from_cache(ah,al,am);if(aj){return aj}aj=this.load_data(ah,al,am,ai,ak);this.set_data(ah,al,am,aj);return aj},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ap,ak,ao,aj,an,al){var aq=this.get_data_from_cache(ap,ak,ao);if(!aq){console.log("ERROR: no current data for: ",this.track,ap,ak,ao,aj,an);return}aq.stale=true;var ai=ap;if(al===this.DEEP_DATA_REQ){$.extend(an,{start_val:aq.data.length+1})}else{if(al===this.BROAD_DATA_REQ){ai=(aq.max_high?aq.max_high:aq.data[aq.data.length-1][2])+1}}var ah=this,am=this.load_data(ai,ak,ao,aj,an);new_data_available=$.Deferred();this.set_data(ap,ak,ao,new_data_available);$.when(am).then(function(ar){if(ar.data){ar.data=aq.data.concat(ar.data);if(ar.max_low){ar.max_low=aq.max_low}if(ar.message){ar.message=ar.message.replace(/[0-9]+/,ar.data.length)}}ah.set_data(ap,ak,ao,ar);new_data_available.resolve(ar)});return new_data_available},get_data_from_cache:function(ah,ai,aj){return this.get(this.gen_key(ah,ai,aj))},set_data:function(ai,aj,ak,ah){return this.set(this.gen_key(ai,aj,ak),ah)},gen_key:function(ah,aj,ak){var ai=ah+"_"+aj+"_"+ak;return ai},split_key:function(ah){return ah.split("_")}});var J=function(ai,ah,aj){T.call(this,ai,ah,aj)};q(J.prototype,T.prototype,c.prototype,{load_data:function(aj,ah,al,am,ai,ak){if(ai>1){return}return T.prototype.load_data.call(this,aj,ah,al,am,ai,ak)}});var r=function(ak,ai,ah,aj,al){this.name=ak;this.view=ai;this.container=ah;this.drag_handle_class=al;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak}],saved_values:aj,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values};q(r.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},make_name_popup_menu:function(){},set_name:function(ah){this.old_name=this.name;this.name=ah;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var z=function(al,ak,ai,ah,aj,am){r.call(this,ak,ai,ah,aj,am);this.obj_type=al;this.drawables=[]};q(z.prototype,r.prototype,{init:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah].init()}},_draw:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah]._draw()}},to_json:function(){var ai=[];for(var ah=0;ah<this.drawables.length;ah++){ai.push(this.drawables[ah].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ai}},add_drawable:function(ah){this.drawables.push(ah);ah.container=this},add_drawable_before:function(aj,ah){var ai=this.drawables.indexOf(ah);if(ai!=-1){this.drawables.splice(ai,0,aj);return true}return false},remove_drawable:function(ai){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);ai.container=null;return true}return false},move_drawable:function(ai,aj){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);this.drawables.splice(aj,0,ai);return true}return false}});var R=function(ak,ai,ah,aj){z.call(this,"DrawableGroup",ak,ai,ah,aj,"group-handle");if(!R.id_counter){R.id_counter=0}var al=R.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+al).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+al+"_content_div").appendTo(this.container_div);m(this.container_div,this);m(this.content_div,this);n(this.container_div,this.drag_handle_class,".group",this);this.make_name_popup_menu()};q(R.prototype,r.prototype,z.prototype,{make_name_popup_menu:function(){var ai=this;var ah={};ah["Edit configuration"]=function(){var al=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aj=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(am){if((am.keyCode||am.which)===27){al()}else{if((am.keyCode||am.which)===13){aj()}}};$(window).bind("keypress.check_enter_esc",ak);show_modal("Configure Group",ai.config.build_form(),{Cancel:al,OK:aj})};ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)}});var ae=function(ah,ak,aj,ai){z.call(this,"View");this.container=ah;this.chrom=null;this.vis_id=aj;this.dbkey=ai;this.title=ak;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ag(ah.get(0).ownerDocument);this.reset()};q(ae.prototype,z.prototype,{init:function(){var aj=this.container,ah=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aj);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;m(this.viewport_container,ah);this.intro_div=$("<div/>").addClass("intro");var ak=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ai=function(al){if(al.type==="focusout"||(al.keyCode||al.which)===13||(al.keyCode||al.which)===27){if((al.keyCode||al.which)!==27){ah.go_to($(this).val())}$(this).hide();$(this).val("");ah.location_span.show();ah.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ai).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ah.location_span.hide();ah.chrom_select.hide();ah.nav_input.val(ah.chrom+":"+ah.low+"-"+ah.high);ah.nav_input.css("display","inline-block");ah.nav_input.select();ah.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ah.zoom_out();ah.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.browser_content_div.click(function(al){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("<div />").css({height:ah.browser_content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,{content_div:this.top_labeltrack}));this.add_label_track(new ad(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new B(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(am,ai,ao){if(!am||am==="None"){return}var aj=this;if(am==="previous"){aj.load_chroms({low:this.chrom_start_index-x});return}if(am==="next"){aj.load_chroms({low:this.chrom_start_index+x});return}var an=$.grep(aj.chrom_data,function(ap,aq){return ap.chrom===am})[0];if(an===undefined){aj.load_chroms({chrom:am},function(){aj.change_chrom(am,ai,ao)});return}else{if(am!==aj.chrom){aj.chrom=am;aj.chrom_select.val(aj.chrom);aj.max_high=an.len-1;aj.reset();aj.request_redraw(true);for(var al=0,ah=aj.drawables.length;al<ah;al++){var ak=aj.drawables[al];if(ak.init){ak.init()}}}if(ai!==undefined&&ao!==undefined){aj.low=Math.max(ai,0);aj.high=Math.min(ao,aj.max_high)}aj.reset_overview();aj.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){z.prototype.add_drawable.call(this,ah);ah.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;ah.init();this.label_tracks.push(ah)},remove_drawable:function(aj,ai){z.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.drawables),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(D,Math.ceil(Math.log((this.high-this.low)/S)/Math.log(D)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){$.when(ah.get_overview_tile()).then(function(ai){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ai.canvas);view.overview_highlight.show().height(ai.canvas.height());view.overview_viewport.height(ai.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ah;ah.set_is_overview(true)});view.has_changes=true},reset_overview:function(){this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new P(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},al=this.track,aj=ai.tool_id+al.tool_region_and_parameters_str(ai.chrom,ai.low,ai.high),ah,am;if(al.container===view){var ak=new R(this.name,this.track.view,this.track.container);al.container.add_drawable(ak);al.container.remove_drawable(al);ak.add_drawable(al);al.container_div.appendTo(ak.content_div);ah=ak}else{ah=al.container}if(al instanceof e){am=new W(aj,view,ah,"hda");am.change_mode(al.mode);ah.add_drawable(am)}am.content_div.text("Starting job.");this.run(ai,am,function(an){am.dataset_id=an.dataset_id;am.content_div.text("Running job.");am.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(L)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(y+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var P=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){P.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var X=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};q(X.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=ah[this.index];return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(at,aA){this.track=at;this.filters=[];for(var av=0;av<aA.length;av++){var aw=aA[av],aB=aw.name,ah=aw.type,aj=aw.index,az=aw.tool_id,ay=aw.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[av]=new X(aB,aj,az,ay)}else{console.log("ERROR: unsupported filter: ",aB,ah)}}var ak=function(aC,aD,aE){aC.click(function(){var aF=aD.text();max=parseFloat(aE.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aE.slider("option","values")){input_size=2*input_size+1;multi_value=true}aD.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aF).appendTo(aD).focus().select().click(function(aG){aG.stopPropagation()}).blur(function(){$(this).remove();aD.text(aF)}).keyup(function(aK){if(aK.keyCode===27){$(this).trigger("blur")}else{if(aK.keyCode===13){var aI=aE.slider("option","min"),aG=aE.slider("option","max"),aJ=function(aL){return(isNaN(aL)||aL>aG||aL<aI)},aH=$(this).val();if(!multi_value){aH=parseFloat(aH);if(aJ(aH)){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}else{aH=aH.split("-");aH=[parseFloat(aH[0]),parseFloat(aH[1])];if(aJ(aH[0])||aJ(aH[1])){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}aE.slider((multi_value?"values":"value"),aH)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aC){aC.stopPropagation()}).click(function(aC){aC.stopPropagation()}).bind("dblclick",function(aC){aC.stopPropagation()}).bind("keydown",function(aC){aC.stopPropagation()});var ax=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aF,aH){aH.container=$("<div/>").addClass("filter-row slider-row").appendTo(ax);var aG=$("<div/>").addClass("elt-label").appendTo(aH.container);var aE=$("<span/>").addClass("slider-name").text(aH.name+"  ").appendTo(aG);var aD=$("<span/>");var aJ=$("<span/>").addClass("slider-value").appendTo(aG).append("[").append(aD).append("]");var aC=$("<div/>").addClass("slider").appendTo(aH.container);aH.control_element=$("<div/>").attr("id",aH.name+"-filter-control").appendTo(aC);var aI=[0,0];aH.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aL,aM){var aK=aM.values;aD.text(aK[0]+"-"+aK[1]);aH.low=aK[0];aH.high=aK[1];ap.track.request_draw(true,true)},change:function(aK,aL){aH.control_element.slider("option","slide").call(aH.control_element,aK,aL)}});aH.slider=aH.control_element;aH.slider_label=aD;ak(aJ,aD,aH.control_element);$("<div style='clear: both;'/>").appendTo(aH.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(ax);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var ai=this;ao.click(function(){ai.run_on_dataset()})}var ar=$("<div/>").addClass("display-controls").appendTo(this.parent_div),au,an,aq,al={Transparency:function(aC){ap.alpha_filter=aC},Height:function(aC){ap.height_filter=aC}};$.each(al,function(aE,aD){au=$("<div/>").addClass("filter-row").appendTo(ar),an=$("<span/>").addClass("elt-label").text(aE+":").appendTo(au),aq=$("<select/>").attr("name",aE+"_dropdown").css("float","right").appendTo(au);$("<option/>").attr("value",-1).text("== None ==").appendTo(aq);for(var aC=0;aC<ap.filters.length;aC++){$("<option/>").attr("value",aC).text(ap.filters[aC].name).appendTo(aq)}aq.change(function(){$(this).children("option:selected").each(function(){var aF=parseInt($(this).val());al[aE]((aF>=0?ap.filters[aF]:null));ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(au)});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var E=function(ah,ai){N.Scaler.call(this,ai);this.filter=ah};E.prototype.gen_val=function(ah){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var H=function(ah){this.track=ah.track;this.params=ah.params;this.values={};this.restore_values((ah.saved_values?ah.saved_values:{}));this.onchange=ah.onchange};q(H.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(ah,ak,aj,ai,al){this.track=ah;this.index=ak;this.low=ak*S*aj;this.high=(ak+1)*S*aj;this.resolution=aj;this.canvas=$("<div class='track-tile'/>").append(ai);this.data=al;this.stale=false};b.prototype.predisplay_actions=function(){};var l=function(ah,ak,aj,ai,al,am){b.call(this,ah,ak,aj,ai,al);this.max_val=am};q(l.prototype,b.prototype);var Q=function(ah,al,ak,aj,an,ao,am,ai){b.call(this,ah,al,ak,aj,an);this.mode=ao;this.message=am;this.feature_mapper=ai};q(Q.prototype,b.prototype);Q.prototype.predisplay_actions=function(){var ai=this,ah={};if(ai.mode!=="Pack"){return}$(this.canvas).mousemove(function(au){var ao=$(this).offset(),at=au.pageX-ao.left,ar=au.pageY-ao.top,ay=ai.feature_mapper.get_feature_data(at,ar),ap=(ay?ay[0]:null);$(this).siblings(".feature-popup").each(function(){if(!ap||$(this).attr("id")!==ap.toString()){$(this).remove()}});if(ay){var ak=ah[ap];if(!ak){var ap=ay[0],av={name:ay[3],start:ay[1],end:ay[2],strand:ay[4]},an=ai.track.filters_manager.filters,am;for(var aq=0;aq<an.length;aq++){am=an[aq];av[am.name]=ay[am.index]}var ak=$("<div/>").attr("id",ap).addClass("feature-popup"),ax,aw,az=$("<table/>").appendTo(ak),aA;for(ax in av){aw=av[ax];aA=$("<tr/>").appendTo(az);$("<th/>").appendTo(aA).text(ax);$("<td/>").attr("align","left").appendTo(aA).text(typeof(aw)=="number"?ab(aw,2):aw)}ah[ap]=ak}ak.appendTo($(ai.canvas).parent());var al=at+parseInt(ai.canvas.css("left"))+7,aj=ar+parseInt(ai.canvas.css("top"))+7;ak.css("left",al+"px").css("top",aj+"px")}else{if(!au.isPropagationStopped()){au.stopPropagation();$(this).siblings().each(function(){$(this).trigger(au)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var j=function(ak,ai,ah,aj,al,am){r.call(this,ak,ai,ah,{},"draghandle");this.data_url=(al?al:default_data_url);this.data_url_extra_params={};this.data_query_wait=(am?am:M);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.container_div=$("<div />").addClass("track").attr("id","track_"+j.id_counter++).css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Y){return"ReadTrack"}else{if(this instanceof W){return"ToolDataFeatureTrack"}else{if(this instanceof V){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(L)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(G)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.make_name_popup_menu()}ah.content_div.text(aa);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}})},predraw_init:function(){},});var O=function(ao,am){var ai=this,ap=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=new ac(this,(ao!==undefined?ao:{}));this.filters_available=false;this.filters_visible=false;this.tool=(am!==undefined&&obj_length(am)>0?new s(this,am):undefined);this.is_overview=false;if(ai.hidden){return}if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(ai.display_modes!==undefined){if(ai.mode_div===undefined){ai.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ai.header_div);var aj=(ai.config&&ai.config.values.mode?ai.config.values.mode:ai.display_modes[0]);ai.mode=aj;ai.mode_div.text(aj);var ah={};for(var ak=0,an=ai.display_modes.length;ak<an;ak++){var al=ai.display_modes[ak];ah[al]=function(aq){return function(){ai.change_mode(aq)}}(al)}make_popupmenu(ai.mode_div,ah)}else{ai.mode_div.hide()}}this.make_name_popup_menu()};q(O.prototype,r.prototype,j.prototype,{to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw();return ah},make_name_popup_menu:function(){var ai=this;var ah={};ah[(this.is_overview?"Hide overview":"Set as overview")]=function(){if(ai.is_overview){ai.view.reset_overview()}else{ai.view.set_overview(ai)}};ah["Edit configuration"]=function(){var am=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},al=function(an){if((an.keyCode||an.which)===27){am()}else{if((an.keyCode||an.which)===13){ak()}}};$(window).bind("keypress.check_enter_esc",al);show_modal("Configure Track",ai.config.build_form(),{Cancel:am,OK:ak})};if(ai.filters_available>0){var aj=(ai.filters_div.is(":visible")?"Hide filters":"Show filters");ah[aj]=function(){ai.filters_visible=(ai.filters_div.is(":visible"));if(ai.filters_visible){ai.filters_manager.reset_filters()}ai.filters_div.toggle();ai.make_name_popup_menu()}}if(ai.tool){var aj=(ai.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");ah[aj]=function(){if(!ai.dynamic_tool_div.is(":visible")){ai.set_name(ai.name+ai.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ai.revert_name()}ai.dynamic_tool_div.toggle();ai.make_name_popup_menu()}}ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)},set_is_overview:function(ah){this.is_overview=ah;this.make_name_popup_menu()},get_overview_tile:function(){var ah=this;view=ah.view,resolution=Math.pow(D,Math.ceil(Math.log((view.max_high-view.max_low)/S)/Math.log(D))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ah.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ah.data_url_extra_params)).then(function(ai){var ak=ah._gen_tile_cache_key(view_width,w_scale,0),am=ah.tile_cache.get(ak);if(!am){am=ah.draw_tile(ai,"Auto",resolution,0,w_scale);ah.tile_cache.set(ak,am)}var ap=$(am.canvas.find("canvas")),al=ap.clone(),ao=ap.get(0).getContext("2d"),aj=al.get(0).getContext("2d"),an=ao.getImageData(0,0,ao.canvas.width,ao.canvas.height);aj.putImageData(an,-ah.left_offset,(am.data.dataset_type==="summary_tree"?U:0));new_tile=new b(ah,-1,resolution,al);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof B)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/S);var ap=true;var at=[];var ah=0;while((ai*S*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",F)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*S*an,ax=ap+S*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);if(aq!==undefined){al.tile_cache.set(at,aq);al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw()});return null},show_tile:function(ao,aq,ar){var aj=this,ai=ao.canvas,an=ai;if(ao.message){var at=$("<div/>"),ap=$("<div/>").addClass("tile-message").text(ao.message).css({height:F-1,width:ao.canvas.width}).appendTo(at),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ap),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ap);at.append(ai);an=at;al.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()});ah.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()})}ao.predisplay_actions();var am=this.view.high-this.view.low,ak=(ao.low-this.view.low)*ar;if(this.left_offset){ak-=this.left_offset}an.css({position:"absolute",top:0,left:ak,height:""});aq.append(an);aj.max_height=Math.max(aj.max_height,an.height());aj.content_div.css("height",aj.max_height+"px");aq.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*S*ai,al=S*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ai,ah){this.hidden=true;j.call(this,"label",ai,ah,{});this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{init:function(){this.enabled=true},_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var B=function(ah){this.hidden=true;j.call(this,"reference",ah,{content_div:ah.top_labeltrack},{});O.call(this);ah.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ah.dbkey};this.data_manager=new J(C,this,false);this.tile_cache=new c(v)};q(B.prototype,r.prototype,O.prototype,{init:function(){this.enabled=true},draw_tile:function(ar,an,am,ai,at){var al=this,aj=S*am;if(at>this.view.canvas_manager.char_width_px){if(ar===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(al,ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(am,ak,aj,an,ah,al){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,am,ak,aj,al);O.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=an;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new T(C,this);this.tile_cache=new c(v);this.left_offset=0;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:am},{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:al,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.dataset_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.dataset_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};q(k.prototype,r.prototype,O.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this;ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(ai){ah.container_div.addClass("line-track");var ak=ai.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=ak.min;ah.prefs.max_value=ak.max;$("#track_"+ah.dataset_id+"_minval").val(ah.prefs.min_value);$("#track_"+ah.dataset_id+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=ak.total_frequency;ah.container_div.find(".yaxislabel").remove();var al=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_minval").text(ab(ah.prefs.min_value,3));var aj=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_maxval").text(ab(ah.prefs.max_value,3));aj.css({position:"absolute",top:"24px",left:"10px"});aj.prependTo(ah.container_div);al.css({position:"absolute",bottom:"2px",left:"10px"});al.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new N.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(this.track,aj,al,ak,au.data)}});var e=function(ah,an,ai,am,ap,ao,ak,al){var aj=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];j.call(this,ah,an,ai,ao);O.call(this,ak,al);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){aj.set_name(aj.prefs.name);aj.tile_cache.clear();aj.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=am;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new T(20,this);this.left_offset=200;this.painter=N.LinkedFeaturePainter};q(e.prototype,r.prototype,O.prototype,{postdraw_actions:function(ax,ah,ay,aw){O.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.make_name_popup_menu()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",A,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aD,aH,ar,ak){var aA=this,am=aA._get_tile_bounds(aH,aD),aK=am[0],ai=am[1],ay=ai-aK,aB=Math.ceil(ay*ar),aQ=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"){az="no_detail"}else{var aP=aw.data;if(this.view.high-this.view.low>K){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aB+al;aj.height=an+U;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aK,ai,200);if(aw.max){at.max=aw.max}aw=at}var aM=new N.SummaryTreePainter(aw,aK,ai,this.prefs);var aC=aj.getContext("2d");aC.translate(al,U);aM.draw(aC,aB,an);return new l(aA,aH,aD,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aE=0,aG=aw.data.length;aE<aG;aE++){var ao=aw.data[aE];var aF=false;var av;for(var aJ=0,aO=au.length;aJ<aO;aJ++){av=au[aJ];av.update_attrs(ao);if(!av.keep(ao)){aF=true;break}}if(!aF){aq.push(ao)}}}var aN=(this.filters_manager.alpha_filter?new E(this.filters_manager.alpha_filter):null);var aL=(this.filters_manager.height_filter?new E(this.filters_manager.height_filter):null);var aM=new (this.painter)(aq,aK,ai,this.prefs,az,aN,aL,ak);var an=Math.max(af,aM.get_required_height(ap));var aj=this.view.canvas_manager.new_canvas();var aI=null;aj.width=aB+al;aj.height=an;var aC=aj.getContext("2d");aC.fillStyle=this.prefs.block_color;aC.font=aC.canvas.manager.default_font;aC.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aw.data){aC.translate(al,0);aI=aM.draw(aC,aB,an,ax);aI.translation=-al}return new Q(aA,aH,aD,aj,aw.data,az,aw.message,aI)}});var V=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.painter=N.VariantPainter};q(V.prototype,r.prototype,O.prototype,e.prototype);var Y=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ak,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=N.ReadPainter;this.make_name_popup_menu()};q(Y.prototype,r.prototype,O.prototype,e.prototype);var W=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am,{});this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};q(W.prototype,r.prototype,O.prototype,e.prototype,{predraw_init:function(){var ai=this;var ah=function(){if(ai.data_manager.size()===0){setTimeout(ah,300)}else{ai.data_url=default_data_url;ai.data_query_wait=M;ai.dataset_state_url=converted_datasets_state_url;$.getJSON(ai.dataset_state_url,{dataset_id:ai.dataset_id,hda_ldda:ai.hda_ldda},function(aj){})}};ah()}});Z.View=ae;Z.DrawableGroup=R;Z.LineTrack=k;Z.FeatureTrack=e;Z.ReadTrack=Y};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(k,y){var v=k("class").extend;var q=function(J,B,H,A,G,E){if(E===undefined){E=4}var D=A-B;var C=G-H;var F=Math.floor(Math.sqrt(D*D+C*C)/E);var K=D/F;var I=C/F;var z;for(z=0;z<F;z++,B+=K,H+=I){if(z%2!==0){continue}J.fillRect(B,H,E,1)}};var r=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var e=function(z){this.default_val=(z?z:1)};e.prototype.gen_val=function(z){return this.default_val};var n=function(B,D,z,A,C){this.data=B;this.view_start=D;this.view_end=z;this.prefs=v({},this.default_prefs,A);this.mode=C};n.prototype.default_prefs={};var w=function(B,D,z,A,C){n.call(this,B,D,z,A,C)};w.prototype.default_prefs={show_counts:false};w.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var c=function(z,D,F,G,B){n.call(this,z,D,F,G,B);if(this.prefs.min_value===undefined){var H=Infinity;for(var A=0,C=this.data.length;A<C;A++){H=Math.min(H,this.data[A][1])}this.prefs.min_value=H}if(this.prefs.max_value===undefined){var E=-Infinity;for(var A=0,C=this.data.length;A<C;A++){E=Math.max(E,this.data[A][1])}this.prefs.max_value=E}};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var o=function(z){this.feature_positions={};this.slot_height=z;this.translation=0};o.prototype.map_feature_data=function(A,C,z,B){if(!this.feature_positions[C]){this.feature_positions[C]=[]}this.feature_positions[C].push({data:A,x_start:z,x_end:B})};o.prototype.get_feature_data=function(z,D){var C=Math.floor(D/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var p=function(B,E,z,A,D,F,C){n.call(this,B,E,z,A,D);this.alpha_scaler=(F?F:new e());this.height_scaler=(C?C:new e())};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};v(p.prototype,{get_required_height:function(A){var z=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){z=A*y_scale}return z+Math.max(Math.round(y_scale/2),5)},draw:function(L,J,H,G){var R=this.data,E=this.view_start,N=this.view_end;L.save();L.fillStyle=this.prefs.block_color;L.textAlign="right";var I=this.view_end-this.view_start,F=J/I,M=this.get_row_height(),Q=new o(M),C;for(var O=0,P=R.length;O<P;O++){var B=R[O],D=B[0],K=B[1],z=B[2],A=(G&&G[D]!==undefined?G[D]:null);if((K<N&&z>E)&&(this.mode=="Dense"||A!==null)){C=this.draw_element(L,this.mode,B,A,E,N,F,M,J);Q.map_feature_data(B,A,C[0],C[1])}}L.restore();return Q},draw_element:function(F,B,H,D,C,E,G,A,z){console.log("WARNING: Unimplemented function.");return[0,0]}});var d=10,j=3,m=5,x=10,g=1,t=3,f=3,a=9,l=2,h="#ccc";var s=function(B,E,z,A,D,F,C){p.call(this,B,E,z,A,D,F,C)};v(s.prototype,p.prototype,{get_row_height:function(){var A=this.mode,z;if(A==="Dense"){z=d}else{if(A==="no_detail"){z=j}else{if(A==="Squish"){z=m}else{z=x}}}return z},draw_element:function(N,E,W,I,P,ah,al,an,z){var T=W[0],aj=W[1],ab=W[2],R=W[3],ac=Math.floor(Math.max(0,(aj-P)*al)),O=Math.ceil(Math.min(z,Math.max(0,(ab-P)*al))),aa=ac,am=O,Z=(E==="Dense"?0:(0+I))*an,M,af,S=null,ap=null,C=this.prefs.block_color,ae=this.prefs.label_color;N.globalAlpha=this.alpha_scaler.gen_val(W);if(E=="Dense"){I=1}if(E==="no_detail"){N.fillStyle=C;N.fillRect(ac,Z+5,O-ac,g)}else{var L=W[4],Y=W[5],ad=W[6],D=W[7];if(Y&&ad){S=Math.floor(Math.max(0,(Y-P)*al));ap=Math.ceil(Math.min(z,Math.max(0,(ad-P)*al)))}var ak,U;if(E==="Squish"||E==="Dense"){ak=1;U=f}else{ak=5;U=a}if(!D){if(W.strand){if(W.strand==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand_inv")}else{if(W.strand==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand_inv")}}}else{N.fillStyle=C}N.fillRect(ac,Z,O-ac,U)}else{var K,V;if(E==="Squish"||E==="Dense"){N.fillStyle=h;K=Z+Math.floor(f/2)+1;V=1}else{if(L){var K=Z;var V=U;if(L==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand")}else{if(L==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand")}}}else{N.fillStyle=h;K+=(f/2)+1;V=1}}N.fillRect(ac,K,O-ac,V);var F;for(var ai=0,B=D.length;ai<B;ai++){var G=D[ai],A=Math.floor(Math.max(0,(G[0]-P)*al)),X=Math.ceil(Math.min(z,Math.max((G[1]-P)*al)));if(A>X){continue}N.fillStyle=C;N.fillRect(A,Z+(U-ak)/2+1,X-A,ak);if(S!==undefined&&ad>Y&&!(A>ap||X<S)){var ag=Math.max(A,S),J=Math.min(X,ap);N.fillRect(ag,Z+1,J-ag,U);if(D.length==1&&E=="Pack"){if(L==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand_inv")}else{if(L==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand_inv")}}if(ag+14<J){ag+=2;J-=2}N.fillRect(ag,Z+1,J-ag,U)}}}if(E==="Pack"){N.globalAlpha=1;N.fillStyle="white";var H=this.height_scaler.gen_val(W),Q=Math.ceil(U*H),ao=Math.round((U-Q)/2);if(H!==1){N.fillRect(ac,K+1,O-ac,ao);N.fillRect(ac,K+U-ao+1,O-ac,ao)}}}N.globalAlpha=1;if(E==="Pack"&&aj>P){N.fillStyle=ae;if(P===0&&ac-N.measureText(R).width<0){N.textAlign="left";N.fillText(R,O+l,Z+8);am+=N.measureText(R).width+l}else{N.textAlign="right";N.fillText(R,ac-l,Z+8);aa-=N.measureText(R).width+l}}}N.globalAlpha=1;return[aa,am]}});var b=function(B,E,z,A,D,F,C){p.call(this,B,E,z,A,D,F,C)};v(b.prototype,p.prototype,{draw_element:function(S,N,H,D,V,B,K,T,Q){var H=data[i],J=H[0],R=H[1],C=H[2],M=H[3],F=Math.floor(Math.max(0,(R-V)*K)),I=Math.ceil(Math.min(Q,Math.max(0,(C-V)*K))),E=(N==="Dense"?0:(0+D))*T,z,W,A=null,L=null;if(no_label){S.fillStyle=block_color;S.fillRect(F+left_offset,E+5,I-F,1)}else{var U=H[4],P=H[5],G=H[6];z=9;W=1;S.fillRect(F+left_offset,E,I-F,z);if(N!=="Dense"&&M!==undefined&&R>V){S.fillStyle=label_color;if(V===0&&F-S.measureText(M).width<0){S.textAlign="left";S.fillText(M,I+2+left_offset,E+8)}else{S.textAlign="right";S.fillText(M,F-2+left_offset,E+8)}S.fillStyle=block_color}var O=U+" / "+P;if(R>V&&S.measureText(O).width<(I-F)){S.fillStyle="white";S.textAlign="center";S.fillText(O,left_offset+F+(I-F)/2,E+8);S.fillStyle=block_color}}return[F,I]}});var u=function(C,F,z,B,E,G,D,A){p.call(this,C,F,z,B,E,G,D);this.ref_seq=A};u.prototype.default_prefs=v({},p.prototype.default_prefs,{show_insertions:false});v(u.prototype,p.prototype,{get_row_height:function(){var z,A=this.mode;if(A==="Dense"){z=d}else{if(A==="Squish"){z=m}else{z=x;if(this.prefs.show_insertions){z*=2}}}return z},draw_read:function(V,Q,M,aa,B,U,J,G,F){V.textAlign="center";var T=this,A=[aa,B],P=0,W=0,S=0;ref_seq=this.ref_seq,char_width_px=V.canvas.manager.char_width_px;var 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Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",u="Currently indexing... please wait",y="Tool cannot be rerun: ",a="Loading data...",aa="Ready for display",d=10,v=5,C=5;function ab(ai,ah){if(!ah){ah=0}var aj=Math.pow(10,ah);return Math.round(ai*aj)/aj}var c=function(ah){this.num_elements=ah;this.clear()};q(c.prototype,{get:function(ai){var ah=this.key_ary.indexOf(ai);if(ah!==-1){if(this.obj_cache[ai].stale){this.key_ary.splice(ah,1);delete this.obj_cache[ai]}else{this.move_key_to_end(ai,ah)}}return this.obj_cache[ai]},set:function(ai,aj){if(!this.obj_cache[ai]){if(this.key_ary.length>=this.num_elements){var ah=this.key_ary.shift();delete this.obj_cache[ah]}this.key_ary.push(ai)}this.obj_cache[ai]=aj;return aj},move_key_to_end:function(ai,ah){this.key_ary.splice(ah,1);this.key_ary.push(ai)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var 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ai=ap;if(al===this.DEEP_DATA_REQ){$.extend(an,{start_val:aq.data.length+1})}else{if(al===this.BROAD_DATA_REQ){ai=(aq.max_high?aq.max_high:aq.data[aq.data.length-1][2])+1}}var ah=this,am=this.load_data(ai,ak,ao,aj,an);new_data_available=$.Deferred();this.set_data(ap,ak,ao,new_data_available);$.when(am).then(function(ar){if(ar.data){ar.data=aq.data.concat(ar.data);if(ar.max_low){ar.max_low=aq.max_low}if(ar.message){ar.message=ar.message.replace(/[0-9]+/,ar.data.length)}}ah.set_data(ap,ak,ao,ar);new_data_available.resolve(ar)});return new_data_available},get_data_from_cache:function(ah,ai,aj){return this.get(this.gen_key(ah,ai,aj))},set_data:function(ai,aj,ak,ah){return this.set(this.gen_key(ai,aj,ak),ah)},gen_key:function(ah,aj,ak){var ai=ah+"_"+aj+"_"+ak;return ai},split_key:function(ah){return ah.split("_")}});var J=function(ai,ah,aj){T.call(this,ai,ah,aj)};q(J.prototype,T.prototype,c.prototype,{load_data:function(aj,ah,al,am,ai,ak){if(ai>1){return}return 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aj=this.container,ah=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aj);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;m(this.viewport_container,ah);this.intro_div=$("<div/>").addClass("intro");var ak=$("<div/>").text("Add Datasets to 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focusout",ai).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ah.location_span.hide();ah.chrom_select.hide();ah.nav_input.val(ah.chrom+":"+ah.low+"-"+ah.high);ah.nav_input.css("display","inline-block");ah.nav_input.select();ah.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ah.zoom_out();ah.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.browser_content_div.click(function(al){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("<div />").css({height:ah.browser_content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,{content_div:this.top_labeltrack}));this.add_label_track(new ad(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new B(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(am,ai,ao){if(!am||am==="None"){return}var aj=this;if(am==="previous"){aj.load_chroms({low:this.chrom_start_index-x});return}if(am==="next"){aj.load_chroms({low:this.chrom_start_index+x});return}var an=$.grep(aj.chrom_data,function(ap,aq){return ap.chrom===am})[0];if(an===undefined){aj.load_chroms({chrom:am},function(){aj.change_chrom(am,ai,ao)});return}else{if(am!==aj.chrom){aj.chrom=am;aj.chrom_select.val(aj.chrom);aj.max_high=an.len-1;aj.reset();aj.request_redraw(true);for(var al=0,ah=aj.drawables.length;al<ah;al++){var ak=aj.drawables[al];if(ak.init){ak.init()}}}if(ai!==undefined&&ao!==undefined){aj.low=Math.max(ai,0);aj.high=Math.min(ao,aj.max_high)}aj.reset_overview();aj.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){z.prototype.add_drawable.call(this,ah);ah.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;ah.init();this.label_tracks.push(ah)},remove_drawable:function(aj,ai){z.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.drawables),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(D,Math.ceil(Math.log((this.high-this.low)/S)/Math.log(D)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){$.when(ah.get_overview_tile()).then(function(ai){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ai.canvas);view.overview_highlight.show().height(ai.canvas.height());view.overview_viewport.height(ai.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ah;ah.set_is_overview(true)});view.has_changes=true},reset_overview:function(){this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new P(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},al=this.track,aj=ai.tool_id+al.tool_region_and_parameters_str(ai.chrom,ai.low,ai.high),ah,am;if(al.container===view){var ak=new R(this.name,this.track.view,this.track.container);al.container.add_drawable(ak);al.container.remove_drawable(al);ak.add_drawable(al);al.container_div.appendTo(ak.content_div);ah=ak}else{ah=al.container}if(al instanceof e){am=new W(aj,view,ah,"hda");am.change_mode(al.mode);ah.add_drawable(am)}am.content_div.text("Starting job.");this.run(ai,am,function(an){am.dataset_id=an.dataset_id;am.content_div.text("Running job.");am.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(L)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(y+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var P=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){P.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var X=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};q(X.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=ah[this.index];return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(at,aA){this.track=at;this.filters=[];for(var av=0;av<aA.length;av++){var aw=aA[av],aB=aw.name,ah=aw.type,aj=aw.index,az=aw.tool_id,ay=aw.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[av]=new X(aB,aj,az,ay)}else{console.log("ERROR: unsupported filter: ",aB,ah)}}var ak=function(aC,aD,aE){aC.click(function(){var aF=aD.text();max=parseFloat(aE.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aE.slider("option","values")){input_size=2*input_size+1;multi_value=true}aD.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aF).appendTo(aD).focus().select().click(function(aG){aG.stopPropagation()}).blur(function(){$(this).remove();aD.text(aF)}).keyup(function(aK){if(aK.keyCode===27){$(this).trigger("blur")}else{if(aK.keyCode===13){var aI=aE.slider("option","min"),aG=aE.slider("option","max"),aJ=function(aL){return(isNaN(aL)||aL>aG||aL<aI)},aH=$(this).val();if(!multi_value){aH=parseFloat(aH);if(aJ(aH)){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}else{aH=aH.split("-");aH=[parseFloat(aH[0]),parseFloat(aH[1])];if(aJ(aH[0])||aJ(aH[1])){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}aE.slider((multi_value?"values":"value"),aH)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aC){aC.stopPropagation()}).click(function(aC){aC.stopPropagation()}).bind("dblclick",function(aC){aC.stopPropagation()}).bind("keydown",function(aC){aC.stopPropagation()});var ax=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aF,aH){aH.container=$("<div/>").addClass("filter-row slider-row").appendTo(ax);var aG=$("<div/>").addClass("elt-label").appendTo(aH.container);var aE=$("<span/>").addClass("slider-name").text(aH.name+"  ").appendTo(aG);var aD=$("<span/>");var aJ=$("<span/>").addClass("slider-value").appendTo(aG).append("[").append(aD).append("]");var aC=$("<div/>").addClass("slider").appendTo(aH.container);aH.control_element=$("<div/>").attr("id",aH.name+"-filter-control").appendTo(aC);var aI=[0,0];aH.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aL,aM){var aK=aM.values;aD.text(aK[0]+"-"+aK[1]);aH.low=aK[0];aH.high=aK[1];ap.track.request_draw(true,true)},change:function(aK,aL){aH.control_element.slider("option","slide").call(aH.control_element,aK,aL)}});aH.slider=aH.control_element;aH.slider_label=aD;ak(aJ,aD,aH.control_element);$("<div style='clear: both;'/>").appendTo(aH.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(ax);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var ai=this;ao.click(function(){ai.run_on_dataset()})}var ar=$("<div/>").addClass("display-controls").appendTo(this.parent_div),au,an,aq,al={Transparency:function(aC){ap.alpha_filter=aC},Height:function(aC){ap.height_filter=aC}};$.each(al,function(aE,aD){au=$("<div/>").addClass("filter-row").appendTo(ar),an=$("<span/>").addClass("elt-label").text(aE+":").appendTo(au),aq=$("<select/>").attr("name",aE+"_dropdown").css("float","right").appendTo(au);$("<option/>").attr("value",-1).text("== None ==").appendTo(aq);for(var aC=0;aC<ap.filters.length;aC++){$("<option/>").attr("value",aC).text(ap.filters[aC].name).appendTo(aq)}aq.change(function(){$(this).children("option:selected").each(function(){var aF=parseInt($(this).val());al[aE]((aF>=0?ap.filters[aF]:null));ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(au)});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var E=function(ah,ai){N.Scaler.call(this,ai);this.filter=ah};E.prototype.gen_val=function(ah){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var H=function(ah){this.track=ah.track;this.params=ah.params;this.values={};this.restore_values((ah.saved_values?ah.saved_values:{}));this.onchange=ah.onchange};q(H.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(ah,ak,aj,ai,al){this.track=ah;this.index=ak;this.low=ak*S*aj;this.high=(ak+1)*S*aj;this.resolution=aj;this.canvas=$("<div class='track-tile'/>").append(ai);this.data=al;this.stale=false};b.prototype.predisplay_actions=function(){};var l=function(ah,ak,aj,ai,al,am){b.call(this,ah,ak,aj,ai,al);this.max_val=am};q(l.prototype,b.prototype);var Q=function(ah,al,ak,aj,an,ao,am,ai){b.call(this,ah,al,ak,aj,an);this.mode=ao;this.message=am;this.feature_mapper=ai};q(Q.prototype,b.prototype);Q.prototype.predisplay_actions=function(){var ai=this,ah={};if(ai.mode!=="Pack"){return}$(this.canvas).mousemove(function(au){var ao=$(this).offset(),at=au.pageX-ao.left,ar=au.pageY-ao.top,ay=ai.feature_mapper.get_feature_data(at,ar),ap=(ay?ay[0]:null);$(this).siblings(".feature-popup").each(function(){if(!ap||$(this).attr("id")!==ap.toString()){$(this).remove()}});if(ay){var ak=ah[ap];if(!ak){var ap=ay[0],av={name:ay[3],start:ay[1],end:ay[2],strand:ay[4]},an=ai.track.filters_manager.filters,am;for(var aq=0;aq<an.length;aq++){am=an[aq];av[am.name]=ay[am.index]}var ak=$("<div/>").attr("id",ap).addClass("feature-popup"),ax,aw,az=$("<table/>").appendTo(ak),aA;for(ax in av){aw=av[ax];aA=$("<tr/>").appendTo(az);$("<th/>").appendTo(aA).text(ax);$("<td/>").attr("align","left").appendTo(aA).text(typeof(aw)=="number"?ab(aw,2):aw)}ah[ap]=ak}ak.appendTo($(ai.canvas).parent());var al=at+parseInt(ai.canvas.css("left"))+7,aj=ar+parseInt(ai.canvas.css("top"))+7;ak.css("left",al+"px").css("top",aj+"px")}else{if(!au.isPropagationStopped()){au.stopPropagation();$(this).siblings().each(function(){$(this).trigger(au)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var j=function(ak,ai,ah,aj,al,am){r.call(this,ak,ai,ah,{},"draghandle");this.data_url=(al?al:default_data_url);this.data_url_extra_params={};this.data_query_wait=(am?am:M);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.container_div=$("<div />").addClass("track").attr("id","track_"+j.id_counter++).css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Y){return"ReadTrack"}else{if(this instanceof W){return"ToolDataFeatureTrack"}else{if(this instanceof V){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(L)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(G)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.make_name_popup_menu()}ah.content_div.text(aa);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}})},predraw_init:function(){},});var O=function(ao,am){var ai=this,ap=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=new ac(this,(ao!==undefined?ao:{}));this.filters_available=false;this.filters_visible=false;this.tool=(am!==undefined&&obj_length(am)>0?new s(this,am):undefined);this.is_overview=false;if(ai.hidden){return}if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(ai.display_modes!==undefined){if(ai.mode_div===undefined){ai.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ai.header_div);var aj=(ai.config&&ai.config.values.mode?ai.config.values.mode:ai.display_modes[0]);ai.mode=aj;ai.mode_div.text(aj);var ah={};for(var ak=0,an=ai.display_modes.length;ak<an;ak++){var al=ai.display_modes[ak];ah[al]=function(aq){return function(){ai.change_mode(aq)}}(al)}make_popupmenu(ai.mode_div,ah)}else{ai.mode_div.hide()}}this.make_name_popup_menu()};q(O.prototype,r.prototype,j.prototype,{to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw();return ah},make_name_popup_menu:function(){var ai=this;var ah={};ah[(this.is_overview?"Hide overview":"Set as overview")]=function(){if(ai.is_overview){ai.view.reset_overview()}else{ai.view.set_overview(ai)}};ah["Edit configuration"]=function(){var am=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},al=function(an){if((an.keyCode||an.which)===27){am()}else{if((an.keyCode||an.which)===13){ak()}}};$(window).bind("keypress.check_enter_esc",al);show_modal("Configure Track",ai.config.build_form(),{Cancel:am,OK:ak})};if(ai.filters_available>0){var aj=(ai.filters_div.is(":visible")?"Hide filters":"Show filters");ah[aj]=function(){ai.filters_visible=(ai.filters_div.is(":visible"));if(ai.filters_visible){ai.filters_manager.reset_filters()}ai.filters_div.toggle();ai.make_name_popup_menu()}}if(ai.tool){var aj=(ai.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");ah[aj]=function(){if(!ai.dynamic_tool_div.is(":visible")){ai.set_name(ai.name+ai.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ai.revert_name()}ai.dynamic_tool_div.toggle();ai.make_name_popup_menu()}}ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)},set_is_overview:function(ah){this.is_overview=ah;this.make_name_popup_menu()},get_overview_tile:function(){var ah=this;view=ah.view,resolution=Math.pow(D,Math.ceil(Math.log((view.max_high-view.max_low)/S)/Math.log(D))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ah.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ah.data_url_extra_params)).then(function(ai){var ak=ah._gen_tile_cache_key(view_width,w_scale,0),am=ah.tile_cache.get(ak);if(!am){am=ah.draw_tile(ai,"Auto",resolution,0,w_scale);ah.tile_cache.set(ak,am)}var ap=$(am.canvas.find("canvas")),al=ap.clone(),ao=ap.get(0).getContext("2d"),aj=al.get(0).getContext("2d"),an=ao.getImageData(0,0,ao.canvas.width,ao.canvas.height);aj.putImageData(an,-ah.left_offset,(am.data.dataset_type==="summary_tree"?U:0));new_tile=new b(ah,-1,resolution,al);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof B)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/S);var ap=true;var at=[];var ah=0;while((ai*S*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",F)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*S*an,ax=ap+S*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);if(aq!==undefined){al.tile_cache.set(at,aq);al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw()});return null},show_tile:function(ao,aq,ar){var aj=this,ai=ao.canvas,an=ai;if(ao.message){var at=$("<div/>"),ap=$("<div/>").addClass("tile-message").text(ao.message).css({height:F-1,width:ao.canvas.width}).appendTo(at),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ap),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ap);at.append(ai);an=at;al.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()});ah.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()})}ao.predisplay_actions();var am=this.view.high-this.view.low,ak=(ao.low-this.view.low)*ar;if(this.left_offset){ak-=this.left_offset}an.css({position:"absolute",top:0,left:ak,height:""});aq.append(an);aj.max_height=Math.max(aj.max_height,an.height());aj.content_div.css("height",aj.max_height+"px");aq.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*S*ai,al=S*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ai,ah){this.hidden=true;j.call(this,"label",ai,ah,{});this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{init:function(){this.enabled=true},_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var B=function(ah){this.hidden=true;j.call(this,"reference",ah,{content_div:ah.top_labeltrack},{});O.call(this);ah.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ah.dbkey};this.data_manager=new J(C,this,false);this.tile_cache=new c(v)};q(B.prototype,r.prototype,O.prototype,{init:function(){this.enabled=true},draw_tile:function(ar,an,am,ai,at){var al=this,aj=S*am;if(at>this.view.canvas_manager.char_width_px){if(ar===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(al,ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(am,ak,aj,an,ah,al){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,am,ak,aj,al);O.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=an;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new T(C,this);this.tile_cache=new c(v);this.left_offset=0;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:am},{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:al,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.dataset_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.dataset_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};q(k.prototype,r.prototype,O.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this;ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(ai){ah.container_div.addClass("line-track");var ak=ai.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=ak.min;ah.prefs.max_value=ak.max;$("#track_"+ah.dataset_id+"_minval").val(ah.prefs.min_value);$("#track_"+ah.dataset_id+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=ak.total_frequency;ah.container_div.find(".yaxislabel").remove();var al=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_minval").text(ab(ah.prefs.min_value,3));var aj=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_maxval").text(ab(ah.prefs.max_value,3));aj.css({position:"absolute",top:"24px",left:"10px"});aj.prependTo(ah.container_div);al.css({position:"absolute",bottom:"2px",left:"10px"});al.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new N.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(this.track,aj,al,ak,au.data)}});var e=function(ah,an,ai,am,ap,ao,ak,al){var aj=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];j.call(this,ah,an,ai,ao);O.call(this,ak,al);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){aj.set_name(aj.prefs.name);aj.tile_cache.clear();aj.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=am;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new T(20,this);this.left_offset=200;this.painter=N.LinkedFeaturePainter};q(e.prototype,r.prototype,O.prototype,{postdraw_actions:function(ax,ah,ay,aw){O.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.make_name_popup_menu()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",A,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aD,aH,ar,ak){var aA=this,am=aA._get_tile_bounds(aH,aD),aK=am[0],ai=am[1],ay=ai-aK,aB=Math.ceil(ay*ar),aQ=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"){az="no_detail"}else{var aP=aw.data;if(this.view.high-this.view.low>K){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aB+al;aj.height=an+U;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aK,ai,200);if(aw.max){at.max=aw.max}aw=at}var aM=new N.SummaryTreePainter(aw,aK,ai,this.prefs);var aC=aj.getContext("2d");aC.translate(al,U);aM.draw(aC,aB,an);return new l(aA,aH,aD,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aE=0,aG=aw.data.length;aE<aG;aE++){var ao=aw.data[aE];var aF=false;var av;for(var aJ=0,aO=au.length;aJ<aO;aJ++){av=au[aJ];av.update_attrs(ao);if(!av.keep(ao)){aF=true;break}}if(!aF){aq.push(ao)}}}var aN=(this.filters_manager.alpha_filter?new E(this.filters_manager.alpha_filter):null);var aL=(this.filters_manager.height_filter?new E(this.filters_manager.height_filter):null);var aM=new (this.painter)(aq,aK,ai,this.prefs,az,aN,aL,ak);var an=Math.max(af,aM.get_required_height(ap));var aj=this.view.canvas_manager.new_canvas();var aI=null;aj.width=aB+al;aj.height=an;var aC=aj.getContext("2d");aC.fillStyle=this.prefs.block_color;aC.font=aC.canvas.manager.default_font;aC.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aw.data){aC.translate(al,0);aI=aM.draw(aC,aB,an,ax);aI.translation=-al}return new Q(aA,aH,aD,aj,aw.data,az,aw.message,aI)}});var V=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.painter=N.VariantPainter};q(V.prototype,r.prototype,O.prototype,e.prototype);var Y=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ak,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=N.ReadPainter;this.make_name_popup_menu()};q(Y.prototype,r.prototype,O.prototype,e.prototype);var W=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am,{});this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};q(W.prototype,r.prototype,O.prototype,e.prototype,{predraw_init:function(){var ai=this;var ah=function(){if(ai.data_manager.size()===0){setTimeout(ah,300)}else{ai.data_url=default_data_url;ai.data_query_wait=M;ai.dataset_state_url=converted_datasets_state_url;$.getJSON(ai.dataset_state_url,{dataset_id:ai.dataset_id,hda_ldda:ai.hda_ldda},function(aj){})}};ah()}});Z.View=ae;Z.DrawableGroup=R;Z.LineTrack=k;Z.FeatureTrack=e;Z.ReadTrack=Y};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(k,y){var v=k("class").extend;var q=function(J,B,H,A,G,E){if(E===undefined){E=4}var D=A-B;var C=G-H;var F=Math.floor(Math.sqrt(D*D+C*C)/E);var K=D/F;var I=C/F;var z;for(z=0;z<F;z++,B+=K,H+=I){if(z%2!==0){continue}J.fillRect(B,H,E,1)}};var r=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var e=function(z){this.default_val=(z?z:1)};e.prototype.gen_val=function(z){return this.default_val};var n=function(B,D,z,A,C){this.data=B;this.view_start=D;this.view_end=z;this.prefs=v({},this.default_prefs,A);this.mode=C};n.prototype.default_prefs={};var w=function(B,D,z,A,C){n.call(this,B,D,z,A,C)};w.prototype.default_prefs={show_counts:false};w.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var c=function(z,D,F,G,B){n.call(this,z,D,F,G,B);if(this.prefs.min_value===undefined){var H=Infinity;for(var A=0,C=this.data.length;A<C;A++){H=Math.min(H,this.data[A][1])}this.prefs.min_value=H}if(this.prefs.max_value===undefined){var E=-Infinity;for(var A=0,C=this.data.length;A<C;A++){E=Math.max(E,this.data[A][1])}this.prefs.max_value=E}};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var o=function(z){this.feature_positions={};this.slot_height=z;this.translation=0};o.prototype.map_feature_data=function(A,C,z,B){if(!this.feature_positions[C]){this.feature_positions[C]=[]}this.feature_positions[C].push({data:A,x_start:z,x_end:B})};o.prototype.get_feature_data=function(z,D){var C=Math.floor(D/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var p=function(B,E,z,A,D,F,C){n.call(this,B,E,z,A,D);this.alpha_scaler=(F?F:new e());this.height_scaler=(C?C:new e())};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};v(p.prototype,{get_required_height:function(A){var z=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){z=A*y_scale}return z+Math.max(Math.round(y_scale/2),5)},draw:function(L,J,H,G){var R=this.data,E=this.view_start,N=this.view_end;L.save();L.fillStyle=this.prefs.block_color;L.textAlign="right";var I=this.view_end-this.view_start,F=J/I,M=this.get_row_height(),Q=new o(M),C;for(var O=0,P=R.length;O<P;O++){var B=R[O],D=B[0],K=B[1],z=B[2],A=(G&&G[D]!==undefined?G[D]:null);if((K<N&&z>E)&&(this.mode=="Dense"||A!==null)){C=this.draw_element(L,this.mode,B,A,E,N,F,M,J);Q.map_feature_data(B,A,C[0],C[1])}}L.restore();return Q},draw_element:function(F,B,H,D,C,E,G,A,z){console.log("WARNING: Unimplemented function.");return[0,0]}});var d=10,j=3,m=5,x=10,g=1,t=3,f=3,a=9,l=2,h="#ccc";var s=function(B,E,z,A,D,F,C){p.call(this,B,E,z,A,D,F,C)};v(s.prototype,p.prototype,{get_row_height:function(){var A=this.mode,z;if(A==="Dense"){z=d}else{if(A==="no_detail"){z=j}else{if(A==="Squish"){z=m}else{z=x}}}return z},draw_element:function(N,E,W,I,P,ah,al,an,z){var T=W[0],aj=W[1],ab=W[2],R=W[3],ac=Math.floor(Math.max(0,(aj-P)*al)),O=Math.ceil(Math.min(z,Math.max(0,(ab-P)*al))),aa=ac,am=O,Z=(E==="Dense"?0:(0+I))*an,M,af,S=null,ap=null,C=this.prefs.block_color,ae=this.prefs.label_color;N.globalAlpha=this.alpha_scaler.gen_val(W);if(E=="Dense"){I=1}if(E==="no_detail"){N.fillStyle=C;N.fillRect(ac,Z+5,O-ac,g)}else{var L=W[4],Y=W[5],ad=W[6],D=W[7];if(Y&&ad){S=Math.floor(Math.max(0,(Y-P)*al));ap=Math.ceil(Math.min(z,Math.max(0,(ad-P)*al)))}var ak,U;if(E==="Squish"||E==="Dense"){ak=1;U=f}else{ak=5;U=a}if(!D){if(W.strand){if(W.strand==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand_inv")}else{if(W.strand==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand_inv")}}}else{N.fillStyle=C}N.fillRect(ac,Z,O-ac,U)}else{var K,V;if(E==="Squish"||E==="Dense"){N.fillStyle=h;K=Z+Math.floor(f/2)+1;V=1}else{if(L){var K=Z;var V=U;if(L==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand")}else{if(L==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand")}}}else{N.fillStyle=h;K+=(f/2)+1;V=1}}N.fillRect(ac,K,O-ac,V);var F;for(var ai=0,B=D.length;ai<B;ai++){var G=D[ai],A=Math.floor(Math.max(0,(G[0]-P)*al)),X=Math.ceil(Math.min(z,Math.max((G[1]-P)*al)));if(A>X){continue}N.fillStyle=C;N.fillRect(A,Z+(U-ak)/2+1,X-A,ak);if(S!==undefined&&ad>Y&&!(A>ap||X<S)){var ag=Math.max(A,S),J=Math.min(X,ap);N.fillRect(ag,Z+1,J-ag,U);if(D.length==1&&E=="Pack"){if(L==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand_inv")}else{if(L==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand_inv")}}if(ag+14<J){ag+=2;J-=2}N.fillRect(ag,Z+1,J-ag,U)}}}if(E==="Pack"){N.globalAlpha=1;N.fillStyle="white";var H=this.height_scaler.gen_val(W),Q=Math.ceil(U*H),ao=Math.round((U-Q)/2);if(H!==1){N.fillRect(ac,K+1,O-ac,ao);N.fillRect(ac,K+U-ao+1,O-ac,ao)}}}N.globalAlpha=1;if(E==="Pack"&&aj>P){N.fillStyle=ae;if(P===0&&ac-N.measureText(R).width<0){N.textAlign="left";N.fillText(R,O+l,Z+8);am+=N.measureText(R).width+l}else{N.textAlign="right";N.fillText(R,ac-l,Z+8);aa-=N.measureText(R).width+l}}}N.globalAlpha=1;return[aa,am]}});var b=function(B,E,z,A,D,F,C){p.call(this,B,E,z,A,D,F,C)};v(b.prototype,p.prototype,{draw_element:function(S,N,H,D,V,B,K,T,Q){var H=data[i],J=H[0],R=H[1],C=H[2],M=H[3],F=Math.floor(Math.max(0,(R-V)*K)),I=Math.ceil(Math.min(Q,Math.max(0,(C-V)*K))),E=(N==="Dense"?0:(0+D))*T,z,W,A=null,L=null;if(no_label){S.fillStyle=block_color;S.fillRect(F+left_offset,E+5,I-F,1)}else{var U=H[4],P=H[5],G=H[6];z=9;W=1;S.fillRect(F+left_offset,E,I-F,z);if(N!=="Dense"&&M!==undefined&&R>V){S.fillStyle=label_color;if(V===0&&F-S.measureText(M).width<0){S.textAlign="left";S.fillText(M,I+2+left_offset,E+8)}else{S.textAlign="right";S.fillText(M,F-2+left_offset,E+8)}S.fillStyle=block_color}var O=U+" / "+P;if(R>V&&S.measureText(O).width<(I-F)){S.fillStyle="white";S.textAlign="center";S.fillText(O,left_offset+F+(I-F)/2,E+8);S.fillStyle=block_color}}return[F,I]}});var u=function(C,F,z,B,E,G,D,A){p.call(this,C,F,z,B,E,G,D);this.ref_seq=A};u.prototype.default_prefs=v({},p.prototype.default_prefs,{show_insertions:false});v(u.prototype,p.prototype,{get_row_height:function(){var z,A=this.mode;if(A==="Dense"){z=d}else{if(A==="Squish"){z=m}else{z=x;if(this.prefs.show_insertions){z*=2}}}return z},draw_read:function(V,Q,M,aa,B,U,J,G,F){V.textAlign="center";var T=this,A=[aa,B],P=0,W=0,S=0;ref_seq=this.ref_seq.data,char_width_px=V.canvas.manager.char_width_px;var af=[];if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){S=Math.round(M/2)}if(!J){J=[[0,G.length]]}for(var N=0,Y=J.length;N<Y;N++){var K=J[N],C="MIDNSHP=X"[K[0]],O=K[1];if(C==="H"||C==="S"){P-=O}var H=U+P,ae=Math.floor(Math.max(0,(H-aa)*M)),I=Math.floor(Math.max(0,(H+O-aa)*M));if(ae===I){I+=1}switch(C){case"H":break;case"S":case"M":case"=":if(is_overlap([H,H+O],A)){var R=G.slice(W,W+O);if(S>0){V.fillStyle=this.prefs.block_color;V.fillRect(ae-S,F+1,I-ae,9);V.fillStyle=h;for(var ac=0,z=R.length;ac<z;ac++){if(this.prefs.show_differences&&ref_seq){var L=ref_seq[H-aa+ac];if(!L||L.toLowerCase()===R[ac].toLowerCase()){continue}}if(H+ac>=aa&&H+ac<=B){var ad=Math.floor(Math.max(0,(H+ac-aa)*M));V.fillText(R[ac],ad,F+9)}}}else{V.fillStyle=this.prefs.block_color;V.fillRect(ae,F+4,I-ae,f)}}W+=O;P+=O;break;case"N":V.fillStyle=h;V.fillRect(ae-S,F+5,I-ae,1);P+=O;break;case"D":V.fillStyle="red";V.fillRect(ae-S,F+4,I-ae,3);P+=O;break;case"P":break;case"I":var Z=ae-S;if(is_overlap([H,H+O],A)){var R=G.slice(W,W+O);if(this.prefs.show_insertions){var E=ae-(I-ae)/2;if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){V.fillStyle="yellow";V.fillRect(E-S,F-9,I-ae,9);af[af.length]={type:"triangle",data:[Z,F+4,5]};V.fillStyle=h;switch(seq_tile_overlap){case (OVERLAP_START):R=R.slice(aa-H);break;case (OVERLAP_END):R=R.slice(0,H-B);break;case (CONTAINED_BY):break;case (CONTAINS):R=R.slice(aa-H,H-B);break}for(var ac=0,z=R.length;ac<z;ac++){var ad=Math.floor(Math.max(0,(H+ac-aa)*M));V.fillText(R[ac],ad-(I-ae)/2,F)}}else{V.fillStyle="yellow";V.fillRect(E,F+(this.mode!=="Dense"?2:5),I-ae,(Q!=="Dense"?f:t))}}else{if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){af[af.length]={type:"text",data:[R.length,Z,F+9]}}else{}}}W+=O;break;case"X":W+=O;break}}V.fillStyle="yellow";var ab,D,ag;for(var X=0;X<af.length;X++){ab=af[X];D=ab.type;ag=ab.data;if(D==="text"){V.save();V.font="bold "+V.font;V.fillText(ag[0],ag[1],ag[2]);V.restore()}else{if(D=="triangle"){r(V,ag[0],ag[1],ag[2])}}}},draw_element:function(S,N,F,C,V,A,J,T,Q){var I=F[0],R=F[1],B=F[2],K=F[3],E=Math.floor(Math.max(0,(R-V)*J)),G=Math.ceil(Math.min(Q,Math.max(0,(B-V)*J))),D=(N==="Dense"?0:(0+C))*T,W=this.prefs.block_color,H=this.prefs.label_color,P=0;if((N==="Pack"||this.mode==="Auto")&&J>S.canvas.manager.char_width_px){var P=Math.round(J/2)}S.fillStyle=W;if(F[5] instanceof Array){var O=Math.floor(Math.max(0,(F[4][0]-V)*J)),M=Math.ceil(Math.min(Q,Math.max(0,(F[4][1]-V)*J))),L=Math.floor(Math.max(0,(F[5][0]-V)*J)),z=Math.ceil(Math.min(Q,Math.max(0,(F[5][1]-V)*J)));if(F[4][1]>=V&&F[4][0]<=A&&F[4][2]){this.draw_read(S,N,J,V,A,F[4][0],F[4][2],F[4][3],D)}if(F[5][1]>=V&&F[5][0]<=A&&F[5][2]){this.draw_read(S,N,J,V,A,F[5][0],F[5][2],F[5][3],D)}if(L>M){S.fillStyle=h;q(S,M-P,D+5,L-P,D+5)}}else{S.fillStyle=W;this.draw_read(S,N,J,V,A,R,F[4],F[5],D)}if(N==="Pack"&&R>V){S.fillStyle=this.prefs.label_color;var U=1;if(U===0&&E-S.measureText(K).width<0){S.textAlign="left";S.fillText(K,G+l-P,D+8)}else{S.textAlign="right";S.fillText(K,E-l-P,D+8)}S.fillStyle=W}return[0,0]}});y.Scaler=e;y.SummaryTreePainter=w;y.LinePainter=c;y.LinkedFeaturePainter=s;y.ReadPainter=u;y.VariantPainter=b};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window);
\ No newline at end of file
diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index 5eac12b6dc5..97f20dc435c 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -4411,7 +4411,7 @@ extend(ReadPainter.prototype, FeaturePainter.prototype, {
             base_offset = 0,
             seq_offset = 0,
             gap = 0
-            ref_seq = this.ref_seq,
+            ref_seq = this.ref_seq.data,
             char_width_px = ctx.canvas.manager.char_width_px;
             
         // Keep list of items that need to be drawn on top of initial drawing layer.

From 98da2311bb2b9413975ef5d3c8f579d815125e13 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Mon, 17 Oct 2011 17:41:10 -0400
Subject: [PATCH 065/362] Encode the tool shed repository information and
 include in the request when installing into local Galaxy instances rather
 than using cookies.

---
 lib/galaxy/web/controllers/admin.py           | 53 ++++++++++--------
 lib/galaxy/web/controllers/workflow.py        |  4 +-
 .../community/controllers/repository.py       | 55 ++++++++++---------
 .../admin/select_tool_panel_section.mako      |  2 +-
 4 files changed, 60 insertions(+), 54 deletions(-)

diff --git a/lib/galaxy/web/controllers/admin.py b/lib/galaxy/web/controllers/admin.py
index dd60f6d30c3..2e595510c46 100644
--- a/lib/galaxy/web/controllers/admin.py
+++ b/lib/galaxy/web/controllers/admin.py
@@ -3,7 +3,9 @@ from galaxy import model
 from galaxy.model.orm import *
 from galaxy.web.framework.helpers import time_ago, iff, grids
 from galaxy.tools.search import ToolBoxSearch
-import logging
+from galaxy.tools import json_fix
+from galaxy.util.hash_util import *
+import simplejson, binascii, logging
 log = logging.getLogger( __name__ )
 
 from galaxy.actions.admin import AdminActions
@@ -688,9 +690,19 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
     @web.require_admin
     def browse_tool_shed( self, trans, **kwd ):
         tool_shed_url = kwd[ 'tool_shed_url' ]
-        trans.set_cookie( trans.request.host, name='toolshedgalaxyurl' )
-        url = '%s/repository/browse_downloadable_repositories?webapp=galaxy' % tool_shed_url
+        galaxy_url = trans.request.host
+        url = '%s/repository/browse_downloadable_repositories?galaxy_url=%s&webapp=community' % ( tool_shed_url, galaxy_url )
         return trans.response.send_redirect( url )
+    def _decode( self, trans, value, secure=True ):
+        if secure:
+            # Extract and verify hash
+            a, b = value.split( ":" )
+            value = binascii.unhexlify( b )
+            test = hmac_new( trans.app.config.tool_secret, value )
+            assert a == test
+        # Restore from string
+        values = json_fix( simplejson.loads( value ) )
+        return values
     @web.expose
     @web.require_admin
     def install_tool_shed_repository( self, trans, **kwd ):
@@ -703,10 +715,10 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
             message += 'target=_blank">Automatic installation of Galaxy tool shed repository tools into a local Galaxy instance</a> section of the '
             message += '<a href="http://wiki.g2.bx.psu.edu/Tool%20Shed" target="_blank">Galaxy tool shed wiki</a> for all of the details.'
             return trans.show_error_message( message )
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        status = params.get( 'status', 'done' )
-        tool_shed_url = trans.get_cookie( name='galaxytoolshedurl' )
+        message = kwd.get( 'message', ''  )
+        status = kwd.get( 'status', 'done' )
+        tool_shed_url = kwd[ 'tool_shed_url' ]
+        repo_info_dict = kwd[ 'repo_info_dict' ]
         if kwd.get( 'select_tool_panel_section_button', False ):
             shed_tool_conf = kwd[ 'shed_tool_conf' ]
             # Get the tool path.
@@ -716,18 +728,12 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
             if 'tool_panel_section' in kwd:
                 section_key = 'section_%s' % kwd[ 'tool_panel_section' ]
                 tool_section = trans.app.toolbox.tool_panel[ section_key ]
-                # Get the number of repositories to clone from a cookie.
-                num_repos_to_clone = int( trans.get_cookie( name='numrepostoclone' ) )
+                # Decode the encoded repo_info_dict param value.
+                repo_info_dict = self._decode( trans, repo_info_dict )
                 # Clone the repository to the configured location.
                 current_working_dir = os.getcwd()
-                for index in range( 0, num_repos_to_clone ):
-                    cookie_name = 'toolshedrepository%i' % index
-                    clone_repo_info_str = trans.get_cookie( name=cookie_name )
-                    clone_repo_info_items = clone_repo_info_str.split( '&' )
-                    name = clone_repo_info_items[ 0 ]
-                    description = clone_repo_info_items[ 1 ]
-                    repository_clone_url = clone_repo_info_items[ 2 ]
-                    changeset_revision = clone_repo_info_items[ 3 ]
+                for name, repo_info_tuple in repo_info_dict.items():
+                    description, repository_clone_url, changeset_revision = repo_info_tuple
                     clone_dir = os.path.join( tool_path, self.__generate_tool_path( repository_clone_url, changeset_revision ) )
                     if os.path.exists( clone_dir ):
                         # Repository and revision has already been cloned.
@@ -825,6 +831,8 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
             shed_tool_conf_select_field = None
         tool_panel_section_select_field = build_tool_panel_section_select_field( trans )
         return trans.fill_template( '/admin/select_tool_panel_section.mako',
+                                    tool_shed_url=tool_shed_url,
+                                    repo_info_dict=repo_info_dict,
                                     shed_tool_conf=shed_tool_conf,
                                     shed_tool_conf_select_field=shed_tool_conf_select_field,
                                     tool_panel_section_select_field=tool_panel_section_select_field,
@@ -836,12 +844,11 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
         params = util.Params( kwd )
         repository_id = params.get( 'id', None )
         repository = get_repository( trans, repository_id )
-        trans.set_cookie( trans.request.host, name='toolshedgalaxyurl' )
+        galaxy_url = trans.request.host
         # Send a request to the relevant tool shed to see if there are any updates.
         # TODO: support https in the following url.
-        # TODO: Set cookies for name, owner, changeset-revision instead of sending in request
-        url = 'http://%s/repository/check_for_updates?name=%s&owner=%s&changeset_revision=%s&webapp=community' % \
-            ( repository.tool_shed, repository.name, repository.owner, repository.changeset_revision )
+        url = 'http://%s/repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=community' % \
+            ( repository.tool_shed, galaxy_url, repository.name, repository.owner, repository.changeset_revision )
         return trans.response.send_redirect( url )
     @web.expose
     @web.require_admin
@@ -1087,10 +1094,10 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
             # http://test@bx.psu.edu:9009/repos/some_username/column
             items = repository_clone_url.split( '@' )
             tmp_url = items[ 1 ]
-        elif repository_clone_url.find( '\/\/' ) > 0:
+        elif repository_clone_url.find( '//' ) > 0:
             # We have an url that includes only a protocol, something like:
             # http://bx.psu.edu:9009/repos/some_username/column
-            items = repository_clone_url.split( '\/\/' )
+            items = repository_clone_url.split( '//' )
             tmp_url = items[ 1 ]
         else:
             tmp_url = repository_clone_url
diff --git a/lib/galaxy/web/controllers/workflow.py b/lib/galaxy/web/controllers/workflow.py
index 3ee7a50d07f..3e7245b0125 100644
--- a/lib/galaxy/web/controllers/workflow.py
+++ b/lib/galaxy/web/controllers/workflow.py
@@ -1156,14 +1156,12 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
                             # involved in workflow development needs to figure out what it will take to be able to switch
                             # back and forth between Galaxy (with panels ) and the workflow view (without panels ), having 
                             # the Galaxy panels displayed whenever in Galaxy.
-                            trans.set_cookie( trans.request.host, name='toolshedgalaxyurl' )
-                            galaxy_url = trans.request.host
                             message += "The workflow requires the following tools that are not available in this Galaxy instance."
                             message += "You can likely install the required tools from one of the Galaxy tool sheds listed below.<br/><br/>"
                             for tool_shed_name, tool_shed_url in trans.app.tool_shed_registry.tool_sheds.items():
                                 if tool_shed_url.endswith( '/' ):
                                     tool_shed_url = tool_shed_url.rstrip( '/' )
-                                    url = '%s/repository/find_tools?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, galaxy_url )
+                                    url = '%s/repository/find_tools?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, trans.request.host )
                                     for missing_tool_tup in missing_tool_tups:
                                         missing_tool_id = missing_tool_tup[0]
                                         url += '&tool_id=%s' % missing_tool_id
diff --git a/lib/galaxy/webapps/community/controllers/repository.py b/lib/galaxy/webapps/community/controllers/repository.py
index 288b8a58823..bfa7f12ce4c 100644
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -9,6 +9,7 @@ from galaxy.webapps.community import model
 from galaxy.webapps.community.model import directory_hash_id
 from galaxy.web.framework.helpers import time_ago, iff, grids
 from galaxy.util.json import from_json_string, to_json_string
+from galaxy.util.hash_util import *
 from galaxy.model.orm import *
 from common import *
 from mercurial import hg, ui, patch, commands
@@ -283,7 +284,7 @@ class MatchedRepositoryListGrid( grids.Grid ):
 class InstallMatchedRepositoryListGrid( MatchedRepositoryListGrid ):
     # Grid definition
     title = "Repositories with required tools"
-    operations = [ grids.GridOperation( "Preview and install tools",
+    operations = [ grids.GridOperation( "Install tools",
                                         url_args = dict( controller='repository',
                                                          action='find_tools',
                                                          webapp='community' ),
@@ -408,17 +409,22 @@ class RepositoryController( BaseUIController, ItemRatings ):
                     return trans.response.send_redirect( web.url_for( controller='repository',
                                                                       action='view_repository',
                                                                       **kwd ) )
-            if operation == "preview and install tools":
+            if operation == "install tools":
+                repo_info_dict = {}
                 galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' )
-                trans.set_cookie( trans.request.host, name='galaxytoolshedurl' )
                 # TODO: support https in the following url.
-                url = 'http://%s/admin/install_tool_shed_repository' % ( galaxy_url )
-                repos_to_clone = util.listify( kwd[ 'id' ] )
-                num_repos_to_clone = len( repos_to_clone )
-                trans.set_cookie( num_repos_to_clone, name='numrepostoclone' )
-                for index in range( 0, num_repos_to_clone ):
-                    repository_metadata_id = repos_to_clone[ index ]
-                    self._set_clone_repository_cookie( trans, index, repository_metadata_id )
+                url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s' % ( galaxy_url, trans.request.host )
+                repository_metadata_ids = util.listify( kwd[ 'id' ] )
+                for repository_metadata_id in repository_metadata_ids:
+                    #self._set_clone_repository_cookie( trans, index, repository_metadata_id )
+                    repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id )
+                    repository = get_repository( trans, trans.security.encode_id( repository_metadata.repository_id ) )
+                    repository_id = trans.security.encode_id( repository.id )
+                    changeset_revision = repository_metadata.changeset_revision
+                    repository_clone_url = generate_clone_url( trans, repository_id )
+                    repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, changeset_revision )
+                encoded_repo_info_dict = self._encode( trans, repo_info_dict, secure=True )
+                url += '&repo_info_dict=%s' % encoded_repo_info_dict
                 return trans.response.send_redirect( url )
         tool_ids = [ tid.lower() for tid in util.listify( kwd.get( 'tool_id', '' ) ) ]
         tool_names = [ tn.lower() for tn in util.listify( kwd.get( 'tool_name', '' ) ) ]
@@ -548,16 +554,15 @@ class RepositoryController( BaseUIController, ItemRatings ):
             found = ( tool_version == tool_dict_tool_version and tool_name == tool_dict_tool_name ) or \
                     ( not exact_matches_checked and tool_dict_tool_version.find( tool_version ) >= 0 and tool_dict_tool_name.find( tool_name ) >= 0 )
         return found
-    def _set_clone_repository_cookie( self, trans, index, repository_metadata_id ):
-        cookie_name = 'toolshedrepository%i' % index
-        repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id )
-        repository = get_repository( trans, trans.security.encode_id( repository_metadata.repository_id ) )
-        repository_id = trans.security.encode_id( repository.id )
-        changeset_revision = repository_metadata.changeset_revision
-        # Redirect back to local Galaxy to perform install.
-        repository_clone_url = generate_clone_url( trans, repository_id )
-        cookie_value = '%s&%s&%s&%s' % ( repository.name, repository.description, repository_clone_url, changeset_revision )
-        trans.set_cookie( cookie_value, name=cookie_name )
+    def _encode( self, trans, repo_info_dict, secure=True ):
+        value = simplejson.dumps( repo_info_dict )
+        # Make it secure
+        if secure:
+            a = hmac_new( trans.app.config.tool_secret, value )
+            b = binascii.hexlify( value )
+            return "%s:%s" % ( a, b )
+        else:
+            return value
     @web.expose
     def preview_tools_in_changeset( self, trans, repository_id, **kwd ):
         params = util.Params( kwd )
@@ -593,28 +598,24 @@ class RepositoryController( BaseUIController, ItemRatings ):
         repository = get_repository( trans, repository_id )
         changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) )
         # Redirect back to local Galaxy to perform install.
-        trans.set_cookie( trans.request.host, name='galaxytoolshedurl' )
         repository_clone_url = generate_clone_url( trans, repository_id )
         # TODO: support https in the following url.
-        url = 'http://%s/admin/install_tool_shed_repository?name=%s&description=%s&repository_clone_url=%s&changeset_revision=%s' % \
-            ( galaxy_url, repository.name, repository.description, repository_clone_url, changeset_revision )
+        url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s&name=%s&description=%s&repository_clone_url=%s&changeset_revision=%s' % \
+            ( galaxy_url, trans.request.host, repository.name, repository.description, repository_clone_url, changeset_revision )
         return trans.response.send_redirect( url )
     @web.expose
     def check_for_updates( self, trans, **kwd ):
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
-        # The sender didn't store galaxy_url in a cookie since
-        # this method immediately redirects back to the caller.
         galaxy_url = kwd[ 'galaxy_url' ]
         name = params.get( 'name', None )
         owner = params.get( 'owner', None )
         changeset_revision = params.get( 'changeset_revision', None )
         webapp = params.get( 'webapp', None )
-        trans.set_cookie( trans.request.host, name='galaxytoolshedurl' )
         # Start building up the url to redirect back to the calling Galaxy instance.
         # TODO: support https in the following url.
-        url = 'http://%s/admin/update_to_changeset_revision' % galaxy_url
+        url = 'http://%s/admin/update_to_changeset_revision?tool_shed_url=%s' % ( galaxy_url, trans.request.host )
         repository = get_repository_by_name_and_owner( trans, name, owner )
         url += '&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % \
             ( repository.name, repository.user.username, changeset_revision )
diff --git a/templates/admin/select_tool_panel_section.mako b/templates/admin/select_tool_panel_section.mako
index bd618db12b0..045c418143a 100644
--- a/templates/admin/select_tool_panel_section.mako
+++ b/templates/admin/select_tool_panel_section.mako
@@ -25,7 +25,7 @@
 <div class="toolForm">
     <div class="toolFormTitle">Load tools into tool panel</div>
     <div class="toolFormBody">
-    <form name="select_tool_panel_section" id="select_tool_panel_section" action="${h.url_for( controller='admin', action='install_tool_shed_repository' )}" method="post" >
+    <form name="select_tool_panel_section" id="select_tool_panel_section" action="${h.url_for( controller='admin', action='install_tool_shed_repository', tool_shed_url=tool_shed_url, repo_info_dict=repo_info_dict )}" method="post" >
         %if shed_tool_conf_select_field:
             <div class="form-row">
                 <label>Shed tool configuration file:</label>

From 1e2ae076d640bb0f7eb598c506fc7087bae5acfb Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Mon, 17 Oct 2011 19:57:54 -0400
Subject: [PATCH 066/362] Better handling of reference data in Trackster read
 tracks.

---
 static/scripts/trackster.js | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index 97f20dc435c..3941f3438a2 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -4375,7 +4375,7 @@ extend(VariantPainter.prototype, FeaturePainter.prototype, {
 
 var ReadPainter = function(data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler, ref_seq) {
     FeaturePainter.call(this, data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler);
-    this.ref_seq = ref_seq;
+    this.ref_seq = (ref_seq ? ref_seq.data : null);
 };
 
 ReadPainter.prototype.default_prefs = extend({}, FeaturePainter.prototype.default_prefs, { show_insertions: false });
@@ -4410,8 +4410,7 @@ extend(ReadPainter.prototype, FeaturePainter.prototype, {
             tile_region = [tile_low, tile_high],
             base_offset = 0,
             seq_offset = 0,
-            gap = 0
-            ref_seq = this.ref_seq.data,
+            gap = 0,
             char_width_px = ctx.canvas.manager.char_width_px;
             
         // Keep list of items that need to be drawn on top of initial drawing layer.
@@ -4465,8 +4464,8 @@ extend(ReadPainter.prototype, FeaturePainter.prototype, {
                             // TODO: this can be made much more efficient by computing the complete sequence
                             // to draw and then drawing it.
                             for (var c = 0, str_len = seq.length; c < str_len; c++) {
-                                if (this.prefs.show_differences && ref_seq) {
-                                    var ref_char = ref_seq[seq_start - tile_low + c];
+                                if (this.prefs.show_differences && this.ref_seq) {
+                                    var ref_char = this.ref_seq[seq_start - tile_low + c];
                                     if (!ref_char || ref_char.toLowerCase() === seq[c].toLowerCase()) {
                                         continue;
                                     }

From ece2f3a90fc666c06c311ea731a219230ab376eb Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Tue, 18 Oct 2011 08:43:30 -0400
Subject: [PATCH 067/362] Make sure the same key is used in encoding and
 decoding between Galaxy and the tool sheds.

---
 lib/galaxy/web/controllers/admin.py               | 15 +++++++--------
 .../webapps/community/controllers/repository.py   | 14 +++++---------
 2 files changed, 12 insertions(+), 17 deletions(-)

diff --git a/lib/galaxy/web/controllers/admin.py b/lib/galaxy/web/controllers/admin.py
index 2e595510c46..8b1acf85dca 100644
--- a/lib/galaxy/web/controllers/admin.py
+++ b/lib/galaxy/web/controllers/admin.py
@@ -693,13 +693,12 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
         galaxy_url = trans.request.host
         url = '%s/repository/browse_downloadable_repositories?galaxy_url=%s&webapp=community' % ( tool_shed_url, galaxy_url )
         return trans.response.send_redirect( url )
-    def _decode( self, trans, value, secure=True ):
-        if secure:
-            # Extract and verify hash
-            a, b = value.split( ":" )
-            value = binascii.unhexlify( b )
-            test = hmac_new( trans.app.config.tool_secret, value )
-            assert a == test
+    def _decode( self, value ):
+        # Extract and verify hash
+        a, b = value.split( ":" )
+        value = binascii.unhexlify( b )
+        test = hmac_new( 'ToolShedAndGalaxyMustHaveThisSameKey', value )
+        assert a == test
         # Restore from string
         values = json_fix( simplejson.loads( value ) )
         return values
@@ -729,7 +728,7 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
                 section_key = 'section_%s' % kwd[ 'tool_panel_section' ]
                 tool_section = trans.app.toolbox.tool_panel[ section_key ]
                 # Decode the encoded repo_info_dict param value.
-                repo_info_dict = self._decode( trans, repo_info_dict )
+                repo_info_dict = self._decode( repo_info_dict )
                 # Clone the repository to the configured location.
                 current_working_dir = os.getcwd()
                 for name, repo_info_tuple in repo_info_dict.items():
diff --git a/lib/galaxy/webapps/community/controllers/repository.py b/lib/galaxy/webapps/community/controllers/repository.py
index bfa7f12ce4c..1a33fae36f8 100644
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -423,7 +423,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
                     changeset_revision = repository_metadata.changeset_revision
                     repository_clone_url = generate_clone_url( trans, repository_id )
                     repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, changeset_revision )
-                encoded_repo_info_dict = self._encode( trans, repo_info_dict, secure=True )
+                encoded_repo_info_dict = self._encode( repo_info_dict )
                 url += '&repo_info_dict=%s' % encoded_repo_info_dict
                 return trans.response.send_redirect( url )
         tool_ids = [ tid.lower() for tid in util.listify( kwd.get( 'tool_id', '' ) ) ]
@@ -554,15 +554,11 @@ class RepositoryController( BaseUIController, ItemRatings ):
             found = ( tool_version == tool_dict_tool_version and tool_name == tool_dict_tool_name ) or \
                     ( not exact_matches_checked and tool_dict_tool_version.find( tool_version ) >= 0 and tool_dict_tool_name.find( tool_name ) >= 0 )
         return found
-    def _encode( self, trans, repo_info_dict, secure=True ):
+    def _encode( self, repo_info_dict ):
         value = simplejson.dumps( repo_info_dict )
-        # Make it secure
-        if secure:
-            a = hmac_new( trans.app.config.tool_secret, value )
-            b = binascii.hexlify( value )
-            return "%s:%s" % ( a, b )
-        else:
-            return value
+        a = hmac_new( 'ToolShedAndGalaxyMustHaveThisSameKey', value )
+        b = binascii.hexlify( value )
+        return "%s:%s" % ( a, b )
     @web.expose
     def preview_tools_in_changeset( self, trans, repository_id, **kwd ):
         params = util.Params( kwd )

From 5d86e1bbbc5118d6bc355996aa872940e90f2926 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Tue, 18 Oct 2011 09:51:39 -0400
Subject: [PATCH 068/362] Fix for job.compute_outputs() when
 outputs_to_working_directory is True.

---
 lib/galaxy/jobs/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 4c0b441007c..a8ffb49512f 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -765,7 +765,7 @@ class JobWrapper( object ):
         jeha_false_path = None
         if self.app.config.outputs_to_working_directory:
             self.output_paths = []
-            output_dataset_paths = {}
+            self.output_dataset_paths = {}
             for name, data in [ ( da.name, da.dataset.dataset ) for da in job.output_datasets + job.output_library_datasets ]:
                 false_path = os.path.abspath( os.path.join( self.working_directory, "galaxy_dataset_%d.dat" % data.id ) )
                 dsp = DatasetPath( data.id, data.file_name, false_path )

From a7fba00f219090b4284c1e7d5898781b17588b81 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Tue, 18 Oct 2011 10:50:16 -0400
Subject: [PATCH 069/362] Bug fixes to Trackster ReferenceDataManager.

---
 static/scripts/trackster.js | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index 3941f3438a2..3f802895ee7 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -561,13 +561,13 @@ var ReferenceTrackDataManager = function(num_elements, track, subset) {
     DataManager.call(this, num_elements, track, subset);
 };
 extend(ReferenceTrackDataManager.prototype, DataManager.prototype, Cache.prototype, {
-    load_data: function(chrom, low, high, mode, resolution, extra_params) {
+    load_data: function(low, high, mode, resolution, extra_params) {
         if (resolution > 1) {
             // Now that data is pre-fetched before draw, we don't load reference tracks
-            // unless it's at the bottom level
-            return;
+            // unless it's at the bottom level.
+            return { data: null };
         }
-        return DataManager.prototype.load_data.call(this, chrom, low, high, mode, resolution, extra_params);
+        return DataManager.prototype.load_data.call(this, low, high, mode, resolution, extra_params);
     }
 });
 

From db1d316a7c29453847e500fdbace32ec945712ff Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Tue, 18 Oct 2011 11:41:08 -0400
Subject: [PATCH 070/362] Add new tool attributes to hold information about
 tools installed from a Galaxy tool shed.  Enhance the toolbox's <tool> tag
 parser to handle these new tool attributes for installed tools.  Enhance the
 Workflow import and load functions to search these new attributes when
 looking for required tools in the Galaxy instance.

---
 lib/galaxy/tools/__init__.py   | 31 ++++++++++++++++++++++---------
 lib/galaxy/workflow/modules.py | 20 ++++++--------------
 2 files changed, 28 insertions(+), 23 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index dcc20347c0d..32f4c3f866a 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -104,6 +104,14 @@ class ToolBox( object ):
         try:
             path = elem.get( "file" )
             tool = self.load_tool( os.path.join( tool_path, path ), guid=guid )
+            if guid is not None:
+                # Tool was installed from a Galaxy tool shed.
+                tool.tool_shed = elem.find( "tool_shed" ).text
+                tool.repository_name = elem.find( "repository_name" ).text
+                tool.repository_owner = elem.find( "repository_owner" ).text
+                tool.changeset_revision = elem.find( "changeset_revision" ).text
+                tool.old_id = elem.find( "id" ).text
+                tool.version = elem.find( "version" ).text
             if self.app.config.get_bool( 'enable_tool_tags', False ):
                 tag_names = elem.get( "tags", "" ).split( "," )
                 for tag_name in tag_names:
@@ -364,9 +372,7 @@ class ToolParallelismInfo(object):
             # legacy basic mode - provide compatible defaults
             self.attributes['split_size'] = 20
             self.attributes['split_mode'] = 'number_of_parts'
-            
-        
-    
+
 class Tool:
     """
     Represents a computational tool that can be executed through Galaxy. 
@@ -387,6 +393,13 @@ class Tool:
         # easily ensure that parameter dependencies like index files or
         # tool_data_table_conf.xml entries exist.
         self.input_params = []
+        # Attributes of tools installed from Galaxy tool sheds.
+        self.tool_shed = None
+        self.repository_name = None
+        self.repository_owner = None
+        self.changeset_revision = None
+        self.old_id = None
+        self.version = None
         # Parse XML element containing configuration
         self.parse( root, guid=guid )
     
@@ -407,14 +420,14 @@ class Tool:
             raise Exception, "Missing tool 'name'"
         # Get the UNIQUE id for the tool 
         # TODO: can this be generated automatically?
-        if guid is not None:
-            self.id = guid
-        else:
+        if guid is None:
             self.id = root.get( "id" )
+            self.version = root.get( "version" )
+        else:
+            self.id = guid
         if not self.id: 
-            raise Exception, "Missing tool 'id'" 
-        self.version = root.get( "version" )
-        if not self.version: 
+            raise Exception, "Missing tool 'id'"
+        if not self.version:
             # For backward compatibility, some tools may not have versions yet.
             self.version = "1.0.0"
         # Support multi-byte tools
diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
index 2ab95083370..f4dc32667a5 100644
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -171,15 +171,10 @@ class ToolModule( WorkflowModule ):
         except KeyError, e:
             # Handle the case where the workflow requires a tool not available in the local Galaxy instance.
             self.tool = None
-            # TODO: Instead of parsing the guid, get the tool_id and version from the shed_tool_conf.xml,
-            # which requires enhancements to the tool loading process.
+            # The id value of tools installed from a Galaxy tool shed is a guid, but
+            # these tool's old_id attribute should contain what we're looking for.
             for available_tool_id, available_tool in trans.app.toolbox.tools_by_id.items():
-                if available_tool_id.find( tool_id ) >=0:
-                    # We're attempting to match tool id against a tool guid.
-                    # TODO: match by tool_id (and version if we attempt that, but 
-                    # workflows will break) is not good enough because
-                    # 2 tools installed from a tool shed could both match this.  We
-                    # need to present a select list here.
+                if tool_id == available_tool.old_id:
                     self.tool = available_tool
                     break
         self.post_job_actions = {}
@@ -211,13 +206,10 @@ class ToolModule( WorkflowModule ):
         tool_id = step.tool_id
         install_tool_id = None
         if tool_id not in trans.app.toolbox.tools_by_id:
+            # The id value of tools installed from a Galaxy tool shed is a guid, but
+            # these tool's old_id attribute should contain what we're looking for.
             for available_tool_id, available_tool in trans.app.toolbox.tools_by_id.items():
-                if available_tool_id.find( tool_id ) >=0:
-                    # We're attempting to match tool id against a tool guid.
-                    # TODO: match by tool_id (and version if we attempt that, but 
-                    # workflows will break) is not good enough because
-                    # 2 tools installed from a tool shed could both match this.  We
-                    # need to present a select list here.
+                if tool_id == available_tool.old_id:
                     install_tool_id = available_tool_id
                     break
         if tool_id in trans.app.toolbox.tools_by_id or install_tool_id:

From 47019804f542d261553f8d3634794eb03cdc360b Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Tue, 18 Oct 2011 16:57:45 -0400
Subject: [PATCH 071/362] Fixes and code cleanup for searching for tools in
 tool shed repositories.

---
 .../community/controllers/repository.py       | 205 ++++++++++--------
 1 file changed, 114 insertions(+), 91 deletions(-)

diff --git a/lib/galaxy/webapps/community/controllers/repository.py b/lib/galaxy/webapps/community/controllers/repository.py
index 1a33fae36f8..d704014fc58 100644
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -340,8 +340,6 @@ class RepositoryController( BaseUIController, ItemRatings ):
         return self.category_list_grid( trans, **kwd )
     @web.expose
     def browse_downloadable_repositories( self, trans, **kwd ):
-        # Set the toolshedgalaxyurl cookie so we can get back
-        # to the calling local Galaxy instance.
         galaxy_url = kwd.get( 'galaxy_url', None )
         if galaxy_url:
             trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' )
@@ -354,7 +352,6 @@ class RepositoryController( BaseUIController, ItemRatings ):
                                                                   action='preview_tools_in_changeset',
                                                                   repository_id=repository_id,
                                                                   changeset_revision=repository.tip ) )
-
         # The changeset_revision_select_field in the RepositoryListGrid performs a refresh_on_change
         # which sends in request parameters like changeset_revison_1, changeset_revision_2, etc.  One
         # of the many select fields on the grid performed the refresh_on_change, so we loop through 
@@ -385,9 +382,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', '' ) )
         status = params.get( 'status', 'done' )
-        webapp = params.get( 'webapp', 'galaxy' )
-        # Set the toolshedgalaxyurl cookie so we can get back
-        # to the calling local Galaxy instance.
+        webapp = params.get( 'webapp', 'community' )
         galaxy_url = kwd.get( 'galaxy_url', None )
         if galaxy_url:
             trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' )
@@ -395,20 +390,19 @@ class RepositoryController( BaseUIController, ItemRatings ):
             operation = kwd[ 'operation' ].lower()
             is_admin = trans.user_is_admin()
             if operation == "view_or_manage_repository":
+                # The received id is a RepositoryMetadata id, so we have to get the repository id.
                 repository_metadata = get_repository_metadata_by_id( trans, kwd[ 'id' ] )
                 repository_id = trans.security.encode_id( repository_metadata.repository.id )
                 repository = get_repository( trans, repository_id )
-                # The received id is a RepositoryMetadata.id, so we have to get the repository id.
                 kwd[ 'id' ] = repository_id
                 kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision
                 if is_admin or repository.user == trans.user:
-                    return trans.response.send_redirect( web.url_for( controller='repository',
-                                                                      action='manage_repository',
-                                                                      **kwd ) )
+                    a = 'manage_repository'
                 else:
-                    return trans.response.send_redirect( web.url_for( controller='repository',
-                                                                      action='view_repository',
-                                                                      **kwd ) )
+                    a = 'view_repository'
+                return trans.response.send_redirect( web.url_for( controller='repository',
+                                                                  action=a,
+                                                                  **kwd ) )
             if operation == "install tools":
                 repo_info_dict = {}
                 galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' )
@@ -416,7 +410,6 @@ class RepositoryController( BaseUIController, ItemRatings ):
                 url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s' % ( galaxy_url, trans.request.host )
                 repository_metadata_ids = util.listify( kwd[ 'id' ] )
                 for repository_metadata_id in repository_metadata_ids:
-                    #self._set_clone_repository_cookie( trans, index, repository_metadata_id )
                     repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id )
                     repository = get_repository( trans, trans.security.encode_id( repository_metadata.repository_id ) )
                     repository_id = trans.security.encode_id( repository.id )
@@ -426,60 +419,15 @@ class RepositoryController( BaseUIController, ItemRatings ):
                 encoded_repo_info_dict = self._encode( repo_info_dict )
                 url += '&repo_info_dict=%s' % encoded_repo_info_dict
                 return trans.response.send_redirect( url )
-        tool_ids = [ tid.lower() for tid in util.listify( kwd.get( 'tool_id', '' ) ) ]
-        tool_names = [ tn.lower() for tn in util.listify( kwd.get( 'tool_name', '' ) ) ]
-        tool_versions = [ tv.lower() for tv in util.listify( kwd.get( 'tool_version', '' ) ) ]
+        tool_ids = [ item.lower() for item in util.listify( kwd.get( 'tool_id', '' ) ) ]
+        tool_names = [ item.lower() for item in util.listify( kwd.get( 'tool_name', '' ) ) ]
+        tool_versions = [ item.lower() for item in util.listify( kwd.get( 'tool_version', '' ) ) ]
         exact_matches = params.get( 'exact_matches', '' )
         exact_matches_checked = CheckboxField.is_checked( exact_matches )
         match_tuples = []
         ok = True
         if tool_ids or tool_names or tool_versions:
-            for repository_metadata in trans.sa_session.query( model.RepositoryMetadata ):
-                metadata = repository_metadata.metadata
-                tools = metadata[ 'tools' ]
-                for tool_dict in tools:
-                    if tool_ids and not tool_names and not tool_versions:
-                        for tool_id in tool_ids:
-                            if self._in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id ):
-                                match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
-                    elif tool_names and not tool_ids and not tool_versions:
-                        for tool_name in tool_names:
-                            if self._in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name ):
-                                match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
-                    elif tool_versions and not tool_ids and not tool_names:
-                        for tool_version in tool_versions:
-                            if self._in_tool_dict( tool_dict, exact_matches_checked, tool_version=tool_version ):
-                                match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
-                    elif tool_ids and tool_names and not tool_versions:
-                        if len( tool_ids ) == len( tool_names ):
-                            for i, tool_id in enumerate( tool_ids ):
-                                tool_name = tool_names[ i ]
-                                if self._in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name ):
-                                    match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
-                        else:
-                            message = "No search performed - each field must contain the same number of comma-separated items."
-                            status = "error"
-                            ok = False
-                    elif tool_ids and tool_versions and not tool_names:
-                        if len( tool_ids )  == len( tool_versions ):
-                            for i, tool_id in enumerate( tool_ids ):
-                                tool_version = tool_versions[ i ]
-                                if self._in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_version=tool_version ):
-                                    match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
-                        else:
-                            message = "No search performed - each field must contain the same number of comma-separated items."
-                            status = "error"
-                            ok = False
-                    elif tool_versions and tool_names and not tool_ids:
-                        if len( tool_versions ) == len( tool_names ):
-                            for i, tool_version in enumerate( tool_versions ):
-                                tool_name = tool_names[ i ]
-                                if self._in_tool_dict( tool_dict, exact_matches_checked, tool_version=tool_version, tool_name=tool_name ):
-                                    match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
-                        else:
-                            message = "No search performed - each field must contain the same number of comma-separated items."
-                            status = "error"
-                            ok = False
+            ok, match_tuples = self._search_repository_metadata( trans, tool_ids, tool_names, tool_versions, exact_matches_checked )
             if ok:
                 kwd[ 'match_tuples' ] = match_tuples
                 # Render the list view
@@ -488,42 +436,74 @@ class RepositoryController( BaseUIController, ItemRatings ):
                     # that have been found for a workflow in Galaxy.
                     return self.install_matched_repository_list_grid( trans, **kwd )
                 else:
-                    if tool_ids:
-                        tool_id_str = ','.join( tool_ids )
-                    else:
-                        tool_id_str = ''
-                    if tool_names:
-                        tool_name_str = ','.join( tool_names )
-                    else:
-                        tool_name_str = ''
-                    if tool_versions:
-                        tool_version_str = ','.join( tool_versions )
-                    else:
-                        tool_version_str = ''
                     kwd[ 'message' ] = "tool id: <b>%s</b><br/>tool name: <b>%s</b><br/>tool version: <b>%s</b><br/>exact matches only: <b>%s</b>" % \
-                        ( tool_id_str, tool_name_str, tool_version_str, str( exact_matches_checked ) )
+                        ( self._stringify( tool_ids ), self._stringify( tool_names ), self._stringify( tool_versions ), str( exact_matches_checked ) )
                     return self.matched_repository_list_grid( trans, **kwd )
+            else:
+                message = "No search performed - each field must contain the same number of comma-separated items."
+                status = "error"
         exact_matches_check_box = CheckboxField( 'exact_matches', checked=exact_matches_checked )
-        if tool_ids:
-            tool_id = ','.join( tool_ids )
-        else:
-            tool_id = ''
-        if tool_names:
-            tool_name = ','.join( tool_names )
-        else:
-            tool_name = ''
-        if tool_versions:
-            tool_version = ','.join( tool_versions )
-        else:
-            tool_version = ''
         return trans.fill_template( '/webapps/community/repository/find_tools.mako',
                                     webapp=webapp,
-                                    tool_id=tool_id,
-                                    tool_name=tool_name,
-                                    tool_version=tool_version,
+                                    tool_id=self._stringify( tool_ids ),
+                                    tool_name=self._stringify( tool_names ),
+                                    tool_version=self._stringify( tool_versions ),
                                     exact_matches_check_box=exact_matches_check_box,
                                     message=message,
                                     status=status )
+    def _search_repository_metadata( self, trans, tool_ids, tool_names, tool_versions, exact_matches_checked ):
+        match_tuples = []
+        ok = True
+        for repository_metadata in trans.sa_session.query( model.RepositoryMetadata ):
+            metadata = repository_metadata.metadata
+            tools = metadata[ 'tools' ]
+            for tool_dict in tools:
+                if tool_ids and not tool_names and not tool_versions:
+                    for tool_id in tool_ids:
+                        if self._in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id ):
+                            match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
+                elif tool_names and not tool_ids and not tool_versions:
+                    for tool_name in tool_names:
+                        if self._in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name ):
+                            match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
+                elif tool_versions and not tool_ids and not tool_names:
+                    for tool_version in tool_versions:
+                        if self._in_tool_dict( tool_dict, exact_matches_checked, tool_version=tool_version ):
+                            match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
+                elif tool_ids and tool_names and not tool_versions:
+                    if len( tool_ids ) == len( tool_names ):
+                        match_tuples = self._search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names )
+                    elif len( tool_ids ) == 1 or len( tool_names ) == 1:
+                        tool_ids, tool_names = self._make_same_length( tool_ids, tool_names )
+                        match_tuples = self._search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names )
+                    else:
+                        ok = False
+                elif tool_ids and tool_versions and not tool_names:
+                    if len( tool_ids )  == len( tool_versions ):
+                        match_tuples = self._search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions )
+                    elif len( tool_ids ) == 1 or len( tool_versions ) == 1:
+                        tool_ids, tool_versions = self._make_same_length( tool_ids, tool_versions )
+                        match_tuples = self._search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions )
+                    else:
+                        ok = False
+                elif tool_versions and tool_names and not tool_ids:
+                    if len( tool_versions ) == len( tool_names ):
+                        match_tuples = self._search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions )
+                    elif len( tool_versions ) == 1 or len( tool_names ) == 1:
+                        tool_versions, tool_names = self._make_same_length( tool_versions, tool_names )
+                        match_tuples = self._search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions )
+                    else:
+                        ok = False
+                elif tool_versions and tool_names and tool_ids:
+                    if len( tool_versions ) == len( tool_names ) and len( tool_names ) == len( tool_ids ):
+                        for i, tool_version in enumerate( tool_versions ):
+                            tool_name = tool_names[ i ]
+                            tool_id = tool_ids[ i ]
+                            if self._in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name, tool_version=tool_version ):
+                                match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
+                    else:
+                        ok = False
+        return ok, match_tuples
     def _in_tool_dict( self, tool_dict, exact_matches_checked, tool_id=None, tool_name=None, tool_version=None ):
         found = False
         if tool_id and not tool_name and not tool_version:
@@ -553,7 +533,50 @@ class RepositoryController( BaseUIController, ItemRatings ):
             tool_dict_tool_name = tool_dict[ 'name' ].lower()
             found = ( tool_version == tool_dict_tool_version and tool_name == tool_dict_tool_name ) or \
                     ( not exact_matches_checked and tool_dict_tool_version.find( tool_version ) >= 0 and tool_dict_tool_name.find( tool_name ) >= 0 )
+        elif tool_version and tool_name and tool_id:
+            tool_dict_tool_version = tool_dict[ 'version' ].lower()
+            tool_dict_tool_name = tool_dict[ 'name' ].lower()
+            tool_dict_tool_id = tool_dict[ 'id' ].lower()
+            found = ( tool_version == tool_dict_tool_version and \
+                      tool_name == tool_dict_tool_name and \
+                      tool_id == tool_dict_tool_id ) or \
+                    ( not exact_matches_checked and \
+                      tool_dict_tool_version.find( tool_version ) >= 0 and \
+                      tool_dict_tool_name.find( tool_name ) >= 0 and \
+                      tool_dict_tool_id.find( tool_id ) >= 0 )
         return found
+    def _stringify( self, list ):
+        if list:
+            return ','.join( list )
+        return ''
+    def _make_same_length( self, list1, list2 ):
+        # If either list is 1 item, we'll append to it until its 
+        #length is the same as the other.
+        if len( list1 ) == 1:
+            for i in range( 1, len( list2 ) ):
+                list1.append( list1[ 0 ] )
+        elif len( list2 ) == 1:
+            for i in range( 1, len( list1 ) ):
+                list2.append( list2[ 0 ] )
+        return list1, list2
+    def _search_ids_names( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ):
+        for i, tool_id in enumerate( tool_ids ):
+            tool_name = tool_names[ i ]
+            if self._in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name ):
+                match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
+        return match_tuples
+    def _search_ids_versions( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ):
+        for i, tool_id in enumerate( tool_ids ):
+            tool_version = tool_versions[ i ]
+            if self._in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_version=tool_version ):
+                match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
+        return match_tuples
+    def _search_names_versions( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ):
+        for i, tool_name in enumerate( tool_names ):
+            tool_version = tool_versions[ i ]
+            if self._in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name, tool_version=tool_version ):
+                match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
+        return match_tuples
     def _encode( self, repo_info_dict ):
         value = simplejson.dumps( repo_info_dict )
         a = hmac_new( 'ToolShedAndGalaxyMustHaveThisSameKey', value )

From 8532d5e47b5b21e35a0ad54e218afa26d3568ad3 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Wed, 19 Oct 2011 10:14:51 -0400
Subject: [PATCH 072/362] Add dataset_metadata_in_data_table validator. Mimics
 behavior of dataset_metadata_in_file, but uses data tables.

---
 lib/galaxy/tools/parameters/validation.py | 42 ++++++++++++++++++++++-
 1 file changed, 41 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/tools/parameters/validation.py b/lib/galaxy/tools/parameters/validation.py
index 3f2d3ee9cbd..969522841ac 100644
--- a/lib/galaxy/tools/parameters/validation.py
+++ b/lib/galaxy/tools/parameters/validation.py
@@ -189,7 +189,7 @@ class MetadataValidator( Validator ):
 
 class UnspecifiedBuildValidator( Validator ):
     """
-    Validator that checks for missing metadata
+    Validator that checks for dbkey not equal to '?'
     """
     def __init__( self, message=None ):
         if message is None:
@@ -268,6 +268,45 @@ class MetadataInFileColumnValidator( Validator ):
                 return
         raise ValueError( self.message )
 
+class MetadataInDataTableColumnValidator( Validator ):
+    """
+    Validator that checks if the value for a dataset's metadata item exists in a file.
+    """
+    @classmethod
+    def from_element( cls, param, elem ):
+        table_name = elem.get( "table_name", None )
+        assert table_name, 'You must specify a table_name.'
+        tool_data_table = param.tool.app.tool_data_tables[ table_name ]
+        metadata_name = elem.get( "metadata_name", None )
+        if metadata_name:
+            metadata_name = metadata_name.strip()
+        metadata_column = elem.get( "metadata_column", 0 )
+        try:
+            metadata_column = int( metadata_column )
+        except:
+            pass
+        message = elem.get( "message", "Value for metadata %s was not found in %s." % ( metadata_name, table_name ) )
+        line_startswith = elem.get( "line_startswith", None  )
+        if line_startswith:
+            line_startswith = line_startswith.strip()
+        return cls( tool_data_table, metadata_name, metadata_column, message, line_startswith )
+    def __init__( self, tool_data_table, metadata_name, metadata_column, message="Value for metadata not found.", line_startswith=None ):
+        self.metadata_name = metadata_name
+        self.message = message
+        self.valid_values = []
+        if isinstance( metadata_column, basestring ):
+            metadata_column = tool_data_table.columns[ metadata_column ]
+        for fields in tool_data_table.get_fields():
+            if metadata_column < len( fields ):
+                self.valid_values.append( fields[ metadata_column ] )
+    def validate( self, value, history = None ):
+        if not value: return
+        if hasattr( value, "metadata" ):
+            if value.metadata.spec[self.metadata_name].param.to_string( value.metadata.get( self.metadata_name ) ) in self.valid_values:
+                return
+        raise ValueError( self.message )
+
+
 validator_types = dict( expression=ExpressionValidator,
                         regex=RegexValidator,
                         in_range=InRangeValidator,
@@ -277,6 +316,7 @@ validator_types = dict( expression=ExpressionValidator,
                         no_options=NoOptionsValidator,
                         empty_field=EmptyTextfieldValidator,
                         dataset_metadata_in_file=MetadataInFileColumnValidator,
+                        dataset_metadata_in_data_table=MetadataInDataTableColumnValidator,
                         dataset_ok_validator=DatasetOkValidator )
                         
 def get_suite():

From 34a565096a8189a82f22321909f7c9d669bcd38f Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Wed, 19 Oct 2011 16:47:25 -0400
Subject: [PATCH 073/362] Enhanced Galaxy instance <=> Galaxy tool shed
 integration: 1. All accessible tool sheds are now displayed in a mako
 template in teh Admin view rather than the left tool panel 2. From Galaxy you
 can now search for tools by id, name, version in a selected Galaxy tool shed.
 3. Tools found using the above search can now be installed in the local
 Galaxy instance.

---
 lib/galaxy/web/controllers/admin.py           |  41 ++++--
 .../community/controllers/repository.py       | 119 ++++++++++--------
 .../webapps/community/controllers/upload.py   |   1 +
 .../repository/browse_repository.mako         |   4 +-
 .../webapps/community/repository/common.mako  |   6 +-
 .../community/repository/contact_owner.mako   |   6 +-
 .../community/repository/find_tools.mako      |   5 +-
 .../repository/manage_repository.mako         |   8 +-
 .../preview_tools_in_changeset.mako           |   4 +-
 .../community/repository/rate_repository.mako |   6 +-
 .../community/repository/tool_form.mako       |  16 +--
 .../webapps/community/repository/upload.mako  |   6 +-
 .../community/repository/view_changelog.mako  |   4 +-
 .../community/repository/view_changeset.mako  |   6 +-
 .../community/repository/view_repository.mako |  74 +++++------
 .../repository/view_tool_metadata.mako        |  24 ++--
 templates/webapps/galaxy/admin/index.mako     |   5 +-
 .../webapps/galaxy/admin/tool_sheds.mako      |  40 ++++++
 18 files changed, 225 insertions(+), 150 deletions(-)
 create mode 100644 templates/webapps/galaxy/admin/tool_sheds.mako

diff --git a/lib/galaxy/web/controllers/admin.py b/lib/galaxy/web/controllers/admin.py
index 8b1acf85dca..2168f811ddb 100644
--- a/lib/galaxy/web/controllers/admin.py
+++ b/lib/galaxy/web/controllers/admin.py
@@ -688,20 +688,28 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
         return self.repository_list_grid( trans, **kwd )
     @web.expose
     @web.require_admin
+    def browse_tool_sheds( self, trans, **kwd ):
+        params = util.Params( kwd )
+        message = util.restore_text( params.get( 'message', ''  ) )
+        status = params.get( 'status', 'done' )
+        return trans.fill_template( '/webapps/galaxy/admin/tool_sheds.mako',
+                                    webapp='galaxy',
+                                    message=message,
+                                    status='error' )
+    @web.expose
+    @web.require_admin
+    def find_tools_in_tool_shed( self, trans, **kwd ):
+        tool_shed_url = kwd[ 'tool_shed_url' ]
+        galaxy_url = trans.request.host
+        url = '%s/repository/find_tools?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, galaxy_url )
+        return trans.response.send_redirect( url )
+    @web.expose
+    @web.require_admin
     def browse_tool_shed( self, trans, **kwd ):
         tool_shed_url = kwd[ 'tool_shed_url' ]
         galaxy_url = trans.request.host
-        url = '%s/repository/browse_downloadable_repositories?galaxy_url=%s&webapp=community' % ( tool_shed_url, galaxy_url )
+        url = '%s/repository/browse_downloadable_repositories?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, galaxy_url )
         return trans.response.send_redirect( url )
-    def _decode( self, value ):
-        # Extract and verify hash
-        a, b = value.split( ":" )
-        value = binascii.unhexlify( b )
-        test = hmac_new( 'ToolShedAndGalaxyMustHaveThisSameKey', value )
-        assert a == test
-        # Restore from string
-        values = json_fix( simplejson.loads( value ) )
-        return values
     @web.expose
     @web.require_admin
     def install_tool_shed_repository( self, trans, **kwd ):
@@ -728,7 +736,7 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
                 section_key = 'section_%s' % kwd[ 'tool_panel_section' ]
                 tool_section = trans.app.toolbox.tool_panel[ section_key ]
                 # Decode the encoded repo_info_dict param value.
-                repo_info_dict = self._decode( repo_info_dict )
+                repo_info_dict = self.__decode( repo_info_dict )
                 # Clone the repository to the configured location.
                 current_working_dir = os.getcwd()
                 for name, repo_info_tuple in repo_info_dict.items():
@@ -846,7 +854,7 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
         galaxy_url = trans.request.host
         # Send a request to the relevant tool shed to see if there are any updates.
         # TODO: support https in the following url.
-        url = 'http://%s/repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=community' % \
+        url = 'http://%s/repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \
             ( repository.tool_shed, galaxy_url, repository.name, repository.owner, repository.changeset_revision )
         return trans.response.send_redirect( url )
     @web.expose
@@ -1149,6 +1157,15 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
             section_str += '        </tool>\n'
         section_str += '    </section>\n'
         return section_str
+    def __decode( self, value ):
+        # Extract and verify hash
+        a, b = value.split( ":" )
+        value = binascii.unhexlify( b )
+        test = hmac_new( 'ToolShedAndGalaxyMustHaveThisSameKey', value )
+        assert a == test
+        # Restore from string
+        values = json_fix( simplejson.loads( value ) )
+        return values
 
 ## ---- Utility methods -------------------------------------------------------
 
diff --git a/lib/galaxy/webapps/community/controllers/repository.py b/lib/galaxy/webapps/community/controllers/repository.py
index d704014fc58..f130be58949 100644
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -283,13 +283,14 @@ class MatchedRepositoryListGrid( grids.Grid ):
 
 class InstallMatchedRepositoryListGrid( MatchedRepositoryListGrid ):
     # Grid definition
-    title = "Repositories with required tools"
-    operations = [ grids.GridOperation( "Install tools",
-                                        url_args = dict( controller='repository',
-                                                         action='find_tools',
-                                                         webapp='community' ),
-                                        allow_multiple=True,
-                                        async_compatible=False ) ]
+    title = "Repositories that contain tools matching search criteria"
+    columns = [ col for col in MatchedRepositoryListGrid.columns ]
+    # Override the NameColumn
+    columns[ 0 ] = MatchedRepositoryListGrid.NameColumn( "Name",
+                                                         link=( lambda item: dict( operation="view_or_manage_repository",
+                                                                                   id=item.id,
+                                                                                   webapp="galaxy" ) ),
+                                                         attach_popup=True )
 
 class RepositoryController( BaseUIController, ItemRatings ):
 
@@ -340,6 +341,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
         return self.category_list_grid( trans, **kwd )
     @web.expose
     def browse_downloadable_repositories( self, trans, **kwd ):
+        webapp = kwd.get( 'webapp', 'community' )
         galaxy_url = kwd.get( 'galaxy_url', None )
         if galaxy_url:
             trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' )
@@ -366,12 +368,14 @@ class RepositoryController( BaseUIController, ItemRatings ):
                 if repository.tip != v:
                     return trans.response.send_redirect( web.url_for( controller='repository',
                                                                       action='preview_tools_in_changeset',
+                                                                      webapp=webapp,
                                                                       repository_id=trans.security.encode_id( repository.id ),
                                                                       changeset_revision=v ) )
         url_args = dict( action='browse_downloadable_repositories',
                          operation='preview_tools_in_changeset',
+                         webapp=webapp,
                          repository_id=repository_id )
-        self.downloadable_repository_list_grid.operations = [ grids.GridOperation( "Preview and install tools",
+        self.downloadable_repository_list_grid.operations = [ grids.GridOperation( "Preview and install",
                                                                                    url_args=url_args,
                                                                                    allow_multiple=False,
                                                                                    async_compatible=False ) ]
@@ -396,18 +400,18 @@ class RepositoryController( BaseUIController, ItemRatings ):
                 repository = get_repository( trans, repository_id )
                 kwd[ 'id' ] = repository_id
                 kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision
-                if is_admin or repository.user == trans.user:
+                if webapp == 'community' and ( is_admin or repository.user == trans.user ):
                     a = 'manage_repository'
                 else:
                     a = 'view_repository'
                 return trans.response.send_redirect( web.url_for( controller='repository',
                                                                   action=a,
                                                                   **kwd ) )
-            if operation == "install tools":
+            if operation == "install":
                 repo_info_dict = {}
                 galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' )
                 # TODO: support https in the following url.
-                url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s' % ( galaxy_url, trans.request.host )
+                url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s&webapp=%s' % ( galaxy_url, trans.request.host, webapp )
                 repository_metadata_ids = util.listify( kwd[ 'id' ] )
                 for repository_metadata_id in repository_metadata_ids:
                     repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id )
@@ -416,7 +420,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
                     changeset_revision = repository_metadata.changeset_revision
                     repository_clone_url = generate_clone_url( trans, repository_id )
                     repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, changeset_revision )
-                encoded_repo_info_dict = self._encode( repo_info_dict )
+                encoded_repo_info_dict = self.__encode( repo_info_dict )
                 url += '&repo_info_dict=%s' % encoded_repo_info_dict
                 return trans.response.send_redirect( url )
         tool_ids = [ item.lower() for item in util.listify( kwd.get( 'tool_id', '' ) ) ]
@@ -427,17 +431,19 @@ class RepositoryController( BaseUIController, ItemRatings ):
         match_tuples = []
         ok = True
         if tool_ids or tool_names or tool_versions:
-            ok, match_tuples = self._search_repository_metadata( trans, tool_ids, tool_names, tool_versions, exact_matches_checked )
+            ok, match_tuples = self.__search_repository_metadata( trans, tool_ids, tool_names, tool_versions, exact_matches_checked )
             if ok:
                 kwd[ 'match_tuples' ] = match_tuples
                 # Render the list view
-                if galaxy_url:
-                    # Our request originated from a Galaxy instance, so we're listing tools
-                    # that have been found for a workflow in Galaxy.
+                if webapp == 'galaxy':
+                    # Our request originated from a Galaxy instance.
+                    install_url_args = dict( controller='repository', action='find_tools', webapp=webapp )
+                    operations = [ grids.GridOperation( "Install", url_args=install_url_args, allow_multiple=True, async_compatible=False ) ]
+                    self.install_matched_repository_list_grid.operations = operations
                     return self.install_matched_repository_list_grid( trans, **kwd )
                 else:
                     kwd[ 'message' ] = "tool id: <b>%s</b><br/>tool name: <b>%s</b><br/>tool version: <b>%s</b><br/>exact matches only: <b>%s</b>" % \
-                        ( self._stringify( tool_ids ), self._stringify( tool_names ), self._stringify( tool_versions ), str( exact_matches_checked ) )
+                        ( self.__stringify( tool_ids ), self.__stringify( tool_names ), self.__stringify( tool_versions ), str( exact_matches_checked ) )
                     return self.matched_repository_list_grid( trans, **kwd )
             else:
                 message = "No search performed - each field must contain the same number of comma-separated items."
@@ -445,13 +451,13 @@ class RepositoryController( BaseUIController, ItemRatings ):
         exact_matches_check_box = CheckboxField( 'exact_matches', checked=exact_matches_checked )
         return trans.fill_template( '/webapps/community/repository/find_tools.mako',
                                     webapp=webapp,
-                                    tool_id=self._stringify( tool_ids ),
-                                    tool_name=self._stringify( tool_names ),
-                                    tool_version=self._stringify( tool_versions ),
+                                    tool_id=self.__stringify( tool_ids ),
+                                    tool_name=self.__stringify( tool_names ),
+                                    tool_version=self.__stringify( tool_versions ),
                                     exact_matches_check_box=exact_matches_check_box,
                                     message=message,
                                     status=status )
-    def _search_repository_metadata( self, trans, tool_ids, tool_names, tool_versions, exact_matches_checked ):
+    def __search_repository_metadata( self, trans, tool_ids, tool_names, tool_versions, exact_matches_checked ):
         match_tuples = []
         ok = True
         for repository_metadata in trans.sa_session.query( model.RepositoryMetadata ):
@@ -460,38 +466,38 @@ class RepositoryController( BaseUIController, ItemRatings ):
             for tool_dict in tools:
                 if tool_ids and not tool_names and not tool_versions:
                     for tool_id in tool_ids:
-                        if self._in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id ):
+                        if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id ):
                             match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
                 elif tool_names and not tool_ids and not tool_versions:
                     for tool_name in tool_names:
-                        if self._in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name ):
+                        if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name ):
                             match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
                 elif tool_versions and not tool_ids and not tool_names:
                     for tool_version in tool_versions:
-                        if self._in_tool_dict( tool_dict, exact_matches_checked, tool_version=tool_version ):
+                        if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_version=tool_version ):
                             match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
                 elif tool_ids and tool_names and not tool_versions:
                     if len( tool_ids ) == len( tool_names ):
-                        match_tuples = self._search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names )
+                        match_tuples = self.__search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names )
                     elif len( tool_ids ) == 1 or len( tool_names ) == 1:
-                        tool_ids, tool_names = self._make_same_length( tool_ids, tool_names )
-                        match_tuples = self._search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names )
+                        tool_ids, tool_names = self.__make_same_length( tool_ids, tool_names )
+                        match_tuples = self.__search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names )
                     else:
                         ok = False
                 elif tool_ids and tool_versions and not tool_names:
                     if len( tool_ids )  == len( tool_versions ):
-                        match_tuples = self._search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions )
+                        match_tuples = self.__search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions )
                     elif len( tool_ids ) == 1 or len( tool_versions ) == 1:
-                        tool_ids, tool_versions = self._make_same_length( tool_ids, tool_versions )
-                        match_tuples = self._search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions )
+                        tool_ids, tool_versions = self.__make_same_length( tool_ids, tool_versions )
+                        match_tuples = self.__search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions )
                     else:
                         ok = False
                 elif tool_versions and tool_names and not tool_ids:
                     if len( tool_versions ) == len( tool_names ):
-                        match_tuples = self._search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions )
+                        match_tuples = self.__search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions )
                     elif len( tool_versions ) == 1 or len( tool_names ) == 1:
-                        tool_versions, tool_names = self._make_same_length( tool_versions, tool_names )
-                        match_tuples = self._search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions )
+                        tool_versions, tool_names = self.__make_same_length( tool_versions, tool_names )
+                        match_tuples = self.__search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions )
                     else:
                         ok = False
                 elif tool_versions and tool_names and tool_ids:
@@ -499,12 +505,12 @@ class RepositoryController( BaseUIController, ItemRatings ):
                         for i, tool_version in enumerate( tool_versions ):
                             tool_name = tool_names[ i ]
                             tool_id = tool_ids[ i ]
-                            if self._in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name, tool_version=tool_version ):
+                            if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name, tool_version=tool_version ):
                                 match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
                     else:
                         ok = False
         return ok, match_tuples
-    def _in_tool_dict( self, tool_dict, exact_matches_checked, tool_id=None, tool_name=None, tool_version=None ):
+    def __in_tool_dict( self, tool_dict, exact_matches_checked, tool_id=None, tool_name=None, tool_version=None ):
         found = False
         if tool_id and not tool_name and not tool_version:
             tool_dict_tool_id = tool_dict[ 'id' ].lower()
@@ -545,13 +551,13 @@ class RepositoryController( BaseUIController, ItemRatings ):
                       tool_dict_tool_name.find( tool_name ) >= 0 and \
                       tool_dict_tool_id.find( tool_id ) >= 0 )
         return found
-    def _stringify( self, list ):
+    def __stringify( self, list ):
         if list:
             return ','.join( list )
         return ''
-    def _make_same_length( self, list1, list2 ):
+    def __make_same_length( self, list1, list2 ):
         # If either list is 1 item, we'll append to it until its 
-        #length is the same as the other.
+        # length is the same as the other.
         if len( list1 ) == 1:
             for i in range( 1, len( list2 ) ):
                 list1.append( list1[ 0 ] )
@@ -559,25 +565,25 @@ class RepositoryController( BaseUIController, ItemRatings ):
             for i in range( 1, len( list1 ) ):
                 list2.append( list2[ 0 ] )
         return list1, list2
-    def _search_ids_names( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ):
+    def __search_ids_names( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ):
         for i, tool_id in enumerate( tool_ids ):
             tool_name = tool_names[ i ]
-            if self._in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name ):
+            if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name ):
                 match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
         return match_tuples
-    def _search_ids_versions( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ):
+    def __search_ids_versions( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ):
         for i, tool_id in enumerate( tool_ids ):
             tool_version = tool_versions[ i ]
-            if self._in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_version=tool_version ):
+            if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_version=tool_version ):
                 match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
         return match_tuples
-    def _search_names_versions( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ):
+    def __search_names_versions( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ):
         for i, tool_name in enumerate( tool_names ):
             tool_version = tool_versions[ i ]
-            if self._in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name, tool_version=tool_version ):
+            if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name, tool_version=tool_version ):
                 match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
         return match_tuples
-    def _encode( self, repo_info_dict ):
+    def __encode( self, repo_info_dict ):
         value = simplejson.dumps( repo_info_dict )
         a = hmac_new( 'ToolShedAndGalaxyMustHaveThisSameKey', value )
         b = binascii.hexlify( value )
@@ -587,6 +593,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', '' ) )
         status = params.get( 'status', 'done' )
+        webapp = params.get( 'webapp', 'community' )
         repository = get_repository( trans, repository_id )
         changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) )
         repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision )
@@ -605,7 +612,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
                                     revision_label=revision_label,
                                     changeset_revision_select_field=changeset_revision_select_field,
                                     metadata=metadata,
-                                    display_for_install=True,
+                                    webapp=webapp,
                                     message=message,
                                     status=status )
     @web.expose
@@ -631,7 +638,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
         name = params.get( 'name', None )
         owner = params.get( 'owner', None )
         changeset_revision = params.get( 'changeset_revision', None )
-        webapp = params.get( 'webapp', None )
+        webapp = params.get( 'webapp', 'community' )
         # Start building up the url to redirect back to the calling Galaxy instance.
         # TODO: support https in the following url.
         url = 'http://%s/admin/update_to_changeset_revision?tool_shed_url=%s' % ( galaxy_url, trans.request.host )
@@ -713,6 +720,8 @@ class RepositoryController( BaseUIController, ItemRatings ):
         # We add params to the keyword dict in this method in order to rename the param
         # with an "f-" prefix, simulating filtering by clicking a search link.  We have
         # to take this approach because the "-" character is illegal in HTTP requests.
+        if 'webapp' not in kwd:
+            kwd[ 'webapp' ] = 'community'
         if 'operation' in kwd:
             operation = kwd['operation'].lower()
             if operation == "view_or_manage_repository":
@@ -855,6 +864,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
                 message = "Repository '%s' has been created." % repository.name
                 trans.response.send_redirect( web.url_for( controller='repository',
                                                            action='view_repository',
+                                                           webapp='community',
                                                            message=message,
                                                            id=trans.security.encode_id( repository.id ) ) )
         return trans.fill_template( '/webapps/community/repository/create_repository.mako',
@@ -945,6 +955,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
+        webapp = params.get( 'webapp', 'community' )
         commit_message = util.restore_text( params.get( 'commit_message', 'Deleted selected files' ) )
         repository = get_repository( trans, id )
         repo = hg.repository( get_configured_ui(), repository.repo_path )
@@ -957,6 +968,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
                                     repository=repository,
                                     commit_message=commit_message,
                                     is_malicious=is_malicious,
+                                    webapp=webapp,
                                     message=message,
                                     status=status )
     @web.expose
@@ -1098,6 +1110,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
         repository = get_repository( trans, id )
+        webapp = params.get( 'webapp', 'community' )
         repo = hg.repository( get_configured_ui(), repository.repo_path )
         avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model )
         changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) )
@@ -1155,6 +1168,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
                                     changeset_revision_select_field=changeset_revision_select_field,
                                     revision_label=revision_label,
                                     is_malicious=is_malicious,
+                                    webapp=webapp,
                                     message=message,
                                     status=status )
     @web.expose
@@ -1191,6 +1205,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
                 return trans.response.send_redirect( web.url_for( controller='repository',
                                                                   action='view_repository',
                                                                   id=id,
+                                                                  webapp='community',
                                                                   message=message,
                                                                   status=status ) )
             if repo_name != repository.name:
@@ -1482,7 +1497,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
-        display_for_install = util.string_as_bool( params.get( 'display_for_install', False ) )
+        webapp = params.get( 'webapp', 'community' )
         repository = get_repository( trans, repository_id )
         repo = hg.repository( get_configured_ui(), repository.repo_path )          
         try:
@@ -1523,12 +1538,12 @@ class RepositoryController( BaseUIController, ItemRatings ):
                                         tool=tool,
                                         tool_state=tool_state,
                                         is_malicious=is_malicious,
-                                        display_for_install=display_for_install,
+                                        webapp=webapp,
                                         message=message,
                                         status=status )
         except Exception, e:
             message = "Error loading tool: %s.  Click <b>Reset metadata</b> to correct this error." % str( e )
-        if display_for_install:
+        if webapp == 'galaxy':
             return trans.response.send_redirect( web.url_for( controller='repository',
                                                               action='preview_tools_in_changeset',
                                                               repository_id=repository_id,
@@ -1558,7 +1573,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
-        display_for_install = util.string_as_bool( params.get( 'display_for_install', False ) )
+        webapp = params.get( 'webapp', 'community' )
         repository = get_repository( trans, repository_id )
         metadata = {}
         tool = None
@@ -1587,7 +1602,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
                                     revision_label=revision_label,
                                     changeset_revision_select_field=changeset_revision_select_field,
                                     is_malicious=is_malicious,
-                                    display_for_install=display_for_install,
+                                    webapp=webapp,
                                     message=message,
                                     status=status )
     @web.expose
diff --git a/lib/galaxy/webapps/community/controllers/upload.py b/lib/galaxy/webapps/community/controllers/upload.py
index bc206ac6693..9a691eb5250 100644
--- a/lib/galaxy/webapps/community/controllers/upload.py
+++ b/lib/galaxy/webapps/community/controllers/upload.py
@@ -138,6 +138,7 @@ class UploadController( BaseUIController ):
                                                                action='browse_repository',
                                                                id=repository_id,
                                                                commit_message='Deleted selected files',
+                                                               webapp='community',
                                                                message=message,
                                                                status=status ) )
                 else:
diff --git a/templates/webapps/community/repository/browse_repository.mako b/templates/webapps/community/repository/browse_repository.mako
index 2f27355af7a..054e682fc48 100644
--- a/templates/webapps/community/repository/browse_repository.mako
+++ b/templates/webapps/community/repository/browse_repository.mako
@@ -71,13 +71,13 @@
             %if can_manage:
                 <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a>
             %else:
-                <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a>
+                <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View repository</a>
             %endif
             %if can_upload:
                 <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a>
             %endif
             %if can_view_change_log:
-                <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a>
+                <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View change log</a>
             %endif
             %if can_rate:
                 <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a>
diff --git a/templates/webapps/community/repository/common.mako b/templates/webapps/community/repository/common.mako
index c239f515c7c..acdf665fe91 100644
--- a/templates/webapps/community/repository/common.mako
+++ b/templates/webapps/community/repository/common.mako
@@ -83,7 +83,7 @@
     hg clone <a href="${clone_str}">${clone_str}</a>
 </%def>
 
-<%def name="render_repository_tools_and_workflows( metadata, can_set_metadata=False, display_for_install=False )">
+<%def name="render_repository_tools_and_workflows( metadata, can_set_metadata=False, webapp='community' )">
     %if metadata or can_set_metadata:
         <p/>
         <div class="toolForm">
@@ -111,12 +111,12 @@
                                     <tr>
                                         <td>
                                             <div style="float: left; margin-left: 1px;" class="menubutton split popup" id="tool-${tool_dict[ 'id' ].replace( ' ', '_' )}-popup">
-                                                <a class="view-info" href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ], changeset_revision=changeset_revision, display_for_install=display_for_install )}">
+                                                <a class="view-info" href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ], changeset_revision=changeset_revision, webapp=webapp )}">
                                                     ${tool_dict[ 'name' ]}
                                                 </a>
                                             </div>
                                             <div popupmenu="tool-${tool_dict[ 'id' ].replace( ' ', '_' )}-popup">
-                                                <a class="action-button" href="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision, tool_id=tool_dict[ 'id' ], display_for_install=display_for_install )}">View tool metadata</a>
+                                                <a class="action-button" href="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision, tool_id=tool_dict[ 'id' ], webapp=webapp )}">View tool metadata</a>
                                             </div>
                                         </td>
                                         <td>${tool_dict[ 'description' ]}</td>
diff --git a/templates/webapps/community/repository/contact_owner.mako b/templates/webapps/community/repository/contact_owner.mako
index 66a5e7358a3..d8a27beaf55 100644
--- a/templates/webapps/community/repository/contact_owner.mako
+++ b/templates/webapps/community/repository/contact_owner.mako
@@ -37,16 +37,16 @@
             %if can_manage:
                 <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ) )}">Manage repository</a>
             %else:
-                <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ) )}">View repository</a>
+                <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View repository</a>
             %endif
             %if can_upload:
                 <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a>
             %endif
             %if can_view_change_log:
-                <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a>
+                <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View change log</a>
             %endif
             %if can_browse_contents:
-                <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a>
+                <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">${browse_label}</a>
             %endif
             %if can_download:
                 <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='gz' )}">Download as a .tar.gz file</a>
diff --git a/templates/webapps/community/repository/find_tools.mako b/templates/webapps/community/repository/find_tools.mako
index ef1fb01f8f5..71390a7857c 100644
--- a/templates/webapps/community/repository/find_tools.mako
+++ b/templates/webapps/community/repository/find_tools.mako
@@ -18,9 +18,10 @@
     <div class="toolFormTitle">Search repositories for valid tools</div>
     <div class="toolFormBody">
         <div class="form-row">
-            Valid tools are those that properly load in Galaxy.  Enter any combination of the following tool attributes to locate matching valid tools.
+            Valid tools are those that properly load in Galaxy.  Enter any combination of the following tool attributes to find repositories that contain 
+            valid tools matching the search criteria.<br/><br/>
             Comma-separated strings may be entered in each field to expand search criteria.  Each field must contain the same number of comma-separated
-            strings if these types of strings are entered in more than one field.
+            strings if these types of search strings are entered in more than one field.
         </div>
         <div style="clear: both"></div>
         <form name="find_tools" id="find_tools" action="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}" method="post" >
diff --git a/templates/webapps/community/repository/manage_repository.mako b/templates/webapps/community/repository/manage_repository.mako
index fc910f69fbb..46ae1d7a69d 100644
--- a/templates/webapps/community/repository/manage_repository.mako
+++ b/templates/webapps/community/repository/manage_repository.mako
@@ -77,13 +77,13 @@
                 <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a>
             %endif
             %if can_view_change_log:
-                <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a>
+                <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View change log</a>
             %endif
             %if can_rate:
                 <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a>
             %endif
             %if can_browse_contents:
-                <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a>
+                <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">${browse_label}</a>
             %endif
             %if can_contact_owner:
                 <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp='community' )}">Contact repository owner</a>
@@ -290,7 +290,7 @@ ${render_repository_tools_and_workflows( metadata, can_set_metadata=True )}
         <div class="toolFormBody">
             %if display_reviews:
                 <div class="form-row">
-                    <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=False )}"><label>Hide Reviews</label></a>
+                    <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=False, webapp='community' )}"><label>Hide Reviews</label></a>
                 </div>
                 <table class="grid">
                     <thead>
@@ -317,7 +317,7 @@ ${render_repository_tools_and_workflows( metadata, can_set_metadata=True )}
                 </table>
             %else:
                 <div class="form-row">
-                    <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=True )}"><label>Display Reviews</label></a>
+                    <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=True, webapp='community' )}"><label>Display Reviews</label></a>
                 </div>
             %endif
         </div>
diff --git a/templates/webapps/community/repository/preview_tools_in_changeset.mako b/templates/webapps/community/repository/preview_tools_in_changeset.mako
index 3c55005e576..ab496e4fc26 100644
--- a/templates/webapps/community/repository/preview_tools_in_changeset.mako
+++ b/templates/webapps/community/repository/preview_tools_in_changeset.mako
@@ -64,7 +64,7 @@
 
 <br/><br/>
 <ul class="manage-table-actions">
-    <a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp='community', changeset_revision=changeset_revision )}">Install to local Galaxy</a>
+    <a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a>
 </ul>
 
 %if message:
@@ -98,4 +98,4 @@
     </div>
 </div>
 <p/>
-${render_repository_tools_and_workflows( metadata, display_for_install=display_for_install )}
+${render_repository_tools_and_workflows( metadata, webapp=webapp )}
diff --git a/templates/webapps/community/repository/rate_repository.mako b/templates/webapps/community/repository/rate_repository.mako
index 1ce234a9c17..23baa8fc031 100644
--- a/templates/webapps/community/repository/rate_repository.mako
+++ b/templates/webapps/community/repository/rate_repository.mako
@@ -78,16 +78,16 @@
             %if can_manage:
                 <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a>
             %else:
-                <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a>
+                <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View repository</a>
             %endif
             %if can_upload:
                 <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a>
             %endif
             %if can_view_change_log:
-                <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a>
+                <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View change log</a>
             %endif
             %if can_browse_contents:
-                <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a>
+                <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">${browse_label}</a>
             %endif
             %if can_contact_owner:
                 <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp='community' )}">Contact repository owner</a>
diff --git a/templates/webapps/community/repository/tool_form.mako b/templates/webapps/community/repository/tool_form.mako
index f0f89b3914e..8cbcd5aec40 100644
--- a/templates/webapps/community/repository/tool_form.mako
+++ b/templates/webapps/community/repository/tool_form.mako
@@ -110,33 +110,33 @@
 
         <br/><br/>
         <ul class="manage-table-actions">
-            %if display_for_install:
-                <a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp='community', changeset_revision=changeset_revision )}">Install to local Galaxy</a>
+            %if webapp == 'galaxy':
+                <a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a>
             %else:
                 %if is_new:
-                    <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a>
+                    <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp=webapp )}">Upload files to repository</a>
                 %else:
                     <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li>
                     <div popupmenu="repository-${repository.id}-popup">
                         %if can_manage:
                             <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">Manage repository</a>
                         %else:
-                            <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">View repository</a>
+                            <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, webapp=webapp )}">View repository</a>
                         %endif
                         %if can_upload:
-                            <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a>
+                            <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp=webapp )}">Upload files to repository</a>
                         %endif
                         %if can_view_change_log:
-                            <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a>
+                            <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">View change log</a>
                         %endif
                         %if can_browse_contents:
-                            <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a>
+                            <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">${browse_label}</a>
                         %endif
                         %if can_rate:
                             <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a>
                         %endif
                         %if can_contact_owner:
-                            <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp='community' )}">Contact repository owner</a>
+                            <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp=webapp )}">Contact repository owner</a>
                         %endif
                         %if can_download:
                             <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a>
diff --git a/templates/webapps/community/repository/upload.mako b/templates/webapps/community/repository/upload.mako
index 2bc4fae421f..20df043cc8d 100644
--- a/templates/webapps/community/repository/upload.mako
+++ b/templates/webapps/community/repository/upload.mako
@@ -50,13 +50,13 @@
         %if can_manage:
             <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a>
         %else:
-            <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a>
+            <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View repository</a>
         %endif
         %if can_view_change_log:
-            <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a>
+            <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View change log</a>
         %endif
         %if can_browse_contents:
-            <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">Browse or delete repository files</a>
+            <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">Browse or delete repository files</a>
         %endif
     </div>
 </ul>
diff --git a/templates/webapps/community/repository/view_changelog.mako b/templates/webapps/community/repository/view_changelog.mako
index b31c3e36979..38ba45a8bb5 100644
--- a/templates/webapps/community/repository/view_changelog.mako
+++ b/templates/webapps/community/repository/view_changelog.mako
@@ -49,13 +49,13 @@
         %if can_manage:
             <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a>
         %else:
-            <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a>
+            <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View repository</a>
         %endif
         %if can_rate:
             <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a>
         %endif
         %if can_browse_contents:
-            <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a>
+            <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">${browse_label}</a>
         %endif
         %if can_contact_owner:
             <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp='community' )}">Contact repository owner</a>
diff --git a/templates/webapps/community/repository/view_changeset.mako b/templates/webapps/community/repository/view_changeset.mako
index f25a61a6026..4c2aa5a0551 100644
--- a/templates/webapps/community/repository/view_changeset.mako
+++ b/templates/webapps/community/repository/view_changeset.mako
@@ -50,16 +50,16 @@
         %if can_manage:
             <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a>
         %else:
-            <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a>
+            <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View repository</a>
         %endif
         %if can_view_change_log:
-            <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a>
+            <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View change log</a>
         %endif
         %if can_rate:
             <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a>
         %endif
         %if can_browse_contents:
-            <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a>
+            <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">${browse_label}</a>
         %endif
         %if can_contact_owner:
             <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp='community' )}">Contact repository owner</a>
diff --git a/templates/webapps/community/repository/view_repository.mako b/templates/webapps/community/repository/view_repository.mako
index 563aad4fc88..82a8c8fb2cb 100644
--- a/templates/webapps/community/repository/view_repository.mako
+++ b/templates/webapps/community/repository/view_repository.mako
@@ -11,8 +11,8 @@
     can_rate = not is_new and trans.user and repository.user != trans.user
     can_upload = can_push
     can_download = not is_new and ( not is_malicious or can_push )
-    can_browse_contents = not is_new
-    can_view_change_log = not is_new
+    can_browse_contents = webapp == 'community' and not is_new
+    can_view_change_log = webapp == 'community' and not is_new
     if can_push:
         browse_label = 'Browse or delete repository files'
     else:
@@ -65,32 +65,36 @@
 
 <br/><br/>
 <ul class="manage-table-actions">
-    %if is_new and can_upload:
-        <li><a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a></li>
+    %if webapp == 'community':
+        %if is_new and can_upload:
+            <li><a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp=webapp )}">Upload files to repository</a></li>
+        %else:
+            <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li>
+            <div popupmenu="repository-${repository.id}-popup">
+                %if can_upload:
+                    <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp=webapp )}">Upload files to repository</a>
+                %endif
+                %if can_view_change_log:
+                    <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">View change log</a>
+                %endif
+                %if can_rate:
+                    <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">Rate repository</a>
+                %endif
+                %if can_browse_contents:
+                    <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">${browse_label}</a>
+                %endif
+                %if can_contact_owner:
+                    <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp=webapp )}">Contact repository owner</a>
+                %endif
+                %if can_download:
+                    <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz', webapp=webapp )}">Download as a .tar.gz file</a>
+                    <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='bz2', webapp=webapp )}">Download as a .tar.bz2 file</a>
+                    <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='zip', webapp=webapp )}">Download as a zip file</a>
+                %endif
+            </div>
+        %endif
     %else:
-        <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li>
-        <div popupmenu="repository-${repository.id}-popup">
-            %if can_upload:
-                <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a>
-            %endif
-            %if can_view_change_log:
-                <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a>
-            %endif
-            %if can_rate:
-                <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a>
-            %endif
-            %if can_browse_contents:
-                <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a>
-            %endif
-            %if can_contact_owner:
-                <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp='community' )}">Contact repository owner</a>
-            %endif
-            %if can_download:
-                <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a>
-                <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='bz2' )}">Download as a .tar.bz2 file</a>
-                <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='zip' )}">Download as a zip file</a>
-            %endif
-        </div>
+        <a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a>
     %endif
 </ul>
 
@@ -102,7 +106,7 @@
     <div class="toolForm">
         <div class="toolFormTitle">Repository revision</div>
         <div class="toolFormBody">
-            <form name="change_revision" id="change_revision" action="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ) )}" method="post" >
+            <form name="change_revision" id="change_revision" action="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), webapp=webapp )}" method="post" >
                 <div class="form-row">
                     <%
                         if changeset_revision == repository.tip:
@@ -132,7 +136,7 @@
         <div class="form-row">
             <label>Name:</label>
             %if can_browse_contents:
-                <a href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${repository.name}</a>
+                <a href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">${repository.name}</a>
             %else:
                 ${repository.name}
             %endif
@@ -151,7 +155,7 @@
         <div class="form-row">
             <label>Revision:</label>
             %if can_view_change_log:
-                <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">${revision_label}</a>
+                <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">${revision_label}</a>
             %else:
                 ${revision_label}
             %endif
@@ -176,7 +180,7 @@
         %endif
     </div>
 </div>
-${render_repository_tools_and_workflows( metadata )}
+${render_repository_tools_and_workflows( metadata, webapp=webapp )}
 %if repository.categories:
     <p/>
     <div class="toolForm">
@@ -191,12 +195,12 @@ ${render_repository_tools_and_workflows( metadata )}
         </div>
     </div>
 %endif
-%if trans.user and trans.app.config.smtp_server:
+%if webapp == 'community' and trans.user and trans.app.config.smtp_server:
     <p/>
     <div class="toolForm">
         <div class="toolFormTitle">Notification on update</div>
         <div class="toolFormBody">
-            <form name="receive_email_alerts" id="receive_email_alerts" action="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ) )}" method="post" >
+            <form name="receive_email_alerts" id="receive_email_alerts" action="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), webapp=webapp )}" method="post" >
                 <div class="form-row">
                     <label>Receive email alerts:</label>
                     ${alerts_check_box.get_html()}
@@ -233,7 +237,7 @@ ${render_repository_tools_and_workflows( metadata )}
         <div class="toolFormBody">
             %if display_reviews:
                 <div class="form-row">
-                    <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=False )}"><label>Hide Reviews</label></a>
+                    <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=False, webapp=webapp )}"><label>Hide Reviews</label></a>
                 </div>
                 <table class="grid">
                     <thead>
@@ -260,7 +264,7 @@ ${render_repository_tools_and_workflows( metadata )}
                 </table>
             %else:
                 <div class="form-row">
-                    <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=True )}"><label>Display Reviews</label></a>
+                    <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=True, webapp=webapp )}"><label>Display Reviews</label></a>
                 </div>
             %endif
         </div>
diff --git a/templates/webapps/community/repository/view_tool_metadata.mako b/templates/webapps/community/repository/view_tool_metadata.mako
index 1c43727543b..c8a3bc421a6 100644
--- a/templates/webapps/community/repository/view_tool_metadata.mako
+++ b/templates/webapps/community/repository/view_tool_metadata.mako
@@ -12,10 +12,10 @@
     can_push = trans.app.security_agent.can_push( trans.user, repository )
     can_upload = can_push
     can_download = not is_new and ( not is_malicious or can_push )
-    can_browse_contents = not is_new
+    can_browse_contents = webapp == 'community' and not is_new
     can_rate = repository.user != trans.user
     can_manage = is_admin or repository.user == trans.user
-    can_view_change_log = not is_new
+    can_view_change_log = webapp == 'community' and not is_new
     if can_push:
         browse_label = 'Browse or delete repository files'
     else:
@@ -33,30 +33,30 @@
 
 <br/><br/>
 <ul class="manage-table-actions">
-    %if display_for_install:
-        <a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp='community', changeset_revision=changeset_revision )}">Install to local Galaxy</a>
+    %if webapp == 'galaxy':
+        <a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a>
     %else:
         %if is_new:
-            <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a>
+            <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp=webapp )}">Upload files to repository</a>
         %else:
             <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li>
             <div popupmenu="repository-${repository.id}-popup">
                 %if can_manage:
                     <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">Manage repository</a>
                 %else:
-                    <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">View repository</a>
+                    <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, webapp=webapp )}">View repository</a>
                 %endif
                 %if can_upload:
-                    <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a>
+                    <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp=webapp )}">Upload files to repository</a>
                 %endif
                 %if can_view_change_log:
-                    <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a>
+                    <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">View change log</a>
                 %endif
                 %if can_browse_contents:
-                    <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a>
+                    <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">${browse_label}</a>
                 %endif
                 %if can_contact_owner:
-                    <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp='community' )}">Contact repository owner</a>
+                    <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp=webapp )}">Contact repository owner</a>
                 %endif
                 %if can_download:
                     <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a>
@@ -76,7 +76,7 @@
     <div class="toolFormTitle">Repository revision</div>
     <div class="toolFormBody">
         %if len( changeset_revision_select_field.options ) > 1:
-            <form name="change_revision" id="change_revision" action="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), tool_id=metadata[ 'id' ], display_for_install=display_for_install )}" method="post" >
+            <form name="change_revision" id="change_revision" action="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), tool_id=metadata[ 'id' ], webapp=webapp )}" method="post" >
                 <div class="form-row">
                     <%
                         if changeset_revision == repository.tip:
@@ -124,7 +124,7 @@
         <div class="toolFormBody">
             <div class="form-row">
                 <label>Name:</label>
-                <a href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=metadata[ 'tool_config' ], changeset_revision=changeset_revision )}">${metadata[ 'name' ]}</a>
+                <a href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=metadata[ 'tool_config' ], changeset_revision=changeset_revision, webapp=webapp )}">${metadata[ 'name' ]}</a>
                 <div style="clear: both"></div>
             </div>
             %if 'description' in metadata:
diff --git a/templates/webapps/galaxy/admin/index.mako b/templates/webapps/galaxy/admin/index.mako
index 9c2edd7f498..a54f5706b78 100644
--- a/templates/webapps/galaxy/admin/index.mako
+++ b/templates/webapps/galaxy/admin/index.mako
@@ -73,10 +73,7 @@
                     <div class="toolSectionTitle">Tool sheds</div>
                     <div class="toolSectionBody">
                         <div class="toolSectionBg">                        
-                            %for name, url in trans.app.tool_shed_registry.tool_sheds.items():
-                                <div class="toolTitle"><a href="${h.url_for( controller='admin', action='browse_tool_shed', tool_shed_url=url )}" target="galaxy_main">${name}</a></div>
-                            %endfor
-                            </div>
+                            <div class="toolTitle"><a href="${h.url_for( controller='admin', action='browse_tool_sheds' )}" target="galaxy_main">Browse tool sheds</a></div>
                         </div>
                     </div>
                 %endif
diff --git a/templates/webapps/galaxy/admin/tool_sheds.mako b/templates/webapps/galaxy/admin/tool_sheds.mako
new file mode 100644
index 00000000000..659449f55d9
--- /dev/null
+++ b/templates/webapps/galaxy/admin/tool_sheds.mako
@@ -0,0 +1,40 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+<%def name="title()">Configured Galaxy tool sheds</%def>
+
+<%def name="stylesheets()">
+    ${parent.stylesheets()}
+    ${h.css( "library" )}
+</%def>
+
+%if message:
+    ${render_msg( message, status )}
+%endif
+
+<div class="toolForm">
+    <div class="toolFormTitle">Accessible Galaxy tool sheds</div>
+    <div class="toolFormBody">
+        <div class="form-row">
+            <table cellspacing="0" cellpadding="0" border="0" width="100%" class="grid" id="library-grid">
+                <% shed_id = 0 %>
+                %for name, url in trans.app.tool_shed_registry.tool_sheds.items():
+                    <tr class="libraryTitle">
+                        <td>
+                            <div style="float: left; margin-left: 1px;" class="menubutton split popup" id="dataset-${shed_id}-popup">
+                                <a class="view-info" href="${h.url_for( controller='admin', action='browse_tool_shed', tool_shed_url=url )}">${name}</a>
+                            </div>
+                            <div popupmenu="dataset-${shed_id}-popup">
+                                <a class="action-button" href="${h.url_for( controller='admin', action='browse_tool_shed', tool_shed_url=url )}">Browse downloadable repositories</a>
+                                <a class="action-button" href="${h.url_for( controller='admin', action='find_tools_in_tool_shed', tool_shed_url=url )}">Search for valid tools</a>
+                            </div>
+                        </td>
+                    </tr>
+                    <% shed_id += 1 %>
+                %endfor
+                </tr>
+            </table>
+        </div>
+        <div style="clear: both"></div>
+    </div>
+</div>

From cdddeb3f34f9516c57ce5152e30ece3f8cb57c6b Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Thu, 20 Oct 2011 09:37:02 -0400
Subject: [PATCH 074/362] Allow specifying a help attribute for repeat
 parameter grouping.

---
 lib/galaxy/tools/__init__.py            | 3 ++-
 lib/galaxy/tools/parameters/grouping.py | 1 +
 templates/tool_form.mako                | 8 +++++++-
 3 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 32f4c3f866a..493d7ba86ee 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -814,7 +814,8 @@ class Tool:
             if elem.tag == "repeat":
                 group = Repeat()
                 group.name = elem.get( "name" )
-                group.title = elem.get( "title" ) 
+                group.title = elem.get( "title" )
+                group.help = elem.get( "help", None )
                 group.inputs = self.parse_input_elem( elem, enctypes, context )
                 group.default = int( elem.get( "default", 0 ) )
                 group.min = int( elem.get( "min", 0 ) )
diff --git a/lib/galaxy/tools/parameters/grouping.py b/lib/galaxy/tools/parameters/grouping.py
index 13a2e4b5091..37cca05f880 100644
--- a/lib/galaxy/tools/parameters/grouping.py
+++ b/lib/galaxy/tools/parameters/grouping.py
@@ -45,6 +45,7 @@ class Repeat( Group ):
         Group.__init__( self )
         self.title = None
         self.inputs = None
+        self.help = None
         self.default = 0
         self.min = None
         self.max = None
diff --git a/templates/tool_form.mako b/templates/tool_form.mako
index eabb338449d..2bc185be038 100644
--- a/templates/tool_form.mako
+++ b/templates/tool_form.mako
@@ -120,7 +120,13 @@
             <% pass %>
         %elif input.type == "repeat":
           <div class="repeat-group">
-              <div class="form-title-row"><strong>${input.title_plural}</strong></div>
+              <div class="form-title-row"><strong>${input.title_plural}</strong>
+              %if input.help:
+                  <div class="toolParamHelp" style="clear: both;">
+                      ${input.help}
+                  </div>
+              %endif
+              </div>
               <% repeat_state = tool_state[input.name] %>
               %for i in range( len( repeat_state ) ):
                 <div class="repeat-group-item">

From eefc21c0303f4a0fba3d63f87c3b1b5a03aa7491 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Thu, 20 Oct 2011 10:03:28 -0400
Subject: [PATCH 075/362] Allow toolbox tests to test 0 instances of a repeat.

---
 test/functional/test_toolbox.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/functional/test_toolbox.py b/test/functional/test_toolbox.py
index 68aa7f0a54e..1843ada7ede 100644
--- a/test/functional/test_toolbox.py
+++ b/test/functional/test_toolbox.py
@@ -59,7 +59,7 @@ class ToolTestCase( TwillTestCase ):
         # See if we have a grouping.Repeat element
         repeat_name = None
         for input_name, input_value in testdef.tool.inputs_by_page[0].items():
-            if isinstance( input_value, grouping.Repeat ):
+            if isinstance( input_value, grouping.Repeat ) and all_inputs.get( input_name, 1 ) not in [ 0, "0" ]: #default behavior is to test 1 repeat, for backwards compatibility
                 repeat_name = input_name
                 break
         #check if we need to verify number of outputs created dynamically by tool

From b7e0e1a291b0270db1c8240c7784d602bc404d83 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Thu, 20 Oct 2011 10:24:19 -0400
Subject: [PATCH 076/362] First pass at updating GATK tools to version 1.2.
 Changes are not backwards compatible with workflows. Still considered BETA,
 and so future changes are like to also not be backwards compatible.

---
 tools/gatk/analyze_covariates.xml          |   9 +-
 tools/gatk/count_covariates.xml            |   9 +-
 tools/gatk/indel_realigner.xml             |  19 +-
 tools/gatk/realigner_target_creator.xml    |  35 ++-
 tools/gatk/table_recalibration.xml         |   9 +-
 tools/gatk/unified_genotyper.xml           | 113 ++++++---
 tools/gatk/variant_annotator.xml           | 273 ++++++++++-----------
 tools/gatk/variant_apply_recalibration.xml |  61 +++--
 tools/gatk/variant_combine.xml             |  35 +--
 tools/gatk/variant_eval.xml                | 115 ++++-----
 tools/gatk/variant_filtration.xml          |  97 ++++----
 tools/gatk/variant_recalibrator.xml        | 120 +++++----
 tools/gatk/variants_validate.xml           |  79 +++---
 13 files changed, 514 insertions(+), 460 deletions(-)

diff --git a/tools/gatk/analyze_covariates.xml b/tools/gatk/analyze_covariates.xml
index 9ad4715514e..ab62a089cdf 100644
--- a/tools/gatk/analyze_covariates.xml
+++ b/tools/gatk/analyze_covariates.xml
@@ -1,7 +1,10 @@
-<tool id="gatk_analyze_covariates" name="Analyze Covariates" version="0.0.2">
+<tool id="gatk_analyze_covariates" name="Analyze Covariates" version="0.0.3">
   <description>- draw plots</description>
-<command interpreter="python">gatk_wrapper.py
-   --max_jvm_heap_fraction "2"
+  <requirements>
+      <requirement type="package" version="1.2">gatk</requirement>
+  </requirements>
+  <command interpreter="python">gatk_wrapper.py
+   --max_jvm_heap_fraction "1"
    --stdout "${output_log}"
    --html_report_from_directory "${output_html}" "${output_html.files_path}"
    -p 'java 
diff --git a/tools/gatk/count_covariates.xml b/tools/gatk/count_covariates.xml
index 418f6a100e3..89491b08308 100644
--- a/tools/gatk/count_covariates.xml
+++ b/tools/gatk/count_covariates.xml
@@ -1,7 +1,10 @@
-<tool id="gatk_count_covariates" name="Count Covariates" version="0.0.2">
+<tool id="gatk_count_covariates" name="Count Covariates" version="0.0.3">
   <description>on BAM files</description>
+  <requirements>
+      <requirement type="package" version="1.2">gatk</requirement>
+  </requirements>
   <command interpreter="python">gatk_wrapper.py
-   --max_jvm_heap_fraction "2"
+   --max_jvm_heap_fraction "1"
    --stdout "${output_log}"
    -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
    -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
@@ -35,7 +38,7 @@
             #set $snp_dataset_provided = True
         #end if
         #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
-        -d "-B:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
+        -d "--knownSites:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
         #if str( $rod_binding.rod_bind_type.rodToIntervalTrackName ):
             -p '--rodToIntervalTrackName "${rod_bind_name}"'
         #end if
diff --git a/tools/gatk/indel_realigner.xml b/tools/gatk/indel_realigner.xml
index 9165dbfd91c..0702d2d656b 100644
--- a/tools/gatk/indel_realigner.xml
+++ b/tools/gatk/indel_realigner.xml
@@ -1,7 +1,10 @@
-<tool id="gatk_indel_realigner" name="Indel Realigner" version="0.0.2">
+<tool id="gatk_indel_realigner" name="Indel Realigner" version="0.0.3">
   <description>- perform local realignment</description>
+  <requirements>
+      <requirement type="package" version="1.2">gatk</requirement>
+  </requirements>
   <command interpreter="python">gatk_wrapper.py
-   --max_jvm_heap_fraction "2"
+   --max_jvm_heap_fraction "1"
    --stdout "${output_log}"
    -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
    -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
@@ -26,7 +29,7 @@
             #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector
         #end if
         #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
-        -d "-B:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
+        -d "-known:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
         #if str( $rod_binding.rod_bind_type.rodToIntervalTrackName ):
             -p '--rodToIntervalTrackName "${rod_bind_name}"'
         #end if
@@ -104,7 +107,7 @@
       <when value="cached">
         <param name="input_bam" type="data" format="bam" label="BAM file">
           <validator type="unspecified_build" />
-          <validator type="dataset_metadata_in_file" filename="picard_index.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
+          <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
         </param>
         <param name="ref_file" type="select" label="Using reference genome">
           <options from_data_table="picard_indexes">
@@ -114,7 +117,11 @@
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
         <param name="input_bam" type="data" format="bam" label="BAM file" />
-        <param name="ref_file" type="data" format="fasta" label="Using reference file" />
+        <param name="ref_file" type="data" format="fasta" label="Using reference file">
+          <options>
+            <filter type="data_meta" key="dbkey" ref="input_bam" /> <!-- FIX ME!!!! -->
+          </options>
+        </param>
       </when>
     </conditional>
     <param name="target_intervals" type="data" format="gatk_interval,bed,picard_interval_list" label="Restrict realignment to provided intervals" />
@@ -277,7 +284,7 @@
           <param name="input_bam" value="gatk/fake_phiX_reads_1.bam" ftype="bam" />
           <param name="rod_bind_type_selector" value="snps" />
           <param name="rodToIntervalTrackName" />
-          <param name="input_rod" value="gatk/fake_phiX_variant_locations.bed" ftype="bed" />
+          <param name="input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" />
           <param name="lod_threshold" value="5.0" />
           <param name="knowns_only" />
           <param name="gatk_param_type_selector" value="basic" />
diff --git a/tools/gatk/realigner_target_creator.xml b/tools/gatk/realigner_target_creator.xml
index 877480f6070..c2ccdd02aae 100644
--- a/tools/gatk/realigner_target_creator.xml
+++ b/tools/gatk/realigner_target_creator.xml
@@ -1,7 +1,10 @@
-<tool id="gatk_realigner_target_creator" name="Realigner Target Creator" version="0.0.2">
+<tool id="gatk_realigner_target_creator" name="Realigner Target Creator" version="0.0.3">
   <description>for use in local realignment</description>
+  <requirements>
+      <requirement type="package" version="1.2">gatk</requirement>
+  </requirements>
   <command interpreter="python">gatk_wrapper.py
-   --max_jvm_heap_fraction "2"
+   --max_jvm_heap_fraction "1"
    --stdout "${output_log}"
    -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
    -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
@@ -23,7 +26,7 @@
             #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector
         #end if
         #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
-        -d "-B:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
+        -d "-known:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
         #if str( $rod_binding.rod_bind_type.rodToIntervalTrackName ):
             -p '--rodToIntervalTrackName "${rod_bind_name}"'
         #end if
@@ -92,7 +95,7 @@
       <when value="cached">
         <param name="input_bam" type="data" format="bam" label="BAM file">
           <validator type="unspecified_build" />
-          <validator type="dataset_metadata_in_file" filename="picard_index.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
+          <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
         </param>
         <param name="ref_file" type="select" label="Using reference genome">
           <options from_data_table="picard_indexes">
@@ -100,9 +103,13 @@
           </options>
         </param>
       </when>
-      <when value="history"> <!-- FIX ME!!!! -->
+      <when value="history">
         <param name="input_bam" type="data" format="bam" label="BAM file" />
-        <param name="ref_file" type="data" format="fasta" label="Using reference file" />
+        <param name="ref_file" type="data" format="fasta" label="Using reference file">
+          <options>
+            <filter type="data_meta" key="dbkey" ref="input_bam" /> <!-- FIX ME!!!! -->
+          </options>
+        </param>
       </when>
     </conditional>
     
@@ -115,20 +122,20 @@
 	        <option value="custom">Custom</option>
 	      </param>
           <when value="dbsnp">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
               <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
           </when>
           <when value="snps">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
               <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
           </when>
           <when value="indels">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
               <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
           </when>
           <when value="custom">
               <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/>
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
               <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
           </when>
         </conditional>
@@ -254,9 +261,13 @@
           <param name="input_bam" value="gatk/fake_phiX_reads_1.bam" ftype="bam" />
           <param name="rod_bind_type_selector" value="dbsnp" />
           <param name="rodToIntervalTrackName" />
-          <param name="input_rod" value="gatk/fake_phiX_variant_locations.bed" ftype="bed" />
+          <param name="input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" />
           <param name="gatk_param_type_selector" value="basic" />
-          <param name="analysis_param_type_selector" value="basic" />
+          <param name="analysis_param_type_selector" value="advanced" />
+          <param name="windowSize" value="10" />
+          <param name="mismatchFraction" value="0.15" />
+          <param name="minReadsAtLocus" value="4" />
+          <param name="maxIntervalSize" value="500" />
           <output name="output_interval" file="gatk/gatk_realigner_target_creator/gatk_realigner_target_creator_out_1.gatk_interval" /> 
           <output name="output_log" file="gatk/gatk_realigner_target_creator/gatk_realigner_target_creator_out_1.log.contains" compare="contains"/>
       </test>
diff --git a/tools/gatk/table_recalibration.xml b/tools/gatk/table_recalibration.xml
index 0da4d4afbe8..631ff2e65bc 100644
--- a/tools/gatk/table_recalibration.xml
+++ b/tools/gatk/table_recalibration.xml
@@ -1,7 +1,10 @@
-<tool id="gatk_table_recalibration" name="Table Recalibration" version="0.0.2">
+<tool id="gatk_table_recalibration" name="Table Recalibration" version="0.0.3">
   <description>on BAM files</description>
+  <requirements>
+      <requirement type="package" version="1.2">gatk</requirement>
+  </requirements>
   <command interpreter="python">gatk_wrapper.py
-   --max_jvm_heap_fraction "2"
+   --max_jvm_heap_fraction "1"
    --stdout "${output_log}"
    -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
    -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
@@ -120,7 +123,7 @@
       <when value="cached">
         <param name="input_bam" type="data" format="bam" label="BAM file">
           <validator type="unspecified_build" />
-          <validator type="dataset_metadata_in_file" filename="picard_index.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
+          <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
         </param>
         <param name="ref_file" type="select" label="Using reference genome">
           <options from_data_table="picard_indexes">
diff --git a/tools/gatk/unified_genotyper.xml b/tools/gatk/unified_genotyper.xml
index 5d88fb35420..f33a3da4651 100644
--- a/tools/gatk/unified_genotyper.xml
+++ b/tools/gatk/unified_genotyper.xml
@@ -1,9 +1,14 @@
-<tool id="gatk_unified_genotyper" name="Unified Genotyper" version="0.0.2">
+<tool id="gatk_unified_genotyper" name="Unified Genotyper" version="0.0.3">
   <description>SNP and indel caller</description>
+  <requirements>
+      <requirement type="package" version="1.2">gatk</requirement>
+  </requirements>
   <command interpreter="python">gatk_wrapper.py
-   --max_jvm_heap_fraction "2"
+   --max_jvm_heap_fraction "1"
    --stdout "${output_log}"
    #for $i, $input_bam in enumerate( $reference_source.input_bams ):
+       ${dir( $input_bam.input_bam )}
+       ${dir( $input_bam.input_bam.dataset )}
        -d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "gatk_input_${i}"
        -d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index
    #end for
@@ -11,12 +16,14 @@
     -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar"
     -T "UnifiedGenotyper"
     --num_threads 4 ##hard coded, for now
-    -o "${output_vcf}"
+    --out "${output_vcf}"
+    --metrics_file "${output_metrics}"
     -et "NO_ET" ##ET no phone home
     ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
     #if $reference_source.reference_source_selector != "history":
         -R "${reference_source.ref_file.fields.path}"
     #end if
+    --genotype_likelihoods_model "${genotype_likelihoods_model}"
     --standard_min_confidence_threshold_for_calling "${standard_min_confidence_threshold_for_calling}"
     --standard_min_confidence_threshold_for_emitting "${standard_min_confidence_threshold_for_emitting}"
    '
@@ -28,7 +35,7 @@
             #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector
         #end if
         #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
-        -d "-B:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
+        -d "--dbsnp:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
         #if str( $rod_binding.rod_bind_type.rodToIntervalTrackName ):
             -p '--rodToIntervalTrackName "${rod_bind_name}"'
         #end if
@@ -81,13 +88,15 @@
     ##start analysis specific options
     #if $analysis_param_type.analysis_param_type_selector == "advanced":
         -p '
-        --genotype_likelihoods_model "${analysis_param_type.genotype_likelihoods_model}"
         --p_nonref_model "${analysis_param_type.p_nonref_model}"
         --heterozygosity "${analysis_param_type.heterozygosity}"
         --pcr_error_rate "${analysis_param_type.pcr_error_rate}"
-        --genotyping_mode "${analysis_param_type.genotyping_mode}"
+        --genotyping_mode "${analysis_param_type.genotyping_mode_type.genotyping_mode}"
+        #if str( $analysis_param_type.genotyping_mode_type.genotyping_mode ) == 'GENOTYPE_GIVEN_ALLELES':
+            --alleles "${analysis_param_type.genotyping_mode_type.input_alleles_rod}"
+        #end if
         --output_mode "${analysis_param_type.output_mode}"
-        ${analysis_param_type.noSLOD}
+        ${analysis_param_type.compute_SLOD}
         --min_base_quality_score "${analysis_param_type.min_base_quality_score}"
         --min_mapping_quality_score "${analysis_param_type.min_mapping_quality_score}"
         --max_deletion_fraction "${analysis_param_type.max_deletion_fraction}"
@@ -120,7 +129,7 @@
         <repeat name="input_bams" title="Sample BAM file" min="1">
             <param name="input_bam" type="data" format="bam" label="BAM file">
               <validator type="unspecified_build" />
-              <validator type="dataset_metadata_in_file" filename="picard_index.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
+              <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
             </param>
         </repeat>
         <param name="ref_file" type="select" label="Using reference genome">
@@ -146,25 +155,31 @@
 	        <option value="custom">Custom</option>
 	      </param>
           <when value="dbsnp">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
               <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
           </when>
           <when value="snps">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
               <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
           </when>
           <when value="indels">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
               <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
           </when>
           <when value="custom">
               <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/>
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
               <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
           </when>
         </conditional>
     </repeat>
     
+    <param name="genotype_likelihoods_model" type="select" label="Genotype likelihoods calculation model to employ">
+      <option value="BOTH" selected="True">BOTH</option>
+      <option value="SNP">SNP</option>
+      <option value="INDEL">INDEL</option>
+    </param>
+    
     <param name="standard_min_confidence_threshold_for_calling" type="float" value="30.0" label="The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be called" />
     <param name="standard_min_confidence_threshold_for_emitting" type="float" value="30.0" label="The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be emitted (and filtered if less than the calling threshold)" />
 
@@ -271,27 +286,30 @@
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <param name="genotype_likelihoods_model" type="select" label="Genotype likelihoods calculation model to employ">
-          <option value="BOTH" selected="True">BOTH</option>
-          <option value="SNP">SNP</option>
-          <option value="INDEL">INDEL</option>
-        </param>
         <param name="p_nonref_model" type="select" label="Non-reference probability calculation model to employ">
           <option value="EXACT" selected="True">EXACT</option>
           <option value="GRID_SEARCH">GRID_SEARCH</option>
         </param>
         <param name="heterozygosity" type="float" value="1e-3" label="Heterozygosity value used to compute prior likelihoods for any locus" />
         <param name="pcr_error_rate" type="float" value="1e-4" label="The PCR error rate to be used for computing fragment-based likelihoods" />
-        <param name="genotyping_mode" type="select" label="How to determine the alternate allele to use for genotyping">
-          <option value="DISCOVERY" selected="True">DISCOVERY</option>
-          <option value="GENOTYPE_GIVEN_ALLELES">GENOTYPE_GIVEN_ALLELES</option>
-        </param>
+        <conditional name="genotyping_mode_type">
+          <param name="genotyping_mode" type="select" label="How to determine the alternate allele to use for genotyping">
+            <option value="DISCOVERY" selected="True">DISCOVERY</option>
+            <option value="GENOTYPE_GIVEN_ALLELES">GENOTYPE_GIVEN_ALLELES</option>
+          </param>
+          <when value="DISCOVERY">
+            <!-- Do nothing here -->
+          </when>
+          <when value="GENOTYPE_GIVEN_ALLELES">
+            <param name="input_alleles_rod" type="data" format="vcf" label="Alleles ROD file" />
+          </when>
+        </conditional>
         <param name="output_mode" type="select" label="Should we output confident genotypes (i.e. including ref calls) or just the variants?">
           <option value="EMIT_VARIANTS_ONLY" selected="True">EMIT_VARIANTS_ONLY</option>
           <option value="EMIT_ALL_CONFIDENT_SITES">EMIT_ALL_CONFIDENT_SITES</option>
           <option value="EMIT_ALL_SITES">EMIT_ALL_SITES</option>
         </param>
-        <param name="noSLOD" type="boolean" truevalue="--noSLOD" falsevalue="" label="Do not calculate the SLOD" />
+        <param name="compute_SLOD" type="boolean" truevalue="--computeSLOD" falsevalue="" label="Compute the SLOD" />
         <param name="min_base_quality_score" type="integer" value="17" label="Minimum base quality required to consider a base for calling" />
         <param name="min_mapping_quality_score" type="integer" value="20" label="Minimum read mapping quality required to consider a read for calling" />
         <param name="max_deletion_fraction" type="float" value="0.05" label="Maximum fraction of reads with deletions spanning this locus for it to be callable" help="to disable, set to &lt; 0 or &gt; 1" />
@@ -302,16 +320,35 @@
         <param name="indelHaplotypeSize" type="integer" value="80" label="Indel haplotype size" />
         <param name="doContextDependentGapPenalties" type="boolean" truevalue="--doContextDependentGapPenalties" falsevalue="" label="Vary gap penalties by context" />
 	    <param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types">
-	      <option value="AlleleBalance">AlleleBalance</option>
-	      <option value="BaseQualityRankSumTest">BaseQualityRankSumTest</option>
-	      <option value="DepthOfCoverage">DepthOfCoverage</option>
-	      <option value="HomopolymerRun">HomopolymerRun</option>
-	      <option value="MappingQualityRankSumTest">MappingQualityRankSumTest</option>
-	      <option value="MappingQualityZero">MappingQualityZero</option>
-	      <option value="QualByDepth">QualByDepth</option>
-	      <option value="RMSMappingQuality">RMSMappingQuality</option>
-	      <option value="SpanningDeletions">SpanningDeletions</option>
-	      <option value="HaplotypeScore">HaplotypeScore</option>
+          <option value="ChromosomeCounts"/>
+          <option value="IndelType"/>
+          <option value="SpanningDeletions"/>
+          <option value="HardyWeinberg"/>
+          <option value="NBaseCount"/>
+          <option value="MappingQualityZero"/>
+          <option value="AlleleBalance"/>
+          <option value="BaseCounts"/>
+          <option value="LowMQ"/>
+          <option value="InbreedingCoeff"/>
+          <option value="RMSMappingQuality"/>
+          <option value="HaplotypeScore"/>
+          <option value="TechnologyComposition"/>
+          <option value="SampleList"/>
+          <option value="FisherStrand"/>
+          <option value="HomopolymerRun"/>
+          <option value="DepthOfCoverage"/>
+          <option value="SnpEff"/>
+          <option value="MappingQualityZeroFraction"/>
+          <option value="GCContent"/>
+          <option value="MappingQualityRankSumTest"/>
+          <option value="ReadPosRankSumTest"/>
+          <option value="BaseQualityRankSumTest"/>
+          <option value="QualByDepth"/>
+          <option value="SBByDepth"/>
+          <option value="ReadDepthAndAllelicFractionBySample"/>
+          <option value="AlleleBalanceBySample"/>
+          <option value="DepthPerAlleleBySample"/>
+          <option value="MappingQualityZeroBySample"/>
 	    </param>
 	    <param name="group" type="select" multiple="True" display="checkboxes" label="Annotation Interfaces/Groups">
 	      <option value="Standard">Standard</option>
@@ -324,6 +361,7 @@
   </inputs>
   <outputs>
     <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (VCF)" />
+    <data format="txt" name="output_metrics" label="${tool.name} on ${on_string} (metrics)" />
     <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
   </outputs>
   <!-- FIXME! <trackster_conf/> -->
@@ -333,9 +371,9 @@
           <param name="ref_file" value="phiX.fasta" ftype="fasta" />
           <param name="input_bam" value="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" />
           <param name="rod_bind_type_selector" value="dbsnp" />
-          <param name="input_rod" value="gatk/fake_phiX_variant_locations.bed" ftype="bed" />
+          <param name="input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" />
           <param name="rodToIntervalTrackName" />
-          <param name="standard_min_confidence_threshold_for_calling" value="4" />
+          <param name="standard_min_confidence_threshold_for_calling" value="0" />
           <param name="standard_min_confidence_threshold_for_emitting" value="4" />
           <param name="gatk_param_type_selector" value="basic" />
           <param name="analysis_param_type_selector" value="advanced" />
@@ -345,7 +383,7 @@
           <param name="pcr_error_rate" value="0.0001" />
           <param name="genotyping_mode" value="DISCOVERY" />
           <param name="output_mode" value="EMIT_ALL_CONFIDENT_SITES" />
-          <param name="noSLOD" />
+          <param name="compute_SLOD" />
           <param name="min_base_quality_score" value="17" />
           <param name="min_mapping_quality_score" value="20" />
           <param name="max_deletion_fraction" value="-1" />
@@ -357,8 +395,9 @@
           <param name="doContextDependentGapPenalties" />
           <!-- <param name="annotation" value="" />
           <param name="group" value="" /> -->
-          <output name="output_vcf" file="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.vcf" lines_diff="2"/> 
-          <output name="output_log" file="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.log.contains" compare="contains"/>
+          <output name="output_vcf" file="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.vcf" lines_diff="4" /> 
+          <output name="output_metrics" file="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.metrics" /> 
+          <output name="output_log" file="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.log.contains" compare="contains" />
       </test>
   </tests>
   <help>
diff --git a/tools/gatk/variant_annotator.xml b/tools/gatk/variant_annotator.xml
index 49e3702acfd..cfaaaa680f4 100644
--- a/tools/gatk/variant_annotator.xml
+++ b/tools/gatk/variant_annotator.xml
@@ -1,13 +1,16 @@
-<tool id="gatk_variant_annotator" name="Variant Annotator" version="0.0.1">
+<tool id="gatk_variant_annotator" name="Variant Annotator" version="0.0.2">
   <description></description>
+  <requirements>
+      <requirement type="package" version="1.2">gatk</requirement>
+  </requirements>
   <command interpreter="python">gatk_wrapper.py
-   --max_jvm_heap_fraction "2"
+   --max_jvm_heap_fraction "1"
    --stdout "${output_log}"
    #if str( $reference_source.input_bam ) != "None":
        -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
        -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
    #end if
-   -d "-B:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
+   -d "--variant" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
    -p 'java 
     -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar"
     -T "VariantAnnotator"
@@ -35,26 +38,40 @@
 ##            #end if
 ##        #end for
 ##    #end for
-    #if str( $reference_source.input_variant_name ):
-        --sampleName "${reference_source.input_variant_name}"
-    #end if
     ${reference_source.input_variant_bti}
    '
     
-    #set $rod_binding_names = dict()
-    #for $rod_binding in $rod_bind:
-        #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom':
-            #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name
-        #elif str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'comp':
-            #set $rod_bind_name = "comp" + str( $rod_binding.rod_bind_type.custom_rod_name )
-        #else 
-            #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector
+    #for $rod_binding in $comp_rod_bind:
+        -d "--comp:${rod_binding.comp_rod_name},%(file_type)s" "${rod_binding.comp_input_rod}" "${rod_binding.comp_input_rod.ext}" "input_comp_${rod_binding.comp_rod_name}"
+        #if str( $rod_binding.comp_rodToIntervalTrackName ):
+            -p '--rodToIntervalTrackName "${rod_binding.comp_rod_name}"'
         #end if
-        #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
-        -d "-B:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
-        #if str( $rod_binding.rod_bind_type.rodToIntervalTrackName ):
-            -p '--rodToIntervalTrackName "${rod_bind_name}"'
+    #end for
+    
+    #if str( $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector ) == 'set_dbsnp':
+        -d "--dbsnp:${dbsnp_rod_bind_type.dbsnp_rod_name},%(file_type)s" "${dbsnp_rod_bind_type.dbsnp_input_rod}" "${dbsnp_rod_bind_type.dbsnp_input_rod.ext}" "input_dbsnp_${dbsnp_rod_bind_type.dbsnp_rod_name}"
+        #if str( $dbsnp_rod_bind_type.dbsnp_rodToIntervalTrackName ):
+            -p '--rodToIntervalTrackName "${dbsnp_rod_bind_type.dbsnp_rod_name}"'
         #end if
+    #end if
+    
+    
+    #for $rod_binding in $resource_rod_bind:
+        -d "--resource:${rod_binding.resource_rod_name},%(file_type)s" "${rod_binding.resource_input_rod}" "${rod_binding.resource_input_rod.ext}" "input_resource_${rod_binding.resource_rod_name}"
+        #if str( $rod_binding.resource_rodToIntervalTrackName ):
+            -p '--rodToIntervalTrackName "${rod_binding.resource_rod_name}"'
+        #end if
+    #end for
+    
+    #if str( $snpEff_rod_bind_type.snpEff_rod_bind_type_selector ) == 'set_snpEff':
+        -d "--snpEff:${snpEff_rod_bind_type.snpEff_rod_name},%(file_type)s" "${snpEff_rod_bind_type.snpEff_input_rod}" "${snpEff_rod_bind_type.snpEff_input_rod.ext}" "input_snpEff_${snpEff_rod_bind_type.snpEff_rod_name}"
+        #if str( $snpEff_rod_bind_type.snpEff_rodToIntervalTrackName ):
+            -p '--rodToIntervalTrackName "${snpEff_rod_bind_type.snpEff_rod_name}"'
+        #end if
+    #end if
+    
+    #for $expression in $expressions:
+        -p '--expression "${expression.expression}"'
     #end for
     
     ##start standard gatk options
@@ -101,16 +118,13 @@
     #end if
     ##end standard gatk options
     
-    ##start analysis specific options
-    #if $analysis_param_type.analysis_param_type_selector == "advanced":
-        -p '
-        #if $analysis_param_type.group.value:
-            #for $annotation_group in str( $analysis_param_type.group ).split( ',' ):
-                --group "${annotation_group}"
-            #end for
-        #end if
-        '
+    -p '
+    #if $annotation_group.value:
+        #for $group in str( $annotation_group ).split( ',' ):
+            --group "${group}"
+        #end for
     #end if
+        '
   </command>
   <inputs>
     <conditional name="reference_source">
@@ -119,12 +133,11 @@
         <option value="history">History</option>
       </param>
       <when value="cached">
-        <param name="input_variant" type="data" format="vcf,gatk_dbsnp,bed" label="Variant file to annotate" />
-        <param name="input_variant_name" type="text" value="" label="Variant Name" help="Not needed for VCF inputs."/>
+        <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" />
         <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." />
         <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" help="Not needed for all annotations." >
           <validator type="unspecified_build" />
-          <validator type="dataset_metadata_in_file" filename="picard_index.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
+          <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
         </param>
         <param name="ref_file" type="select" label="Using reference genome">
           <options from_data_table="picard_indexes">
@@ -133,8 +146,7 @@
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
-        <param name="input_variant" type="data" format="vcf,gatk_dbsnp,bed" label="Variant file to annotate" />
-        <param name="input_variant_name" type="text" value="" label="Variant Name" help="Not needed for VCF inputs."/>
+        <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" />
         <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." />
         <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" />
         <param name="ref_file" type="data" format="fasta" label="Using reference file" />
@@ -151,90 +163,83 @@
       <when value="choose">
         <param name="annotations" type="select" multiple="True" display="checkboxes" label="Annotations to apply" >
           <!-- might we want to load the available annotations from an external configuration file, since additional ones can be added to local installs? -->
-          <option value="AlleleBalance" />
-          <option value="BaseQualityRankSumTest" />
-          <option value="DepthOfCoverage" />
-          <option value="HomopolymerRun" />
-          <option value="MappingQualityRankSumTest" />
-          <option value="MappingQualityZero" />
-          <option value="QualByDepth" />
-          <option value="RMSMappingQuality" />
-          <option value="SpanningDeletions" />
-          <option value="HaplotypeScore" />
-          <!-- annotations below were pulled from list option -->
-          <option value="ChromosomeCounts" />
-          <option value="IndelType" />
-          <option value="HardyWeinberg" />
-          <option value="BaseCounts" />
-          <option value="LowMQ" />
-          <option value="FisherStrand" />
-          <option value="GenomicAnnotation" />
-          <option value="GCContent" />
-          <option value="ReadPosRankSumTest" />
-          <option value="SBByDepth" />
-          <option value="ReadDepthAndAllelicFractionBySample" />
-          <option value="AlleleBalanceBySample" />
-          <option value="DepthPerAlleleBySample" />
-          <option value="MappingQualityZeroBySample" />
-          <option value="NBaseCount" />
-          <option value="GLstats" />
-          <option value="SampleList" />
-          <option value="MappingQualityZeroFraction" />
+          <option value="ChromosomeCounts"/>
+          <option value="IndelType"/>
+          <option value="SpanningDeletions"/>
+          <option value="HardyWeinberg"/>
+          <option value="NBaseCount"/>
+          <option value="MappingQualityZero"/>
+          <option value="AlleleBalance"/>
+          <option value="BaseCounts"/>
+          <option value="LowMQ"/>
+          <option value="InbreedingCoeff"/>
+          <option value="RMSMappingQuality"/>
+          <option value="HaplotypeScore"/>
+          <option value="TechnologyComposition"/>
+          <option value="SampleList"/>
+          <option value="FisherStrand"/>
+          <option value="HomopolymerRun"/>
+          <option value="DepthOfCoverage"/>
+          <option value="SnpEff"/>
+          <option value="MappingQualityZeroFraction"/>
+          <option value="GCContent"/>
+          <option value="MappingQualityRankSumTest"/>
+          <option value="ReadPosRankSumTest"/>
+          <option value="BaseQualityRankSumTest"/>
+          <option value="QualByDepth"/>
+          <option value="SBByDepth"/>
+          <option value="ReadDepthAndAllelicFractionBySample"/>
+          <option value="AlleleBalanceBySample"/>
+          <option value="DepthPerAlleleBySample"/>
+          <option value="MappingQualityZeroBySample"/>
         </param>
       </when>
     </conditional>
-    <!-- <repeat name="additional_annotations" title="Additional annotation">
-        <conditional name="additional_annotation_type">
-          <param name="additional_annotation_type_selector" type="select" label="Choose annotation type">
-            <option value="SnpEff">snpEff</option>
-          </param>
-          <when value="SnpEff">
-            <param name="snpEffFile" type="data" format="snpEff" label="snpEff output file" />
-          </when>
-        </conditional>
-    </repeat> -->
-    <repeat name="rod_bind" title="Binding for reference-ordered data">
-        <conditional name="rod_bind_type">
-          <param name="rod_bind_type_selector" type="select" label="Binding Type">
-            <option value="variant">Variants</option>
-	        <option value="dbsnp">dbSNP</option>
-	        <option value="snps">SNPs</option>
-            <option value="comp" selected="True">Comps</option>
-            <option value="indels">INDELs</option>
-            <option value="mask">Mask</option>
-            <option value="custom">Custom</option>
-          </param>
-          <when value="variant">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="Variant ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
-          </when>
-          <when value="comp">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp" label="ROD file" />
-              <param name="custom_rod_name" type="text" value="Unnamed" label="ROD Name"/>
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
-          </when>
-          <when value="dbsnp">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
-          </when>
-          <when value="snps">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
-          </when>
-          <when value="indels">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
-          </when>
-          <when value="mask">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
-          </when>
-          <when value="custom">
-              <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/>
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
-          </when>
-        </conditional>
+    
+    <repeat name="comp_rod_bind" title="Binding for reference-ordered comparison data">
+      <param name="comp_input_rod" type="data" format="vcf" label="ROD file" />
+      <param name="comp_rod_name" type="text" value="Unnamed" label="ROD Name"/>
+      <param name="comp_rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
+    </repeat>
+    
+    <conditional name="dbsnp_rod_bind_type">
+      <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP reference-ordered data file">
+        <option value="set_dbsnp" selected="True">Set dbSNP</option>
+        <option value="exclude_dbsnp">Don't set dbSNP</option>
+      </param>
+      <when value="exclude_dbsnp">
+        <!-- Do nothing here -->
+      </when>
+      <when value="set_dbsnp">
+        <param name="dbsnp_input_rod" type="data" format="vcf" label="ROD file" />
+        <param name="dbsnp_rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
+        <param name="dbsnp_rod_name" type="hidden" value="dbsnp" label="ROD Name"/>
+      </when>
+    </conditional>
+    
+    <repeat name="resource_rod_bind" title="Binding for reference-ordered resource data">
+      <param name="resource_input_rod" type="data" format="vcf" label="ROD file" />
+      <param name="resource_rod_name" type="text" value="Unnamed" label="ROD Name"/>
+      <param name="resource_rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
+    </repeat>
+    
+    <conditional name="snpEff_rod_bind_type">
+      <param name="snpEff_rod_bind_type_selector" type="select" label="Provide a snpEff reference-ordered data file">
+        <option value="set_snpEff">Set snpEff</option>
+        <option value="exclude_snpEff" selected="True">Don't set snpEff</option>
+      </param>
+      <when value="exclude_snpEff">
+        <!-- Do nothing here -->
+      </when>
+      <when value="set_snpEff">
+        <param name="snpEff_input_rod" type="data" format="vcf" label="ROD file" />
+        <param name="snpEff_rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
+        <param name="snpEff_rod_name" type="hidden" value="snpEff" label="ROD Name"/>
+      </when>
+    </conditional>
+    
+    <repeat name="expressions" title="Expression">
+      <param name="expression" type="text" value="" label="Expression"/>
     </repeat>
     
     <conditional name="gatk_param_type">
@@ -328,23 +333,14 @@
       </when>
     </conditional>
     
-    <conditional name="analysis_param_type">
-      <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
-        <option value="basic" selected="True">Basic</option>
-        <option value="advanced">Advanced</option>
-      </param>
-      <when value="basic">
-        <!-- Do nothing here -->
-      </when>
-      <when value="advanced">
-        <param name="group" type="select" multiple="True" display="checkboxes" label="annotation interfaces/groups to apply to variant calls">
-          <option value="Standard">Standard</option>
-          <option value="Experimental">Experimental</option>
-          <option value="WorkInProgress">WorkInProgress</option>
-        </param>
-
-      </when>
-    </conditional>
+    <param name="annotation_group" type="select" multiple="True" display="checkboxes" label="annotation interfaces/groups to apply to variant calls">
+      <option value="RodRequiringAnnotation">RodRequiringAnnotation</option>
+      <option value="Standard">Standard</option>
+      <option value="Experimental">Experimental</option>
+      <option value="WorkInProgress">WorkInProgress</option>
+      <option value="RankSumTest">RankSumTest</option>
+    </param>
+        
   </inputs>
   <outputs>
     <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (Variant File)" />
@@ -356,17 +352,20 @@
           <param name="ref_file" value="phiX.fasta" ftype="fasta" />
           <param name="input_bam" value="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" />
           <param name="input_variant" value="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.vcf" ftype="vcf" />
+          <param name="input_variant_bti" />
           <param name="annotations_type_selector" value="choose" />
           <param name="annotations" value="AlleleBalance,BaseQualityRankSumTest,DepthOfCoverage,HomopolymerRun,MappingQualityRankSumTest,MappingQualityZero,QualByDepth,RMSMappingQuality,SpanningDeletions,HaplotypeScore" />
-          <!-- <param name="additional_annotation_type_selector" value="snpEff" />
-          <param name="snpEffFile" value="single_comment.dat" ftype="snpEff" /> -->
-          <param name="rod_bind_type_selector" value="dbsnp" />
-          <param name="rodToIntervalTrackName" />
-          <param name="input_rod" value="gatk/fake_phiX_variant_locations.bed" ftype="bed" />
+          <param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" />
+          <param name="dbsnp_rodToIntervalTrackName" />
+          <param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" />
+          <param name="snpEff_rod_bind_type_selector" value="exclude_snpEff" />
           <param name="gatk_param_type_selector" value="basic" />
-          <param name="analysis_param_type_selector" value="basic" />
-          <output name="output_vcf" file="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" lines_diff="2" /> 
+          <output name="output_vcf" file="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" lines_diff="4" /> 
           <output name="output_log" file="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.log.contains" compare="contains" />
+          <param name="comp_rod_bind" value="0" />
+          <param name="resource_rod_bind" value="0" />
+          <param name="expressions" value="0" />
+          <!-- <param name="annotation_group" /> -->
       </test>
   </tests>
   <help>
diff --git a/tools/gatk/variant_apply_recalibration.xml b/tools/gatk/variant_apply_recalibration.xml
index e920a6b8257..bb0c1f90637 100644
--- a/tools/gatk/variant_apply_recalibration.xml
+++ b/tools/gatk/variant_apply_recalibration.xml
@@ -1,9 +1,14 @@
-<tool id="gatk_variant_apply_recalibration" name="Apply Variant Recalibration" version="0.0.1">
+<tool id="gatk_variant_apply_recalibration" name="Apply Variant Recalibration" version="0.0.2">
   <description></description>
+  <requirements>
+      <requirement type="package" version="1.2">gatk</requirement>
+  </requirements>
   <command interpreter="python">gatk_wrapper.py
-   --max_jvm_heap_fraction "2"
+   --max_jvm_heap_fraction "1"
    --stdout "${output_log}"
-   -d "-B:input,%(file_type)s" "${reference_source.input_variants}" "${reference_source.input_variants.ext}" "input_variants"
+   #for $var_count, $variant in enumerate( $reference_source.variants ):
+      -d "--input:input_${var_count},%(file_type)s" "${variant.input_variants}" "${variant.input_variants.ext}" "input_variants_${var_count}"
+   #end for
    -p 'java 
     -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar"
     -T "ApplyRecalibration"
@@ -62,21 +67,18 @@
     ##end standard gatk options
     
     ##start analysis specific options
+    -p '
+    --mode "${mode}"
     
-    #if $analysis_param_type.analysis_param_type_selector == "advanced":
-        -p '
-        --mode "${analysis_param_type.mode}"
-        
-        #for $ignore_filter in $analysis_param_type.ignore_filters:
-            #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.ignore_filter_type_selector )
-            #if $ignore_filter_name == "custom":
-              #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.filter_name )
-            #end if
-            --ignore_filter "${ignore_filter_name}"
-        #end for
-        '
-    #end if
-    -p '--ts_filter_level "${ts_filter_level}"'
+    #for $ignore_filter in $ignore_filters:
+        #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.ignore_filter_type_selector )
+        #if $ignore_filter_name == "custom":
+          #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.filter_name )
+        #end if
+        --ignore_filter "${ignore_filter_name}"
+    #end for
+    --ts_filter_level "${ts_filter_level}"
+    '
   </command>
   <inputs>
     <conditional name="reference_source">
@@ -85,17 +87,21 @@
         <option value="history">History</option>
       </param>
       <when value="cached">
-        <param name="input_variants" type="data" format="vcf,gatk_dbsnp,bed" label="Variant file to annotate" />
+        <repeat name="variants" title="Variant" min="1">
+          <param name="input_variants" type="data" format="vcf" label="Variant file to annotate" />
+        </repeat>
         <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" />
         <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" />
         <param name="ref_file" type="select" label="Using reference genome">
-          <options from_data_table="picard_indexes">
-            <filter type="data_meta" key="dbkey" ref="input_variants" column="dbkey"/>
-          </options>
+         <!--  <options from_data_table="picard_indexes">
+            <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/>
+          </options> -->
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
-        <param name="input_variants" type="data" format="vcf,gatk_dbsnp,bed" label="Variant file to annotate" />
+        <repeat name="variants" title="Variant" min="1">
+          <param name="input_variants" type="data" format="vcf" label="Variant file to annotate" />
+        </repeat>
         <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" />
         <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" />
         <param name="ref_file" type="data" format="fasta" label="Using reference file" />
@@ -193,15 +199,6 @@
       </when>
     </conditional>
     
-    <conditional name="analysis_param_type">
-      <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
-        <option value="basic" selected="True">Basic</option>
-        <option value="advanced">Advanced</option>
-      </param>
-      <when value="basic">
-        <!-- Do nothing here -->
-      </when>
-      <when value="advanced">
         <param name="mode" type="select" label="Recalibration mode">
           <option value="SNP" selected="True">SNP</option>
           <option value="INDEL">INDEL</option>
@@ -219,8 +216,6 @@
             </when>
           </conditional>
         </repeat>
-      </when>
-    </conditional>
     <param name="ts_filter_level" type="float" label="truth sensitivity level at which to start filtering, used here to indicate filtered variants in plots" value="99.0"/>
   </inputs>
   <outputs>
diff --git a/tools/gatk/variant_combine.xml b/tools/gatk/variant_combine.xml
index e6510ce7581..7494cb7ebe4 100644
--- a/tools/gatk/variant_combine.xml
+++ b/tools/gatk/variant_combine.xml
@@ -1,12 +1,15 @@
-<tool id="gatk_variant_combine" name="Combine Variants" version="0.0.1">
+<tool id="gatk_variant_combine" name="Combine Variants" version="0.0.2">
   <description></description>
+  <requirements>
+      <requirement type="package" version="1.2">gatk</requirement>
+  </requirements>
   <command interpreter="python">gatk_wrapper.py
-   --max_jvm_heap_fraction "2"
+   --max_jvm_heap_fraction "1"
    --stdout "${output_log}"
    
    #set $priority_order = []
    #for $input_variant in $reference_source.input_variants:
-       -d "-B:${input_variant.input_variant_name},%(file_type)s" "${input_variant.input_variant}" "${input_variant.input_variant.ext}" "input_variant_${input_variant.input_variant_name}"
+       -d "--variant:${input_variant.input_variant_name},%(file_type)s" "${input_variant.input_variant}" "${input_variant.input_variant.ext}" "input_variant_${input_variant.input_variant_name}"
        #set $input_variant_name = str( $input_variant.input_variant_name )
        #assert $input_variant_name not in $priority_order, "Variant Names must be unique" ##this should be handled by a validator
        #silent $priority_order.append( $input_variant_name )
@@ -21,6 +24,7 @@
     #if $reference_source.reference_source_selector != "history":
         -R "${reference_source.ref_file.fields.path}"
     #end if
+   --genotypemergeoption "${genotype_merge_option}"
    --rod_priority_list "${ ','.join( $priority_order ) }"
    '
    
@@ -72,7 +76,6 @@
     ##start analysis specific options
     #if $analysis_param_type.analysis_param_type_selector == "advanced":
         -p '
-        --genotypemergeoption "${analysis_param_type.genotype_merge_option}"
         --filteredrecordsmergetype "${analysis_param_type.filtered_records_merge_type}"
         ${analysis_param_type.print_complex_merges}
         ${analysis_param_type.filtered_are_uncalled}
@@ -95,7 +98,7 @@
         <option value="history">History</option>
       </param>
       <when value="cached">
-        <repeat min="1" name="input_variants" title="Variants to Merge">
+        <repeat min="1" name="input_variants" title="Variants to Merge" help="Records will be prioritized in the order that you list them here.">
           <param name="input_variant" type="data" format="vcf" label="Input variant file" />
           <param name="input_variant_name" type="text" value="" label="Variant name" help="Names must be unique">
             <validator type="length" min="1" message="You must provide a unique name for this set of variants" />
@@ -108,7 +111,7 @@
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
-        <repeat min="1" name="input_variants" title="Variants to Merge">
+        <repeat min="1" name="input_variants" title="Variants to Merge" help="Records will be prioritized in the order that you list them here.">
           <param name="input_variant" type="data" format="vcf" label="Input variant file" />
           <param name="input_variant_name" type="text" value="" label="Variant name" help="Names must be unique">
             <validator type="length" min="1" message="You must provide a unique name for this set of variants" />
@@ -117,7 +120,14 @@
         <param name="ref_file" type="data" format="fasta" label="Using reference file" />
       </when>
     </conditional>
-        
+    
+    <param name="genotype_merge_option" type="select" label="How should we merge genotype records across records for samples shared across the ROD files" >
+      <option value="UNIQUIFY" />
+      <option value="PRIORITIZE" selected="true"/>
+      <option value="UNSORTED" />
+      <option value="REQUIRE_UNIQUE" />
+    </param>
+    
     <conditional name="gatk_param_type">
       <param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options">
         <option value="basic" selected="True">Basic</option>
@@ -219,16 +229,10 @@
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <param name="genotype_merge_option" type="select" label="How should we merge genotype records across records for samples shared across the ROD files" >
-          <option value="UNIQUIFY" />
-          <option value="PRIORITIZE" selected="true"/>
-          <option value="UNSORTED" />
-          <option value="REQUIRE_UNIQUE" />
-        </param> 
         <param name="filtered_records_merge_type" type="select" label="How should we deal with records seen at the same site in the VCF, but with different FILTER fields? " >
           <option value="KEEP_IF_ANY_UNFILTERED" selected="true"/>
           <option value="KEEP_IF_ALL_UNFILTERED" />
-        </param> 
+        </param>
         
         <param name="print_complex_merges" checked="false" type="boolean" truevalue="--printComplexMerges" falsevalue="" label="Print out interesting sites requiring complex compatibility merging" />
         <param name="filtered_are_uncalled" checked="false" type="boolean" truevalue="--filteredAreUncalled" falsevalue="" label="If true, then filtered VCFs are treated as uncalled, so that filtered set annotation don't appear in the combined VCF" />
@@ -253,9 +257,10 @@
           <param name="ref_file" value="phiX.fasta" ftype="fasta" />
           <param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" />
           <param name="input_variant_name" value="from_variant_annotator" />
+          <param name="genotype_merge_option" value="PRIORITIZE" />
           <param name="gatk_param_type_selector" value="basic" />
           <param name="analysis_param_type_selector" value="basic" />
-          <output name="output_variants" file="gatk/gatk_variant_combine/gatk_variant_combine_out_1.vcf" lines_diff="2" />
+          <output name="output_variants" file="gatk/gatk_variant_combine/gatk_variant_combine_out_1.vcf" lines_diff="4" />
           <output name="output_log" file="gatk/gatk_variant_combine/gatk_variant_combine_out_1.log.contains" compare="contains" />
       </test>
   </tests>
diff --git a/tools/gatk/variant_eval.xml b/tools/gatk/variant_eval.xml
index 77886f688a8..4ea0f6b92c1 100644
--- a/tools/gatk/variant_eval.xml
+++ b/tools/gatk/variant_eval.xml
@@ -1,9 +1,14 @@
-<tool id="gatk_variant_eval" name="Eval Variants" version="0.0.1">
+<tool id="gatk_variant_eval" name="Eval Variants" version="0.0.2">
   <description></description>
+  <requirements>
+      <requirement type="package" version="1.2">gatk</requirement>
+  </requirements>
   <command interpreter="python">gatk_wrapper.py
-   --max_jvm_heap_fraction "2"
+   --max_jvm_heap_fraction "1"
    --stdout "${output_log}"
-   -d "-B:eval,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
+   #for $var_count, $variant in enumerate( $reference_source.variants ):
+      -d "--eval:input_${var_count},%(file_type)s" "${variant.input_variant}" "${variant.input_variant.ext}" "input_variants_${var_count}"
+   #end for
    -p 'java 
     -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar"
     -T "VariantEval"
@@ -16,23 +21,25 @@
     #end if
    '
    
-    #set $rod_binding_names = dict()
-    #for $rod_binding in $rod_bind:
-        #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom':
-            #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name
-        #else
-            #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector
+    #for $rod_binding in $comp_rod_bind:
+        -d "--comp:${rod_binding.comp_rod_name},%(file_type)s" "${rod_binding.comp_input_rod}" "${rod_binding.comp_input_rod.ext}" "input_comp_${rod_binding.comp_rod_name}"
+        #if str( $rod_binding.comp_rodToIntervalTrackName ):
+            -p '--rodToIntervalTrackName "${rod_binding.comp_rod_name}"'
         #end if
-        #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
-        -d "-B:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
-        #if str( $rod_binding.rod_bind_type.rodToIntervalTrackName ):
-            -p '--rodToIntervalTrackName "${rod_bind_name}"'
+        #if str( $rod_binding.comp_known_names ):
+            -p '--known_names "${rod_binding.comp_rod_name}"'
         #end if
-        #if str( $rod_binding.rod_bind_type.known_names ):
-            -p '--known_names "${rod_bind_name}"'
-        #end if
-        
     #end for
+    
+    #if str( $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector ) == 'set_dbsnp':
+        -d "--dbsnp:${dbsnp_rod_bind_type.dbsnp_rod_name},%(file_type)s" "${dbsnp_rod_bind_type.dbsnp_input_rod}" "${dbsnp_rod_bind_type.dbsnp_input_rod.ext}" "input_dbsnp_${dbsnp_rod_bind_type.dbsnp_rod_name}"
+        #if str( $dbsnp_rod_bind_type.dbsnp_rodToIntervalTrackName ):
+            -p '--rodToIntervalTrackName "${dbsnp_rod_bind_type.dbsnp_rod_name}"'
+            #if str( $dbsnp_rod_bind_type.dbsnp_known_names ):
+                -p '--known_names "${dbsnp_rod_bind_type.dbsnp_rod_name}"'
+            #end if
+        #end if
+    #end if
    
     ##start standard gatk options
     #if $gatk_param_type.gatk_param_type_selector == "advanced":
@@ -138,51 +145,46 @@
         <option value="history">History</option>
       </param>
       <when value="cached">
-        <param name="input_variant" type="data" format="vcf" label="Input variant file" />
+        <repeat name="variants" title="Variant" min="1">
+          <param name="input_variant" type="data" format="vcf" label="Input variant file" />
+        </repeat>
         <param name="ref_file" type="select" label="Using reference genome">
-          <options from_data_table="picard_indexes">
+          <!--<options from_data_table="picard_indexes">
             <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/>
-          </options>
+          </options>-->
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
-        <param name="input_variant" type="data" format="vcf" label="Input variant file" />
+        <repeat name="variants" title="Variant" min="1">
+          <param name="input_variant" type="data" format="vcf" label="Input variant file" />
+        </repeat>
         <param name="ref_file" type="data" format="fasta" label="Using reference file" />
       </when>
     </conditional>
     
-    <repeat name="rod_bind" title="Binding for reference-ordered data">
-        <conditional name="rod_bind_type">
-	      <param name="rod_bind_type_selector" type="select" label="Binding Type">
-	        <option value="dbsnp" selected="True">dbSNP</option>
-	        <option value="snps">SNPs</option>
-	        <option value="indels">INDELs</option>
-	        <option value="custom">Custom</option>
-	      </param>
-          <when value="dbsnp">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
-              <param name="known_names" type="boolean" truevalue="--known_names" falsevalue="" label="Treat ROD as known when splitting eval rods into known and novel subsets" />
-          </when>
-          <when value="snps">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
-              <param name="known_names" type="boolean" truevalue="--known_names" falsevalue="" label="Treat ROD as known when splitting eval rods into known and novel subsets" />
-          </when>
-          <when value="indels">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
-              <param name="known_names" type="boolean" truevalue="--known_names" falsevalue="" label="Treat ROD as known when splitting eval rods into known and novel subsets" />
-          </when>
-          <when value="custom">
-              <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/>
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
-              <param name="known_names" type="boolean" truevalue="--known_names" falsevalue="" label="Treat ROD as known when splitting eval rods into known and novel subsets" />
-          </when>
-        </conditional>
+    <repeat name="comp_rod_bind" title="Binding for reference-ordered comparison data">
+      <param name="comp_input_rod" type="data" format="vcf" label="Comparison ROD file" />
+      <param name="comp_rod_name" type="text" value="Unnamed" label="Comparison ROD Name"/>
+      <param name="comp_rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use Comparison ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
+      <param name="comp_known_names" type="boolean" truevalue="--known_names" falsevalue="" label="Use Comparison ROD as known_names" />
     </repeat>
     
+    <conditional name="dbsnp_rod_bind_type">
+      <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP reference-ordered data file">
+        <option value="set_dbsnp" selected="True">Set dbSNP</option>
+        <option value="exclude_dbsnp">Don't set dbSNP</option>
+      </param>
+      <when value="exclude_dbsnp">
+        <!-- Do nothing here -->
+      </when>
+      <when value="set_dbsnp">
+        <param name="dbsnp_input_rod" type="data" format="vcf" label="dbSNP ROD file" />
+        <param name="dbsnp_rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use dbSNP ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
+        <param name="dbsnp_rod_name" type="hidden" value="dbsnp" label="dbSNP ROD Name"/>
+        <param name="dbsnp_known_names" type="boolean" truevalue="--known_names" falsevalue="" label="Use dbSNP ROD as known_names" />
+      </when>
+    </conditional>
+    
     <conditional name="gatk_param_type">
       <param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options">
         <option value="basic" selected="True">Basic</option>
@@ -293,7 +295,7 @@
           <param name="sample" value="" type="text" label="Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context"/>
         </repeat>
         
-        <param name="stratification_modules" type="select" multiple="True" display="checkboxes" label="Stratification modules to apply to the eval track(s)" >
+        <param name="stratification_modules" type="select" multiple="True" display="checkboxes" label="Stratification modules to apply to the w track(s)" >
           <!-- do these need individual options also? gatk wiki has little info -->
           <option value="AlleleFrequency" />
           <option value="AlleleCount" />
@@ -356,10 +358,11 @@
           <param name="reference_source_selector" value="history" />
           <param name="ref_file" value="phiX.fasta" ftype="fasta" />
           <param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" />
-          <param name="rod_bind_type_selector" value="dbsnp" />
-          <param name="rodToIntervalTrackName" />
-          <param name="input_rod" value="gatk/fake_phiX_variant_locations.bed" ftype="bed" />
-          <param name="known_names" value="True"/>
+          <param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" />
+          <param name="dbsnp_rodToIntervalTrackName" />
+          <param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" />
+          <param name="dbsnp_known_names" value="True"/>
+          <param name="comp_rod_bind" value="0" />
           <param name="gatk_param_type_selector" value="basic" />
           <param name="analysis_param_type_selector" value="basic" />
           <output name="output_table" file="gatk/gatk_variant_eval/gatk_variant_eval_out_1.tabular" />
diff --git a/tools/gatk/variant_filtration.xml b/tools/gatk/variant_filtration.xml
index 4f076b811df..9c435c72123 100644
--- a/tools/gatk/variant_filtration.xml
+++ b/tools/gatk/variant_filtration.xml
@@ -1,9 +1,12 @@
-<tool id="gatk_variant_filtration" name="Variant Filtration" version="0.0.1">
+<tool id="gatk_variant_filtration" name="Variant Filtration" version="0.0.2">
   <description>on VCF files</description>
+  <requirements>
+      <requirement type="package" version="1.2">gatk</requirement>
+  </requirements>
   <command interpreter="python">gatk_wrapper.py
-   --max_jvm_heap_fraction "2"
+   --max_jvm_heap_fraction "1"
    --stdout "${output_log}"
-   -d "-B:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
+   -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
    -p 'java 
     -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar"
     -T "VariantFiltration"
@@ -20,22 +23,17 @@
     #end for
    '
     
-    #set $rod_binding_names = dict()
-    #for $rod_binding in $rod_bind:
-        #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom':
-            #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name
-        #else
-            #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector
+    
+    #if str( $mask_rod_bind_type.mask_rod_bind_type_selector ) == 'set_mask':
+        -d "--mask:${mask_rod_bind_type.mask_rod_name},%(file_type)s" "${mask_rod_bind_type.input_mask_rod}" "${mask_rod_bind_type.input_mask_rod.ext}" "input_mask_${mask_rod_bind_type.mask_rod_name}"
+        -p '
+        --maskExtension "${mask_rod_bind_type.mask_extension}"
+        --maskName "${mask_rod_bind_type.mask_rod_name}"
+        '
+        #if str( $mask_rod_bind_type.mask_rodToIntervalTrackName ):
+            -p '--rodToIntervalTrackName "${mask_rod_bind_type.mask_rod_name}"'
         #end if
-        #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
-        -d "-B:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
-        #if $rod_binding.rod_bind_type.rod_bind_type_selector == "mask":
-            --maskName "${rod_binding.rod_bind_type.mask_rod_name}"
-        #end if
-        #if str( $rod_binding.rod_bind_type.rodToIntervalTrackName ):
-            -p '--rodToIntervalTrackName "${rod_bind_name}"'
-        #end if
-    #end for
+    #end if
     
     ##start standard gatk options
     #if $gatk_param_type.gatk_param_type_selector == "advanced":
@@ -97,7 +95,7 @@
         <option value="history">History</option>
       </param>
       <when value="cached">
-        <param name="input_variant" type="data" format="vcf,gatk_dbsnp,bed" label="Variant file to annotate" />
+        <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" />
         <param name="ref_file" type="select" label="Using reference genome">
           <options from_data_table="picard_indexes">
             <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/>
@@ -105,7 +103,7 @@
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
-        <param name="input_variant" type="data" format="vcf,gatk_dbsnp,bed" label="Variant file to annotate" />
+        <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" />
         <param name="ref_file" type="data" format="fasta" label="Using reference file" />
       </when>
     </conditional>
@@ -125,39 +123,24 @@
         <param name="is_genotype_filter" type="boolean" truevalue="genotypeFilter" falsevalue="filter" label="Use filter at the individual sample level" />
     </repeat>
     
-    <repeat name="rod_bind" title="Binding for reference-ordered data">
-        <conditional name="rod_bind_type">
-	      <param name="rod_bind_type_selector" type="select" label="Binding Type">
-	        <option value="dbsnp">dbSNP</option>
-	        <option value="snps">SNPs</option>
-	        <option value="indels">INDELs</option>
-	        <option value="mask" selected="True">Mask</option>
-	        <option value="custom">Custom</option>
-	      </param>
-          <when value="dbsnp">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
-          </when>
-          <when value="snps">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
-          </when>
-          <when value="indels">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
-          </when>
-          <when value="custom">
-              <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/>
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
-          </when>
-          <when value="mask">
-              <param name="mask_rod_name" type="text" value="Unknown" label="Mask Name"/>
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
-          </when>
-        </conditional>
-    </repeat>
+
+    
+    <conditional name="mask_rod_bind_type">
+      <param name="mask_rod_bind_type_selector" type="select" label="Provide a Mask reference-ordered data file">
+        <option value="set_mask" selected="True">Set maskP</option>
+        <option value="exclude_mask">Don't set mask</option>
+      </param>
+      <when value="exclude_mask">
+        <!-- Do nothing here -->
+      </when>
+      <when value="set_mask">
+        <param name="input_mask_rod" type="data" format="bed,gatk_dbsnp,vcf" label="Mask ROD file" />
+        <param name="mask_rod_name" type="text" value="Mask" label="Mask Name"/>
+        <param name="mask_extension" type="integer" value="0" label="Mask Extension"/>
+        <param name="mask_rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use Mask ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
+      </when>
+    </conditional>    
+    
     
     <conditional name="gatk_param_type">
       <param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options">
@@ -279,9 +262,11 @@
           <param name="filter_expression" value="MQ &lt; 37.74 || MQ0 &gt; 50" />
           <param name="filter_name" value="Galaxy_filter" />
           <param name="is_genotype_filter" />
-          <param name="rod_bind_type_selector" value="dbsnp" />
-          <param name="rodToIntervalTrackName" />
-          <param name="input_rod" value="gatk/fake_phiX_variant_locations.bed" ftype="bed" />
+          <param name="mask_rod_bind_type_selector" value="set_mask" />
+          <param name="mask_rodToIntervalTrackName" />
+          <param name="input_mask_rod" value="gatk/fake_phiX_variant_locations.bed" ftype="bed" />
+          <param name="mask_rod_name" value="." />
+          <param name="mask_extension" value="0" />
           <param name="gatk_param_type_selector" value="basic" />
           <param name="cluster_snp_type_selector" value="do_not_cluster_snp" />
           <param name="missing_values_in_expressions_should_evaluate_as_failing" />
diff --git a/tools/gatk/variant_recalibrator.xml b/tools/gatk/variant_recalibrator.xml
index 7aae76119fc..58e762b2242 100644
--- a/tools/gatk/variant_recalibrator.xml
+++ b/tools/gatk/variant_recalibrator.xml
@@ -1,9 +1,14 @@
-<tool id="gatk_variant_recalibrator" name="Variant Recalibrator" version="0.0.1">
+<tool id="gatk_variant_recalibrator" name="Variant Recalibrator" version="0.0.2">
   <description></description>
+  <requirements>
+      <requirement type="package" version="1.2">gatk</requirement>
+  </requirements>
   <command interpreter="python">gatk_wrapper.py
-   --max_jvm_heap_fraction "2"
+   --max_jvm_heap_fraction "1"
    --stdout "${output_log}"
-   -d "-B:input,%(file_type)s" "${reference_source.input_variants}" "${reference_source.input_variants.ext}" "input_variants"
+   #for $var_count, $variant in enumerate( $reference_source.variants ):
+      -d "--input:input_${var_count},%(file_type)s" "${variant.input_variants}" "${variant.input_variants.ext}" "input_variants_${var_count}"
+   #end for
    -p 'java 
     -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar"
     -T "VariantRecalibrator"
@@ -29,9 +34,9 @@
         #end if
         #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
         #if $rod_binding.rod_bind_type.rod_training_type.rod_training_type_selector == "not_training_truth_known":
-        -d "-B:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
+        -d "--resource:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
         #else:
-        -d "-B:${rod_bind_name},%(file_type)s,known=${rod_binding.rod_bind_type.rod_training_type.known},training=${rod_binding.rod_bind_type.rod_training_type.training},truth=${rod_binding.rod_bind_type.rod_training_type.truth},bad=${rod_binding.rod_bind_type.rod_training_type.bad},prior=${rod_binding.rod_bind_type.rod_training_type.prior}" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
+        -d "--resource:${rod_bind_name},%(file_type)s,known=${rod_binding.rod_bind_type.rod_training_type.known},training=${rod_binding.rod_bind_type.rod_training_type.training},truth=${rod_binding.rod_bind_type.rod_training_type.truth},bad=${rod_binding.rod_bind_type.rod_training_type.bad},prior=${rod_binding.rod_bind_type.rod_training_type.prior}" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
         #end if
         #if str( $rod_binding.rod_bind_type.rodToIntervalTrackName ):
             -p '--rodToIntervalTrackName "${rod_bind_name}"'
@@ -89,11 +94,11 @@
             --use_annotation "${annotation}"
         #end for
     #end if
+    --mode "${mode}"
     '
     
     #if $analysis_param_type.analysis_param_type_selector == "advanced":
         -p '
-        --mode "${analysis_param_type.mode}"
         --maxGaussians "${analysis_param_type.max_gaussians}"
         --maxIterations "${analysis_param_type.max_iterations}"
         --numKMeans "${analysis_param_type.num_k_means}"
@@ -102,8 +107,11 @@
         --shrinkage "${analysis_param_type.shrinkage}"
         --dirichlet "${analysis_param_type.dirichlet}"
         --priorCounts "${analysis_param_type.prior_counts}"
-        --percentBadVariants "${analysis_param_type.percent_bad_variants}"
-        --minNumBadVariants "${analysis_param_type.min_num_bad_variants}"
+        #if str( $analysis_param_type.bad_variant_selector.bad_variant_selector_type ) == 'percent':
+            --percentBadVariants "${analysis_param_type.bad_variant_selector.percent_bad_variants}"
+        #else:
+            --minNumBadVariants "${analysis_param_type.bad_variant_selector.min_num_bad_variants}"
+        #end if
         --target_titv "${analysis_param_type.target_titv}"
         #for $tranche in [ $tranche.strip() for $tranche in str( $analysis_param_type.ts_tranche ).split( ',' ) if $tranche.strip() ]
             --TStranche "${tranche}"
@@ -131,15 +139,19 @@
         <option value="history">History</option>
       </param>
       <when value="cached">
-        <param name="input_variants" type="data" format="vcf,gatk_dbsnp,bed" label="Variant file to annotate" />
+        <repeat name="variants" title="Variant" min="1">
+          <param name="input_variants" type="data" format="vcf" label="Variant file to recalibrate" />
+        </repeat>
         <param name="ref_file" type="select" label="Using reference genome">
-          <options from_data_table="picard_indexes">
-            <filter type="data_meta" key="dbkey" ref="input_variants" column="dbkey"/>
-          </options>
+          <!-- <options from_data_table="picard_indexes">
+            <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/>
+          </options> -->
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
-        <param name="input_variants" type="data" format="vcf,gatk_dbsnp,bed" label="Variant file to annotate" />
+        <repeat name="variants" title="Variant" min="1">
+          <param name="input_variants" type="data" format="vcf" label="Variant file to recalibrate" />
+        </repeat>
         <param name="ref_file" type="data" format="fasta" label="Using reference file" />
       </when>
     </conditional>
@@ -323,37 +335,42 @@
     
     <param name="annotations" type="select" multiple="True" display="checkboxes" label="annotations which should used for calculations">
       <!-- might we want to load the available annotations from an external configuration file, since additional ones can be added to local installs? -->
-      <option value="AlleleBalance" />
-      <option value="BaseQualityRankSumTest" />
-      <option value="DepthOfCoverage" />
-      <option value="HomopolymerRun" />
-      <option value="MappingQualityRankSumTest" />
-      <option value="MappingQualityZero" />
-      <option value="QualByDepth" />
-      <option value="RMSMappingQuality" />
-      <option value="SpanningDeletions" />
-      <option value="HaplotypeScore" />
-      <!-- annotations below were pulled from list option -->
-      <option value="ChromosomeCounts" />
-      <option value="IndelType" />
-      <option value="HardyWeinberg" />
-      <option value="BaseCounts" />
-      <option value="LowMQ" />
-      <option value="FisherStrand" />
-      <option value="GenomicAnnotation" />
-      <option value="GCContent" />
-      <option value="ReadPosRankSumTest" />
-      <option value="SBByDepth" />
-      <option value="ReadDepthAndAllelicFractionBySample" />
-      <option value="AlleleBalanceBySample" />
-      <option value="DepthPerAlleleBySample" />
-      <option value="MappingQualityZeroBySample" />
-      <option value="NBaseCount" />
-      <option value="GLstats" />
-      <option value="SampleList" />
-      <option value="MappingQualityZeroFraction" />
+      <option value="ChromosomeCounts"/>
+      <option value="IndelType"/>
+      <option value="SpanningDeletions"/>
+      <option value="HardyWeinberg"/>
+      <option value="NBaseCount"/>
+      <option value="MappingQualityZero"/>
+      <option value="AlleleBalance"/>
+      <option value="BaseCounts"/>
+      <option value="LowMQ"/>
+      <option value="InbreedingCoeff"/>
+      <option value="RMSMappingQuality"/>
+      <option value="HaplotypeScore"/>
+      <option value="TechnologyComposition"/>
+      <option value="SampleList"/>
+      <option value="FisherStrand"/>
+      <option value="HomopolymerRun"/>
+      <option value="DepthOfCoverage"/>
+      <option value="SnpEff"/>
+      <option value="MappingQualityZeroFraction"/>
+      <option value="GCContent"/>
+      <option value="MappingQualityRankSumTest"/>
+      <option value="ReadPosRankSumTest"/>
+      <option value="BaseQualityRankSumTest"/>
+      <option value="QualByDepth"/>
+      <option value="SBByDepth"/>
+      <option value="ReadDepthAndAllelicFractionBySample"/>
+      <option value="AlleleBalanceBySample"/>
+      <option value="DepthPerAlleleBySample"/>
+      <option value="MappingQualityZeroBySample"/>
     </param>
     
+        <param name="mode" type="select" label="Recalibration mode">
+          <option value="SNP" selected="True">SNP</option>
+          <option value="INDEL">INDEL</option>
+          <option value="BOTH">BOTH</option>
+        </param>
     
     <conditional name="gatk_param_type">
       <param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options">
@@ -455,11 +472,6 @@
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <param name="mode" type="select" label="Recalibration mode">
-          <option value="SNP" selected="True">SNP</option>
-          <option value="INDEL">INDEL</option>
-          <option value="BOTH">BOTH</option>
-        </param>
         <param name="max_gaussians" type="integer" label="maximum number of Gaussians to try during variational Bayes Algorithm" value="10"/>
         <param name="max_iterations" type="integer" label="maximum number of maximum number of VBEM iterations to be performed in variational Bayes Algorithm" value="100"/>
         <param name="num_k_means" type="integer" label="number of k-means iterations to perform in order to initialize the means of the Gaussians in the Gaussian mixture model" value="30"/>
@@ -468,8 +480,18 @@
         <param name="shrinkage" type="float" label="shrinkage parameter in variational Bayes algorithm" value="1.0"/>
         <param name="dirichlet" type="float" label="dirichlet parameter in variational Bayes algorithm" value="0.001"/>
         <param name="prior_counts" type="float" label="number of prior counts to use in variational Bayes algorithm" value="20.0"/>
-        <param name="percent_bad_variants" type="float" label="percentage of the worst scoring variants to use when building the Gaussian mixture model of bad variants. 0.07 means bottom 7 percent." value="0.03"/>
-        <param name="min_num_bad_variants" type="integer" label="minimum amount of worst scoring variants to use when building the Gaussian mixture model of bad variants. Will override -percentBad arugment if necessary" value="2000"/>
+        <conditional name="bad_variant_selector">
+          <param name="bad_variant_selector_type" type="select" label="Basic or Advanced Analysis options">
+            <option value="percent" selected="True">Percent</option>
+            <option value="min_num">Number</option>
+          </param>
+          <when value="percent">
+            <param name="percent_bad_variants" type="float" label="percentage of the worst scoring variants to use when building the Gaussian mixture model of bad variants. 0.07 means bottom 7 percent." value="0.03"/>
+          </when>
+          <when value="min_num">
+            <param name="min_num_bad_variants" type="integer" label="minimum amount of worst scoring variants to use when building the Gaussian mixture model of bad variants. Will override -percentBad arugment if necessary" value="2000"/>
+          </when>
+        </conditional>
         <param name="target_titv" type="float" label="expected novel Ti/Tv ratio to use when calculating FDR tranches and for display on optimization curve output figures. (approx 2.15 for whole genome experiments). ONLY USED FOR PLOTTING PURPOSES!" value="2.15"/>
         <param name="ts_tranche" type="text" label="levels of novel false discovery rate (FDR, implied by ti/tv) at which to slice the data. (in percent, that is 1.0 for 1 percent)" value="100.0, 99.9, 99.0, 90.0"/>
         <repeat name="ignore_filters" title="Ignore Filter">
diff --git a/tools/gatk/variants_validate.xml b/tools/gatk/variants_validate.xml
index ccec64b8f27..67a325f23f7 100644
--- a/tools/gatk/variants_validate.xml
+++ b/tools/gatk/variants_validate.xml
@@ -1,9 +1,12 @@
-<tool id="gatk_validate_variants" name="Validate Variants" version="0.0.1">
+<tool id="gatk_validate_variants" name="Validate Variants" version="0.0.2">
   <description></description>
+  <requirements>
+      <requirement type="package" version="1.2">gatk</requirement>
+  </requirements>
   <command interpreter="python">gatk_wrapper.py
-   --max_jvm_heap_fraction "2"
+   --max_jvm_heap_fraction "1"
    --stdout "${output_log}"
-   -d "-B:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
+   -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
    -p 'java 
     -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar"
     -T "ValidateVariants"
@@ -17,19 +20,12 @@
     ${do_not_validate_filtered_records}
    '
    
-    #set $rod_binding_names = dict()
-    #for $rod_binding in $rod_bind:
-        #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom':
-            #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name
-        #else
-            #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector
+    #if str( $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector ) == 'set_dbsnp':
+        -d "--dbsnp:${dbsnp_rod_bind_type.dbsnp_rod_name},%(file_type)s" "${dbsnp_rod_bind_type.dbsnp_input_rod}" "${dbsnp_rod_bind_type.dbsnp_input_rod.ext}" "input_dbsnp_${dbsnp_rod_bind_type.dbsnp_rod_name}"
+        #if str( $dbsnp_rod_bind_type.dbsnp_rodToIntervalTrackName ):
+            -p '--rodToIntervalTrackName "${dbsnp_rod_bind_type.dbsnp_rod_name}"'
         #end if
-        #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
-        -d "-B:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
-        #if str( $rod_binding.rod_bind_type.rodToIntervalTrackName ):
-            -p '--rodToIntervalTrackName "${rod_bind_name}"'
-        #end if
-    #end for
+    #end if
    
     ##start standard gatk options
     #if $gatk_param_type.gatk_param_type_selector == "advanced":
@@ -96,38 +92,21 @@
       </when>
     </conditional>
     
-    <repeat name="rod_bind" title="Binding for reference-ordered data">
-        <conditional name="rod_bind_type">
-	      <param name="rod_bind_type_selector" type="select" label="Binding Type">
-	        <!--  <option value="variant" selected="True">Variant</option> -->
-	        <option value="dbsnp" selected="True">dbSNP</option>
-	        <option value="snps">SNPs</option>
-	        <!-- <option value="indels">INDELs</option>
-	        <option value="custom">Custom</option> -->
-	      </param>
-          <when value="variant">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> <!-- this should be restricted to genome type, or genome type should be limited as a result of this selection -->
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
-          </when>
-          <when value="dbsnp">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
-          </when>
-          <when value="snps">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
-          </when>
-          <when value="indels">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
-          </when>
-          <when value="custom">
-              <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/>
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
-          </when>
-        </conditional>
-    </repeat>
+    <conditional name="dbsnp_rod_bind_type">
+      <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP reference-ordered data file">
+        <option value="set_dbsnp" selected="True">Set dbSNP</option>
+        <option value="exclude_dbsnp">Don't set dbSNP</option>
+      </param>
+      <when value="exclude_dbsnp">
+        <!-- Do nothing here -->
+      </when>
+      <when value="set_dbsnp">
+        <param name="dbsnp_input_rod" type="data" format="vcf" label="ROD file" />
+        <param name="dbsnp_rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
+        <param name="dbsnp_rod_name" type="hidden" value="dbsnp" label="ROD Name"/>
+      </when>
+    </conditional>
+    
     <param name="warn_on_errors" type="boolean" checked="False" truevalue="-warnOnErrors" falsevalue="" label="instead of terminating the run at the first error, print warning messages for each error seen. "/>
     <param name="do_not_validate_filtered_records" type="boolean" checked="False" truevalue="-doNotValidateFilteredRecords" falsevalue="" label="do not try to validate records that are FILTERed. "/>
     
@@ -231,9 +210,9 @@
           <param name="reference_source_selector" value="history" />
           <param name="ref_file" value="phiX.fasta" ftype="fasta" />
           <param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" />
-          <param name="rod_bind_type_selector" value="dbsnp" />
-          <param name="rodToIntervalTrackName" />
-          <param name="input_rod" value="gatk/fake_phiX_variant_locations.bed" ftype="bed" />
+          <param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" />
+          <param name="dbsnp_rodToIntervalTrackName" />
+          <param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" />
           <param name="warn_on_errors" value="True"/>
           <param name="do_not_validate_filtered_records" />
           <param name="gatk_param_type_selector" value="basic" />

From 9f9e55f3200a07c12a216354bb07fa1c0c3140f5 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Thu, 20 Oct 2011 16:38:14 -0400
Subject: [PATCH 077/362] Update sff extractor to version 0.2.10.

---
 tools/filters/sff_extract.py    | 21 ++++++++++++++-------
 tools/filters/sff_extractor.xml |  2 +-
 2 files changed, 15 insertions(+), 8 deletions(-)

diff --git a/tools/filters/sff_extract.py b/tools/filters/sff_extract.py
index 1b2013226b5..42fb328b591 100644
--- a/tools/filters/sff_extract.py
+++ b/tools/filters/sff_extract.py
@@ -27,7 +27,7 @@ sequence will be removed, even if occuring multiple times.'''
 __author__ = 'Jose Blanca and Bastien Chevreux'
 __copyright__ = 'Copyright 2008, Jose Blanca, COMAV, and Bastien Chevreux'
 __license__ = 'GPLv3 or later'
-__version__ = '0.2.8'
+__version__ = '0.2.10'
 __email__ = 'jblanca@btc.upv.es'
 __status__ = 'beta'
 
@@ -298,7 +298,8 @@ def remove_last_xmltag_in_file(fname, tag=None):
     
     #we check that we're removing the asked tag
     if tag is not None and tag != last_tag:
-        raise RuntimeError("The given xml tag wasn't the last one in the file")
+        etxt=join('The given xml tag (',tag,') was not the last one in the file');
+        raise RuntimeError(etxt)
 
     # while we are at it: also remove all white spaces in that line :-)
     i -= 1
@@ -843,7 +844,7 @@ def split_paired_end(data, sff_fh, seq_fh, qual_fh, xml_fh):
             if len(boundaries) == 3:
                 # case: mask char on both sides of sequence
                 #print "bounds3"
-                data['clip_adapter_left']=1+boundaries[0][1]
+                data['clip_adapter_left']=boundaries[0][1]
                 data['clip_adapter_right']=boundaries[2][0]
             elif len(boundaries) == 2:
                 # case: mask char left or right of sequence
@@ -851,7 +852,7 @@ def split_paired_end(data, sff_fh, seq_fh, qual_fh, xml_fh):
                 if maskedseq[0] == maskchar :
                     # case: mask char left
                     #print "left"
-                    data['clip_adapter_left']=1+boundaries[0][1]
+                    data['clip_adapter_left']=boundaries[0][1]
                 else:
                     # case: mask char right
                     #print "right"
@@ -1192,7 +1193,11 @@ def sequence_case(data):
     '''
     left, right = return_merged_clips(data)
     seq = data['bases']
-    new_seq = ''.join((seq[:left-1].lower(), seq[left-1:right], seq[right:].lower()))
+    if left >= right:
+        new_seq = seq.lower()
+    else:
+        new_seq = ''.join((seq[:left-1].lower(), seq[left-1:right], seq[right:].lower()))
+
     return new_seq
 
 def clip_read(data):
@@ -1209,14 +1214,14 @@ def clip_read(data):
 
 
 
-def tests_for_ssaha(linker_fname):
+def tests_for_ssaha():
     '''Tests whether SSAHA2 can be successfully called.'''
     
     try:
         print "Testing whether SSAHA2 is installed and can be launched ... ",
         sys.stdout.flush()
         fh = open('/dev/null', 'w')
-        retcode = subprocess.call(["ssaha2", "-v"], stdout = fh)
+        retcode = subprocess.call(["ssaha2"], stdout = fh)
         fh.close()
         print "ok."
     except :
@@ -1247,6 +1252,8 @@ def launch_ssaha(linker_fname, query_fname, output_fh):
     '''Launches SSAHA2 on the linker and query file, string SSAHA2 output
     into the output filehandle'''
 
+    tests_for_ssaha()
+
     try:
         print "Searching linker sequences with SSAHA2 (this may take a while) ... ",
         sys.stdout.flush()
diff --git a/tools/filters/sff_extractor.xml b/tools/filters/sff_extractor.xml
index a777674df59..2beb7548b21 100644
--- a/tools/filters/sff_extractor.xml
+++ b/tools/filters/sff_extractor.xml
@@ -1,4 +1,4 @@
-<tool id="Sff_extractor" name="SFF converter" version="1.0.0">
+<tool id="Sff_extractor" name="SFF converter" version="1.0.1">
     <description></description>
     <command interpreter="python">
         #if   str($fastq_output) == "fastq_false"  #sff_extract.py $clip --seq_file=$out_file3 --qual_file=$out_file4 --xml_file=$out_file2 $input

From 58c158c54566dc4286b96a82d13a73019718647e Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Thu, 20 Oct 2011 16:57:09 -0400
Subject: [PATCH 078/362] Fixes for searching for and installing tools from a
 tool shed.  The value of the webapp request parameter is heavily used
 throughout this process, and has been added to all grid forms that include
 operation buttons.

---
 lib/galaxy/web/controllers/admin.py           |   2 +-
 .../community/controllers/repository.py       | 127 ++++++++++--------
 templates/grid_base.mako                      |   1 +
 .../community/repository/find_tools.mako      |   7 +
 .../preview_tools_in_changeset.mako           |   7 +-
 .../community/repository/tool_form.mako       |   7 +-
 .../community/repository/view_repository.mako |   7 +-
 .../repository/view_tool_metadata.mako        |   7 +-
 .../webapps/galaxy/admin/tool_sheds.mako      |   4 +-
 9 files changed, 105 insertions(+), 64 deletions(-)

diff --git a/lib/galaxy/web/controllers/admin.py b/lib/galaxy/web/controllers/admin.py
index 2168f811ddb..90713fa0169 100644
--- a/lib/galaxy/web/controllers/admin.py
+++ b/lib/galaxy/web/controllers/admin.py
@@ -708,7 +708,7 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
     def browse_tool_shed( self, trans, **kwd ):
         tool_shed_url = kwd[ 'tool_shed_url' ]
         galaxy_url = trans.request.host
-        url = '%s/repository/browse_downloadable_repositories?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, galaxy_url )
+        url = '%s/repository/browse_valid_repositories?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, galaxy_url )
         return trans.response.send_redirect( url )
     @web.expose
     @web.require_admin
diff --git a/lib/galaxy/webapps/community/controllers/repository.py b/lib/galaxy/webapps/community/controllers/repository.py
index f130be58949..01e7c62a4e5 100644
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -183,7 +183,7 @@ class RepositoryListGrid( grids.Grid ):
                                .outerjoin( model.RepositoryCategoryAssociation.table ) \
                                .outerjoin( model.Category.table )
 
-class DownloadableRepositoryListGrid( RepositoryListGrid ):
+class ValidRepositoryListGrid( RepositoryListGrid ):
     class RevisionColumn( grids.GridColumn ):
         def __init__( self, col_name ):
             grids.GridColumn.__init__( self, col_name )
@@ -196,7 +196,7 @@ class DownloadableRepositoryListGrid( RepositoryListGrid ):
             if len( select_field.options ) > 1:
                 return select_field.get_html()
             return repository.revision
-    title = "Downloadable repositories"
+    title = "Valid repositories"
     columns = [
         RepositoryListGrid.NameColumn( "Name",
                                        key="name",
@@ -210,11 +210,6 @@ class DownloadableRepositoryListGrid( RepositoryListGrid ):
                                        attach_popup=False,
                                        key="User.username" )
     ]
-    columns.append( grids.MulticolFilterColumn( "Search repository name, description", 
-                                                cols_to_filter=[ columns[0], columns[1] ],
-                                                key="free-text-search",
-                                                visible=False,
-                                                filterable="standard" ) )
     operations = []
     def build_initial_query( self, trans, **kwd ):
         return trans.sa_session.query( self.model_class ) \
@@ -237,7 +232,7 @@ class MatchedRepositoryListGrid( grids.Grid ):
                 return repository_metadata.repository.user.username
             return 'no user'
     # Grid definition
-    title = "Matched repositories"
+    title = "Repositories with matching tools"
     model_class = model.RepositoryMetadata
     template='/webapps/community/repository/grid.mako'
     default_sort_key = "Repository.name"
@@ -282,21 +277,19 @@ class MatchedRepositoryListGrid( grids.Grid ):
                                .filter( self.model_class.table.c.repository_id == 0 )
 
 class InstallMatchedRepositoryListGrid( MatchedRepositoryListGrid ):
-    # Grid definition
-    title = "Repositories that contain tools matching search criteria"
     columns = [ col for col in MatchedRepositoryListGrid.columns ]
     # Override the NameColumn
     columns[ 0 ] = MatchedRepositoryListGrid.NameColumn( "Name",
                                                          link=( lambda item: dict( operation="view_or_manage_repository",
                                                                                    id=item.id,
                                                                                    webapp="galaxy" ) ),
-                                                         attach_popup=True )
+                                                         attach_popup=False )
 
 class RepositoryController( BaseUIController, ItemRatings ):
 
     install_matched_repository_list_grid = InstallMatchedRepositoryListGrid()
     matched_repository_list_grid = MatchedRepositoryListGrid()
-    downloadable_repository_list_grid = DownloadableRepositoryListGrid()
+    valid_repository_list_grid = ValidRepositoryListGrid()
     repository_list_grid = RepositoryListGrid()
     category_list_grid = CategoryListGrid()
 
@@ -340,7 +333,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
         # Render the list view
         return self.category_list_grid( trans, **kwd )
     @web.expose
-    def browse_downloadable_repositories( self, trans, **kwd ):
+    def browse_valid_repositories( self, trans, **kwd ):
         webapp = kwd.get( 'webapp', 'community' )
         galaxy_url = kwd.get( 'galaxy_url', None )
         if galaxy_url:
@@ -352,6 +345,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
                 repository = get_repository( trans, repository_id )
                 return trans.response.send_redirect( web.url_for( controller='repository',
                                                                   action='preview_tools_in_changeset',
+                                                                  webapp=webapp,
                                                                   repository_id=repository_id,
                                                                   changeset_revision=repository.tip ) )
         # The changeset_revision_select_field in the RepositoryListGrid performs a refresh_on_change
@@ -371,16 +365,16 @@ class RepositoryController( BaseUIController, ItemRatings ):
                                                                       webapp=webapp,
                                                                       repository_id=trans.security.encode_id( repository.id ),
                                                                       changeset_revision=v ) )
-        url_args = dict( action='browse_downloadable_repositories',
+        url_args = dict( action='browse_valid_repositories',
                          operation='preview_tools_in_changeset',
                          webapp=webapp,
                          repository_id=repository_id )
-        self.downloadable_repository_list_grid.operations = [ grids.GridOperation( "Preview and install",
-                                                                                   url_args=url_args,
-                                                                                   allow_multiple=False,
-                                                                                   async_compatible=False ) ]
+        self.valid_repository_list_grid.operations = [ grids.GridOperation( "Preview and install",
+                                                                            url_args=url_args,
+                                                                            allow_multiple=False,
+                                                                            async_compatible=False ) ]
         # Render the list view
-        return self.downloadable_repository_list_grid( trans, **kwd )
+        return self.valid_repository_list_grid( trans, **kwd )
     @web.expose
     def find_tools( self, trans, **kwd ):
         params = util.Params( kwd )
@@ -391,38 +385,35 @@ class RepositoryController( BaseUIController, ItemRatings ):
         if galaxy_url:
             trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' )
         if 'operation' in kwd:
-            operation = kwd[ 'operation' ].lower()
-            is_admin = trans.user_is_admin()
-            if operation == "view_or_manage_repository":
-                # The received id is a RepositoryMetadata id, so we have to get the repository id.
-                repository_metadata = get_repository_metadata_by_id( trans, kwd[ 'id' ] )
-                repository_id = trans.security.encode_id( repository_metadata.repository.id )
-                repository = get_repository( trans, repository_id )
-                kwd[ 'id' ] = repository_id
-                kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision
-                if webapp == 'community' and ( is_admin or repository.user == trans.user ):
-                    a = 'manage_repository'
-                else:
-                    a = 'view_repository'
-                return trans.response.send_redirect( web.url_for( controller='repository',
-                                                                  action=a,
-                                                                  **kwd ) )
-            if operation == "install":
-                repo_info_dict = {}
-                galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' )
-                # TODO: support https in the following url.
-                url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s&webapp=%s' % ( galaxy_url, trans.request.host, webapp )
-                repository_metadata_ids = util.listify( kwd[ 'id' ] )
-                for repository_metadata_id in repository_metadata_ids:
-                    repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id )
-                    repository = get_repository( trans, trans.security.encode_id( repository_metadata.repository_id ) )
-                    repository_id = trans.security.encode_id( repository.id )
-                    changeset_revision = repository_metadata.changeset_revision
-                    repository_clone_url = generate_clone_url( trans, repository_id )
-                    repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, changeset_revision )
-                encoded_repo_info_dict = self.__encode( repo_info_dict )
-                url += '&repo_info_dict=%s' % encoded_repo_info_dict
-                return trans.response.send_redirect( url )
+            item_id = kwd.get( 'id', '' )
+            if item_id:
+                operation = kwd[ 'operation' ].lower()
+                is_admin = trans.user_is_admin()
+                if operation == "view_or_manage_repository":
+                    # The received id is a RepositoryMetadata id, so we have to get the repository id.
+                    repository_metadata = get_repository_metadata_by_id( trans, item_id )
+                    repository_id = trans.security.encode_id( repository_metadata.repository.id )
+                    repository = get_repository( trans, repository_id )
+                    kwd[ 'id' ] = repository_id
+                    kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision
+                    if webapp == 'community' and ( is_admin or repository.user == trans.user ):
+                        a = 'manage_repository'
+                    else:
+                        a = 'view_repository'
+                    return trans.response.send_redirect( web.url_for( controller='repository',
+                                                                      action=a,
+                                                                      **kwd ) )
+                if operation == "install":
+                    galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' )
+                    encoded_repo_info_dict = self.__encode_repo_info_dict( trans, webapp, util.listify( item_id ) )
+                    # TODO: support https in the following url.
+                    url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s&webapp=%s&repo_info_dict=%s' % \
+                        ( galaxy_url, trans.request.host, webapp, encoded_repo_info_dict )
+                    return trans.response.send_redirect( url )
+            else:
+                # This can only occur when there is a multi-select grid with check boxes and an operation,
+                # and the user clicked the operation button without checking any of the check boxes.
+                return trans.show_error_message( "No items were selected." )
         tool_ids = [ item.lower() for item in util.listify( kwd.get( 'tool_id', '' ) ) ]
         tool_names = [ item.lower() for item in util.listify( kwd.get( 'tool_name', '' ) ) ]
         tool_versions = [ item.lower() for item in util.listify( kwd.get( 'tool_version', '' ) ) ]
@@ -436,7 +427,12 @@ class RepositoryController( BaseUIController, ItemRatings ):
                 kwd[ 'match_tuples' ] = match_tuples
                 # Render the list view
                 if webapp == 'galaxy':
-                    # Our request originated from a Galaxy instance.
+                    # Our initial request originated from a Galaxy instance.
+                    global_actions = [ grids.GridAction( "Browse valid repositories",
+                                                         dict( controller='repository', action='browse_valid_repositories', webapp=webapp ) ),
+                                       grids.GridAction( "Search for valid tools",
+                                                         dict( controller='repository', action='find_tools', webapp=webapp ) ) ]
+                    self.install_matched_repository_list_grid.global_actions = global_actions
                     install_url_args = dict( controller='repository', action='find_tools', webapp=webapp )
                     operations = [ grids.GridOperation( "Install", url_args=install_url_args, allow_multiple=True, async_compatible=False ) ]
                     self.install_matched_repository_list_grid.operations = operations
@@ -583,8 +579,21 @@ class RepositoryController( BaseUIController, ItemRatings ):
             if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name, tool_version=tool_version ):
                 match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
         return match_tuples
-    def __encode( self, repo_info_dict ):
-        value = simplejson.dumps( repo_info_dict )
+    def __encode_repo_info_dict( self, trans, webapp, repository_metadata_ids ):
+        repo_info_dict = {}
+        for repository_metadata_id in repository_metadata_ids:
+            repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id )
+            repository = get_repository( trans, trans.security.encode_id( repository_metadata.repository_id ) )
+            repository_id = trans.security.encode_id( repository.id )
+            changeset_revision = repository_metadata.changeset_revision
+            repository_clone_url = generate_clone_url( trans, repository_id )
+            repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, changeset_revision )
+        return self.__encode( repo_info_dict )
+    def __encode( self, val ):
+        if isinstance( val, dict ):
+            value = simplejson.dumps( val )
+        else:
+            value = val
         a = hmac_new( 'ToolShedAndGalaxyMustHaveThisSameKey', value )
         b = binascii.hexlify( value )
         return "%s:%s" % ( a, b )
@@ -620,14 +629,18 @@ class RepositoryController( BaseUIController, ItemRatings ):
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
+        webapp = params.get( 'webapp', 'community' )
         galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' )
+        repository_clone_url = generate_clone_url( trans, repository_id )        
         repository = get_repository( trans, repository_id )
         changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) )
+        repo_info_dict = {}
+        repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, changeset_revision )
+        encoded_repo_info_dict = self.__encode( repo_info_dict )
         # Redirect back to local Galaxy to perform install.
-        repository_clone_url = generate_clone_url( trans, repository_id )
         # TODO: support https in the following url.
-        url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s&name=%s&description=%s&repository_clone_url=%s&changeset_revision=%s' % \
-            ( galaxy_url, trans.request.host, repository.name, repository.description, repository_clone_url, changeset_revision )
+        url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s&repo_info_dict=%s' % \
+            ( galaxy_url, trans.request.host, encoded_repo_info_dict )
         return trans.response.send_redirect( url )
     @web.expose
     def check_for_updates( self, trans, **kwd ):
diff --git a/templates/grid_base.mako b/templates/grid_base.mako
index 4121d115023..cda18fdb3ec 100644
--- a/templates/grid_base.mako
+++ b/templates/grid_base.mako
@@ -777,6 +777,7 @@
             show_item_checkboxes = True
     %>
     <form action="${url()}" method="post" onsubmit="return false;">
+        <input type="hidden" name="webapp" value="${webapp}"/>
         <table id="grid-table" class="grid">
             <thead id="grid-table-header">
                 <tr>
diff --git a/templates/webapps/community/repository/find_tools.mako b/templates/webapps/community/repository/find_tools.mako
index 71390a7857c..fcc50f4c6de 100644
--- a/templates/webapps/community/repository/find_tools.mako
+++ b/templates/webapps/community/repository/find_tools.mako
@@ -10,6 +10,13 @@
 %>
 <%inherit file="${inherit(context)}"/>
 
+%if webapp == 'galaxy':
+    <br/><br/>
+    <ul class="manage-table-actions">
+        <li><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a></li>
+    </ul>
+%endif
+
 %if message:
     ${render_msg( message, status )}
 %endif
diff --git a/templates/webapps/community/repository/preview_tools_in_changeset.mako b/templates/webapps/community/repository/preview_tools_in_changeset.mako
index ab496e4fc26..0420217dfed 100644
--- a/templates/webapps/community/repository/preview_tools_in_changeset.mako
+++ b/templates/webapps/community/repository/preview_tools_in_changeset.mako
@@ -64,7 +64,12 @@
 
 <br/><br/>
 <ul class="manage-table-actions">
-    <a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a>
+    <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a></li>
+    <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li>
+    <div popupmenu="repository-${repository.id}-popup">
+        <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a>
+        <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a>
+    </div>
 </ul>
 
 %if message:
diff --git a/templates/webapps/community/repository/tool_form.mako b/templates/webapps/community/repository/tool_form.mako
index 8cbcd5aec40..6c15a726942 100644
--- a/templates/webapps/community/repository/tool_form.mako
+++ b/templates/webapps/community/repository/tool_form.mako
@@ -111,7 +111,12 @@
         <br/><br/>
         <ul class="manage-table-actions">
             %if webapp == 'galaxy':
-                <a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a>
+                <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a></li>
+                <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li>
+                <div popupmenu="repository-${repository.id}-popup">
+                    <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a>
+                    <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a>
+                </div>
             %else:
                 %if is_new:
                     <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp=webapp )}">Upload files to repository</a>
diff --git a/templates/webapps/community/repository/view_repository.mako b/templates/webapps/community/repository/view_repository.mako
index 82a8c8fb2cb..2e110a26cf9 100644
--- a/templates/webapps/community/repository/view_repository.mako
+++ b/templates/webapps/community/repository/view_repository.mako
@@ -94,7 +94,12 @@
             </div>
         %endif
     %else:
-        <a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a>
+        <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a></li>
+        <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li>
+        <div popupmenu="repository-${repository.id}-popup">
+            <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a>
+            <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a>
+        </div>
     %endif
 </ul>
 
diff --git a/templates/webapps/community/repository/view_tool_metadata.mako b/templates/webapps/community/repository/view_tool_metadata.mako
index c8a3bc421a6..1cb87659326 100644
--- a/templates/webapps/community/repository/view_tool_metadata.mako
+++ b/templates/webapps/community/repository/view_tool_metadata.mako
@@ -34,7 +34,12 @@
 <br/><br/>
 <ul class="manage-table-actions">
     %if webapp == 'galaxy':
-        <a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a>
+        <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a></li>
+        <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li>
+        <div popupmenu="repository-${repository.id}-popup">
+            <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a>
+            <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a>
+        </div>
     %else:
         %if is_new:
             <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp=webapp )}">Upload files to repository</a>
diff --git a/templates/webapps/galaxy/admin/tool_sheds.mako b/templates/webapps/galaxy/admin/tool_sheds.mako
index 659449f55d9..d83b2d53fa6 100644
--- a/templates/webapps/galaxy/admin/tool_sheds.mako
+++ b/templates/webapps/galaxy/admin/tool_sheds.mako
@@ -16,7 +16,7 @@
     <div class="toolFormTitle">Accessible Galaxy tool sheds</div>
     <div class="toolFormBody">
         <div class="form-row">
-            <table cellspacing="0" cellpadding="0" border="0" width="100%" class="grid" id="library-grid">
+            <table class="grid">
                 <% shed_id = 0 %>
                 %for name, url in trans.app.tool_shed_registry.tool_sheds.items():
                     <tr class="libraryTitle">
@@ -25,7 +25,7 @@
                                 <a class="view-info" href="${h.url_for( controller='admin', action='browse_tool_shed', tool_shed_url=url )}">${name}</a>
                             </div>
                             <div popupmenu="dataset-${shed_id}-popup">
-                                <a class="action-button" href="${h.url_for( controller='admin', action='browse_tool_shed', tool_shed_url=url )}">Browse downloadable repositories</a>
+                                <a class="action-button" href="${h.url_for( controller='admin', action='browse_tool_shed', tool_shed_url=url )}">Browse valid repositories</a>
                                 <a class="action-button" href="${h.url_for( controller='admin', action='find_tools_in_tool_shed', tool_shed_url=url )}">Search for valid tools</a>
                             </div>
                         </td>

From 8c29dc20d77f6474702afa4df2f24f04a45377f3 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Fri, 21 Oct 2011 13:48:24 -0400
Subject: [PATCH 079/362] Update generic GATK command line options.

---
 tools/gatk/count_covariates.xml            |  66 +++++++---
 tools/gatk/indel_realigner.xml             |  39 ++++--
 tools/gatk/realigner_target_creator.xml    |  63 +++++++---
 tools/gatk/table_recalibration.xml         | 102 ++++++++-------
 tools/gatk/unified_genotyper.xml           |  63 +++++++---
 tools/gatk/variant_annotator.xml           | 137 ++++++++++++--------
 tools/gatk/variant_apply_recalibration.xml | 138 +++++++++++++--------
 tools/gatk/variant_combine.xml             |  68 +++++++---
 tools/gatk/variant_eval.xml                |  67 +++++++---
 tools/gatk/variant_filtration.xml          |  66 +++++++---
 tools/gatk/variant_recalibrator.xml        | 138 +++++++++++++--------
 tools/gatk/variants_validate.xml           |  67 +++++++---
 12 files changed, 685 insertions(+), 329 deletions(-)

diff --git a/tools/gatk/count_covariates.xml b/tools/gatk/count_covariates.xml
index 89491b08308..ac29c1e6e2a 100644
--- a/tools/gatk/count_covariates.xml
+++ b/tools/gatk/count_covariates.xml
@@ -59,14 +59,16 @@
             #end for
             '
         #end for
-        #if str( $gatk_param_type.input_intervals ) != "None":
-            -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals"
-        #end if
-        #if str( $gatk_param_type.input_exclude_intervals ) != "None":
-            -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals"
-        #end if
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
+            -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
+        #end for
         
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
+            -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
+        #end for
+
         -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
             -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
@@ -78,11 +80,18 @@
         --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
+        ${gatk_param_type.disable_experimental_low_memory_sharding}
+        ${gatk_param_type.non_deterministic_random_seed}
         '
-        #if str( $gatk_param_type.read_group_black_list ) != "None":
-            -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list"
-        #end if
+        #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
+            #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
+                -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
+            #else
+                -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
+            #end if
+        #end for
     #end if
+    
     #if str( $reference_source.reference_source_selector ) == "history":
         -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
     #end if
@@ -202,7 +211,7 @@
       </when>
       <when value="advanced">
         <repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" />
+            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" />
         </repeat>
         <repeat name="read_filter" title="Read Filter">
             <conditional name="read_filter_type">
@@ -218,12 +227,18 @@
 	          </when>
             </conditional>
         </repeat>
-        <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" />
-        <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" />
+        <repeat name="input_interval_repeat" title="Operate on Genomic intervals">
+          <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
+        </repeat>
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
+          <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
+        </repeat>
+        
         <param name="BTI_merge_rule" type="select" label="BTI merge rule">
           <option value="UNION" selected="True">UNION</option>
           <option value="INTERSECTION">INTERSECTION</option>
         </param>
+        
         <conditional name="downsampling_type">
           <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
             <option value="NONE" selected="True">NONE</option>
@@ -240,7 +255,7 @@
 	                  <option value="downsample_to_coverage">Downsample by Coverage</option>
 	              </param>
 	              <when value="downsample_to_fraction">
-	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
 	              </when>
 	              <when value="downsample_to_coverage">
 	                  <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
@@ -254,7 +269,7 @@
 	                  <option value="downsample_to_coverage">Downsample by Coverage</option>
 	              </param>
 	              <when value="downsample_to_fraction">
-	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
 	              </when>
 	              <when value="downsample_to_coverage">
 	                  <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
@@ -267,19 +282,38 @@
           <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
           <option value="RECALCULATE">RECALCULATE</option>
         </param>
-        <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
+        <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
         <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" />
         <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/>
         <param name="validation_strictness" type="select" label="How strict should we be with validation">
           <option value="STRICT" selected="True">STRICT</option>
           <option value="LENIENT">LENIENT</option>
           <option value="SILENT">SILENT</option>
+          <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
         </param>
         <param name="interval_merging" type="select" label="Interval merging rule">
           <option value="ALL" selected="True">ALL</option>
           <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
         </param>
-        <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" />
+        
+        <repeat name="read_group_black_list_repeat" title="Read group black list">
+          <conditional name="read_group_black_list_type">
+            <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
+              <option value="file" selected="True">Filters in file</option>
+              <option value="text">Specify filters as a string</option>
+            </param>
+            <when value="file">
+	          <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
+	        </when>
+            <when value="text">
+	          <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
+	        </when>
+          </conditional>
+        </repeat>
+        
+        <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
+        <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
+        
       </when>
     </conditional>
     
diff --git a/tools/gatk/indel_realigner.xml b/tools/gatk/indel_realigner.xml
index 0702d2d656b..f4077016952 100644
--- a/tools/gatk/indel_realigner.xml
+++ b/tools/gatk/indel_realigner.xml
@@ -165,7 +165,7 @@
       </when>
       <when value="advanced">
         <repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" />
+            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" />
         </repeat>
         <repeat name="read_filter" title="Read Filter">
             <conditional name="read_filter_type">
@@ -181,12 +181,18 @@
 	          </when>
             </conditional>
         </repeat>
-        <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" />
-        <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" />
+        <repeat name="input_interval_repeat" title="Operate on Genomic intervals">
+          <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
+        </repeat>
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
+          <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
+        </repeat>
+        
         <param name="BTI_merge_rule" type="select" label="BTI merge rule">
           <option value="UNION" selected="True">UNION</option>
           <option value="INTERSECTION">INTERSECTION</option>
         </param>
+        
         <conditional name="downsampling_type">
           <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
             <option value="NONE" selected="True">NONE</option>
@@ -203,7 +209,7 @@
 	                  <option value="downsample_to_coverage">Downsample by Coverage</option>
 	              </param>
 	              <when value="downsample_to_fraction">
-	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
 	              </when>
 	              <when value="downsample_to_coverage">
 	                  <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
@@ -217,7 +223,7 @@
 	                  <option value="downsample_to_coverage">Downsample by Coverage</option>
 	              </param>
 	              <when value="downsample_to_fraction">
-	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
 	              </when>
 	              <when value="downsample_to_coverage">
 	                  <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
@@ -230,19 +236,38 @@
           <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
           <option value="RECALCULATE">RECALCULATE</option>
         </param>
-        <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
+        <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
         <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" />
         <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/>
         <param name="validation_strictness" type="select" label="How strict should we be with validation">
           <option value="STRICT" selected="True">STRICT</option>
           <option value="LENIENT">LENIENT</option>
           <option value="SILENT">SILENT</option>
+          <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
         </param>
         <param name="interval_merging" type="select" label="Interval merging rule">
           <option value="ALL" selected="True">ALL</option>
           <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
         </param>
-        <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" />
+        
+        <repeat name="read_group_black_list_repeat" title="Read group black list">
+          <conditional name="read_group_black_list_type">
+            <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
+              <option value="file" selected="True">Filters in file</option>
+              <option value="text">Specify filters as a string</option>
+            </param>
+            <when value="file">
+	          <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
+	        </when>
+            <when value="text">
+	          <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
+	        </when>
+          </conditional>
+        </repeat>
+        
+        <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
+        <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
+        
       </when>
     </conditional>
     
diff --git a/tools/gatk/realigner_target_creator.xml b/tools/gatk/realigner_target_creator.xml
index c2ccdd02aae..0513c75cd5f 100644
--- a/tools/gatk/realigner_target_creator.xml
+++ b/tools/gatk/realigner_target_creator.xml
@@ -47,12 +47,13 @@
             #end for
             '
         #end for
-        #if str( $gatk_param_type.input_intervals ) != "None":
-            -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals"
-        #end if
-        #if str( $gatk_param_type.input_exclude_intervals ) != "None":
-            -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals"
-        #end if
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
+            -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
+        #end for
+        
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
+            -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
+        #end for
 
         -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
         
@@ -67,11 +68,18 @@
         --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
+        ${gatk_param_type.disable_experimental_low_memory_sharding}
+        ${gatk_param_type.non_deterministic_random_seed}
         '
-        #if str( $gatk_param_type.read_group_black_list ) != "None":
-            -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list"
-        #end if
+        #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
+            #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
+                -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
+            #else
+                -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
+            #end if
+        #end for
     #end if
+    
     #if $reference_source.reference_source_selector == "history":
         -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
     #end if
@@ -151,7 +159,7 @@
       </when>
       <when value="advanced">
         <repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" />
+            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" />
         </repeat>
         <repeat name="read_filter" title="Read Filter">
             <conditional name="read_filter_type">
@@ -167,8 +175,12 @@
 	          </when>
             </conditional>
         </repeat>
-        <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" />
-        <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" />
+        <repeat name="input_interval_repeat" title="Operate on Genomic intervals">
+          <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
+        </repeat>
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
+          <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
+        </repeat>
         
         <param name="BTI_merge_rule" type="select" label="BTI merge rule">
           <option value="UNION" selected="True">UNION</option>
@@ -191,7 +203,7 @@
 	                  <option value="downsample_to_coverage">Downsample by Coverage</option>
 	              </param>
 	              <when value="downsample_to_fraction">
-	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
 	              </when>
 	              <when value="downsample_to_coverage">
 	                  <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
@@ -205,7 +217,7 @@
 	                  <option value="downsample_to_coverage">Downsample by Coverage</option>
 	              </param>
 	              <when value="downsample_to_fraction">
-	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
 	              </when>
 	              <when value="downsample_to_coverage">
 	                  <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
@@ -218,19 +230,38 @@
           <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
           <option value="RECALCULATE">RECALCULATE</option>
         </param>
-        <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
+        <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
         <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" />
         <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/>
         <param name="validation_strictness" type="select" label="How strict should we be with validation">
           <option value="STRICT" selected="True">STRICT</option>
           <option value="LENIENT">LENIENT</option>
           <option value="SILENT">SILENT</option>
+          <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
         </param>
         <param name="interval_merging" type="select" label="Interval merging rule">
           <option value="ALL" selected="True">ALL</option>
           <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
         </param>
-        <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" />
+        
+        <repeat name="read_group_black_list_repeat" title="Read group black list">
+          <conditional name="read_group_black_list_type">
+            <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
+              <option value="file" selected="True">Filters in file</option>
+              <option value="text">Specify filters as a string</option>
+            </param>
+            <when value="file">
+	          <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
+	        </when>
+            <when value="text">
+	          <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
+	        </when>
+          </conditional>
+        </repeat>
+        
+        <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
+        <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
+        
       </when>
     </conditional>
     
diff --git a/tools/gatk/table_recalibration.xml b/tools/gatk/table_recalibration.xml
index 631ff2e65bc..e2a0448d1c9 100644
--- a/tools/gatk/table_recalibration.xml
+++ b/tools/gatk/table_recalibration.xml
@@ -35,29 +35,16 @@
             #end for
             '
         #end for
-        #if str( $gatk_param_type.input_intervals ) != "None":
-            -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals"
-        #end if
-        #if str( $gatk_param_type.input_exclude_intervals ) != "None":
-            -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals"
-        #end if
-        #set $rod_binding_names = dict()
-        #for $rod_binding in $gatk_param_type.rod_bind:
-            #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom':
-                #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name
-            #else
-                #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector
-            #end if
-            #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
-            -d "-B:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
-            #if str( $rod_binding.rod_bind_type.rodToIntervalTrackName ):
-                -p '--rodToIntervalTrackName "${rod_bind_name}"'
-            #end if
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
+            -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
         #end for
+        
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
+            -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
+        #end for
+
         -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
-        #if str( $gatk_param_type.input_dbsnp_rod ) != "None":
-            -d "-D" "${gatk_param_type.input_dbsnp_rod}" "${gatk_param_type.input_dbsnp_rod.ext}" "dbsnp_rod"
-        #end if
+        
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
             -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
@@ -69,11 +56,18 @@
         --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
+        ${gatk_param_type.disable_experimental_low_memory_sharding}
+        ${gatk_param_type.non_deterministic_random_seed}
         '
-        #if str( $gatk_param_type.read_group_black_list ) != "None":
-            -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list"
-        #end if
+        #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
+            #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
+                -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
+            #else
+                -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
+            #end if
+        #end for
     #end if
+    
     #if str( $reference_source.reference_source_selector ) == "history":
         -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
     #end if
@@ -147,7 +141,7 @@
       </when>
       <when value="advanced">
         <repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" />
+            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" />
         </repeat>
         <repeat name="read_filter" title="Read Filter">
             <conditional name="read_filter_type">
@@ -163,35 +157,18 @@
 	          </when>
             </conditional>
         </repeat>
-        <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" />
-        <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" />
-        <repeat name="rod_bind" title="Binding for reference-ordered data">
-            <conditional name="rod_bind_type">
-		      <param name="rod_bind_type_selector" type="select" label="Binding Type">
-		        <option value="snps" selected="True">SNPs</option>
-		        <option value="indels">INDELs</option>
-		        <option value="custom">Custom</option>
-		      </param>
-	          <when value="snps">
-	              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-	              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
-	          </when>
-	          <when value="indels">
-	              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-	              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
-	          </when>
-	          <when value="custom">
-	              <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/>
-	              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-	              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
-	          </when>
-            </conditional>
+        <repeat name="input_interval_repeat" title="Operate on Genomic intervals">
+          <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
         </repeat>
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
+          <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
+        </repeat>
+        
         <param name="BTI_merge_rule" type="select" label="BTI merge rule">
           <option value="UNION" selected="True">UNION</option>
           <option value="INTERSECTION">INTERSECTION</option>
         </param>
-        <param name="input_dbsnp_rod" type="data" format="gatk_dbsnp" optional="True" label="dbSNP reference ordered data (ROD)" />
+        
         <conditional name="downsampling_type">
           <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
             <option value="NONE" selected="True">NONE</option>
@@ -208,7 +185,7 @@
 	                  <option value="downsample_to_coverage">Downsample by Coverage</option>
 	              </param>
 	              <when value="downsample_to_fraction">
-	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
 	              </when>
 	              <when value="downsample_to_coverage">
 	                  <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
@@ -222,7 +199,7 @@
 	                  <option value="downsample_to_coverage">Downsample by Coverage</option>
 	              </param>
 	              <when value="downsample_to_fraction">
-	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
 	              </when>
 	              <when value="downsample_to_coverage">
 	                  <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
@@ -235,19 +212,38 @@
           <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
           <option value="RECALCULATE">RECALCULATE</option>
         </param>
-        <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
+        <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
         <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" />
         <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/>
         <param name="validation_strictness" type="select" label="How strict should we be with validation">
           <option value="STRICT" selected="True">STRICT</option>
           <option value="LENIENT">LENIENT</option>
           <option value="SILENT">SILENT</option>
+          <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
         </param>
         <param name="interval_merging" type="select" label="Interval merging rule">
           <option value="ALL" selected="True">ALL</option>
           <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
         </param>
-        <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" />
+        
+        <repeat name="read_group_black_list_repeat" title="Read group black list">
+          <conditional name="read_group_black_list_type">
+            <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
+              <option value="file" selected="True">Filters in file</option>
+              <option value="text">Specify filters as a string</option>
+            </param>
+            <when value="file">
+	          <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
+	        </when>
+            <when value="text">
+	          <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
+	        </when>
+          </conditional>
+        </repeat>
+        
+        <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
+        <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
+        
       </when>
     </conditional>
     
diff --git a/tools/gatk/unified_genotyper.xml b/tools/gatk/unified_genotyper.xml
index f33a3da4651..98cc56faaf3 100644
--- a/tools/gatk/unified_genotyper.xml
+++ b/tools/gatk/unified_genotyper.xml
@@ -56,12 +56,13 @@
             #end for
             '
         #end for
-        #if str( $gatk_param_type.input_intervals ) != "None":
-            -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals"
-        #end if
-        #if str( $gatk_param_type.input_exclude_intervals ) != "None":
-            -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals"
-        #end if
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
+            -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
+        #end for
+        
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
+            -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
+        #end for
 
         -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
         
@@ -76,11 +77,18 @@
         --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
+        ${gatk_param_type.disable_experimental_low_memory_sharding}
+        ${gatk_param_type.non_deterministic_random_seed}
         '
-        #if str( $gatk_param_type.read_group_black_list ) != "None":
-            -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list"
-        #end if
+        #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
+            #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
+                -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
+            #else
+                -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
+            #end if
+        #end for
     #end if
+    
     #if $reference_source.reference_source_selector == "history":
         -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
     #end if
@@ -194,7 +202,7 @@
       </when>
       <when value="advanced">
         <repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" />
+            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" />
         </repeat>
         <repeat name="read_filter" title="Read Filter">
             <conditional name="read_filter_type">
@@ -210,8 +218,12 @@
 	          </when>
             </conditional>
         </repeat>
-        <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" />
-        <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" />
+        <repeat name="input_interval_repeat" title="Operate on Genomic intervals">
+          <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
+        </repeat>
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
+          <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
+        </repeat>
         
         <param name="BTI_merge_rule" type="select" label="BTI merge rule">
           <option value="UNION" selected="True">UNION</option>
@@ -234,7 +246,7 @@
 	                  <option value="downsample_to_coverage">Downsample by Coverage</option>
 	              </param>
 	              <when value="downsample_to_fraction">
-	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
 	              </when>
 	              <when value="downsample_to_coverage">
 	                  <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
@@ -248,7 +260,7 @@
 	                  <option value="downsample_to_coverage">Downsample by Coverage</option>
 	              </param>
 	              <when value="downsample_to_fraction">
-	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
 	              </when>
 	              <when value="downsample_to_coverage">
 	                  <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
@@ -261,19 +273,38 @@
           <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
           <option value="RECALCULATE">RECALCULATE</option>
         </param>
-        <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
+        <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
         <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" />
         <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/>
         <param name="validation_strictness" type="select" label="How strict should we be with validation">
           <option value="STRICT" selected="True">STRICT</option>
           <option value="LENIENT">LENIENT</option>
           <option value="SILENT">SILENT</option>
+          <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
         </param>
         <param name="interval_merging" type="select" label="Interval merging rule">
           <option value="ALL" selected="True">ALL</option>
           <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
         </param>
-        <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" />
+        
+        <repeat name="read_group_black_list_repeat" title="Read group black list">
+          <conditional name="read_group_black_list_type">
+            <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
+              <option value="file" selected="True">Filters in file</option>
+              <option value="text">Specify filters as a string</option>
+            </param>
+            <when value="file">
+	          <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
+	        </when>
+            <when value="text">
+	          <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
+	        </when>
+          </conditional>
+        </repeat>
+        
+        <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
+        <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
+        
       </when>
     </conditional>
     
diff --git a/tools/gatk/variant_annotator.xml b/tools/gatk/variant_annotator.xml
index cfaaaa680f4..c15689f3035 100644
--- a/tools/gatk/variant_annotator.xml
+++ b/tools/gatk/variant_annotator.xml
@@ -89,14 +89,16 @@
             #end for
             '
         #end for
-        #if str( $gatk_param_type.input_intervals ) != "None":
-            -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals"
-        #end if
-        #if str( $gatk_param_type.input_exclude_intervals ) != "None":
-            -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals"
-        #end if
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
+            -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
+        #end for
         
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
+            -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
+        #end for
+
         -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
             -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
@@ -108,10 +110,16 @@
         --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
+        ${gatk_param_type.disable_experimental_low_memory_sharding}
+        ${gatk_param_type.non_deterministic_random_seed}
         '
-        #if str( $gatk_param_type.read_group_black_list ) != "None":
-            -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list"
-        #end if
+        #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
+            #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
+                -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
+            #else
+                -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
+            #end if
+        #end for
     #end if
     #if str( $reference_source.reference_source_selector ) == "history":
         -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
@@ -252,28 +260,34 @@
       </when>
       <when value="advanced">
         <repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" />
+            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" />
         </repeat>
         <repeat name="read_filter" title="Read Filter">
             <conditional name="read_filter_type">
-              <param name="read_filter_type_selector" type="select" label="Read Filter Type">
-                <option value="MaxReadLength" selected="True">MaxReadLength</option>
-                <option value="ZeroMappingQualityRead">ZeroMappingQualityRead</option>
-              </param>
-              <when value="ZeroMappingQualityRead">
-                  <!-- no extra options -->
-              </when>
-              <when value="MaxReadLength">
-                  <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
-              </when>
+		      <param name="read_filter_type_selector" type="select" label="Read Filter Type">
+		        <option value="MaxReadLength" selected="True">MaxReadLength</option>
+		        <option value="ZeroMappingQualityRead">ZeroMappingQualityRead</option>
+		      </param>
+	          <when value="ZeroMappingQualityRead">
+	              <!-- no extra options -->
+	          </when>
+	          <when value="MaxReadLength">
+	              <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
+	          </when>
             </conditional>
         </repeat>
-        <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" />
-        <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" />
+        <repeat name="input_interval_repeat" title="Operate on Genomic intervals">
+          <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
+        </repeat>
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
+          <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
+        </repeat>
+        
         <param name="BTI_merge_rule" type="select" label="BTI merge rule">
           <option value="UNION" selected="True">UNION</option>
           <option value="INTERSECTION">INTERSECTION</option>
         </param>
+        
         <conditional name="downsampling_type">
           <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
             <option value="NONE" selected="True">NONE</option>
@@ -281,55 +295,74 @@
             <option value="BY_SAMPLE">BY_SAMPLE</option>
           </param>
           <when value="NONE">
-              <!-- no more options here -->
-          </when>
+	          <!-- no more options here -->
+	      </when>
           <when value="ALL_READS">
-              <conditional name="downsample_to_type">
-                  <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
-                      <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
-                      <option value="downsample_to_coverage">Downsample by Coverage</option>
-                  </param>
-                  <when value="downsample_to_fraction">
-                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
-                  </when>
-                  <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
-                  </when>
-              </conditional>
-          </when>
+	          <conditional name="downsample_to_type">
+	              <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
+	                  <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
+	                  <option value="downsample_to_coverage">Downsample by Coverage</option>
+	              </param>
+	              <when value="downsample_to_fraction">
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
+	              </when>
+	              <when value="downsample_to_coverage">
+	                  <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
+	              </when>
+	          </conditional>
+	      </when>
           <when value="BY_SAMPLE">
-              <conditional name="downsample_to_type">
-                  <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
-                      <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
-                      <option value="downsample_to_coverage">Downsample by Coverage</option>
-                  </param>
-                  <when value="downsample_to_fraction">
-                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
-                  </when>
-                  <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
-                  </when>
-              </conditional>
-          </when>
+	          <conditional name="downsample_to_type">
+	              <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
+	                  <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
+	                  <option value="downsample_to_coverage">Downsample by Coverage</option>
+	              </param>
+	              <when value="downsample_to_fraction">
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
+	              </when>
+	              <when value="downsample_to_coverage">
+	                  <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
+	              </when>
+	          </conditional>
+	      </when>
         </conditional>
         <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine">
           <option value="OFF" selected="True">OFF</option>
           <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
           <option value="RECALCULATE">RECALCULATE</option>
         </param>
-        <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
+        <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
         <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" />
         <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/>
         <param name="validation_strictness" type="select" label="How strict should we be with validation">
           <option value="STRICT" selected="True">STRICT</option>
           <option value="LENIENT">LENIENT</option>
           <option value="SILENT">SILENT</option>
+          <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
         </param>
         <param name="interval_merging" type="select" label="Interval merging rule">
           <option value="ALL" selected="True">ALL</option>
           <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
         </param>
-        <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" />
+        
+        <repeat name="read_group_black_list_repeat" title="Read group black list">
+          <conditional name="read_group_black_list_type">
+            <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
+              <option value="file" selected="True">Filters in file</option>
+              <option value="text">Specify filters as a string</option>
+            </param>
+            <when value="file">
+	          <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
+	        </when>
+            <when value="text">
+	          <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
+	        </when>
+          </conditional>
+        </repeat>
+        
+        <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
+        <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
+        
       </when>
     </conditional>
     
diff --git a/tools/gatk/variant_apply_recalibration.xml b/tools/gatk/variant_apply_recalibration.xml
index bb0c1f90637..81a52f718ba 100644
--- a/tools/gatk/variant_apply_recalibration.xml
+++ b/tools/gatk/variant_apply_recalibration.xml
@@ -37,14 +37,16 @@
             #end for
             '
         #end for
-        #if str( $gatk_param_type.input_intervals ) != "None":
-            -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals"
-        #end if
-        #if str( $gatk_param_type.input_exclude_intervals ) != "None":
-            -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals"
-        #end if
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
+            -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
+        #end for
         
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
+            -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
+        #end for
+
         -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
             -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
@@ -56,11 +58,18 @@
         --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
+        ${gatk_param_type.disable_experimental_low_memory_sharding}
+        ${gatk_param_type.non_deterministic_random_seed}
         '
-        #if str( $gatk_param_type.read_group_black_list ) != "None":
-            -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list"
-        #end if
+        #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
+            #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
+                -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
+            #else
+                -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
+            #end if
+        #end for
     #end if
+    
     #if str( $reference_source.reference_source_selector ) == "history":
         -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
     #end if
@@ -118,28 +127,34 @@
       </when>
       <when value="advanced">
         <repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" />
+            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" />
         </repeat>
         <repeat name="read_filter" title="Read Filter">
             <conditional name="read_filter_type">
-              <param name="read_filter_type_selector" type="select" label="Read Filter Type">
-                <option value="MaxReadLength" selected="True">MaxReadLength</option>
-                <option value="ZeroMappingQualityRead">ZeroMappingQualityRead</option>
-              </param>
-              <when value="ZeroMappingQualityRead">
-                  <!-- no extra options -->
-              </when>
-              <when value="MaxReadLength">
-                  <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
-              </when>
+		      <param name="read_filter_type_selector" type="select" label="Read Filter Type">
+		        <option value="MaxReadLength" selected="True">MaxReadLength</option>
+		        <option value="ZeroMappingQualityRead">ZeroMappingQualityRead</option>
+		      </param>
+	          <when value="ZeroMappingQualityRead">
+	              <!-- no extra options -->
+	          </when>
+	          <when value="MaxReadLength">
+	              <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
+	          </when>
             </conditional>
         </repeat>
-        <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" />
-        <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" />
+        <repeat name="input_interval_repeat" title="Operate on Genomic intervals">
+          <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
+        </repeat>
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
+          <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
+        </repeat>
+        
         <param name="BTI_merge_rule" type="select" label="BTI merge rule">
           <option value="UNION" selected="True">UNION</option>
           <option value="INTERSECTION">INTERSECTION</option>
         </param>
+        
         <conditional name="downsampling_type">
           <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
             <option value="NONE" selected="True">NONE</option>
@@ -147,55 +162,74 @@
             <option value="BY_SAMPLE">BY_SAMPLE</option>
           </param>
           <when value="NONE">
-              <!-- no more options here -->
-          </when>
+	          <!-- no more options here -->
+	      </when>
           <when value="ALL_READS">
-              <conditional name="downsample_to_type">
-                  <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
-                      <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
-                      <option value="downsample_to_coverage">Downsample by Coverage</option>
-                  </param>
-                  <when value="downsample_to_fraction">
-                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
-                  </when>
-                  <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
-                  </when>
-              </conditional>
-          </when>
+	          <conditional name="downsample_to_type">
+	              <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
+	                  <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
+	                  <option value="downsample_to_coverage">Downsample by Coverage</option>
+	              </param>
+	              <when value="downsample_to_fraction">
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
+	              </when>
+	              <when value="downsample_to_coverage">
+	                  <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
+	              </when>
+	          </conditional>
+	      </when>
           <when value="BY_SAMPLE">
-              <conditional name="downsample_to_type">
-                  <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
-                      <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
-                      <option value="downsample_to_coverage">Downsample by Coverage</option>
-                  </param>
-                  <when value="downsample_to_fraction">
-                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
-                  </when>
-                  <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
-                  </when>
-              </conditional>
-          </when>
+	          <conditional name="downsample_to_type">
+	              <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
+	                  <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
+	                  <option value="downsample_to_coverage">Downsample by Coverage</option>
+	              </param>
+	              <when value="downsample_to_fraction">
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
+	              </when>
+	              <when value="downsample_to_coverage">
+	                  <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
+	              </when>
+	          </conditional>
+	      </when>
         </conditional>
         <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine">
           <option value="OFF" selected="True">OFF</option>
           <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
           <option value="RECALCULATE">RECALCULATE</option>
         </param>
-        <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
+        <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
         <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" />
         <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/>
         <param name="validation_strictness" type="select" label="How strict should we be with validation">
           <option value="STRICT" selected="True">STRICT</option>
           <option value="LENIENT">LENIENT</option>
           <option value="SILENT">SILENT</option>
+          <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
         </param>
         <param name="interval_merging" type="select" label="Interval merging rule">
           <option value="ALL" selected="True">ALL</option>
           <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
         </param>
-        <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" />
+        
+        <repeat name="read_group_black_list_repeat" title="Read group black list">
+          <conditional name="read_group_black_list_type">
+            <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
+              <option value="file" selected="True">Filters in file</option>
+              <option value="text">Specify filters as a string</option>
+            </param>
+            <when value="file">
+	          <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
+	        </when>
+            <when value="text">
+	          <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
+	        </when>
+          </conditional>
+        </repeat>
+        
+        <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
+        <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
+        
       </when>
     </conditional>
     
diff --git a/tools/gatk/variant_combine.xml b/tools/gatk/variant_combine.xml
index 7494cb7ebe4..1b51fe17bd6 100644
--- a/tools/gatk/variant_combine.xml
+++ b/tools/gatk/variant_combine.xml
@@ -28,7 +28,6 @@
    --rod_priority_list "${ ','.join( $priority_order ) }"
    '
    
-   
     ##start standard gatk options
     #if $gatk_param_type.gatk_param_type_selector == "advanced":
         #for $sample_metadata in $gatk_param_type.sample_metadata:
@@ -44,13 +43,16 @@
             #end for
             '
         #end for
-        #if str( $gatk_param_type.input_intervals ) != "None":
-            -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals"
-        #end if
-        #if str( $gatk_param_type.input_exclude_intervals ) != "None":
-            -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals"
-        #end if
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
+            -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
+        #end for
+        
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
+            -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
+        #end for
+
         -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
             -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
@@ -62,11 +64,18 @@
         --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
+        ${gatk_param_type.disable_experimental_low_memory_sharding}
+        ${gatk_param_type.non_deterministic_random_seed}
         '
-        #if str( $gatk_param_type.read_group_black_list ) != "None":
-            -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list"
-        #end if
+        #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
+            #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
+                -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
+            #else
+                -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
+            #end if
+        #end for
     #end if
+    
     #if $reference_source.reference_source_selector == "history":
         -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
     #end if
@@ -138,7 +147,7 @@
       </when>
       <when value="advanced">
         <repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" />
+            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" />
         </repeat>
         <repeat name="read_filter" title="Read Filter">
             <conditional name="read_filter_type">
@@ -154,12 +163,18 @@
 	          </when>
             </conditional>
         </repeat>
-        <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" />
-        <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" />
+        <repeat name="input_interval_repeat" title="Operate on Genomic intervals">
+          <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
+        </repeat>
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
+          <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
+        </repeat>
+        
         <param name="BTI_merge_rule" type="select" label="BTI merge rule">
           <option value="UNION" selected="True">UNION</option>
           <option value="INTERSECTION">INTERSECTION</option>
         </param>
+        
         <conditional name="downsampling_type">
           <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
             <option value="NONE" selected="True">NONE</option>
@@ -176,7 +191,7 @@
 	                  <option value="downsample_to_coverage">Downsample by Coverage</option>
 	              </param>
 	              <when value="downsample_to_fraction">
-	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
 	              </when>
 	              <when value="downsample_to_coverage">
 	                  <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
@@ -190,7 +205,7 @@
 	                  <option value="downsample_to_coverage">Downsample by Coverage</option>
 	              </param>
 	              <when value="downsample_to_fraction">
-	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
 	              </when>
 	              <when value="downsample_to_coverage">
 	                  <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
@@ -203,19 +218,38 @@
           <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
           <option value="RECALCULATE">RECALCULATE</option>
         </param>
-        <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
+        <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
         <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" />
         <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/>
         <param name="validation_strictness" type="select" label="How strict should we be with validation">
           <option value="STRICT" selected="True">STRICT</option>
           <option value="LENIENT">LENIENT</option>
           <option value="SILENT">SILENT</option>
+          <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
         </param>
         <param name="interval_merging" type="select" label="Interval merging rule">
           <option value="ALL" selected="True">ALL</option>
           <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
         </param>
-        <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" />
+        
+        <repeat name="read_group_black_list_repeat" title="Read group black list">
+          <conditional name="read_group_black_list_type">
+            <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
+              <option value="file" selected="True">Filters in file</option>
+              <option value="text">Specify filters as a string</option>
+            </param>
+            <when value="file">
+	          <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
+	        </when>
+            <when value="text">
+	          <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
+	        </when>
+          </conditional>
+        </repeat>
+        
+        <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
+        <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
+        
       </when>
     </conditional>
     
diff --git a/tools/gatk/variant_eval.xml b/tools/gatk/variant_eval.xml
index 4ea0f6b92c1..e337e737c2f 100644
--- a/tools/gatk/variant_eval.xml
+++ b/tools/gatk/variant_eval.xml
@@ -56,13 +56,16 @@
             #end for
             '
         #end for
-        #if str( $gatk_param_type.input_intervals ) != "None":
-            -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals"
-        #end if
-        #if str( $gatk_param_type.input_exclude_intervals ) != "None":
-            -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals"
-        #end if
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
+            -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
+        #end for
+        
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
+            -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
+        #end for
+
         -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
             -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
@@ -74,11 +77,18 @@
         --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
+        ${gatk_param_type.disable_experimental_low_memory_sharding}
+        ${gatk_param_type.non_deterministic_random_seed}
         '
-        #if str( $gatk_param_type.read_group_black_list ) != "None":
-            -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list"
-        #end if
+        #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
+            #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
+                -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
+            #else
+                -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
+            #end if
+        #end for
     #end if
+    
     #if $reference_source.reference_source_selector == "history":
         -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
     #end if
@@ -195,7 +205,7 @@
       </when>
       <when value="advanced">
         <repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" />
+            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" />
         </repeat>
         <repeat name="read_filter" title="Read Filter">
             <conditional name="read_filter_type">
@@ -211,12 +221,18 @@
 	          </when>
             </conditional>
         </repeat>
-        <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" />
-        <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" />
+        <repeat name="input_interval_repeat" title="Operate on Genomic intervals">
+          <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
+        </repeat>
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
+          <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
+        </repeat>
+        
         <param name="BTI_merge_rule" type="select" label="BTI merge rule">
           <option value="UNION" selected="True">UNION</option>
           <option value="INTERSECTION">INTERSECTION</option>
         </param>
+        
         <conditional name="downsampling_type">
           <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
             <option value="NONE" selected="True">NONE</option>
@@ -233,7 +249,7 @@
 	                  <option value="downsample_to_coverage">Downsample by Coverage</option>
 	              </param>
 	              <when value="downsample_to_fraction">
-	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
 	              </when>
 	              <when value="downsample_to_coverage">
 	                  <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
@@ -247,7 +263,7 @@
 	                  <option value="downsample_to_coverage">Downsample by Coverage</option>
 	              </param>
 	              <when value="downsample_to_fraction">
-	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
 	              </when>
 	              <when value="downsample_to_coverage">
 	                  <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
@@ -260,19 +276,38 @@
           <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
           <option value="RECALCULATE">RECALCULATE</option>
         </param>
-        <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
+        <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
         <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" />
         <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/>
         <param name="validation_strictness" type="select" label="How strict should we be with validation">
           <option value="STRICT" selected="True">STRICT</option>
           <option value="LENIENT">LENIENT</option>
           <option value="SILENT">SILENT</option>
+          <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
         </param>
         <param name="interval_merging" type="select" label="Interval merging rule">
           <option value="ALL" selected="True">ALL</option>
           <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
         </param>
-        <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" />
+        
+        <repeat name="read_group_black_list_repeat" title="Read group black list">
+          <conditional name="read_group_black_list_type">
+            <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
+              <option value="file" selected="True">Filters in file</option>
+              <option value="text">Specify filters as a string</option>
+            </param>
+            <when value="file">
+	          <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
+	        </when>
+            <when value="text">
+	          <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
+	        </when>
+          </conditional>
+        </repeat>
+        
+        <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
+        <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
+        
       </when>
     </conditional>
     
diff --git a/tools/gatk/variant_filtration.xml b/tools/gatk/variant_filtration.xml
index 9c435c72123..1e1a79286aa 100644
--- a/tools/gatk/variant_filtration.xml
+++ b/tools/gatk/variant_filtration.xml
@@ -50,14 +50,16 @@
             #end for
             '
         #end for
-        #if str( $gatk_param_type.input_intervals ) != "None":
-            -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals"
-        #end if
-        #if str( $gatk_param_type.input_exclude_intervals ) != "None":
-            -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals"
-        #end if
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
+            -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
+        #end for
         
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
+            -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
+        #end for
+
         -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
             -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
@@ -69,11 +71,18 @@
         --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
+        ${gatk_param_type.disable_experimental_low_memory_sharding}
+        ${gatk_param_type.non_deterministic_random_seed}
         '
-        #if str( $gatk_param_type.read_group_black_list ) != "None":
-            -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list"
-        #end if
+        #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
+            #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
+                -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
+            #else
+                -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
+            #end if
+        #end for
     #end if
+    
     #if str( $reference_source.reference_source_selector ) == "history":
         -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
     #end if
@@ -152,7 +161,7 @@
       </when>
       <when value="advanced">
         <repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" />
+            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" />
         </repeat>
         <repeat name="read_filter" title="Read Filter">
             <conditional name="read_filter_type">
@@ -168,12 +177,18 @@
 	          </when>
             </conditional>
         </repeat>
-        <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" />
-        <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" />
+        <repeat name="input_interval_repeat" title="Operate on Genomic intervals">
+          <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
+        </repeat>
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
+          <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
+        </repeat>
+        
         <param name="BTI_merge_rule" type="select" label="BTI merge rule">
           <option value="UNION" selected="True">UNION</option>
           <option value="INTERSECTION">INTERSECTION</option>
         </param>
+        
         <conditional name="downsampling_type">
           <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
             <option value="NONE" selected="True">NONE</option>
@@ -190,7 +205,7 @@
 	                  <option value="downsample_to_coverage">Downsample by Coverage</option>
 	              </param>
 	              <when value="downsample_to_fraction">
-	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
 	              </when>
 	              <when value="downsample_to_coverage">
 	                  <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
@@ -204,7 +219,7 @@
 	                  <option value="downsample_to_coverage">Downsample by Coverage</option>
 	              </param>
 	              <when value="downsample_to_fraction">
-	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
 	              </when>
 	              <when value="downsample_to_coverage">
 	                  <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
@@ -217,19 +232,38 @@
           <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
           <option value="RECALCULATE">RECALCULATE</option>
         </param>
-        <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
+        <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
         <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" />
         <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/>
         <param name="validation_strictness" type="select" label="How strict should we be with validation">
           <option value="STRICT" selected="True">STRICT</option>
           <option value="LENIENT">LENIENT</option>
           <option value="SILENT">SILENT</option>
+          <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
         </param>
         <param name="interval_merging" type="select" label="Interval merging rule">
           <option value="ALL" selected="True">ALL</option>
           <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
         </param>
-        <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" />
+        
+        <repeat name="read_group_black_list_repeat" title="Read group black list">
+          <conditional name="read_group_black_list_type">
+            <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
+              <option value="file" selected="True">Filters in file</option>
+              <option value="text">Specify filters as a string</option>
+            </param>
+            <when value="file">
+	          <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
+	        </when>
+            <when value="text">
+	          <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
+	        </when>
+          </conditional>
+        </repeat>
+        
+        <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
+        <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
+        
       </when>
     </conditional>
     
diff --git a/tools/gatk/variant_recalibrator.xml b/tools/gatk/variant_recalibrator.xml
index 58e762b2242..511320c26ad 100644
--- a/tools/gatk/variant_recalibrator.xml
+++ b/tools/gatk/variant_recalibrator.xml
@@ -58,14 +58,16 @@
             #end for
             '
         #end for
-        #if str( $gatk_param_type.input_intervals ) != "None":
-            -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals"
-        #end if
-        #if str( $gatk_param_type.input_exclude_intervals ) != "None":
-            -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals"
-        #end if
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
+            -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
+        #end for
         
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
+            -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
+        #end for
+
         -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
             -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
@@ -77,11 +79,18 @@
         --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
+        ${gatk_param_type.disable_experimental_low_memory_sharding}
+        ${gatk_param_type.non_deterministic_random_seed}
         '
-        #if str( $gatk_param_type.read_group_black_list ) != "None":
-            -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list"
-        #end if
+        #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
+            #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
+                -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
+            #else
+                -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
+            #end if
+        #end for
     #end if
+    
     #if str( $reference_source.reference_source_selector ) == "history":
         -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
     #end if
@@ -382,28 +391,34 @@
       </when>
       <when value="advanced">
         <repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" />
+            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" />
         </repeat>
         <repeat name="read_filter" title="Read Filter">
             <conditional name="read_filter_type">
-              <param name="read_filter_type_selector" type="select" label="Read Filter Type">
-                <option value="MaxReadLength" selected="True">MaxReadLength</option>
-                <option value="ZeroMappingQualityRead">ZeroMappingQualityRead</option>
-              </param>
-              <when value="ZeroMappingQualityRead">
-                  <!-- no extra options -->
-              </when>
-              <when value="MaxReadLength">
-                  <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
-              </when>
+		      <param name="read_filter_type_selector" type="select" label="Read Filter Type">
+		        <option value="MaxReadLength" selected="True">MaxReadLength</option>
+		        <option value="ZeroMappingQualityRead">ZeroMappingQualityRead</option>
+		      </param>
+	          <when value="ZeroMappingQualityRead">
+	              <!-- no extra options -->
+	          </when>
+	          <when value="MaxReadLength">
+	              <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
+	          </when>
             </conditional>
         </repeat>
-        <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" />
-        <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" />
+        <repeat name="input_interval_repeat" title="Operate on Genomic intervals">
+          <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
+        </repeat>
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
+          <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
+        </repeat>
+        
         <param name="BTI_merge_rule" type="select" label="BTI merge rule">
           <option value="UNION" selected="True">UNION</option>
           <option value="INTERSECTION">INTERSECTION</option>
         </param>
+        
         <conditional name="downsampling_type">
           <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
             <option value="NONE" selected="True">NONE</option>
@@ -411,55 +426,74 @@
             <option value="BY_SAMPLE">BY_SAMPLE</option>
           </param>
           <when value="NONE">
-              <!-- no more options here -->
-          </when>
+	          <!-- no more options here -->
+	      </when>
           <when value="ALL_READS">
-              <conditional name="downsample_to_type">
-                  <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
-                      <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
-                      <option value="downsample_to_coverage">Downsample by Coverage</option>
-                  </param>
-                  <when value="downsample_to_fraction">
-                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
-                  </when>
-                  <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
-                  </when>
-              </conditional>
-          </when>
+	          <conditional name="downsample_to_type">
+	              <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
+	                  <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
+	                  <option value="downsample_to_coverage">Downsample by Coverage</option>
+	              </param>
+	              <when value="downsample_to_fraction">
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
+	              </when>
+	              <when value="downsample_to_coverage">
+	                  <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
+	              </when>
+	          </conditional>
+	      </when>
           <when value="BY_SAMPLE">
-              <conditional name="downsample_to_type">
-                  <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
-                      <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
-                      <option value="downsample_to_coverage">Downsample by Coverage</option>
-                  </param>
-                  <when value="downsample_to_fraction">
-                      <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
-                  </when>
-                  <when value="downsample_to_coverage">
-                      <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
-                  </when>
-              </conditional>
-          </when>
+	          <conditional name="downsample_to_type">
+	              <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
+	                  <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
+	                  <option value="downsample_to_coverage">Downsample by Coverage</option>
+	              </param>
+	              <when value="downsample_to_fraction">
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
+	              </when>
+	              <when value="downsample_to_coverage">
+	                  <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
+	              </when>
+	          </conditional>
+	      </when>
         </conditional>
         <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine">
           <option value="OFF" selected="True">OFF</option>
           <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
           <option value="RECALCULATE">RECALCULATE</option>
         </param>
-        <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
+        <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
         <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" />
         <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/>
         <param name="validation_strictness" type="select" label="How strict should we be with validation">
           <option value="STRICT" selected="True">STRICT</option>
           <option value="LENIENT">LENIENT</option>
           <option value="SILENT">SILENT</option>
+          <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
         </param>
         <param name="interval_merging" type="select" label="Interval merging rule">
           <option value="ALL" selected="True">ALL</option>
           <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
         </param>
-        <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" />
+        
+        <repeat name="read_group_black_list_repeat" title="Read group black list">
+          <conditional name="read_group_black_list_type">
+            <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
+              <option value="file" selected="True">Filters in file</option>
+              <option value="text">Specify filters as a string</option>
+            </param>
+            <when value="file">
+	          <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
+	        </when>
+            <when value="text">
+	          <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
+	        </when>
+          </conditional>
+        </repeat>
+        
+        <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
+        <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
+        
       </when>
     </conditional>
     
diff --git a/tools/gatk/variants_validate.xml b/tools/gatk/variants_validate.xml
index 67a325f23f7..e8acb244817 100644
--- a/tools/gatk/variants_validate.xml
+++ b/tools/gatk/variants_validate.xml
@@ -42,13 +42,16 @@
             #end for
             '
         #end for
-        #if str( $gatk_param_type.input_intervals ) != "None":
-            -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals"
-        #end if
-        #if str( $gatk_param_type.input_exclude_intervals ) != "None":
-            -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals"
-        #end if
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
+            -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
+        #end for
+        
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
+            -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
+        #end for
+
         -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
             -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
@@ -60,11 +63,18 @@
         --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
+        ${gatk_param_type.disable_experimental_low_memory_sharding}
+        ${gatk_param_type.non_deterministic_random_seed}
         '
-        #if str( $gatk_param_type.read_group_black_list ) != "None":
-            -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list"
-        #end if
+        #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
+            #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
+                -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
+            #else
+                -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
+            #end if
+        #end for
     #end if
+    
     #if $reference_source.reference_source_selector == "history":
         -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
     #end if
@@ -120,7 +130,7 @@
       </when>
       <when value="advanced">
         <repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" />
+            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" />
         </repeat>
         <repeat name="read_filter" title="Read Filter">
             <conditional name="read_filter_type">
@@ -136,12 +146,18 @@
 	          </when>
             </conditional>
         </repeat>
-        <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" />
-        <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" />
+        <repeat name="input_interval_repeat" title="Operate on Genomic intervals">
+          <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
+        </repeat>
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
+          <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
+        </repeat>
+        
         <param name="BTI_merge_rule" type="select" label="BTI merge rule">
           <option value="UNION" selected="True">UNION</option>
           <option value="INTERSECTION">INTERSECTION</option>
         </param>
+        
         <conditional name="downsampling_type">
           <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
             <option value="NONE" selected="True">NONE</option>
@@ -158,7 +174,7 @@
 	                  <option value="downsample_to_coverage">Downsample by Coverage</option>
 	              </param>
 	              <when value="downsample_to_fraction">
-	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
 	              </when>
 	              <when value="downsample_to_coverage">
 	                  <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
@@ -172,7 +188,7 @@
 	                  <option value="downsample_to_coverage">Downsample by Coverage</option>
 	              </param>
 	              <when value="downsample_to_fraction">
-	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
 	              </when>
 	              <when value="downsample_to_coverage">
 	                  <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
@@ -185,19 +201,38 @@
           <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
           <option value="RECALCULATE">RECALCULATE</option>
         </param>
-        <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
+        <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
         <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" />
         <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/>
         <param name="validation_strictness" type="select" label="How strict should we be with validation">
           <option value="STRICT" selected="True">STRICT</option>
           <option value="LENIENT">LENIENT</option>
           <option value="SILENT">SILENT</option>
+          <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
         </param>
         <param name="interval_merging" type="select" label="Interval merging rule">
           <option value="ALL" selected="True">ALL</option>
           <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
         </param>
-        <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" />
+        
+        <repeat name="read_group_black_list_repeat" title="Read group black list">
+          <conditional name="read_group_black_list_type">
+            <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
+              <option value="file" selected="True">Filters in file</option>
+              <option value="text">Specify filters as a string</option>
+            </param>
+            <when value="file">
+	          <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
+	        </when>
+            <when value="text">
+	          <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
+	        </when>
+          </conditional>
+        </repeat>
+        
+        <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
+        <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
+        
       </when>
     </conditional>
     

From f1fdbf7b4dabcd55d31567725fa69967320a942c Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Fri, 21 Oct 2011 20:00:27 -0400
Subject: [PATCH 080/362] Trackster: replace menus with icons + tooltips.
 Overview is not yet implemented.

---
 static/images/fugue/block--plus-bw.png    | Bin 0 -> 1346 bytes
 static/images/fugue/block--plus.png       | Bin 0 -> 689 bytes
 static/images/fugue/bookmarks-bw.png      | Bin 0 -> 1353 bytes
 static/images/fugue/bookmarks.png         | Bin 0 -> 596 bytes
 static/images/fugue/cross-circle-bw.png   | Bin 0 -> 1422 bytes
 static/images/fugue/cross-circle.png      | Bin 0 -> 689 bytes
 static/images/fugue/cross-small-bw.png    | Bin 0 -> 1053 bytes
 static/images/fugue/disk--arrow-bw.png    | Bin 0 -> 1333 bytes
 static/images/fugue/disk--arrow.png       | Bin 0 -> 603 bytes
 static/images/fugue/gear-bw.png           | Bin 0 -> 1424 bytes
 static/images/fugue/gear.png              | Bin 0 -> 721 bytes
 static/images/fugue/plus-button-bw.png    | Bin 0 -> 1309 bytes
 static/images/fugue/plus-button.png       | Bin 0 -> 544 bytes
 static/images/fugue/toolbox-bw.png        | Bin 0 -> 1243 bytes
 static/images/fugue/toolbox.png           | Bin 0 -> 488 bytes
 static/images/fugue/ui-slider-050-bw.png  | Bin 0 -> 1155 bytes
 static/images/fugue/ui-slider-050.png     | Bin 0 -> 454 bytes
 static/june_2007_style/blue/trackster.css |  24 +-
 static/june_2007_style/trackster.css.tmpl |  68 +++++-
 static/scripts/galaxy.base.js             |   2 +
 static/scripts/packed/trackster.js        |   2 +-
 static/scripts/trackster.js               | 258 ++++++++++++----------
 templates/tracks/browser.mako             | 115 +++++-----
 23 files changed, 294 insertions(+), 175 deletions(-)
 create mode 100644 static/images/fugue/block--plus-bw.png
 create mode 100755 static/images/fugue/block--plus.png
 create mode 100644 static/images/fugue/bookmarks-bw.png
 create mode 100755 static/images/fugue/bookmarks.png
 create mode 100644 static/images/fugue/cross-circle-bw.png
 create mode 100755 static/images/fugue/cross-circle.png
 create mode 100644 static/images/fugue/cross-small-bw.png
 create mode 100644 static/images/fugue/disk--arrow-bw.png
 create mode 100755 static/images/fugue/disk--arrow.png
 create mode 100644 static/images/fugue/gear-bw.png
 create mode 100755 static/images/fugue/gear.png
 create mode 100644 static/images/fugue/plus-button-bw.png
 create mode 100755 static/images/fugue/plus-button.png
 create mode 100755 static/images/fugue/toolbox-bw.png
 create mode 100755 static/images/fugue/toolbox.png
 create mode 100644 static/images/fugue/ui-slider-050-bw.png
 create mode 100755 static/images/fugue/ui-slider-050.png

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diff --git a/static/images/fugue/block--plus.png b/static/images/fugue/block--plus.png
new file mode 100755
index 0000000000000000000000000000000000000000..2ab7975480369444e6cdcecccb2f181b71e8d999
GIT binary patch
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diff --git a/static/images/fugue/bookmarks-bw.png b/static/images/fugue/bookmarks-bw.png
new file mode 100644
index 0000000000000000000000000000000000000000..65bd8ce007092a0f6ae164e72cd56e819da30a07
GIT binary patch
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literal 0
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diff --git a/static/images/fugue/bookmarks.png b/static/images/fugue/bookmarks.png
new file mode 100755
index 0000000000000000000000000000000000000000..b06c71287ba2c570eb405c7ae76404e616a70529
GIT binary patch
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literal 0
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diff --git a/static/images/fugue/cross-circle-bw.png b/static/images/fugue/cross-circle-bw.png
new file mode 100644
index 0000000000000000000000000000000000000000..715f2a5712aed11830b21161520b15db65336d29
GIT binary patch
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diff --git a/static/images/fugue/cross-circle.png b/static/images/fugue/cross-circle.png
new file mode 100755
index 0000000000000000000000000000000000000000..d3b37afb85093a9b9578adf66d543559e9578143
GIT binary patch
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literal 0
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diff --git a/static/images/fugue/cross-small-bw.png b/static/images/fugue/cross-small-bw.png
new file mode 100644
index 0000000000000000000000000000000000000000..76830247db7a1ad569b7d746f560490f49fa3997
GIT binary patch
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literal 0
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diff --git a/static/images/fugue/disk--arrow-bw.png b/static/images/fugue/disk--arrow-bw.png
new file mode 100644
index 0000000000000000000000000000000000000000..b0da0aaa1d1bc1e5770003accadeb651ee289cb4
GIT binary patch
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diff --git a/static/images/fugue/disk--arrow.png b/static/images/fugue/disk--arrow.png
new file mode 100755
index 0000000000000000000000000000000000000000..37cbf99819e9066f828f88b57410068bf4489a3c
GIT binary patch
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diff --git a/static/images/fugue/gear-bw.png b/static/images/fugue/gear-bw.png
new file mode 100644
index 0000000000000000000000000000000000000000..8f37acdfae167b6207468d755916cac98bebabd7
GIT binary patch
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diff --git a/static/images/fugue/gear.png b/static/images/fugue/gear.png
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GIT binary patch
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diff --git a/static/images/fugue/plus-button-bw.png b/static/images/fugue/plus-button-bw.png
new file mode 100644
index 0000000000000000000000000000000000000000..80b2efbfb0ac3adf36360941601d27f578e9423f
GIT binary patch
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diff --git a/static/images/fugue/plus-button.png b/static/images/fugue/plus-button.png
new file mode 100755
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GIT binary patch
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diff --git a/static/images/fugue/toolbox-bw.png b/static/images/fugue/toolbox-bw.png
new file mode 100755
index 0000000000000000000000000000000000000000..c800f2cb7a678bb0b0cb542ba34ccc5a7aacc181
GIT binary patch
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diff --git a/static/images/fugue/toolbox.png b/static/images/fugue/toolbox.png
new file mode 100755
index 0000000000000000000000000000000000000000..12f988e94e6f299cfdca183fb487f393afe6f7c6
GIT binary patch
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diff --git a/static/images/fugue/ui-slider-050-bw.png b/static/images/fugue/ui-slider-050-bw.png
new file mode 100644
index 0000000000000000000000000000000000000000..5b5277500a867d37079c835c709b48c98a95950a
GIT binary patch
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diff --git a/static/images/fugue/ui-slider-050.png b/static/images/fugue/ui-slider-050.png
new file mode 100755
index 0000000000000000000000000000000000000000..9878961bfbe0e226725953748aefaa7a1edba88a
GIT binary patch
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diff --git a/static/june_2007_style/blue/trackster.css b/static/june_2007_style/blue/trackster.css
index 0c758a277d8..f9a490c000a 100644
--- a/static/june_2007_style/blue/trackster.css
+++ b/static/june_2007_style/blue/trackster.css
@@ -3,9 +3,28 @@
 .content{font:10px verdana;}
 .nav-controls{text-align:center;padding:1px 0;}
 .nav-controls input{margin:0 5px;}
+.menu-button{padding: 0px 4px 0px 4px;}
 #zoom-in,#zoom-out{display:inline-block;height:16px;width:16px;margin-bottom:-3px;cursor:pointer;}
 #zoom-out{background:transparent url(../images/fugue/magnifier-zoom-out.png) center center no-repeat;}
 #zoom-in{margin-left:10px;background:transparent url(../images/fugue/magnifier-zoom.png) center center no-repeat;}
+.settings-icon{background:transparent url(../images/fugue/gear-bw.png) no-repeat;}
+.settings-icon:hover{background:transparent url(../images/fugue/gear.png) no-repeat;}
+.tools-icon{background:transparent url(../images/fugue/toolbox-bw.png) no-repeat;}
+.tools-icon:hover{background:transparent url(../images/fugue/toolbox.png) no-repeat;}
+.filters-icon{background:transparent url(../images/fugue/ui-slider-050-bw.png) no-repeat;}
+.filters-icon:hover{background:transparent url(../images/fugue/ui-slider-050.png) no-repeat;}
+.remove-icon{background:transparent url(../images/fugue/cross-small-bw.png) no-repeat;}
+.remove-icon:hover{background:transparent url(../images/fugue/cross-circle.png) no-repeat;}
+#close-icon{background:transparent url(../images/fugue/cross-circle-bw.png) no-repeat;margin-right:0px;}
+#close-icon:hover{background:transparent url(../images/fugue/cross-circle.png) no-repeat;}
+#add-tracks-icon{background:transparent url(../images/fugue/plus-button-bw.png) no-repeat;}
+#add-tracks-icon:hover{background:transparent url(../images/fugue/plus-button.png) no-repeat;}
+#add-group-icon{background:transparent url(../images/fugue/block--plus-bw.png) no-repeat;}
+#add-group-icon:hover{background:transparent url(../images/fugue/block--plus.png) no-repeat;}
+#bookmarks-icon{background:transparent url(../images/fugue/bookmarks-bw.png) no-repeat;}
+#bookmarks-icon:hover{background:transparent url(../images/fugue/bookmarks.png) no-repeat;}
+#save-icon{background:transparent url(../images/fugue/disk--arrow-bw.png) no-repeat;}
+#save-icon:hover{background:transparent url(../images/fugue/disk--arrow.png) no-repeat;}
 .nav-input{font-size:12px;width:30em;z-index:1000;}
 .location{display:inline-block;width:15em;margin:0 10px;}
 .draghandle{margin-top:2px;cursor:move;float:left;background:transparent url(../images/visualization/draggable_horizontal.png) center center no-repeat;width:10px;height:12px;}
@@ -19,12 +38,13 @@
 .viewport-canvas{width:100%;height:100px;}
 .yaxislabel{color:#777;z-index:100;}
 .line-track .track-content{border-top:1px solid #eee;border-bottom:1px solid #eee;}
-.group-handle{cursor:move;float:left;background:#eee url('/static/images/tracks/block.png');width:12px;height:12px;}
+.group-handle{cursor:move;float:left;background:#eee url('../images/tracks/block.png');width:12px;height:12px;}
 .group{min-height:20px;border-top:2px solid #888;border-bottom:2px solid #888;}
 .track{background:white;}
 .track-header{text-align:left;padding:4px 0px;color:#666;}
 .track-header .menubutton{margin-left:0px;}
-.track-content{text-align:center;border-top:1px solid #eee;border-bottom:2px solid #eee;background:#eee url('/static/images/tracks/diag_bg.gif');min-height:16px;}
+.track-content{text-align:center;border-top:1px solid #eee;border-bottom:2px solid #eee;background:#eee url('../images/tracks/diag_bg.gif');min-height:16px;}
+.track-name{float:left;margin-top:2px;height:16px;}
 .label-track .track-content{background:white;}
 .track-tile{background:white;}
 .track-tile canvas{position:relative;z-index:100;}
diff --git a/static/june_2007_style/trackster.css.tmpl b/static/june_2007_style/trackster.css.tmpl
index 11419a08032..8fbfac3482c 100644
--- a/static/june_2007_style/trackster.css.tmpl
+++ b/static/june_2007_style/trackster.css.tmpl
@@ -130,7 +130,7 @@
 .group-handle {
     cursor: move;
     float: left;
-    background: #eee url('/static/images/tracks/block.png');
+    background: #eee url('../images/tracks/block.png');
     width: 12px;
     height: 12px;
 }
@@ -159,10 +159,16 @@
     text-align: center;
     border-top: 1px solid #eee;
     border-bottom: 2px solid #eee;
-    background: #eee url('/static/images/tracks/diag_bg.gif');
+    background: #eee url('../images/tracks/diag_bg.gif');
     min-height: 16px;
 }
 
+.track-name {
+    float: left;
+    margin-top: 2px;
+    height: 16px;
+}
+
 .label-track .track-content {
     background: white;
 }
@@ -288,6 +294,63 @@ input {
     font-weight: bold;
     padding-top: 0.2em;
 }
+.menu-button {
+    padding: 0px 4px 0px 4px;
+}
+.settings-icon {
+    background: transparent url(../images/fugue/gear-bw.png) no-repeat;
+}
+.settings-icon:hover {
+    background: transparent url(../images/fugue/gear.png) no-repeat;
+}
+.tools-icon {
+    background: transparent url(../images/fugue/toolbox-bw.png) no-repeat;
+}
+.tools-icon:hover {
+    background: transparent url(../images/fugue/toolbox.png) no-repeat;
+}
+.filters-icon {
+    background: transparent url(../images/fugue/ui-slider-050-bw.png) no-repeat;
+}
+.filters-icon:hover {
+    background: transparent url(../images/fugue/ui-slider-050.png) no-repeat;
+}
+.remove-icon {
+    background: transparent url(../images/fugue/cross-small-bw.png) no-repeat;
+}
+.remove-icon:hover {
+    background: transparent url(../images/fugue/cross-circle.png) no-repeat;
+}
+#close-icon {
+    background: transparent url(../images/fugue/cross-circle-bw.png) no-repeat;margin-right:0px;
+}
+#close-icon:hover {
+    background: transparent url(../images/fugue/cross-circle.png) no-repeat;
+}
+#add-tracks-icon {
+    background: transparent url(../images/fugue/plus-button-bw.png) no-repeat;
+}
+#add-tracks-icon:hover {
+    background: transparent url(../images/fugue/plus-button.png) no-repeat;
+}
+#add-group-icon {
+    background: transparent url(../images/fugue/block--plus-bw.png) no-repeat;
+}
+#add-group-icon:hover {
+    background: transparent url(../images/fugue/block--plus.png) no-repeat;
+}
+#bookmarks-icon {
+    background: transparent url(../images/fugue/bookmarks-bw.png) no-repeat;
+}
+#bookmarks-icon:hover {
+    background: transparent url(../images/fugue/bookmarks.png) no-repeat;
+}
+#save-icon {
+    background: transparent url(../images/fugue/disk--arrow-bw.png) no-repeat;
+}
+#save-icon:hover {
+    background: transparent url(../images/fugue/disk--arrow.png) no-repeat;
+}
 .child-track-icon {
     background:url('../images/fugue/arrow-000-small-bw.png') no-repeat;
     width: 30px;
@@ -317,7 +380,6 @@ input {
 .delete-icon-container {
     float:right;
 }
-
 .icon {
     display:inline-block;
     width:16px;
diff --git a/static/scripts/galaxy.base.js b/static/scripts/galaxy.base.js
index fa0fe391dd2..1c501c8533d 100644
--- a/static/scripts/galaxy.base.js
+++ b/static/scripts/galaxy.base.js
@@ -698,6 +698,8 @@ $(document).ready( function() {
     });
     // Tooltips
     if ( $.fn.tipsy ) {
+        // FIXME: tipsy gravity cannot be updated, so need classes that specify N/S gravity and 
+        // initialize each separately.
         $(".tooltip").tipsy( { gravity: 's' } );
     }
     // Make popup menus.
diff --git a/static/scripts/packed/trackster.js b/static/scripts/packed/trackster.js
index d759f8f88cf..418440169db 100644
--- a/static/scripts/packed/trackster.js
+++ b/static/scripts/packed/trackster.js
@@ -1 +1 @@
-var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var trackster_module=function(f,Z){var q=f("class").extend,t=f("slotting"),N=f("painters");var ag=function(ah,ai){this.document=ah;this.default_font=ai!==undefined?ai:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};q(ag.prototype,{load_pattern:function(ah,al){var ai=this.patterns,aj=this.dummy_context,ak=new Image();ak.src=image_path+al;ak.onload=function(){ai[ah]=aj.createPattern(ak,"repeat")}},get_pattern:function(ah){return this.patterns[ah]},new_canvas:function(){var ah=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ah)}ah.manager=this;return ah}});var o={};var m=function(ah,ai){o[ah.attr("id")]=ai};var n=function(ah,aj,al,ak){al=".group";var ai={};o[ah.attr("id")]=ak;ah.bind("drag",{handle:"."+aj,relative:true},function(au,av){var at=$(this);var ay=$(this).parent(),ap=ay.children(),ar=o[$(this).attr("id")],ao,an,aw,am,aq;an=$(this).parents(al);if(an.length!==0){aw=an.position().top;am=aw+an.outerHeight();if(av.offsetY<aw){$(this).insertBefore(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable_before(ar,ax);return}else{if(av.offsetY>am){$(this).insertAfter(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable(ar);return}}}an=null;for(aq=0;aq<ap.length;aq++){ao=$(ap.get(aq));aw=ao.position().top;am=aw+ao.outerHeight();if(ao.is(al)&&this!==ao.get(0)&&av.offsetY>=aw&&av.offsetY<=am){if(av.offsetY-aw<am-av.offsetY){ao.find(".content-div").prepend(this)}else{ao.find(".content-div").append(this)}if(ar.container){ar.container.remove_drawable(ar)}o[ao.attr("id")].add_drawable(ar);return}}for(aq=0;aq<ap.length;aq++){if(av.offsetY<$(ap.get(aq)).position().top){break}}if(aq===ap.length){if(this!==ap.get(aq-1)){ay.append(this);o[ay.attr("id")].move_drawable(ar,aq)}}else{if(this!==ap.get(aq)){$(this).insertBefore(ap.get(aq));o[ay.attr("id")].move_drawable(ar,(av.deltaY>0?aq-1:aq))}}}).bind("dragstart",function(){ai["border-top"]=ah.css("border-top");ai["border-bottom"]=ah.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ai)})};Z.moveable=n;var af=16,I=9,F=20,U=I+2,A=100,K=12000,S=200,D=5,w=10,M=5000,x=100,p="There was an error in indexing this dataset. 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Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",u="Currently indexing... please wait",y="Tool cannot be rerun: ",a="Loading data...",aa="Ready for display",d=10,v=5,C=5;function ab(ai,ah){if(!ah){ah=0}var aj=Math.pow(10,ah);return Math.round(ai*aj)/aj}var c=function(ah){this.num_elements=ah;this.clear()};q(c.prototype,{get:function(ai){var ah=this.key_ary.indexOf(ai);if(ah!==-1){if(this.obj_cache[ai].stale){this.key_ary.splice(ah,1);delete this.obj_cache[ai]}else{this.move_key_to_end(ai,ah)}}return this.obj_cache[ai]},set:function(ai,aj){if(!this.obj_cache[ai]){if(this.key_ary.length>=this.num_elements){var ah=this.key_ary.shift();delete this.obj_cache[ah]}this.key_ary.push(ai)}this.obj_cache[ai]=aj;return aj},move_key_to_end:function(ai,ah){this.key_ary.splice(ah,1);this.key_ary.push(ai)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var T=function(ai,ah,aj){c.call(this,ai);this.track=ah;this.subset=(aj!==undefined?aj:true)};q(T.prototype,c.prototype,{load_data:function(aq,al,ao,ai,an){var ap=this.track.view.chrom,ak={chrom:ap,low:aq,high:al,mode:ao,resolution:ai,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ak,an);if(this.track.filters_manager){var ar=[];var ah=this.track.filters_manager.filters;for(var am=0;am<ah.length;am++){ar[ar.length]=ah[am].name}ak.filter_cols=JSON.stringify(ar)}var aj=this;return $.getJSON(this.track.data_url,ak,function(at){aj.set_data(aq,al,ao,at)})},get_data:function(ah,al,am,ai,ak){var aj=this.get_data_from_cache(ah,al,am);if(aj){return aj}aj=this.load_data(ah,al,am,ai,ak);this.set_data(ah,al,am,aj);return aj},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ap,ak,ao,aj,an,al){var aq=this.get_data_from_cache(ap,ak,ao);if(!aq){console.log("ERROR: no current data for: ",this.track,ap,ak,ao,aj,an);return}aq.stale=true;var ai=ap;if(al===this.DEEP_DATA_REQ){$.extend(an,{start_val:aq.data.length+1})}else{if(al===this.BROAD_DATA_REQ){ai=(aq.max_high?aq.max_high:aq.data[aq.data.length-1][2])+1}}var ah=this,am=this.load_data(ai,ak,ao,aj,an);new_data_available=$.Deferred();this.set_data(ap,ak,ao,new_data_available);$.when(am).then(function(ar){if(ar.data){ar.data=aq.data.concat(ar.data);if(ar.max_low){ar.max_low=aq.max_low}if(ar.message){ar.message=ar.message.replace(/[0-9]+/,ar.data.length)}}ah.set_data(ap,ak,ao,ar);new_data_available.resolve(ar)});return new_data_available},get_data_from_cache:function(ah,ai,aj){return this.get(this.gen_key(ah,ai,aj))},set_data:function(ai,aj,ak,ah){return this.set(this.gen_key(ai,aj,ak),ah)},gen_key:function(ah,aj,ak){var ai=ah+"_"+aj+"_"+ak;return ai},split_key:function(ah){return ah.split("_")}});var J=function(ai,ah,aj){T.call(this,ai,ah,aj)};q(J.prototype,T.prototype,c.prototype,{load_data:function(aj,ah,al,am,ai,ak){if(ai>1){return}return T.prototype.load_data.call(this,aj,ah,al,am,ai,ak)}});var r=function(ak,ai,ah,aj,al){this.name=ak;this.view=ai;this.container=ah;this.drag_handle_class=al;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak}],saved_values:aj,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values};q(r.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},make_name_popup_menu:function(){},set_name:function(ah){this.old_name=this.name;this.name=ah;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var z=function(al,ak,ai,ah,aj,am){r.call(this,ak,ai,ah,aj,am);this.obj_type=al;this.drawables=[]};q(z.prototype,r.prototype,{init:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah].init()}},_draw:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah]._draw()}},to_json:function(){var ai=[];for(var ah=0;ah<this.drawables.length;ah++){ai.push(this.drawables[ah].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ai}},add_drawable:function(ah){this.drawables.push(ah);ah.container=this},add_drawable_before:function(aj,ah){var ai=this.drawables.indexOf(ah);if(ai!=-1){this.drawables.splice(ai,0,aj);return true}return false},remove_drawable:function(ai){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);ai.container=null;return true}return false},move_drawable:function(ai,aj){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);this.drawables.splice(aj,0,ai);return true}return false}});var R=function(ak,ai,ah,aj){z.call(this,"DrawableGroup",ak,ai,ah,aj,"group-handle");if(!R.id_counter){R.id_counter=0}var al=R.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+al).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+al+"_content_div").appendTo(this.container_div);m(this.container_div,this);m(this.content_div,this);n(this.container_div,this.drag_handle_class,".group",this);this.make_name_popup_menu()};q(R.prototype,r.prototype,z.prototype,{make_name_popup_menu:function(){var ai=this;var ah={};ah["Edit configuration"]=function(){var al=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aj=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(am){if((am.keyCode||am.which)===27){al()}else{if((am.keyCode||am.which)===13){aj()}}};$(window).bind("keypress.check_enter_esc",ak);show_modal("Configure Group",ai.config.build_form(),{Cancel:al,OK:aj})};ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)}});var ae=function(ah,ak,aj,ai){z.call(this,"View");this.container=ah;this.chrom=null;this.vis_id=aj;this.dbkey=ai;this.title=ak;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ag(ah.get(0).ownerDocument);this.reset()};q(ae.prototype,z.prototype,{init:function(){var aj=this.container,ah=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aj);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;m(this.viewport_container,ah);this.intro_div=$("<div/>").addClass("intro");var ak=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ai=function(al){if(al.type==="focusout"||(al.keyCode||al.which)===13||(al.keyCode||al.which)===27){if((al.keyCode||al.which)!==27){ah.go_to($(this).val())}$(this).hide();$(this).val("");ah.location_span.show();ah.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ai).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ah.location_span.hide();ah.chrom_select.hide();ah.nav_input.val(ah.chrom+":"+ah.low+"-"+ah.high);ah.nav_input.css("display","inline-block");ah.nav_input.select();ah.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ah.zoom_out();ah.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.browser_content_div.click(function(al){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("<div />").css({height:ah.browser_content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,{content_div:this.top_labeltrack}));this.add_label_track(new ad(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new B(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(am,ai,ao){if(!am||am==="None"){return}var aj=this;if(am==="previous"){aj.load_chroms({low:this.chrom_start_index-x});return}if(am==="next"){aj.load_chroms({low:this.chrom_start_index+x});return}var an=$.grep(aj.chrom_data,function(ap,aq){return ap.chrom===am})[0];if(an===undefined){aj.load_chroms({chrom:am},function(){aj.change_chrom(am,ai,ao)});return}else{if(am!==aj.chrom){aj.chrom=am;aj.chrom_select.val(aj.chrom);aj.max_high=an.len-1;aj.reset();aj.request_redraw(true);for(var al=0,ah=aj.drawables.length;al<ah;al++){var ak=aj.drawables[al];if(ak.init){ak.init()}}}if(ai!==undefined&&ao!==undefined){aj.low=Math.max(ai,0);aj.high=Math.min(ao,aj.max_high)}aj.reset_overview();aj.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){z.prototype.add_drawable.call(this,ah);ah.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;ah.init();this.label_tracks.push(ah)},remove_drawable:function(aj,ai){z.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.drawables),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(D,Math.ceil(Math.log((this.high-this.low)/S)/Math.log(D)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){$.when(ah.get_overview_tile()).then(function(ai){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ai.canvas);view.overview_highlight.show().height(ai.canvas.height());view.overview_viewport.height(ai.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ah;ah.set_is_overview(true)});view.has_changes=true},reset_overview:function(){this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new P(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},al=this.track,aj=ai.tool_id+al.tool_region_and_parameters_str(ai.chrom,ai.low,ai.high),ah,am;if(al.container===view){var ak=new R(this.name,this.track.view,this.track.container);al.container.add_drawable(ak);al.container.remove_drawable(al);ak.add_drawable(al);al.container_div.appendTo(ak.content_div);ah=ak}else{ah=al.container}if(al instanceof e){am=new W(aj,view,ah,"hda");am.change_mode(al.mode);ah.add_drawable(am)}am.content_div.text("Starting job.");this.run(ai,am,function(an){am.dataset_id=an.dataset_id;am.content_div.text("Running job.");am.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(L)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(y+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var P=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){P.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var X=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};q(X.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=ah[this.index];return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(at,aA){this.track=at;this.filters=[];for(var av=0;av<aA.length;av++){var aw=aA[av],aB=aw.name,ah=aw.type,aj=aw.index,az=aw.tool_id,ay=aw.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[av]=new X(aB,aj,az,ay)}else{console.log("ERROR: unsupported filter: ",aB,ah)}}var ak=function(aC,aD,aE){aC.click(function(){var aF=aD.text();max=parseFloat(aE.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aE.slider("option","values")){input_size=2*input_size+1;multi_value=true}aD.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aF).appendTo(aD).focus().select().click(function(aG){aG.stopPropagation()}).blur(function(){$(this).remove();aD.text(aF)}).keyup(function(aK){if(aK.keyCode===27){$(this).trigger("blur")}else{if(aK.keyCode===13){var aI=aE.slider("option","min"),aG=aE.slider("option","max"),aJ=function(aL){return(isNaN(aL)||aL>aG||aL<aI)},aH=$(this).val();if(!multi_value){aH=parseFloat(aH);if(aJ(aH)){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}else{aH=aH.split("-");aH=[parseFloat(aH[0]),parseFloat(aH[1])];if(aJ(aH[0])||aJ(aH[1])){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}aE.slider((multi_value?"values":"value"),aH)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aC){aC.stopPropagation()}).click(function(aC){aC.stopPropagation()}).bind("dblclick",function(aC){aC.stopPropagation()}).bind("keydown",function(aC){aC.stopPropagation()});var ax=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aF,aH){aH.container=$("<div/>").addClass("filter-row slider-row").appendTo(ax);var aG=$("<div/>").addClass("elt-label").appendTo(aH.container);var aE=$("<span/>").addClass("slider-name").text(aH.name+"  ").appendTo(aG);var aD=$("<span/>");var aJ=$("<span/>").addClass("slider-value").appendTo(aG).append("[").append(aD).append("]");var aC=$("<div/>").addClass("slider").appendTo(aH.container);aH.control_element=$("<div/>").attr("id",aH.name+"-filter-control").appendTo(aC);var aI=[0,0];aH.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aL,aM){var aK=aM.values;aD.text(aK[0]+"-"+aK[1]);aH.low=aK[0];aH.high=aK[1];ap.track.request_draw(true,true)},change:function(aK,aL){aH.control_element.slider("option","slide").call(aH.control_element,aK,aL)}});aH.slider=aH.control_element;aH.slider_label=aD;ak(aJ,aD,aH.control_element);$("<div style='clear: both;'/>").appendTo(aH.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(ax);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var ai=this;ao.click(function(){ai.run_on_dataset()})}var ar=$("<div/>").addClass("display-controls").appendTo(this.parent_div),au,an,aq,al={Transparency:function(aC){ap.alpha_filter=aC},Height:function(aC){ap.height_filter=aC}};$.each(al,function(aE,aD){au=$("<div/>").addClass("filter-row").appendTo(ar),an=$("<span/>").addClass("elt-label").text(aE+":").appendTo(au),aq=$("<select/>").attr("name",aE+"_dropdown").css("float","right").appendTo(au);$("<option/>").attr("value",-1).text("== None ==").appendTo(aq);for(var aC=0;aC<ap.filters.length;aC++){$("<option/>").attr("value",aC).text(ap.filters[aC].name).appendTo(aq)}aq.change(function(){$(this).children("option:selected").each(function(){var aF=parseInt($(this).val());al[aE]((aF>=0?ap.filters[aF]:null));ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(au)});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var E=function(ah,ai){N.Scaler.call(this,ai);this.filter=ah};E.prototype.gen_val=function(ah){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var H=function(ah){this.track=ah.track;this.params=ah.params;this.values={};this.restore_values((ah.saved_values?ah.saved_values:{}));this.onchange=ah.onchange};q(H.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(ah,ak,aj,ai,al){this.track=ah;this.index=ak;this.low=ak*S*aj;this.high=(ak+1)*S*aj;this.resolution=aj;this.canvas=$("<div class='track-tile'/>").append(ai);this.data=al;this.stale=false};b.prototype.predisplay_actions=function(){};var l=function(ah,ak,aj,ai,al,am){b.call(this,ah,ak,aj,ai,al);this.max_val=am};q(l.prototype,b.prototype);var Q=function(ah,al,ak,aj,an,ao,am,ai){b.call(this,ah,al,ak,aj,an);this.mode=ao;this.message=am;this.feature_mapper=ai};q(Q.prototype,b.prototype);Q.prototype.predisplay_actions=function(){var ai=this,ah={};if(ai.mode!=="Pack"){return}$(this.canvas).mousemove(function(au){var ao=$(this).offset(),at=au.pageX-ao.left,ar=au.pageY-ao.top,ay=ai.feature_mapper.get_feature_data(at,ar),ap=(ay?ay[0]:null);$(this).siblings(".feature-popup").each(function(){if(!ap||$(this).attr("id")!==ap.toString()){$(this).remove()}});if(ay){var ak=ah[ap];if(!ak){var ap=ay[0],av={name:ay[3],start:ay[1],end:ay[2],strand:ay[4]},an=ai.track.filters_manager.filters,am;for(var aq=0;aq<an.length;aq++){am=an[aq];av[am.name]=ay[am.index]}var ak=$("<div/>").attr("id",ap).addClass("feature-popup"),ax,aw,az=$("<table/>").appendTo(ak),aA;for(ax in av){aw=av[ax];aA=$("<tr/>").appendTo(az);$("<th/>").appendTo(aA).text(ax);$("<td/>").attr("align","left").appendTo(aA).text(typeof(aw)=="number"?ab(aw,2):aw)}ah[ap]=ak}ak.appendTo($(ai.canvas).parent());var al=at+parseInt(ai.canvas.css("left"))+7,aj=ar+parseInt(ai.canvas.css("top"))+7;ak.css("left",al+"px").css("top",aj+"px")}else{if(!au.isPropagationStopped()){au.stopPropagation();$(this).siblings().each(function(){$(this).trigger(au)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var j=function(ak,ai,ah,aj,al,am){r.call(this,ak,ai,ah,{},"draghandle");this.data_url=(al?al:default_data_url);this.data_url_extra_params={};this.data_query_wait=(am?am:M);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.container_div=$("<div />").addClass("track").attr("id","track_"+j.id_counter++).css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Y){return"ReadTrack"}else{if(this instanceof W){return"ToolDataFeatureTrack"}else{if(this instanceof V){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(L)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(G)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.make_name_popup_menu()}ah.content_div.text(aa);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}})},predraw_init:function(){},});var O=function(ao,am){var ai=this,ap=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=new ac(this,(ao!==undefined?ao:{}));this.filters_available=false;this.filters_visible=false;this.tool=(am!==undefined&&obj_length(am)>0?new s(this,am):undefined);this.is_overview=false;if(ai.hidden){return}if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(ai.display_modes!==undefined){if(ai.mode_div===undefined){ai.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ai.header_div);var aj=(ai.config&&ai.config.values.mode?ai.config.values.mode:ai.display_modes[0]);ai.mode=aj;ai.mode_div.text(aj);var ah={};for(var ak=0,an=ai.display_modes.length;ak<an;ak++){var al=ai.display_modes[ak];ah[al]=function(aq){return function(){ai.change_mode(aq)}}(al)}make_popupmenu(ai.mode_div,ah)}else{ai.mode_div.hide()}}this.make_name_popup_menu()};q(O.prototype,r.prototype,j.prototype,{to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw();return ah},make_name_popup_menu:function(){var ai=this;var ah={};ah[(this.is_overview?"Hide overview":"Set as overview")]=function(){if(ai.is_overview){ai.view.reset_overview()}else{ai.view.set_overview(ai)}};ah["Edit configuration"]=function(){var am=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},al=function(an){if((an.keyCode||an.which)===27){am()}else{if((an.keyCode||an.which)===13){ak()}}};$(window).bind("keypress.check_enter_esc",al);show_modal("Configure Track",ai.config.build_form(),{Cancel:am,OK:ak})};if(ai.filters_available>0){var aj=(ai.filters_div.is(":visible")?"Hide filters":"Show filters");ah[aj]=function(){ai.filters_visible=(ai.filters_div.is(":visible"));if(ai.filters_visible){ai.filters_manager.reset_filters()}ai.filters_div.toggle();ai.make_name_popup_menu()}}if(ai.tool){var aj=(ai.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");ah[aj]=function(){if(!ai.dynamic_tool_div.is(":visible")){ai.set_name(ai.name+ai.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ai.revert_name()}ai.dynamic_tool_div.toggle();ai.make_name_popup_menu()}}ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)},set_is_overview:function(ah){this.is_overview=ah;this.make_name_popup_menu()},get_overview_tile:function(){var ah=this;view=ah.view,resolution=Math.pow(D,Math.ceil(Math.log((view.max_high-view.max_low)/S)/Math.log(D))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ah.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ah.data_url_extra_params)).then(function(ai){var ak=ah._gen_tile_cache_key(view_width,w_scale,0),am=ah.tile_cache.get(ak);if(!am){am=ah.draw_tile(ai,"Auto",resolution,0,w_scale);ah.tile_cache.set(ak,am)}var ap=$(am.canvas.find("canvas")),al=ap.clone(),ao=ap.get(0).getContext("2d"),aj=al.get(0).getContext("2d"),an=ao.getImageData(0,0,ao.canvas.width,ao.canvas.height);aj.putImageData(an,-ah.left_offset,(am.data.dataset_type==="summary_tree"?U:0));new_tile=new b(ah,-1,resolution,al);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof B)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/S);var ap=true;var at=[];var ah=0;while((ai*S*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",F)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*S*an,ax=ap+S*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);if(aq!==undefined){al.tile_cache.set(at,aq);al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw()});return null},show_tile:function(ao,aq,ar){var aj=this,ai=ao.canvas,an=ai;if(ao.message){var at=$("<div/>"),ap=$("<div/>").addClass("tile-message").text(ao.message).css({height:F-1,width:ao.canvas.width}).appendTo(at),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ap),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ap);at.append(ai);an=at;al.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()});ah.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()})}ao.predisplay_actions();var am=this.view.high-this.view.low,ak=(ao.low-this.view.low)*ar;if(this.left_offset){ak-=this.left_offset}an.css({position:"absolute",top:0,left:ak,height:""});aq.append(an);aj.max_height=Math.max(aj.max_height,an.height());aj.content_div.css("height",aj.max_height+"px");aq.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*S*ai,al=S*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ai,ah){this.hidden=true;j.call(this,"label",ai,ah,{});this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{init:function(){this.enabled=true},_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var B=function(ah){this.hidden=true;j.call(this,"reference",ah,{content_div:ah.top_labeltrack},{});O.call(this);ah.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ah.dbkey};this.data_manager=new J(C,this,false);this.tile_cache=new c(v)};q(B.prototype,r.prototype,O.prototype,{init:function(){this.enabled=true},draw_tile:function(ar,an,am,ai,at){var al=this,aj=S*am;if(at>this.view.canvas_manager.char_width_px){if(ar===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(al,ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(am,ak,aj,an,ah,al){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,am,ak,aj,al);O.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=an;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new T(C,this);this.tile_cache=new c(v);this.left_offset=0;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:am},{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:al,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.dataset_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.dataset_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};q(k.prototype,r.prototype,O.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this;ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(ai){ah.container_div.addClass("line-track");var ak=ai.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=ak.min;ah.prefs.max_value=ak.max;$("#track_"+ah.dataset_id+"_minval").val(ah.prefs.min_value);$("#track_"+ah.dataset_id+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=ak.total_frequency;ah.container_div.find(".yaxislabel").remove();var al=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_minval").text(ab(ah.prefs.min_value,3));var aj=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_maxval").text(ab(ah.prefs.max_value,3));aj.css({position:"absolute",top:"24px",left:"10px"});aj.prependTo(ah.container_div);al.css({position:"absolute",bottom:"2px",left:"10px"});al.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new N.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(this.track,aj,al,ak,au.data)}});var e=function(ah,an,ai,am,ap,ao,ak,al){var aj=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];j.call(this,ah,an,ai,ao);O.call(this,ak,al);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){aj.set_name(aj.prefs.name);aj.tile_cache.clear();aj.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=am;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new T(20,this);this.left_offset=200;this.painter=N.LinkedFeaturePainter};q(e.prototype,r.prototype,O.prototype,{postdraw_actions:function(ax,ah,ay,aw){O.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.make_name_popup_menu()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",A,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aD,aH,ar,ak){var aA=this,am=aA._get_tile_bounds(aH,aD),aK=am[0],ai=am[1],ay=ai-aK,aB=Math.ceil(ay*ar),aQ=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"){az="no_detail"}else{var aP=aw.data;if(this.view.high-this.view.low>K){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aB+al;aj.height=an+U;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aK,ai,200);if(aw.max){at.max=aw.max}aw=at}var aM=new N.SummaryTreePainter(aw,aK,ai,this.prefs);var aC=aj.getContext("2d");aC.translate(al,U);aM.draw(aC,aB,an);return new l(aA,aH,aD,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aE=0,aG=aw.data.length;aE<aG;aE++){var ao=aw.data[aE];var aF=false;var av;for(var aJ=0,aO=au.length;aJ<aO;aJ++){av=au[aJ];av.update_attrs(ao);if(!av.keep(ao)){aF=true;break}}if(!aF){aq.push(ao)}}}var aN=(this.filters_manager.alpha_filter?new E(this.filters_manager.alpha_filter):null);var aL=(this.filters_manager.height_filter?new E(this.filters_manager.height_filter):null);var aM=new (this.painter)(aq,aK,ai,this.prefs,az,aN,aL,ak);var an=Math.max(af,aM.get_required_height(ap));var aj=this.view.canvas_manager.new_canvas();var aI=null;aj.width=aB+al;aj.height=an;var aC=aj.getContext("2d");aC.fillStyle=this.prefs.block_color;aC.font=aC.canvas.manager.default_font;aC.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aw.data){aC.translate(al,0);aI=aM.draw(aC,aB,an,ax);aI.translation=-al}return new Q(aA,aH,aD,aj,aw.data,az,aw.message,aI)}});var V=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.painter=N.VariantPainter};q(V.prototype,r.prototype,O.prototype,e.prototype);var Y=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ak,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=N.ReadPainter;this.make_name_popup_menu()};q(Y.prototype,r.prototype,O.prototype,e.prototype);var W=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am,{});this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};q(W.prototype,r.prototype,O.prototype,e.prototype,{predraw_init:function(){var ai=this;var ah=function(){if(ai.data_manager.size()===0){setTimeout(ah,300)}else{ai.data_url=default_data_url;ai.data_query_wait=M;ai.dataset_state_url=converted_datasets_state_url;$.getJSON(ai.dataset_state_url,{dataset_id:ai.dataset_id,hda_ldda:ai.hda_ldda},function(aj){})}};ah()}});Z.View=ae;Z.DrawableGroup=R;Z.LineTrack=k;Z.FeatureTrack=e;Z.ReadTrack=Y};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(k,y){var v=k("class").extend;var q=function(J,B,H,A,G,E){if(E===undefined){E=4}var D=A-B;var C=G-H;var F=Math.floor(Math.sqrt(D*D+C*C)/E);var K=D/F;var I=C/F;var z;for(z=0;z<F;z++,B+=K,H+=I){if(z%2!==0){continue}J.fillRect(B,H,E,1)}};var r=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var e=function(z){this.default_val=(z?z:1)};e.prototype.gen_val=function(z){return this.default_val};var n=function(B,D,z,A,C){this.data=B;this.view_start=D;this.view_end=z;this.prefs=v({},this.default_prefs,A);this.mode=C};n.prototype.default_prefs={};var w=function(B,D,z,A,C){n.call(this,B,D,z,A,C)};w.prototype.default_prefs={show_counts:false};w.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var c=function(z,D,F,G,B){n.call(this,z,D,F,G,B);if(this.prefs.min_value===undefined){var H=Infinity;for(var A=0,C=this.data.length;A<C;A++){H=Math.min(H,this.data[A][1])}this.prefs.min_value=H}if(this.prefs.max_value===undefined){var E=-Infinity;for(var A=0,C=this.data.length;A<C;A++){E=Math.max(E,this.data[A][1])}this.prefs.max_value=E}};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var o=function(z){this.feature_positions={};this.slot_height=z;this.translation=0};o.prototype.map_feature_data=function(A,C,z,B){if(!this.feature_positions[C]){this.feature_positions[C]=[]}this.feature_positions[C].push({data:A,x_start:z,x_end:B})};o.prototype.get_feature_data=function(z,D){var C=Math.floor(D/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var p=function(B,E,z,A,D,F,C){n.call(this,B,E,z,A,D);this.alpha_scaler=(F?F:new e());this.height_scaler=(C?C:new e())};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};v(p.prototype,{get_required_height:function(A){var z=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){z=A*y_scale}return z+Math.max(Math.round(y_scale/2),5)},draw:function(L,J,H,G){var R=this.data,E=this.view_start,N=this.view_end;L.save();L.fillStyle=this.prefs.block_color;L.textAlign="right";var I=this.view_end-this.view_start,F=J/I,M=this.get_row_height(),Q=new o(M),C;for(var O=0,P=R.length;O<P;O++){var B=R[O],D=B[0],K=B[1],z=B[2],A=(G&&G[D]!==undefined?G[D]:null);if((K<N&&z>E)&&(this.mode=="Dense"||A!==null)){C=this.draw_element(L,this.mode,B,A,E,N,F,M,J);Q.map_feature_data(B,A,C[0],C[1])}}L.restore();return Q},draw_element:function(F,B,H,D,C,E,G,A,z){console.log("WARNING: Unimplemented function.");return[0,0]}});var d=10,j=3,m=5,x=10,g=1,t=3,f=3,a=9,l=2,h="#ccc";var s=function(B,E,z,A,D,F,C){p.call(this,B,E,z,A,D,F,C)};v(s.prototype,p.prototype,{get_row_height:function(){var A=this.mode,z;if(A==="Dense"){z=d}else{if(A==="no_detail"){z=j}else{if(A==="Squish"){z=m}else{z=x}}}return z},draw_element:function(N,E,W,I,P,ah,al,an,z){var 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ah=0;ah<this.drawables.length;ah++){this.drawables[ah].init()}},_draw:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah]._draw()}},to_json:function(){var ai=[];for(var ah=0;ah<this.drawables.length;ah++){ai.push(this.drawables[ah].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ai}},add_drawable:function(ah){this.drawables.push(ah);ah.container=this},add_drawable_before:function(aj,ah){var ai=this.drawables.indexOf(ah);if(ai!=-1){this.drawables.splice(ai,0,aj);return true}return false},remove_drawable:function(ai){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);ai.container=null;return true}return false},move_drawable:function(ai,aj){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);this.drawables.splice(aj,0,ai);return true}return false}});var R=function(ak,ai,ah,aj){z.call(this,"DrawableGroup",ak,ai,ah,aj,"group-handle");if(!R.id_counter){R.id_counter=0}var al=R.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+al).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+al+"_content_div").appendTo(this.container_div);m(this.container_div,this);m(this.content_div,this);n(this.container_div,this.drag_handle_class,".group",this);this.update_track_icons()};q(R.prototype,r.prototype,z.prototype,{update_track_icons:function(){var ai=this;var ah={};ah["Edit configuration"]=function(){var al=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aj=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(am){if((am.keyCode||am.which)===27){al()}else{if((am.keyCode||am.which)===13){aj()}}};$(window).bind("keypress.check_enter_esc",ak);show_modal("Configure Group",ai.config.build_form(),{Cancel:al,OK:aj})};ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)}});var ae=function(ah,ak,aj,ai){z.call(this,"View");this.container=ah;this.chrom=null;this.vis_id=aj;this.dbkey=ai;this.title=ak;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ag(ah.get(0).ownerDocument);this.reset()};q(ae.prototype,z.prototype,{init:function(){var aj=this.container,ah=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aj);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;m(this.viewport_container,ah);this.intro_div=$("<div/>").addClass("intro");var ak=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ai=function(al){if(al.type==="focusout"||(al.keyCode||al.which)===13||(al.keyCode||al.which)===27){if((al.keyCode||al.which)!==27){ah.go_to($(this).val())}$(this).hide();$(this).val("");ah.location_span.show();ah.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ai).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ah.location_span.hide();ah.chrom_select.hide();ah.nav_input.val(ah.chrom+":"+ah.low+"-"+ah.high);ah.nav_input.css("display","inline-block");ah.nav_input.select();ah.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ah.zoom_out();ah.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.browser_content_div.click(function(al){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("<div />").css({height:ah.browser_content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,{content_div:this.top_labeltrack}));this.add_label_track(new ad(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new B(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(am,ai,ao){if(!am||am==="None"){return}var aj=this;if(am==="previous"){aj.load_chroms({low:this.chrom_start_index-x});return}if(am==="next"){aj.load_chroms({low:this.chrom_start_index+x});return}var an=$.grep(aj.chrom_data,function(ap,aq){return ap.chrom===am})[0];if(an===undefined){aj.load_chroms({chrom:am},function(){aj.change_chrom(am,ai,ao)});return}else{if(am!==aj.chrom){aj.chrom=am;aj.chrom_select.val(aj.chrom);aj.max_high=an.len-1;aj.reset();aj.request_redraw(true);for(var al=0,ah=aj.drawables.length;al<ah;al++){var ak=aj.drawables[al];if(ak.init){ak.init()}}}if(ai!==undefined&&ao!==undefined){aj.low=Math.max(ai,0);aj.high=Math.min(ao,aj.max_high)}aj.reset_overview();aj.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){z.prototype.add_drawable.call(this,ah);ah.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;ah.init();this.label_tracks.push(ah)},remove_drawable:function(aj,ai){z.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.drawables),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(D,Math.ceil(Math.log((this.high-this.low)/S)/Math.log(D)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){$.when(ah.get_overview_tile()).then(function(ai){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ai.canvas);view.overview_highlight.show().height(ai.canvas.height());view.overview_viewport.height(ai.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ah;ah.set_is_overview(true)});view.has_changes=true},reset_overview:function(){this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new P(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},al=this.track,aj=ai.tool_id+al.tool_region_and_parameters_str(ai.chrom,ai.low,ai.high),ah,am;if(al.container===view){var ak=new R(this.name,this.track.view,this.track.container);al.container.add_drawable(ak);al.container.remove_drawable(al);ak.add_drawable(al);al.container_div.appendTo(ak.content_div);ah=ak}else{ah=al.container}if(al instanceof e){am=new W(aj,view,ah,"hda");am.change_mode(al.mode);ah.add_drawable(am)}am.content_div.text("Starting job.");this.run(ai,am,function(an){am.dataset_id=an.dataset_id;am.content_div.text("Running job.");am.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(L)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(y+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var P=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){P.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var X=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};q(X.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=ah[this.index];return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(at,aA){this.track=at;this.filters=[];for(var av=0;av<aA.length;av++){var aw=aA[av],aB=aw.name,ah=aw.type,aj=aw.index,az=aw.tool_id,ay=aw.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[av]=new X(aB,aj,az,ay)}else{console.log("ERROR: unsupported filter: ",aB,ah)}}var ak=function(aC,aD,aE){aC.click(function(){var aF=aD.text();max=parseFloat(aE.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aE.slider("option","values")){input_size=2*input_size+1;multi_value=true}aD.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aF).appendTo(aD).focus().select().click(function(aG){aG.stopPropagation()}).blur(function(){$(this).remove();aD.text(aF)}).keyup(function(aK){if(aK.keyCode===27){$(this).trigger("blur")}else{if(aK.keyCode===13){var aI=aE.slider("option","min"),aG=aE.slider("option","max"),aJ=function(aL){return(isNaN(aL)||aL>aG||aL<aI)},aH=$(this).val();if(!multi_value){aH=parseFloat(aH);if(aJ(aH)){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}else{aH=aH.split("-");aH=[parseFloat(aH[0]),parseFloat(aH[1])];if(aJ(aH[0])||aJ(aH[1])){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}aE.slider((multi_value?"values":"value"),aH)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aC){aC.stopPropagation()}).click(function(aC){aC.stopPropagation()}).bind("dblclick",function(aC){aC.stopPropagation()}).bind("keydown",function(aC){aC.stopPropagation()});var ax=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aF,aH){aH.container=$("<div/>").addClass("filter-row slider-row").appendTo(ax);var aG=$("<div/>").addClass("elt-label").appendTo(aH.container);var aE=$("<span/>").addClass("slider-name").text(aH.name+"  ").appendTo(aG);var aD=$("<span/>");var aJ=$("<span/>").addClass("slider-value").appendTo(aG).append("[").append(aD).append("]");var aC=$("<div/>").addClass("slider").appendTo(aH.container);aH.control_element=$("<div/>").attr("id",aH.name+"-filter-control").appendTo(aC);var aI=[0,0];aH.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aL,aM){var aK=aM.values;aD.text(aK[0]+"-"+aK[1]);aH.low=aK[0];aH.high=aK[1];ap.track.request_draw(true,true)},change:function(aK,aL){aH.control_element.slider("option","slide").call(aH.control_element,aK,aL)}});aH.slider=aH.control_element;aH.slider_label=aD;ak(aJ,aD,aH.control_element);$("<div style='clear: both;'/>").appendTo(aH.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(ax);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var ai=this;ao.click(function(){ai.run_on_dataset()})}var ar=$("<div/>").addClass("display-controls").appendTo(this.parent_div),au,an,aq,al={Transparency:function(aC){ap.alpha_filter=aC},Height:function(aC){ap.height_filter=aC}};$.each(al,function(aE,aD){au=$("<div/>").addClass("filter-row").appendTo(ar),an=$("<span/>").addClass("elt-label").text(aE+":").appendTo(au),aq=$("<select/>").attr("name",aE+"_dropdown").css("float","right").appendTo(au);$("<option/>").attr("value",-1).text("== None ==").appendTo(aq);for(var aC=0;aC<ap.filters.length;aC++){$("<option/>").attr("value",aC).text(ap.filters[aC].name).appendTo(aq)}aq.change(function(){$(this).children("option:selected").each(function(){var aF=parseInt($(this).val());al[aE]((aF>=0?ap.filters[aF]:null));ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(au)});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var E=function(ah,ai){N.Scaler.call(this,ai);this.filter=ah};E.prototype.gen_val=function(ah){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var H=function(ah){this.track=ah.track;this.params=ah.params;this.values={};this.restore_values((ah.saved_values?ah.saved_values:{}));this.onchange=ah.onchange};q(H.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(ah,ak,aj,ai,al){this.track=ah;this.index=ak;this.low=ak*S*aj;this.high=(ak+1)*S*aj;this.resolution=aj;this.canvas=$("<div class='track-tile'/>").append(ai);this.data=al;this.stale=false};b.prototype.predisplay_actions=function(){};var l=function(ah,ak,aj,ai,al,am){b.call(this,ah,ak,aj,ai,al);this.max_val=am};q(l.prototype,b.prototype);var Q=function(ah,al,ak,aj,an,ao,am,ai){b.call(this,ah,al,ak,aj,an);this.mode=ao;this.message=am;this.feature_mapper=ai};q(Q.prototype,b.prototype);Q.prototype.predisplay_actions=function(){var ai=this,ah={};if(ai.mode!=="Pack"){return}$(this.canvas).mousemove(function(au){var ao=$(this).offset(),at=au.pageX-ao.left,ar=au.pageY-ao.top,ay=ai.feature_mapper.get_feature_data(at,ar),ap=(ay?ay[0]:null);$(this).siblings(".feature-popup").each(function(){if(!ap||$(this).attr("id")!==ap.toString()){$(this).remove()}});if(ay){var ak=ah[ap];if(!ak){var ap=ay[0],av={name:ay[3],start:ay[1],end:ay[2],strand:ay[4]},an=ai.track.filters_manager.filters,am;for(var aq=0;aq<an.length;aq++){am=an[aq];av[am.name]=ay[am.index]}var ak=$("<div/>").attr("id",ap).addClass("feature-popup"),ax,aw,az=$("<table/>").appendTo(ak),aA;for(ax in av){aw=av[ax];aA=$("<tr/>").appendTo(az);$("<th/>").appendTo(aA).text(ax);$("<td/>").attr("align","left").appendTo(aA).text(typeof(aw)=="number"?ab(aw,2):aw)}ah[ap]=ak}ak.appendTo($(ai.canvas).parent());var al=at+parseInt(ai.canvas.css("left"))+7,aj=ar+parseInt(ai.canvas.css("top"))+7;ak.css("left",al+"px").css("top",aj+"px")}else{if(!au.isPropagationStopped()){au.stopPropagation();$(this).siblings().each(function(){$(this).trigger(au)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var j=function(ak,ar,al,at,aj,ai){r.call(this,ak,ar,al,{},"draghandle");this.data_url=(aj?aj:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ai?ai:M);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.id=j.id_counter++;this.container_div=$("<div />").addClass("track").attr("id","track_"+this.id).css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div/>").addClass("track-name").appendTo(this.header_div).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());this.icons_div=$("<div/>").css("float","left").appendTo(this.header_div).hide();this.settings_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Edit settings").addClass("icon-button settings-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.filters_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Filters").addClass("icon-button filters-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.tools_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Tools").addClass("icon-button tools-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.remove_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Remove").addClass("icon-button remove-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);var am=this;this.header_div.dblclick(function(au){au.stopPropagation()});this.settings_icon.click(function(){var aw=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},au=function(){am.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},av=function(ax){if((ax.keyCode||ax.which)===27){aw()}else{if((ax.keyCode||ax.which)===13){au()}}};$(window).bind("keypress.check_enter_esc",av);show_modal("Configure Track",am.config.build_form(),{Cancel:aw,OK:au})});this.filters_icon.click(function(){am.filters_div.toggle();am.filters_manager.reset_filters()});this.tools_icon.click(function(){am.dynamic_tool_div.toggle();if(am.dynamic_tool_div.is(":visible")){am.set_name(am.name+am.tool_region_and_parameters_str())}else{am.revert_name()}$(".tipsy").remove()});this.remove_icon.click(function(){$(".tipsy").remove();am.remove()});if(am.display_modes!==undefined){if(am.mode_div===undefined){am.mode_div=$("<div class='right-float menubutton popup' />").appendTo(am.header_div);var an=(am.config&&am.config.values.mode?am.config.values.mode:am.display_modes[0]);am.mode=an;am.mode_div.text(an);var ah={};for(var ao=0,aq=am.display_modes.length;ao<aq;ao++){var ap=am.display_modes[ao];ah[ap]=function(au){return function(){am.change_mode(au)}}(ap)}make_popupmenu(am.mode_div,ah)}else{am.mode_div.hide()}this.header_div.append($("<div/>").css("clear","both"));this.container_div.hover(function(){am.icons_div.show()},function(){am.icons_div.hide()})}}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Y){return"ReadTrack"}else{if(this instanceof W){return"ToolDataFeatureTrack"}else{if(this instanceof V){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(L)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(G)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.update_track_icons()}ah.content_div.text(aa);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}});this.update_track_icons()},predraw_init:function(){},});var O=function(ak,aj){var ai=this,ah=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=new ac(this,(ak!==undefined?ak:{}));this.filters_available=false;this.filters_visible=false;this.tool=(aj!==undefined&&obj_length(aj)>0?new s(this,aj):undefined);this.is_overview=false;if(ai.hidden){return}if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}};q(O.prototype,r.prototype,j.prototype,{to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw();return ah},update_track_icons:function(){var ah=this;if(ah.filters_available>0){ah.filters_icon.show()}else{ah.filters_icon.hide()}if(ah.tool){ah.tools_icon.show()}else{ah.tools_icon.hide()}},set_is_overview:function(ah){this.is_overview=ah;this.update_track_icons()},get_overview_tile:function(){var ah=this;view=ah.view,resolution=Math.pow(D,Math.ceil(Math.log((view.max_high-view.max_low)/S)/Math.log(D))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ah.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ah.data_url_extra_params)).then(function(ai){var ak=ah._gen_tile_cache_key(view_width,w_scale,0),am=ah.tile_cache.get(ak);if(!am){am=ah.draw_tile(ai,"Auto",resolution,0,w_scale);ah.tile_cache.set(ak,am)}var ap=$(am.canvas.find("canvas")),al=ap.clone(),ao=ap.get(0).getContext("2d"),aj=al.get(0).getContext("2d"),an=ao.getImageData(0,0,ao.canvas.width,ao.canvas.height);aj.putImageData(an,-ah.left_offset,(am.data.dataset_type==="summary_tree"?U:0));new_tile=new b(ah,-1,resolution,al);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof B)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/S);var ap=true;var at=[];var ah=0;while((ai*S*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",F)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*S*an,ax=ap+S*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);if(aq!==undefined){al.tile_cache.set(at,aq);al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw()});return null},show_tile:function(ao,aq,ar){var aj=this,ai=ao.canvas,an=ai;if(ao.message){var at=$("<div/>"),ap=$("<div/>").addClass("tile-message").text(ao.message).css({height:F-1,width:ao.canvas.width}).appendTo(at),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ap),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ap);at.append(ai);an=at;al.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()});ah.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()})}ao.predisplay_actions();var am=this.view.high-this.view.low,ak=(ao.low-this.view.low)*ar;if(this.left_offset){ak-=this.left_offset}an.css({position:"absolute",top:0,left:ak,height:""});aq.append(an);aj.max_height=Math.max(aj.max_height,an.height());aj.content_div.css("height",aj.max_height+"px");aq.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*S*ai,al=S*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ai,ah){this.hidden=true;j.call(this,"label",ai,ah,{});this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{init:function(){this.enabled=true},_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var B=function(ah){this.hidden=true;j.call(this,"reference",ah,{content_div:ah.top_labeltrack},{});O.call(this);ah.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ah.dbkey};this.data_manager=new J(C,this,false);this.tile_cache=new c(v)};q(B.prototype,r.prototype,O.prototype,{init:function(){this.enabled=true},draw_tile:function(ar,an,am,ai,at){var al=this,aj=S*am;if(at>this.view.canvas_manager.char_width_px){if(ar===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(al,ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(am,ak,aj,an,ah,al){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,am,ak,aj,al);O.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=an;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new T(C,this);this.tile_cache=new c(v);this.left_offset=0;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:am},{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:al,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.dataset_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.dataset_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};q(k.prototype,r.prototype,O.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this;ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(ai){ah.container_div.addClass("line-track");var ak=ai.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=ak.min;ah.prefs.max_value=ak.max;$("#track_"+ah.dataset_id+"_minval").val(ah.prefs.min_value);$("#track_"+ah.dataset_id+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=ak.total_frequency;ah.container_div.find(".yaxislabel").remove();var al=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_minval").text(ab(ah.prefs.min_value,3));var aj=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_maxval").text(ab(ah.prefs.max_value,3));aj.css({position:"absolute",top:"24px",left:"10px"});aj.prependTo(ah.container_div);al.css({position:"absolute",bottom:"2px",left:"10px"});al.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new N.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(this.track,aj,al,ak,au.data)}});var e=function(ah,an,ai,am,ap,ao,ak,al){var aj=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];j.call(this,ah,an,ai,ao);O.call(this,ak,al);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){aj.set_name(aj.prefs.name);aj.tile_cache.clear();aj.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=am;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new T(20,this);this.left_offset=200;this.painter=N.LinkedFeaturePainter};q(e.prototype,r.prototype,O.prototype,{postdraw_actions:function(ax,ah,ay,aw){O.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.update_track_icons()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",A,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aD,aH,ar,ak){var aA=this,am=aA._get_tile_bounds(aH,aD),aK=am[0],ai=am[1],ay=ai-aK,aB=Math.ceil(ay*ar),aQ=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"){az="no_detail"}else{var aP=aw.data;if(this.view.high-this.view.low>K){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aB+al;aj.height=an+U;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aK,ai,200);if(aw.max){at.max=aw.max}aw=at}var aM=new N.SummaryTreePainter(aw,aK,ai,this.prefs);var aC=aj.getContext("2d");aC.translate(al,U);aM.draw(aC,aB,an);return new l(aA,aH,aD,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aE=0,aG=aw.data.length;aE<aG;aE++){var ao=aw.data[aE];var aF=false;var av;for(var aJ=0,aO=au.length;aJ<aO;aJ++){av=au[aJ];av.update_attrs(ao);if(!av.keep(ao)){aF=true;break}}if(!aF){aq.push(ao)}}}var aN=(this.filters_manager.alpha_filter?new E(this.filters_manager.alpha_filter):null);var aL=(this.filters_manager.height_filter?new E(this.filters_manager.height_filter):null);var aM=new (this.painter)(aq,aK,ai,this.prefs,az,aN,aL,ak);var an=Math.max(af,aM.get_required_height(ap));var aj=this.view.canvas_manager.new_canvas();var aI=null;aj.width=aB+al;aj.height=an;var aC=aj.getContext("2d");aC.fillStyle=this.prefs.block_color;aC.font=aC.canvas.manager.default_font;aC.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aw.data){aC.translate(al,0);aI=aM.draw(aC,aB,an,ax);aI.translation=-al}return new Q(aA,aH,aD,aj,aw.data,az,aw.message,aI)}});var V=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.painter=N.VariantPainter};q(V.prototype,r.prototype,O.prototype,e.prototype);var Y=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ak,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=N.ReadPainter;this.update_track_icons()};q(Y.prototype,r.prototype,O.prototype,e.prototype);var W=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am,{});this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};q(W.prototype,r.prototype,O.prototype,e.prototype,{predraw_init:function(){var ai=this;var ah=function(){if(ai.data_manager.size()===0){setTimeout(ah,300)}else{ai.data_url=default_data_url;ai.data_query_wait=M;ai.dataset_state_url=converted_datasets_state_url;$.getJSON(ai.dataset_state_url,{dataset_id:ai.dataset_id,hda_ldda:ai.hda_ldda},function(aj){})}};ah()}});Z.View=ae;Z.DrawableGroup=R;Z.LineTrack=k;Z.FeatureTrack=e;Z.ReadTrack=Y};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(k,y){var v=k("class").extend;var q=function(J,B,H,A,G,E){if(E===undefined){E=4}var D=A-B;var C=G-H;var F=Math.floor(Math.sqrt(D*D+C*C)/E);var K=D/F;var I=C/F;var z;for(z=0;z<F;z++,B+=K,H+=I){if(z%2!==0){continue}J.fillRect(B,H,E,1)}};var r=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var e=function(z){this.default_val=(z?z:1)};e.prototype.gen_val=function(z){return this.default_val};var n=function(B,D,z,A,C){this.data=B;this.view_start=D;this.view_end=z;this.prefs=v({},this.default_prefs,A);this.mode=C};n.prototype.default_prefs={};var w=function(B,D,z,A,C){n.call(this,B,D,z,A,C)};w.prototype.default_prefs={show_counts:false};w.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var c=function(z,D,F,G,B){n.call(this,z,D,F,G,B);if(this.prefs.min_value===undefined){var H=Infinity;for(var A=0,C=this.data.length;A<C;A++){H=Math.min(H,this.data[A][1])}this.prefs.min_value=H}if(this.prefs.max_value===undefined){var E=-Infinity;for(var A=0,C=this.data.length;A<C;A++){E=Math.max(E,this.data[A][1])}this.prefs.max_value=E}};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var o=function(z){this.feature_positions={};this.slot_height=z;this.translation=0};o.prototype.map_feature_data=function(A,C,z,B){if(!this.feature_positions[C]){this.feature_positions[C]=[]}this.feature_positions[C].push({data:A,x_start:z,x_end:B})};o.prototype.get_feature_data=function(z,D){var C=Math.floor(D/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var p=function(B,E,z,A,D,F,C){n.call(this,B,E,z,A,D);this.alpha_scaler=(F?F:new e());this.height_scaler=(C?C:new e())};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};v(p.prototype,{get_required_height:function(A){var z=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){z=A*y_scale}return z+Math.max(Math.round(y_scale/2),5)},draw:function(L,J,H,G){var R=this.data,E=this.view_start,N=this.view_end;L.save();L.fillStyle=this.prefs.block_color;L.textAlign="right";var I=this.view_end-this.view_start,F=J/I,M=this.get_row_height(),Q=new o(M),C;for(var O=0,P=R.length;O<P;O++){var B=R[O],D=B[0],K=B[1],z=B[2],A=(G&&G[D]!==undefined?G[D]:null);if((K<N&&z>E)&&(this.mode=="Dense"||A!==null)){C=this.draw_element(L,this.mode,B,A,E,N,F,M,J);Q.map_feature_data(B,A,C[0],C[1])}}L.restore();return Q},draw_element:function(F,B,H,D,C,E,G,A,z){console.log("WARNING: Unimplemented function.");return[0,0]}});var d=10,j=3,m=5,x=10,g=1,t=3,f=3,a=9,l=2,h="#ccc";var s=function(B,E,z,A,D,F,C){p.call(this,B,E,z,A,D,F,C)};v(s.prototype,p.prototype,{get_row_height:function(){var A=this.mode,z;if(A==="Dense"){z=d}else{if(A==="no_detail"){z=j}else{if(A==="Squish"){z=m}else{z=x}}}return z},draw_element:function(N,E,W,I,P,ah,al,an,z){var T=W[0],aj=W[1],ab=W[2],R=W[3],ac=Math.floor(Math.max(0,(aj-P)*al)),O=Math.ceil(Math.min(z,Math.max(0,(ab-P)*al))),aa=ac,am=O,Z=(E==="Dense"?0:(0+I))*an,M,af,S=null,ap=null,C=this.prefs.block_color,ae=this.prefs.label_color;N.globalAlpha=this.alpha_scaler.gen_val(W);if(E=="Dense"){I=1}if(E==="no_detail"){N.fillStyle=C;N.fillRect(ac,Z+5,O-ac,g)}else{var L=W[4],Y=W[5],ad=W[6],D=W[7];if(Y&&ad){S=Math.floor(Math.max(0,(Y-P)*al));ap=Math.ceil(Math.min(z,Math.max(0,(ad-P)*al)))}var ak,U;if(E==="Squish"||E==="Dense"){ak=1;U=f}else{ak=5;U=a}if(!D){if(W.strand){if(W.strand==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand_inv")}else{if(W.strand==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand_inv")}}}else{N.fillStyle=C}N.fillRect(ac,Z,O-ac,U)}else{var K,V;if(E==="Squish"||E==="Dense"){N.fillStyle=h;K=Z+Math.floor(f/2)+1;V=1}else{if(L){var K=Z;var V=U;if(L==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand")}else{if(L==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand")}}}else{N.fillStyle=h;K+=(f/2)+1;V=1}}N.fillRect(ac,K,O-ac,V);var F;for(var ai=0,B=D.length;ai<B;ai++){var G=D[ai],A=Math.floor(Math.max(0,(G[0]-P)*al)),X=Math.ceil(Math.min(z,Math.max((G[1]-P)*al)));if(A>X){continue}N.fillStyle=C;N.fillRect(A,Z+(U-ak)/2+1,X-A,ak);if(S!==undefined&&ad>Y&&!(A>ap||X<S)){var ag=Math.max(A,S),J=Math.min(X,ap);N.fillRect(ag,Z+1,J-ag,U);if(D.length==1&&E=="Pack"){if(L==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand_inv")}else{if(L==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand_inv")}}if(ag+14<J){ag+=2;J-=2}N.fillRect(ag,Z+1,J-ag,U)}}}if(E==="Pack"){N.globalAlpha=1;N.fillStyle="white";var H=this.height_scaler.gen_val(W),Q=Math.ceil(U*H),ao=Math.round((U-Q)/2);if(H!==1){N.fillRect(ac,K+1,O-ac,ao);N.fillRect(ac,K+U-ao+1,O-ac,ao)}}}N.globalAlpha=1;if(E==="Pack"&&aj>P){N.fillStyle=ae;if(P===0&&ac-N.measureText(R).width<0){N.textAlign="left";N.fillText(R,O+l,Z+8);am+=N.measureText(R).width+l}else{N.textAlign="right";N.fillText(R,ac-l,Z+8);aa-=N.measureText(R).width+l}}}N.globalAlpha=1;return[aa,am]}});var b=function(B,E,z,A,D,F,C){p.call(this,B,E,z,A,D,F,C)};v(b.prototype,p.prototype,{draw_element:function(S,N,H,D,V,B,K,T,Q){var H=data[i],J=H[0],R=H[1],C=H[2],M=H[3],F=Math.floor(Math.max(0,(R-V)*K)),I=Math.ceil(Math.min(Q,Math.max(0,(C-V)*K))),E=(N==="Dense"?0:(0+D))*T,z,W,A=null,L=null;if(no_label){S.fillStyle=block_color;S.fillRect(F+left_offset,E+5,I-F,1)}else{var U=H[4],P=H[5],G=H[6];z=9;W=1;S.fillRect(F+left_offset,E,I-F,z);if(N!=="Dense"&&M!==undefined&&R>V){S.fillStyle=label_color;if(V===0&&F-S.measureText(M).width<0){S.textAlign="left";S.fillText(M,I+2+left_offset,E+8)}else{S.textAlign="right";S.fillText(M,F-2+left_offset,E+8)}S.fillStyle=block_color}var O=U+" / "+P;if(R>V&&S.measureText(O).width<(I-F)){S.fillStyle="white";S.textAlign="center";S.fillText(O,left_offset+F+(I-F)/2,E+8);S.fillStyle=block_color}}return[F,I]}});var u=function(C,F,z,B,E,G,D,A){p.call(this,C,F,z,B,E,G,D);this.ref_seq=(A?A.data:null)};u.prototype.default_prefs=v({},p.prototype.default_prefs,{show_insertions:false});v(u.prototype,p.prototype,{get_row_height:function(){var z,A=this.mode;if(A==="Dense"){z=d}else{if(A==="Squish"){z=m}else{z=x;if(this.prefs.show_insertions){z*=2}}}return z},draw_read:function(W,R,N,ab,C,V,K,H,G){W.textAlign="center";var U=this,B=[ab,C],Q=0,X=0,T=0,z=W.canvas.manager.char_width_px;var ag=[];if((R==="Pack"||this.mode==="Auto")&&H!==undefined&&N>z){T=Math.round(N/2)}if(!K){K=[[0,H.length]]}for(var O=0,Z=K.length;O<Z;O++){var L=K[O],D="MIDNSHP=X"[L[0]],P=L[1];if(D==="H"||D==="S"){Q-=P}var I=V+Q,af=Math.floor(Math.max(0,(I-ab)*N)),J=Math.floor(Math.max(0,(I+P-ab)*N));if(af===J){J+=1}switch(D){case"H":break;case"S":case"M":case"=":if(is_overlap([I,I+P],B)){var S=H.slice(X,X+P);if(T>0){W.fillStyle=this.prefs.block_color;W.fillRect(af-T,G+1,J-af,9);W.fillStyle=h;for(var ad=0,A=S.length;ad<A;ad++){if(this.prefs.show_differences&&this.ref_seq){var M=this.ref_seq[I-ab+ad];if(!M||M.toLowerCase()===S[ad].toLowerCase()){continue}}if(I+ad>=ab&&I+ad<=C){var ae=Math.floor(Math.max(0,(I+ad-ab)*N));W.fillText(S[ad],ae,G+9)}}}else{W.fillStyle=this.prefs.block_color;W.fillRect(af,G+4,J-af,f)}}X+=P;Q+=P;break;case"N":W.fillStyle=h;W.fillRect(af-T,G+5,J-af,1);Q+=P;break;case"D":W.fillStyle="red";W.fillRect(af-T,G+4,J-af,3);Q+=P;break;case"P":break;case"I":var aa=af-T;if(is_overlap([I,I+P],B)){var S=H.slice(X,X+P);if(this.prefs.show_insertions){var F=af-(J-af)/2;if((R==="Pack"||this.mode==="Auto")&&H!==undefined&&N>z){W.fillStyle="yellow";W.fillRect(F-T,G-9,J-af,9);ag[ag.length]={type:"triangle",data:[aa,G+4,5]};W.fillStyle=h;switch(seq_tile_overlap){case (OVERLAP_START):S=S.slice(ab-I);break;case (OVERLAP_END):S=S.slice(0,I-C);break;case (CONTAINED_BY):break;case (CONTAINS):S=S.slice(ab-I,I-C);break}for(var ad=0,A=S.length;ad<A;ad++){var ae=Math.floor(Math.max(0,(I+ad-ab)*N));W.fillText(S[ad],ae-(J-af)/2,G)}}else{W.fillStyle="yellow";W.fillRect(F,G+(this.mode!=="Dense"?2:5),J-af,(R!=="Dense"?f:t))}}else{if((R==="Pack"||this.mode==="Auto")&&H!==undefined&&N>z){ag[ag.length]={type:"text",data:[S.length,aa,G+9]}}else{}}}X+=P;break;case"X":X+=P;break}}W.fillStyle="yellow";var ac,E,ah;for(var Y=0;Y<ag.length;Y++){ac=ag[Y];E=ac.type;ah=ac.data;if(E==="text"){W.save();W.font="bold "+W.font;W.fillText(ah[0],ah[1],ah[2]);W.restore()}else{if(E=="triangle"){r(W,ah[0],ah[1],ah[2])}}}},draw_element:function(S,N,F,C,V,A,J,T,Q){var I=F[0],R=F[1],B=F[2],K=F[3],E=Math.floor(Math.max(0,(R-V)*J)),G=Math.ceil(Math.min(Q,Math.max(0,(B-V)*J))),D=(N==="Dense"?0:(0+C))*T,W=this.prefs.block_color,H=this.prefs.label_color,P=0;if((N==="Pack"||this.mode==="Auto")&&J>S.canvas.manager.char_width_px){var P=Math.round(J/2)}S.fillStyle=W;if(F[5] instanceof Array){var O=Math.floor(Math.max(0,(F[4][0]-V)*J)),M=Math.ceil(Math.min(Q,Math.max(0,(F[4][1]-V)*J))),L=Math.floor(Math.max(0,(F[5][0]-V)*J)),z=Math.ceil(Math.min(Q,Math.max(0,(F[5][1]-V)*J)));if(F[4][1]>=V&&F[4][0]<=A&&F[4][2]){this.draw_read(S,N,J,V,A,F[4][0],F[4][2],F[4][3],D)}if(F[5][1]>=V&&F[5][0]<=A&&F[5][2]){this.draw_read(S,N,J,V,A,F[5][0],F[5][2],F[5][3],D)}if(L>M){S.fillStyle=h;q(S,M-P,D+5,L-P,D+5)}}else{S.fillStyle=W;this.draw_read(S,N,J,V,A,R,F[4],F[5],D)}if(N==="Pack"&&R>V){S.fillStyle=this.prefs.label_color;var U=1;if(U===0&&E-S.measureText(K).width<0){S.textAlign="left";S.fillText(K,G+l-P,D+8)}else{S.textAlign="right";S.fillText(K,E-l-P,D+8)}S.fillStyle=W}return[0,0]}});y.Scaler=e;y.SummaryTreePainter=w;y.LinePainter=c;y.LinkedFeaturePainter=s;y.ReadPainter=u;y.VariantPainter=b};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window);
\ No newline at end of file
diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index 3f802895ee7..1a2adff9380 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -608,7 +608,7 @@ extend(Drawable.prototype, {
     request_draw: function() {},
     _draw: function() {},
     to_json: function() {},
-    make_name_popup_menu: function() {},
+    update_track_icons: function() {},
     /**
      * Set drawable name.
      */ 
@@ -750,14 +750,14 @@ var DrawableGroup = function(name, view, container, prefs) {
     is_container(this.content_div, this);
     moveable(this.container_div, this.drag_handle_class, ".group", this);
     
-    this.make_name_popup_menu();
+    this.update_track_icons();
 };
 
 extend(DrawableGroup.prototype, Drawable.prototype, DrawableCollection.prototype, {
     /**
      * Make popup menu for group.
      */
-    make_name_popup_menu: function() {
+    update_track_icons: function() {
         var group = this;
         
         var group_dropdown = {};
@@ -2254,18 +2254,133 @@ var Track = function(name, view, container, prefs, data_url, data_query_wait) {
     this.data_url_extra_params = {}
     this.data_query_wait = (data_query_wait ? data_query_wait : DEFAULT_DATA_QUERY_WAIT);
     this.dataset_check_url = converted_datasets_state_url;
+
+    if (!Track.id_counter) { Track.id_counter = 0; }
+    this.id = Track.id_counter++;
     
     //
     // Create HTML element structure for track.
     //
-    if (!Track.id_counter) { Track.id_counter = 0; }
-    this.container_div = $("<div />").addClass('track').attr("id", "track_" + Track.id_counter++).css("position", "relative");
+    this.container_div = $("<div />").addClass('track').attr("id", "track_" + this.id).css("position", "relative");
+    
+    // Create and initialize track header and icons. Only non-hidden tracks have headers.
     if (!this.hidden) {
         this.header_div = $("<div class='track-header' />").appendTo(this.container_div);
         if (this.view.editor) { this.drag_div = $("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div); }
-        this.name_div = $("<div class='menubutton popup' />").appendTo(this.header_div);
-        this.name_div.text(this.name);
-        this.name_div.attr( "id", this.name.replace(/\s+/g,'-').replace(/[^a-zA-Z0-9\-]/g,'').toLowerCase() );
+        this.name_div = $("<div/>").addClass("track-name").appendTo(this.header_div).text(this.name)
+                        .attr( "id", this.name.replace(/\s+/g,'-').replace(/[^a-zA-Z0-9\-]/g,'').toLowerCase() );
+        this.icons_div = $("<div/>").css("float", "left").appendTo(this.header_div).hide();
+    
+        // Track icons.
+        this.settings_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Edit settings")
+                                      .addClass("icon-button settings-icon").tipsy( {gravity: 's'} )
+                                      .appendTo(this.icons_div);
+        this.filters_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Filters")
+                                     .addClass("icon-button filters-icon").tipsy( {gravity: 's'} )
+                                     .appendTo(this.icons_div).hide();
+        this.tools_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Tools")
+                                   .addClass("icon-button tools-icon").tipsy( {gravity: 's'} )
+                                   .appendTo(this.icons_div).hide();
+        this.remove_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Remove")
+                                    .addClass("icon-button remove-icon").tipsy( {gravity: 's'} )
+                                    .appendTo(this.icons_div);
+        var track = this;
+            
+        // Suppress double clicks in header so that they do not impact viz.
+        this.header_div.dblclick( function(e) { e.stopPropagation(); } );
+        
+        // Clicking on settings icon opens track config.
+        this.settings_icon.click( function() {
+            var cancel_fn = function() { hide_modal(); $(window).unbind("keypress.check_enter_esc"); },
+                ok_fn = function() { 
+                    track.config.update_from_form( $(".dialog-box") );
+                    hide_modal(); 
+                    $(window).unbind("keypress.check_enter_esc"); 
+                },
+                check_enter_esc = function(e) {
+                    if ((e.keyCode || e.which) === 27) { // Escape key
+                        cancel_fn();
+                    } else if ((e.keyCode || e.which) === 13) { // Enter key
+                        ok_fn();
+                    }
+                };
+
+            $(window).bind("keypress.check_enter_esc", check_enter_esc);        
+            show_modal("Configure Track", track.config.build_form(), {
+                "Cancel": cancel_fn,
+                "OK": ok_fn
+            });
+        });
+        
+        // FIXME: old code for overview.
+        /*
+        track_dropdown[(this.is_overview ? "Hide overview" : "Set as overview")] = function() {
+            if (track.is_overview) {
+                track.view.reset_overview();
+            }
+            else {
+                track.view.set_overview(track);
+            }
+        };
+        */
+        
+        this.filters_icon.click( function() {
+            // TODO: update tipsy text.            
+            track.filters_div.toggle();
+            track.filters_manager.reset_filters();
+        });
+        
+        this.tools_icon.click( function() {
+            // TODO: update tipsy text.
+            
+            track.dynamic_tool_div.toggle();
+            
+            // Update track name.
+            if (track.dynamic_tool_div.is(":visible")) {
+                track.set_name(track.name + track.tool_region_and_parameters_str());
+            }
+            else {
+                track.revert_name();
+            }
+            // HACK: name change modifies icon placement, which leaves tooltip incorrectly placed.
+            $(".tipsy").remove();
+        });
+        
+        // Clicking on remove icon removes track.
+        this.remove_icon.click( function() {
+            // Tipsy for remove icon must be deleted when track is deleted.
+            $(".tipsy").remove();
+            track.remove();
+        });
+        
+        // Set up behavior for modes popup.
+        if (track.display_modes !== undefined) {
+            if (track.mode_div === undefined) {
+                track.mode_div = $("<div class='right-float menubutton popup' />").appendTo(track.header_div);
+                var init_mode = (track.config && track.config.values['mode'] ? 
+                                 track.config.values['mode'] : track.display_modes[0]);
+                track.mode = init_mode;
+                track.mode_div.text(init_mode);
+
+                var mode_mapping = {};
+                for (var i = 0, len = track.display_modes.length; i < len; i++) {
+                    var mode = track.display_modes[i];
+                    mode_mapping[mode] = function(mode) {
+                        return function() { track.change_mode(mode); };
+                    }(mode);
+                }
+                make_popupmenu(track.mode_div, mode_mapping);
+            } else {
+                track.mode_div.hide();
+            }
+
+            this.header_div.append( $("<div/>").css("clear", "both") );        
+        
+            // Set up config icon.
+        
+            // Show icons when users is hovering over track.
+            this.container_div.hover( function() { track.icons_div.show(); }, function() { track.icons_div.hide(); } );
+        }
     }
     
     //
@@ -2352,7 +2467,7 @@ extend(Track.prototype, Drawable.prototype, {
             } else if (result['status'] === "data") {
                 if (result['valid_chroms']) {
                     track.valid_chroms = result['valid_chroms'];
-                    track.make_name_popup_menu();
+                    track.update_track_icons();
                 }
                 track.content_div.text(DATA_OK);
                 if (track.view.chrom) {
@@ -2367,6 +2482,8 @@ extend(Track.prototype, Drawable.prototype, {
                 }
             }
         });
+        
+        this.update_track_icons();
     },
     /**
      * Additional initialization required before drawing track for the first time.
@@ -2405,33 +2522,7 @@ var TiledTrack = function(filters_list, tool_dict) {
     if (this.tool) {  
         this.dynamic_tool_div = this.tool.parent_div;
         this.header_div.after(this.dynamic_tool_div);
-    }    
-    
-    //
-    // Create modes control.
-    //
-    if (track.display_modes !== undefined) {
-        if (track.mode_div === undefined) {
-            track.mode_div = $("<div class='right-float menubutton popup' />").appendTo(track.header_div);
-            var init_mode = (track.config && track.config.values['mode'] ? 
-                             track.config.values['mode'] : track.display_modes[0]);
-            track.mode = init_mode;
-            track.mode_div.text(init_mode);
-        
-            var mode_mapping = {};
-            for (var i = 0, len = track.display_modes.length; i < len; i++) {
-                var mode = track.display_modes[i];
-                mode_mapping[mode] = function(mode) {
-                    return function() { track.change_mode(mode); };
-                }(mode);
-            }
-            make_popupmenu(track.mode_div, mode_mapping);
-        } else {
-            track.mode_div.hide();
-        }
     }
-    
-    this.make_name_popup_menu();
 };
 extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
     /**
@@ -2461,87 +2552,31 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
         return track;
      },
     /**
-     * Make popup menu for track name.
+     * Update track's buttons.
      */
-    make_name_popup_menu: function() {
+    update_track_icons: function() {
         var track = this;
         
-        var track_dropdown = {};
-        
         //
-        // Make track overview option.
-        //
-        track_dropdown[(this.is_overview ? "Hide overview" : "Set as overview")] = function() {
-            if (track.is_overview) {
-                track.view.reset_overview();
-            }
-            else {
-                track.view.set_overview(track);
-            }
-        };
-        
-        //
-        // Edit config option.
-        //
-        track_dropdown["Edit configuration"] = function() {
-            var cancel_fn = function() { hide_modal(); $(window).unbind("keypress.check_enter_esc"); },
-                ok_fn = function() { 
-                    track.config.update_from_form( $(".dialog-box") );
-                    hide_modal(); 
-                    $(window).unbind("keypress.check_enter_esc"); 
-                },
-                check_enter_esc = function(e) {
-                    if ((e.keyCode || e.which) === 27) { // Escape key
-                        cancel_fn();
-                    } else if ((e.keyCode || e.which) === 13) { // Enter key
-                        ok_fn();
-                    }
-                };
-
-            $(window).bind("keypress.check_enter_esc", check_enter_esc);        
-            show_modal("Configure Track", track.config.build_form(), {
-                "Cancel": cancel_fn,
-                "OK": ok_fn
-            });
-        };
-
-        //
-        // Show/hide filters option.
+        // Show/hide filter icon.
         //
         if (track.filters_available > 0) {
-            // Show/hide filters menu item.
-            var text = (track.filters_div.is(":visible") ? "Hide filters" : "Show filters");
-            track_dropdown[text] = function() {
-                // Toggle filtering div, reset filters, and remake menu.
-                track.filters_visible = (track.filters_div.is(":visible"));
-                if (track.filters_visible) {
-                    track.filters_manager.reset_filters();
-                }
-                track.filters_div.toggle();
-                track.make_name_popup_menu();
-            };
+            track.filters_icon.show();
+        }
+        else {
+            track.filters_icon.hide();
         }
         
         //
-        // Show/hide tool option.
+        // Show/hide tool icon.
         //
         if (track.tool) {
-            // Show/hide dynamic tool menu item.
-            var text = (track.dynamic_tool_div.is(":visible") ? "Hide tool" : "Show tool");
-            track_dropdown[text] = function() {
-                // Set track name, toggle tool div, and remake menu.
-                if (!track.dynamic_tool_div.is(":visible")) {
-                    track.set_name(track.name + track.tool_region_and_parameters_str());
-                }
-                else {
-                    menu_option_text = "Show dynamic tool";
-                    track.revert_name();
-                }
-                track.dynamic_tool_div.toggle();
-                track.make_name_popup_menu();
-            };
+            track.tools_icon.show();
         }
-                
+        else {
+            track.tools_icon.hide();
+        }
+                        
         //
         // List chrom/contigs with data option.
         //
@@ -2552,22 +2587,13 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
             };
         }
         */
-        
-        //
-        // Remove option.
-        //
-        track_dropdown.Remove = function() {
-            track.remove();
-        };
-        
-        make_popupmenu(track.name_div, track_dropdown);
     },
     /**
      * Set track's overview status.
      */
     set_is_overview: function(is_overview) {
         this.is_overview = is_overview;
-        this.make_name_popup_menu();
+        this.update_track_icons();
     },
     /**
      * Returns a jQuery Deferred object that resolves to a Tile with track's overview.
@@ -3203,7 +3229,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
                 if (!track.filters_available) {
                     track.filters_div.hide();
                 }
-                track.make_name_popup_menu();
+                track.update_track_icons();
             }
         }
     },
@@ -3495,7 +3521,7 @@ var ReadTrack = function (name, view, container, hda_ldda, dataset_id, prefs, fi
     this.prefs = this.config.values;
     
     this.painter = painters.ReadPainter;
-    this.make_name_popup_menu();
+    this.update_track_icons();
 };
 extend(ReadTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype);
 
diff --git a/templates/tracks/browser.mako b/templates/tracks/browser.mako
index e14f723cf84..565aa4743d2 100644
--- a/templates/tracks/browser.mako
+++ b/templates/tracks/browser.mako
@@ -42,10 +42,9 @@ ${parent.javascripts()}
   <script type='text/javascript' src="${h.url_for('/static/scripts/excanvas.js')}"></script>
 <![endif]-->
 
-${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.event.drag", "jquery.mousewheel", "jquery.autocomplete", "trackster", "trackster_ui", "jquery.ui.sortable.slider", "jquery.scrollTo", "farbtastic" )}
+${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.event.drag", "jquery.mousewheel", "jquery.autocomplete", "trackster", "trackster_ui", "jquery.ui.sortable.slider", "jquery.scrollTo", "farbtastic", "jquery.tipsy" )}
 
 <script type="text/javascript">
-
     //
     // Place URLs here so that url_for can be used to generate them.
     // 
@@ -113,6 +112,9 @@ ${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.e
     };
     
     $(function() {
+        // Manual tipsy config because default gravity is S and cannot be changed.
+        $(".menu-button").tipsy( {gravity: 'n'} );
+        
         // Hide bookmarks by default right now.
         parent.force_right_panel("hide"); 
         
@@ -172,59 +174,61 @@ ${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.e
             %endif
             
             //
-            // Make actions menu.
+            // Initialize icons.
             //
-            $("#viz-actions-button").css( "position", "relative" );
-            make_popupmenu( $("#viz-actions-button"), {
-                "Add Tracks": add_tracks,
-                "Add Group": function() {
-                    var group = new DrawableGroup("New Group", view, view);
-                    view.add_drawable(group);
-                },
-                "Save": function() {
-                    // Show saving dialog box
-                    show_modal("Saving...", "<img src='${h.url_for('/static/images/yui/rel_interstitial_loading.gif')}'/>");
-                                        
-                    // Save bookmarks.
-                    var bookmarks = [];
-                    $(".bookmark").each(function() { 
-                        bookmarks[bookmarks.length] = {
-                            position: $(this).children(".position").text(),
-                            annotation: $(this).children(".annotation").text()
-                        };
-                    });
-
-                    var overview_track_name = (view.overview_track ? view.overview_track.name : null);
-                    var payload = { 
-                        'view': view.to_json(), 
-                        'viewport': { 'chrom': view.chrom, 'start': view.low , 'end': view.high, 'overview': overview_track_name },
-                        'bookmarks': bookmarks
-                    };
-
-                    $.ajax({
-                        url: "${h.url_for( action='save' )}",
-                        type: "POST",
-                        data: {
-                            'vis_id': view.vis_id,
-                            'vis_title': view.title,
-                            'dbkey': view.dbkey,
-                            'payload': JSON.stringify(payload)
-                        },
-                        success: function(vis_id) {
-                            view.vis_id = vis_id;
-                            view.has_changes = false;
-                            hide_modal();
-                        },
-                        error: function() { alert("Could not save visualization"); }
-                    });
-                },
-                "Bookmarks": function() {
-                    // HACK -- use style to determine if panel is hidden and hide/show accordingly.
-                    parent.force_right_panel(($("div#right").css("right") == "0px" ? "hide" : "show")); 
-                },
-                "Close": function() { window.location = "${h.url_for( controller='visualization', action='list' )}"; }
+            $("#add-tracks-icon").click( function() { add_tracks(); } );
+            
+            $("#add-group-icon").click( function() {
+                view.add_drawable( new DrawableGroup("New Group", view, view) );                
             });
             
+            $("#save-icon").click( function() {                
+                // Show saving dialog box
+                show_modal("Saving...", "<img src='${h.url_for('/static/images/yui/rel_interstitial_loading.gif')}'/>");
+                                    
+                // Save bookmarks.
+                var bookmarks = [];
+                $(".bookmark").each(function() { 
+                    bookmarks[bookmarks.length] = {
+                        position: $(this).children(".position").text(),
+                        annotation: $(this).children(".annotation").text()
+                    };
+                });
+
+                var overview_track_name = (view.overview_track ? view.overview_track.name : null);
+                var payload = { 
+                    'view': view.to_json(), 
+                    'viewport': { 'chrom': view.chrom, 'start': view.low , 'end': view.high, 'overview': overview_track_name },
+                    'bookmarks': bookmarks
+                };
+
+                $.ajax({
+                    url: "${h.url_for( action='save' )}",
+                    type: "POST",
+                    data: {
+                        'vis_id': view.vis_id,
+                        'vis_title': view.title,
+                        'dbkey': view.dbkey,
+                        'payload': JSON.stringify(payload)
+                    },
+                    success: function(vis_id) {
+                        view.vis_id = vis_id;
+                        view.has_changes = false;
+                        hide_modal();
+                    },
+                    error: function() { alert("Could not save visualization"); }
+                });
+            });
+            
+            $("#bookmarks-icon").click( function() {
+                // HACK -- use style to determine if panel is hidden and hide/show accordingly.
+                parent.force_right_panel(($("div#right").css("right") == "0px" ? "hide" : "show"));                 
+            });
+
+            $("#close-icon").click( function() {
+                window.location = "${h.url_for( controller='visualization', action='list' )}";
+            });  
+        
             $("#add-bookmark-button").click(function() {
                 // Add new bookmark.
                 var position = view.chrom + ":" + view.low + "-" + view.high,
@@ -245,9 +249,14 @@ ${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.e
     <div class="unified-panel-header-inner">
         <div style="float:left;" id="title"></div>
         <div style="float: right">
-            <a id="viz-actions-button" class='panel-header-button popup' href="javascript:void(0)" target="galaxy_main">${_('Actions')}</a>
+            <a id="add-tracks-icon" class='icon-button menu-button' href="javascript:void(0);" title="Add tracks"></a>
+            <a id="add-group-icon" class='icon-button menu-button' href="javascript:void(0);" title="Add new group"></a>
+            <a id="bookmarks-icon" class='icon-button menu-button' href="javascript:void(0);" title="Bookmarks"></a>
+            <a id="save-icon" class='icon-button menu-button' href="javascript:void(0);" title="Save"></a>
+            <a id="close-icon" class='icon-button menu-button' href="javascript:void(0);" title="Close"></a>
         </div>
     </div>
+    <div style="clear: both"></div>
 </div>
 <div id="browser-container" class="unified-panel-body"></div>
 

From 7eb7390360962ccf8d0cb8f8a1ba97e362c620a4 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Sat, 22 Oct 2011 21:22:43 -0400
Subject: [PATCH 081/362] Fix bug in saving trackster bookmarks.

---
 lib/galaxy/web/controllers/tracks.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/web/controllers/tracks.py b/lib/galaxy/web/controllers/tracks.py
index 2962554c02b..d9b464eede6 100644
--- a/lib/galaxy/web/controllers/tracks.py
+++ b/lib/galaxy/web/controllers/tracks.py
@@ -646,7 +646,7 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
 
         # TODO: unpack and validate bookmarks:
         def unpack_bookmarks( bookmarks_json ):
-            return 
+            return bookmarks_json
         
         # Unpack and validate view content.
         view_content = unpack_collection( decoded_payload[ 'view' ] )

From b57d60caf2e8772e6320dca7450ee0e7b90c642f Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Sun, 23 Oct 2011 11:13:40 -0400
Subject: [PATCH 082/362] Trackster: fix bug in drawing reference track.

---
 static/scripts/trackster.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index 1a2adff9380..1cfe3963793 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -463,7 +463,7 @@ extend(DataManager.prototype, Cache.prototype, {
         // data is ready, it then replaces itself with the actual data
         entry = this.load_data(low, high, mode, resolution, extra_params);
         this.set_data(low, high, mode, entry);
-        return entry
+        return entry;
     },
     /** "Deep" data request; used as a parameter for DataManager.get_more_data() */
     DEEP_DATA_REQ: "deep",
@@ -2935,7 +2935,7 @@ extend(ReferenceTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
             tile_length = DENSITY * resolution;
         
         if (w_scale > this.view.canvas_manager.char_width_px) {
-            if (seq === null) {
+            if (seq.data === null) {
                 track.content_div.css("height", "0px");
                 return;
             }

From 7800c6fe1cbdb494a1de22dce6dbee070dfd442e Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Sun, 23 Oct 2011 16:32:04 -0400
Subject: [PATCH 083/362] Trackster: make overview its own track, add icons for
 showing/hiding overview, and make track header optional.

---
 .../images/fugue/application-dock-270-bw.png  | Bin 0 -> 1288 bytes
 static/images/fugue/application-dock-270.png  | Bin 0 -> 516 bytes
 static/june_2007_style/blue/trackster.css     |   6 +-
 static/june_2007_style/trackster.css.tmpl     |  11 +-
 static/scripts/packed/trackster.js            |   2 +-
 static/scripts/packed/trackster_ui.js         |   2 +-
 static/scripts/trackster.js                   | 198 ++++++++----------
 static/scripts/trackster_ui.js                |   2 +-
 templates/tracks/browser.mako                 |   3 +-
 9 files changed, 100 insertions(+), 124 deletions(-)
 create mode 100644 static/images/fugue/application-dock-270-bw.png
 create mode 100755 static/images/fugue/application-dock-270.png

diff --git a/static/images/fugue/application-dock-270-bw.png b/static/images/fugue/application-dock-270-bw.png
new file mode 100644
index 0000000000000000000000000000000000000000..1d0ad1bb6ce468022d7d7cf0314144905cccf5a9
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diff --git a/static/june_2007_style/blue/trackster.css b/static/june_2007_style/blue/trackster.css
index f9a490c000a..e59b26677a9 100644
--- a/static/june_2007_style/blue/trackster.css
+++ b/static/june_2007_style/blue/trackster.css
@@ -7,14 +7,16 @@
 #zoom-in,#zoom-out{display:inline-block;height:16px;width:16px;margin-bottom:-3px;cursor:pointer;}
 #zoom-out{background:transparent url(../images/fugue/magnifier-zoom-out.png) center center no-repeat;}
 #zoom-in{margin-left:10px;background:transparent url(../images/fugue/magnifier-zoom.png) center center no-repeat;}
+.overview-icon{background:transparent url(../images/fugue/application-dock-270-bw.png) no-repeat;}
+.overview-icon:hover{background:transparent url(../images/fugue/application-dock-270.png) no-repeat;}
 .settings-icon{background:transparent url(../images/fugue/gear-bw.png) no-repeat;}
 .settings-icon:hover{background:transparent url(../images/fugue/gear.png) no-repeat;}
 .tools-icon{background:transparent url(../images/fugue/toolbox-bw.png) no-repeat;}
 .tools-icon:hover{background:transparent url(../images/fugue/toolbox.png) no-repeat;}
 .filters-icon{background:transparent url(../images/fugue/ui-slider-050-bw.png) no-repeat;}
 .filters-icon:hover{background:transparent url(../images/fugue/ui-slider-050.png) no-repeat;}
-.remove-icon{background:transparent url(../images/fugue/cross-small-bw.png) no-repeat;}
-.remove-icon:hover{background:transparent url(../images/fugue/cross-circle.png) no-repeat;}
+.remove-icon,.overview-close{background:transparent url(../images/fugue/cross-small-bw.png) no-repeat;}
+.remove-icon:hover,.overview-close:hover{background:transparent url(../images/fugue/cross-circle.png) no-repeat;}
 #close-icon{background:transparent url(../images/fugue/cross-circle-bw.png) no-repeat;margin-right:0px;}
 #close-icon:hover{background:transparent url(../images/fugue/cross-circle.png) no-repeat;}
 #add-tracks-icon{background:transparent url(../images/fugue/plus-button-bw.png) no-repeat;}
diff --git a/static/june_2007_style/trackster.css.tmpl b/static/june_2007_style/trackster.css.tmpl
index 8fbfac3482c..16e92729a7c 100644
--- a/static/june_2007_style/trackster.css.tmpl
+++ b/static/june_2007_style/trackster.css.tmpl
@@ -303,6 +303,13 @@ input {
 .settings-icon:hover {
     background: transparent url(../images/fugue/gear.png) no-repeat;
 }
+.overview-icon {
+    background:transparent url(../images/fugue/application-dock-270-bw.png) no-repeat;
+}
+.overview-icon:hover {
+    background:transparent url(../images/fugue/application-dock-270.png) no-repeat;
+}
+
 .tools-icon {
     background: transparent url(../images/fugue/toolbox-bw.png) no-repeat;
 }
@@ -315,10 +322,10 @@ input {
 .filters-icon:hover {
     background: transparent url(../images/fugue/ui-slider-050.png) no-repeat;
 }
-.remove-icon {
+.remove-icon, .overview-close {
     background: transparent url(../images/fugue/cross-small-bw.png) no-repeat;
 }
-.remove-icon:hover {
+.remove-icon:hover, .overview-close:hover {
     background: transparent url(../images/fugue/cross-circle.png) no-repeat;
 }
 #close-icon {
diff --git a/static/scripts/packed/trackster.js b/static/scripts/packed/trackster.js
index 418440169db..42d148ff92a 100644
--- a/static/scripts/packed/trackster.js
+++ b/static/scripts/packed/trackster.js
@@ -1 +1 @@
-var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var trackster_module=function(f,Z){var q=f("class").extend,t=f("slotting"),N=f("painters");var ag=function(ah,ai){this.document=ah;this.default_font=ai!==undefined?ai:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};q(ag.prototype,{load_pattern:function(ah,al){var ai=this.patterns,aj=this.dummy_context,ak=new Image();ak.src=image_path+al;ak.onload=function(){ai[ah]=aj.createPattern(ak,"repeat")}},get_pattern:function(ah){return this.patterns[ah]},new_canvas:function(){var ah=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ah)}ah.manager=this;return ah}});var o={};var m=function(ah,ai){o[ah.attr("id")]=ai};var n=function(ah,aj,al,ak){al=".group";var ai={};o[ah.attr("id")]=ak;ah.bind("drag",{handle:"."+aj,relative:true},function(au,av){var at=$(this);var ay=$(this).parent(),ap=ay.children(),ar=o[$(this).attr("id")],ao,an,aw,am,aq;an=$(this).parents(al);if(an.length!==0){aw=an.position().top;am=aw+an.outerHeight();if(av.offsetY<aw){$(this).insertBefore(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable_before(ar,ax);return}else{if(av.offsetY>am){$(this).insertAfter(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable(ar);return}}}an=null;for(aq=0;aq<ap.length;aq++){ao=$(ap.get(aq));aw=ao.position().top;am=aw+ao.outerHeight();if(ao.is(al)&&this!==ao.get(0)&&av.offsetY>=aw&&av.offsetY<=am){if(av.offsetY-aw<am-av.offsetY){ao.find(".content-div").prepend(this)}else{ao.find(".content-div").append(this)}if(ar.container){ar.container.remove_drawable(ar)}o[ao.attr("id")].add_drawable(ar);return}}for(aq=0;aq<ap.length;aq++){if(av.offsetY<$(ap.get(aq)).position().top){break}}if(aq===ap.length){if(this!==ap.get(aq-1)){ay.append(this);o[ay.attr("id")].move_drawable(ar,aq)}}else{if(this!==ap.get(aq)){$(this).insertBefore(ap.get(aq));o[ay.attr("id")].move_drawable(ar,(av.deltaY>0?aq-1:aq))}}}).bind("dragstart",function(){ai["border-top"]=ah.css("border-top");ai["border-bottom"]=ah.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ai)})};Z.moveable=n;var af=16,I=9,F=20,U=I+2,A=100,K=12000,S=200,D=5,w=10,M=5000,x=100,p="There was an error in indexing this dataset. ",L="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",u="Currently indexing... please wait",y="Tool cannot be rerun: ",a="Loading data...",aa="Ready for display",d=10,v=5,C=5;function ab(ai,ah){if(!ah){ah=0}var aj=Math.pow(10,ah);return Math.round(ai*aj)/aj}var c=function(ah){this.num_elements=ah;this.clear()};q(c.prototype,{get:function(ai){var ah=this.key_ary.indexOf(ai);if(ah!==-1){if(this.obj_cache[ai].stale){this.key_ary.splice(ah,1);delete this.obj_cache[ai]}else{this.move_key_to_end(ai,ah)}}return this.obj_cache[ai]},set:function(ai,aj){if(!this.obj_cache[ai]){if(this.key_ary.length>=this.num_elements){var ah=this.key_ary.shift();delete this.obj_cache[ah]}this.key_ary.push(ai)}this.obj_cache[ai]=aj;return aj},move_key_to_end:function(ai,ah){this.key_ary.splice(ah,1);this.key_ary.push(ai)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var T=function(ai,ah,aj){c.call(this,ai);this.track=ah;this.subset=(aj!==undefined?aj:true)};q(T.prototype,c.prototype,{load_data:function(aq,al,ao,ai,an){var ap=this.track.view.chrom,ak={chrom:ap,low:aq,high:al,mode:ao,resolution:ai,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ak,an);if(this.track.filters_manager){var ar=[];var ah=this.track.filters_manager.filters;for(var am=0;am<ah.length;am++){ar[ar.length]=ah[am].name}ak.filter_cols=JSON.stringify(ar)}var aj=this;return $.getJSON(this.track.data_url,ak,function(at){aj.set_data(aq,al,ao,at)})},get_data:function(ah,al,am,ai,ak){var aj=this.get_data_from_cache(ah,al,am);if(aj){return aj}aj=this.load_data(ah,al,am,ai,ak);this.set_data(ah,al,am,aj);return aj},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ap,ak,ao,aj,an,al){var aq=this.get_data_from_cache(ap,ak,ao);if(!aq){console.log("ERROR: no current data for: ",this.track,ap,ak,ao,aj,an);return}aq.stale=true;var ai=ap;if(al===this.DEEP_DATA_REQ){$.extend(an,{start_val:aq.data.length+1})}else{if(al===this.BROAD_DATA_REQ){ai=(aq.max_high?aq.max_high:aq.data[aq.data.length-1][2])+1}}var ah=this,am=this.load_data(ai,ak,ao,aj,an);new_data_available=$.Deferred();this.set_data(ap,ak,ao,new_data_available);$.when(am).then(function(ar){if(ar.data){ar.data=aq.data.concat(ar.data);if(ar.max_low){ar.max_low=aq.max_low}if(ar.message){ar.message=ar.message.replace(/[0-9]+/,ar.data.length)}}ah.set_data(ap,ak,ao,ar);new_data_available.resolve(ar)});return new_data_available},get_data_from_cache:function(ah,ai,aj){return this.get(this.gen_key(ah,ai,aj))},set_data:function(ai,aj,ak,ah){return this.set(this.gen_key(ai,aj,ak),ah)},gen_key:function(ah,aj,ak){var ai=ah+"_"+aj+"_"+ak;return ai},split_key:function(ah){return ah.split("_")}});var J=function(ai,ah,aj){T.call(this,ai,ah,aj)};q(J.prototype,T.prototype,c.prototype,{load_data:function(ah,ak,al,ai,aj){if(ai>1){return{data:null}}return T.prototype.load_data.call(this,ah,ak,al,ai,aj)}});var r=function(ak,ai,ah,aj,al){this.name=ak;this.view=ai;this.container=ah;this.drag_handle_class=al;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak}],saved_values:aj,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values};q(r.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},update_track_icons:function(){},set_name:function(ah){this.old_name=this.name;this.name=ah;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var z=function(al,ak,ai,ah,aj,am){r.call(this,ak,ai,ah,aj,am);this.obj_type=al;this.drawables=[]};q(z.prototype,r.prototype,{init:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah].init()}},_draw:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah]._draw()}},to_json:function(){var ai=[];for(var ah=0;ah<this.drawables.length;ah++){ai.push(this.drawables[ah].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ai}},add_drawable:function(ah){this.drawables.push(ah);ah.container=this},add_drawable_before:function(aj,ah){var ai=this.drawables.indexOf(ah);if(ai!=-1){this.drawables.splice(ai,0,aj);return true}return false},remove_drawable:function(ai){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);ai.container=null;return true}return false},move_drawable:function(ai,aj){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);this.drawables.splice(aj,0,ai);return true}return false}});var R=function(ak,ai,ah,aj){z.call(this,"DrawableGroup",ak,ai,ah,aj,"group-handle");if(!R.id_counter){R.id_counter=0}var al=R.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+al).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+al+"_content_div").appendTo(this.container_div);m(this.container_div,this);m(this.content_div,this);n(this.container_div,this.drag_handle_class,".group",this);this.update_track_icons()};q(R.prototype,r.prototype,z.prototype,{update_track_icons:function(){var ai=this;var ah={};ah["Edit configuration"]=function(){var al=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aj=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(am){if((am.keyCode||am.which)===27){al()}else{if((am.keyCode||am.which)===13){aj()}}};$(window).bind("keypress.check_enter_esc",ak);show_modal("Configure Group",ai.config.build_form(),{Cancel:al,OK:aj})};ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)}});var ae=function(ah,ak,aj,ai){z.call(this,"View");this.container=ah;this.chrom=null;this.vis_id=aj;this.dbkey=ai;this.title=ak;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ag(ah.get(0).ownerDocument);this.reset()};q(ae.prototype,z.prototype,{init:function(){var aj=this.container,ah=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aj);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;m(this.viewport_container,ah);this.intro_div=$("<div/>").addClass("intro");var ak=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ai=function(al){if(al.type==="focusout"||(al.keyCode||al.which)===13||(al.keyCode||al.which)===27){if((al.keyCode||al.which)!==27){ah.go_to($(this).val())}$(this).hide();$(this).val("");ah.location_span.show();ah.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ai).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ah.location_span.hide();ah.chrom_select.hide();ah.nav_input.val(ah.chrom+":"+ah.low+"-"+ah.high);ah.nav_input.css("display","inline-block");ah.nav_input.select();ah.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ah.zoom_out();ah.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.browser_content_div.click(function(al){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("<div />").css({height:ah.browser_content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,{content_div:this.top_labeltrack}));this.add_label_track(new ad(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new B(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(am,ai,ao){if(!am||am==="None"){return}var aj=this;if(am==="previous"){aj.load_chroms({low:this.chrom_start_index-x});return}if(am==="next"){aj.load_chroms({low:this.chrom_start_index+x});return}var an=$.grep(aj.chrom_data,function(ap,aq){return ap.chrom===am})[0];if(an===undefined){aj.load_chroms({chrom:am},function(){aj.change_chrom(am,ai,ao)});return}else{if(am!==aj.chrom){aj.chrom=am;aj.chrom_select.val(aj.chrom);aj.max_high=an.len-1;aj.reset();aj.request_redraw(true);for(var al=0,ah=aj.drawables.length;al<ah;al++){var ak=aj.drawables[al];if(ak.init){ak.init()}}}if(ai!==undefined&&ao!==undefined){aj.low=Math.max(ai,0);aj.high=Math.min(ao,aj.max_high)}aj.reset_overview();aj.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){z.prototype.add_drawable.call(this,ah);ah.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;ah.init();this.label_tracks.push(ah)},remove_drawable:function(aj,ai){z.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.drawables),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(D,Math.ceil(Math.log((this.high-this.low)/S)/Math.log(D)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){$.when(ah.get_overview_tile()).then(function(ai){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ai.canvas);view.overview_highlight.show().height(ai.canvas.height());view.overview_viewport.height(ai.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ah;ah.set_is_overview(true)});view.has_changes=true},reset_overview:function(){this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new P(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},al=this.track,aj=ai.tool_id+al.tool_region_and_parameters_str(ai.chrom,ai.low,ai.high),ah,am;if(al.container===view){var ak=new R(this.name,this.track.view,this.track.container);al.container.add_drawable(ak);al.container.remove_drawable(al);ak.add_drawable(al);al.container_div.appendTo(ak.content_div);ah=ak}else{ah=al.container}if(al instanceof e){am=new W(aj,view,ah,"hda");am.change_mode(al.mode);ah.add_drawable(am)}am.content_div.text("Starting job.");this.run(ai,am,function(an){am.dataset_id=an.dataset_id;am.content_div.text("Running job.");am.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(L)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(y+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var P=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){P.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var X=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};q(X.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=ah[this.index];return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(at,aA){this.track=at;this.filters=[];for(var av=0;av<aA.length;av++){var aw=aA[av],aB=aw.name,ah=aw.type,aj=aw.index,az=aw.tool_id,ay=aw.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[av]=new X(aB,aj,az,ay)}else{console.log("ERROR: unsupported filter: ",aB,ah)}}var ak=function(aC,aD,aE){aC.click(function(){var aF=aD.text();max=parseFloat(aE.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aE.slider("option","values")){input_size=2*input_size+1;multi_value=true}aD.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aF).appendTo(aD).focus().select().click(function(aG){aG.stopPropagation()}).blur(function(){$(this).remove();aD.text(aF)}).keyup(function(aK){if(aK.keyCode===27){$(this).trigger("blur")}else{if(aK.keyCode===13){var aI=aE.slider("option","min"),aG=aE.slider("option","max"),aJ=function(aL){return(isNaN(aL)||aL>aG||aL<aI)},aH=$(this).val();if(!multi_value){aH=parseFloat(aH);if(aJ(aH)){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}else{aH=aH.split("-");aH=[parseFloat(aH[0]),parseFloat(aH[1])];if(aJ(aH[0])||aJ(aH[1])){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}aE.slider((multi_value?"values":"value"),aH)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aC){aC.stopPropagation()}).click(function(aC){aC.stopPropagation()}).bind("dblclick",function(aC){aC.stopPropagation()}).bind("keydown",function(aC){aC.stopPropagation()});var ax=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aF,aH){aH.container=$("<div/>").addClass("filter-row slider-row").appendTo(ax);var aG=$("<div/>").addClass("elt-label").appendTo(aH.container);var aE=$("<span/>").addClass("slider-name").text(aH.name+"  ").appendTo(aG);var aD=$("<span/>");var aJ=$("<span/>").addClass("slider-value").appendTo(aG).append("[").append(aD).append("]");var aC=$("<div/>").addClass("slider").appendTo(aH.container);aH.control_element=$("<div/>").attr("id",aH.name+"-filter-control").appendTo(aC);var aI=[0,0];aH.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aL,aM){var aK=aM.values;aD.text(aK[0]+"-"+aK[1]);aH.low=aK[0];aH.high=aK[1];ap.track.request_draw(true,true)},change:function(aK,aL){aH.control_element.slider("option","slide").call(aH.control_element,aK,aL)}});aH.slider=aH.control_element;aH.slider_label=aD;ak(aJ,aD,aH.control_element);$("<div style='clear: both;'/>").appendTo(aH.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(ax);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var ai=this;ao.click(function(){ai.run_on_dataset()})}var ar=$("<div/>").addClass("display-controls").appendTo(this.parent_div),au,an,aq,al={Transparency:function(aC){ap.alpha_filter=aC},Height:function(aC){ap.height_filter=aC}};$.each(al,function(aE,aD){au=$("<div/>").addClass("filter-row").appendTo(ar),an=$("<span/>").addClass("elt-label").text(aE+":").appendTo(au),aq=$("<select/>").attr("name",aE+"_dropdown").css("float","right").appendTo(au);$("<option/>").attr("value",-1).text("== None ==").appendTo(aq);for(var aC=0;aC<ap.filters.length;aC++){$("<option/>").attr("value",aC).text(ap.filters[aC].name).appendTo(aq)}aq.change(function(){$(this).children("option:selected").each(function(){var aF=parseInt($(this).val());al[aE]((aF>=0?ap.filters[aF]:null));ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(au)});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var E=function(ah,ai){N.Scaler.call(this,ai);this.filter=ah};E.prototype.gen_val=function(ah){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var H=function(ah){this.track=ah.track;this.params=ah.params;this.values={};this.restore_values((ah.saved_values?ah.saved_values:{}));this.onchange=ah.onchange};q(H.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(ah,ak,aj,ai,al){this.track=ah;this.index=ak;this.low=ak*S*aj;this.high=(ak+1)*S*aj;this.resolution=aj;this.canvas=$("<div class='track-tile'/>").append(ai);this.data=al;this.stale=false};b.prototype.predisplay_actions=function(){};var l=function(ah,ak,aj,ai,al,am){b.call(this,ah,ak,aj,ai,al);this.max_val=am};q(l.prototype,b.prototype);var Q=function(ah,al,ak,aj,an,ao,am,ai){b.call(this,ah,al,ak,aj,an);this.mode=ao;this.message=am;this.feature_mapper=ai};q(Q.prototype,b.prototype);Q.prototype.predisplay_actions=function(){var ai=this,ah={};if(ai.mode!=="Pack"){return}$(this.canvas).mousemove(function(au){var ao=$(this).offset(),at=au.pageX-ao.left,ar=au.pageY-ao.top,ay=ai.feature_mapper.get_feature_data(at,ar),ap=(ay?ay[0]:null);$(this).siblings(".feature-popup").each(function(){if(!ap||$(this).attr("id")!==ap.toString()){$(this).remove()}});if(ay){var ak=ah[ap];if(!ak){var ap=ay[0],av={name:ay[3],start:ay[1],end:ay[2],strand:ay[4]},an=ai.track.filters_manager.filters,am;for(var aq=0;aq<an.length;aq++){am=an[aq];av[am.name]=ay[am.index]}var ak=$("<div/>").attr("id",ap).addClass("feature-popup"),ax,aw,az=$("<table/>").appendTo(ak),aA;for(ax in av){aw=av[ax];aA=$("<tr/>").appendTo(az);$("<th/>").appendTo(aA).text(ax);$("<td/>").attr("align","left").appendTo(aA).text(typeof(aw)=="number"?ab(aw,2):aw)}ah[ap]=ak}ak.appendTo($(ai.canvas).parent());var al=at+parseInt(ai.canvas.css("left"))+7,aj=ar+parseInt(ai.canvas.css("top"))+7;ak.css("left",al+"px").css("top",aj+"px")}else{if(!au.isPropagationStopped()){au.stopPropagation();$(this).siblings().each(function(){$(this).trigger(au)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var j=function(ak,ar,al,at,aj,ai){r.call(this,ak,ar,al,{},"draghandle");this.data_url=(aj?aj:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ai?ai:M);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.id=j.id_counter++;this.container_div=$("<div />").addClass("track").attr("id","track_"+this.id).css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div/>").addClass("track-name").appendTo(this.header_div).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());this.icons_div=$("<div/>").css("float","left").appendTo(this.header_div).hide();this.settings_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Edit settings").addClass("icon-button settings-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.filters_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Filters").addClass("icon-button filters-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.tools_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Tools").addClass("icon-button tools-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.remove_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Remove").addClass("icon-button remove-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);var am=this;this.header_div.dblclick(function(au){au.stopPropagation()});this.settings_icon.click(function(){var aw=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},au=function(){am.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},av=function(ax){if((ax.keyCode||ax.which)===27){aw()}else{if((ax.keyCode||ax.which)===13){au()}}};$(window).bind("keypress.check_enter_esc",av);show_modal("Configure Track",am.config.build_form(),{Cancel:aw,OK:au})});this.filters_icon.click(function(){am.filters_div.toggle();am.filters_manager.reset_filters()});this.tools_icon.click(function(){am.dynamic_tool_div.toggle();if(am.dynamic_tool_div.is(":visible")){am.set_name(am.name+am.tool_region_and_parameters_str())}else{am.revert_name()}$(".tipsy").remove()});this.remove_icon.click(function(){$(".tipsy").remove();am.remove()});if(am.display_modes!==undefined){if(am.mode_div===undefined){am.mode_div=$("<div class='right-float menubutton popup' />").appendTo(am.header_div);var an=(am.config&&am.config.values.mode?am.config.values.mode:am.display_modes[0]);am.mode=an;am.mode_div.text(an);var ah={};for(var ao=0,aq=am.display_modes.length;ao<aq;ao++){var ap=am.display_modes[ao];ah[ap]=function(au){return function(){am.change_mode(au)}}(ap)}make_popupmenu(am.mode_div,ah)}else{am.mode_div.hide()}this.header_div.append($("<div/>").css("clear","both"));this.container_div.hover(function(){am.icons_div.show()},function(){am.icons_div.hide()})}}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Y){return"ReadTrack"}else{if(this instanceof W){return"ToolDataFeatureTrack"}else{if(this instanceof V){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(L)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(G)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.update_track_icons()}ah.content_div.text(aa);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}});this.update_track_icons()},predraw_init:function(){},});var O=function(ak,aj){var ai=this,ah=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=new ac(this,(ak!==undefined?ak:{}));this.filters_available=false;this.filters_visible=false;this.tool=(aj!==undefined&&obj_length(aj)>0?new s(this,aj):undefined);this.is_overview=false;if(ai.hidden){return}if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}};q(O.prototype,r.prototype,j.prototype,{to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw();return ah},update_track_icons:function(){var ah=this;if(ah.filters_available>0){ah.filters_icon.show()}else{ah.filters_icon.hide()}if(ah.tool){ah.tools_icon.show()}else{ah.tools_icon.hide()}},set_is_overview:function(ah){this.is_overview=ah;this.update_track_icons()},get_overview_tile:function(){var ah=this;view=ah.view,resolution=Math.pow(D,Math.ceil(Math.log((view.max_high-view.max_low)/S)/Math.log(D))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ah.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ah.data_url_extra_params)).then(function(ai){var ak=ah._gen_tile_cache_key(view_width,w_scale,0),am=ah.tile_cache.get(ak);if(!am){am=ah.draw_tile(ai,"Auto",resolution,0,w_scale);ah.tile_cache.set(ak,am)}var ap=$(am.canvas.find("canvas")),al=ap.clone(),ao=ap.get(0).getContext("2d"),aj=al.get(0).getContext("2d"),an=ao.getImageData(0,0,ao.canvas.width,ao.canvas.height);aj.putImageData(an,-ah.left_offset,(am.data.dataset_type==="summary_tree"?U:0));new_tile=new b(ah,-1,resolution,al);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof B)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/S);var ap=true;var at=[];var ah=0;while((ai*S*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",F)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*S*an,ax=ap+S*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);if(aq!==undefined){al.tile_cache.set(at,aq);al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw()});return null},show_tile:function(ao,aq,ar){var aj=this,ai=ao.canvas,an=ai;if(ao.message){var at=$("<div/>"),ap=$("<div/>").addClass("tile-message").text(ao.message).css({height:F-1,width:ao.canvas.width}).appendTo(at),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ap),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ap);at.append(ai);an=at;al.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()});ah.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()})}ao.predisplay_actions();var am=this.view.high-this.view.low,ak=(ao.low-this.view.low)*ar;if(this.left_offset){ak-=this.left_offset}an.css({position:"absolute",top:0,left:ak,height:""});aq.append(an);aj.max_height=Math.max(aj.max_height,an.height());aj.content_div.css("height",aj.max_height+"px");aq.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*S*ai,al=S*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ai,ah){this.hidden=true;j.call(this,"label",ai,ah,{});this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{init:function(){this.enabled=true},_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var B=function(ah){this.hidden=true;j.call(this,"reference",ah,{content_div:ah.top_labeltrack},{});O.call(this);ah.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ah.dbkey};this.data_manager=new J(C,this,false);this.tile_cache=new c(v)};q(B.prototype,r.prototype,O.prototype,{init:function(){this.enabled=true},draw_tile:function(ar,an,am,ai,at){var al=this,aj=S*am;if(at>this.view.canvas_manager.char_width_px){if(ar===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(al,ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(am,ak,aj,an,ah,al){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,am,ak,aj,al);O.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=an;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new T(C,this);this.tile_cache=new c(v);this.left_offset=0;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:am},{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:al,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.dataset_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.dataset_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};q(k.prototype,r.prototype,O.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this;ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(ai){ah.container_div.addClass("line-track");var ak=ai.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=ak.min;ah.prefs.max_value=ak.max;$("#track_"+ah.dataset_id+"_minval").val(ah.prefs.min_value);$("#track_"+ah.dataset_id+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=ak.total_frequency;ah.container_div.find(".yaxislabel").remove();var al=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_minval").text(ab(ah.prefs.min_value,3));var aj=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_maxval").text(ab(ah.prefs.max_value,3));aj.css({position:"absolute",top:"24px",left:"10px"});aj.prependTo(ah.container_div);al.css({position:"absolute",bottom:"2px",left:"10px"});al.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new N.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(this.track,aj,al,ak,au.data)}});var e=function(ah,an,ai,am,ap,ao,ak,al){var aj=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];j.call(this,ah,an,ai,ao);O.call(this,ak,al);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){aj.set_name(aj.prefs.name);aj.tile_cache.clear();aj.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=am;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new T(20,this);this.left_offset=200;this.painter=N.LinkedFeaturePainter};q(e.prototype,r.prototype,O.prototype,{postdraw_actions:function(ax,ah,ay,aw){O.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.update_track_icons()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",A,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aD,aH,ar,ak){var aA=this,am=aA._get_tile_bounds(aH,aD),aK=am[0],ai=am[1],ay=ai-aK,aB=Math.ceil(ay*ar),aQ=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"){az="no_detail"}else{var aP=aw.data;if(this.view.high-this.view.low>K){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aB+al;aj.height=an+U;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aK,ai,200);if(aw.max){at.max=aw.max}aw=at}var aM=new N.SummaryTreePainter(aw,aK,ai,this.prefs);var aC=aj.getContext("2d");aC.translate(al,U);aM.draw(aC,aB,an);return new l(aA,aH,aD,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aE=0,aG=aw.data.length;aE<aG;aE++){var ao=aw.data[aE];var aF=false;var av;for(var aJ=0,aO=au.length;aJ<aO;aJ++){av=au[aJ];av.update_attrs(ao);if(!av.keep(ao)){aF=true;break}}if(!aF){aq.push(ao)}}}var aN=(this.filters_manager.alpha_filter?new E(this.filters_manager.alpha_filter):null);var aL=(this.filters_manager.height_filter?new E(this.filters_manager.height_filter):null);var aM=new (this.painter)(aq,aK,ai,this.prefs,az,aN,aL,ak);var an=Math.max(af,aM.get_required_height(ap));var aj=this.view.canvas_manager.new_canvas();var aI=null;aj.width=aB+al;aj.height=an;var aC=aj.getContext("2d");aC.fillStyle=this.prefs.block_color;aC.font=aC.canvas.manager.default_font;aC.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aw.data){aC.translate(al,0);aI=aM.draw(aC,aB,an,ax);aI.translation=-al}return new Q(aA,aH,aD,aj,aw.data,az,aw.message,aI)}});var V=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.painter=N.VariantPainter};q(V.prototype,r.prototype,O.prototype,e.prototype);var Y=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ak,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=N.ReadPainter;this.update_track_icons()};q(Y.prototype,r.prototype,O.prototype,e.prototype);var W=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am,{});this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};q(W.prototype,r.prototype,O.prototype,e.prototype,{predraw_init:function(){var ai=this;var ah=function(){if(ai.data_manager.size()===0){setTimeout(ah,300)}else{ai.data_url=default_data_url;ai.data_query_wait=M;ai.dataset_state_url=converted_datasets_state_url;$.getJSON(ai.dataset_state_url,{dataset_id:ai.dataset_id,hda_ldda:ai.hda_ldda},function(aj){})}};ah()}});Z.View=ae;Z.DrawableGroup=R;Z.LineTrack=k;Z.FeatureTrack=e;Z.ReadTrack=Y};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(k,y){var v=k("class").extend;var q=function(J,B,H,A,G,E){if(E===undefined){E=4}var D=A-B;var C=G-H;var F=Math.floor(Math.sqrt(D*D+C*C)/E);var K=D/F;var I=C/F;var z;for(z=0;z<F;z++,B+=K,H+=I){if(z%2!==0){continue}J.fillRect(B,H,E,1)}};var r=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var e=function(z){this.default_val=(z?z:1)};e.prototype.gen_val=function(z){return this.default_val};var n=function(B,D,z,A,C){this.data=B;this.view_start=D;this.view_end=z;this.prefs=v({},this.default_prefs,A);this.mode=C};n.prototype.default_prefs={};var w=function(B,D,z,A,C){n.call(this,B,D,z,A,C)};w.prototype.default_prefs={show_counts:false};w.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var c=function(z,D,F,G,B){n.call(this,z,D,F,G,B);if(this.prefs.min_value===undefined){var H=Infinity;for(var A=0,C=this.data.length;A<C;A++){H=Math.min(H,this.data[A][1])}this.prefs.min_value=H}if(this.prefs.max_value===undefined){var E=-Infinity;for(var A=0,C=this.data.length;A<C;A++){E=Math.max(E,this.data[A][1])}this.prefs.max_value=E}};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var o=function(z){this.feature_positions={};this.slot_height=z;this.translation=0};o.prototype.map_feature_data=function(A,C,z,B){if(!this.feature_positions[C]){this.feature_positions[C]=[]}this.feature_positions[C].push({data:A,x_start:z,x_end:B})};o.prototype.get_feature_data=function(z,D){var C=Math.floor(D/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var p=function(B,E,z,A,D,F,C){n.call(this,B,E,z,A,D);this.alpha_scaler=(F?F:new e());this.height_scaler=(C?C:new e())};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};v(p.prototype,{get_required_height:function(A){var z=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){z=A*y_scale}return z+Math.max(Math.round(y_scale/2),5)},draw:function(L,J,H,G){var R=this.data,E=this.view_start,N=this.view_end;L.save();L.fillStyle=this.prefs.block_color;L.textAlign="right";var I=this.view_end-this.view_start,F=J/I,M=this.get_row_height(),Q=new o(M),C;for(var O=0,P=R.length;O<P;O++){var B=R[O],D=B[0],K=B[1],z=B[2],A=(G&&G[D]!==undefined?G[D]:null);if((K<N&&z>E)&&(this.mode=="Dense"||A!==null)){C=this.draw_element(L,this.mode,B,A,E,N,F,M,J);Q.map_feature_data(B,A,C[0],C[1])}}L.restore();return Q},draw_element:function(F,B,H,D,C,E,G,A,z){console.log("WARNING: Unimplemented function.");return[0,0]}});var d=10,j=3,m=5,x=10,g=1,t=3,f=3,a=9,l=2,h="#ccc";var s=function(B,E,z,A,D,F,C){p.call(this,B,E,z,A,D,F,C)};v(s.prototype,p.prototype,{get_row_height:function(){var A=this.mode,z;if(A==="Dense"){z=d}else{if(A==="no_detail"){z=j}else{if(A==="Squish"){z=m}else{z=x}}}return z},draw_element:function(N,E,W,I,P,ah,al,an,z){var T=W[0],aj=W[1],ab=W[2],R=W[3],ac=Math.floor(Math.max(0,(aj-P)*al)),O=Math.ceil(Math.min(z,Math.max(0,(ab-P)*al))),aa=ac,am=O,Z=(E==="Dense"?0:(0+I))*an,M,af,S=null,ap=null,C=this.prefs.block_color,ae=this.prefs.label_color;N.globalAlpha=this.alpha_scaler.gen_val(W);if(E=="Dense"){I=1}if(E==="no_detail"){N.fillStyle=C;N.fillRect(ac,Z+5,O-ac,g)}else{var L=W[4],Y=W[5],ad=W[6],D=W[7];if(Y&&ad){S=Math.floor(Math.max(0,(Y-P)*al));ap=Math.ceil(Math.min(z,Math.max(0,(ad-P)*al)))}var ak,U;if(E==="Squish"||E==="Dense"){ak=1;U=f}else{ak=5;U=a}if(!D){if(W.strand){if(W.strand==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand_inv")}else{if(W.strand==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand_inv")}}}else{N.fillStyle=C}N.fillRect(ac,Z,O-ac,U)}else{var K,V;if(E==="Squish"||E==="Dense"){N.fillStyle=h;K=Z+Math.floor(f/2)+1;V=1}else{if(L){var K=Z;var V=U;if(L==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand")}else{if(L==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand")}}}else{N.fillStyle=h;K+=(f/2)+1;V=1}}N.fillRect(ac,K,O-ac,V);var F;for(var ai=0,B=D.length;ai<B;ai++){var G=D[ai],A=Math.floor(Math.max(0,(G[0]-P)*al)),X=Math.ceil(Math.min(z,Math.max((G[1]-P)*al)));if(A>X){continue}N.fillStyle=C;N.fillRect(A,Z+(U-ak)/2+1,X-A,ak);if(S!==undefined&&ad>Y&&!(A>ap||X<S)){var ag=Math.max(A,S),J=Math.min(X,ap);N.fillRect(ag,Z+1,J-ag,U);if(D.length==1&&E=="Pack"){if(L==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand_inv")}else{if(L==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand_inv")}}if(ag+14<J){ag+=2;J-=2}N.fillRect(ag,Z+1,J-ag,U)}}}if(E==="Pack"){N.globalAlpha=1;N.fillStyle="white";var H=this.height_scaler.gen_val(W),Q=Math.ceil(U*H),ao=Math.round((U-Q)/2);if(H!==1){N.fillRect(ac,K+1,O-ac,ao);N.fillRect(ac,K+U-ao+1,O-ac,ao)}}}N.globalAlpha=1;if(E==="Pack"&&aj>P){N.fillStyle=ae;if(P===0&&ac-N.measureText(R).width<0){N.textAlign="left";N.fillText(R,O+l,Z+8);am+=N.measureText(R).width+l}else{N.textAlign="right";N.fillText(R,ac-l,Z+8);aa-=N.measureText(R).width+l}}}N.globalAlpha=1;return[aa,am]}});var b=function(B,E,z,A,D,F,C){p.call(this,B,E,z,A,D,F,C)};v(b.prototype,p.prototype,{draw_element:function(S,N,H,D,V,B,K,T,Q){var H=data[i],J=H[0],R=H[1],C=H[2],M=H[3],F=Math.floor(Math.max(0,(R-V)*K)),I=Math.ceil(Math.min(Q,Math.max(0,(C-V)*K))),E=(N==="Dense"?0:(0+D))*T,z,W,A=null,L=null;if(no_label){S.fillStyle=block_color;S.fillRect(F+left_offset,E+5,I-F,1)}else{var U=H[4],P=H[5],G=H[6];z=9;W=1;S.fillRect(F+left_offset,E,I-F,z);if(N!=="Dense"&&M!==undefined&&R>V){S.fillStyle=label_color;if(V===0&&F-S.measureText(M).width<0){S.textAlign="left";S.fillText(M,I+2+left_offset,E+8)}else{S.textAlign="right";S.fillText(M,F-2+left_offset,E+8)}S.fillStyle=block_color}var O=U+" / "+P;if(R>V&&S.measureText(O).width<(I-F)){S.fillStyle="white";S.textAlign="center";S.fillText(O,left_offset+F+(I-F)/2,E+8);S.fillStyle=block_color}}return[F,I]}});var u=function(C,F,z,B,E,G,D,A){p.call(this,C,F,z,B,E,G,D);this.ref_seq=(A?A.data:null)};u.prototype.default_prefs=v({},p.prototype.default_prefs,{show_insertions:false});v(u.prototype,p.prototype,{get_row_height:function(){var z,A=this.mode;if(A==="Dense"){z=d}else{if(A==="Squish"){z=m}else{z=x;if(this.prefs.show_insertions){z*=2}}}return z},draw_read:function(W,R,N,ab,C,V,K,H,G){W.textAlign="center";var U=this,B=[ab,C],Q=0,X=0,T=0,z=W.canvas.manager.char_width_px;var ag=[];if((R==="Pack"||this.mode==="Auto")&&H!==undefined&&N>z){T=Math.round(N/2)}if(!K){K=[[0,H.length]]}for(var O=0,Z=K.length;O<Z;O++){var L=K[O],D="MIDNSHP=X"[L[0]],P=L[1];if(D==="H"||D==="S"){Q-=P}var I=V+Q,af=Math.floor(Math.max(0,(I-ab)*N)),J=Math.floor(Math.max(0,(I+P-ab)*N));if(af===J){J+=1}switch(D){case"H":break;case"S":case"M":case"=":if(is_overlap([I,I+P],B)){var S=H.slice(X,X+P);if(T>0){W.fillStyle=this.prefs.block_color;W.fillRect(af-T,G+1,J-af,9);W.fillStyle=h;for(var ad=0,A=S.length;ad<A;ad++){if(this.prefs.show_differences&&this.ref_seq){var M=this.ref_seq[I-ab+ad];if(!M||M.toLowerCase()===S[ad].toLowerCase()){continue}}if(I+ad>=ab&&I+ad<=C){var ae=Math.floor(Math.max(0,(I+ad-ab)*N));W.fillText(S[ad],ae,G+9)}}}else{W.fillStyle=this.prefs.block_color;W.fillRect(af,G+4,J-af,f)}}X+=P;Q+=P;break;case"N":W.fillStyle=h;W.fillRect(af-T,G+5,J-af,1);Q+=P;break;case"D":W.fillStyle="red";W.fillRect(af-T,G+4,J-af,3);Q+=P;break;case"P":break;case"I":var aa=af-T;if(is_overlap([I,I+P],B)){var S=H.slice(X,X+P);if(this.prefs.show_insertions){var F=af-(J-af)/2;if((R==="Pack"||this.mode==="Auto")&&H!==undefined&&N>z){W.fillStyle="yellow";W.fillRect(F-T,G-9,J-af,9);ag[ag.length]={type:"triangle",data:[aa,G+4,5]};W.fillStyle=h;switch(seq_tile_overlap){case (OVERLAP_START):S=S.slice(ab-I);break;case (OVERLAP_END):S=S.slice(0,I-C);break;case (CONTAINED_BY):break;case (CONTAINS):S=S.slice(ab-I,I-C);break}for(var ad=0,A=S.length;ad<A;ad++){var ae=Math.floor(Math.max(0,(I+ad-ab)*N));W.fillText(S[ad],ae-(J-af)/2,G)}}else{W.fillStyle="yellow";W.fillRect(F,G+(this.mode!=="Dense"?2:5),J-af,(R!=="Dense"?f:t))}}else{if((R==="Pack"||this.mode==="Auto")&&H!==undefined&&N>z){ag[ag.length]={type:"text",data:[S.length,aa,G+9]}}else{}}}X+=P;break;case"X":X+=P;break}}W.fillStyle="yellow";var ac,E,ah;for(var Y=0;Y<ag.length;Y++){ac=ag[Y];E=ac.type;ah=ac.data;if(E==="text"){W.save();W.font="bold 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+var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var trackster_module=function(f,Z){var q=f("class").extend,t=f("slotting"),N=f("painters");var ag=function(ah,ai){this.document=ah;this.default_font=ai!==undefined?ai:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};q(ag.prototype,{load_pattern:function(ah,al){var ai=this.patterns,aj=this.dummy_context,ak=new Image();ak.src=image_path+al;ak.onload=function(){ai[ah]=aj.createPattern(ak,"repeat")}},get_pattern:function(ah){return this.patterns[ah]},new_canvas:function(){var ah=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ah)}ah.manager=this;return ah}});var o={};var m=function(ah,ai){o[ah.attr("id")]=ai};var n=function(ah,aj,al,ak){al=".group";var ai={};o[ah.attr("id")]=ak;ah.bind("drag",{handle:"."+aj,relative:true},function(au,av){var at=$(this);var ay=$(this).parent(),ap=ay.children(),ar=o[$(this).attr("id")],ao,an,aw,am,aq;an=$(this).parents(al);if(an.length!==0){aw=an.position().top;am=aw+an.outerHeight();if(av.offsetY<aw){$(this).insertBefore(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable_before(ar,ax);return}else{if(av.offsetY>am){$(this).insertAfter(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable(ar);return}}}an=null;for(aq=0;aq<ap.length;aq++){ao=$(ap.get(aq));aw=ao.position().top;am=aw+ao.outerHeight();if(ao.is(al)&&this!==ao.get(0)&&av.offsetY>=aw&&av.offsetY<=am){if(av.offsetY-aw<am-av.offsetY){ao.find(".content-div").prepend(this)}else{ao.find(".content-div").append(this)}if(ar.container){ar.container.remove_drawable(ar)}o[ao.attr("id")].add_drawable(ar);return}}for(aq=0;aq<ap.length;aq++){if(av.offsetY<$(ap.get(aq)).position().top){break}}if(aq===ap.length){if(this!==ap.get(aq-1)){ay.append(this);o[ay.attr("id")].move_drawable(ar,aq)}}else{if(this!==ap.get(aq)){$(this).insertBefore(ap.get(aq));o[ay.attr("id")].move_drawable(ar,(av.deltaY>0?aq-1:aq))}}}).bind("dragstart",function(){ai["border-top"]=ah.css("border-top");ai["border-bottom"]=ah.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ai)})};Z.moveable=n;var af=16,I=9,F=20,U=I+2,A=100,K=12000,S=200,D=5,w=10,M=5000,x=100,p="There was an error in indexing this dataset. ",L="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",u="Currently indexing... please wait",y="Tool cannot be rerun: ",a="Loading data...",aa="Ready for display",d=10,v=5,C=5;function ab(ai,ah){if(!ah){ah=0}var aj=Math.pow(10,ah);return Math.round(ai*aj)/aj}var c=function(ah){this.num_elements=ah;this.clear()};q(c.prototype,{get:function(ai){var ah=this.key_ary.indexOf(ai);if(ah!==-1){if(this.obj_cache[ai].stale){this.key_ary.splice(ah,1);delete this.obj_cache[ai]}else{this.move_key_to_end(ai,ah)}}return this.obj_cache[ai]},set:function(ai,aj){if(!this.obj_cache[ai]){if(this.key_ary.length>=this.num_elements){var ah=this.key_ary.shift();delete this.obj_cache[ah]}this.key_ary.push(ai)}this.obj_cache[ai]=aj;return aj},move_key_to_end:function(ai,ah){this.key_ary.splice(ah,1);this.key_ary.push(ai)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var T=function(ai,ah,aj){c.call(this,ai);this.track=ah;this.subset=(aj!==undefined?aj:true)};q(T.prototype,c.prototype,{load_data:function(aq,al,ao,ai,an){var ap=this.track.view.chrom,ak={chrom:ap,low:aq,high:al,mode:ao,resolution:ai,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ak,an);if(this.track.filters_manager){var ar=[];var ah=this.track.filters_manager.filters;for(var am=0;am<ah.length;am++){ar[ar.length]=ah[am].name}ak.filter_cols=JSON.stringify(ar)}var aj=this;return $.getJSON(this.track.data_url,ak,function(at){aj.set_data(aq,al,ao,at)})},get_data:function(ah,al,am,ai,ak){var aj=this.get_data_from_cache(ah,al,am);if(aj){return aj}aj=this.load_data(ah,al,am,ai,ak);this.set_data(ah,al,am,aj);return aj},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ap,ak,ao,aj,an,al){var aq=this.get_data_from_cache(ap,ak,ao);if(!aq){console.log("ERROR: no current data for: ",this.track,ap,ak,ao,aj,an);return}aq.stale=true;var ai=ap;if(al===this.DEEP_DATA_REQ){$.extend(an,{start_val:aq.data.length+1})}else{if(al===this.BROAD_DATA_REQ){ai=(aq.max_high?aq.max_high:aq.data[aq.data.length-1][2])+1}}var ah=this,am=this.load_data(ai,ak,ao,aj,an);new_data_available=$.Deferred();this.set_data(ap,ak,ao,new_data_available);$.when(am).then(function(ar){if(ar.data){ar.data=aq.data.concat(ar.data);if(ar.max_low){ar.max_low=aq.max_low}if(ar.message){ar.message=ar.message.replace(/[0-9]+/,ar.data.length)}}ah.set_data(ap,ak,ao,ar);new_data_available.resolve(ar)});return new_data_available},get_data_from_cache:function(ah,ai,aj){return this.get(this.gen_key(ah,ai,aj))},set_data:function(ai,aj,ak,ah){return this.set(this.gen_key(ai,aj,ak),ah)},gen_key:function(ah,aj,ak){var ai=ah+"_"+aj+"_"+ak;return ai},split_key:function(ah){return ah.split("_")}});var J=function(ai,ah,aj){T.call(this,ai,ah,aj)};q(J.prototype,T.prototype,c.prototype,{load_data:function(ah,ak,al,ai,aj){if(ai>1){return{data:null}}return T.prototype.load_data.call(this,ah,ak,al,ai,aj)}});var r=function(ak,ai,ah,aj,al){this.name=ak;this.view=ai;this.container=ah;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak}],saved_values:aj,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=al;this.is_overview=false};q(r.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},update_track_icons:function(){},set_name:function(ah){this.old_name=this.name;this.name=ah;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var z=function(al,ak,ai,ah,aj,am){r.call(this,ak,ai,ah,aj,am);this.obj_type=al;this.drawables=[]};q(z.prototype,r.prototype,{init:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah].init()}},_draw:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah]._draw()}},to_json:function(){var ai=[];for(var ah=0;ah<this.drawables.length;ah++){ai.push(this.drawables[ah].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ai}},add_drawable:function(ah){this.drawables.push(ah);ah.container=this},add_drawable_before:function(aj,ah){var ai=this.drawables.indexOf(ah);if(ai!=-1){this.drawables.splice(ai,0,aj);return true}return false},remove_drawable:function(ai){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);ai.container=null;return true}return false},move_drawable:function(ai,aj){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);this.drawables.splice(aj,0,ai);return true}return false}});var R=function(ak,ai,ah,aj){z.call(this,"DrawableGroup",ak,ai,ah,aj,"group-handle");if(!R.id_counter){R.id_counter=0}var al=R.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+al).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+al+"_content_div").appendTo(this.container_div);m(this.container_div,this);m(this.content_div,this);n(this.container_div,this.drag_handle_class,".group",this);this.update_track_icons()};q(R.prototype,r.prototype,z.prototype,{update_track_icons:function(){var ai=this;var ah={};ah["Edit configuration"]=function(){var al=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aj=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(am){if((am.keyCode||am.which)===27){al()}else{if((am.keyCode||am.which)===13){aj()}}};$(window).bind("keypress.check_enter_esc",ak);show_modal("Configure Group",ai.config.build_form(),{Cancel:al,OK:aj})};ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)}});var ae=function(ah,ak,aj,ai){z.call(this,"View");this.container=ah;this.chrom=null;this.vis_id=aj;this.dbkey=ai;this.title=ak;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ag(ah.get(0).ownerDocument);this.reset()};q(ae.prototype,z.prototype,{init:function(){var aj=this.container,ah=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aj);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;m(this.viewport_container,ah);this.intro_div=$("<div/>").addClass("intro");var ak=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ai=function(al){if(al.type==="focusout"||(al.keyCode||al.which)===13||(al.keyCode||al.which)===27){if((al.keyCode||al.which)!==27){ah.go_to($(this).val())}$(this).hide();$(this).val("");ah.location_span.show();ah.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ai).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ah.location_span.hide();ah.chrom_select.hide();ah.nav_input.val(ah.chrom+":"+ah.low+"-"+ah.high);ah.nav_input.css("display","inline-block");ah.nav_input.select();ah.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ah.zoom_out();ah.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.browser_content_div.click(function(al){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("<div />").css({height:ah.browser_content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,{content_div:this.top_labeltrack}));this.add_label_track(new ad(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new B(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(am,ai,ao){if(!am||am==="None"){return}var aj=this;if(am==="previous"){aj.load_chroms({low:this.chrom_start_index-x});return}if(am==="next"){aj.load_chroms({low:this.chrom_start_index+x});return}var an=$.grep(aj.chrom_data,function(ap,aq){return ap.chrom===am})[0];if(an===undefined){aj.load_chroms({chrom:am},function(){aj.change_chrom(am,ai,ao)});return}else{if(am!==aj.chrom){aj.chrom=am;aj.chrom_select.val(aj.chrom);aj.max_high=an.len-1;aj.reset();aj.request_redraw(true);for(var al=0,ah=aj.drawables.length;al<ah;al++){var ak=aj.drawables[al];if(ak.init){ak.init()}}}if(ai!==undefined&&ao!==undefined){aj.low=Math.max(ai,0);aj.high=Math.min(ao,aj.max_high)}aj.reset_overview();aj.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){z.prototype.add_drawable.call(this,ah);ah.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;ah.init();this.label_tracks.push(ah)},remove_drawable:function(aj,ai){z.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.drawables),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(D,Math.ceil(Math.log((this.high-this.low)/S)/Math.log(D)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(aj){if(this.overview_drawable){if(this.overview_drawable.dataset_id===aj.dataset_id){return}this.overview_viewport.find(".track").remove()}var ai=aj.copy({content_div:this.overview_viewport}),ah=this;ai.header_div.hide();ai.is_overview=true;ah.overview_drawable=ai;this.overview_drawable.postdraw_actions=function(){ah.overview_highlight.show().height(ah.overview_drawable.content_div.height());ah.overview_viewport.height(ah.overview_drawable.content_div.height()+ah.overview_box.outerHeight());ah.overview_close.show();ah.resize_window()};this.overview_drawable.init();ah.has_changes=true},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new P(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},al=this.track,aj=ai.tool_id+al.tool_region_and_parameters_str(ai.chrom,ai.low,ai.high),ah,am;if(al.container===view){var ak=new R(this.name,this.track.view,this.track.container);al.container.add_drawable(ak);al.container.remove_drawable(al);ak.add_drawable(al);al.container_div.appendTo(ak.content_div);ah=ak}else{ah=al.container}if(al instanceof e){am=new W(aj,view,ah,"hda");am.change_mode(al.mode);ah.add_drawable(am)}am.content_div.text("Starting job.");this.run(ai,am,function(an){am.dataset_id=an.dataset_id;am.content_div.text("Running job.");am.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(L)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(y+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var P=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){P.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var X=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};q(X.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=ah[this.index];return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(at,aA){this.track=at;this.filters=[];for(var av=0;av<aA.length;av++){var aw=aA[av],aB=aw.name,ah=aw.type,aj=aw.index,az=aw.tool_id,ay=aw.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[av]=new X(aB,aj,az,ay)}else{console.log("ERROR: unsupported filter: ",aB,ah)}}var ak=function(aC,aD,aE){aC.click(function(){var aF=aD.text();max=parseFloat(aE.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aE.slider("option","values")){input_size=2*input_size+1;multi_value=true}aD.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aF).appendTo(aD).focus().select().click(function(aG){aG.stopPropagation()}).blur(function(){$(this).remove();aD.text(aF)}).keyup(function(aK){if(aK.keyCode===27){$(this).trigger("blur")}else{if(aK.keyCode===13){var aI=aE.slider("option","min"),aG=aE.slider("option","max"),aJ=function(aL){return(isNaN(aL)||aL>aG||aL<aI)},aH=$(this).val();if(!multi_value){aH=parseFloat(aH);if(aJ(aH)){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}else{aH=aH.split("-");aH=[parseFloat(aH[0]),parseFloat(aH[1])];if(aJ(aH[0])||aJ(aH[1])){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}aE.slider((multi_value?"values":"value"),aH)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aC){aC.stopPropagation()}).click(function(aC){aC.stopPropagation()}).bind("dblclick",function(aC){aC.stopPropagation()}).bind("keydown",function(aC){aC.stopPropagation()});var ax=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aF,aH){aH.container=$("<div/>").addClass("filter-row slider-row").appendTo(ax);var aG=$("<div/>").addClass("elt-label").appendTo(aH.container);var aE=$("<span/>").addClass("slider-name").text(aH.name+"  ").appendTo(aG);var aD=$("<span/>");var aJ=$("<span/>").addClass("slider-value").appendTo(aG).append("[").append(aD).append("]");var aC=$("<div/>").addClass("slider").appendTo(aH.container);aH.control_element=$("<div/>").attr("id",aH.name+"-filter-control").appendTo(aC);var aI=[0,0];aH.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aL,aM){var aK=aM.values;aD.text(aK[0]+"-"+aK[1]);aH.low=aK[0];aH.high=aK[1];ap.track.request_draw(true,true)},change:function(aK,aL){aH.control_element.slider("option","slide").call(aH.control_element,aK,aL)}});aH.slider=aH.control_element;aH.slider_label=aD;ak(aJ,aD,aH.control_element);$("<div style='clear: both;'/>").appendTo(aH.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(ax);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var ai=this;ao.click(function(){ai.run_on_dataset()})}var ar=$("<div/>").addClass("display-controls").appendTo(this.parent_div),au,an,aq,al={Transparency:function(aC){ap.alpha_filter=aC},Height:function(aC){ap.height_filter=aC}};$.each(al,function(aE,aD){au=$("<div/>").addClass("filter-row").appendTo(ar),an=$("<span/>").addClass("elt-label").text(aE+":").appendTo(au),aq=$("<select/>").attr("name",aE+"_dropdown").css("float","right").appendTo(au);$("<option/>").attr("value",-1).text("== None ==").appendTo(aq);for(var aC=0;aC<ap.filters.length;aC++){$("<option/>").attr("value",aC).text(ap.filters[aC].name).appendTo(aq)}aq.change(function(){$(this).children("option:selected").each(function(){var aF=parseInt($(this).val());al[aE]((aF>=0?ap.filters[aF]:null));ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(au)});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var E=function(ah,ai){N.Scaler.call(this,ai);this.filter=ah};E.prototype.gen_val=function(ah){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var H=function(ah){this.track=ah.track;this.params=ah.params;this.values={};this.restore_values((ah.saved_values?ah.saved_values:{}));this.onchange=ah.onchange};q(H.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(ah,ak,aj,ai,al){this.track=ah;this.index=ak;this.low=ak*S*aj;this.high=(ak+1)*S*aj;this.resolution=aj;this.canvas=$("<div class='track-tile'/>").append(ai);this.data=al;this.stale=false};b.prototype.predisplay_actions=function(){};var l=function(ah,ak,aj,ai,al,am){b.call(this,ah,ak,aj,ai,al);this.max_val=am};q(l.prototype,b.prototype);var Q=function(ah,al,ak,aj,an,ao,am,ai){b.call(this,ah,al,ak,aj,an);this.mode=ao;this.message=am;this.feature_mapper=ai};q(Q.prototype,b.prototype);Q.prototype.predisplay_actions=function(){var ai=this,ah={};if(ai.mode!=="Pack"){return}$(this.canvas).mousemove(function(au){var ao=$(this).offset(),at=au.pageX-ao.left,ar=au.pageY-ao.top,ay=ai.feature_mapper.get_feature_data(at,ar),ap=(ay?ay[0]:null);$(this).siblings(".feature-popup").each(function(){if(!ap||$(this).attr("id")!==ap.toString()){$(this).remove()}});if(ay){var ak=ah[ap];if(!ak){var ap=ay[0],av={name:ay[3],start:ay[1],end:ay[2],strand:ay[4]},an=ai.track.filters_manager.filters,am;for(var aq=0;aq<an.length;aq++){am=an[aq];av[am.name]=ay[am.index]}var ak=$("<div/>").attr("id",ap).addClass("feature-popup"),ax,aw,az=$("<table/>").appendTo(ak),aA;for(ax in av){aw=av[ax];aA=$("<tr/>").appendTo(az);$("<th/>").appendTo(aA).text(ax);$("<td/>").attr("align","left").appendTo(aA).text(typeof(aw)=="number"?ab(aw,2):aw)}ah[ap]=ak}ak.appendTo($(ai.canvas).parent());var al=at+parseInt(ai.canvas.css("left"))+7,aj=ar+parseInt(ai.canvas.css("top"))+7;ak.css("left",al+"px").css("top",aj+"px")}else{if(!au.isPropagationStopped()){au.stopPropagation();$(this).siblings().each(function(){$(this).trigger(au)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var j=function(ak,at,al,ao,au,aj,ai){r.call(this,ak,at,al,{},"draghandle");this.data_url=(aj?aj:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ai?ai:M);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.id=j.id_counter++;this.container_div=$("<div />").addClass("track").attr("id","track_"+this.id).css("position","relative");if(ao){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div/>").addClass("track-name").appendTo(this.header_div).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());this.icons_div=$("<div/>").css("float","left").appendTo(this.header_div).hide();this.settings_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Edit settings").addClass("icon-button settings-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.overview_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Set as overview").addClass("icon-button overview-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.filters_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Filters").addClass("icon-button filters-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.tools_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Tools").addClass("icon-button tools-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.remove_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Remove").addClass("icon-button remove-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);var am=this;this.header_div.dblclick(function(av){av.stopPropagation()});this.settings_icon.click(function(){var ax=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},av=function(){am.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},aw=function(ay){if((ay.keyCode||ay.which)===27){ax()}else{if((ay.keyCode||ay.which)===13){av()}}};$(window).bind("keypress.check_enter_esc",aw);show_modal("Configure Track",am.config.build_form(),{Cancel:ax,OK:av})});this.overview_icon.click(function(){am.view.set_overview(am)});this.filters_icon.click(function(){am.filters_div.toggle();am.filters_manager.reset_filters()});this.tools_icon.click(function(){am.dynamic_tool_div.toggle();if(am.dynamic_tool_div.is(":visible")){am.set_name(am.name+am.tool_region_and_parameters_str())}else{am.revert_name()}$(".tipsy").remove()});this.remove_icon.click(function(){$(".tipsy").remove();am.remove()});if(am.display_modes!==undefined){if(am.mode_div===undefined){am.mode_div=$("<div class='right-float menubutton popup' />").appendTo(am.header_div);var an=(am.config&&am.config.values.mode?am.config.values.mode:am.display_modes[0]);am.mode=an;am.mode_div.text(an);var ah={};for(var ap=0,ar=am.display_modes.length;ap<ar;ap++){var aq=am.display_modes[ap];ah[aq]=function(av){return function(){am.change_mode(av)}}(aq)}make_popupmenu(am.mode_div,ah)}else{am.mode_div.hide()}this.header_div.append($("<div/>").css("clear","both"));this.container_div.hover(function(){am.icons_div.show()},function(){am.icons_div.hide()})}}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Y){return"ReadTrack"}else{if(this instanceof W){return"ToolDataFeatureTrack"}else{if(this instanceof V){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(L)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(G)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.update_track_icons()}ah.content_div.text(aa);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}});this.update_track_icons()},predraw_init:function(){}});var O=function(ak,aj){var ai=this,ah=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=new ac(this,(ak!==undefined?ak:{}));this.filters_available=false;this.filters_visible=false;this.tool=(aj!==undefined&&obj_length(aj)>0?new s(this,aj):undefined);if(this.header_div){if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}};q(O.prototype,r.prototype,j.prototype,{copy:function(ah){return new this.constructor(this.name,this.view,ah,this.hda_ldda,this.dataset_id,this.prefs,this.filters,this.tool)},to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw();return ah},update_track_icons:function(){var ah=this;if(ah.filters_available>0){ah.filters_icon.show()}else{ah.filters_icon.hide()}if(ah.tool){ah.tools_icon.show()}else{ah.tools_icon.hide()}},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof B)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(this.is_overview){aq=this.view.max_low;an=this.view.max_high;am=Math.pow(D,Math.ceil(Math.log((view.max_high-view.max_low)/S)/Math.log(D)));av=ak/(view.max_high-view.max_low)}if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/S);var ap=true;var at=[];var ah=0;while((ai*S*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",F)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*S*an,ax=ap+S*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);if(aq!==undefined){al.tile_cache.set(at,aq);al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw(false,false,false,al)});return null},show_tile:function(an,ap,aq){var aj=this,ai=an.canvas,am=ai;if(an.message){var ar=$("<div/>"),ao=$("<div/>").addClass("tile-message").text(an.message).css({height:F-1,width:an.canvas.width}).appendTo(ar),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ao),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ao);ar.append(ai);am=ar;al.click(function(){an.stale=true;aj.data_manager.get_more_data(an.low,an.high,aj.mode,an.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(at){at.stopPropagation()});ah.click(function(){an.stale=true;aj.data_manager.get_more_data(an.low,an.high,aj.mode,an.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(at){at.stopPropagation()})}an.predisplay_actions();var ak=(an.low-(this.is_overview?this.view.max_low:this.view.low))*aq;if(this.left_offset){ak-=this.left_offset}am.css({position:"absolute",top:0,left:ak,height:""});ap.append(am);aj.max_height=Math.max(aj.max_height,am.height());aj.content_div.css("height",aj.max_height+"px");ap.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*S*ai,al=S*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ai,ah){j.call(this,"label",ai,ah,false,{});this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{init:function(){this.enabled=true},_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var B=function(ah){j.call(this,"reference",ah,{content_div:ah.top_labeltrack},false,{});O.call(this);ah.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ah.dbkey};this.data_manager=new J(C,this,false);this.tile_cache=new c(v)};q(B.prototype,r.prototype,O.prototype,{init:function(){this.enabled=true},draw_tile:function(ar,an,am,ai,at){var al=this,aj=S*am;if(at>this.view.canvas_manager.char_width_px){if(ar.data===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(al,ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(am,ak,aj,an,ah,al){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,am,ak,aj,al);O.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=an;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new T(C,this);this.tile_cache=new c(v);this.left_offset=0;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:am},{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:al,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.dataset_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.dataset_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};q(k.prototype,r.prototype,O.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this;ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(ai){ah.container_div.addClass("line-track");var ak=ai.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=ak.min;ah.prefs.max_value=ak.max;$("#track_"+ah.dataset_id+"_minval").val(ah.prefs.min_value);$("#track_"+ah.dataset_id+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=ak.total_frequency;ah.container_div.find(".yaxislabel").remove();var al=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_minval").text(ab(ah.prefs.min_value,3));var aj=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_maxval").text(ab(ah.prefs.max_value,3));aj.css({position:"absolute",top:"24px",left:"10px"});aj.prependTo(ah.container_div);al.css({position:"absolute",bottom:"2px",left:"10px"});al.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new N.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(this.track,aj,al,ak,au.data)}});var e=function(ah,an,ai,am,ap,ao,ak,al){var aj=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];j.call(this,ah,an,ai,true,ao);O.call(this,ak,al);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){aj.set_name(aj.prefs.name);aj.tile_cache.clear();aj.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=am;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new T(20,this);this.left_offset=200;this.painter=N.LinkedFeaturePainter};q(e.prototype,r.prototype,O.prototype,{postdraw_actions:function(ax,ah,ay,aw){O.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.update_track_icons()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",A,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aD,aH,ar,ak){var aA=this,am=aA._get_tile_bounds(aH,aD),aK=am[0],ai=am[1],ay=ai-aK,aB=Math.ceil(ay*ar),aQ=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"||aA.is_overview){az="no_detail"}else{var aP=aw.data;if(this.view.high-this.view.low>K){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aB+al;aj.height=an+U;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aK,ai,200);if(aw.max){at.max=aw.max}aw=at}var aM=new N.SummaryTreePainter(aw,aK,ai,this.prefs);var aC=aj.getContext("2d");aC.translate(al,U);aM.draw(aC,aB,an);return new l(aA,aH,aD,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aE=0,aG=aw.data.length;aE<aG;aE++){var ao=aw.data[aE];var aF=false;var av;for(var aJ=0,aO=au.length;aJ<aO;aJ++){av=au[aJ];av.update_attrs(ao);if(!av.keep(ao)){aF=true;break}}if(!aF){aq.push(ao)}}}var aN=(this.filters_manager.alpha_filter?new E(this.filters_manager.alpha_filter):null);var aL=(this.filters_manager.height_filter?new E(this.filters_manager.height_filter):null);var aM=new (this.painter)(aq,aK,ai,this.prefs,az,aN,aL,ak);var an=Math.max(af,aM.get_required_height(ap));var aj=this.view.canvas_manager.new_canvas();var aI=null;aj.width=aB+al;aj.height=an;var aC=aj.getContext("2d");aC.fillStyle=this.prefs.block_color;aC.font=aC.canvas.manager.default_font;aC.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aw.data){aC.translate(al,0);aI=aM.draw(aC,aB,an,ax);aI.translation=-al}return new Q(aA,aH,aD,aj,aw.data,az,aw.message,aI)}});var V=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.painter=N.VariantPainter};q(V.prototype,r.prototype,O.prototype,e.prototype);var Y=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ak,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=N.ReadPainter;this.update_track_icons()};q(Y.prototype,r.prototype,O.prototype,e.prototype);var W=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am,{});this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};q(W.prototype,r.prototype,O.prototype,e.prototype,{predraw_init:function(){var ai=this;var ah=function(){if(ai.data_manager.size()===0){setTimeout(ah,300)}else{ai.data_url=default_data_url;ai.data_query_wait=M;ai.dataset_state_url=converted_datasets_state_url;$.getJSON(ai.dataset_state_url,{dataset_id:ai.dataset_id,hda_ldda:ai.hda_ldda},function(aj){})}};ah()}});Z.View=ae;Z.DrawableGroup=R;Z.LineTrack=k;Z.FeatureTrack=e;Z.ReadTrack=Y};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(k,y){var v=k("class").extend;var q=function(J,B,H,A,G,E){if(E===undefined){E=4}var D=A-B;var C=G-H;var F=Math.floor(Math.sqrt(D*D+C*C)/E);var K=D/F;var I=C/F;var z;for(z=0;z<F;z++,B+=K,H+=I){if(z%2!==0){continue}J.fillRect(B,H,E,1)}};var r=function(B,A,z,E){var 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aa=af-T;if(is_overlap([I,I+P],B)){var S=H.slice(X,X+P);if(this.prefs.show_insertions){var F=af-(J-af)/2;if((R==="Pack"||this.mode==="Auto")&&H!==undefined&&N>z){W.fillStyle="yellow";W.fillRect(F-T,G-9,J-af,9);ag[ag.length]={type:"triangle",data:[aa,G+4,5]};W.fillStyle=h;switch(seq_tile_overlap){case (OVERLAP_START):S=S.slice(ab-I);break;case (OVERLAP_END):S=S.slice(0,I-C);break;case (CONTAINED_BY):break;case (CONTAINS):S=S.slice(ab-I,I-C);break}for(var ad=0,A=S.length;ad<A;ad++){var ae=Math.floor(Math.max(0,(I+ad-ab)*N));W.fillText(S[ad],ae-(J-af)/2,G)}}else{W.fillStyle="yellow";W.fillRect(F,G+(this.mode!=="Dense"?2:5),J-af,(R!=="Dense"?f:t))}}else{if((R==="Pack"||this.mode==="Auto")&&H!==undefined&&N>z){ag[ag.length]={type:"text",data:[S.length,aa,G+9]}}else{}}}X+=P;break;case"X":X+=P;break}}W.fillStyle="yellow";var ac,E,ah;for(var Y=0;Y<ag.length;Y++){ac=ag[Y];E=ac.type;ah=ac.data;if(E==="text"){W.save();W.font="bold 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\ No newline at end of file
diff --git a/static/scripts/packed/trackster_ui.js b/static/scripts/packed/trackster_ui.js
index 67fef91ff89..0915be0fc30 100644
--- a/static/scripts/packed/trackster_ui.js
+++ b/static/scripts/packed/trackster_ui.js
@@ -1 +1 @@
-var add_bookmark=function(b,a){var g=$("#bookmarks-container"),d=$("<div/>").addClass("bookmark").appendTo(g),c=$("<div/>").addClass("delete-icon-container").appendTo(d).click(function(){d.slideUp("fast");d.remove();view.has_changes=true;return false}),e=$("<a href=''/>").addClass("icon-button delete").appendTo(c),f=$("<div/>").addClass("position").appendTo(d),h=$("<a href=''/>").text(b).appendTo(f).click(function(){view.go_to(b);return false});annotation_div=get_editable_text_elt(a,true).addClass("annotation").appendTo(d);view.has_changes=true;return d};var addable_objects={LineTrack:LineTrack,FeatureTrack:FeatureTrack,ReadTrack:ReadTrack,DrawableGroup:DrawableGroup};var track_from_dict=function(c,b){var a=new addable_objects[c.track_type](c.name,view,b,c.hda_ldda,c.dataset_id,c.prefs,c.filters,c.tool);if(c.mode){a.change_mode(c.mode)}return a};var drawable_collection_from_dict=function(f,a){var e=new addable_objects[f.obj_type](f.name,view,a,f.prefs,view.viewport_container,view);for(var d=0;d<f.drawables.length;d++){var b=f.drawables[d],c;if(b.track_type){c=track_from_dict(b,e)}else{c=drawable_collection_from_dict(b)}e.add_drawable(c);e.content_div.append(c.container_div)}return e};var drawable_from_dict=function(b,a){return(b.track_type?track_from_dict(b,a):drawable_collection_from_dict(b,a))};var create_visualization=function(b,e,g,c,a,d,f){view=new View(b,e,g,c);view.editor=true;$.when(view.load_chroms_deferred).then(function(){if(a){var k=a.chrom,p=a.start,h=a.end,m=a.overview;if(k&&(p!==undefined)&&h){view.change_chrom(k,p,h)}}if(d){var o;for(var j=0;j<d.length;j++){o=d[j];view.add_drawable(drawable_from_dict(o,view))}}var n;for(var j=0;j<view.drawables.length;j++){if(view.drawables[j].name==m){view.set_overview(view.drawables[j]);break}}if(f){var l;for(var j=0;j<f.length;j++){l=f[j];add_bookmark(l.position,l.annotation)}}view.has_changes=false});return view};var init_keyboard_nav=function(a){$(document).keydown(function(b){if($(b.srcElement).is(":input")){return}switch(b.which){case 37:a.move_fraction(0.25);break;case 38:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("-="+c+"px");break;case 39:a.move_fraction(-0.25);break;case 40:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("+="+c+"px");break}})};
\ No newline at end of file
+var add_bookmark=function(b,a){var g=$("#bookmarks-container"),d=$("<div/>").addClass("bookmark").appendTo(g),c=$("<div/>").addClass("delete-icon-container").appendTo(d).click(function(){d.slideUp("fast");d.remove();view.has_changes=true;return false}),e=$("<a href=''/>").addClass("icon-button delete").appendTo(c),f=$("<div/>").addClass("position").appendTo(d),h=$("<a href=''/>").text(b).appendTo(f).click(function(){view.go_to(b);return false});annotation_div=get_editable_text_elt(a,true).addClass("annotation").appendTo(d);view.has_changes=true;return d};var addable_objects={LineTrack:LineTrack,FeatureTrack:FeatureTrack,ReadTrack:ReadTrack,DrawableGroup:DrawableGroup};var track_from_dict=function(c,b){var a=new addable_objects[c.track_type](c.name,view,b,c.hda_ldda,c.dataset_id,c.prefs,c.filters,c.tool);if(c.mode){a.change_mode(c.mode)}return a};var drawable_collection_from_dict=function(f,a){var e=new addable_objects[f.obj_type](f.name,view,a,f.prefs,view.viewport_container,view);for(var d=0;d<f.drawables.length;d++){var b=f.drawables[d],c;if(b.track_type){c=track_from_dict(b,e)}else{c=drawable_collection_from_dict(b)}e.add_drawable(c);e.content_div.append(c.container_div)}return e};var drawable_from_dict=function(b,a){return(b.track_type?track_from_dict(b,a):drawable_collection_from_dict(b,a))};var create_visualization=function(b,e,g,c,a,d,f){view=new View(b,e,g,c);view.editor=true;$.when(view.load_chroms_deferred).then(function(){if(a){var k=a.chrom,p=a.start,h=a.end,m=a.overview;if(k&&(p!==undefined)&&h){view.change_chrom(k,p,h)}}if(d){var o;for(var j=0;j<d.length;j++){o=d[j];view.add_drawable(drawable_from_dict(o,view))}}var n;for(var j=0;j<view.drawables.length;j++){if(view.drawables[j].name===m){view.set_overview(view.drawables[j]);break}}if(f){var l;for(var j=0;j<f.length;j++){l=f[j];add_bookmark(l.position,l.annotation)}}view.has_changes=false});return view};var init_keyboard_nav=function(a){$(document).keydown(function(b){if($(b.srcElement).is(":input")){return}switch(b.which){case 37:a.move_fraction(0.25);break;case 38:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("-="+c+"px");break;case 39:a.move_fraction(-0.25);break;case 40:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("+="+c+"px");break}})};
\ No newline at end of file
diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index 1cfe3963793..fec93fd3600 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -589,7 +589,6 @@ var Drawable = function(name, view, container, prefs, drag_handle_class) {
     this.name = name;
     this.view = view;
     this.container = container;
-    this.drag_handle_class = drag_handle_class;
     this.config = new DrawableConfig({
         track: this,
         params: [ 
@@ -601,6 +600,8 @@ var Drawable = function(name, view, container, prefs, drag_handle_class) {
         }
     });
     this.prefs = this.config.values;
+    this.drag_handle_class = drag_handle_class;
+    this.is_overview = false;
 };
 
 extend(Drawable.prototype, {
@@ -852,7 +853,7 @@ extend( View.prototype, DrawableCollection.prototype, {
         // Overview (scrollbar and overview plot) at bottom
         this.overview = $("<div/>").addClass("overview").appendTo(this.bottom_container);
         this.overview_viewport = $("<div/>").addClass("overview-viewport").appendTo(this.overview);
-        this.overview_close = $("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);
+        this.overview_close = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);
         this.overview_highlight = $("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);
         this.overview_box_background = $("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);
         this.overview_box = $("<div/>").addClass("overview-box").appendTo(this.overview_viewport);
@@ -1195,13 +1196,14 @@ extend( View.prototype, DrawableCollection.prototype, {
     /**
      * Request that view redraw some or all tracks. If a track is not specificied, redraw all tracks.
      */
+    // FIXME: change method call so that track is first and additional parameters are optional.
     request_redraw: function(nodraw, force, clear_after, track) {
         var 
             view = this,
-            // Either redrawing a single track or all view's tracks.
+            // Either redrawing a single drawable or all view's drawables.
             track_list = (track ? [track] : view.drawables),
             track_index;
-        
+            
         // Add/update tracks in track list to redraw list.
         var track;
         for (var i = 0; i < track_list.length; i++) {
@@ -1318,42 +1320,44 @@ extend( View.prototype, DrawableCollection.prototype, {
         this.nav_container.width( this.container.width() );
         this.request_redraw();
     },
-    /** Show a track in the overview. */
-    set_overview: function(track) {
-        // Get data and draw tile.
-        $.when(track.get_overview_tile()).then(function(tile) {
-            // Update UI.
-            view.overview_viewport.find(".track-tile").remove();
-            view.overview_close.show();
-            view.overview_viewport.append(tile.canvas);
-            view.overview_highlight.show().height(tile.canvas.height());
-            view.overview_viewport.height(tile.canvas.height() + view.overview_box.outerHeight());
-            view.resize_window();
-            
-            // Update view, track states.
-            if (view.overview_track) {
-                view.overview_track.set_is_overview(false);
+    /** Show a Drawable in the overview. */
+    set_overview: function(drawable) {
+        if (this.overview_drawable) {
+            // If drawable to be set as overview is already in overview, do nothing.
+            // Otherwise, remove overview.
+            if (this.overview_drawable.dataset_id === drawable.dataset_id) {
+                return;
             }
-            view.overview_track = track;
-            track.set_is_overview(true);
-        });
+            this.overview_viewport.find(".track").remove();
+        }
+        
+        // Set new overview.
+        var 
+            overview_drawable = drawable.copy( { content_div: this.overview_viewport } ),
+            view = this;
+        overview_drawable.header_div.hide();
+        overview_drawable.is_overview = true;
+        view.overview_drawable = overview_drawable;
+        this.overview_drawable.postdraw_actions = function() {
+            view.overview_highlight.show().height(view.overview_drawable.content_div.height());
+            view.overview_viewport.height(view.overview_drawable.content_div.height() + view.overview_box.outerHeight());
+            view.overview_close.show();
+            view.resize_window();
+        };
+        this.overview_drawable.init();
         view.has_changes = true;
     },
     /** Close and reset overview. */
     reset_overview: function() {
         // Update UI.
+        $(".tipsy").remove();
         this.overview_viewport.find(".track-tile").remove();
         this.overview_viewport.height(this.default_overview_height);
         this.overview_box.height(this.default_overview_height);
         this.overview_close.hide();
         this.overview_highlight.hide();
         view.resize_window();
-        
-        // Update view, track states.
-        if (view.overview_track) {
-            view.overview_track.set_is_overview(false);
-        }
-        view.overview_track = null;
+        view.overview_drawable = null;
     }
 });
 
@@ -2243,7 +2247,7 @@ FeatureTrackTile.prototype.predisplay_actions = function() {
  * -------> ToolDataFeatureTrack
  * -------> VcfTrack
  */
-var Track = function(name, view, container, prefs, data_url, data_query_wait) {
+var Track = function(name, view, container, show_header, prefs, data_url, data_query_wait) {
     // For now, track's container is always view.
     Drawable.call(this, name, view, container, {}, "draghandle");
     
@@ -2263,8 +2267,8 @@ var Track = function(name, view, container, prefs, data_url, data_query_wait) {
     //
     this.container_div = $("<div />").addClass('track').attr("id", "track_" + this.id).css("position", "relative");
     
-    // Create and initialize track header and icons. Only non-hidden tracks have headers.
-    if (!this.hidden) {
+    // Create and initialize track header and icons.
+    if (show_header) {
         this.header_div = $("<div class='track-header' />").appendTo(this.container_div);
         if (this.view.editor) { this.drag_div = $("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div); }
         this.name_div = $("<div/>").addClass("track-name").appendTo(this.header_div).text(this.name)
@@ -2275,6 +2279,9 @@ var Track = function(name, view, container, prefs, data_url, data_query_wait) {
         this.settings_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Edit settings")
                                       .addClass("icon-button settings-icon").tipsy( {gravity: 's'} )
                                       .appendTo(this.icons_div);
+        this.overview_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Set as overview")
+                                      .addClass("icon-button overview-icon").tipsy( {gravity: 's'} )
+                                      .appendTo(this.icons_div);
         this.filters_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Filters")
                                      .addClass("icon-button filters-icon").tipsy( {gravity: 's'} )
                                      .appendTo(this.icons_div).hide();
@@ -2312,18 +2319,10 @@ var Track = function(name, view, container, prefs, data_url, data_query_wait) {
             });
         });
         
-        // FIXME: old code for overview.
-        /*
-        track_dropdown[(this.is_overview ? "Hide overview" : "Set as overview")] = function() {
-            if (track.is_overview) {
-                track.view.reset_overview();
-            }
-            else {
-                track.view.set_overview(track);
-            }
-        };
-        */
-        
+        this.overview_icon.click( function() {
+            track.view.set_overview(track);
+        });
+                
         this.filters_icon.click( function() {
             // TODO: update tipsy text.            
             track.filters_div.toggle();
@@ -2488,7 +2487,7 @@ extend(Track.prototype, Drawable.prototype, {
     /**
      * Additional initialization required before drawing track for the first time.
      */
-    predraw_init: function() {},
+    predraw_init: function() {}
 });
 
 var TiledTrack = function(filters_list, tool_dict) {
@@ -2504,27 +2503,32 @@ var TiledTrack = function(filters_list, tool_dict) {
     this.filters_available = false;
     this.filters_visible = false;
     this.tool = (tool_dict !== undefined && obj_length(tool_dict) > 0 ? new Tool(this, tool_dict) : undefined);
-    this.is_overview = false;
     
-    if (track.hidden) { return; }
+    if (this.header_div) {
+        //
+        // Create filters div.
+        //
+        if (this.filters_manager) {
+            this.filters_div = this.filters_manager.parent_div
+            this.header_div.after(this.filters_div);
+        }
         
-    //
-    // Create filters div.
-    //
-    if (this.filters_manager) {
-        this.filters_div = this.filters_manager.parent_div
-        this.header_div.after(this.filters_div);
-    }
-        
-    //
-    // Create dynamic tool div.
-    //
-    if (this.tool) {  
-        this.dynamic_tool_div = this.tool.parent_div;
-        this.header_div.after(this.dynamic_tool_div);
+        //
+        // Create dynamic tool div.
+        //
+        if (this.tool) {  
+            this.dynamic_tool_div = this.tool.parent_div;
+            this.header_div.after(this.dynamic_tool_div);
+        }
     }
 };
 extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
+    /**
+     * Returns a copy of the track.
+     */
+    copy: function(container) {        
+        return new this.constructor(this.name, this.view, container, this.hda_ldda, this.dataset_id, this.prefs, this.filters, this.tool);
+    },
     /**
      * Convert track to JSON object.
      */
@@ -2588,52 +2592,6 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
         }
         */
     },
-    /**
-     * Set track's overview status.
-     */
-    set_is_overview: function(is_overview) {
-        this.is_overview = is_overview;
-        this.update_track_icons();
-    },
-    /**
-     * Returns a jQuery Deferred object that resolves to a Tile with track's overview.
-     * TODO: this should be the approach used when drawing any tile so that tile drawing is not blocking.
-     */
-    get_overview_tile: function() {
-        var 
-            track = this;
-            view = track.view,
-            resolution = Math.pow(RESOLUTION, Math.ceil( Math.log( (view.max_high - view.max_low) / DENSITY ) / Math.log(RESOLUTION) )),
-            view_width = view.container.width(),
-            // w_scale units are pixels per base.
-            w_scale =  view_width / (view.max_high - view.max_low),
-            overview_tile = $.Deferred();
-        $.when(track.data_manager.get_data(view.max_low, view.max_high, "Auto", resolution, track.data_url_extra_params)).then(function(overview_data) {
-            var 
-                key = track._gen_tile_cache_key(view_width, w_scale, 0),
-                tile = track.tile_cache.get(key);
-                
-            // Draw tile if necessary.
-            if (!tile) {
-                tile = track.draw_tile(overview_data, "Auto", resolution, 0, w_scale);
-                track.tile_cache.set(key, tile);                
-            }
-            
-            // Always copy tile because it may need to be used in viz.
-            var 
-                src_canvas = $(tile.canvas.find("canvas")),
-                new_canvas = src_canvas.clone(), 
-                src_ctx = src_canvas.get(0).getContext("2d"),
-                tgt_ctx = new_canvas.get(0).getContext("2d"),
-                data = src_ctx.getImageData(0, 0, src_ctx.canvas.width, src_ctx.canvas.height);
-            // Need to undo offsets when placing image data.
-            tgt_ctx.putImageData(data, -track.left_offset, (tile.data.dataset_type === "summary_tree" ? SUMMARY_TREE_TOP_PADDING : 0));
-            new_tile = new Tile(track, -1, resolution, new_canvas);
-            overview_tile.resolve(new_tile);
-        });
-        
-        return overview_tile;
-    },
     /**
      * Generate a key for the tile cache.
      * TODO: create a TileCache object (like DataCache) and generate key internally.
@@ -2667,6 +2625,14 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
             w_scale = width / range,
             resolution = this.view.resolution,
             parent_element = $("<div style='position: relative;'></div>");
+            
+        // For overview, adjust high, low, resolution, and w_scale.
+        if (this.is_overview) {
+            low = this.view.max_low;
+            high = this.view.max_high;
+            resolution = Math.pow(RESOLUTION, Math.ceil( Math.log( (view.max_high - view.max_low) / DENSITY ) / Math.log(RESOLUTION) ));
+            w_scale = width / (view.max_high - view.max_low);
+        }
         
         if (!clear_after) { this.content_div.children().remove(); }
         this.content_div.append( parent_element );
@@ -2777,7 +2743,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
          
         // Can't draw now, so trigger another redraw when the data is ready
         $.when( tile_data, seq_data ).then( function() {
-            view.request_redraw();
+            view.request_redraw(false, false, false, track);
         });
         
         // Indicate to caller that this tile could not be drawn
@@ -2837,8 +2803,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
         tile.predisplay_actions();
       
         // Position tile element, recalculate left position at display time
-        var range = this.view.high - this.view.low,
-            left = (tile.low - this.view.low) * w_scale;
+        var left = ( tile.low - (this.is_overview? this.view.max_low : this.view.low) ) * w_scale;
         if (this.left_offset) {
             left -= this.left_offset;
         }
@@ -2875,8 +2840,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
 });
 
 var LabelTrack = function (view, container) {
-    this.hidden = true;
-    Track.call(this, "label", view, container, {} );
+    Track.call(this, "label", view, container, false, {} );
     this.container_div.addClass( "label-track" );
 };
 extend(LabelTrack.prototype, Track.prototype, {
@@ -2906,8 +2870,7 @@ extend(LabelTrack.prototype, Track.prototype, {
 });
 
 var ReferenceTrack = function (view) {
-    this.hidden = true;
-    Track.call(this, "reference", view, { content_div: view.top_labeltrack }, {});
+    Track.call(this, "reference", view, { content_div: view.top_labeltrack }, false, {});
     TiledTrack.call(this);
     
     view.reference_track = this;
@@ -3109,7 +3072,7 @@ var FeatureTrack = function(name, view, container, hda_ldda, dataset_id, prefs,
     //
     
     // FIXME: cleaner init needed; should just be able to call TiledTrack()
-    Track.call(this, name, view, container, prefs);
+    Track.call(this, name, view, container, true, prefs);
     TiledTrack.call(this, filters, tool);
 
     // Define and restore track configuration.
@@ -3371,9 +3334,12 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
         if (mode === "Auto") {
             if (result.dataset_type === "summary_tree") {
                 mode = result.dataset_type;
-            } else if (result.extra_info === "no_detail") {
+            } 
+            // HACK: use no_detail mode track is in overview to prevent overview from being too large.
+            else if (result.extra_info === "no_detail" || track.is_overview) {
                 mode = "no_detail";
-            } else {
+            } 
+            else {
                 // Choose b/t Squish and Pack.
                 // Proxy measures for using Squish: 
                 // (a) error message re: limiting number of features shown; 
diff --git a/static/scripts/trackster_ui.js b/static/scripts/trackster_ui.js
index 900dfc6a929..87b0f68e2b7 100644
--- a/static/scripts/trackster_ui.js
+++ b/static/scripts/trackster_ui.js
@@ -114,7 +114,7 @@ var create_visualization = function(parent_elt, title, id, dbkey, viewport_confi
         // Set overview.
         var overview_track;
         for (var i = 0; i < view.drawables.length; i++) {
-            if (view.drawables[i].name == overview_track_name) {
+            if (view.drawables[i].name === overview_track_name) {
                 view.set_overview(view.drawables[i]);
                 break;
             }
diff --git a/templates/tracks/browser.mako b/templates/tracks/browser.mako
index 565aa4743d2..86d860a2289 100644
--- a/templates/tracks/browser.mako
+++ b/templates/tracks/browser.mako
@@ -195,7 +195,8 @@ ${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.e
                     };
                 });
 
-                var overview_track_name = (view.overview_track ? view.overview_track.name : null);
+                // FIXME: give unique IDs to Drawables and save overview as ID.
+                var overview_track_name = (view.overview_drawable ? view.overview_drawable.name : null);
                 var payload = { 
                     'view': view.to_json(), 
                     'viewport': { 'chrom': view.chrom, 'start': view.low , 'end': view.high, 'overview': overview_track_name },

From 613d2cfc899fcfc1222364fc893e3293b7e95de8 Mon Sep 17 00:00:00 2001
From: Jim Johnson <jj@umn.edu>
Date: Mon, 24 Oct 2011 15:02:07 -0500
Subject: [PATCH 084/362] FASTQ de-interlacer - fix for memory leak

---
 tools/fastq/fastq_paired_end_deinterlacer.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/tools/fastq/fastq_paired_end_deinterlacer.py b/tools/fastq/fastq_paired_end_deinterlacer.py
index b409544ca21..558326411e3 100644
--- a/tools/fastq/fastq_paired_end_deinterlacer.py
+++ b/tools/fastq/fastq_paired_end_deinterlacer.py
@@ -21,12 +21,14 @@ def main():
     i = None
     skip_count = 0
     found = {}
-    for i, mate1 in enumerate( fastqReader( open( input_filename, 'rb' ), format = type ) ):
+    for i, read in enumerate( fastqReader( open( input_filename, 'rb' ), format = type ) ):
      
-        if mate1.identifier in found:
-            del found[mate1.identifier]
+        if read.identifier in found:
+            del found[read.identifier]
             continue
 
+        mate1 = input.get( read.identifier )
+
         mate2 = input.get( joiner.get_paired_identifier( mate1 ) )
 
         if mate2:

From 5d964a4a24495dc8f18826cced18b176fb3f8026 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Mon, 24 Oct 2011 16:11:20 -0400
Subject: [PATCH 085/362] Add Picard tools FASTQ to SAM (makes BAM) tool. Add
 Picard tools SAM to FASTQ tool.

---
 tool_conf.xml.sample               |   4 +-
 tools/picard/picard_FastqToSam.xml | 143 ++++++++++++++++++++++++++
 tools/picard/picard_SamToFastq.xml | 160 +++++++++++++++++++++++++++++
 3 files changed, 306 insertions(+), 1 deletion(-)
 create mode 100644 tools/picard/picard_FastqToSam.xml
 create mode 100644 tools/picard/picard_SamToFastq.xml

diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index 3f02ba7cbd3..d309da3e364 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -295,6 +295,9 @@
     <tool file="fastx_toolkit/fastx_trimmer.xml" />
   </section>
   <section name="NGS: Picard (beta)" id="picard_beta">
+    <label text="Conversion" id="picard_conversion"/>
+    <tool file="picard/picard_FastqToSam.xml" />
+    <tool file="picard/picard_SamToFastq.xml" />
     
     <label text="QC/Metrics for sam/bam" id="qcsambam"/>
     <tool file="picard/picard_BamIndexStats.xml" />
@@ -390,7 +393,6 @@
     
     <label text="Filtration" id="gatk_filtration" />
     <tool file="gatk/variant_filtration.xml" />
-    <tool file="gatk/variant_filtration.xml" />
     
     <label text="Variant Quality Score Recalibration" id="gatk_variant_quality_score_recalibration" />
     <tool file="gatk/variant_recalibrator.xml" />
diff --git a/tools/picard/picard_FastqToSam.xml b/tools/picard/picard_FastqToSam.xml
new file mode 100644
index 00000000000..0eafc51e76a
--- /dev/null
+++ b/tools/picard/picard_FastqToSam.xml
@@ -0,0 +1,143 @@
+<tool id="picard_FastqToSam" name="FASTQ to BAM" version="0.0.1">
+  <description>creates an unaligned BAM file</description>
+  <command>java  -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC
+    -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/FastqToSam.jar"
+    FASTQ="${input_fastq1}"
+    #if str( $input_fastq2) != "None":
+        FASTQ2="${input_fastq2}"
+    #end if
+    QUALITY_FORMAT="${ dict( fastqsanger='Standard', fastqcssanger='Standard', fastqillumina='Illumina', fastqsolexa='Solexa' )[ $input_fastq1.ext ] }" ##Solexa, Illumina, Standard
+    OUTPUT="${output_bam}"
+    READ_GROUP_NAME="${read_group_name}"
+    SAMPLE_NAME="${sample_name}" 
+    #if $param_type.param_type_selector == "advanced":
+        #if str( $param_type.library_name ) != "":
+            LIBRARY_NAME="${param_type.library_name}" 
+        #end if
+        #if str( $param_type.platform_unit ) != "":
+            PLATFORM_UNIT="${param_type.platform_unit}"
+        #end if
+        #if str( $param_type.platform ) != "":
+            PLATFORM="${param_type.platform}"
+        #end if 
+        #if str( $param_type.sequencing_center ) != "":
+            SEQUENCING_CENTER="${param_type.sequencing_center}"
+        #end if 
+        #if str( $param_type.predicted_insert_size ) != "":
+            PREDICTED_INSERT_SIZE="${param_type.predicted_insert_size}"
+        #end if 
+        #if str( $param_type.description.value ) != "":
+            DESCRIPTION="${param_type.description}"
+        #end if 
+        #if str( $param_type.run_date ) != "":
+            RUN_DATE="${param_type.run_date}"
+        #end if
+        #if str( $param_type.min_q ) != "":
+            MIN_Q="${param_type.min_q}"
+        #end if
+        #if str( $param_type.min_q ) != "":
+            MAX_Q="${param_type.max_q}"
+        #end if
+        SORT_ORDER="${param_type.sort_order}"
+    #else:
+        SORT_ORDER=coordinate ##unsorted, queryname, coordinate; always use coordinate
+    #end if
+  2&gt;&amp;1 
+  || echo "Error running Picard FastqToSAM" >&amp;2
+  </command>
+  <inputs>
+    <param name="input_fastq1" type="data" format="fastqsanger,fastqillumina,fastqsolexa,fastqcssanger" label="FASTQ file" /> <!-- confirm that fastqcssanger also works -->
+    <param name="input_fastq2" type="data" format="fastqsanger,fastqillumina,fastqsolexa,fastqcssanger" optional="True" label="Second FASTQ of paired end data" help="Only needed when using paired end data." >
+      <options options_filter_attribute="ext" from_parameter="tool.app.datatypes_registry.datatypes_by_extension" transform_lines="obj.keys()">
+        <column name="name" index="0"/>
+        <column name="value" index="0"/>
+        <filter type="param_value" ref="input_fastq1" ref_attribute="ext" column="0"/> 
+      </options>
+    </param>
+    <param name="read_group_name" type="text" value="A" label="Read Group Name" />
+    <param name="sample_name" type="text" value="unknown sample" label="Sample Name" />
+    <conditional name="param_type">
+      <param name="param_type_selector" type="select" label="Basic or Advanced options">
+        <option value="basic" selected="True">Basic</option>
+        <option value="advanced">Advanced</option>
+      </param>
+      <when value="basic">
+        <!-- Do nothing here -->
+      </when>
+      <when value="advanced">
+        <param name="library_name" type="text" value="" label="Library Name" />
+        <param name="platform_unit" type="text" value="" label="Platform Unit" />
+        <param name="platform" type="text" value="" label="Platform" />
+        <param name="sequencing_center" type="text" value="" label="Sequencing Center" />
+        <param name="predicted_insert_size" type="integer" value="" optional="True" label="Predicted Insert Size" />
+        <param name="description" type="text" value="" label="Description" />
+        <param name="run_date" type="text" value="" label="Run Date" />
+        <param name="min_q" type="integer" optional="True" value="0" label="Min Q" />
+        <param name="max_q" type="integer" optional="True" value="93" label="Max Q" />
+        <param name="sort_order" type="select" label="Sort order">
+          <option value="coordinate" selected="True">coordinate</option>
+          <option value="queryname">queryname</option>
+          <option value="unsorted">unsorted</option>
+        </param>
+      </when>
+    </conditional>
+  </inputs>
+  <outputs>
+    <data format="bam" name="output_bam" />
+  </outputs>
+  <tests>
+      <test>
+          <param name="input_fastq1" value="bwa_wrapper_in2.fastqsanger" ftype="fastqsanger" />
+          <param name="input_fastq2" />
+          <param name="read_group_name" value="A" />
+          <param name="sample_name" value="unknown sample" />
+          <param name="param_type_selector" value="basic" />
+          <output name="output_bam" file="picard_fastq_to_sam_out1.bam" ftype="bam"/> 
+      </test>
+      <test>
+          <param name="input_fastq1" value="bwa_wrapper_in2.fastqsanger" ftype="fastqsanger" />
+          <param name="input_fastq2" value="bwa_wrapper_in3.fastqsanger" ftype="fastqsanger" />
+          <param name="read_group_name" value="A" />
+          <param name="sample_name" value="unknown sample" />
+          <param name="param_type_selector" value="basic" />
+          <output name="output_bam" file="picard_fastq_to_sam_out2.bam" ftype="bam"/> 
+      </test>
+  </tests>
+  <help>
+**What it does**
+
+Picard: FastqToSam converts FASTQ files to unaligned BAM files.
+
+------
+
+Please cite the website "http://picard.sourceforge.net".
+
+------
+
+
+**Input formats**
+
+FastqToSam accepts FASTQ input files. If using paired-end data, you should select two FASTQ files.
+
+------
+
+**Outputs**
+
+The output is in BAM format, see http://samtools.sourceforge.net for more details.
+
+-------
+
+**FastqToSam settings**
+
+This is list of FastqToSam options::
+
+ READ_GROUP_NAME=String	Read group name Default value: A. This option can be set to 'null' to clear the default value.
+ SAMPLE_NAME=String	Sample name to insert into the read group header Required.
+ LIBRARY_NAME=String	The library name to place into the LB attribute in the read group header Default value: null.
+ PLATFORM_UNIT=String	The platform unit (often run_barcode.lane) to insert into the read group header Default value: null.
+ PLATFORM=String	The platform type (e.g. illumina, solid) to insert into the read group header Default value: null.
+ SEQUENCING_CENTER=String	The sequencing center from which the data originated Default value: null.
+ PREDICTED_INSERT_SIZE=Integer	Predicted median insert size, to insert into the read group header Default value: null.
+ DESCRIPTION=String	Inserted into the read group header Default value: null. 
+  </help>
+</tool>
diff --git a/tools/picard/picard_SamToFastq.xml b/tools/picard/picard_SamToFastq.xml
new file mode 100644
index 00000000000..d123a42d27f
--- /dev/null
+++ b/tools/picard/picard_SamToFastq.xml
@@ -0,0 +1,160 @@
+<tool id="picard_SamToFastq" name="SAM to FASTQ" version="0.0.1">
+  <description>creates a FASTQ file</description>
+  <command>java -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC
+    -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/SamToFastq.jar"
+    INPUT="${input_sam}"
+    RE_REVERSE=${re_reverse}
+    INCLUDE_NON_PF_READS=${include_non_pf_reads}
+    #if str( $clipping_attribute ):
+        CLIPPING_ATTRIBUTE="${clipping_attribute}"
+    #end if
+    #if str( $clipping_action ):
+        CLIPPING_ACTION="${clipping_action}"
+    #end if
+    #if str( $read1_trim ):
+        READ1_TRIM="${read1_trim}"
+    #end if
+    #if str( $read1_max_bases_to_write ):
+        READ1_MAX_BASES_TO_WRITE="${read1_max_bases_to_write}"
+    #end if
+    INCLUDE_NON_PRIMARY_ALIGNMENTS=${include_non_primary_alignments}
+    
+    #if str( $output_per_read_group.output_per_read_group_selector ) == 'per_sam_file':
+        ##OUTPUT_PER_RG=false
+        FASTQ="${output_fastq1}"
+        
+        #if str( $output_per_read_group.single_paired_end_type.single_paired_end_type_selector ) == 'paired':
+            SECOND_END_FASTQ="${output_fastq2}"
+            #if str( $output_per_read_group.single_paired_end_type.read2_trim ): 
+                READ2_TRIM="${output_per_read_group.single_paired_end_type.read2_trim}"
+            #end if
+            #if str( $output_per_read_group.single_paired_end_type.read2_max_bases_to_write ):
+                READ2_MAX_BASES_TO_WRITE="${output_per_read_group.single_paired_end_type.read2_max_bases_to_write}"
+            #end if
+        #end if
+    #else:
+        #raise Exception( 'Per Read Group not yet supported.' )
+        OUTPUT_PER_RG=true
+        OUTPUT_DIR="./picard_sam_to_fastq_tmp_dir/"
+    #end if
+  2&gt;&amp;1 
+  || echo "Error running SamToFastq" >&amp;2
+  ##&amp;&amp; echo "die die die" >&amp;2
+  </command>
+  <inputs>
+    <param name="input_sam" type="data" format="sam" label="SAM file" />
+    <param name="read1_trim" type="integer" value="" optional="True" label="The number of bases to trim from the beginning of read 1." />
+    <param name="read1_max_bases_to_write" type="integer" optional="True" value="" label="The maximum number of bases to write from read 1 after trimming." />
+    <conditional name="output_per_read_group">
+      <param name="output_per_read_group_selector" type="select" label="Output per read group">
+        <option value="per_sam_file" selected="True">Per SAM file</option>
+        <option value="per_read_group">Per Read Group</option>
+        <validator type="expression" message="Per Read Group selection is not yet implemented">value == 'per_sam_file'</validator>
+      </param>
+      <when value="per_sam_file">
+        <conditional name="single_paired_end_type">
+          <param name="single_paired_end_type_selector" type="select" label="Single or Paired end">
+            <option value="single" selected="True">Single</option>
+            <option value="paired">Paired end</option>
+          </param>
+          <when value="single">
+            <!-- nothing yet -->
+          </when>
+          <when value="paired">
+            <param name="read2_trim" type="integer" value="" optional="True" label="The number of bases to trim from the beginning of read 2." />
+            <param name="read2_max_bases_to_write" type="integer" optional="True" value="" label="The maximum number of bases to write from read 2 after trimming." />
+          </when>
+        </conditional>
+      </when>
+      <when value="per_read_group">
+        <!-- Fix me -->
+      </when>
+    </conditional>
+    <param name="re_reverse" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Re-reverse bases and qualities of reads on negative strand"/>
+    <param name="include_non_pf_reads" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Include non-PF reads from the SAM file into the output FASTQ files."/>
+    <param name="clipping_attribute" type="text" value="" label="The attribute that stores the position at which the SAM record should be clipped" help="Leave blank for null" />
+    <param name="clipping_action" type="text" value="" label="The action that should be taken with clipped reads" help="'X' means the reads and qualities should be trimmed at the clipped position; 'N' means the bases should be changed to Ns in the clipped region; and any integer means that the base qualities should be set to that value in the clipped region. Leave blank for null" />
+    <param name="include_non_primary_alignments" type="boolean" truevalue="true" falsevalue="false" checked="False" label="If true, include non-primary alignments in the output." help="Support of non-primary alignments in SamToFastq is not comprehensive, so there may be exceptions if this is set to true and there are paired reads with non-primary alignments."/>
+    
+  </inputs>
+  <outputs>
+    <data format="fastqsanger" name="output_fastq1" label="${tool.name} on ${on_string}: FASTQ 1" />
+    <data format="fastqsanger" name="output_fastq2" label="${tool.name} on ${on_string}: FASTQ 2" >
+        <filter>output_per_read_group['single_paired_end_type']['single_paired_end_type_selector'] == 'paired'</filter>
+    </data>
+  </outputs>
+  <tests>
+      <test>
+          <param name="input_sam" value="bfast_out1.sam" ftype="sam" />
+          <param name="output_per_read_group_selector" value="per_sam_file" />
+          <param name="single_paired_end_type_selector" value="single" />
+          <param name="read1_trim" value="" />
+          <param name="read1_max_bases_to_write" value="" />
+          <param name="re_reverse" value="True" />
+          <param name="include_non_pf_reads" value="False" />
+          <param name="clipping_attribute" value="" />
+          <param name="include_non_primary_alignments" value="False" />
+          <output name="output_fastq1" file="random_phiX_1.fastqsanger"/> 
+      </test>
+      <test>
+          <param name="input_sam" value="bwa_wrapper_out3.sam" ftype="sam" />
+          <param name="output_per_read_group_selector" value="per_sam_file" />
+          <param name="single_paired_end_type_selector" value="paired" />
+          <param name="read1_trim" value="" />
+          <param name="read1_max_bases_to_write" value="" />
+          <param name="read2_trim" value="" />
+          <param name="read2_max_bases_to_write" value="" />
+          <param name="re_reverse" value="True" />
+          <param name="include_non_pf_reads" value="False" />
+          <param name="clipping_attribute" value="" />
+          <param name="include_non_primary_alignments" value="False" />
+          <output name="output_fastq1" file="bwa_wrapper_in2.fastqsanger" lines_diff="64"/> <!-- 16 unaligned fastq blocks not present in original sam file -->
+          <output name="output_fastq2" file="bwa_wrapper_in3.fastqsanger" lines_diff="64"/> <!-- 16 unaligned fastq blocks not present in original sam file -->
+      </test>
+  </tests>
+  <help>
+**What it does**
+
+Picard: SamToFastq converts SAM files to FASTQ files.
+
+Extracts read sequences and qualities from the input SAM/BAM file and writes them into the output file in Sanger fastq format. In the RC mode (default is True), if the read is aligned and the alignment is to the reverse strand on the genome, the read's sequence from input SAM file will be reverse-complemented prior to writing it to fastq in order restore correctly the original read sequence as it was generated by the sequencer.
+
+------
+
+Please cite the website "http://picard.sourceforge.net".
+
+------
+
+
+**Input formats**
+
+FastqToSam accepts SAM input files, see http://samtools.sourceforge.net for more details.
+
+------
+
+**Outputs**
+
+The output is in FASTQ format. If using Paired end data, 2 fastq files are created.
+
+-------
+
+**FastqToSam settings**
+
+This is list of SamToFastq options::
+
+NPUT=File	Input SAM/BAM file to extract reads from Required.
+FASTQ=File	Output fastq file (single-end fastq or, if paired, first end of the pair fastq). Required. Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG)
+SECOND_END_FASTQ=File	Output fastq file (if paired, second end of the pair fastq). Default value: null. Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG)
+OUTPUT_PER_RG=Boolean	Output a fastq file per read group (two fastq files per read group if the group is paired). Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false} Cannot be used in conjuction with option(s) SECOND_END_FASTQ (F2) FASTQ (F)
+OUTPUT_DIR=File	Directory in which to output the fastq file(s). Used only when OUTPUT_PER_RG is true. Default value: null.
+RE_REVERSE=Boolean	Re-reverse bases and qualities of reads with negative strand flag set before writing them to fastq Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false}
+INCLUDE_NON_PF_READS=Boolean	Include non-PF reads from the SAM file into the output FASTQ files. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
+CLIPPING_ATTRIBUTE=String	The attribute that stores the position at which the SAM record should be clipped Default value: null.
+CLIPPING_ACTION=String	The action that should be taken with clipped reads: 'X' means the reads and qualities should be trimmed at the clipped position; 'N' means the bases should be changed to Ns in the clipped region; and any integer means that the base qualities should be set to that value in the clipped region. Default value: null.
+READ1_TRIM=Integer	The number of bases to trim from the beginning of read 1. Default value: 0. This option can be set to 'null' to clear the default value.
+READ1_MAX_BASES_TO_WRITE=Integer	The maximum number of bases to write from read 1 after trimming. If there are fewer than this many bases left after trimming, all will be written. If this value is null then all bases left after trimming will be written. Default value: null.
+READ2_TRIM=Integer	The number of bases to trim from the beginning of read 2. Default value: 0. This option can be set to 'null' to clear the default value.
+READ2_MAX_BASES_TO_WRITE=Integer	The maximum number of bases to write from read 2 after trimming. If there are fewer than this many bases left after trimming, all will be written. If this value is null then all bases left after trimming will be written. Default value: null.
+INCLUDE_NON_PRIMARY_ALIGNMENTS=Boolean	If true, include non-primary alignments in the output. Support of non-primary alignments in SamToFastq is not comprehensive, so there may be exceptions if this is set to true and there are paired reads with non-primary alignments. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false} 
+  </help>
+</tool>

From 15f3277e9ff0d0a796f87406b40435ee9ae299d1 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 24 Oct 2011 15:27:17 -0500
Subject: [PATCH 086/362] Creating branch for JJ's fastq-deinterlacer memory
 hole fix.


From 25a4ac338d7f878df630ee750abb0be3194474ff Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Mon, 24 Oct 2011 16:32:13 -0400
Subject: [PATCH 087/362] Update for Sam to Fastq.

---
 tools/picard/picard_SamToFastq.xml | 79 ++++++++++++++----------------
 1 file changed, 37 insertions(+), 42 deletions(-)

diff --git a/tools/picard/picard_SamToFastq.xml b/tools/picard/picard_SamToFastq.xml
index d123a42d27f..7ac90d17e14 100644
--- a/tools/picard/picard_SamToFastq.xml
+++ b/tools/picard/picard_SamToFastq.xml
@@ -19,17 +19,17 @@
     #end if
     INCLUDE_NON_PRIMARY_ALIGNMENTS=${include_non_primary_alignments}
     
-    #if str( $output_per_read_group.output_per_read_group_selector ) == 'per_sam_file':
+    #if str( $output_per_read_group_selector ) == 'per_sam_file':
         ##OUTPUT_PER_RG=false
         FASTQ="${output_fastq1}"
         
-        #if str( $output_per_read_group.single_paired_end_type.single_paired_end_type_selector ) == 'paired':
+        #if str( $single_paired_end_type.single_paired_end_type_selector ) == 'paired':
             SECOND_END_FASTQ="${output_fastq2}"
-            #if str( $output_per_read_group.single_paired_end_type.read2_trim ): 
-                READ2_TRIM="${output_per_read_group.single_paired_end_type.read2_trim}"
+            #if str( $single_paired_end_type.read2_trim ): 
+                READ2_TRIM="${single_paired_end_type.read2_trim}"
             #end if
-            #if str( $output_per_read_group.single_paired_end_type.read2_max_bases_to_write ):
-                READ2_MAX_BASES_TO_WRITE="${output_per_read_group.single_paired_end_type.read2_max_bases_to_write}"
+            #if str( $single_paired_end_type.read2_max_bases_to_write ):
+                READ2_MAX_BASES_TO_WRITE="${single_paired_end_type.read2_max_bases_to_write}"
             #end if
         #end if
     #else:
@@ -45,29 +45,22 @@
     <param name="input_sam" type="data" format="sam" label="SAM file" />
     <param name="read1_trim" type="integer" value="" optional="True" label="The number of bases to trim from the beginning of read 1." />
     <param name="read1_max_bases_to_write" type="integer" optional="True" value="" label="The maximum number of bases to write from read 1 after trimming." />
-    <conditional name="output_per_read_group">
-      <param name="output_per_read_group_selector" type="select" label="Output per read group">
-        <option value="per_sam_file" selected="True">Per SAM file</option>
-        <option value="per_read_group">Per Read Group</option>
-        <validator type="expression" message="Per Read Group selection is not yet implemented">value == 'per_sam_file'</validator>
+    <param name="output_per_read_group_selector" type="select" label="Output per read group">
+      <option value="per_sam_file" selected="True">Per SAM file</option>
+      <!-- <option value="per_read_group">Per Read Group</option> -->
+      <validator type="expression" message="Per Read Group selection is not yet implemented">value == 'per_sam_file'</validator>
+    </param>
+    <conditional name="single_paired_end_type">
+      <param name="single_paired_end_type_selector" type="select" label="Single or Paired end">
+        <option value="single" selected="True">Single</option>
+        <option value="paired">Paired end</option>
       </param>
-      <when value="per_sam_file">
-        <conditional name="single_paired_end_type">
-          <param name="single_paired_end_type_selector" type="select" label="Single or Paired end">
-            <option value="single" selected="True">Single</option>
-            <option value="paired">Paired end</option>
-          </param>
-          <when value="single">
-            <!-- nothing yet -->
-          </when>
-          <when value="paired">
-            <param name="read2_trim" type="integer" value="" optional="True" label="The number of bases to trim from the beginning of read 2." />
-            <param name="read2_max_bases_to_write" type="integer" optional="True" value="" label="The maximum number of bases to write from read 2 after trimming." />
-          </when>
-        </conditional>
+      <when value="single">
+        <!-- nothing yet -->
       </when>
-      <when value="per_read_group">
-        <!-- Fix me -->
+      <when value="paired">
+        <param name="read2_trim" type="integer" value="" optional="True" label="The number of bases to trim from the beginning of read 2." />
+        <param name="read2_max_bases_to_write" type="integer" optional="True" value="" label="The maximum number of bases to write from read 2 after trimming." />
       </when>
     </conditional>
     <param name="re_reverse" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Re-reverse bases and qualities of reads on negative strand"/>
@@ -80,7 +73,7 @@
   <outputs>
     <data format="fastqsanger" name="output_fastq1" label="${tool.name} on ${on_string}: FASTQ 1" />
     <data format="fastqsanger" name="output_fastq2" label="${tool.name} on ${on_string}: FASTQ 2" >
-        <filter>output_per_read_group['single_paired_end_type']['single_paired_end_type_selector'] == 'paired'</filter>
+        <filter>single_paired_end_type['single_paired_end_type_selector'] == 'paired'</filter>
     </data>
   </outputs>
   <tests>
@@ -141,20 +134,22 @@ The output is in FASTQ format. If using Paired end data, 2 fastq files are creat
 **FastqToSam settings**
 
 This is list of SamToFastq options::
+  
+  INPUT=File	Input SAM/BAM file to extract reads from Required.
+  FASTQ=File	Output fastq file (single-end fastq or, if paired, first end of the pair fastq). Required. Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG)
+  SECOND_END_FASTQ=File	Output fastq file (if paired, second end of the pair fastq). Default value: null. Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG)
+  OUTPUT_PER_RG=Boolean	Output a fastq file per read group (two fastq files per read group if the group is paired). Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false} Cannot be used in conjuction with option(s) SECOND_END_FASTQ (F2) FASTQ (F)
+  OUTPUT_DIR=File	Directory in which to output the fastq file(s). Used only when OUTPUT_PER_RG is true. Default value: null.
+  RE_REVERSE=Boolean	Re-reverse bases and qualities of reads with negative strand flag set before writing them to fastq Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false}
+  INCLUDE_NON_PF_READS=Boolean	Include non-PF reads from the SAM file into the output FASTQ files. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
+  CLIPPING_ATTRIBUTE=String	The attribute that stores the position at which the SAM record should be clipped Default value: null.
+  CLIPPING_ACTION=String	The action that should be taken with clipped reads: 'X' means the reads and qualities should be trimmed at the clipped position; 'N' means the bases should be changed to Ns in the clipped region; and any integer means that the base qualities should be set to that value in the clipped region. Default value: null.
+  READ1_TRIM=Integer	The number of bases to trim from the beginning of read 1. Default value: 0. This option can be set to 'null' to clear the default value.
+  READ1_MAX_BASES_TO_WRITE=Integer	The maximum number of bases to write from read 1 after trimming. If there are fewer than this many bases left after trimming, all will be written. If this value is null then all bases left after trimming will be written. Default value: null.
+  READ2_TRIM=Integer	The number of bases to trim from the beginning of read 2. Default value: 0. This option can be set to 'null' to clear the default value.
+  READ2_MAX_BASES_TO_WRITE=Integer	The maximum number of bases to write from read 2 after trimming. If there are fewer than this many bases left after trimming, all will be written. If this value is null then all bases left after trimming will be written. Default value: null.
+  INCLUDE_NON_PRIMARY_ALIGNMENTS=Boolean	If true, include non-primary alignments in the output. Support of non-primary alignments in SamToFastq is not comprehensive, so there may be exceptions if this is set to true and there are paired reads with non-primary alignments. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false} 
+
 
-NPUT=File	Input SAM/BAM file to extract reads from Required.
-FASTQ=File	Output fastq file (single-end fastq or, if paired, first end of the pair fastq). Required. Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG)
-SECOND_END_FASTQ=File	Output fastq file (if paired, second end of the pair fastq). Default value: null. Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG)
-OUTPUT_PER_RG=Boolean	Output a fastq file per read group (two fastq files per read group if the group is paired). Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false} Cannot be used in conjuction with option(s) SECOND_END_FASTQ (F2) FASTQ (F)
-OUTPUT_DIR=File	Directory in which to output the fastq file(s). Used only when OUTPUT_PER_RG is true. Default value: null.
-RE_REVERSE=Boolean	Re-reverse bases and qualities of reads with negative strand flag set before writing them to fastq Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false}
-INCLUDE_NON_PF_READS=Boolean	Include non-PF reads from the SAM file into the output FASTQ files. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
-CLIPPING_ATTRIBUTE=String	The attribute that stores the position at which the SAM record should be clipped Default value: null.
-CLIPPING_ACTION=String	The action that should be taken with clipped reads: 'X' means the reads and qualities should be trimmed at the clipped position; 'N' means the bases should be changed to Ns in the clipped region; and any integer means that the base qualities should be set to that value in the clipped region. Default value: null.
-READ1_TRIM=Integer	The number of bases to trim from the beginning of read 1. Default value: 0. This option can be set to 'null' to clear the default value.
-READ1_MAX_BASES_TO_WRITE=Integer	The maximum number of bases to write from read 1 after trimming. If there are fewer than this many bases left after trimming, all will be written. If this value is null then all bases left after trimming will be written. Default value: null.
-READ2_TRIM=Integer	The number of bases to trim from the beginning of read 2. Default value: 0. This option can be set to 'null' to clear the default value.
-READ2_MAX_BASES_TO_WRITE=Integer	The maximum number of bases to write from read 2 after trimming. If there are fewer than this many bases left after trimming, all will be written. If this value is null then all bases left after trimming will be written. Default value: null.
-INCLUDE_NON_PRIMARY_ALIGNMENTS=Boolean	If true, include non-primary alignments in the output. Support of non-primary alignments in SamToFastq is not comprehensive, so there may be exceptions if this is set to true and there are paired reads with non-primary alignments. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false} 
   </help>
 </tool>

From 9bcaef6c9fc6623a083e10d2f6fe29c1eda50876 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Mon, 24 Oct 2011 17:47:50 -0400
Subject: [PATCH 088/362] Trackster: set new track color randomly using W3C
 metrics.

---
 static/scripts/packed/trackster.js |  2 +-
 static/scripts/trackster.js        | 76 ++++++++++++++++++++++++++++--
 2 files changed, 73 insertions(+), 5 deletions(-)

diff --git a/static/scripts/packed/trackster.js b/static/scripts/packed/trackster.js
index 42d148ff92a..8f447b2887e 100644
--- a/static/scripts/packed/trackster.js
+++ b/static/scripts/packed/trackster.js
@@ -1 +1 @@
-var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var trackster_module=function(f,Z){var q=f("class").extend,t=f("slotting"),N=f("painters");var ag=function(ah,ai){this.document=ah;this.default_font=ai!==undefined?ai:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};q(ag.prototype,{load_pattern:function(ah,al){var ai=this.patterns,aj=this.dummy_context,ak=new Image();ak.src=image_path+al;ak.onload=function(){ai[ah]=aj.createPattern(ak,"repeat")}},get_pattern:function(ah){return this.patterns[ah]},new_canvas:function(){var ah=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ah)}ah.manager=this;return ah}});var o={};var m=function(ah,ai){o[ah.attr("id")]=ai};var n=function(ah,aj,al,ak){al=".group";var ai={};o[ah.attr("id")]=ak;ah.bind("drag",{handle:"."+aj,relative:true},function(au,av){var at=$(this);var ay=$(this).parent(),ap=ay.children(),ar=o[$(this).attr("id")],ao,an,aw,am,aq;an=$(this).parents(al);if(an.length!==0){aw=an.position().top;am=aw+an.outerHeight();if(av.offsetY<aw){$(this).insertBefore(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable_before(ar,ax);return}else{if(av.offsetY>am){$(this).insertAfter(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable(ar);return}}}an=null;for(aq=0;aq<ap.length;aq++){ao=$(ap.get(aq));aw=ao.position().top;am=aw+ao.outerHeight();if(ao.is(al)&&this!==ao.get(0)&&av.offsetY>=aw&&av.offsetY<=am){if(av.offsetY-aw<am-av.offsetY){ao.find(".content-div").prepend(this)}else{ao.find(".content-div").append(this)}if(ar.container){ar.container.remove_drawable(ar)}o[ao.attr("id")].add_drawable(ar);return}}for(aq=0;aq<ap.length;aq++){if(av.offsetY<$(ap.get(aq)).position().top){break}}if(aq===ap.length){if(this!==ap.get(aq-1)){ay.append(this);o[ay.attr("id")].move_drawable(ar,aq)}}else{if(this!==ap.get(aq)){$(this).insertBefore(ap.get(aq));o[ay.attr("id")].move_drawable(ar,(av.deltaY>0?aq-1:aq))}}}).bind("dragstart",function(){ai["border-top"]=ah.css("border-top");ai["border-bottom"]=ah.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ai)})};Z.moveable=n;var af=16,I=9,F=20,U=I+2,A=100,K=12000,S=200,D=5,w=10,M=5000,x=100,p="There was an error in indexing this dataset. ",L="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",u="Currently indexing... please wait",y="Tool cannot be rerun: ",a="Loading data...",aa="Ready for display",d=10,v=5,C=5;function ab(ai,ah){if(!ah){ah=0}var aj=Math.pow(10,ah);return Math.round(ai*aj)/aj}var c=function(ah){this.num_elements=ah;this.clear()};q(c.prototype,{get:function(ai){var ah=this.key_ary.indexOf(ai);if(ah!==-1){if(this.obj_cache[ai].stale){this.key_ary.splice(ah,1);delete this.obj_cache[ai]}else{this.move_key_to_end(ai,ah)}}return this.obj_cache[ai]},set:function(ai,aj){if(!this.obj_cache[ai]){if(this.key_ary.length>=this.num_elements){var ah=this.key_ary.shift();delete this.obj_cache[ah]}this.key_ary.push(ai)}this.obj_cache[ai]=aj;return aj},move_key_to_end:function(ai,ah){this.key_ary.splice(ah,1);this.key_ary.push(ai)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var T=function(ai,ah,aj){c.call(this,ai);this.track=ah;this.subset=(aj!==undefined?aj:true)};q(T.prototype,c.prototype,{load_data:function(aq,al,ao,ai,an){var ap=this.track.view.chrom,ak={chrom:ap,low:aq,high:al,mode:ao,resolution:ai,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ak,an);if(this.track.filters_manager){var ar=[];var ah=this.track.filters_manager.filters;for(var am=0;am<ah.length;am++){ar[ar.length]=ah[am].name}ak.filter_cols=JSON.stringify(ar)}var aj=this;return $.getJSON(this.track.data_url,ak,function(at){aj.set_data(aq,al,ao,at)})},get_data:function(ah,al,am,ai,ak){var aj=this.get_data_from_cache(ah,al,am);if(aj){return aj}aj=this.load_data(ah,al,am,ai,ak);this.set_data(ah,al,am,aj);return aj},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ap,ak,ao,aj,an,al){var aq=this.get_data_from_cache(ap,ak,ao);if(!aq){console.log("ERROR: no current data for: ",this.track,ap,ak,ao,aj,an);return}aq.stale=true;var ai=ap;if(al===this.DEEP_DATA_REQ){$.extend(an,{start_val:aq.data.length+1})}else{if(al===this.BROAD_DATA_REQ){ai=(aq.max_high?aq.max_high:aq.data[aq.data.length-1][2])+1}}var ah=this,am=this.load_data(ai,ak,ao,aj,an);new_data_available=$.Deferred();this.set_data(ap,ak,ao,new_data_available);$.when(am).then(function(ar){if(ar.data){ar.data=aq.data.concat(ar.data);if(ar.max_low){ar.max_low=aq.max_low}if(ar.message){ar.message=ar.message.replace(/[0-9]+/,ar.data.length)}}ah.set_data(ap,ak,ao,ar);new_data_available.resolve(ar)});return new_data_available},get_data_from_cache:function(ah,ai,aj){return this.get(this.gen_key(ah,ai,aj))},set_data:function(ai,aj,ak,ah){return this.set(this.gen_key(ai,aj,ak),ah)},gen_key:function(ah,aj,ak){var ai=ah+"_"+aj+"_"+ak;return ai},split_key:function(ah){return ah.split("_")}});var J=function(ai,ah,aj){T.call(this,ai,ah,aj)};q(J.prototype,T.prototype,c.prototype,{load_data:function(ah,ak,al,ai,aj){if(ai>1){return{data:null}}return T.prototype.load_data.call(this,ah,ak,al,ai,aj)}});var r=function(ak,ai,ah,aj,al){this.name=ak;this.view=ai;this.container=ah;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak}],saved_values:aj,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=al;this.is_overview=false};q(r.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},update_track_icons:function(){},set_name:function(ah){this.old_name=this.name;this.name=ah;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var z=function(al,ak,ai,ah,aj,am){r.call(this,ak,ai,ah,aj,am);this.obj_type=al;this.drawables=[]};q(z.prototype,r.prototype,{init:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah].init()}},_draw:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah]._draw()}},to_json:function(){var ai=[];for(var ah=0;ah<this.drawables.length;ah++){ai.push(this.drawables[ah].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ai}},add_drawable:function(ah){this.drawables.push(ah);ah.container=this},add_drawable_before:function(aj,ah){var ai=this.drawables.indexOf(ah);if(ai!=-1){this.drawables.splice(ai,0,aj);return true}return false},remove_drawable:function(ai){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);ai.container=null;return true}return false},move_drawable:function(ai,aj){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);this.drawables.splice(aj,0,ai);return true}return false}});var R=function(ak,ai,ah,aj){z.call(this,"DrawableGroup",ak,ai,ah,aj,"group-handle");if(!R.id_counter){R.id_counter=0}var al=R.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+al).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+al+"_content_div").appendTo(this.container_div);m(this.container_div,this);m(this.content_div,this);n(this.container_div,this.drag_handle_class,".group",this);this.update_track_icons()};q(R.prototype,r.prototype,z.prototype,{update_track_icons:function(){var ai=this;var ah={};ah["Edit configuration"]=function(){var al=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aj=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(am){if((am.keyCode||am.which)===27){al()}else{if((am.keyCode||am.which)===13){aj()}}};$(window).bind("keypress.check_enter_esc",ak);show_modal("Configure Group",ai.config.build_form(),{Cancel:al,OK:aj})};ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)}});var ae=function(ah,ak,aj,ai){z.call(this,"View");this.container=ah;this.chrom=null;this.vis_id=aj;this.dbkey=ai;this.title=ak;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ag(ah.get(0).ownerDocument);this.reset()};q(ae.prototype,z.prototype,{init:function(){var aj=this.container,ah=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aj);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;m(this.viewport_container,ah);this.intro_div=$("<div/>").addClass("intro");var ak=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ai=function(al){if(al.type==="focusout"||(al.keyCode||al.which)===13||(al.keyCode||al.which)===27){if((al.keyCode||al.which)!==27){ah.go_to($(this).val())}$(this).hide();$(this).val("");ah.location_span.show();ah.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup 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/>").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.browser_content_div.click(function(al){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("<div />").css({height:ah.browser_content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,{content_div:this.top_labeltrack}));this.add_label_track(new ad(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new B(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(am,ai,ao){if(!am||am==="None"){return}var aj=this;if(am==="previous"){aj.load_chroms({low:this.chrom_start_index-x});return}if(am==="next"){aj.load_chroms({low:this.chrom_start_index+x});return}var an=$.grep(aj.chrom_data,function(ap,aq){return ap.chrom===am})[0];if(an===undefined){aj.load_chroms({chrom:am},function(){aj.change_chrom(am,ai,ao)});return}else{if(am!==aj.chrom){aj.chrom=am;aj.chrom_select.val(aj.chrom);aj.max_high=an.len-1;aj.reset();aj.request_redraw(true);for(var al=0,ah=aj.drawables.length;al<ah;al++){var ak=aj.drawables[al];if(ak.init){ak.init()}}}if(ai!==undefined&&ao!==undefined){aj.low=Math.max(ai,0);aj.high=Math.min(ao,aj.max_high)}aj.reset_overview();aj.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){z.prototype.add_drawable.call(this,ah);ah.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;ah.init();this.label_tracks.push(ah)},remove_drawable:function(aj,ai){z.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.drawables),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(D,Math.ceil(Math.log((this.high-this.low)/S)/Math.log(D)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(aj){if(this.overview_drawable){if(this.overview_drawable.dataset_id===aj.dataset_id){return}this.overview_viewport.find(".track").remove()}var ai=aj.copy({content_div:this.overview_viewport}),ah=this;ai.header_div.hide();ai.is_overview=true;ah.overview_drawable=ai;this.overview_drawable.postdraw_actions=function(){ah.overview_highlight.show().height(ah.overview_drawable.content_div.height());ah.overview_viewport.height(ah.overview_drawable.content_div.height()+ah.overview_box.outerHeight());ah.overview_close.show();ah.resize_window()};this.overview_drawable.init();ah.has_changes=true},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new P(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},al=this.track,aj=ai.tool_id+al.tool_region_and_parameters_str(ai.chrom,ai.low,ai.high),ah,am;if(al.container===view){var ak=new R(this.name,this.track.view,this.track.container);al.container.add_drawable(ak);al.container.remove_drawable(al);ak.add_drawable(al);al.container_div.appendTo(ak.content_div);ah=ak}else{ah=al.container}if(al instanceof e){am=new W(aj,view,ah,"hda");am.change_mode(al.mode);ah.add_drawable(am)}am.content_div.text("Starting job.");this.run(ai,am,function(an){am.dataset_id=an.dataset_id;am.content_div.text("Running job.");am.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(L)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(y+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var P=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){P.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var X=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};q(X.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=ah[this.index];return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(at,aA){this.track=at;this.filters=[];for(var av=0;av<aA.length;av++){var aw=aA[av],aB=aw.name,ah=aw.type,aj=aw.index,az=aw.tool_id,ay=aw.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[av]=new X(aB,aj,az,ay)}else{console.log("ERROR: unsupported filter: ",aB,ah)}}var ak=function(aC,aD,aE){aC.click(function(){var aF=aD.text();max=parseFloat(aE.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aE.slider("option","values")){input_size=2*input_size+1;multi_value=true}aD.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aF).appendTo(aD).focus().select().click(function(aG){aG.stopPropagation()}).blur(function(){$(this).remove();aD.text(aF)}).keyup(function(aK){if(aK.keyCode===27){$(this).trigger("blur")}else{if(aK.keyCode===13){var aI=aE.slider("option","min"),aG=aE.slider("option","max"),aJ=function(aL){return(isNaN(aL)||aL>aG||aL<aI)},aH=$(this).val();if(!multi_value){aH=parseFloat(aH);if(aJ(aH)){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}else{aH=aH.split("-");aH=[parseFloat(aH[0]),parseFloat(aH[1])];if(aJ(aH[0])||aJ(aH[1])){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}aE.slider((multi_value?"values":"value"),aH)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aC){aC.stopPropagation()}).click(function(aC){aC.stopPropagation()}).bind("dblclick",function(aC){aC.stopPropagation()}).bind("keydown",function(aC){aC.stopPropagation()});var ax=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aF,aH){aH.container=$("<div/>").addClass("filter-row slider-row").appendTo(ax);var aG=$("<div/>").addClass("elt-label").appendTo(aH.container);var aE=$("<span/>").addClass("slider-name").text(aH.name+"  ").appendTo(aG);var aD=$("<span/>");var aJ=$("<span/>").addClass("slider-value").appendTo(aG).append("[").append(aD).append("]");var aC=$("<div/>").addClass("slider").appendTo(aH.container);aH.control_element=$("<div/>").attr("id",aH.name+"-filter-control").appendTo(aC);var aI=[0,0];aH.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aL,aM){var aK=aM.values;aD.text(aK[0]+"-"+aK[1]);aH.low=aK[0];aH.high=aK[1];ap.track.request_draw(true,true)},change:function(aK,aL){aH.control_element.slider("option","slide").call(aH.control_element,aK,aL)}});aH.slider=aH.control_element;aH.slider_label=aD;ak(aJ,aD,aH.control_element);$("<div style='clear: both;'/>").appendTo(aH.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(ax);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var ai=this;ao.click(function(){ai.run_on_dataset()})}var ar=$("<div/>").addClass("display-controls").appendTo(this.parent_div),au,an,aq,al={Transparency:function(aC){ap.alpha_filter=aC},Height:function(aC){ap.height_filter=aC}};$.each(al,function(aE,aD){au=$("<div/>").addClass("filter-row").appendTo(ar),an=$("<span/>").addClass("elt-label").text(aE+":").appendTo(au),aq=$("<select/>").attr("name",aE+"_dropdown").css("float","right").appendTo(au);$("<option/>").attr("value",-1).text("== None ==").appendTo(aq);for(var aC=0;aC<ap.filters.length;aC++){$("<option/>").attr("value",aC).text(ap.filters[aC].name).appendTo(aq)}aq.change(function(){$(this).children("option:selected").each(function(){var aF=parseInt($(this).val());al[aE]((aF>=0?ap.filters[aF]:null));ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(au)});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var E=function(ah,ai){N.Scaler.call(this,ai);this.filter=ah};E.prototype.gen_val=function(ah){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var H=function(ah){this.track=ah.track;this.params=ah.params;this.values={};this.restore_values((ah.saved_values?ah.saved_values:{}));this.onchange=ah.onchange};q(H.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(ah,ak,aj,ai,al){this.track=ah;this.index=ak;this.low=ak*S*aj;this.high=(ak+1)*S*aj;this.resolution=aj;this.canvas=$("<div class='track-tile'/>").append(ai);this.data=al;this.stale=false};b.prototype.predisplay_actions=function(){};var l=function(ah,ak,aj,ai,al,am){b.call(this,ah,ak,aj,ai,al);this.max_val=am};q(l.prototype,b.prototype);var Q=function(ah,al,ak,aj,an,ao,am,ai){b.call(this,ah,al,ak,aj,an);this.mode=ao;this.message=am;this.feature_mapper=ai};q(Q.prototype,b.prototype);Q.prototype.predisplay_actions=function(){var ai=this,ah={};if(ai.mode!=="Pack"){return}$(this.canvas).mousemove(function(au){var ao=$(this).offset(),at=au.pageX-ao.left,ar=au.pageY-ao.top,ay=ai.feature_mapper.get_feature_data(at,ar),ap=(ay?ay[0]:null);$(this).siblings(".feature-popup").each(function(){if(!ap||$(this).attr("id")!==ap.toString()){$(this).remove()}});if(ay){var ak=ah[ap];if(!ak){var ap=ay[0],av={name:ay[3],start:ay[1],end:ay[2],strand:ay[4]},an=ai.track.filters_manager.filters,am;for(var aq=0;aq<an.length;aq++){am=an[aq];av[am.name]=ay[am.index]}var ak=$("<div/>").attr("id",ap).addClass("feature-popup"),ax,aw,az=$("<table/>").appendTo(ak),aA;for(ax in av){aw=av[ax];aA=$("<tr/>").appendTo(az);$("<th/>").appendTo(aA).text(ax);$("<td/>").attr("align","left").appendTo(aA).text(typeof(aw)=="number"?ab(aw,2):aw)}ah[ap]=ak}ak.appendTo($(ai.canvas).parent());var al=at+parseInt(ai.canvas.css("left"))+7,aj=ar+parseInt(ai.canvas.css("top"))+7;ak.css("left",al+"px").css("top",aj+"px")}else{if(!au.isPropagationStopped()){au.stopPropagation();$(this).siblings().each(function(){$(this).trigger(au)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var j=function(ak,at,al,ao,au,aj,ai){r.call(this,ak,at,al,{},"draghandle");this.data_url=(aj?aj:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ai?ai:M);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.id=j.id_counter++;this.container_div=$("<div />").addClass("track").attr("id","track_"+this.id).css("position","relative");if(ao){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div/>").addClass("track-name").appendTo(this.header_div).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());this.icons_div=$("<div/>").css("float","left").appendTo(this.header_div).hide();this.settings_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Edit settings").addClass("icon-button settings-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.overview_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Set as overview").addClass("icon-button overview-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.filters_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Filters").addClass("icon-button filters-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.tools_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Tools").addClass("icon-button tools-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.remove_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Remove").addClass("icon-button remove-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);var am=this;this.header_div.dblclick(function(av){av.stopPropagation()});this.settings_icon.click(function(){var ax=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},av=function(){am.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},aw=function(ay){if((ay.keyCode||ay.which)===27){ax()}else{if((ay.keyCode||ay.which)===13){av()}}};$(window).bind("keypress.check_enter_esc",aw);show_modal("Configure Track",am.config.build_form(),{Cancel:ax,OK:av})});this.overview_icon.click(function(){am.view.set_overview(am)});this.filters_icon.click(function(){am.filters_div.toggle();am.filters_manager.reset_filters()});this.tools_icon.click(function(){am.dynamic_tool_div.toggle();if(am.dynamic_tool_div.is(":visible")){am.set_name(am.name+am.tool_region_and_parameters_str())}else{am.revert_name()}$(".tipsy").remove()});this.remove_icon.click(function(){$(".tipsy").remove();am.remove()});if(am.display_modes!==undefined){if(am.mode_div===undefined){am.mode_div=$("<div class='right-float menubutton popup' />").appendTo(am.header_div);var an=(am.config&&am.config.values.mode?am.config.values.mode:am.display_modes[0]);am.mode=an;am.mode_div.text(an);var ah={};for(var ap=0,ar=am.display_modes.length;ap<ar;ap++){var aq=am.display_modes[ap];ah[aq]=function(av){return function(){am.change_mode(av)}}(aq)}make_popupmenu(am.mode_div,ah)}else{am.mode_div.hide()}this.header_div.append($("<div/>").css("clear","both"));this.container_div.hover(function(){am.icons_div.show()},function(){am.icons_div.hide()})}}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Y){return"ReadTrack"}else{if(this instanceof W){return"ToolDataFeatureTrack"}else{if(this instanceof V){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(L)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(G)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.update_track_icons()}ah.content_div.text(aa);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}});this.update_track_icons()},predraw_init:function(){}});var O=function(ak,aj){var ai=this,ah=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=new ac(this,(ak!==undefined?ak:{}));this.filters_available=false;this.filters_visible=false;this.tool=(aj!==undefined&&obj_length(aj)>0?new s(this,aj):undefined);if(this.header_div){if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}};q(O.prototype,r.prototype,j.prototype,{copy:function(ah){return new this.constructor(this.name,this.view,ah,this.hda_ldda,this.dataset_id,this.prefs,this.filters,this.tool)},to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw();return ah},update_track_icons:function(){var ah=this;if(ah.filters_available>0){ah.filters_icon.show()}else{ah.filters_icon.hide()}if(ah.tool){ah.tools_icon.show()}else{ah.tools_icon.hide()}},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof B)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(this.is_overview){aq=this.view.max_low;an=this.view.max_high;am=Math.pow(D,Math.ceil(Math.log((view.max_high-view.max_low)/S)/Math.log(D)));av=ak/(view.max_high-view.max_low)}if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/S);var ap=true;var at=[];var ah=0;while((ai*S*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",F)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*S*an,ax=ap+S*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);if(aq!==undefined){al.tile_cache.set(at,aq);al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw(false,false,false,al)});return null},show_tile:function(an,ap,aq){var aj=this,ai=an.canvas,am=ai;if(an.message){var ar=$("<div/>"),ao=$("<div/>").addClass("tile-message").text(an.message).css({height:F-1,width:an.canvas.width}).appendTo(ar),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ao),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ao);ar.append(ai);am=ar;al.click(function(){an.stale=true;aj.data_manager.get_more_data(an.low,an.high,aj.mode,an.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(at){at.stopPropagation()});ah.click(function(){an.stale=true;aj.data_manager.get_more_data(an.low,an.high,aj.mode,an.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(at){at.stopPropagation()})}an.predisplay_actions();var ak=(an.low-(this.is_overview?this.view.max_low:this.view.low))*aq;if(this.left_offset){ak-=this.left_offset}am.css({position:"absolute",top:0,left:ak,height:""});ap.append(am);aj.max_height=Math.max(aj.max_height,am.height());aj.content_div.css("height",aj.max_height+"px");ap.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*S*ai,al=S*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ai,ah){j.call(this,"label",ai,ah,false,{});this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{init:function(){this.enabled=true},_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var B=function(ah){j.call(this,"reference",ah,{content_div:ah.top_labeltrack},false,{});O.call(this);ah.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ah.dbkey};this.data_manager=new J(C,this,false);this.tile_cache=new c(v)};q(B.prototype,r.prototype,O.prototype,{init:function(){this.enabled=true},draw_tile:function(ar,an,am,ai,at){var al=this,aj=S*am;if(at>this.view.canvas_manager.char_width_px){if(ar.data===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(al,ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(am,ak,aj,an,ah,al){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,am,ak,aj,al);O.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=an;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new T(C,this);this.tile_cache=new c(v);this.left_offset=0;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:am},{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:al,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.dataset_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.dataset_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};q(k.prototype,r.prototype,O.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this;ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(ai){ah.container_div.addClass("line-track");var ak=ai.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=ak.min;ah.prefs.max_value=ak.max;$("#track_"+ah.dataset_id+"_minval").val(ah.prefs.min_value);$("#track_"+ah.dataset_id+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=ak.total_frequency;ah.container_div.find(".yaxislabel").remove();var al=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_minval").text(ab(ah.prefs.min_value,3));var aj=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_maxval").text(ab(ah.prefs.max_value,3));aj.css({position:"absolute",top:"24px",left:"10px"});aj.prependTo(ah.container_div);al.css({position:"absolute",bottom:"2px",left:"10px"});al.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new N.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(this.track,aj,al,ak,au.data)}});var e=function(ah,an,ai,am,ap,ao,ak,al){var aj=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];j.call(this,ah,an,ai,true,ao);O.call(this,ak,al);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){aj.set_name(aj.prefs.name);aj.tile_cache.clear();aj.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=am;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new T(20,this);this.left_offset=200;this.painter=N.LinkedFeaturePainter};q(e.prototype,r.prototype,O.prototype,{postdraw_actions:function(ax,ah,ay,aw){O.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.update_track_icons()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",A,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aD,aH,ar,ak){var aA=this,am=aA._get_tile_bounds(aH,aD),aK=am[0],ai=am[1],ay=ai-aK,aB=Math.ceil(ay*ar),aQ=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"||aA.is_overview){az="no_detail"}else{var aP=aw.data;if(this.view.high-this.view.low>K){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aB+al;aj.height=an+U;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aK,ai,200);if(aw.max){at.max=aw.max}aw=at}var aM=new N.SummaryTreePainter(aw,aK,ai,this.prefs);var aC=aj.getContext("2d");aC.translate(al,U);aM.draw(aC,aB,an);return new l(aA,aH,aD,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aE=0,aG=aw.data.length;aE<aG;aE++){var ao=aw.data[aE];var aF=false;var av;for(var aJ=0,aO=au.length;aJ<aO;aJ++){av=au[aJ];av.update_attrs(ao);if(!av.keep(ao)){aF=true;break}}if(!aF){aq.push(ao)}}}var aN=(this.filters_manager.alpha_filter?new E(this.filters_manager.alpha_filter):null);var aL=(this.filters_manager.height_filter?new E(this.filters_manager.height_filter):null);var aM=new (this.painter)(aq,aK,ai,this.prefs,az,aN,aL,ak);var an=Math.max(af,aM.get_required_height(ap));var aj=this.view.canvas_manager.new_canvas();var aI=null;aj.width=aB+al;aj.height=an;var aC=aj.getContext("2d");aC.fillStyle=this.prefs.block_color;aC.font=aC.canvas.manager.default_font;aC.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aw.data){aC.translate(al,0);aI=aM.draw(aC,aB,an,ax);aI.translation=-al}return new Q(aA,aH,aD,aj,aw.data,az,aw.message,aI)}});var V=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.painter=N.VariantPainter};q(V.prototype,r.prototype,O.prototype,e.prototype);var Y=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ak,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=N.ReadPainter;this.update_track_icons()};q(Y.prototype,r.prototype,O.prototype,e.prototype);var W=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am,{});this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};q(W.prototype,r.prototype,O.prototype,e.prototype,{predraw_init:function(){var ai=this;var ah=function(){if(ai.data_manager.size()===0){setTimeout(ah,300)}else{ai.data_url=default_data_url;ai.data_query_wait=M;ai.dataset_state_url=converted_datasets_state_url;$.getJSON(ai.dataset_state_url,{dataset_id:ai.dataset_id,hda_ldda:ai.hda_ldda},function(aj){})}};ah()}});Z.View=ae;Z.DrawableGroup=R;Z.LineTrack=k;Z.FeatureTrack=e;Z.ReadTrack=Y};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(k,y){var v=k("class").extend;var q=function(J,B,H,A,G,E){if(E===undefined){E=4}var D=A-B;var C=G-H;var F=Math.floor(Math.sqrt(D*D+C*C)/E);var K=D/F;var I=C/F;var z;for(z=0;z<F;z++,B+=K,H+=I){if(z%2!==0){continue}J.fillRect(B,H,E,1)}};var r=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var e=function(z){this.default_val=(z?z:1)};e.prototype.gen_val=function(z){return this.default_val};var n=function(B,D,z,A,C){this.data=B;this.view_start=D;this.view_end=z;this.prefs=v({},this.default_prefs,A);this.mode=C};n.prototype.default_prefs={};var w=function(B,D,z,A,C){n.call(this,B,D,z,A,C)};w.prototype.default_prefs={show_counts:false};w.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var c=function(z,D,F,G,B){n.call(this,z,D,F,G,B);if(this.prefs.min_value===undefined){var H=Infinity;for(var A=0,C=this.data.length;A<C;A++){H=Math.min(H,this.data[A][1])}this.prefs.min_value=H}if(this.prefs.max_value===undefined){var E=-Infinity;for(var A=0,C=this.data.length;A<C;A++){E=Math.max(E,this.data[A][1])}this.prefs.max_value=E}};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var o=function(z){this.feature_positions={};this.slot_height=z;this.translation=0};o.prototype.map_feature_data=function(A,C,z,B){if(!this.feature_positions[C]){this.feature_positions[C]=[]}this.feature_positions[C].push({data:A,x_start:z,x_end:B})};o.prototype.get_feature_data=function(z,D){var C=Math.floor(D/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var p=function(B,E,z,A,D,F,C){n.call(this,B,E,z,A,D);this.alpha_scaler=(F?F:new e());this.height_scaler=(C?C:new e())};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};v(p.prototype,{get_required_height:function(A){var z=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){z=A*y_scale}return z+Math.max(Math.round(y_scale/2),5)},draw:function(L,J,H,G){var R=this.data,E=this.view_start,N=this.view_end;L.save();L.fillStyle=this.prefs.block_color;L.textAlign="right";var I=this.view_end-this.view_start,F=J/I,M=this.get_row_height(),Q=new o(M),C;for(var O=0,P=R.length;O<P;O++){var B=R[O],D=B[0],K=B[1],z=B[2],A=(G&&G[D]!==undefined?G[D]:null);if((K<N&&z>E)&&(this.mode=="Dense"||A!==null)){C=this.draw_element(L,this.mode,B,A,E,N,F,M,J);Q.map_feature_data(B,A,C[0],C[1])}}L.restore();return Q},draw_element:function(F,B,H,D,C,E,G,A,z){console.log("WARNING: Unimplemented function.");return[0,0]}});var d=10,j=3,m=5,x=10,g=1,t=3,f=3,a=9,l=2,h="#ccc";var s=function(B,E,z,A,D,F,C){p.call(this,B,E,z,A,D,F,C)};v(s.prototype,p.prototype,{get_row_height:function(){var A=this.mode,z;if(A==="Dense"){z=d}else{if(A==="no_detail"){z=j}else{if(A==="Squish"){z=m}else{z=x}}}return z},draw_element:function(N,E,W,I,P,ah,al,an,z){var T=W[0],aj=W[1],ab=W[2],R=W[3],ac=Math.floor(Math.max(0,(aj-P)*al)),O=Math.ceil(Math.min(z,Math.max(0,(ab-P)*al))),aa=ac,am=O,Z=(E==="Dense"?0:(0+I))*an,M,af,S=null,ap=null,C=this.prefs.block_color,ae=this.prefs.label_color;N.globalAlpha=this.alpha_scaler.gen_val(W);if(E=="Dense"){I=1}if(E==="no_detail"){N.fillStyle=C;N.fillRect(ac,Z+5,O-ac,g)}else{var L=W[4],Y=W[5],ad=W[6],D=W[7];if(Y&&ad){S=Math.floor(Math.max(0,(Y-P)*al));ap=Math.ceil(Math.min(z,Math.max(0,(ad-P)*al)))}var ak,U;if(E==="Squish"||E==="Dense"){ak=1;U=f}else{ak=5;U=a}if(!D){if(W.strand){if(W.strand==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand_inv")}else{if(W.strand==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand_inv")}}}else{N.fillStyle=C}N.fillRect(ac,Z,O-ac,U)}else{var K,V;if(E==="Squish"||E==="Dense"){N.fillStyle=h;K=Z+Math.floor(f/2)+1;V=1}else{if(L){var K=Z;var V=U;if(L==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand")}else{if(L==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand")}}}else{N.fillStyle=h;K+=(f/2)+1;V=1}}N.fillRect(ac,K,O-ac,V);var F;for(var ai=0,B=D.length;ai<B;ai++){var G=D[ai],A=Math.floor(Math.max(0,(G[0]-P)*al)),X=Math.ceil(Math.min(z,Math.max((G[1]-P)*al)));if(A>X){continue}N.fillStyle=C;N.fillRect(A,Z+(U-ak)/2+1,X-A,ak);if(S!==undefined&&ad>Y&&!(A>ap||X<S)){var ag=Math.max(A,S),J=Math.min(X,ap);N.fillRect(ag,Z+1,J-ag,U);if(D.length==1&&E=="Pack"){if(L==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand_inv")}else{if(L==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand_inv")}}if(ag+14<J){ag+=2;J-=2}N.fillRect(ag,Z+1,J-ag,U)}}}if(E==="Pack"){N.globalAlpha=1;N.fillStyle="white";var H=this.height_scaler.gen_val(W),Q=Math.ceil(U*H),ao=Math.round((U-Q)/2);if(H!==1){N.fillRect(ac,K+1,O-ac,ao);N.fillRect(ac,K+U-ao+1,O-ac,ao)}}}N.globalAlpha=1;if(E==="Pack"&&aj>P){N.fillStyle=ae;if(P===0&&ac-N.measureText(R).width<0){N.textAlign="left";N.fillText(R,O+l,Z+8);am+=N.measureText(R).width+l}else{N.textAlign="right";N.fillText(R,ac-l,Z+8);aa-=N.measureText(R).width+l}}}N.globalAlpha=1;return[aa,am]}});var b=function(B,E,z,A,D,F,C){p.call(this,B,E,z,A,D,F,C)};v(b.prototype,p.prototype,{draw_element:function(S,N,H,D,V,B,K,T,Q){var H=data[i],J=H[0],R=H[1],C=H[2],M=H[3],F=Math.floor(Math.max(0,(R-V)*K)),I=Math.ceil(Math.min(Q,Math.max(0,(C-V)*K))),E=(N==="Dense"?0:(0+D))*T,z,W,A=null,L=null;if(no_label){S.fillStyle=block_color;S.fillRect(F+left_offset,E+5,I-F,1)}else{var U=H[4],P=H[5],G=H[6];z=9;W=1;S.fillRect(F+left_offset,E,I-F,z);if(N!=="Dense"&&M!==undefined&&R>V){S.fillStyle=label_color;if(V===0&&F-S.measureText(M).width<0){S.textAlign="left";S.fillText(M,I+2+left_offset,E+8)}else{S.textAlign="right";S.fillText(M,F-2+left_offset,E+8)}S.fillStyle=block_color}var O=U+" / "+P;if(R>V&&S.measureText(O).width<(I-F)){S.fillStyle="white";S.textAlign="center";S.fillText(O,left_offset+F+(I-F)/2,E+8);S.fillStyle=block_color}}return[F,I]}});var u=function(C,F,z,B,E,G,D,A){p.call(this,C,F,z,B,E,G,D);this.ref_seq=(A?A.data:null)};u.prototype.default_prefs=v({},p.prototype.default_prefs,{show_insertions:false});v(u.prototype,p.prototype,{get_row_height:function(){var z,A=this.mode;if(A==="Dense"){z=d}else{if(A==="Squish"){z=m}else{z=x;if(this.prefs.show_insertions){z*=2}}}return z},draw_read:function(W,R,N,ab,C,V,K,H,G){W.textAlign="center";var U=this,B=[ab,C],Q=0,X=0,T=0,z=W.canvas.manager.char_width_px;var ag=[];if((R==="Pack"||this.mode==="Auto")&&H!==undefined&&N>z){T=Math.round(N/2)}if(!K){K=[[0,H.length]]}for(var O=0,Z=K.length;O<Z;O++){var L=K[O],D="MIDNSHP=X"[L[0]],P=L[1];if(D==="H"||D==="S"){Q-=P}var I=V+Q,af=Math.floor(Math.max(0,(I-ab)*N)),J=Math.floor(Math.max(0,(I+P-ab)*N));if(af===J){J+=1}switch(D){case"H":break;case"S":case"M":case"=":if(is_overlap([I,I+P],B)){var S=H.slice(X,X+P);if(T>0){W.fillStyle=this.prefs.block_color;W.fillRect(af-T,G+1,J-af,9);W.fillStyle=h;for(var ad=0,A=S.length;ad<A;ad++){if(this.prefs.show_differences&&this.ref_seq){var M=this.ref_seq[I-ab+ad];if(!M||M.toLowerCase()===S[ad].toLowerCase()){continue}}if(I+ad>=ab&&I+ad<=C){var ae=Math.floor(Math.max(0,(I+ad-ab)*N));W.fillText(S[ad],ae,G+9)}}}else{W.fillStyle=this.prefs.block_color;W.fillRect(af,G+4,J-af,f)}}X+=P;Q+=P;break;case"N":W.fillStyle=h;W.fillRect(af-T,G+5,J-af,1);Q+=P;break;case"D":W.fillStyle="red";W.fillRect(af-T,G+4,J-af,3);Q+=P;break;case"P":break;case"I":var 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aj=this.container,ah=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aj);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;m(this.viewport_container,ah);this.intro_div=$("<div/>").addClass("intro");var ak=$("<div/>").text("Add Datasets to 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/>").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.browser_content_div.click(function(al){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("<div />").css({height:ah.browser_content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,{content_div:this.top_labeltrack}));this.add_label_track(new ad(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new B(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(am,ai,ao){if(!am||am==="None"){return}var aj=this;if(am==="previous"){aj.load_chroms({low:this.chrom_start_index-x});return}if(am==="next"){aj.load_chroms({low:this.chrom_start_index+x});return}var an=$.grep(aj.chrom_data,function(ap,aq){return ap.chrom===am})[0];if(an===undefined){aj.load_chroms({chrom:am},function(){aj.change_chrom(am,ai,ao)});return}else{if(am!==aj.chrom){aj.chrom=am;aj.chrom_select.val(aj.chrom);aj.max_high=an.len-1;aj.reset();aj.request_redraw(true);for(var al=0,ah=aj.drawables.length;al<ah;al++){var ak=aj.drawables[al];if(ak.init){ak.init()}}}if(ai!==undefined&&ao!==undefined){aj.low=Math.max(ai,0);aj.high=Math.min(ao,aj.max_high)}aj.reset_overview();aj.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){z.prototype.add_drawable.call(this,ah);ah.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;ah.init();this.label_tracks.push(ah)},remove_drawable:function(aj,ai){z.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.drawables),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(D,Math.ceil(Math.log((this.high-this.low)/S)/Math.log(D)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(aj){if(this.overview_drawable){if(this.overview_drawable.dataset_id===aj.dataset_id){return}this.overview_viewport.find(".track").remove()}var ai=aj.copy({content_div:this.overview_viewport}),ah=this;ai.header_div.hide();ai.is_overview=true;ah.overview_drawable=ai;this.overview_drawable.postdraw_actions=function(){ah.overview_highlight.show().height(ah.overview_drawable.content_div.height());ah.overview_viewport.height(ah.overview_drawable.content_div.height()+ah.overview_box.outerHeight());ah.overview_close.show();ah.resize_window()};this.overview_drawable.init();ah.has_changes=true},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new P(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},al=this.track,aj=ai.tool_id+al.tool_region_and_parameters_str(ai.chrom,ai.low,ai.high),ah,am;if(al.container===view){var ak=new R(this.name,this.track.view,this.track.container);al.container.add_drawable(ak);al.container.remove_drawable(al);ak.add_drawable(al);al.container_div.appendTo(ak.content_div);ah=ak}else{ah=al.container}if(al instanceof e){am=new W(aj,view,ah,"hda");am.change_mode(al.mode);ah.add_drawable(am)}am.content_div.text("Starting job.");this.run(ai,am,function(an){am.dataset_id=an.dataset_id;am.content_div.text("Running job.");am.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(L)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(y+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var P=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){P.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var X=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};q(X.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=ah[this.index];return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(at,aA){this.track=at;this.filters=[];for(var av=0;av<aA.length;av++){var aw=aA[av],aB=aw.name,ah=aw.type,aj=aw.index,az=aw.tool_id,ay=aw.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[av]=new X(aB,aj,az,ay)}else{console.log("ERROR: unsupported filter: ",aB,ah)}}var ak=function(aC,aD,aE){aC.click(function(){var aF=aD.text();max=parseFloat(aE.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aE.slider("option","values")){input_size=2*input_size+1;multi_value=true}aD.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aF).appendTo(aD).focus().select().click(function(aG){aG.stopPropagation()}).blur(function(){$(this).remove();aD.text(aF)}).keyup(function(aK){if(aK.keyCode===27){$(this).trigger("blur")}else{if(aK.keyCode===13){var aI=aE.slider("option","min"),aG=aE.slider("option","max"),aJ=function(aL){return(isNaN(aL)||aL>aG||aL<aI)},aH=$(this).val();if(!multi_value){aH=parseFloat(aH);if(aJ(aH)){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}else{aH=aH.split("-");aH=[parseFloat(aH[0]),parseFloat(aH[1])];if(aJ(aH[0])||aJ(aH[1])){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}aE.slider((multi_value?"values":"value"),aH)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aC){aC.stopPropagation()}).click(function(aC){aC.stopPropagation()}).bind("dblclick",function(aC){aC.stopPropagation()}).bind("keydown",function(aC){aC.stopPropagation()});var ax=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aF,aH){aH.container=$("<div/>").addClass("filter-row slider-row").appendTo(ax);var aG=$("<div/>").addClass("elt-label").appendTo(aH.container);var aE=$("<span/>").addClass("slider-name").text(aH.name+"  ").appendTo(aG);var aD=$("<span/>");var aJ=$("<span/>").addClass("slider-value").appendTo(aG).append("[").append(aD).append("]");var aC=$("<div/>").addClass("slider").appendTo(aH.container);aH.control_element=$("<div/>").attr("id",aH.name+"-filter-control").appendTo(aC);var aI=[0,0];aH.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aL,aM){var aK=aM.values;aD.text(aK[0]+"-"+aK[1]);aH.low=aK[0];aH.high=aK[1];ap.track.request_draw(true,true)},change:function(aK,aL){aH.control_element.slider("option","slide").call(aH.control_element,aK,aL)}});aH.slider=aH.control_element;aH.slider_label=aD;ak(aJ,aD,aH.control_element);$("<div style='clear: both;'/>").appendTo(aH.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(ax);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var ai=this;ao.click(function(){ai.run_on_dataset()})}var ar=$("<div/>").addClass("display-controls").appendTo(this.parent_div),au,an,aq,al={Transparency:function(aC){ap.alpha_filter=aC},Height:function(aC){ap.height_filter=aC}};$.each(al,function(aE,aD){au=$("<div/>").addClass("filter-row").appendTo(ar),an=$("<span/>").addClass("elt-label").text(aE+":").appendTo(au),aq=$("<select/>").attr("name",aE+"_dropdown").css("float","right").appendTo(au);$("<option/>").attr("value",-1).text("== None ==").appendTo(aq);for(var aC=0;aC<ap.filters.length;aC++){$("<option/>").attr("value",aC).text(ap.filters[aC].name).appendTo(aq)}aq.change(function(){$(this).children("option:selected").each(function(){var aF=parseInt($(this).val());al[aE]((aF>=0?ap.filters[aF]:null));ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(au)});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var E=function(ah,ai){N.Scaler.call(this,ai);this.filter=ah};E.prototype.gen_val=function(ah){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var H=function(ah){this.track=ah.track;this.params=ah.params;this.values={};this.restore_values((ah.saved_values?ah.saved_values:{}));this.onchange=ah.onchange};q(H.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(ah,ak,aj,ai,al){this.track=ah;this.index=ak;this.low=ak*S*aj;this.high=(ak+1)*S*aj;this.resolution=aj;this.canvas=$("<div class='track-tile'/>").append(ai);this.data=al;this.stale=false};b.prototype.predisplay_actions=function(){};var l=function(ah,ak,aj,ai,al,am){b.call(this,ah,ak,aj,ai,al);this.max_val=am};q(l.prototype,b.prototype);var Q=function(ah,al,ak,aj,an,ao,am,ai){b.call(this,ah,al,ak,aj,an);this.mode=ao;this.message=am;this.feature_mapper=ai};q(Q.prototype,b.prototype);Q.prototype.predisplay_actions=function(){var ai=this,ah={};if(ai.mode!=="Pack"){return}$(this.canvas).mousemove(function(au){var ao=$(this).offset(),at=au.pageX-ao.left,ar=au.pageY-ao.top,ay=ai.feature_mapper.get_feature_data(at,ar),ap=(ay?ay[0]:null);$(this).siblings(".feature-popup").each(function(){if(!ap||$(this).attr("id")!==ap.toString()){$(this).remove()}});if(ay){var ak=ah[ap];if(!ak){var ap=ay[0],av={name:ay[3],start:ay[1],end:ay[2],strand:ay[4]},an=ai.track.filters_manager.filters,am;for(var aq=0;aq<an.length;aq++){am=an[aq];av[am.name]=ay[am.index]}var ak=$("<div/>").attr("id",ap).addClass("feature-popup"),ax,aw,az=$("<table/>").appendTo(ak),aA;for(ax in av){aw=av[ax];aA=$("<tr/>").appendTo(az);$("<th/>").appendTo(aA).text(ax);$("<td/>").attr("align","left").appendTo(aA).text(typeof(aw)=="number"?ab(aw,2):aw)}ah[ap]=ak}ak.appendTo($(ai.canvas).parent());var al=at+parseInt(ai.canvas.css("left"))+7,aj=ar+parseInt(ai.canvas.css("top"))+7;ak.css("left",al+"px").css("top",aj+"px")}else{if(!au.isPropagationStopped()){au.stopPropagation();$(this).siblings().each(function(){$(this).trigger(au)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var j=function(ak,at,al,ao,au,aj,ai){r.call(this,ak,at,al,{},"draghandle");this.data_url=(aj?aj:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ai?ai:M);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.id=j.id_counter++;this.container_div=$("<div />").addClass("track").attr("id","track_"+this.id).css("position","relative");if(ao){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div/>").addClass("track-name").appendTo(this.header_div).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());this.icons_div=$("<div/>").css("float","left").appendTo(this.header_div).hide();this.settings_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Edit settings").addClass("icon-button settings-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.overview_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Set as overview").addClass("icon-button overview-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.filters_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Filters").addClass("icon-button filters-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.tools_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Tools").addClass("icon-button tools-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.remove_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Remove").addClass("icon-button remove-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);var am=this;this.header_div.dblclick(function(av){av.stopPropagation()});this.settings_icon.click(function(){var ax=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},av=function(){am.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},aw=function(ay){if((ay.keyCode||ay.which)===27){ax()}else{if((ay.keyCode||ay.which)===13){av()}}};$(window).bind("keypress.check_enter_esc",aw);show_modal("Configure Track",am.config.build_form(),{Cancel:ax,OK:av})});this.overview_icon.click(function(){am.view.set_overview(am)});this.filters_icon.click(function(){am.filters_div.toggle();am.filters_manager.reset_filters()});this.tools_icon.click(function(){am.dynamic_tool_div.toggle();if(am.dynamic_tool_div.is(":visible")){am.set_name(am.name+am.tool_region_and_parameters_str())}else{am.revert_name()}$(".tipsy").remove()});this.remove_icon.click(function(){$(".tipsy").remove();am.remove()});if(am.display_modes!==undefined){if(am.mode_div===undefined){am.mode_div=$("<div class='right-float menubutton popup' />").appendTo(am.header_div);var an=(am.config&&am.config.values.mode?am.config.values.mode:am.display_modes[0]);am.mode=an;am.mode_div.text(an);var ah={};for(var ap=0,ar=am.display_modes.length;ap<ar;ap++){var aq=am.display_modes[ap];ah[aq]=function(av){return function(){am.change_mode(av)}}(aq)}make_popupmenu(am.mode_div,ah)}else{am.mode_div.hide()}this.header_div.append($("<div/>").css("clear","both"));this.container_div.hover(function(){am.icons_div.show()},function(){am.icons_div.hide()})}}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Y){return"ReadTrack"}else{if(this instanceof W){return"ToolDataFeatureTrack"}else{if(this instanceof V){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(L)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(G)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.update_track_icons()}ah.content_div.text(aa);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}});this.update_track_icons()},predraw_init:function(){}});var O=function(ak,aj){var ai=this,ah=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=new ac(this,(ak!==undefined?ak:{}));this.filters_available=false;this.filters_visible=false;this.tool=(aj!==undefined&&obj_length(aj)>0?new s(this,aj):undefined);if(this.header_div){if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}};q(O.prototype,r.prototype,j.prototype,{copy:function(ah){return new this.constructor(this.name,this.view,ah,this.hda_ldda,this.dataset_id,this.prefs,this.filters,this.tool)},to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw();return ah},update_track_icons:function(){var ah=this;if(ah.filters_available>0){ah.filters_icon.show()}else{ah.filters_icon.hide()}if(ah.tool){ah.tools_icon.show()}else{ah.tools_icon.hide()}},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof B)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(this.is_overview){aq=this.view.max_low;an=this.view.max_high;am=Math.pow(D,Math.ceil(Math.log((view.max_high-view.max_low)/S)/Math.log(D)));av=ak/(view.max_high-view.max_low)}if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/S);var ap=true;var at=[];var ah=0;while((ai*S*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",F)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*S*an,ax=ap+S*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);if(aq!==undefined){al.tile_cache.set(at,aq);al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw(false,false,false,al)});return null},show_tile:function(an,ap,aq){var aj=this,ai=an.canvas,am=ai;if(an.message){var ar=$("<div/>"),ao=$("<div/>").addClass("tile-message").text(an.message).css({height:F-1,width:an.canvas.width}).appendTo(ar),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ao),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ao);ar.append(ai);am=ar;al.click(function(){an.stale=true;aj.data_manager.get_more_data(an.low,an.high,aj.mode,an.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(at){at.stopPropagation()});ah.click(function(){an.stale=true;aj.data_manager.get_more_data(an.low,an.high,aj.mode,an.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(at){at.stopPropagation()})}an.predisplay_actions();var ak=(an.low-(this.is_overview?this.view.max_low:this.view.low))*aq;if(this.left_offset){ak-=this.left_offset}am.css({position:"absolute",top:0,left:ak,height:""});ap.append(am);aj.max_height=Math.max(aj.max_height,am.height());aj.content_div.css("height",aj.max_height+"px");ap.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*S*ai,al=S*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ai,ah){j.call(this,"label",ai,ah,false,{});this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{init:function(){this.enabled=true},_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var B=function(ah){j.call(this,"reference",ah,{content_div:ah.top_labeltrack},false,{});O.call(this);ah.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ah.dbkey};this.data_manager=new J(C,this,false);this.tile_cache=new c(v)};q(B.prototype,r.prototype,O.prototype,{init:function(){this.enabled=true},draw_tile:function(ar,an,am,ai,at){var al=this,aj=S*am;if(at>this.view.canvas_manager.char_width_px){if(ar.data===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(al,ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(am,ak,aj,an,ah,al){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,am,ak,aj,al);O.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=an;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new T(C,this);this.tile_cache=new c(v);this.left_offset=0;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:am},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:al,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.dataset_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.dataset_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};q(k.prototype,r.prototype,O.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this;ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(ai){ah.container_div.addClass("line-track");var ak=ai.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=ak.min;ah.prefs.max_value=ak.max;$("#track_"+ah.dataset_id+"_minval").val(ah.prefs.min_value);$("#track_"+ah.dataset_id+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=ak.total_frequency;ah.container_div.find(".yaxislabel").remove();var al=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_minval").text(ab(ah.prefs.min_value,3));var aj=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_maxval").text(ab(ah.prefs.max_value,3));aj.css({position:"absolute",top:"24px",left:"10px"});aj.prependTo(ah.container_div);al.css({position:"absolute",bottom:"2px",left:"10px"});al.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new N.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(this.track,aj,al,ak,au.data)}});var e=function(ah,an,ai,am,ap,ao,ak,al){var aj=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];j.call(this,ah,an,ai,true,ao);O.call(this,ak,al);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){aj.set_name(aj.prefs.name);aj.tile_cache.clear();aj.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=am;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new T(20,this);this.left_offset=200;this.painter=N.LinkedFeaturePainter};q(e.prototype,r.prototype,O.prototype,{postdraw_actions:function(ax,ah,ay,aw){O.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.update_track_icons()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",A,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aD,aH,ar,ak){var aA=this,am=aA._get_tile_bounds(aH,aD),aK=am[0],ai=am[1],ay=ai-aK,aB=Math.ceil(ay*ar),aQ=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"||aA.is_overview){az="no_detail"}else{var aP=aw.data;if(this.view.high-this.view.low>K){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aB+al;aj.height=an+U;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aK,ai,200);if(aw.max){at.max=aw.max}aw=at}var aM=new N.SummaryTreePainter(aw,aK,ai,this.prefs);var aC=aj.getContext("2d");aC.translate(al,U);aM.draw(aC,aB,an);return new l(aA,aH,aD,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aE=0,aG=aw.data.length;aE<aG;aE++){var ao=aw.data[aE];var aF=false;var av;for(var aJ=0,aO=au.length;aJ<aO;aJ++){av=au[aJ];av.update_attrs(ao);if(!av.keep(ao)){aF=true;break}}if(!aF){aq.push(ao)}}}var aN=(this.filters_manager.alpha_filter?new E(this.filters_manager.alpha_filter):null);var aL=(this.filters_manager.height_filter?new E(this.filters_manager.height_filter):null);var aM=new (this.painter)(aq,aK,ai,this.prefs,az,aN,aL,ak);var an=Math.max(af,aM.get_required_height(ap));var aj=this.view.canvas_manager.new_canvas();var aI=null;aj.width=aB+al;aj.height=an;var aC=aj.getContext("2d");aC.fillStyle=this.prefs.block_color;aC.font=aC.canvas.manager.default_font;aC.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aw.data){aC.translate(al,0);aI=aM.draw(aC,aB,an,ax);aI.translation=-al}return new Q(aA,aH,aD,aj,aw.data,az,aw.message,aI)}});var V=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.painter=N.VariantPainter};q(V.prototype,r.prototype,O.prototype,e.prototype);var Y=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ak,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=N.ReadPainter;this.update_track_icons()};q(Y.prototype,r.prototype,O.prototype,e.prototype);var W=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am,{});this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};q(W.prototype,r.prototype,O.prototype,e.prototype,{predraw_init:function(){var ai=this;var ah=function(){if(ai.data_manager.size()===0){setTimeout(ah,300)}else{ai.data_url=default_data_url;ai.data_query_wait=M;ai.dataset_state_url=converted_datasets_state_url;$.getJSON(ai.dataset_state_url,{dataset_id:ai.dataset_id,hda_ldda:ai.hda_ldda},function(aj){})}};ah()}});Z.View=ae;Z.DrawableGroup=R;Z.LineTrack=k;Z.FeatureTrack=e;Z.ReadTrack=Y};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(k,y){var v=k("class").extend;var q=function(J,B,H,A,G,E){if(E===undefined){E=4}var D=A-B;var C=G-H;var F=Math.floor(Math.sqrt(D*D+C*C)/E);var K=D/F;var I=C/F;var z;for(z=0;z<F;z++,B+=K,H+=I){if(z%2!==0){continue}J.fillRect(B,H,E,1)}};var r=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var e=function(z){this.default_val=(z?z:1)};e.prototype.gen_val=function(z){return this.default_val};var n=function(B,D,z,A,C){this.data=B;this.view_start=D;this.view_end=z;this.prefs=v({},this.default_prefs,A);this.mode=C};n.prototype.default_prefs={};var w=function(B,D,z,A,C){n.call(this,B,D,z,A,C)};w.prototype.default_prefs={show_counts:false};w.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var c=function(z,D,F,G,B){n.call(this,z,D,F,G,B);if(this.prefs.min_value===undefined){var H=Infinity;for(var A=0,C=this.data.length;A<C;A++){H=Math.min(H,this.data[A][1])}this.prefs.min_value=H}if(this.prefs.max_value===undefined){var E=-Infinity;for(var A=0,C=this.data.length;A<C;A++){E=Math.max(E,this.data[A][1])}this.prefs.max_value=E}};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var o=function(z){this.feature_positions={};this.slot_height=z;this.translation=0};o.prototype.map_feature_data=function(A,C,z,B){if(!this.feature_positions[C]){this.feature_positions[C]=[]}this.feature_positions[C].push({data:A,x_start:z,x_end:B})};o.prototype.get_feature_data=function(z,D){var C=Math.floor(D/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var p=function(B,E,z,A,D,F,C){n.call(this,B,E,z,A,D);this.alpha_scaler=(F?F:new e());this.height_scaler=(C?C:new e())};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};v(p.prototype,{get_required_height:function(A){var z=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){z=A*y_scale}return z+Math.max(Math.round(y_scale/2),5)},draw:function(L,J,H,G){var R=this.data,E=this.view_start,N=this.view_end;L.save();L.fillStyle=this.prefs.block_color;L.textAlign="right";var I=this.view_end-this.view_start,F=J/I,M=this.get_row_height(),Q=new o(M),C;for(var O=0,P=R.length;O<P;O++){var B=R[O],D=B[0],K=B[1],z=B[2],A=(G&&G[D]!==undefined?G[D]:null);if((K<N&&z>E)&&(this.mode=="Dense"||A!==null)){C=this.draw_element(L,this.mode,B,A,E,N,F,M,J);Q.map_feature_data(B,A,C[0],C[1])}}L.restore();return Q},draw_element:function(F,B,H,D,C,E,G,A,z){console.log("WARNING: Unimplemented function.");return[0,0]}});var d=10,j=3,m=5,x=10,g=1,t=3,f=3,a=9,l=2,h="#ccc";var s=function(B,E,z,A,D,F,C){p.call(this,B,E,z,A,D,F,C)};v(s.prototype,p.prototype,{get_row_height:function(){var A=this.mode,z;if(A==="Dense"){z=d}else{if(A==="no_detail"){z=j}else{if(A==="Squish"){z=m}else{z=x}}}return z},draw_element:function(N,E,W,I,P,ah,al,an,z){var T=W[0],aj=W[1],ab=W[2],R=W[3],ac=Math.floor(Math.max(0,(aj-P)*al)),O=Math.ceil(Math.min(z,Math.max(0,(ab-P)*al))),aa=ac,am=O,Z=(E==="Dense"?0:(0+I))*an,M,af,S=null,ap=null,C=this.prefs.block_color,ae=this.prefs.label_color;N.globalAlpha=this.alpha_scaler.gen_val(W);if(E=="Dense"){I=1}if(E==="no_detail"){N.fillStyle=C;N.fillRect(ac,Z+5,O-ac,g)}else{var L=W[4],Y=W[5],ad=W[6],D=W[7];if(Y&&ad){S=Math.floor(Math.max(0,(Y-P)*al));ap=Math.ceil(Math.min(z,Math.max(0,(ad-P)*al)))}var ak,U;if(E==="Squish"||E==="Dense"){ak=1;U=f}else{ak=5;U=a}if(!D){if(W.strand){if(W.strand==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand_inv")}else{if(W.strand==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand_inv")}}}else{N.fillStyle=C}N.fillRect(ac,Z,O-ac,U)}else{var K,V;if(E==="Squish"||E==="Dense"){N.fillStyle=h;K=Z+Math.floor(f/2)+1;V=1}else{if(L){var K=Z;var V=U;if(L==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand")}else{if(L==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand")}}}else{N.fillStyle=h;K+=(f/2)+1;V=1}}N.fillRect(ac,K,O-ac,V);var F;for(var ai=0,B=D.length;ai<B;ai++){var G=D[ai],A=Math.floor(Math.max(0,(G[0]-P)*al)),X=Math.ceil(Math.min(z,Math.max((G[1]-P)*al)));if(A>X){continue}N.fillStyle=C;N.fillRect(A,Z+(U-ak)/2+1,X-A,ak);if(S!==undefined&&ad>Y&&!(A>ap||X<S)){var ag=Math.max(A,S),J=Math.min(X,ap);N.fillRect(ag,Z+1,J-ag,U);if(D.length==1&&E=="Pack"){if(L==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand_inv")}else{if(L==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand_inv")}}if(ag+14<J){ag+=2;J-=2}N.fillRect(ag,Z+1,J-ag,U)}}}if(E==="Pack"){N.globalAlpha=1;N.fillStyle="white";var H=this.height_scaler.gen_val(W),Q=Math.ceil(U*H),ao=Math.round((U-Q)/2);if(H!==1){N.fillRect(ac,K+1,O-ac,ao);N.fillRect(ac,K+U-ao+1,O-ac,ao)}}}N.globalAlpha=1;if(E==="Pack"&&aj>P){N.fillStyle=ae;if(P===0&&ac-N.measureText(R).width<0){N.textAlign="left";N.fillText(R,O+l,Z+8);am+=N.measureText(R).width+l}else{N.textAlign="right";N.fillText(R,ac-l,Z+8);aa-=N.measureText(R).width+l}}}N.globalAlpha=1;return[aa,am]}});var b=function(B,E,z,A,D,F,C){p.call(this,B,E,z,A,D,F,C)};v(b.prototype,p.prototype,{draw_element:function(S,N,H,D,V,B,K,T,Q){var H=data[i],J=H[0],R=H[1],C=H[2],M=H[3],F=Math.floor(Math.max(0,(R-V)*K)),I=Math.ceil(Math.min(Q,Math.max(0,(C-V)*K))),E=(N==="Dense"?0:(0+D))*T,z,W,A=null,L=null;if(no_label){S.fillStyle=block_color;S.fillRect(F+left_offset,E+5,I-F,1)}else{var U=H[4],P=H[5],G=H[6];z=9;W=1;S.fillRect(F+left_offset,E,I-F,z);if(N!=="Dense"&&M!==undefined&&R>V){S.fillStyle=label_color;if(V===0&&F-S.measureText(M).width<0){S.textAlign="left";S.fillText(M,I+2+left_offset,E+8)}else{S.textAlign="right";S.fillText(M,F-2+left_offset,E+8)}S.fillStyle=block_color}var O=U+" / "+P;if(R>V&&S.measureText(O).width<(I-F)){S.fillStyle="white";S.textAlign="center";S.fillText(O,left_offset+F+(I-F)/2,E+8);S.fillStyle=block_color}}return[F,I]}});var u=function(C,F,z,B,E,G,D,A){p.call(this,C,F,z,B,E,G,D);this.ref_seq=(A?A.data:null)};u.prototype.default_prefs=v({},p.prototype.default_prefs,{show_insertions:false});v(u.prototype,p.prototype,{get_row_height:function(){var z,A=this.mode;if(A==="Dense"){z=d}else{if(A==="Squish"){z=m}else{z=x;if(this.prefs.show_insertions){z*=2}}}return z},draw_read:function(W,R,N,ab,C,V,K,H,G){W.textAlign="center";var U=this,B=[ab,C],Q=0,X=0,T=0,z=W.canvas.manager.char_width_px;var ag=[];if((R==="Pack"||this.mode==="Auto")&&H!==undefined&&N>z){T=Math.round(N/2)}if(!K){K=[[0,H.length]]}for(var O=0,Z=K.length;O<Z;O++){var L=K[O],D="MIDNSHP=X"[L[0]],P=L[1];if(D==="H"||D==="S"){Q-=P}var I=V+Q,af=Math.floor(Math.max(0,(I-ab)*N)),J=Math.floor(Math.max(0,(I+P-ab)*N));if(af===J){J+=1}switch(D){case"H":break;case"S":case"M":case"=":if(is_overlap([I,I+P],B)){var S=H.slice(X,X+P);if(T>0){W.fillStyle=this.prefs.block_color;W.fillRect(af-T,G+1,J-af,9);W.fillStyle=h;for(var ad=0,A=S.length;ad<A;ad++){if(this.prefs.show_differences&&this.ref_seq){var M=this.ref_seq[I-ab+ad];if(!M||M.toLowerCase()===S[ad].toLowerCase()){continue}}if(I+ad>=ab&&I+ad<=C){var ae=Math.floor(Math.max(0,(I+ad-ab)*N));W.fillText(S[ad],ae,G+9)}}}else{W.fillStyle=this.prefs.block_color;W.fillRect(af,G+4,J-af,f)}}X+=P;Q+=P;break;case"N":W.fillStyle=h;W.fillRect(af-T,G+5,J-af,1);Q+=P;break;case"D":W.fillStyle="red";W.fillRect(af-T,G+4,J-af,3);Q+=P;break;case"P":break;case"I":var aa=af-T;if(is_overlap([I,I+P],B)){var S=H.slice(X,X+P);if(this.prefs.show_insertions){var F=af-(J-af)/2;if((R==="Pack"||this.mode==="Auto")&&H!==undefined&&N>z){W.fillStyle="yellow";W.fillRect(F-T,G-9,J-af,9);ag[ag.length]={type:"triangle",data:[aa,G+4,5]};W.fillStyle=h;switch(seq_tile_overlap){case (OVERLAP_START):S=S.slice(ab-I);break;case (OVERLAP_END):S=S.slice(0,I-C);break;case (CONTAINED_BY):break;case (CONTAINS):S=S.slice(ab-I,I-C);break}for(var ad=0,A=S.length;ad<A;ad++){var ae=Math.floor(Math.max(0,(I+ad-ab)*N));W.fillText(S[ad],ae-(J-af)/2,G)}}else{W.fillStyle="yellow";W.fillRect(F,G+(this.mode!=="Dense"?2:5),J-af,(R!=="Dense"?f:t))}}else{if((R==="Pack"||this.mode==="Auto")&&H!==undefined&&N>z){ag[ag.length]={type:"text",data:[S.length,aa,G+9]}}else{}}}X+=P;break;case"X":X+=P;break}}W.fillStyle="yellow";var ac,E,ah;for(var Y=0;Y<ag.length;Y++){ac=ag[Y];E=ac.type;ah=ac.data;if(E==="text"){W.save();W.font="bold "+W.font;W.fillText(ah[0],ah[1],ah[2]);W.restore()}else{if(E=="triangle"){r(W,ah[0],ah[1],ah[2])}}}},draw_element:function(S,N,F,C,V,A,J,T,Q){var I=F[0],R=F[1],B=F[2],K=F[3],E=Math.floor(Math.max(0,(R-V)*J)),G=Math.ceil(Math.min(Q,Math.max(0,(B-V)*J))),D=(N==="Dense"?0:(0+C))*T,W=this.prefs.block_color,H=this.prefs.label_color,P=0;if((N==="Pack"||this.mode==="Auto")&&J>S.canvas.manager.char_width_px){var P=Math.round(J/2)}S.fillStyle=W;if(F[5] instanceof Array){var O=Math.floor(Math.max(0,(F[4][0]-V)*J)),M=Math.ceil(Math.min(Q,Math.max(0,(F[4][1]-V)*J))),L=Math.floor(Math.max(0,(F[5][0]-V)*J)),z=Math.ceil(Math.min(Q,Math.max(0,(F[5][1]-V)*J)));if(F[4][1]>=V&&F[4][0]<=A&&F[4][2]){this.draw_read(S,N,J,V,A,F[4][0],F[4][2],F[4][3],D)}if(F[5][1]>=V&&F[5][0]<=A&&F[5][2]){this.draw_read(S,N,J,V,A,F[5][0],F[5][2],F[5][3],D)}if(L>M){S.fillStyle=h;q(S,M-P,D+5,L-P,D+5)}}else{S.fillStyle=W;this.draw_read(S,N,J,V,A,R,F[4],F[5],D)}if(N==="Pack"&&R>V){S.fillStyle=this.prefs.label_color;var U=1;if(U===0&&E-S.measureText(K).width<0){S.textAlign="left";S.fillText(K,G+l-P,D+8)}else{S.textAlign="right";S.fillText(K,E-l-P,D+8)}S.fillStyle=W}return[0,0]}});y.Scaler=e;y.SummaryTreePainter=w;y.LinePainter=c;y.LinkedFeaturePainter=s;y.ReadPainter=u;y.VariantPainter=b};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window);
\ No newline at end of file
diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index fec93fd3600..a84d5129761 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -37,7 +37,6 @@ var requestAnimationFrame = (function(){
             };
 })();
 
-
 /**
  * Compute the type of overlap between two regions. They are assumed to be on the same chrom/contig.
  * The overlap is computed relative to the second region; hence, OVERLAP_START indicates that the first
@@ -74,6 +73,7 @@ var compute_overlap = function(first_region, second_region) {
     
     return overlap;
 };
+
 /**
  * Returns true if regions overlap.
  */
@@ -82,6 +82,74 @@ var is_overlap = function(first_region, second_region) {
     return (overlap !== BEFORE && overlap !== AFTER);
 };
 
+/**
+ * Returns a random color in hexadecimal format that is sufficiently different from a single color
+ * or set of colors.
+ * @param colors a color or list of colors in the format '#RRGGBB'
+ */
+var get_random_color = function(colors) {
+    // Default for colors is white.
+    if (!colors) { colors = "#ffffff" };
+    
+    // If needed, create list of colors.
+    if ( typeof(colors) === "string" ) {
+        colors = [ colors ];
+    }
+    
+    // Convert colors to numbers.
+    for (var i = 0; i < colors.length; i++) {
+        colors[i] = parseInt( colors[i].slice(1), 16 );
+    }
+    
+    // -- Perceived brightness and difference formulas are from 
+    // -- http://www.w3.org/WAI/ER/WD-AERT/#color-contrast
+    
+    // Compute perceived color brightness (based on RGB-YIQ transformation):
+    var brightness = function(r, g, b) {
+        return ( (r * 299) + (g * 587) + (b * 114) ) / 1000;
+    };
+    
+    // Compute color difference:
+    var difference = function(r1, g1, b1, r2, g2, b2) {
+        return ( Math.max(r1, r2) - Math.min(r1, r2) ) + 
+               ( Math.max(g1, g2) - Math.min(g1, g2) ) + 
+               ( Math.max(b1, b2) - Math.min(b1, b2) );
+    };
+    
+    // Create new random color.
+    var new_color, nr, ng, nb,
+        other_color, or, og, ob,
+        n_brightness, o_brightness,
+        diff, ok = false;
+    do {
+        // New color is never white b/c random in [0,1)
+        new_color = Math.random() * 0xffffff;
+        nr = new_color | 0xff0000;
+        ng = new_color | 0x00ff00;
+        nb = new_color | 0x0000ff;
+        n_brightness = brightness(nr, ng, nb);
+        ok = true;
+        for (var i = 0; i < colors.length; i++) {
+            other_color = colors[i];
+            or = other_color | 0xff0000;
+            og = other_color | 0x00ff00;
+            ob = other_color | 0x0000ff;
+            o_brightness = brightness(or, og, ob);
+            diff = difference(nr, ng, nb, or, og, ob);
+            // Thresholds for brightness difference and color difference
+            // are from W3C link above.
+            if ( ( Math.abs(n_brightness - o_brightness) < 125 ) ||
+                 ( diff < 500 ) ) {
+                ok = false;
+                break;         
+            }
+        }
+    } while (!ok);
+    
+    // Add 0x1000000 to left pad number with 0s.
+    return '#' + ( 0x1000000 + new_color ).toString(16).substr(1,6);
+};
+
 // Encapsulate -- anything to be availabe outside this block is added to exports
 var trackster_module = function(require, exports) {
 
@@ -2941,7 +3009,7 @@ var LineTrack = function (name, view, container, hda_ldda, dataset_id, prefs) {
         track: this,
         params: [
             { key: 'name', label: 'Name', type: 'text', default_value: name },
-            { key: 'color', label: 'Color', type: 'color', default_value: 'black' },
+            { key: 'color', label: 'Color', type: 'color', default_value: get_random_color() },
             { key: 'min_value', label: 'Min Value', type: 'float', default_value: undefined },
             { key: 'max_value', label: 'Max Value', type: 'float', default_value: undefined },
             { key: 'mode', type: 'string', default_value: this.mode, hidden: true },
@@ -3080,7 +3148,7 @@ var FeatureTrack = function(name, view, container, hda_ldda, dataset_id, prefs,
         track: this,
         params: [
             { key: 'name', label: 'Name', type: 'text', default_value: name },
-            { key: 'block_color', label: 'Block color', type: 'color', default_value: '#444' },
+            { key: 'block_color', label: 'Block color', type: 'color', default_value: get_random_color() },
             { key: 'label_color', label: 'Label color', type: 'color', default_value: 'black' },
             { key: 'show_counts', label: 'Show summary counts', type: 'bool', default_value: true },
             { key: 'mode', type: 'string', default_value: this.mode, hidden: true },
@@ -3470,7 +3538,7 @@ var ReadTrack = function (name, view, container, hda_ldda, dataset_id, prefs, fi
         track: this,
         params: [
             { key: 'name', label: 'Name', type: 'text', default_value: name },
-            { key: 'block_color', label: 'Block color', type: 'color', default_value: '#444' },
+            { key: 'block_color', label: 'Block color', type: 'color', default_value: get_random_color() },
             { key: 'label_color', label: 'Label color', type: 'color', default_value: 'black' },
             { key: 'show_insertions', label: 'Show insertions', type: 'bool', default_value: false },
             { key: 'show_differences', label: 'Show differences only', type: 'bool', default_value: true },

From 61e1c95fe1d3c6c73d99793121e7e1dd4f34be8b Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Mon, 24 Oct 2011 17:54:48 -0400
Subject: [PATCH 089/362] GATK updates.

---
 tools/gatk/variant_apply_recalibration.xml | 6 +++---
 tools/gatk/variant_eval.xml                | 6 +++---
 tools/gatk/variant_recalibrator.xml        | 6 +++---
 3 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/tools/gatk/variant_apply_recalibration.xml b/tools/gatk/variant_apply_recalibration.xml
index 81a52f718ba..b66cbf9290d 100644
--- a/tools/gatk/variant_apply_recalibration.xml
+++ b/tools/gatk/variant_apply_recalibration.xml
@@ -102,9 +102,9 @@
         <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" />
         <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" />
         <param name="ref_file" type="select" label="Using reference genome">
-         <!--  <options from_data_table="picard_indexes">
-            <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/>
-          </options> -->
+          <options from_data_table="picard_indexes">
+            <!-- <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> -->
+          </options>
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
diff --git a/tools/gatk/variant_eval.xml b/tools/gatk/variant_eval.xml
index e337e737c2f..25fcf14214a 100644
--- a/tools/gatk/variant_eval.xml
+++ b/tools/gatk/variant_eval.xml
@@ -159,9 +159,9 @@
           <param name="input_variant" type="data" format="vcf" label="Input variant file" />
         </repeat>
         <param name="ref_file" type="select" label="Using reference genome">
-          <!--<options from_data_table="picard_indexes">
-            <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/>
-          </options>-->
+          <options from_data_table="picard_indexes">
+            <!-- <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/> -->
+          </options>
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
diff --git a/tools/gatk/variant_recalibrator.xml b/tools/gatk/variant_recalibrator.xml
index 511320c26ad..98c16d3a809 100644
--- a/tools/gatk/variant_recalibrator.xml
+++ b/tools/gatk/variant_recalibrator.xml
@@ -152,9 +152,9 @@
           <param name="input_variants" type="data" format="vcf" label="Variant file to recalibrate" />
         </repeat>
         <param name="ref_file" type="select" label="Using reference genome">
-          <!-- <options from_data_table="picard_indexes">
-            <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/>
-          </options> -->
+          <options from_data_table="picard_indexes">
+          <!--  <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> -->
+          </options>
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->

From 2a5422873526b3c2a5ed991eba26731756629856 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Mon, 24 Oct 2011 20:28:28 -0400
Subject: [PATCH 090/362] Trackster: refactor constructor code for cleaner
 initialization.

---
 static/scripts/trackster.js | 17 +++++++----------
 1 file changed, 7 insertions(+), 10 deletions(-)

diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index a84d5129761..523ec4ca488 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -2558,7 +2558,9 @@ extend(Track.prototype, Drawable.prototype, {
     predraw_init: function() {}
 });
 
-var TiledTrack = function(filters_list, tool_dict) {
+var TiledTrack = function(name, view, container, show_header, prefs, filters_list, tool_dict, data_url, data_query_wait) {
+    Track.call(this, name, view, container, show_header, prefs, data_url, data_query_wait);
+
     var track = this,
         view = track.view;
         
@@ -2938,8 +2940,7 @@ extend(LabelTrack.prototype, Track.prototype, {
 });
 
 var ReferenceTrack = function (view) {
-    Track.call(this, "reference", view, { content_div: view.top_labeltrack }, false, {});
-    TiledTrack.call(this);
+    TiledTrack.call(this, "reference", view, { content_div: view.top_labeltrack }, false, {});
     
     view.reference_track = this;
     this.left_offset = 200;
@@ -2991,8 +2992,7 @@ var LineTrack = function (name, view, container, hda_ldda, dataset_id, prefs) {
     var track = this;
     this.display_modes = ["Histogram", "Line", "Filled", "Intensity"];
     this.mode = "Histogram";
-    Track.call( this, name, view, container, prefs );
-    TiledTrack.call( this );
+    TiledTrack.call( this, name, view, container, true, prefs );
    
     this.min_height_px = 16; 
     this.max_height_px = 400; 
@@ -3137,11 +3137,8 @@ var FeatureTrack = function(name, view, container, hda_ldda, dataset_id, prefs,
     
     //
     // Initialization.
-    //
-    
-    // FIXME: cleaner init needed; should just be able to call TiledTrack()
-    Track.call(this, name, view, container, true, prefs);
-    TiledTrack.call(this, filters, tool);
+    //    
+    TiledTrack.call(this, name, view, container, true, prefs, filters, tool);
 
     // Define and restore track configuration.
     this.config = new DrawableConfig( {

From 06e59f58fe4db308a496565aab9496041a2cf5dd Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Tue, 25 Oct 2011 09:40:26 -0400
Subject: [PATCH 091/362] Minor cleanup in picard_SamToFastq.xml

---
 tools/picard/picard_SamToFastq.xml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tools/picard/picard_SamToFastq.xml b/tools/picard/picard_SamToFastq.xml
index 7ac90d17e14..b7e71d28ee9 100644
--- a/tools/picard/picard_SamToFastq.xml
+++ b/tools/picard/picard_SamToFastq.xml
@@ -39,7 +39,6 @@
     #end if
   2&gt;&amp;1 
   || echo "Error running SamToFastq" >&amp;2
-  ##&amp;&amp; echo "die die die" >&amp;2
   </command>
   <inputs>
     <param name="input_sam" type="data" format="sam" label="SAM file" />
@@ -85,6 +84,7 @@
           <param name="read1_max_bases_to_write" value="" />
           <param name="re_reverse" value="True" />
           <param name="include_non_pf_reads" value="False" />
+          <param name="clipping_action" value="" />
           <param name="clipping_attribute" value="" />
           <param name="include_non_primary_alignments" value="False" />
           <output name="output_fastq1" file="random_phiX_1.fastqsanger"/> 
@@ -99,6 +99,7 @@
           <param name="read2_max_bases_to_write" value="" />
           <param name="re_reverse" value="True" />
           <param name="include_non_pf_reads" value="False" />
+          <param name="clipping_action" value="" />
           <param name="clipping_attribute" value="" />
           <param name="include_non_primary_alignments" value="False" />
           <output name="output_fastq1" file="bwa_wrapper_in2.fastqsanger" lines_diff="64"/> <!-- 16 unaligned fastq blocks not present in original sam file -->

From ea65ae6661dd8e8e1837a320401f4b0bf9b76c05 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Tue, 25 Oct 2011 10:34:35 -0400
Subject: [PATCH 092/362] Update Picard tools to use
 tool-data/shared/jars/picard/* instead of just tool-data/shared/jars/*.

---
 tools/picard/picard_AddOrReplaceReadGroups.xml | 4 ++--
 tools/picard/picard_BamIndexStats.xml          | 4 ++--
 tools/picard/picard_FastqToSam.xml             | 1 +
 tools/picard/picard_MarkDuplicates.xml         | 4 ++--
 tools/picard/picard_ReorderSam.xml             | 4 ++--
 tools/picard/picard_ReplaceSamHeader.xml       | 4 ++--
 tools/picard/picard_SamToFastq.xml             | 1 +
 tools/picard/rgPicardASMetrics.xml             | 4 ++--
 tools/picard/rgPicardFixMate.xml               | 4 ++--
 tools/picard/rgPicardGCBiasMetrics.xml         | 4 ++--
 tools/picard/rgPicardHsMetrics.xml             | 4 ++--
 tools/picard/rgPicardInsertSize.xml            | 4 ++--
 tools/picard/rgPicardLibComplexity.xml         | 4 ++--
 tools/picard/rgPicardMarkDups.xml              | 4 ++--
 14 files changed, 26 insertions(+), 24 deletions(-)

diff --git a/tools/picard/picard_AddOrReplaceReadGroups.xml b/tools/picard/picard_AddOrReplaceReadGroups.xml
index 88c6dcb2772..d70b2294846 100644
--- a/tools/picard/picard_AddOrReplaceReadGroups.xml
+++ b/tools/picard/picard_AddOrReplaceReadGroups.xml
@@ -1,4 +1,4 @@
-<tool name="Add or Replace Groups" id="picard_ARRG" version="0.2.0">
+<tool name="Add or Replace Groups" id="picard_ARRG" version="0.2.1">
   <requirements><requirement type="package">picard</requirement></requirements>
   <command interpreter="python">
     picard_wrapper.py
@@ -15,7 +15,7 @@
       #end if
       --output-format=$outputFormat
       --output=$outFile
-      -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/AddOrReplaceReadGroups.jar"
+      -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/AddOrReplaceReadGroups.jar"
   </command>
   <inputs>
     <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to add or replace read groups in"
diff --git a/tools/picard/picard_BamIndexStats.xml b/tools/picard/picard_BamIndexStats.xml
index b09b24f06a1..53258ae83cf 100644
--- a/tools/picard/picard_BamIndexStats.xml
+++ b/tools/picard/picard_BamIndexStats.xml
@@ -1,4 +1,4 @@
-<tool name="BAM Index Statistics" id="picard_BamIndexStats" version="0.2.0">
+<tool name="BAM Index Statistics" id="picard_BamIndexStats" version="0.2.1">
   <requirements><requirement type="package">picard</requirement></requirements>
   <command interpreter="python">
     picard_wrapper.py
@@ -6,7 +6,7 @@
       --bai-file "$input_file.metadata.bam_index"
       -t "$htmlfile"
       -d "$htmlfile.files_path"
-      -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/BamIndexStats.jar"
+      -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/BamIndexStats.jar"
   </command>
   <inputs>
     <param format="bam" name="input_file" type="data"  label="BAM dataset to generate statistics for"
diff --git a/tools/picard/picard_FastqToSam.xml b/tools/picard/picard_FastqToSam.xml
index 0eafc51e76a..f1674688fb7 100644
--- a/tools/picard/picard_FastqToSam.xml
+++ b/tools/picard/picard_FastqToSam.xml
@@ -1,5 +1,6 @@
 <tool id="picard_FastqToSam" name="FASTQ to BAM" version="0.0.1">
   <description>creates an unaligned BAM file</description>
+  <requirements><requirement type="package">picard</requirement></requirements>
   <command>java  -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC
     -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/FastqToSam.jar"
     FASTQ="${input_fastq1}"
diff --git a/tools/picard/picard_MarkDuplicates.xml b/tools/picard/picard_MarkDuplicates.xml
index b623b8f53b0..61835e209e9 100644
--- a/tools/picard/picard_MarkDuplicates.xml
+++ b/tools/picard/picard_MarkDuplicates.xml
@@ -1,4 +1,4 @@
-<tool name="Mark Duplicates" id="picard_MarkDuplicates" version="0.01">
+<tool name="Mark Duplicates" id="picard_MarkDuplicates" version="0.01.1">
   <command interpreter="python">
     picard_wrapper.py
       --input="$input_file"
@@ -20,7 +20,7 @@
           --output-sam=$outFileBamMarked
         #end if
       #end if
-      -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/"
+      -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/"
       --picard-cmd="MarkDuplicates"
   </command>
   <inputs>
diff --git a/tools/picard/picard_ReorderSam.xml b/tools/picard/picard_ReorderSam.xml
index b5be194419b..71c0059663d 100644
--- a/tools/picard/picard_ReorderSam.xml
+++ b/tools/picard/picard_ReorderSam.xml
@@ -1,4 +1,4 @@
-<tool name="Reorder SAM/BAM" id="picard_ReorderSam" version="0.3.0">
+<tool name="Reorder SAM/BAM" id="picard_ReorderSam" version="0.3.1">
   <requirements><requirement type="package">picard</requirement></requirements>
   <command interpreter="python">
     picard_wrapper.py
@@ -15,7 +15,7 @@
       --allow-contig-len-discord=$allowContigLenDiscord
       --output-format=$outputFormat
       --output=$outFile
-      -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/ReorderSam.jar"
+      -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/ReorderSam.jar"
   </command>
   <inputs>
     <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to be reordered"
diff --git a/tools/picard/picard_ReplaceSamHeader.xml b/tools/picard/picard_ReplaceSamHeader.xml
index dcf7bfbdd63..95a584068da 100644
--- a/tools/picard/picard_ReplaceSamHeader.xml
+++ b/tools/picard/picard_ReplaceSamHeader.xml
@@ -1,4 +1,4 @@
-<tool name="Replace SAM/BAM Header" id="picard_ReplaceSamHeader" version="0.2.0">
+<tool name="Replace SAM/BAM Header" id="picard_ReplaceSamHeader" version="0.2.1">
   <requirements><requirement type="package">picard</requirement></requirements>
   <command interpreter="python">
     picard_wrapper.py
@@ -6,7 +6,7 @@
       -o $outFile
       --header-file $headerFile
       --output-format $outputFormat
-      -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/ReplaceSamHeader.jar"
+      -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/ReplaceSamHeader.jar"
       --tmpdir "${__new_file_path__}" 
   </command>
   <inputs>
diff --git a/tools/picard/picard_SamToFastq.xml b/tools/picard/picard_SamToFastq.xml
index b7e71d28ee9..e40a99cf310 100644
--- a/tools/picard/picard_SamToFastq.xml
+++ b/tools/picard/picard_SamToFastq.xml
@@ -1,5 +1,6 @@
 <tool id="picard_SamToFastq" name="SAM to FASTQ" version="0.0.1">
   <description>creates a FASTQ file</description>
+  <requirements><requirement type="package">picard</requirement></requirements>
   <command>java -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC
     -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/SamToFastq.jar"
     INPUT="${input_sam}"
diff --git a/tools/picard/rgPicardASMetrics.xml b/tools/picard/rgPicardASMetrics.xml
index 7b5080c38c3..abd3d8fab3d 100644
--- a/tools/picard/rgPicardASMetrics.xml
+++ b/tools/picard/rgPicardASMetrics.xml
@@ -1,8 +1,8 @@
-<tool name="SAM/BAM Alignment Summary Metrics" id="PicardASMetrics" version="0.03">
+<tool name="SAM/BAM Alignment Summary Metrics" id="PicardASMetrics" version="0.03.1">
   <command interpreter="python">
     picard_wrapper.py -i "$input_file" -d "$html_file.files_path" -t "$html_file"
     --assumesorted "$sorted" -b "$bisulphite" --adaptors "$adaptors" --maxinsert "$maxinsert" -n "$out_prefix"
-    -j ${GALAXY_DATA_INDEX_DIR}/shared/jars/CollectAlignmentSummaryMetrics.jar
+    -j ${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/CollectAlignmentSummaryMetrics.jar
 #if $genomeSource.refGenomeSource == "history":
     --ref-file "$genomeSource.ownFile"
 #else
diff --git a/tools/picard/rgPicardFixMate.xml b/tools/picard/rgPicardFixMate.xml
index 9598e8e3b9a..5d7ecb6142e 100644
--- a/tools/picard/rgPicardFixMate.xml
+++ b/tools/picard/rgPicardFixMate.xml
@@ -1,8 +1,8 @@
-<tool name="Paired Read Mate Fixer" id="rgPicFixMate" version="0.2.0">
+<tool name="Paired Read Mate Fixer" id="rgPicFixMate" version="0.2.1">
   <description>for paired data</description>
   <command interpreter="python">
    picard_wrapper.py -i "$input_file" -o "$out_file" --tmpdir "${__new_file_path__}" -n "$out_prefix" 
-   --output-format "$outputFormat" -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/FixMateInformation.jar" --sortorder "$sortOrder"
+   --output-format "$outputFormat" -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/FixMateInformation.jar" --sortorder "$sortOrder"
   </command>
   <requirements><requirement type="package">picard</requirement></requirements>
   <inputs>
diff --git a/tools/picard/rgPicardGCBiasMetrics.xml b/tools/picard/rgPicardGCBiasMetrics.xml
index 0372c3ccfa7..f5eab53d0de 100644
--- a/tools/picard/rgPicardGCBiasMetrics.xml
+++ b/tools/picard/rgPicardGCBiasMetrics.xml
@@ -1,8 +1,8 @@
-<tool name="SAM/BAM GC Bias Metrics" id="PicardGCBiasMetrics" version="0.02">
+<tool name="SAM/BAM GC Bias Metrics" id="PicardGCBiasMetrics" version="0.02.1">
   <command interpreter="python">
     picard_wrapper.py -i "$input_file" -d "$html_file.files_path" -t "$html_file"
     --windowsize "$windowsize" --mingenomefrac "$mingenomefrac" -n "$out_prefix" --tmpdir "${__new_file_path__}"
-    -j ${GALAXY_DATA_INDEX_DIR}/shared/jars/CollectGcBiasMetrics.jar
+    -j ${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/CollectGcBiasMetrics.jar
 #if $genomeSource.refGenomeSource == "history":
  --ref-file "$genomeSource.ownFile"
 #else:
diff --git a/tools/picard/rgPicardHsMetrics.xml b/tools/picard/rgPicardHsMetrics.xml
index ddd35d806dc..d2d3017befe 100644
--- a/tools/picard/rgPicardHsMetrics.xml
+++ b/tools/picard/rgPicardHsMetrics.xml
@@ -1,10 +1,10 @@
-<tool name="SAM/BAM Hybrid Selection Metrics" id="PicardHsMetrics" version="0.02">
+<tool name="SAM/BAM Hybrid Selection Metrics" id="PicardHsMetrics" version="0.02.1">
   <description>for targeted resequencing data</description>
   <command interpreter="python">
 
     picard_wrapper.py -i "$input_file" -d "$html_file.files_path" -t "$html_file" --datatype "$input_file.ext"
     --baitbed "$bait_bed" --targetbed "$target_bed" -n "$out_prefix" --tmpdir "${__new_file_path__}"
-    -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/CalculateHsMetrics.jar"
+    -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/CalculateHsMetrics.jar"
 
   </command>
   <requirements><requirement type="package">picard</requirement></requirements>
diff --git a/tools/picard/rgPicardInsertSize.xml b/tools/picard/rgPicardInsertSize.xml
index f6b71fdef8c..6dd937f0f50 100644
--- a/tools/picard/rgPicardInsertSize.xml
+++ b/tools/picard/rgPicardInsertSize.xml
@@ -1,10 +1,10 @@
-<tool name="Insertion size metrics" id="PicardInsertSize" version="0.3.0">
+<tool name="Insertion size metrics" id="PicardInsertSize" version="0.3.1">
   <description>for PAIRED data</description>
   <requirements><requirement type="package">picard</requirement></requirements>
   <command interpreter="python">
    picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --taillimit "$tailLimit"
    --histwidth "$histWidth" --minpct "$minPct"
-   -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/CollectInsertSizeMetrics.jar" -d "$html_file.files_path" -t "$html_file"
+   -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/CollectInsertSizeMetrics.jar" -d "$html_file.files_path" -t "$html_file"
   </command>
   <inputs>
     <param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset to generate statistics for"
diff --git a/tools/picard/rgPicardLibComplexity.xml b/tools/picard/rgPicardLibComplexity.xml
index 28b104f9f87..ab252100ec2 100644
--- a/tools/picard/rgPicardLibComplexity.xml
+++ b/tools/picard/rgPicardLibComplexity.xml
@@ -1,8 +1,8 @@
-<tool name="Estimate Library Complexity" id="rgEstLibComp" version="0.01">
+<tool name="Estimate Library Complexity" id="rgEstLibComp" version="0.01.1">
   <command interpreter="python">
    picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --minid "$minIDbases"
    --maxdiff "$maxDiff" --minmeanq "$minMeanQ" --readregex "$readRegex" --optdupdist "$optDupeDist"
-   -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/EstimateLibraryComplexity.jar" -d "$html_file.files_path" -t "$html_file"
+   -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/EstimateLibraryComplexity.jar" -d "$html_file.files_path" -t "$html_file"
   </command>
   <inputs>
     <param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset"
diff --git a/tools/picard/rgPicardMarkDups.xml b/tools/picard/rgPicardMarkDups.xml
index 152f23d0866..5a6947b85a8 100644
--- a/tools/picard/rgPicardMarkDups.xml
+++ b/tools/picard/rgPicardMarkDups.xml
@@ -1,8 +1,8 @@
-<tool name="Mark Duplicate reads" id="rgPicardMarkDups" version="0.01">
+<tool name="Mark Duplicate reads" id="rgPicardMarkDups" version="0.01.1">
   <command interpreter="python">
    picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" -o "$out_file"
    --remdups "$remDups" --assumesorted "$assumeSorted" --readregex "$readRegex" --optdupdist "$optDupeDist"
-   -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/MarkDuplicates.jar" -d "$html_file.files_path" -t "$html_file" -e "$input_file.ext"
+   -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/MarkDuplicates.jar" -d "$html_file.files_path" -t "$html_file" -e "$input_file.ext"
   </command>
   <requirements><requirement type="package">picard</requirement></requirements>
   <inputs>

From dab195de277a543f4fd908913187bbe9704560e2 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Tue, 25 Oct 2011 10:52:43 -0400
Subject: [PATCH 093/362] Closed fastq-deinterlacer-memfix


From 9057a61438066ff7e87371e4aad2fc598ae5592f Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Tue, 25 Oct 2011 10:54:17 -0400
Subject: [PATCH 094/362] Fix Python versions in README.txt

---
 README.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.txt b/README.txt
index fd2f7f88bb9..459a93ee5a1 100644
--- a/README.txt
+++ b/README.txt
@@ -7,7 +7,7 @@ website above.
 
 HOW TO START
 ============
-Galaxy requires Python 2.4, 2.5 or 2.6. To check your python version, run:
+Galaxy requires Python 2.5, 2.6 or 2.7. To check your python version, run:
 
 % python -V
 Python 2.4.4

From 58b0b674d59f72c3907aae695cb11bd00b813896 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Tue, 25 Oct 2011 13:51:56 -0400
Subject: [PATCH 095/362] Allow picard_SamToFastq to use input BAM files.

---
 tools/picard/picard_SamToFastq.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/picard/picard_SamToFastq.xml b/tools/picard/picard_SamToFastq.xml
index e40a99cf310..2274ad1caed 100644
--- a/tools/picard/picard_SamToFastq.xml
+++ b/tools/picard/picard_SamToFastq.xml
@@ -42,11 +42,11 @@
   || echo "Error running SamToFastq" >&amp;2
   </command>
   <inputs>
-    <param name="input_sam" type="data" format="sam" label="SAM file" />
+    <param name="input_sam" type="data" format="sam,bam" label="BAM/SAM file" />
     <param name="read1_trim" type="integer" value="" optional="True" label="The number of bases to trim from the beginning of read 1." />
     <param name="read1_max_bases_to_write" type="integer" optional="True" value="" label="The maximum number of bases to write from read 1 after trimming." />
     <param name="output_per_read_group_selector" type="select" label="Output per read group">
-      <option value="per_sam_file" selected="True">Per SAM file</option>
+      <option value="per_sam_file" selected="True">Per BAM/SAM file</option>
       <!-- <option value="per_read_group">Per Read Group</option> -->
       <validator type="expression" message="Per Read Group selection is not yet implemented">value == 'per_sam_file'</validator>
     </param>

From 2502d06cc14e67f59cd193b381c5a3b9fbcc9621 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Tue, 25 Oct 2011 13:58:08 -0400
Subject: [PATCH 096/362] Show dataset size of non-purged error state history
 items.

---
 templates/root/history_common.mako | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/templates/root/history_common.mako b/templates/root/history_common.mako
index 6f4064e0cf1..ebe46f6317b 100644
--- a/templates/root/history_common.mako
+++ b/templates/root/history_common.mako
@@ -96,7 +96,7 @@
                             display_url = h.url_for( controller='dataset', action='display', dataset_id=dataset_id, preview=True, filename='' )
                 %>
                 %if data.purged:
-                    <span class="icon-button display_disabled tooltip" title="Cannoy display datasets removed from disk"></span>
+                    <span class="icon-button display_disabled tooltip" title="Cannot display datasets removed from disk"></span>
                 %else:
                     <a class="icon-button display tooltip" title="Display data in browser" href="${display_url}"
                     %if for_editing:
@@ -150,6 +150,9 @@
                 %endif
             </div>
         %elif data_state == "error":
+            %if not data.purged:
+                <div>${data.get_size( nice_size=True )}</div>
+            %endif
             <div>
                 An error occurred running this job: <i>${data.display_info().strip()}</i>
             </div>

From 3bf0297dfda45af4f7394bc8593089b4a857bad5 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Tue, 25 Oct 2011 14:21:49 -0400
Subject: [PATCH 097/362] Remove some debug prints from GATK unified genotyper.

---
 tools/gatk/unified_genotyper.xml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/tools/gatk/unified_genotyper.xml b/tools/gatk/unified_genotyper.xml
index 98cc56faaf3..8fe0bebaaf3 100644
--- a/tools/gatk/unified_genotyper.xml
+++ b/tools/gatk/unified_genotyper.xml
@@ -7,8 +7,6 @@
    --max_jvm_heap_fraction "1"
    --stdout "${output_log}"
    #for $i, $input_bam in enumerate( $reference_source.input_bams ):
-       ${dir( $input_bam.input_bam )}
-       ${dir( $input_bam.input_bam.dataset )}
        -d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "gatk_input_${i}"
        -d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index
    #end for

From 7a1ad5f96705593eb36debd70f4462c7fd5b30fc Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Tue, 25 Oct 2011 14:59:19 -0400
Subject: [PATCH 098/362] Trackster: automatically remove spaces from an
 entered location.

---
 static/scripts/trackster.js | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index 523ec4ca488..ce87c95f0f3 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -1189,6 +1189,10 @@ extend( View.prototype, DrawableCollection.prototype, {
         }
     },
     go_to: function(str) {
+        // Preprocess str to remove spaces and commas.
+        str = str.replace(/ |,/g, "");
+        
+        // Go to new location.
         var view = this,
             new_low, 
             new_high,
@@ -1199,8 +1203,8 @@ extend( View.prototype, DrawableCollection.prototype, {
         if (pos !== undefined) {
             try {
                 var pos_split = pos.split("-");
-                new_low = parseInt(pos_split[0].replace(/,/g, ""), 10);
-                new_high = parseInt(pos_split[1].replace(/,/g, ""), 10);
+                new_low = parseInt(pos_split[0], 10);
+                new_high = parseInt(pos_split[1], 10);
             } catch (e) {
                 return false;
             }

From 03e84bfdd82ad3369dadafaf7522e0c53174219d Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Tue, 25 Oct 2011 15:23:45 -0400
Subject: [PATCH 099/362] Set URL for visualization when it is first saved.

---
 lib/galaxy/web/controllers/tracks.py |  3 ++-
 templates/tracks/browser.mako        | 10 +++++++---
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/web/controllers/tracks.py b/lib/galaxy/web/controllers/tracks.py
index d9b464eede6..a1527438a1f 100644
--- a/lib/galaxy/web/controllers/tracks.py
+++ b/lib/galaxy/web/controllers/tracks.py
@@ -663,7 +663,8 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
         vis.latest_revision = vis_rev
         session.add( vis_rev )
         session.flush()
-        return trans.security.encode_id(vis.id)
+        encoded_id = trans.security.encode_id(vis.id)
+        return { "id": encoded_id, "url": url_for( action='browser', id=encoded_id ) }
         
     @web.expose
     @web.require_login( "see all available libraries" )
diff --git a/templates/tracks/browser.mako b/templates/tracks/browser.mako
index 86d860a2289..1dc017fc469 100644
--- a/templates/tracks/browser.mako
+++ b/templates/tracks/browser.mako
@@ -212,10 +212,14 @@ ${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.e
                         'dbkey': view.dbkey,
                         'payload': JSON.stringify(payload)
                     },
-                    success: function(vis_id) {
-                        view.vis_id = vis_id;
-                        view.has_changes = false;
+                    dataType: "json",
+                    success: function(vis_info) {
                         hide_modal();
+                        view.vis_id = vis_info.vis_id;
+                        view.has_changes = false;
+                        
+                        // Needed to set URL when first saving a visualization.
+                        window.history.pushState({}, "", vis_info.url);
                     },
                     error: function() { alert("Could not save visualization"); }
                 });

From 6703cf25e63c6f7fd25e5e0e08d800df3854a062 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Tue, 25 Oct 2011 15:43:04 -0400
Subject: [PATCH 100/362] Add metadata validator to force input bam files to
 have bam_index metadata files for GATK tools.

---
 tools/gatk/count_covariates.xml         | 5 ++++-
 tools/gatk/indel_realigner.xml          | 5 ++++-
 tools/gatk/realigner_target_creator.xml | 5 ++++-
 tools/gatk/table_recalibration.xml      | 5 ++++-
 tools/gatk/unified_genotyper.xml        | 5 ++++-
 tools/gatk/variant_annotator.xml        | 5 ++++-
 6 files changed, 24 insertions(+), 6 deletions(-)

diff --git a/tools/gatk/count_covariates.xml b/tools/gatk/count_covariates.xml
index ac29c1e6e2a..0a2366fa09a 100644
--- a/tools/gatk/count_covariates.xml
+++ b/tools/gatk/count_covariates.xml
@@ -138,6 +138,7 @@
       <when value="cached">
         <param name="input_bam" type="data" format="bam" label="BAM file">
           <validator type="unspecified_build" />
+          <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
           <validator type="dataset_metadata_in_file" filename="picard_index.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
         </param>
         <param name="ref_file" type="select" label="Using reference genome">
@@ -147,7 +148,9 @@
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
-        <param name="input_bam" type="data" format="bam" label="BAM file" />
+        <param name="input_bam" type="data" format="bam" label="BAM file" >
+          <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
+        </param>
         <param name="ref_file" type="data" format="fasta" label="Using reference file" />
       </when>
     </conditional>
diff --git a/tools/gatk/indel_realigner.xml b/tools/gatk/indel_realigner.xml
index f4077016952..9676467e9c4 100644
--- a/tools/gatk/indel_realigner.xml
+++ b/tools/gatk/indel_realigner.xml
@@ -107,6 +107,7 @@
       <when value="cached">
         <param name="input_bam" type="data" format="bam" label="BAM file">
           <validator type="unspecified_build" />
+          <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
           <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
         </param>
         <param name="ref_file" type="select" label="Using reference genome">
@@ -116,7 +117,9 @@
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
-        <param name="input_bam" type="data" format="bam" label="BAM file" />
+        <param name="input_bam" type="data" format="bam" label="BAM file" >
+          <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
+        </param>
         <param name="ref_file" type="data" format="fasta" label="Using reference file">
           <options>
             <filter type="data_meta" key="dbkey" ref="input_bam" /> <!-- FIX ME!!!! -->
diff --git a/tools/gatk/realigner_target_creator.xml b/tools/gatk/realigner_target_creator.xml
index 0513c75cd5f..7be101ec472 100644
--- a/tools/gatk/realigner_target_creator.xml
+++ b/tools/gatk/realigner_target_creator.xml
@@ -103,6 +103,7 @@
       <when value="cached">
         <param name="input_bam" type="data" format="bam" label="BAM file">
           <validator type="unspecified_build" />
+          <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
           <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
         </param>
         <param name="ref_file" type="select" label="Using reference genome">
@@ -112,7 +113,9 @@
         </param>
       </when>
       <when value="history">
-        <param name="input_bam" type="data" format="bam" label="BAM file" />
+        <param name="input_bam" type="data" format="bam" label="BAM file" >
+          <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
+        </param>
         <param name="ref_file" type="data" format="fasta" label="Using reference file">
           <options>
             <filter type="data_meta" key="dbkey" ref="input_bam" /> <!-- FIX ME!!!! -->
diff --git a/tools/gatk/table_recalibration.xml b/tools/gatk/table_recalibration.xml
index e2a0448d1c9..1e4e6da35f6 100644
--- a/tools/gatk/table_recalibration.xml
+++ b/tools/gatk/table_recalibration.xml
@@ -117,6 +117,7 @@
       <when value="cached">
         <param name="input_bam" type="data" format="bam" label="BAM file">
           <validator type="unspecified_build" />
+          <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
           <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
         </param>
         <param name="ref_file" type="select" label="Using reference genome">
@@ -126,7 +127,9 @@
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
-        <param name="input_bam" type="data" format="bam" label="BAM file" />
+        <param name="input_bam" type="data" format="bam" label="BAM file" >
+          <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
+        </param>
         <param name="ref_file" type="data" format="fasta" label="Using reference file" />
       </when>
     </conditional>
diff --git a/tools/gatk/unified_genotyper.xml b/tools/gatk/unified_genotyper.xml
index 8fe0bebaaf3..ae2cc08c6d1 100644
--- a/tools/gatk/unified_genotyper.xml
+++ b/tools/gatk/unified_genotyper.xml
@@ -135,6 +135,7 @@
         <repeat name="input_bams" title="Sample BAM file" min="1">
             <param name="input_bam" type="data" format="bam" label="BAM file">
               <validator type="unspecified_build" />
+              <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
               <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
             </param>
         </repeat>
@@ -146,7 +147,9 @@
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
         <repeat name="input_bams" title="Sample BAM file" min="1">
-            <param name="input_bam" type="data" format="bam" label="BAM file" />
+            <param name="input_bam" type="data" format="bam" label="BAM file" >
+              <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
+            </param>
         </repeat>
         <param name="ref_file" type="data" format="fasta" label="Using reference file" />
       </when>
diff --git a/tools/gatk/variant_annotator.xml b/tools/gatk/variant_annotator.xml
index c15689f3035..55802641b2f 100644
--- a/tools/gatk/variant_annotator.xml
+++ b/tools/gatk/variant_annotator.xml
@@ -145,6 +145,7 @@
         <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." />
         <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" help="Not needed for all annotations." >
           <validator type="unspecified_build" />
+          <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
           <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
         </param>
         <param name="ref_file" type="select" label="Using reference genome">
@@ -156,7 +157,9 @@
       <when value="history"> <!-- FIX ME!!!! -->
         <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" />
         <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." />
-        <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" />
+        <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" >
+          <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
+        </param>
         <param name="ref_file" type="data" format="fasta" label="Using reference file" />
       </when>
     </conditional>

From fc156c89a0b667d0724f3f9a407573b4345cae09 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Wed, 26 Oct 2011 13:35:17 -0400
Subject: [PATCH 101/362] "Merge BAM Files" under SAM Tools section(???) calls
 Picard MergeSamFiles.jar. Update to new jar location.

---
 tools/samtools/sam_merge.xml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tools/samtools/sam_merge.xml b/tools/samtools/sam_merge.xml
index 2dae5965675..7a0ae80623b 100644
--- a/tools/samtools/sam_merge.xml
+++ b/tools/samtools/sam_merge.xml
@@ -4,7 +4,7 @@
     <requirement type="package">picard</requirement>
   </requirements>
   <command>
-java -Xmx2G -jar ${GALAXY_DATA_INDEX_DIR}/shared/jars/MergeSamFiles.jar MSD=$mergeSD VALIDATION_STRINGENCY=LENIENT O=$output1 I=$input1 I=$input2 
+java -Xmx2G -jar ${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/MergeSamFiles.jar MSD=$mergeSD VALIDATION_STRINGENCY=LENIENT O=$output1 I=$input1 I=$input2 
       #for $i in $inputs
         I=${i.input}
       #end for 
@@ -36,7 +36,7 @@ java -Xmx2G -jar ${GALAXY_DATA_INDEX_DIR}/shared/jars/MergeSamFiles.jar MSD=$mer
       <param name="input1" value="sam_merge_in1.bam" ftype="bam" /> 
       <param name="input2" value="sam_merge_in2.bam" ftype="bam" />
       <output name="output1" file="sam_merge_out1.bam" ftype="bam" />
-      <output name="outlog" file="sam_merge_out1.log" ftype="txt" lines_diff="10"/>
+      <output name="outlog" file="sam_merge_out1.log" ftype="txt" lines_diff="11"/>
     </test>
     <test>
       <param name="title" value="test2" />
@@ -45,7 +45,7 @@ java -Xmx2G -jar ${GALAXY_DATA_INDEX_DIR}/shared/jars/MergeSamFiles.jar MSD=$mer
       <param name="input2" value="sam_merge_in2.bam" ftype="bam" />
       <param name="input" value="sam_merge_in3.bam" ftype="bam" />
       <output name="output1" file="sam_merge_out2.bam" ftype="bam" />
-      <output name="outlog" file="sam_merge_out2.log" ftype="txt" lines_diff="10"/>
+      <output name="outlog" file="sam_merge_out2.log" ftype="txt" lines_diff="11"/>
     </test>
   </tests>
   <help>

From 8e10b7d6fb837b455485a9444342fe4cf18db0f3 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Wed, 26 Oct 2011 16:03:47 -0400
Subject: [PATCH 102/362] Allow Picard based Merge BAM Files tool to work on
 sam inputs as well as the previously accepted bam.

---
 tools/samtools/sam_merge.xml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tools/samtools/sam_merge.xml b/tools/samtools/sam_merge.xml
index 7a0ae80623b..1b9ab0faeda 100644
--- a/tools/samtools/sam_merge.xml
+++ b/tools/samtools/sam_merge.xml
@@ -16,10 +16,10 @@ java -Xmx2G -jar ${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/MergeSamFiles.jar M
     <param name="mergeSD" value="true" type="boolean"  label="Merge all component bam file headers into the merged bam file"
       truevalue="true" falsevalue="false" checked="yes" 
       help="Control the MERGE_SEQUENCE_DICTIONARIES flag for Picard MergeSamFiles. Default (true) correctly propagates read groups and other important metadata" />
-    <param name="input1" label="First file" type="data" format="bam" />
-    <param name="input2" label="with file" type="data" format="bam" help="Need to add more files? Use controls below." />
+    <param name="input1" label="First file" type="data" format="bam,sam" />
+    <param name="input2" label="with file" type="data" format="bam,sam" help="Need to add more files? Use controls below." />
     <repeat name="inputs" title="Input Files">
-      <param name="input" label="Add file" type="data" format="bam" />
+      <param name="input" label="Add file" type="data" format="bam,sam" />
     </repeat>
   </inputs>
   <outputs>

From e3979aae31439d425ad15825927b1714ba471d66 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Wed, 26 Oct 2011 16:11:49 -0400
Subject: [PATCH 103/362] Add the ability to view workflows contained in a tool
 shed repository as svg images.  Add the ability to import a specific workflow
 from a Galaxy tool shed repository to a loacl Galaxy instance.  Fix bugs when
 displaying or running a workflow that requires tools that use the old Galaxy
 tool id, but the local Galaxy instance uses tools installed from a tool shed.

---
 lib/galaxy/web/base/controller.py             |  32 +-
 lib/galaxy/web/controllers/admin.py           |  14 +-
 lib/galaxy/web/controllers/workflow.py        |  37 +-
 lib/galaxy/webapps/community/app.py           |   2 +
 .../webapps/community/controllers/admin.py    |   8 +-
 .../webapps/community/controllers/common.py   |  51 ++-
 .../community/controllers/repository.py       |  27 +-
 .../webapps/community/controllers/workflow.py | 395 ++++++++++++++++++
 .../webapps/community/model/__init__.py       |  28 ++
 lib/galaxy/workflow/modules.py                |   8 +-
 .../webapps/community/repository/common.mako  |  26 +-
 .../repository/manage_repository.mako         |   2 +-
 .../preview_tools_in_changeset.mako           |   2 +-
 .../community/repository/view_repository.mako |   2 +-
 .../community/repository/view_workflow.mako   | 102 +++++
 templates/workflow/display.mako               |  14 +-
 templates/workflow/run.mako                   |  12 +-
 17 files changed, 701 insertions(+), 61 deletions(-)
 create mode 100644 lib/galaxy/webapps/community/controllers/workflow.py
 create mode 100644 templates/webapps/community/repository/view_workflow.mako

diff --git a/lib/galaxy/web/base/controller.py b/lib/galaxy/web/base/controller.py
index 530706451a8..aac24eca02e 100644
--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -1,10 +1,11 @@
 """
 Contains functionality needed in every web interface
 """
-import os, time, logging, re, string, sys, glob, shutil, tempfile, subprocess
+import os, time, logging, re, string, sys, glob, shutil, tempfile, subprocess, binascii
 from datetime import date, datetime, timedelta
 from time import strftime
 from galaxy import config, tools, web, util
+from galaxy.util.hash_util import *
 from galaxy.web import error, form, url_for
 from galaxy.model.orm import *
 from galaxy.workflow.modules import *
@@ -2484,3 +2485,32 @@ def handle_sample_tool_data_table_conf_file( trans, filename ):
             message = "The required file named tool_data_table_conf.xml does not exist in the Galaxy install directory."
             error = True
     return error, message
+def tool_shed_encode( val ):
+    if isinstance( val, dict ):
+        value = simplejson.dumps( val )
+    else:
+        value = val
+    a = hmac_new( 'ToolShedAndGalaxyMustHaveThisSameKey', value )
+    b = binascii.hexlify( value )
+    return "%s:%s" % ( a, b )
+def tool_shed_decode( value ):
+    # Extract and verify hash
+    a, b = value.split( ":" )
+    value = binascii.unhexlify( b )
+    test = hmac_new( 'ToolShedAndGalaxyMustHaveThisSameKey', value )
+    assert a == test
+    # Restore from string
+    values = None
+    try:
+        values = simplejson.loads( value )
+    except Exception, e:
+        log.debug( "Decoding json value from tool shed threw exception: %s" % str( e ) )
+    if values is not None:
+        try:
+            return json_fix( values )
+        except Exception, e:
+            log.debug( "Fixing decoded json value from tool shed threw exception: %s" % str( e ) )
+            fixed_values = values
+    if values is None:
+        values = value
+    return values
diff --git a/lib/galaxy/web/controllers/admin.py b/lib/galaxy/web/controllers/admin.py
index 90713fa0169..34ec1367bf8 100644
--- a/lib/galaxy/web/controllers/admin.py
+++ b/lib/galaxy/web/controllers/admin.py
@@ -4,8 +4,7 @@ from galaxy.model.orm import *
 from galaxy.web.framework.helpers import time_ago, iff, grids
 from galaxy.tools.search import ToolBoxSearch
 from galaxy.tools import json_fix
-from galaxy.util.hash_util import *
-import simplejson, binascii, logging
+import logging
 log = logging.getLogger( __name__ )
 
 from galaxy.actions.admin import AdminActions
@@ -736,7 +735,7 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
                 section_key = 'section_%s' % kwd[ 'tool_panel_section' ]
                 tool_section = trans.app.toolbox.tool_panel[ section_key ]
                 # Decode the encoded repo_info_dict param value.
-                repo_info_dict = self.__decode( repo_info_dict )
+                repo_info_dict = tool_shed_decode( repo_info_dict )
                 # Clone the repository to the configured location.
                 current_working_dir = os.getcwd()
                 for name, repo_info_tuple in repo_info_dict.items():
@@ -1157,15 +1156,6 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
             section_str += '        </tool>\n'
         section_str += '    </section>\n'
         return section_str
-    def __decode( self, value ):
-        # Extract and verify hash
-        a, b = value.split( ":" )
-        value = binascii.unhexlify( b )
-        test = hmac_new( 'ToolShedAndGalaxyMustHaveThisSameKey', value )
-        assert a == test
-        # Restore from string
-        values = json_fix( simplejson.loads( value ) )
-        return values
 
 ## ---- Utility methods -------------------------------------------------------
 
diff --git a/lib/galaxy/web/controllers/workflow.py b/lib/galaxy/web/controllers/workflow.py
index 3e7245b0125..6536d262027 100644
--- a/lib/galaxy/web/controllers/workflow.py
+++ b/lib/galaxy/web/controllers/workflow.py
@@ -4,7 +4,7 @@ import pkg_resources
 pkg_resources.require( "simplejson" )
 pkg_resources.require( "SVGFig" )
 import simplejson
-import base64, httplib, urllib2, sgmllib, svgfig
+import base64, httplib, urllib2, sgmllib, svgfig, urllib, urllib2
 import math
 from galaxy.web.framework.helpers import time_ago, grids
 from galaxy.tools.parameters import *
@@ -1092,13 +1092,35 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
         trans.response.headers["Content-Disposition"] = "attachment; filename=Galaxy-Workflow-%s.ga" % ( sname )
         trans.response.set_content_type( 'application/galaxy-archive' )
         return stored_dict
-
     @web.expose
     def import_workflow( self, trans, **kwd ):
+        """
+        Import a workflow by reading an url, uploading a file, or receiving the textual
+        representation of a workflow.
+        """
         url = kwd.get( 'url', '' )
+        workflow_text = kwd.get( 'workflow_text', '' )
+        webapp = kwd.get( 'webapp', 'galaxy' )
         message = kwd.get( 'message', '' )
         status = kwd.get( 'status', 'done' )
-        if kwd.get( 'import_button', False ):
+        import_button = kwd.get( 'import_button', False )
+        tool_shed_url = kwd.get( 'tool_shed_url', '' )
+        repository_metadata_id = kwd.get( 'repository_metadata_id', '' )
+        # The workflow_name parameter is in the request only if the import originated
+        # from a Galaxy tool shed, in which case the value was encoded.
+        workflow_name = kwd.get( 'workflow_name', '' )
+        if workflow_name:
+            workflow_name = tool_shed_decode( workflow_name )
+        if tool_shed_url and not import_button:
+            # Use urllib (send another request to the tool shed) to retrieve the workflow.
+            workflow_url = 'http://%s/workflow/import_workflow?repository_metadata_id=%s&workflow_name=%s&webapp=%s&open_for_url=true' % \
+                ( tool_shed_url, repository_metadata_id, tool_shed_encode( workflow_name ), webapp )
+            response = urllib2.urlopen( workflow_url )
+            workflow_text = response.read()
+            response.close()
+            workflow_text = workflow_text
+            import_button = True
+        if import_button:
             workflow_data = None
             if url:
                 # Load workflow from external URL
@@ -1108,6 +1130,8 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
                 except Exception, e:
                     message = "Failed to open URL: <b>%s</b><br>Exception: %s" % ( url, str( e ) )
                     status = 'error'
+            elif workflow_text:
+                workflow_data = workflow_text
             else:
                 # Load workflow from browsed file.
                 file_data = kwd.get( 'file_data', '' )
@@ -1175,6 +1199,13 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
                         else:
                             # TODO: Figure out what to do here...
                             pass
+                    if tool_shed_url:
+                        # We've received the textual representation of a workflow from a Galaxy tool shed.
+                        message = "This workflow has been successfully imported into your local Galaxy instance."
+                        # TODO: support https in the following url.
+                        url = 'http://%s/workflow/view_workflow?repository_metadata_id=%s&workflow_name=%s&webapp=%s&message=%s' % \
+                            ( tool_shed_url, repository_metadata_id, tool_shed_encode( workflow_name ), webapp, message )
+                        return trans.response.send_redirect( url )
                     return self.list( trans )
         return trans.fill_template( "workflow/import.mako",
                                     url=url,
diff --git a/lib/galaxy/webapps/community/app.py b/lib/galaxy/webapps/community/app.py
index 3f622002751..00f6f622b01 100644
--- a/lib/galaxy/webapps/community/app.py
+++ b/lib/galaxy/webapps/community/app.py
@@ -35,6 +35,8 @@ class UniverseApplication( object ):
         self.tag_handler = CommunityTagHandler()
         # Tool data tables
         self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( self.config.tool_data_table_config_path )
+        # The tool shed has no toolbox, but this attribute is still required.
+        self.toolbox = None
         # Load security policy
         self.security_agent = self.model.security_agent
         self.quota_agent = galaxy.quota.NoQuotaAgent( self.model )
diff --git a/lib/galaxy/webapps/community/controllers/admin.py b/lib/galaxy/webapps/community/controllers/admin.py
index 040f596eaf1..47bd4b84584 100644
--- a/lib/galaxy/webapps/community/controllers/admin.py
+++ b/lib/galaxy/webapps/community/controllers/admin.py
@@ -332,13 +332,13 @@ class RepositoryMetadataListGrid( grids.Grid ):
                     if 'tools' in metadata:
                         metadata_str += '<b>Tools:</b><br/>'
                         for tool_metadata_dict in metadata[ 'tools' ]:
-                            metadata_str += '%s <b>%s</b><br/>' % \
-                                ( tool_metadata_dict[ 'id' ], tool_metadata_dict[ 'version' ] )
+                            metadata_str += '%s <b>%s</b><br/>' % ( tool_metadata_dict[ 'id' ],
+                                                                    tool_metadata_dict[ 'version' ] )
                     if 'workflows' in metadata:
                         metadata_str += '<b>Workflows:</b><br/>'
                         for workflow_metadata_dict in metadata[ 'workflows' ]:
-                            metadata_str += '%s <b>%s</b><br/>' % \
-                                ( workflow_metadata_dict[ 'name' ], workflow_metadata_dict[ 'format-version' ] )
+                            metadata_str += '%s <b>%s</b><br/>' % ( workflow_metadata_dict[ 'name' ],
+                                                                    workflow_metadata_dict[ 'format-version' ] )
             return metadata_str
     class MaliciousColumn( grids.BooleanColumn ):
         def get_value( self, trans, grid, repository_metadata ):
diff --git a/lib/galaxy/webapps/community/controllers/common.py b/lib/galaxy/webapps/community/controllers/common.py
index 0cbda2eed7d..fa46b95ab8a 100644
--- a/lib/galaxy/webapps/community/controllers/common.py
+++ b/lib/galaxy/webapps/community/controllers/common.py
@@ -1,8 +1,9 @@
-import os, string, socket, logging
+import os, string, socket, logging, simplejson, binascii
 from time import strftime
 from datetime import *
 from galaxy.tools import *
 from galaxy.util.json import from_json_string, to_json_string
+from galaxy.util.hash_util import *
 from galaxy.web.base.controller import *
 from galaxy.webapps.community import model
 from galaxy.model.orm import *
@@ -126,23 +127,18 @@ def get_latest_repository_metadata( trans, id ):
 def generate_workflow_metadata( trans, id, changeset_revision, exported_workflow_dict, metadata_dict ):
     """
     Update the received metadata_dict with changes that have been applied
-    to the received exported_workflow_dict.  Store everything except the
-    workflow steps in the database.
+    to the received exported_workflow_dict.  Store everything in the database.
     """
-    workflow_dict = { 'a_galaxy_workflow' : exported_workflow_dict[ 'a_galaxy_workflow' ],
-                      'name' :exported_workflow_dict[ 'name' ],
-                      'annotation' : exported_workflow_dict[ 'annotation' ],
-                      'format-version' : exported_workflow_dict[ 'format-version' ] }
     if 'workflows' in metadata_dict:
-        metadata_dict[ 'workflows' ].append( workflow_dict )
+        metadata_dict[ 'workflows' ].append( exported_workflow_dict )
     else:
-        metadata_dict[ 'workflows' ] = [ workflow_dict ]
+        metadata_dict[ 'workflows' ] = [ exported_workflow_dict ]
     return metadata_dict
 def new_workflow_metadata_required( trans, id, metadata_dict ):
     """
-    TODO: Currently everything about an exported workflow except the name is hard-coded, so
-    there's no real way to differentiate versions of exported workflows.  If this changes at
-    some future time, this method should be enhanced accordingly...
+    Currently everything about an exported workflow except the name is hard-coded, so there's
+    no real way to differentiate versions of exported workflows.  If this changes at some future
+    time, this method should be enhanced accordingly.
     """
     if 'workflows' in metadata_dict:
         repository_metadata = get_latest_repository_metadata( trans, id )
@@ -425,18 +421,20 @@ def set_repository_metadata( trans, id, changeset_revision, **kwd ):
                 trans.sa_session.add( repository_metadata )
                 trans.sa_session.flush()
         else:
-            message = "Change set revision '%s' includes no tools or exported workflows for which metadata can be set." % str( changeset_revision )
+            message = "Revision '%s' includes no tools or exported workflows for which metadata can be defined " % str( changeset_revision )
+            message += "so this revision cannot be automatically installed into a local Galaxy instance."
             status = "error"
     else:
         # change_set is None
-        message = "Repository does not include change set revision '%s'." % str( changeset_revision )
+        message = "This repository does not include revision '%s'." % str( changeset_revision )
         status = 'error'
     if invalid_files:
         if metadata_dict:
-            message = "Metadata was defined for some items in change set revision '%s'.  " % str( changeset_revision )
+            message = "Metadata was defined for some items in revision '%s'.  " % str( changeset_revision )
             message += "Correct the following problems if necessary and reset metadata.<br/>"
         else:
-            message = "Metadata cannot be defined for change set revision '%s'.  Correct the following problems and reset metadata.<br/>" % str( changeset_revision )
+            message = "Metadata cannot be defined for revision '%s' so this revision cannot be automatically " % str( changeset_revision )
+            message += "installed into a local Galaxy instance.  Correct the following problems and reset metadata.<br/>"
         for itc_tup in invalid_files:
             tool_file, exception_msg = itc_tup
             if exception_msg.find( 'No such file or directory' ) >= 0:
@@ -619,3 +617,24 @@ def build_changeset_revision_select_field( trans, repository, selected_value=Non
         selected = selected_value and option_tup[1] == selected_value
         select_field.add_option( option_tup[0], option_tup[1], selected=selected )
     return select_field
+def encode( val ):
+    if isinstance( val, dict ):
+        value = simplejson.dumps( val )
+    else:
+        value = val
+    a = hmac_new( 'ToolShedAndGalaxyMustHaveThisSameKey', value )
+    b = binascii.hexlify( value )
+    return "%s:%s" % ( a, b )
+def decode( value ):
+    # Extract and verify hash
+    a, b = value.split( ":" )
+    value = binascii.unhexlify( b )
+    test = hmac_new( 'ToolShedAndGalaxyMustHaveThisSameKey', value )
+    assert a == test
+    # Restore from string
+    try:
+        values = json_fix( simplejson.loads( value ) )
+    except Exception, e:
+        # We do not have a json string
+        values = value
+    return values
diff --git a/lib/galaxy/webapps/community/controllers/repository.py b/lib/galaxy/webapps/community/controllers/repository.py
index 01e7c62a4e5..93f32c49c9f 100644
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -9,7 +9,6 @@ from galaxy.webapps.community import model
 from galaxy.webapps.community.model import directory_hash_id
 from galaxy.web.framework.helpers import time_ago, iff, grids
 from galaxy.util.json import from_json_string, to_json_string
-from galaxy.util.hash_util import *
 from galaxy.model.orm import *
 from common import *
 from mercurial import hg, ui, patch, commands
@@ -458,7 +457,10 @@ class RepositoryController( BaseUIController, ItemRatings ):
         ok = True
         for repository_metadata in trans.sa_session.query( model.RepositoryMetadata ):
             metadata = repository_metadata.metadata
-            tools = metadata[ 'tools' ]
+            if 'tools' in metadata:
+                tools = metadata[ 'tools' ]
+            else:
+                tools = []
             for tool_dict in tools:
                 if tool_ids and not tool_names and not tool_versions:
                     for tool_id in tool_ids:
@@ -588,15 +590,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
             changeset_revision = repository_metadata.changeset_revision
             repository_clone_url = generate_clone_url( trans, repository_id )
             repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, changeset_revision )
-        return self.__encode( repo_info_dict )
-    def __encode( self, val ):
-        if isinstance( val, dict ):
-            value = simplejson.dumps( val )
-        else:
-            value = val
-        a = hmac_new( 'ToolShedAndGalaxyMustHaveThisSameKey', value )
-        b = binascii.hexlify( value )
-        return "%s:%s" % ( a, b )
+        return encode( repo_info_dict )
     @web.expose
     def preview_tools_in_changeset( self, trans, repository_id, **kwd ):
         params = util.Params( kwd )
@@ -607,8 +601,10 @@ class RepositoryController( BaseUIController, ItemRatings ):
         changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) )
         repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision )
         if repository_metadata:
+            repository_metadata_id = trans.security.encode_id( repository_metadata.id ),
             metadata = repository_metadata.metadata
         else:
+            repository_metadata_id = None
             metadata = None
         revision_label = get_revision_label( trans, repository, changeset_revision )
         changeset_revision_select_field = build_changeset_revision_select_field( trans,
@@ -617,6 +613,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
                                                                                  add_id_to_name=False )
         return trans.fill_template( '/webapps/community/repository/preview_tools_in_changeset.mako',
                                     repository=repository,
+                                    repository_metadata_id=repository_metadata_id,
                                     changeset_revision=changeset_revision,
                                     revision_label=revision_label,
                                     changeset_revision_select_field=changeset_revision_select_field,
@@ -636,7 +633,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
         changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) )
         repo_info_dict = {}
         repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, changeset_revision )
-        encoded_repo_info_dict = self.__encode( repo_info_dict )
+        encoded_repo_info_dict = encode( repo_info_dict )
         # Redirect back to local Galaxy to perform install.
         # TODO: support https in the following url.
         url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s&repo_info_dict=%s' % \
@@ -1159,8 +1156,10 @@ class RepositoryController( BaseUIController, ItemRatings ):
         revision_label = get_revision_label( trans, repository, changeset_revision )
         repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision )
         if repository_metadata:
+            repository_metadata_id = trans.security.encode_id( repository_metadata.id ),
             metadata = repository_metadata.metadata
         else:
+            repository_metadata_id = None
             metadata = None
         is_malicious = change_set_is_malicious( trans, id, repository.tip )
         if is_malicious:
@@ -1172,6 +1171,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
         return trans.fill_template( '/webapps/community/repository/view_repository.mako',
                                     repo=repo,
                                     repository=repository,
+                                    repository_metadata_id=repository_metadata_id,
                                     metadata=metadata,
                                     avg_rating=avg_rating,
                                     display_reviews=display_reviews,
@@ -1299,9 +1299,11 @@ class RepositoryController( BaseUIController, ItemRatings ):
         revision_label = get_revision_label( trans, repository, changeset_revision )
         repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision )
         if repository_metadata:
+            repository_metadata_id = trans.security.encode_id( repository_metadata.id )
             metadata = repository_metadata.metadata
             is_malicious = repository_metadata.malicious
         else:
+            repository_metadata_id = None
             metadata = None
             is_malicious = False
         if is_malicious:
@@ -1321,6 +1323,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
                                     allow_push_select_field=allow_push_select_field,
                                     repo=repo,
                                     repository=repository,
+                                    repository_metadata_id=repository_metadata_id,
                                     changeset_revision=changeset_revision,
                                     changeset_revision_select_field=changeset_revision_select_field,
                                     revision_label=revision_label,
diff --git a/lib/galaxy/webapps/community/controllers/workflow.py b/lib/galaxy/webapps/community/controllers/workflow.py
new file mode 100644
index 00000000000..8bbc01a701c
--- /dev/null
+++ b/lib/galaxy/webapps/community/controllers/workflow.py
@@ -0,0 +1,395 @@
+import pkg_resources
+pkg_resources.require( "simplejson" )
+pkg_resources.require( "SVGFig" )
+import os, logging, ConfigParser, tempfile, shutil, svgfig
+from galaxy.webapps.community import model
+from galaxy.web.framework.helpers import time_ago, iff, grids
+from galaxy.util.json import from_json_string, to_json_string
+from galaxy.workflow.modules import InputDataModule, ToolModule, WorkflowModuleFactory
+from galaxy.tools import DefaultToolState
+from galaxy.web.controllers.workflow import attach_ordered_steps
+from galaxy.model.orm import *
+from common import *
+
+class RepoInputDataModule( InputDataModule ):
+
+    type = "data_input"
+    name = "Input dataset"
+
+    @classmethod
+    def new( Class, trans, tools_metadata=None, tool_id=None ):
+        module = Class( trans )
+        module.state = dict( name="Input Dataset" )
+        return module
+    @classmethod
+    def from_dict( Class, trans, d, tools_metadata=None, secure=True ):
+        module = Class( trans )
+        state = from_json_string( d[ "tool_state" ] )
+        module.state = dict( name=state.get( "name", "Input Dataset" ) )
+        return module
+    @classmethod
+    def from_workflow_step( Class, trans, tools_metadata, step ):
+        module = Class( trans )
+        module.state = dict( name="Input Dataset" )
+        if step.tool_inputs and "name" in step.tool_inputs:
+            module.state[ 'name' ] = step.tool_inputs[ 'name' ]
+        return module
+
+class RepoToolModule( ToolModule ):
+    
+    type = "tool"
+    
+    def __init__( self, trans, tools_metadata, tool_id ):
+        self.trans = trans
+        self.tools_metadata = tools_metadata
+        self.tool_id = tool_id
+        self.tool = None
+        for tool_dict in tools_metadata:
+            if self.tool_id in [ tool_dict[ 'id' ], tool_dict[ 'guid' ] ]:
+                self.tool = load_tool( trans, os.path.abspath( tool_dict[ 'tool_config' ] ) )
+        self.post_job_actions = {}
+        self.workflow_outputs = []
+        self.state = None
+        self.errors = None
+    @classmethod
+    def new( Class, trans, tools_metadata, tool_id=None ):
+        module = Class( trans, tools_metadata, tool_id )
+        module.state = module.tool.new_state( trans, all_pages=True )
+        return module
+    @classmethod
+    def from_dict( Class, trans, d, tools_metadata, secure=True ):
+        tool_id = d[ 'tool_id' ]
+        module = Class( trans, tools_metadata, tool_id )
+        module.state = DefaultToolState()
+        if module.tool is not None:
+            module.state.decode( d[ "tool_state" ], module.tool, module.trans.app, secure=secure )
+        module.errors = d.get( "tool_errors", None )
+        return module
+    @classmethod
+    def from_workflow_step( Class, trans, tools_metadata, step ):
+        module = Class( trans, tools_metadata, step.tool_id )
+        module.state = DefaultToolState()
+        if module.tool:
+            module.state.inputs = module.tool.params_from_strings( step.tool_inputs, trans.app, ignore_errors=True )
+        else:
+            module.state.inputs = {}
+        module.errors = step.tool_errors
+        return module
+    def get_data_inputs( self ):
+        data_inputs = []
+        def callback( input, value, prefixed_name, prefixed_label ):
+            if isinstance( input, DataToolParameter ):
+                data_inputs.append( dict( name=prefixed_name,
+                                          label=prefixed_label,
+                                          extensions=input.extensions ) )
+        if self.tool:
+            visit_input_values( self.tool.inputs, self.state.inputs, callback )
+        return data_inputs
+    def get_data_outputs( self ):
+        data_outputs = []
+        if self.tool:
+            data_inputs = None
+            for name, tool_output in self.tool.outputs.iteritems():
+                if tool_output.format_source != None:
+                    # Default to special name "input" which remove restrictions on connections
+                    formats = [ 'input' ]
+                    if data_inputs == None:
+                        data_inputs = self.get_data_inputs()
+                    # Find the input parameter referenced by format_source
+                    for di in data_inputs:
+                        # Input names come prefixed with conditional and repeat names separated by '|',
+                        # so remove prefixes when comparing with format_source.
+                        if di[ 'name' ] != None and di[ 'name' ].split( '|' )[ -1 ] == tool_output.format_source:
+                            formats = di[ 'extensions' ]
+                else:
+                    formats = [ tool_output.format ]
+                for change_elem in tool_output.change_format:
+                    for when_elem in change_elem.findall( 'when' ):
+                        format = when_elem.get( 'format', None )
+                        if format and format not in formats:
+                            formats.append( format )
+                data_outputs.append( dict( name=name, extensions=formats ) )
+        return data_outputs
+
+class RepoWorkflowModuleFactory( WorkflowModuleFactory ):
+    def __init__( self, module_types ):
+        self.module_types = module_types
+    def new( self, trans, type, tools_metadata=None, tool_id=None ):
+        """Return module for type and (optional) tool_id intialized with new / default state."""
+        assert type in self.module_types
+        return self.module_types[type].new( trans, tool_id )
+    def from_dict( self, trans, d, **kwargs ):
+        """Return module initialized from the data in dictionary `d`."""
+        type = d[ 'type' ]
+        assert type in self.module_types
+        return self.module_types[ type ].from_dict( trans, d, **kwargs )
+    def from_workflow_step( self, trans, tools_metadata, step ):
+        """Return module initialized from the WorkflowStep object `step`."""
+        type = step.type
+        return self.module_types[ type ].from_workflow_step( trans, tools_metadata, step )
+
+module_factory = RepoWorkflowModuleFactory( dict( data_input=RepoInputDataModule, tool=RepoToolModule ) )
+
+class WorkflowController( BaseUIController ):
+    @web.expose
+    def view_workflow( self, trans, **kwd ):
+        repository_metadata_id = kwd.get( 'repository_metadata_id', '' )
+        workflow_name = kwd.get( 'workflow_name', '' )
+        if workflow_name:
+            workflow_name = decode( workflow_name )
+        webapp = kwd.get( 'webapp', 'community' )
+        message = kwd.get( 'message', '' )
+        status = kwd.get( 'status', 'done' )
+        repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id )
+        repository = get_repository( trans, trans.security.encode_id( repository_metadata.repository_id ) )
+        return trans.fill_template( "/webapps/community/repository/view_workflow.mako",
+                                    repository=repository,
+                                    changeset_revision=repository_metadata.changeset_revision,
+                                    repository_metadata_id=repository_metadata_id,
+                                    workflow_name=workflow_name,
+                                    webapp=webapp,
+                                    message=message,
+                                    status=status )
+    @web.expose
+    def generate_workflow_image( self, trans, repository_metadata_id, workflow_name, webapp='community' ):
+        repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id )
+        metadata = repository_metadata.metadata
+        workflow_name = decode( workflow_name )
+        for workflow_dict in metadata[ 'workflows' ]:
+            if workflow_dict[ 'name' ] == workflow_name:
+                break
+        if 'tools' in metadata:
+            tools_metadata = metadata[ 'tools' ]
+        else:
+            tools_metadata = []
+        workflow, missing_tool_tups = self.__workflow_from_dict( trans, workflow_dict, tools_metadata )
+        data = []
+        canvas = svgfig.canvas( style="stroke:black; fill:none; stroke-width:1px; stroke-linejoin:round; text-anchor:left" )
+        text = svgfig.SVG( "g" )
+        connectors = svgfig.SVG( "g" )
+        boxes = svgfig.SVG( "g" )
+        svgfig.Text.defaults[ "font-size" ] = "10px"
+        in_pos = {}
+        out_pos = {}
+        margin = 5
+        # Spacing between input/outputs.
+        line_px = 16
+        # Store px width for boxes of each step.
+        widths = {}
+        max_width, max_x, max_y = 0, 0, 0
+        for step in workflow.steps:
+            step.upgrade_messages = {}
+            module = module_factory.from_workflow_step( trans, tools_metadata, step )
+            tool_errors = module.type == 'tool' and not module.tool
+            module_data_inputs = self.__get_data_inputs( step, module )
+            module_data_outputs = self.__get_data_outputs( step, module, workflow.steps )
+            step_dict = {
+                'id' : step.order_index,
+                'data_inputs' : module_data_inputs,
+                'data_outputs' : module_data_outputs,
+                'position' : step.position,
+                'tool_errors' : tool_errors
+            }
+            input_conn_dict = {}
+            for conn in step.input_connections:
+                input_conn_dict[ conn.input_name ] = dict( id=conn.output_step.order_index, output_name=conn.output_name )
+            step_dict[ 'input_connections' ] = input_conn_dict
+            data.append( step_dict )
+            x, y = step.position[ 'left' ], step.position[ 'top' ]
+            count = 0
+            module_name = self.__get_name( module, missing_tool_tups )
+            max_len = len( module_name ) * 1.5
+            text.append( svgfig.Text( x, y + 20, module_name, **{ "font-size": "14px" } ).SVG() )
+            y += 45
+            for di in module_data_inputs:
+                cur_y = y + count * line_px
+                if step.order_index not in in_pos:
+                    in_pos[ step.order_index ] = {}
+                in_pos[ step.order_index ][ di[ 'name' ] ] = ( x, cur_y )
+                text.append( svgfig.Text( x, cur_y, di[ 'label' ] ).SVG() )
+                count += 1
+                max_len = max( max_len, len( di[ 'label' ] ) )
+            if len( module.get_data_inputs() ) > 0:
+                y += 15
+            for do in module_data_outputs:
+                cur_y = y + count * line_px
+                if step.order_index not in out_pos:
+                    out_pos[ step.order_index ] = {}
+                out_pos[ step.order_index ][ do[ 'name' ] ] = ( x, cur_y )
+                text.append( svgfig.Text( x, cur_y, do[ 'name' ] ).SVG() )
+                count += 1
+                max_len = max( max_len, len( do['name' ] ) )
+            widths[ step.order_index ] = max_len * 5.5
+            max_x = max( max_x, step.position[ 'left' ] )
+            max_y = max( max_y, step.position[ 'top' ] )
+            max_width = max( max_width, widths[ step.order_index ] )
+        for step_dict in data:
+            tool_unavailable = step_dict[ 'tool_errors' ]
+            width = widths[ step_dict[ 'id' ] ]
+            x, y = step_dict[ 'position' ][ 'left' ], step_dict[ 'position' ][ 'top' ]
+            if tool_unavailable:
+                fill = "#EBBCB2"
+            else:
+                fill = "#EBD9B2"    
+            boxes.append( svgfig.Rect( x - margin, y, x + width - margin, y + 30, fill=fill ).SVG() )
+            box_height = ( len( step_dict[ 'data_inputs' ] ) + len( step_dict[ 'data_outputs' ] ) ) * line_px + margin
+            # Draw separator line.
+            if len( step_dict[ 'data_inputs' ] ) > 0:
+                box_height += 15
+                sep_y = y + len( step_dict[ 'data_inputs' ] ) * line_px + 40
+                text.append( svgfig.Line( x - margin, sep_y, x + width - margin, sep_y ).SVG() )
+            # Define an input/output box.
+            boxes.append( svgfig.Rect( x - margin, y + 30, x + width - margin, y + 30 + box_height, fill="#ffffff" ).SVG() )
+            for conn, output_dict in step_dict[ 'input_connections' ].iteritems():
+                in_coords = in_pos[ step_dict[ 'id' ] ][ conn ]
+                out_conn_pos = out_pos[ output_dict[ 'id' ] ][ output_dict[ 'output_name' ] ]
+                adjusted = ( out_conn_pos[ 0 ] + widths[ output_dict[ 'id' ] ], out_conn_pos[ 1 ] )
+                text.append( svgfig.SVG( "circle",
+                                         cx=out_conn_pos[ 0 ] + widths[ output_dict[ 'id' ] ] - margin,
+                                         cy=out_conn_pos[ 1 ] - margin,
+                                         r = 5,
+                                         fill="#ffffff" ) )
+                connectors.append( svgfig.Line( adjusted[ 0 ],
+                                                adjusted[ 1 ] - margin,
+                                                in_coords[ 0 ] - 10,
+                                                in_coords[ 1 ],
+                                                arrow_end = "true" ).SVG() )
+        canvas.append( connectors )
+        canvas.append( boxes )
+        canvas.append( text )
+        width, height = ( max_x + max_width + 50 ), max_y + 300
+        canvas[ 'width' ] = "%s px" % width
+        canvas[ 'height' ] = "%s px" % height
+        canvas[ 'viewBox' ] = "0 0 %s %s" % ( width, height )
+        trans.response.set_content_type( "image/svg+xml" )
+        return canvas.standalone_xml()
+    def __get_name( self, module, missing_tool_tups ):
+        module_name = module.get_name()
+        if module.type == 'tool' and module_name == 'unavailable':
+            for missing_tool_tup in missing_tool_tups:
+                missing_tool_id, missing_tool_name, missing_tool_version = missing_tool_tup
+                if missing_tool_id == module.tool_id:
+                    module_name = '%s' % missing_tool_name
+        return module_name
+    def __get_data_inputs( self, step, module ):
+        if module.type == 'tool':
+            if module.tool:
+                return module.get_data_inputs()
+            else:
+                data_inputs = []
+                for wfsc in step.input_connections:
+                    data_inputs_dict = {}
+                    data_inputs_dict[ 'extensions' ] = [ '' ]
+                    data_inputs_dict[ 'name' ] = wfsc.input_name
+                    data_inputs_dict[ 'label' ] = 'Unknown'
+                    data_inputs.append( data_inputs_dict )
+                return data_inputs
+        return module.get_data_inputs()
+    def __get_data_outputs( self, step, module, steps ):
+        if module.type == 'tool':
+            if module.tool:
+                return module.get_data_outputs()
+            else:
+                data_outputs = []
+                data_outputs_dict = {}
+                data_outputs_dict[ 'extensions' ] = [ 'input' ]
+                found = False
+                for workflow_step in steps:
+                    for wfsc in workflow_step.input_connections:
+                        if step.name == wfsc.output_step.name:
+                            data_outputs_dict[ 'name' ] = wfsc.output_name
+                            found = True
+                            break
+                    if found:
+                        break
+                if not found:
+                    # We're at the last step of the workflow.
+                    data_outputs_dict[ 'name' ] = 'output'
+                data_outputs.append( data_outputs_dict )       
+                return data_outputs
+        return module.get_data_outputs()
+    def __workflow_from_dict( self, trans, data, tools_metadata ):
+        """Creates and returns workflow object from a dictionary."""
+        trans.workflow_building_mode = True
+        workflow = model.Workflow()
+        workflow.name = data[ 'name' ]
+        workflow.has_errors = False
+        steps = []
+        # Keep ids for each step that we need to use to make connections.
+        steps_by_external_id = {}
+        # Keep track of tools required by the workflow that are not available in
+        # the tool shed repository.  Each tuple in the list of missing_tool_tups
+        # will be ( tool_id, tool_name, tool_version ).
+        missing_tool_tups = []
+        # First pass to build step objects and populate basic values
+        for key, step_dict in data[ 'steps' ].iteritems():
+            # Create the model class for the step
+            step = model.WorkflowStep()
+            step.name = step_dict[ 'name' ]
+            step.position = step_dict[ 'position' ]
+            module = module_factory.from_dict( trans, step_dict, tools_metadata=tools_metadata, secure=False )
+            if module.type == 'tool' and module.tool is None:
+                # A required tool is not available in the current repository.
+                step.tool_errors = 'unavailable'
+                missing_tool_tup = ( step_dict[ 'tool_id' ], step_dict[ 'name' ], step_dict[ 'tool_version' ] )
+                if missing_tool_tup not in missing_tool_tups:
+                    missing_tool_tups.append( missing_tool_tup )
+            module.save_to_step( step )
+            if step.tool_errors:
+                workflow.has_errors = True
+            # Stick this in the step temporarily.
+            step.temp_input_connections = step_dict[ 'input_connections' ]
+            # Unpack and add post-job actions.
+            post_job_actions = step_dict.get( 'post_job_actions', {} )
+            for name, pja_dict in post_job_actions.items():
+                pja = PostJobAction( pja_dict[ 'action_type' ], 
+                                     step, pja_dict[ 'output_name' ], 
+                                     pja_dict[ 'action_arguments' ] )
+            steps.append( step )
+            steps_by_external_id[ step_dict[ 'id' ] ] = step
+        # Second pass to deal with connections between steps.
+        for step in steps:
+            # Input connections.
+            for input_name, conn_dict in step.temp_input_connections.iteritems():
+                if conn_dict:
+                    output_step = steps_by_external_id[ conn_dict[ 'id' ] ]
+                    conn = model.WorkflowStepConnection()
+                    conn.input_step = step
+                    conn.input_name = input_name
+                    conn.output_step = output_step
+                    conn.output_name = conn_dict[ 'output_name' ]
+                    step.input_connections.append( conn )
+            del step.temp_input_connections
+        # Order the steps if possible.
+        attach_ordered_steps( workflow, steps )
+        return workflow, missing_tool_tups
+    @web.expose
+    def import_workflow( self, trans, **kwd ):
+        repository_metadata_id = kwd.get( 'repository_metadata_id', '' )
+        workflow_name = kwd.get( 'workflow_name', '' )
+        if workflow_name:
+            workflow_name = decode( workflow_name )
+        webapp = kwd.get( 'webapp', 'community' )
+        message = kwd.get( 'message', '' )
+        status = kwd.get( 'status', 'done' )
+        repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id )
+        workflows = repository_metadata.metadata[ 'workflows' ]
+        workflow_data = None
+        for workflow_data in workflows:
+            if workflow_data[ 'name' ] == workflow_name:
+                break
+        if workflow_data:
+            if kwd.get( 'open_for_url', False ):
+                tmp_fd, tmp_fname = tempfile.mkstemp()
+                to_file = open( tmp_fname, 'wb' )
+                to_file.write( to_json_string( workflow_data ) )
+                return open( tmp_fname )
+            galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' )
+            # TODO: support https in the following url.
+            url = 'http://%s/workflow/import_workflow?tool_shed_url=%s&repository_metadata_id=%s&workflow_name=%s&webapp=%s' % \
+                ( galaxy_url, trans.request.host, repository_metadata_id, encode( workflow_name ), webapp )
+            return trans.response.send_redirect( url )
+        return trans.response.send_redirect( web.url_for( controller='workflow',
+                                                          action='view_workflow',
+                                                          message=message,
+                                                          status=status ) )
diff --git a/lib/galaxy/webapps/community/model/__init__.py b/lib/galaxy/webapps/community/model/__init__.py
index 31d6d24cc00..f32862cdb04 100644
--- a/lib/galaxy/webapps/community/model/__init__.py
+++ b/lib/galaxy/webapps/community/model/__init__.py
@@ -204,6 +204,34 @@ class ItemTagAssociation ( object ):
         self.value = None
         self.user_value = None
 
+class Workflow( object ):
+    def __init__( self ):
+        self.user = None
+        self.name = None
+        self.has_cycles = None
+        self.has_errors = None
+        self.steps = []
+
+class WorkflowStep( object ):
+    def __init__( self ):
+        self.id = None
+        self.type = None
+        self.name = None
+        self.tool_id = None
+        self.tool_inputs = None
+        self.tool_errors = None
+        self.position = None
+        self.input_connections = []
+        #self.output_connections = []
+        self.config = None
+
+class WorkflowStepConnection( object ):
+    def __init__( self ):
+        self.output_step = None
+        self.output_name = None
+        self.input_step = None
+        self.input_name = None
+
 ## ---- Utility methods -------------------------------------------------------
 def sort_by_attr( seq, attr ):
     """
diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
index f4dc32667a5..8c07d6a34e5 100644
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -205,14 +205,14 @@ class ToolModule( WorkflowModule ):
     def from_workflow_step( Class, trans, step ):
         tool_id = step.tool_id
         install_tool_id = None
-        if tool_id not in trans.app.toolbox.tools_by_id:
+        if trans.app.toolbox and tool_id not in trans.app.toolbox.tools_by_id:
             # The id value of tools installed from a Galaxy tool shed is a guid, but
             # these tool's old_id attribute should contain what we're looking for.
             for available_tool_id, available_tool in trans.app.toolbox.tools_by_id.items():
                 if tool_id == available_tool.old_id:
                     install_tool_id = available_tool_id
                     break
-        if tool_id in trans.app.toolbox.tools_by_id or install_tool_id:
+        if ( trans.app.toolbox and tool_id in trans.app.toolbox.tools_by_id ) or install_tool_id:
             module = Class( trans, tool_id )
             module.state = DefaultToolState()
             module.state.inputs = module.tool.params_from_strings( step.tool_inputs, trans.app, ignore_errors=True )
@@ -247,7 +247,9 @@ class ToolModule( WorkflowModule ):
                 action_arguments = None
             n_p = PostJobAction(v['action_type'], step, output_name, action_arguments)
     def get_name( self ):
-        return self.tool.name
+        if self.tool:
+            return self.tool.name
+        return 'unavailable'
     def get_tool_id( self ):
         return self.tool_id
     def get_tool_version( self ):
diff --git a/templates/webapps/community/repository/common.mako b/templates/webapps/community/repository/common.mako
index acdf665fe91..3bac7f00ffd 100644
--- a/templates/webapps/community/repository/common.mako
+++ b/templates/webapps/community/repository/common.mako
@@ -83,7 +83,8 @@
     hg clone <a href="${clone_str}">${clone_str}</a>
 </%def>
 
-<%def name="render_repository_tools_and_workflows( metadata, can_set_metadata=False, webapp='community' )">
+<%def name="render_repository_tools_and_workflows( repository_metadata_id, metadata, can_set_metadata=False, webapp='community' )">
+    <% from galaxy.webapps.community.controllers.common import encode, decode %>
     %if metadata or can_set_metadata:
         <p/>
         <div class="toolForm">
@@ -160,14 +161,31 @@
                             <table class="grid">
                                 <tr>
                                     <td><b>name</b></td>
+                                    <td><b>steps</b></td>
                                     <td><b>format-version</b></td>
                                     <td><b>annotation</b></td>
                                 </tr>
                                 %for workflow_dict in workflow_dicts:
+                                    <% 
+                                        workflow_name = workflow_dict[ 'name' ]
+                                        steps = workflow_dict[ 'steps' ]
+                                        format_version = workflow_dict[ 'format-version' ]
+                                        annotation = workflow_dict[ 'annotation' ]
+                                    %>
                                     <tr>
-                                        <td>${workflow_dict[ 'name' ]}</td>
-                                        <td>${workflow_dict[ 'format-version' ]}</td>
-                                        <td>${workflow_dict[ 'annotation' ]}</td>
+                                        <td>
+                                            <a href="${h.url_for( controller='workflow', action='view_workflow', repository_metadata_id=repository_metadata_id, workflow_name=encode( workflow_name ), webapp=webapp )}">${workflow_name}</a>
+                                        </td>
+                                        <td>
+                                            %if 'steps' in workflow_dict:
+                                                ## Initially steps were not stored in the metadata record.
+                                                ${len( steps )}
+                                            %else:
+                                                unknown
+                                            %endif
+                                        </td>
+                                        <td>${format_version}</td>
+                                        <td>${annotation}</td>
                                     </tr>
                                 %endfor
                             </table>
diff --git a/templates/webapps/community/repository/manage_repository.mako b/templates/webapps/community/repository/manage_repository.mako
index 46ae1d7a69d..c056413c34e 100644
--- a/templates/webapps/community/repository/manage_repository.mako
+++ b/templates/webapps/community/repository/manage_repository.mako
@@ -184,7 +184,7 @@
         </form>
     </div>
 </div>
-${render_repository_tools_and_workflows( metadata, can_set_metadata=True )}
+${render_repository_tools_and_workflows( repository_metadata_id, metadata, can_set_metadata=True )}
 <p/>
 <div class="toolForm">
     <div class="toolFormTitle">Manage categories</div>
diff --git a/templates/webapps/community/repository/preview_tools_in_changeset.mako b/templates/webapps/community/repository/preview_tools_in_changeset.mako
index 0420217dfed..1807038b253 100644
--- a/templates/webapps/community/repository/preview_tools_in_changeset.mako
+++ b/templates/webapps/community/repository/preview_tools_in_changeset.mako
@@ -103,4 +103,4 @@
     </div>
 </div>
 <p/>
-${render_repository_tools_and_workflows( metadata, webapp=webapp )}
+${render_repository_tools_and_workflows( repository_metadata_id, metadata, webapp=webapp )}
diff --git a/templates/webapps/community/repository/view_repository.mako b/templates/webapps/community/repository/view_repository.mako
index 2e110a26cf9..08866804e7b 100644
--- a/templates/webapps/community/repository/view_repository.mako
+++ b/templates/webapps/community/repository/view_repository.mako
@@ -185,7 +185,7 @@
         %endif
     </div>
 </div>
-${render_repository_tools_and_workflows( metadata, webapp=webapp )}
+${render_repository_tools_and_workflows( repository_metadata_id, metadata, webapp=webapp )}
 %if repository.categories:
     <p/>
     <div class="toolForm">
diff --git a/templates/webapps/community/repository/view_workflow.mako b/templates/webapps/community/repository/view_workflow.mako
new file mode 100644
index 00000000000..7bea2b35daf
--- /dev/null
+++ b/templates/webapps/community/repository/view_workflow.mako
@@ -0,0 +1,102 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+<%namespace file="/webapps/community/common/common.mako" import="*" />
+<%namespace file="/webapps/community/repository/common.mako" import="*" />
+
+<%
+    from galaxy.web.framework.helpers import time_ago
+    from galaxy.webapps.community.controllers.common import encode
+
+    in_tool_shed = webapp == 'community'
+    is_admin = trans.user_is_admin()
+    is_new = repository.is_new
+    can_manage = is_admin or trans.user == repository.user
+    can_contact_owner = in_tool_shed and trans.user and trans.user != repository.user
+    can_push = in_tool_shed and trans.app.security_agent.can_push( trans.user, repository )
+    can_upload = can_push
+    can_download = in_tool_shed and not is_new and ( not is_malicious or can_push )
+    can_browse_contents = in_tool_shed and not is_new
+    can_set_metadata = in_tool_shed and not is_new
+    can_rate = in_tool_shed and not is_new and trans.user and repository.user != trans.user
+    can_view_change_log = in_tool_shed and not is_new
+    if can_push:
+        browse_label = 'Browse or delete repository files'
+    else:
+        browse_label = 'Browse repository files'
+%>
+
+<%!
+   def inherit(context):
+       if context.get('use_panels'):
+           return '/webapps/community/base_panels.mako'
+       else:
+           return '/base.mako'
+%>
+<%inherit file="${inherit(context)}"/>
+
+<%def name="render_workflow( repository_metadata_id, workflow_name, webapp )">
+    <% center_url = h.url_for( controller='workflow', action='generate_workflow_image', repository_metadata_id=repository_metadata_id, workflow_name=encode( workflow_name ), webapp=webapp ) %>
+    <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"> </iframe>
+</%def>
+
+<br/><br/>
+<ul class="manage-table-actions">
+    %if in_tool_shed:
+        %if is_new and can_upload:
+            <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a>
+        %else:
+            <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li>
+            <div popupmenu="repository-${repository.id}-popup">
+                %if can_upload:
+                    <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a>
+                %endif
+                %if can_manage:
+                    <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a>
+                %else:
+                    <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View repository</a>
+                %endif
+                %if can_view_change_log:
+                    <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View change log</a>
+                %endif
+                %if can_rate:
+                    <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a>
+                %endif
+                %if can_browse_contents:
+                    <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">${browse_label}</a>
+                %endif
+                %if can_contact_owner:
+                    <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp='community' )}">Contact repository owner</a>
+                %endif
+                %if can_download:
+                    <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a>
+                    <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='bz2' )}">Download as a .tar.bz2 file</a>
+                    <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='zip' )}">Download as a zip file</a>
+                %endif
+            </div>
+        %endif
+    %else:
+        <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li>
+        <div popupmenu="repository-${repository.id}-popup">
+            <li><a class="action-button" href="${h.url_for( controller='workflow', action='import_workflow', repository_metadata_id=repository_metadata_id, workflow_name=encode( workflow_name ), webapp=webapp )}">Import workflow to local Galaxy</a></li>
+            <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install repository to local Galaxy</a></li>
+        </div>
+        <li><a class="action-button" id="toolshed-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li>
+        <div popupmenu="toolshed-${repository.id}-popup">
+            <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a>
+            <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a>
+        </div>
+    %endif
+</ul>
+
+%if message:
+    ${render_msg( message, status )}
+%endif
+
+<br/>
+<b>Boxes are red when tools are not available in this repository</b>
+<div class="toolParamHelp" style="clear: both;">
+    (this page displays SVG graphics)
+</div>
+<br clear="left"/>
+
+${render_workflow( repository_metadata_id, workflow_name, webapp )}
diff --git a/templates/workflow/display.mako b/templates/workflow/display.mako
index c73225e8a91..969ccdb62ef 100644
--- a/templates/workflow/display.mako
+++ b/templates/workflow/display.mako
@@ -1,7 +1,7 @@
 <%inherit file="/display_base.mako"/>
 <%namespace file="/display_common.mako" import="render_message" />
 
-<%! 
+<%
     from galaxy.tools.parameters import DataToolParameter, RuntimeValue 
     from galaxy.web import form_builder
 %>
@@ -82,7 +82,17 @@
         %for i, step in enumerate( steps ):
             <tr><td>
             %if step.type == 'tool' or step.type is None:
-              <% tool = app.toolbox.tools_by_id[step.tool_id] %>
+              <% 
+                try:
+                    tool = trans.app.toolbox.tools_by_id[ step.tool_id ]
+                except KeyError, e:
+                    # The id value of tools installed from a Galaxy tool shed is a guid, but
+                    # these tool's old_id attribute should contain what we're looking for.
+                    for available_tool_id, available_tool in trans.app.toolbox.tools_by_id.items():
+                        if step.tool_id == available_tool.old_id:
+                            tool = available_tool
+                            break
+              %>
               <div class="toolForm">
                   <div class="toolFormTitle">Step ${int(step.order_index)+1}: ${tool.name}</div>
                   <div class="toolFormBody">
diff --git a/templates/workflow/run.mako b/templates/workflow/run.mako
index afe3f464122..d9139e0ba98 100644
--- a/templates/workflow/run.mako
+++ b/templates/workflow/run.mako
@@ -363,7 +363,17 @@ if wf_parms:
 %endif
 %for i, step in enumerate( steps ):
     %if step.type == 'tool' or step.type is None:
-      <% tool = app.toolbox.tools_by_id[step.tool_id] %>
+      <%
+        try:
+            tool = trans.app.toolbox.tools_by_id[ step.tool_id ]
+        except KeyError, e:
+            # The id value of tools installed from a Galaxy tool shed is a guid, but
+            # these tool's old_id attribute should contain what we're looking for.
+            for available_tool_id, available_tool in trans.app.toolbox.tools_by_id.items():
+                if step.tool_id == available_tool.old_id:
+                    tool = available_tool
+                    break
+      %>
       <input type="hidden" name="${step.id}|tool_state" value="${step.state.encode( tool, app )}">
       <div class="toolForm">
           <div class="toolFormTitle">

From 1143dfe2baec6ca209d173f0284132a56bff2965 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Thu, 27 Oct 2011 10:54:42 -0400
Subject: [PATCH 104/362] Have Picard MergeSamFiles use return code to
 determine tool error.

---
 tools/samtools/sam_merge.xml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tools/samtools/sam_merge.xml b/tools/samtools/sam_merge.xml
index 1b9ab0faeda..625aa082c1a 100644
--- a/tools/samtools/sam_merge.xml
+++ b/tools/samtools/sam_merge.xml
@@ -9,6 +9,7 @@ java -Xmx2G -jar ${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/MergeSamFiles.jar M
         I=${i.input}
       #end for 
     2&gt; $outlog
+    || echo "Error running Picard MergeSamFiles" >&amp;2
   </command>
   <inputs>
     <param name="title" label="Name for the output merged bam file" type="text" default="Merged.bam"

From 8b59cb0f45798545f8c9d437a617e52b6c1efa97 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Thu, 27 Oct 2011 13:26:43 -0400
Subject: [PATCH 105/362] Add the ability to search for workflows by name in a
 Galalxy tool shed, either within the tool shed itself or in a local Galaxy
 instance configured to communicate with the tool shed.

---
 lib/galaxy/web/controllers/admin.py           |   7 +
 .../community/controllers/repository.py       | 200 +++++++++++++-----
 templates/grid_base.mako                      |   2 +-
 templates/webapps/community/index.mako        |  19 +-
 .../community/repository/find_tools.mako      |   1 +
 .../community/repository/find_workflows.mako  |  53 +++++
 .../preview_tools_in_changeset.mako           |   1 +
 .../community/repository/tool_form.mako       |   1 +
 .../community/repository/view_repository.mako |   1 +
 .../repository/view_tool_metadata.mako        |   1 +
 .../community/repository/view_workflow.mako   |  11 +-
 templates/webapps/galaxy/admin/index.mako     |   2 +-
 .../webapps/galaxy/admin/tool_sheds.mako      |   1 +
 13 files changed, 236 insertions(+), 64 deletions(-)
 create mode 100644 templates/webapps/community/repository/find_workflows.mako

diff --git a/lib/galaxy/web/controllers/admin.py b/lib/galaxy/web/controllers/admin.py
index 34ec1367bf8..e56e0c9e02b 100644
--- a/lib/galaxy/web/controllers/admin.py
+++ b/lib/galaxy/web/controllers/admin.py
@@ -704,6 +704,13 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
         return trans.response.send_redirect( url )
     @web.expose
     @web.require_admin
+    def find_workflows_in_tool_shed( self, trans, **kwd ):
+        tool_shed_url = kwd[ 'tool_shed_url' ]
+        galaxy_url = trans.request.host
+        url = '%s/repository/find_workflows?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, galaxy_url )
+        return trans.response.send_redirect( url )
+    @web.expose
+    @web.require_admin
     def browse_tool_shed( self, trans, **kwd ):
         tool_shed_url = kwd[ 'tool_shed_url' ]
         galaxy_url = trans.request.host
diff --git a/lib/galaxy/webapps/community/controllers/repository.py b/lib/galaxy/webapps/community/controllers/repository.py
index 93f32c49c9f..a41b734c140 100644
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -231,7 +231,7 @@ class MatchedRepositoryListGrid( grids.Grid ):
                 return repository_metadata.repository.user.username
             return 'no user'
     # Grid definition
-    title = "Repositories with matching tools"
+    title = "Matching repositories"
     model_class = model.RepositoryMetadata
     template='/webapps/community/repository/grid.mako'
     default_sort_key = "Repository.name"
@@ -375,6 +375,83 @@ class RepositoryController( BaseUIController, ItemRatings ):
         # Render the list view
         return self.valid_repository_list_grid( trans, **kwd )
     @web.expose
+    def find_workflows( self, trans, **kwd ):
+        params = util.Params( kwd )
+        message = util.restore_text( params.get( 'message', '' ) )
+        status = params.get( 'status', 'done' )
+        webapp = params.get( 'webapp', 'community' )
+        galaxy_url = kwd.get( 'galaxy_url', None )
+        if galaxy_url:
+            trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' )
+        if 'operation' in kwd:
+            item_id = kwd.get( 'id', '' )
+            if item_id:
+                operation = kwd[ 'operation' ].lower()
+                is_admin = trans.user_is_admin()
+                if operation == "view_or_manage_repository":
+                    # The received id is a RepositoryMetadata id, so we have to get the repository id.
+                    repository_metadata = get_repository_metadata_by_id( trans, item_id )
+                    repository_id = trans.security.encode_id( repository_metadata.repository.id )
+                    repository = get_repository( trans, repository_id )
+                    kwd[ 'id' ] = repository_id
+                    kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision
+                    if webapp == 'community' and ( is_admin or repository.user == trans.user ):
+                        a = 'manage_repository'
+                    else:
+                        a = 'view_repository'
+                    return trans.response.send_redirect( web.url_for( controller='repository',
+                                                                      action=a,
+                                                                      **kwd ) )
+                if operation == "install":
+                    galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' )
+                    encoded_repo_info_dict = self.__encode_repo_info_dict( trans, webapp, util.listify( item_id ) )
+                    # TODO: support https in the following url.
+                    url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s&webapp=%s&repo_info_dict=%s' % \
+                        ( galaxy_url, trans.request.host, webapp, encoded_repo_info_dict )
+                    return trans.response.send_redirect( url )
+            else:
+                # This can only occur when there is a multi-select grid with check boxes and an operation,
+                # and the user clicked the operation button without checking any of the check boxes.
+                return trans.show_error_message( "No items were selected." )
+        workflow_names = [ item.lower() for item in util.listify( kwd.get( 'workflow_name', '' ) ) ]
+        exact_matches = params.get( 'exact_matches', '' )
+        exact_matches_checked = CheckboxField.is_checked( exact_matches )
+        match_tuples = []
+        ok = True
+        if workflow_names:
+            ok, match_tuples = self.__search_repository_metadata( trans, exact_matches_checked, workflow_names=workflow_names )
+            if ok:
+                kwd[ 'match_tuples' ] = match_tuples
+                # Render the list view
+                if webapp == 'galaxy':
+                    # Our initial request originated from a Galaxy instance.
+                    global_actions = [ grids.GridAction( "Browse valid repositories",
+                                                         dict( controller='repository', action='browse_valid_repositories', webapp=webapp ) ),
+                                       grids.GridAction( "Search for valid tools",
+                                                         dict( controller='repository', action='find_tools', webapp=webapp ) ),
+                                       grids.GridAction( "Search for workflows",
+                                                         dict( controller='repository', action='find_workflows', webapp=webapp ) ) ]
+                    self.install_matched_repository_list_grid.global_actions = global_actions
+                    install_url_args = dict( controller='repository', action='find_workflows', webapp=webapp )
+                    operations = [ grids.GridOperation( "Install", url_args=install_url_args, allow_multiple=True, async_compatible=False ) ]
+                    self.install_matched_repository_list_grid.operations = operations
+                    return self.install_matched_repository_list_grid( trans, **kwd )
+                else:
+                    kwd[ 'message' ] = "workflow name: <b>%s</b><br/>exact matches only: <b>%s</b>" % \
+                        ( self.__stringify( workflow_names ), str( exact_matches_checked ) )
+                    self.matched_repository_list_grid.title = "Repositories with matching workflows"
+                    return self.matched_repository_list_grid( trans, **kwd )
+            else:
+                message = "No search performed - each field must contain the same number of comma-separated items."
+                status = "error"
+        exact_matches_check_box = CheckboxField( 'exact_matches', checked=exact_matches_checked )
+        return trans.fill_template( '/webapps/community/repository/find_workflows.mako',
+                                    webapp=webapp,
+                                    workflow_name=self.__stringify( workflow_names ),
+                                    exact_matches_check_box=exact_matches_check_box,
+                                    message=message,
+                                    status=status )
+    @web.expose
     def find_tools( self, trans, **kwd ):
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', '' ) )
@@ -421,7 +498,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
         match_tuples = []
         ok = True
         if tool_ids or tool_names or tool_versions:
-            ok, match_tuples = self.__search_repository_metadata( trans, tool_ids, tool_names, tool_versions, exact_matches_checked )
+            ok, match_tuples = self.__search_repository_metadata( trans, exact_matches_checked, tool_ids=tool_ids, tool_names=tool_names, tool_versions=tool_versions )
             if ok:
                 kwd[ 'match_tuples' ] = match_tuples
                 # Render the list view
@@ -430,7 +507,9 @@ class RepositoryController( BaseUIController, ItemRatings ):
                     global_actions = [ grids.GridAction( "Browse valid repositories",
                                                          dict( controller='repository', action='browse_valid_repositories', webapp=webapp ) ),
                                        grids.GridAction( "Search for valid tools",
-                                                         dict( controller='repository', action='find_tools', webapp=webapp ) ) ]
+                                                         dict( controller='repository', action='find_tools', webapp=webapp ) ),
+                                       grids.GridAction( "Search for workflows",
+                                                         dict( controller='repository', action='find_workflows', webapp=webapp ) ) ]
                     self.install_matched_repository_list_grid.global_actions = global_actions
                     install_url_args = dict( controller='repository', action='find_tools', webapp=webapp )
                     operations = [ grids.GridOperation( "Install", url_args=install_url_args, allow_multiple=True, async_compatible=False ) ]
@@ -439,6 +518,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
                 else:
                     kwd[ 'message' ] = "tool id: <b>%s</b><br/>tool name: <b>%s</b><br/>tool version: <b>%s</b><br/>exact matches only: <b>%s</b>" % \
                         ( self.__stringify( tool_ids ), self.__stringify( tool_names ), self.__stringify( tool_versions ), str( exact_matches_checked ) )
+                    self.matched_repository_list_grid.title = "Repositories with matching tools"
                     return self.matched_repository_list_grid( trans, **kwd )
             else:
                 message = "No search performed - each field must contain the same number of comma-separated items."
@@ -452,62 +532,76 @@ class RepositoryController( BaseUIController, ItemRatings ):
                                     exact_matches_check_box=exact_matches_check_box,
                                     message=message,
                                     status=status )
-    def __search_repository_metadata( self, trans, tool_ids, tool_names, tool_versions, exact_matches_checked ):
+    def __search_repository_metadata( self, trans, exact_matches_checked, tool_ids='', tool_names='', tool_versions='', workflow_names='' ):
         match_tuples = []
         ok = True
         for repository_metadata in trans.sa_session.query( model.RepositoryMetadata ):
             metadata = repository_metadata.metadata
-            if 'tools' in metadata:
-                tools = metadata[ 'tools' ]
-            else:
-                tools = []
-            for tool_dict in tools:
-                if tool_ids and not tool_names and not tool_versions:
-                    for tool_id in tool_ids:
-                        if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id ):
-                            match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
-                elif tool_names and not tool_ids and not tool_versions:
-                    for tool_name in tool_names:
-                        if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name ):
-                            match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
-                elif tool_versions and not tool_ids and not tool_names:
-                    for tool_version in tool_versions:
-                        if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_version=tool_version ):
-                            match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
-                elif tool_ids and tool_names and not tool_versions:
-                    if len( tool_ids ) == len( tool_names ):
-                        match_tuples = self.__search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names )
-                    elif len( tool_ids ) == 1 or len( tool_names ) == 1:
-                        tool_ids, tool_names = self.__make_same_length( tool_ids, tool_names )
-                        match_tuples = self.__search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names )
-                    else:
-                        ok = False
-                elif tool_ids and tool_versions and not tool_names:
-                    if len( tool_ids )  == len( tool_versions ):
-                        match_tuples = self.__search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions )
-                    elif len( tool_ids ) == 1 or len( tool_versions ) == 1:
-                        tool_ids, tool_versions = self.__make_same_length( tool_ids, tool_versions )
-                        match_tuples = self.__search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions )
-                    else:
-                        ok = False
-                elif tool_versions and tool_names and not tool_ids:
-                    if len( tool_versions ) == len( tool_names ):
-                        match_tuples = self.__search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions )
-                    elif len( tool_versions ) == 1 or len( tool_names ) == 1:
-                        tool_versions, tool_names = self.__make_same_length( tool_versions, tool_names )
-                        match_tuples = self.__search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions )
-                    else:
-                        ok = False
-                elif tool_versions and tool_names and tool_ids:
-                    if len( tool_versions ) == len( tool_names ) and len( tool_names ) == len( tool_ids ):
-                        for i, tool_version in enumerate( tool_versions ):
-                            tool_name = tool_names[ i ]
-                            tool_id = tool_ids[ i ]
-                            if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name, tool_version=tool_version ):
+            if tool_ids or tool_names or tool_versions:
+                if 'tools' in metadata:
+                    tools = metadata[ 'tools' ]
+                else:
+                    tools = []
+                for tool_dict in tools:
+                    if tool_ids and not tool_names and not tool_versions:
+                        for tool_id in tool_ids:
+                            if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id ):
                                 match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
-                    else:
-                        ok = False
+                    elif tool_names and not tool_ids and not tool_versions:
+                        for tool_name in tool_names:
+                            if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name ):
+                                match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
+                    elif tool_versions and not tool_ids and not tool_names:
+                        for tool_version in tool_versions:
+                            if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_version=tool_version ):
+                                match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
+                    elif tool_ids and tool_names and not tool_versions:
+                        if len( tool_ids ) == len( tool_names ):
+                            match_tuples = self.__search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names )
+                        elif len( tool_ids ) == 1 or len( tool_names ) == 1:
+                            tool_ids, tool_names = self.__make_same_length( tool_ids, tool_names )
+                            match_tuples = self.__search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names )
+                        else:
+                            ok = False
+                    elif tool_ids and tool_versions and not tool_names:
+                        if len( tool_ids )  == len( tool_versions ):
+                            match_tuples = self.__search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions )
+                        elif len( tool_ids ) == 1 or len( tool_versions ) == 1:
+                            tool_ids, tool_versions = self.__make_same_length( tool_ids, tool_versions )
+                            match_tuples = self.__search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions )
+                        else:
+                            ok = False
+                    elif tool_versions and tool_names and not tool_ids:
+                        if len( tool_versions ) == len( tool_names ):
+                            match_tuples = self.__search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions )
+                        elif len( tool_versions ) == 1 or len( tool_names ) == 1:
+                            tool_versions, tool_names = self.__make_same_length( tool_versions, tool_names )
+                            match_tuples = self.__search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions )
+                        else:
+                            ok = False
+                    elif tool_versions and tool_names and tool_ids:
+                        if len( tool_versions ) == len( tool_names ) and len( tool_names ) == len( tool_ids ):
+                            for i, tool_version in enumerate( tool_versions ):
+                                tool_name = tool_names[ i ]
+                                tool_id = tool_ids[ i ]
+                                if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name, tool_version=tool_version ):
+                                    match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
+                        else:
+                            ok = False
+            if workflow_names:
+                if 'workflows' in metadata:
+                    workflows = metadata[ 'workflows' ]
+                else:
+                    workflows = []
+                for workflow_dict in workflows:
+                    for workflow_name in workflow_names:
+                        if self.__in_workflow_dict( workflow_dict, exact_matches_checked, workflow_name=workflow_name ):
+                            match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
         return ok, match_tuples
+    def __in_workflow_dict( self, workflow_dict, exact_matches_checked, workflow_name=None ):
+        workflow_dict_workflow_name = workflow_dict[ 'name' ].lower()
+        return ( workflow_name == workflow_dict_workflow_name ) or \
+               ( not exact_matches_checked and workflow_dict_workflow_name.find( workflow_name ) >= 0 )
     def __in_tool_dict( self, tool_dict, exact_matches_checked, tool_id=None, tool_name=None, tool_version=None ):
         found = False
         if tool_id and not tool_name and not tool_version:
diff --git a/templates/grid_base.mako b/templates/grid_base.mako
index cda18fdb3ec..45d4e7d2ce8 100644
--- a/templates/grid_base.mako
+++ b/templates/grid_base.mako
@@ -744,7 +744,7 @@
     
         %if grid.global_actions:
             <ul class="manage-table-actions">
-                %if len( grid.global_actions ) < 4:
+                %if len( grid.global_actions ) < 3:
                     %for action in grid.global_actions:
                         <li><a class="action-button" href="${h.url_for( **action.url_args )}">${action.label}</a></li>
                     %endfor
diff --git a/templates/webapps/community/index.mako b/templates/webapps/community/index.mako
index f29208c2a01..bea7743d006 100644
--- a/templates/webapps/community/index.mako
+++ b/templates/webapps/community/index.mako
@@ -44,6 +44,20 @@
     <div class="page-container" style="padding: 10px;">
         <div class="toolMenu">
             <div class="toolSectionList">
+                %if repository_metadata:
+                    <div class="toolSectionPad"></div>
+                    <div class="toolSectionTitle">
+                        Search
+                    </div>
+                    <div class="toolSectionBody">
+                        <div class="toolTitle">
+                            <a target="galaxy_main" href="${h.url_for( controller='repository', action='find_tools', webapp='community' )}">Search for valid tools</a>
+                        </div>
+                        <div class="toolTitle">
+                            <a target="galaxy_main" href="${h.url_for( controller='repository', action='find_workflows', webapp='community' )}">Search for workflows</a>
+                        </div>
+                    </div>
+                %endif
                 <div class="toolSectionPad"></div>
                 <div class="toolSectionTitle">
                     Repositories
@@ -61,11 +75,6 @@
                                 <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='my_repositories', webapp='community' )}">Browse my repositories</a>
                             </div>
                         %endif
-                        %if repository_metadata:
-                            <div class="toolTitle">
-                                <a target="galaxy_main" href="${h.url_for( controller='repository', action='find_tools', webapp='community' )}">Search for valid tools</a>
-                            </div>
-                        %endif
                     </div>
                 </div>
                 <div class="toolSectionBody">
diff --git a/templates/webapps/community/repository/find_tools.mako b/templates/webapps/community/repository/find_tools.mako
index fcc50f4c6de..1e1b34c7bcd 100644
--- a/templates/webapps/community/repository/find_tools.mako
+++ b/templates/webapps/community/repository/find_tools.mako
@@ -14,6 +14,7 @@
     <br/><br/>
     <ul class="manage-table-actions">
         <li><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a></li>
+        <li><a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a></li>
     </ul>
 %endif
 
diff --git a/templates/webapps/community/repository/find_workflows.mako b/templates/webapps/community/repository/find_workflows.mako
new file mode 100644
index 00000000000..385ff0c7be8
--- /dev/null
+++ b/templates/webapps/community/repository/find_workflows.mako
@@ -0,0 +1,53 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+<%!
+   def inherit(context):
+       if context.get('use_panels'):
+           return '/webapps/community/base_panels.mako'
+       else:
+           return '/base.mako'
+%>
+<%inherit file="${inherit(context)}"/>
+
+%if webapp == 'galaxy':
+    <br/><br/>
+    <ul class="manage-table-actions">
+        <li><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a></li>
+        <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a>
+    </ul>
+%endif
+
+%if message:
+    ${render_msg( message, status )}
+%endif
+
+<div class="toolForm">
+    <div class="toolFormTitle">Search repositories for workflows</div>
+    <div class="toolFormBody">
+        <div class="form-row">
+            Enter a workflow name to find repositories that contain workflows matching the search criteria.<br/><br/>
+            Comma-separated strings may be entered to expand search criteria.
+        </div>
+        <div style="clear: both"></div>
+        <form name="find_workflows" id="find_workflows" action="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}" method="post" >
+            <div style="clear: both"></div>
+            <div class="form-row">
+                <label>Workflow name:</label>
+                <input name="workflow_name" type="textfield" value="${workflow_name}" size="40"/>
+            </div>
+            <div style="clear: both"></div>
+            <div class="form-row">
+                <label>Exact matches only:</label>
+                ${exact_matches_check_box.get_html()}
+                <div class="toolParamHelp" style="clear: both;">
+                    Check the box to match text exactly (text case doesn't matter as all strings are forced to lower case).
+                </div>
+            </div>
+            <div style="clear: both"></div>
+            <div class="form-row">
+                <input type="submit" value="Search repositories"/>
+            </div>
+        </form>
+    </div>
+</div>
diff --git a/templates/webapps/community/repository/preview_tools_in_changeset.mako b/templates/webapps/community/repository/preview_tools_in_changeset.mako
index 1807038b253..25a0ddd1d92 100644
--- a/templates/webapps/community/repository/preview_tools_in_changeset.mako
+++ b/templates/webapps/community/repository/preview_tools_in_changeset.mako
@@ -69,6 +69,7 @@
     <div popupmenu="repository-${repository.id}-popup">
         <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a>
         <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a>
+        <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a>
     </div>
 </ul>
 
diff --git a/templates/webapps/community/repository/tool_form.mako b/templates/webapps/community/repository/tool_form.mako
index 6c15a726942..f1520c79e63 100644
--- a/templates/webapps/community/repository/tool_form.mako
+++ b/templates/webapps/community/repository/tool_form.mako
@@ -116,6 +116,7 @@
                 <div popupmenu="repository-${repository.id}-popup">
                     <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a>
                     <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a>
+                    <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a>
                 </div>
             %else:
                 %if is_new:
diff --git a/templates/webapps/community/repository/view_repository.mako b/templates/webapps/community/repository/view_repository.mako
index 08866804e7b..3cf2ef01fcd 100644
--- a/templates/webapps/community/repository/view_repository.mako
+++ b/templates/webapps/community/repository/view_repository.mako
@@ -99,6 +99,7 @@
         <div popupmenu="repository-${repository.id}-popup">
             <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a>
             <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a>
+            <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a>
         </div>
     %endif
 </ul>
diff --git a/templates/webapps/community/repository/view_tool_metadata.mako b/templates/webapps/community/repository/view_tool_metadata.mako
index 1cb87659326..cb43785f468 100644
--- a/templates/webapps/community/repository/view_tool_metadata.mako
+++ b/templates/webapps/community/repository/view_tool_metadata.mako
@@ -39,6 +39,7 @@
         <div popupmenu="repository-${repository.id}-popup">
             <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a>
             <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a>
+            <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a>
         </div>
     %else:
         %if is_new:
diff --git a/templates/webapps/community/repository/view_workflow.mako b/templates/webapps/community/repository/view_workflow.mako
index 7bea2b35daf..fc79bf889f2 100644
--- a/templates/webapps/community/repository/view_workflow.mako
+++ b/templates/webapps/community/repository/view_workflow.mako
@@ -84,6 +84,7 @@
         <div popupmenu="toolshed-${repository.id}-popup">
             <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a>
             <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a>
+            <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a>
         </div>
     %endif
 </ul>
@@ -92,10 +93,12 @@
     ${render_msg( message, status )}
 %endif
 
-<br/>
-<b>Boxes are red when tools are not available in this repository</b>
-<div class="toolParamHelp" style="clear: both;">
-    (this page displays SVG graphics)
+<div class="toolFormTitle">${workflow_name}</div>
+<div class="form-row">
+    <b>Boxes are red when tools are not available in this repository</b>
+    <div class="toolParamHelp" style="clear: both;">
+        (this page displays SVG graphics)
+    </div>
 </div>
 <br clear="left"/>
 
diff --git a/templates/webapps/galaxy/admin/index.mako b/templates/webapps/galaxy/admin/index.mako
index a54f5706b78..3ec342e2d75 100644
--- a/templates/webapps/galaxy/admin/index.mako
+++ b/templates/webapps/galaxy/admin/index.mako
@@ -73,7 +73,7 @@
                     <div class="toolSectionTitle">Tool sheds</div>
                     <div class="toolSectionBody">
                         <div class="toolSectionBg">                        
-                            <div class="toolTitle"><a href="${h.url_for( controller='admin', action='browse_tool_sheds' )}" target="galaxy_main">Browse tool sheds</a></div>
+                            <div class="toolTitle"><a href="${h.url_for( controller='admin', action='browse_tool_sheds' )}" target="galaxy_main">Search and browse tool sheds</a></div>
                         </div>
                     </div>
                 %endif
diff --git a/templates/webapps/galaxy/admin/tool_sheds.mako b/templates/webapps/galaxy/admin/tool_sheds.mako
index d83b2d53fa6..c3dc8217f3b 100644
--- a/templates/webapps/galaxy/admin/tool_sheds.mako
+++ b/templates/webapps/galaxy/admin/tool_sheds.mako
@@ -27,6 +27,7 @@
                             <div popupmenu="dataset-${shed_id}-popup">
                                 <a class="action-button" href="${h.url_for( controller='admin', action='browse_tool_shed', tool_shed_url=url )}">Browse valid repositories</a>
                                 <a class="action-button" href="${h.url_for( controller='admin', action='find_tools_in_tool_shed', tool_shed_url=url )}">Search for valid tools</a>
+                                <a class="action-button" href="${h.url_for( controller='admin', action='find_workflows_in_tool_shed', tool_shed_url=url )}">Search for workflows</a>
                             </div>
                         </td>
                     </tr>

From f91aec6e0226d3f51fdd84bfee5787da6320da18 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Thu, 27 Oct 2011 13:37:48 -0400
Subject: [PATCH 106/362] Fix for rendering workflow metadata.

---
 templates/webapps/community/repository/common.mako | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/templates/webapps/community/repository/common.mako b/templates/webapps/community/repository/common.mako
index 3bac7f00ffd..63736bacca3 100644
--- a/templates/webapps/community/repository/common.mako
+++ b/templates/webapps/community/repository/common.mako
@@ -168,7 +168,11 @@
                                 %for workflow_dict in workflow_dicts:
                                     <% 
                                         workflow_name = workflow_dict[ 'name' ]
-                                        steps = workflow_dict[ 'steps' ]
+                                        if 'steps' in workflow_dict:
+                                            ## Initially steps were not stored in the metadata record.
+                                            steps = workflow_dict[ 'steps' ]
+                                        else:
+                                            steps = []
                                         format_version = workflow_dict[ 'format-version' ]
                                         annotation = workflow_dict[ 'annotation' ]
                                     %>
@@ -178,7 +182,6 @@
                                         </td>
                                         <td>
                                             %if 'steps' in workflow_dict:
-                                                ## Initially steps were not stored in the metadata record.
                                                 ${len( steps )}
                                             %else:
                                                 unknown

From e988c4ee632c35dab6996ff8fdfe99d5e30d82fd Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Thu, 27 Oct 2011 13:52:05 -0400
Subject: [PATCH 107/362] Eliminate forgotten (and not wanted) PostJobAction
 code when generating a workflow it's dict representation for rendering as an
 svg image in the tool shed.

---
 lib/galaxy/webapps/community/controllers/workflow.py | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/lib/galaxy/webapps/community/controllers/workflow.py b/lib/galaxy/webapps/community/controllers/workflow.py
index 8bbc01a701c..fa5d2a41c2d 100644
--- a/lib/galaxy/webapps/community/controllers/workflow.py
+++ b/lib/galaxy/webapps/community/controllers/workflow.py
@@ -339,12 +339,6 @@ class WorkflowController( BaseUIController ):
                 workflow.has_errors = True
             # Stick this in the step temporarily.
             step.temp_input_connections = step_dict[ 'input_connections' ]
-            # Unpack and add post-job actions.
-            post_job_actions = step_dict.get( 'post_job_actions', {} )
-            for name, pja_dict in post_job_actions.items():
-                pja = PostJobAction( pja_dict[ 'action_type' ], 
-                                     step, pja_dict[ 'output_name' ], 
-                                     pja_dict[ 'action_arguments' ] )
             steps.append( step )
             steps_by_external_id[ step_dict[ 'id' ] ] = step
         # Second pass to deal with connections between steps.

From 690dc8fd92dd57213bcfc2abff9fdb6b62833f00 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Thu, 27 Oct 2011 15:08:07 -0400
Subject: [PATCH 108/362] Create a new ToolShedRepository record only if
 necessary - if one already exists for the installed repository but is marked
 deleted, mark the exisint record undeleted.

---
 lib/galaxy/web/base/controller.py   |  7 ++++++
 lib/galaxy/web/controllers/admin.py | 34 +++++++++++++++++------------
 2 files changed, 27 insertions(+), 14 deletions(-)

diff --git a/lib/galaxy/web/base/controller.py b/lib/galaxy/web/base/controller.py
index aac24eca02e..aaa4be76156 100644
--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -2443,6 +2443,13 @@ def get_quota( trans, id ):
     id = trans.security.decode_id( id )
     quota = trans.sa_session.query( trans.model.Quota ).get( id )
     return quota
+def get_tool_shed_repository( trans, tool_shed, name, owner, changeset_revision ):
+    return trans.sa_session.query( trans.model.ToolShedRepository ) \
+                           .filter( and_( trans.model.ToolShedRepository.table.c.tool_shed == tool_shed,
+                                          trans.model.ToolShedRepository.table.c.name == name,
+                                          trans.model.ToolShedRepository.table.c.owner == owner,
+                                          trans.model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \
+                           .first()
 def handle_sample_tool_data_table_conf_file( trans, filename ):
     """
     Parse the incoming filename and add new entries to the in-memory
diff --git a/lib/galaxy/web/controllers/admin.py b/lib/galaxy/web/controllers/admin.py
index e56e0c9e02b..d2f6fe9354b 100644
--- a/lib/galaxy/web/controllers/admin.py
+++ b/lib/galaxy/web/controllers/admin.py
@@ -766,12 +766,9 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
                         os.chdir( current_working_dir )
                         tmp_stderr.close()
                         if returncode == 0:
-                            # Add a new record to the tool_shed_repository table.
-                            tool_shed_repository = self.__create_tool_shed_repository( trans,
-                                                                                       name,
-                                                                                       description,
-                                                                                       changeset_revision,
-                                                                                       repository_clone_url )
+                            # Add a new record to the tool_shed_repository table if one doesn't
+                            # already exist.  If one exists but is marked deleted, undelete it.
+                            self.__create_or_undelete_tool_shed_repository( trans, name, description, changeset_revision, repository_clone_url )
                             # Update the cloned repository to changeset_revision.
                             repo_files_dir = os.path.join( clone_dir, name )
                             log.debug( 'Updating cloned repository to revision "%s"...' % changeset_revision )
@@ -1055,17 +1052,26 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
                             # We have an invalid .xml file, so not a tool config.
                             log.debug( "Ignoring invalid tool config (%s). Error: %s" % ( str( relative_path ), str( e ) ) )
         return sample_files, repository_tools_tups
-    def __create_tool_shed_repository( self, trans, name, description, changeset_revision, repository_clone_url ):
+    def __create_or_undelete_tool_shed_repository( self, trans, name, description, changeset_revision, repository_clone_url ):
         tmp_url = self.__clean_repository_clone_url( repository_clone_url )
         tool_shed = tmp_url.split( 'repos' )[ 0 ].rstrip( '/' )
         owner = self.__get_repository_owner( tmp_url )
-        tool_shed_repository = trans.model.ToolShedRepository( tool_shed=tool_shed,
-                                                               name=name,
-                                                               description=description,
-                                                               owner=owner,
-                                                               changeset_revision=changeset_revision )
-        trans.sa_session.add( tool_shed_repository )
-        trans.sa_session.flush()
+        flush_needed = False
+        tool_shed_repository = get_tool_shed_repository( trans, tool_shed, name, owner, changeset_revision )
+        if tool_shed_repository:
+            if tool_shed_repository.deleted:
+                tool_shed_repository.deleted = False
+                flush_needed = True
+        else:
+            tool_shed_repository = trans.model.ToolShedRepository( tool_shed=tool_shed,
+                                                                   name=name,
+                                                                   description=description,
+                                                                   owner=owner,
+                                                                   changeset_revision=changeset_revision )
+            flush_needed = True
+        if flush_needed:
+            trans.sa_session.add( tool_shed_repository )
+            trans.sa_session.flush()
     def __add_shed_tool_conf_entry( self, trans, shed_tool_conf, new_tool_section ):
         # Add an entry in the shed_tool_conf file. An entry looks something like:
         # <section name="Filter and Sort" id="filter">

From ef6da827cbef534b9a77474f9e15156ea86f1ded Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Fri, 28 Oct 2011 11:38:55 -0400
Subject: [PATCH 109/362] Fix for refresh on change in workflow run interface
 triggering actual running of workflow.

---
 lib/galaxy/web/controllers/workflow.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/web/controllers/workflow.py b/lib/galaxy/web/controllers/workflow.py
index 6536d262027..7adfda5a2ce 100644
--- a/lib/galaxy/web/controllers/workflow.py
+++ b/lib/galaxy/web/controllers/workflow.py
@@ -1480,10 +1480,10 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
                         trans.sa_session.add( workflow_invocation )
                         invocations.append({'outputs': outputs,
                                             'new_history': new_history})
-                trans.sa_session.flush()
-                return trans.fill_template( "workflow/run_complete.mako",
-                                            workflow=stored,
-                                            invocations=invocations )
+                        trans.sa_session.flush()
+                        return trans.fill_template( "workflow/run_complete.mako",
+                                                    workflow=stored,
+                                                    invocations=invocations )
             else:
                 # Prepare each step
                 missing_tools = []

From ac7d488cb35f42ce9178f8a1036190f5d8a4ba1c Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Fri, 28 Oct 2011 14:05:14 -0400
Subject: [PATCH 110/362] Add basic UI for managng tool shed repositories
 installed into a local Galaxy instance from a tool shed.  Add the ability to
 view the list of tools and workflows included in installed tool shed
 repositories.  Ad the ability to import a workflow from an installed tool
 shed repository into the local Galaxy instance.

---
 lib/galaxy/web/base/controller.py             |   7 -
 lib/galaxy/web/controllers/admin.py           | 166 +++++++++++++++---
 lib/galaxy/web/controllers/workflow.py        |  29 ++-
 .../webapps/community/controllers/common.py   |   5 +-
 .../browse_repository.mako                    | 127 ++++++++++++++
 .../manage_repository.mako                    |  57 ++++++
 templates/webapps/galaxy/admin/index.mako     |   2 +-
 7 files changed, 351 insertions(+), 42 deletions(-)
 create mode 100644 templates/admin/tool_shed_repository/browse_repository.mako
 create mode 100644 templates/admin/tool_shed_repository/manage_repository.mako

diff --git a/lib/galaxy/web/base/controller.py b/lib/galaxy/web/base/controller.py
index aaa4be76156..aac24eca02e 100644
--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -2443,13 +2443,6 @@ def get_quota( trans, id ):
     id = trans.security.decode_id( id )
     quota = trans.sa_session.query( trans.model.Quota ).get( id )
     return quota
-def get_tool_shed_repository( trans, tool_shed, name, owner, changeset_revision ):
-    return trans.sa_session.query( trans.model.ToolShedRepository ) \
-                           .filter( and_( trans.model.ToolShedRepository.table.c.tool_shed == tool_shed,
-                                          trans.model.ToolShedRepository.table.c.name == name,
-                                          trans.model.ToolShedRepository.table.c.owner == owner,
-                                          trans.model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \
-                           .first()
 def handle_sample_tool_data_table_conf_file( trans, filename ):
     """
     Parse the incoming filename and add new entries to the in-memory
diff --git a/lib/galaxy/web/controllers/admin.py b/lib/galaxy/web/controllers/admin.py
index d2f6fe9354b..3c0335120e1 100644
--- a/lib/galaxy/web/controllers/admin.py
+++ b/lib/galaxy/web/controllers/admin.py
@@ -410,7 +410,8 @@ class RepositoryListGrid( grids.Grid ):
     columns = [
         NameColumn( "Name",
                     key="name",
-                    attach_popup=True ),
+                    link=( lambda item: dict( operation="manage_repository", id=item.id, webapp="galaxy" ) ),
+                    attach_popup=False ),
         DescriptionColumn( "Description" ),
         OwnerColumn( "Owner" ),
         RevisionColumn( "Revision" ),
@@ -426,17 +427,14 @@ class RepositoryListGrid( grids.Grid ):
                                                 key="free-text-search",
                                                 visible=False,
                                                 filterable="standard" ) )
-    operations = [ grids.GridOperation( "Get updates",
-                                        allow_multiple=False,
-                                        condition=( lambda item: not item.deleted ),
-                                        async_compatible=False ) ]
     standard_filters = []
     default_filter = dict( deleted="False" )
     num_rows_per_page = 50
     preserve_state = False
     use_paging = True
     def build_initial_query( self, trans, **kwd ):
-        return trans.sa_session.query( self.model_class )
+        return trans.sa_session.query( self.model_class ) \
+                               .filter( self.model_class.table.c.deleted == False )
 
 class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamParser ):
     
@@ -678,11 +676,88 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
         return quota, params
     @web.expose
     @web.require_admin
-    def browse_repositories( self, trans, **kwd ):
+    def browse_tool_shed_repository( self, trans, **kwd ):
+        params = util.Params( kwd )
+        message = util.restore_text( params.get( 'message', ''  ) )
+        status = params.get( 'status', 'done' )
+        repository = get_repository( trans, kwd[ 'id' ] )
+        relative_install_dir = self.__get_relative_install_dir( trans, repository )
+        repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, repository.name ) )
+        tool_dicts = []
+        workflow_dicts = []
+        for root, dirs, files in os.walk( repo_files_dir ):
+            if not root.find( '.hg' ) >= 0 and not root.find( 'hgrc' ) >= 0:
+                if '.hg' in dirs:
+                    # Don't visit .hg directories.
+                    dirs.remove( '.hg' )
+                if 'hgrc' in files:
+                     # Don't include hgrc files.
+                    files.remove( 'hgrc' )
+                for name in files:
+                    # Find all tool configs.
+                    if name.endswith( '.xml' ):
+                        try:
+                            full_path = os.path.abspath( os.path.join( root, name ) )
+                            tool = trans.app.toolbox.load_tool( full_path )
+                            if tool is not None:
+                                tool_config = os.path.join( root, name )
+                                # Handle tool.requirements.
+                                tool_requirements = []
+                                for tr in tool.requirements:
+                                    name=tr.name
+                                    type=tr.type
+                                    if type == 'fabfile':
+                                        version = None
+                                        fabfile = tr.fabfile
+                                        method = tr.method
+                                    else:
+                                        version = tr.version
+                                        fabfile = None
+                                        method = None
+                                    requirement_dict = dict( name=name,
+                                                             type=type,
+                                                             version=version,
+                                                             fabfile=fabfile,
+                                                             method=method )
+                                    tool_requirements.append( requirement_dict )
+                                tool_dict = dict( id=tool.id,
+                                                  old_id=tool.old_id,
+                                                  name=tool.name,
+                                                  version=tool.version,
+                                                  description=tool.description,
+                                                  requirements=tool_requirements,
+                                                  tool_config=tool_config )
+                                tool_dicts.append( tool_dict )
+                        except Exception, e:
+                            # The file is not a Galaxy tool config.
+                            pass
+                    # Find all exported workflows
+                    elif name.endswith( '.ga' ):
+                        try:
+                            full_path = os.path.abspath( os.path.join( root, name ) )
+                            # Convert workflow data from json
+                            fp = open( full_path, 'rb' )
+                            workflow_text = fp.read()
+                            fp.close()
+                            workflow_dict = from_json_string( workflow_text )
+                            if workflow_dict[ 'a_galaxy_workflow' ] == 'true':
+                                workflow_dicts.append( dict( full_path=full_path, workflow_dict=workflow_dict ) )
+                        except Exception, e:
+                            # The file is not a Galaxy workflow.
+                            pass
+        return trans.fill_template( '/admin/tool_shed_repository/browse_repository.mako',
+                                    repository=repository,
+                                    tool_dicts=tool_dicts,
+                                    workflow_dicts=workflow_dicts,
+                                    message=message,
+                                    status=status )
+    @web.expose
+    @web.require_admin
+    def browse_tool_shed_repositories( self, trans, **kwd ):
         if 'operation' in kwd:
-            operation = kwd.pop('operation').lower()
-            if operation == "get updates":
-                return self.check_for_updates( trans, **kwd )
+            operation = kwd.pop( 'operation' ).lower()
+            if operation == "manage_repository":
+                return self.manage_tool_shed_repository( trans, **kwd )
         # Render the list view
         return self.repository_list_grid( trans, **kwd )
     @web.expose
@@ -850,10 +925,35 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
                                     status=status )
     @web.expose
     @web.require_admin
-    def check_for_updates( self, trans, **kwd ):
+    def manage_tool_shed_repository( self, trans, **kwd ):
         params = util.Params( kwd )
+        message = util.restore_text( params.get( 'message', ''  ) )
+        status = params.get( 'status', 'done' )
         repository_id = params.get( 'id', None )
         repository = get_repository( trans, repository_id )
+        description = util.restore_text( params.get( 'description', repository.description ) )
+        if params.get( 'edit_repository_button', False ):
+            if description != repository.description:
+                repository.description = description
+                trans.sa_session.add( repository )
+                trans.sa_session.flush()
+            message = "The repository information has been updated."
+        relative_install_dir = self.__get_relative_install_dir( trans, repository )
+        if relative_install_dir:
+            repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, repository.name ) )
+        else:
+            repo_files_dir = 'unknown'
+        return trans.fill_template( '/admin/tool_shed_repository/manage_repository.mako',
+                                    repository=repository,
+                                    description=description,
+                                    repo_files_dir=repo_files_dir,
+                                    message=message,
+                                    status=status )
+    @web.expose
+    @web.require_admin
+    def check_for_updates( self, trans, **kwd ):
+        params = util.Params( kwd )
+        repository = get_repository( trans, kwd[ 'id' ] )
         galaxy_url = trans.request.host
         # Send a request to the relevant tool shed to see if there are any updates.
         # TODO: support https in the following url.
@@ -872,26 +972,16 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
         owner = params.get( 'owner', None )
         changeset_revision = params.get( 'changeset_revision', None )
         latest_changeset_revision = params.get( 'latest_changeset_revision', None )
+        repository = get_repository_by_shed_name_owner_changeset_revision( trans, tool_shed_url, name, owner, changeset_revision )
         if changeset_revision and latest_changeset_revision:
             if changeset_revision == latest_changeset_revision:
                 message = "The cloned tool shed repository named '%s' is current (there are no updates available)." % name
             else:
-                repository = get_repository_by_name_owner_changeset_revision( trans, name, owner, changeset_revision )
                 current_working_dir = os.getcwd()
-                # Get the directory where the repository is cloned.
-                cleaned_tool_shed_url = self.__clean_tool_shed_url( tool_shed_url )
-                partial_cloned_dir = '%s/repos/%s/%s/%s' % ( cleaned_tool_shed_url, owner, name, changeset_revision )
-                # Get the relative tool installation paths from each of the shed tool configs.
-                shed_tool_confs = trans.app.toolbox.shed_tool_confs
-                relative_cloned_dir = None
-                # The shed_tool_confs dictionary contains shed_conf_filename : tool_path pairs.
-                for shed_conf_filename, tool_path in shed_tool_confs.items():
-                    relative_cloned_dir = os.path.join( tool_path, partial_cloned_dir )
-                    if os.path.isdir( relative_cloned_dir ):
-                        break
-                if relative_cloned_dir:
+                relative_install_dir = self.__get_relative_install_dir( trans, repository )
+                if relative_install_dir:
                     # Update the cloned repository to changeset_revision.
-                    repo_files_dir = os.path.join( relative_cloned_dir, name )
+                    repo_files_dir = os.path.join( relative_install_dir, name )
                     log.debug( "Updating cloned repository named '%s' from revision '%s' to revision '%s'..." % \
                         ( name, changeset_revision, latest_changeset_revision ) )
                     cmd = 'hg pull'
@@ -935,9 +1025,23 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
             message = "The latest changeset revision could not be retrieved for the repository named '%s'." % name
             status = 'error'
         return trans.response.send_redirect( web.url_for( controller='admin',
-                                                          action='browse_repositories',
+                                                          action='manage_tool_shed_repository',
+                                                          id=trans.security.encode_id( repository.id ),
                                                           message=message,
                                                           status=status ) )
+    def __get_relative_install_dir( self, trans, repository ):
+        # Get the directory where the repository is install.
+        tool_shed = self.__clean_tool_shed_url( repository.tool_shed )
+        partial_install_dir = '%s/repos/%s/%s/%s' % ( tool_shed, repository.owner, repository.name, repository.changeset_revision )
+        # Get the relative tool installation paths from each of the shed tool configs.
+        shed_tool_confs = trans.app.toolbox.shed_tool_confs
+        relative_install_dir = None
+        # The shed_tool_confs dictionary contains { shed_conf_filename : tool_path } pairs.
+        for shed_conf_filename, tool_path in shed_tool_confs.items():
+            relative_install_dir = os.path.join( tool_path, partial_install_dir )
+            if os.path.isdir( relative_install_dir ):
+                break
+        return relative_install_dir
     def __handle_missing_data_table_entry( self, trans, tool_path, sample_files, repository_tools_tups ):
         # Inspect each tool to see if any have input parameters that are dynamically
         # generated select lists that require entries in the tool_data_table_conf.xml file.
@@ -1057,7 +1161,7 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
         tool_shed = tmp_url.split( 'repos' )[ 0 ].rstrip( '/' )
         owner = self.__get_repository_owner( tmp_url )
         flush_needed = False
-        tool_shed_repository = get_tool_shed_repository( trans, tool_shed, name, owner, changeset_revision )
+        tool_shed_repository = get_repository_by_shed_name_owner_changeset_revision( trans, tool_shed, name, owner, changeset_revision )
         if tool_shed_repository:
             if tool_shed_repository.deleted:
                 tool_shed_repository.deleted = False
@@ -1200,3 +1304,11 @@ def get_repository_by_name_owner_changeset_revision( trans, name, owner, changes
                                             trans.model.ToolShedRepository.table.c.owner == owner,
                                             trans.model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \
                              .first()
+def get_repository_by_shed_name_owner_changeset_revision( trans, tool_shed, name, owner, changeset_revision ):
+    return trans.sa_session.query( trans.model.ToolShedRepository ) \
+                           .filter( and_( trans.model.ToolShedRepository.table.c.tool_shed == tool_shed,
+                                          trans.model.ToolShedRepository.table.c.name == name,
+                                          trans.model.ToolShedRepository.table.c.owner == owner,
+                                          trans.model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \
+                           .first()
+
diff --git a/lib/galaxy/web/controllers/workflow.py b/lib/galaxy/web/controllers/workflow.py
index 7adfda5a2ce..739cd975eb4 100644
--- a/lib/galaxy/web/controllers/workflow.py
+++ b/lib/galaxy/web/controllers/workflow.py
@@ -1095,8 +1095,8 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
     @web.expose
     def import_workflow( self, trans, **kwd ):
         """
-        Import a workflow by reading an url, uploading a file, or receiving the textual
-        representation of a workflow.
+        Import a workflow by reading an url, uploading a file, opening and reading the contents
+        of a local file, or receiving the textual representation of a workflow via http.
         """
         url = kwd.get( 'url', '' )
         workflow_text = kwd.get( 'workflow_text', '' )
@@ -1104,6 +1104,8 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
         message = kwd.get( 'message', '' )
         status = kwd.get( 'status', 'done' )
         import_button = kwd.get( 'import_button', False )
+        # The following parameters will have values only if the workflow
+        # id being imported from a Galaxy tool shed repository.
         tool_shed_url = kwd.get( 'tool_shed_url', '' )
         repository_metadata_id = kwd.get( 'repository_metadata_id', '' )
         # The workflow_name parameter is in the request only if the import originated
@@ -1111,6 +1113,15 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
         workflow_name = kwd.get( 'workflow_name', '' )
         if workflow_name:
             workflow_name = tool_shed_decode( workflow_name )
+        # The following parameters will have a value only if the import originated
+        # from a tool shed repository installed locally.
+        local_file = kwd.get( 'local_file', '' )
+        repository_id = kwd.get( 'repository_id', '' )
+        if local_file and not import_button:
+            workflow_file = open( local_file, 'rb' )
+            workflow_text = workflow_file.read()
+            workflow_file.close()
+            import_button = True
         if tool_shed_url and not import_button:
             # Use urllib (send another request to the tool shed) to retrieve the workflow.
             workflow_url = 'http://%s/workflow/import_workflow?repository_metadata_id=%s&workflow_name=%s&webapp=%s&open_for_url=true' % \
@@ -1118,7 +1129,6 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
             response = urllib2.urlopen( workflow_url )
             workflow_text = response.read()
             response.close()
-            workflow_text = workflow_text
             import_button = True
         if import_button:
             workflow_data = None
@@ -1131,6 +1141,7 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
                     message = "Failed to open URL: <b>%s</b><br>Exception: %s" % ( url, str( e ) )
                     status = 'error'
             elif workflow_text:
+                # This case occurs when the workflow_text was sent via http from the tool shed.
                 workflow_data = workflow_text
             else:
                 # Load workflow from browsed file.
@@ -1170,7 +1181,7 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
                         message += "Imported, but this workflow contains cycles.  "
                         status = "error"
                     else:
-                        message += "Workflow '%s' imported successfully.  " % workflow.name
+                        message += "Workflow <b>%s</b> imported successfully.  " % workflow.name
                     if missing_tool_tups:
                         if trans.user_is_admin():
                             # A required tool is not available in the local Galaxy instance.
@@ -1201,11 +1212,19 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
                             pass
                     if tool_shed_url:
                         # We've received the textual representation of a workflow from a Galaxy tool shed.
-                        message = "This workflow has been successfully imported into your local Galaxy instance."
+                        message = "Workflow <b>%s</b> imported successfully." % workflow.name
                         # TODO: support https in the following url.
                         url = 'http://%s/workflow/view_workflow?repository_metadata_id=%s&workflow_name=%s&webapp=%s&message=%s' % \
                             ( tool_shed_url, repository_metadata_id, tool_shed_encode( workflow_name ), webapp, message )
                         return trans.response.send_redirect( url )
+                    elif local_file:
+                        # The workflow was read from a file included with an installed tool shed repository.
+                        message = "Workflow <b>%s</b> imported successfully." % workflow.name
+                        return trans.response.send_redirect( web.url_for( controller='admin',
+                                                                          action='browse_tool_shed_repository',
+                                                                          id=repository_id,
+                                                                          message=message,
+                                                                          status=status ) )
                     return self.list( trans )
         return trans.fill_template( "workflow/import.mako",
                                     url=url,
diff --git a/lib/galaxy/webapps/community/controllers/common.py b/lib/galaxy/webapps/community/controllers/common.py
index fa46b95ab8a..2faabb031bf 100644
--- a/lib/galaxy/webapps/community/controllers/common.py
+++ b/lib/galaxy/webapps/community/controllers/common.py
@@ -361,8 +361,9 @@ def set_repository_metadata( trans, id, changeset_revision, **kwd ):
                                 workflow_text = fp.read()
                                 fp.close()
                                 exported_workflow_dict = from_json_string( workflow_text )
-                                # Update the list of metadata dictionaries for workflows in metadata_dict.
-                                metadata_dict = generate_workflow_metadata( trans, id, changeset_revision, exported_workflow_dict, metadata_dict )
+                                if exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true':
+                                    # Update the list of metadata dictionaries for workflows in metadata_dict.
+                                    metadata_dict = generate_workflow_metadata( trans, id, changeset_revision, exported_workflow_dict, metadata_dict )
                             except Exception, e:
                                 invalid_files.append( ( name, str( e ) ) )
         else:
diff --git a/templates/admin/tool_shed_repository/browse_repository.mako b/templates/admin/tool_shed_repository/browse_repository.mako
new file mode 100644
index 00000000000..b8d9ea5a7a7
--- /dev/null
+++ b/templates/admin/tool_shed_repository/browse_repository.mako
@@ -0,0 +1,127 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+<% from galaxy.web.base.controller import tool_shed_encode, tool_shed_decode %>
+
+<br/><br/>
+<ul class="manage-table-actions">
+    <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li>
+    <div popupmenu="repository-${repository.id}-popup">
+        <a class="action-button" href="${h.url_for( controller='admin', action='manage_tool_shed_repository', id=trans.security.encode_id( repository.id ) )}">Manage repository</a>
+        <a class="action-button" href="${h.url_for( controller='admin', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get updates</a>
+    </div>
+</ul>
+
+%if message:
+    ${render_msg( message, status )}
+%endif
+
+<div class="toolForm">
+    <div class="toolFormTitle">Installed tool shed repository '${repository.name}'</div>
+    <div class="toolFormBody">
+
+        %if tool_dicts:
+            <div class="form-row">
+                <table width="100%">
+                    <tr bgcolor="#D8D8D8" width="100%">
+                        <td><b>Tools</b></td>
+                    </tr>
+                </table>
+            </div>
+            <div class="form-row">
+                <table class="grid">
+                    <tr>
+                        <td><b>name</b></td>
+                        <td><b>description</b></td>
+                        <td><b>version</b></td>
+                        <td><b>requirements</b></td>
+                    </tr>
+                    %for tool_dict in tool_dicts:
+                        <tr>
+                            <td>${tool_dict[ 'name' ]}</div>
+                            </td>
+                            <td>${tool_dict[ 'description' ]}</td>
+                            <td>${tool_dict[ 'version' ]}</td>
+                            <td>
+                                <%
+                                    if 'requirements' in tool_dict:
+                                        requirements = tool_dict[ 'requirements' ]
+                                    else:
+                                        requirements = None
+                                %>
+                                %if requirements:
+                                    <%
+                                        requirements_str = ''
+                                        for requirement_dict in tool_dict[ 'requirements' ]:
+                                            requirements_str += '%s (%s), ' % ( requirement_dict[ 'name' ], requirement_dict[ 'type' ] )
+                                        requirements_str = requirements_str.rstrip( ', ' )
+                                    %>
+                                    ${requirements_str}
+                                %else:
+                                    none
+                                %endif
+                            </td>
+                        </tr>
+                    %endfor
+                </table>
+            </div>
+            <div style="clear: both"></div>
+        %endif
+        %if workflow_dicts:
+            <div class="form-row">
+                <table width="100%">
+                    <tr bgcolor="#D8D8D8" width="100%">
+                        <td><b>Workflows</b></td>
+                    </tr>
+                </table>
+            </div>
+            <div style="clear: both"></div>
+            <div class="form-row">
+                <table class="grid">
+                    <tr>
+                        <td><b>name</b></td>
+                        <td><b>steps</b></td>
+                        <td><b>format-version</b></td>
+                        <td><b>annotation</b></td>
+                    </tr>
+                    <% index = 0 %>
+                    %for wf_dict in workflow_dicts:
+                        <%
+                            full_path = wf_dict[ 'full_path' ]
+                            workflow_dict = wf_dict[ 'workflow_dict' ]
+                            workflow_name = workflow_dict[ 'name' ]
+                            if 'steps' in workflow_dict:
+                                ## Initially steps were not stored in the metadata record.
+                                steps = workflow_dict[ 'steps' ]
+                            else:
+                                steps = []
+                            format_version = workflow_dict[ 'format-version' ]
+                            annotation = workflow_dict[ 'annotation' ]
+                        %>
+                        <tr>
+                            <td>
+                                <div class="menubutton" style="float: left;" id="workflow-${index}-popup">
+                                    ${workflow_name}
+                                    <div popupmenu="workflow-${index}-popup">
+                                        <a class="action-button" href="${h.url_for( controller='workflow', action='import_workflow', local_file=full_path, repository_id=trans.security.encode_id( repository.id ) )}">Import to Galaxy</a>
+                                    </div>
+                                </div>
+                            </td>
+                            <td>
+                                %if 'steps' in workflow_dict:
+                                    ${len( steps )}
+                                %else:
+                                    unknown
+                                %endif
+                            </td>
+                            <td>${format_version}</td>
+                            <td>${annotation}</td>
+                        </tr>
+                        <% index += 1 %>
+                    %endfor
+                </table>
+            </div>
+            <div style="clear: both"></div>
+        %endif
+    </div>
+</div>
diff --git a/templates/admin/tool_shed_repository/manage_repository.mako b/templates/admin/tool_shed_repository/manage_repository.mako
new file mode 100644
index 00000000000..2061a8c7a5f
--- /dev/null
+++ b/templates/admin/tool_shed_repository/manage_repository.mako
@@ -0,0 +1,57 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+<br/><br/>
+<ul class="manage-table-actions">
+    <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li>
+    <div popupmenu="repository-${repository.id}-popup">
+        <a class="action-button" href="${h.url_for( controller='admin', action='browse_tool_shed_repository', id=trans.security.encode_id( repository.id ) )}">Browse repository</a>
+        <a class="action-button" href="${h.url_for( controller='admin', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get updates</a>
+    </div>
+</ul>
+
+%if message:
+    ${render_msg( message, status )}
+%endif
+
+<div class="toolForm">
+    <div class="toolFormTitle">${repository.name}</div>
+    <div class="toolFormBody">
+        <form name="edit_repository" id="edit_repository" action="${h.url_for( controller='admin', action='manage_tool_shed_repository', id=trans.security.encode_id( repository.id ) )}" method="post" >
+            <div class="form-row">
+                <label>Tool shed:</label>
+                ${repository.tool_shed}
+                <div style="clear: both"></div>
+            </div>
+            <div class="form-row">
+                <label>Name:</label>
+                ${repository.name}
+                <div style="clear: both"></div>
+            </div>
+            <div class="form-row">
+                <label>Description:</label>
+                <input name="description" type="textfield" value="${description}" size="80"/>
+                <div style="clear: both"></div>
+            </div>
+            <div class="form-row">
+                <label>Revision:</label>
+                ${repository.changeset_revision}
+            </div>
+            <div class="form-row">
+                <label>Owner:</label>
+                ${repository.owner}
+            </div>
+            <div class="form-row">
+                <label>Location:</label>
+                ${repo_files_dir}
+            </div>
+            <div class="form-row">
+                <label>Deleted:</label>
+                ${repository.deleted}
+            </div>
+            <div class="form-row">
+                <input type="submit" name="edit_repository_button" value="Save"/>
+            </div>
+        </form>
+    </div>
+</div>
diff --git a/templates/webapps/galaxy/admin/index.mako b/templates/webapps/galaxy/admin/index.mako
index 3ec342e2d75..c199df5be0a 100644
--- a/templates/webapps/galaxy/admin/index.mako
+++ b/templates/webapps/galaxy/admin/index.mako
@@ -64,7 +64,7 @@
                         <div class="toolTitle"><a href="${h.url_for( controller='admin', action='memdump' )}" target="galaxy_main">Profile memory usage</a></div>
                         <div class="toolTitle"><a href="${h.url_for( controller='admin', action='jobs' )}" target="galaxy_main">Manage jobs</a></div>
                         %if cloned_repositories:
-                            <div class="toolTitle"><a href="${h.url_for( controller='admin', action='browse_repositories' )}" target="galaxy_main">Manage installed tool shed repositories</a></div>
+                            <div class="toolTitle"><a href="${h.url_for( controller='admin', action='browse_tool_shed_repositories' )}" target="galaxy_main">Manage installed tool shed repositories</a></div>
                         %endif
                     </div>
                 </div>

From 2e750be904cb2ea9487f71cea5cb2ecf5f1c98c5 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Fri, 28 Oct 2011 15:19:09 -0400
Subject: [PATCH 111/362] Don't display the "User Info" select field when
 registering as a new user of editing your information as an existing user
 unless there are existing form definitions that provide options for
 selection.

---
 templates/user/register.mako            | 2 +-
 templates/webapps/galaxy/user/info.mako | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/templates/user/register.mako b/templates/user/register.mako
index 2fcb619e2bb..ba420c9e4aa 100644
--- a/templates/user/register.mako
+++ b/templates/user/register.mako
@@ -65,7 +65,7 @@
                     ${subscribe_check_box.get_html()}
                 </div>
             %endif
-            %if user_type_fd_id_select_field:
+            %if len( user_type_fd_id_select_field.options ) > 1:
                 <div class="form-row">
                     <label>User type</label>
                     ${user_type_fd_id_select_field.get_html()}
diff --git a/templates/webapps/galaxy/user/info.mako b/templates/webapps/galaxy/user/info.mako
index f99dfdfe04d..a78e77e2cdd 100644
--- a/templates/webapps/galaxy/user/info.mako
+++ b/templates/webapps/galaxy/user/info.mako
@@ -13,7 +13,7 @@ ${render_user_info()}
     <div class="toolForm">
         <form name="user_info" id="user_info" action="${h.url_for( controller='user', action='edit_info', cntrller=cntrller, user_id=trans.security.encode_id( user.id ) )}" method="post" >
             <div class="toolFormTitle">User information</div>
-            %if user_type_fd_id_select_field:
+            %if len( user_type_fd_id_select_field.options ) > 1:
                 <div class="form-row">
                     <label>User type:</label>
                     ${user_type_fd_id_select_field.get_html()}

From 20f01fcb8faa36794ccafb9dfbd05f63ddf34d24 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Fri, 28 Oct 2011 16:13:21 -0400
Subject: [PATCH 112/362] Fixes for finding tools installed from a tool shed
 when building workflows from the current history or running workflows, and
 the workflow in question references tools using the old tool_id.

---
 lib/galaxy/web/controllers/workflow.py | 22 ++++++++++++++++++++--
 1 file changed, 20 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/web/controllers/workflow.py b/lib/galaxy/web/controllers/workflow.py
index 739cd975eb4..f1efc758a36 100644
--- a/lib/galaxy/web/controllers/workflow.py
+++ b/lib/galaxy/web/controllers/workflow.py
@@ -1296,7 +1296,16 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
             for job_id in job_ids:
                 assert job_id in jobs_by_id, "Attempt to create workflow with job not connected to current history"
                 job = jobs_by_id[ job_id ]
-                tool = trans.app.toolbox.tools_by_id[ job.tool_id ]
+                try:
+                    tool = trans.app.toolbox.tools_by_id[ job.tool_id ]
+                except KeyError, e:
+                    # Handle the case where the workflow requires a tool not available in the local Galaxy instance.
+                    # The id value of tools installed from a Galaxy tool shed is a guid, but these tool's old_id 
+                    # attribute should contain what we're looking for.
+                    for available_tool_id, available_tool in trans.app.toolbox.tools_by_id.items():
+                        if job.tool_id == available_tool.old_id:
+                            tool = available_tool
+                            break
                 param_values = job.get_param_values( trans.app )
                 associations = cleanup_param_values( tool.inputs, param_values )
                 # Doing it this way breaks dynamic parameters, backed out temporarily.
@@ -1463,7 +1472,16 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
                             # Execute module
                             job = None
                             if step.type == 'tool' or step.type is None:
-                                tool = trans.app.toolbox.tools_by_id[ step.tool_id ]
+                                try:
+                                    tool = trans.app.toolbox.tools_by_id[ step.tool_id ]
+                                except KeyError, e:
+                                    # Handle the case where the workflow requires a tool not available in the local Galaxy instance.
+                                    # The id value of tools installed from a Galaxy tool shed is a guid, but these tool's old_id 
+                                    # attribute should contain what we're looking for.
+                                    for available_tool_id, available_tool in trans.app.toolbox.tools_by_id.items():
+                                        if step.tool_id == available_tool.old_id:
+                                            tool = available_tool
+                                            break
                                 input_values = step.state.inputs
                                 # Connect up
                                 def callback( input, value, prefixed_name, prefixed_label ):

From 2a3d2894ddcf7e1f2c8f97f0620d9a52be1ded9f Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Fri, 28 Oct 2011 16:34:28 -0400
Subject: [PATCH 113/362] More menu options when viewing repostiroy tools in a
 tool shed.

---
 templates/webapps/community/repository/tool_form.mako     | 8 ++++++--
 .../webapps/community/repository/view_tool_metadata.mako  | 8 ++++++--
 2 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/templates/webapps/community/repository/tool_form.mako b/templates/webapps/community/repository/tool_form.mako
index f1520c79e63..2ecf77cd4f8 100644
--- a/templates/webapps/community/repository/tool_form.mako
+++ b/templates/webapps/community/repository/tool_form.mako
@@ -111,9 +111,13 @@
         <br/><br/>
         <ul class="manage-table-actions">
             %if webapp == 'galaxy':
-                <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a></li>
-                <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li>
+                <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li>
                 <div popupmenu="repository-${repository.id}-popup">
+                    <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a></li>
+                    <li><a class="action-button" href="${h.url_for( controller='repository', action='preview_tools_in_changeset', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Browse repository</a></li>
+                </div>
+                <li><a class="action-button" id="tool_shed-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li>
+                <div popupmenu="tool_shed-${repository.id}-popup">
                     <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a>
                     <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a>
                     <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a>
diff --git a/templates/webapps/community/repository/view_tool_metadata.mako b/templates/webapps/community/repository/view_tool_metadata.mako
index cb43785f468..d444f5871b6 100644
--- a/templates/webapps/community/repository/view_tool_metadata.mako
+++ b/templates/webapps/community/repository/view_tool_metadata.mako
@@ -34,9 +34,13 @@
 <br/><br/>
 <ul class="manage-table-actions">
     %if webapp == 'galaxy':
-        <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a></li>
-        <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li>
+        <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li>
         <div popupmenu="repository-${repository.id}-popup">
+            <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a></li>
+            <li><a class="action-button" href="${h.url_for( controller='repository', action='preview_tools_in_changeset', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Browse repository</a></li>
+        </div>
+        <li><a class="action-button" id="tool_shed-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li>
+        <div popupmenu="tool_shed-${repository.id}-popup">
             <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a>
             <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a>
             <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a>

From c98ed7820638f3e5a66accc73317997b10deb00b Mon Sep 17 00:00:00 2001
From: James Taylor <james@jamestaylor.org>
Date: Sun, 30 Oct 2011 18:12:22 -0400
Subject: [PATCH 114/362] Modal dialogs now dim the entire page, show_message
 can be used for the old behavior (but should only be used for messages that
 do not require interaction)

---
 static/june_2007_style/blue/panel_layout.css |  2 +
 static/june_2007_style/blue/trackster.css    | 52 ++++++++++----------
 static/june_2007_style/panel_layout.css.tmpl |  8 +++
 static/june_2007_style/trackster.css.tmpl    |  4 +-
 static/scripts/galaxy.panels.js              | 16 ++++--
 templates/workflow/editor.mako               |  4 +-
 6 files changed, 54 insertions(+), 32 deletions(-)

diff --git a/static/june_2007_style/blue/panel_layout.css b/static/june_2007_style/blue/panel_layout.css
index 298ee40af41..5a3e2cf51d7 100644
--- a/static/june_2007_style/blue/panel_layout.css
+++ b/static/june_2007_style/blue/panel_layout.css
@@ -23,9 +23,11 @@ div.unified-panel-body{position:absolute;top:2em;bottom:0;width:100%;margin-top:
 .panel-header-button:hover{color:black;background-color:#ccc;}
 .panel-header-button:active{color:white;background-color:#aaaaaa;}
 #overlay{position:fixed;top:0;left:0;width:100%;height:100%;z-index:20000;}
+#overlay.modal #overlay-background{background:rgba(0,0,0,0.5);}
 .dialog-box-container{position:relative;margin-top:80px;margin-right:auto;margin-left:auto;}
 .dialog-box-wrapper{position:relative;padding:1em;background-color:rgba(0,0,0,0.5);-moz-border-radius:1em;-webkit-border-radius:1em;}
 .dialog-box{border:solid #999 1px;background:white;z-index:80000;}
+#overlay.modal .dialog-box .body{min-width:600px;}
 .dialog-box .body{padding:5px;overflow:auto;max-height:500px;min-width:300px;}
 .dialog-box .buttons{padding:5px;}
 .panel-error-message,.panel-warning-message,.panel-done-message,.panel-info-message{height:24px;line-height:24px;color:#303030;padding:0px;padding-left:26px;background-color:#FFCCCC;background-image:url(error_small.png);background-repeat:no-repeat;background-position:6px 50%;}
diff --git a/static/june_2007_style/blue/trackster.css b/static/june_2007_style/blue/trackster.css
index e59b26677a9..e4f2aad9f4b 100644
--- a/static/june_2007_style/blue/trackster.css
+++ b/static/june_2007_style/blue/trackster.css
@@ -3,30 +3,9 @@
 .content{font:10px verdana;}
 .nav-controls{text-align:center;padding:1px 0;}
 .nav-controls input{margin:0 5px;}
-.menu-button{padding: 0px 4px 0px 4px;}
 #zoom-in,#zoom-out{display:inline-block;height:16px;width:16px;margin-bottom:-3px;cursor:pointer;}
 #zoom-out{background:transparent url(../images/fugue/magnifier-zoom-out.png) center center no-repeat;}
 #zoom-in{margin-left:10px;background:transparent url(../images/fugue/magnifier-zoom.png) center center no-repeat;}
-.overview-icon{background:transparent url(../images/fugue/application-dock-270-bw.png) no-repeat;}
-.overview-icon:hover{background:transparent url(../images/fugue/application-dock-270.png) no-repeat;}
-.settings-icon{background:transparent url(../images/fugue/gear-bw.png) no-repeat;}
-.settings-icon:hover{background:transparent url(../images/fugue/gear.png) no-repeat;}
-.tools-icon{background:transparent url(../images/fugue/toolbox-bw.png) no-repeat;}
-.tools-icon:hover{background:transparent url(../images/fugue/toolbox.png) no-repeat;}
-.filters-icon{background:transparent url(../images/fugue/ui-slider-050-bw.png) no-repeat;}
-.filters-icon:hover{background:transparent url(../images/fugue/ui-slider-050.png) no-repeat;}
-.remove-icon,.overview-close{background:transparent url(../images/fugue/cross-small-bw.png) no-repeat;}
-.remove-icon:hover,.overview-close:hover{background:transparent url(../images/fugue/cross-circle.png) no-repeat;}
-#close-icon{background:transparent url(../images/fugue/cross-circle-bw.png) no-repeat;margin-right:0px;}
-#close-icon:hover{background:transparent url(../images/fugue/cross-circle.png) no-repeat;}
-#add-tracks-icon{background:transparent url(../images/fugue/plus-button-bw.png) no-repeat;}
-#add-tracks-icon:hover{background:transparent url(../images/fugue/plus-button.png) no-repeat;}
-#add-group-icon{background:transparent url(../images/fugue/block--plus-bw.png) no-repeat;}
-#add-group-icon:hover{background:transparent url(../images/fugue/block--plus.png) no-repeat;}
-#bookmarks-icon{background:transparent url(../images/fugue/bookmarks-bw.png) no-repeat;}
-#bookmarks-icon:hover{background:transparent url(../images/fugue/bookmarks.png) no-repeat;}
-#save-icon{background:transparent url(../images/fugue/disk--arrow-bw.png) no-repeat;}
-#save-icon:hover{background:transparent url(../images/fugue/disk--arrow.png) no-repeat;}
 .nav-input{font-size:12px;width:30em;z-index:1000;}
 .location{display:inline-block;width:15em;margin:0 10px;}
 .draghandle{margin-top:2px;cursor:move;float:left;background:transparent url(../images/visualization/draggable_horizontal.png) center center no-repeat;width:10px;height:12px;}
@@ -65,16 +44,39 @@
 input{font:10px verdana;}
 .dynamic-tool,.filters{margin-left:0.25em;padding-bottom:0.5em;}
 .dynamic-tool{width:410px;}
-.filters>.sliders,.display-controls{float:left;margin:1em;}
+.filters > .sliders,.display-controls{float:left;margin:1em;}
 .sliders{width:410px;}
-.display-controls{border-left:solid 2px #DDDDDD;padding-left:1em}
-.filter-row{margin-top:0.4em;}
+.display-controls{border-left:solid 2px #DDDDDD;padding-left:1em
+}
+.filter-row {
+    margin-top:0.4em;}
 .slider-row{margin-left:1em;}
 .elt-label{float:left;font-weight:bold;margin-right:1em;}
 .slider{float:right;width:200px;position:relative;}
 .tool-name{font-size:110%;font-weight:bold;}
 .param-row{margin-top:0.2em;margin-left:1em;}
 .param-label{float:left;font-weight:bold;padding-top:0.2em;}
+.menu-button{padding:0px 4px 0px 4px;}
+.settings-icon{background:transparent url(../images/fugue/gear-bw.png) no-repeat;}
+.settings-icon:hover{background:transparent url(../images/fugue/gear.png) no-repeat;}
+.overview-icon{background:transparent url(../images/fugue/application-dock-270-bw.png) no-repeat;}
+.overview-icon:hover{background:transparent url(../images/fugue/application-dock-270.png) no-repeat;}
+.tools-icon{background:transparent url(../images/fugue/toolbox-bw.png) no-repeat;}
+.tools-icon:hover{background:transparent url(../images/fugue/toolbox.png) no-repeat;}
+.filters-icon{background:transparent url(../images/fugue/ui-slider-050-bw.png) no-repeat;}
+.filters-icon:hover{background:transparent url(../images/fugue/ui-slider-050.png) no-repeat;}
+.remove-icon,.overview-close{background:transparent url(../images/fugue/cross-small-bw.png) no-repeat;}
+.remove-icon:hover,.overview-close:hover{background:transparent url(../images/fugue/cross-circle.png) no-repeat;}
+#close-icon{background:transparent url(../images/fugue/cross-circle-bw.png) no-repeat;margin-right:0px;}
+#close-icon:hover{background:transparent url(../images/fugue/cross-circle.png) no-repeat;}
+#add-tracks-icon{background:transparent url(../images/fugue/plus-button-bw.png) no-repeat;}
+#add-tracks-icon:hover{background:transparent url(../images/fugue/plus-button.png) no-repeat;}
+#add-group-icon{background:transparent url(../images/fugue/block--plus-bw.png) no-repeat;}
+#add-group-icon:hover{background:transparent url(../images/fugue/block--plus.png) no-repeat;}
+#bookmarks-icon{background:transparent url(../images/fugue/bookmarks-bw.png) no-repeat;}
+#bookmarks-icon:hover{background:transparent url(../images/fugue/bookmarks.png) no-repeat;}
+#save-icon{background:transparent url(../images/fugue/disk--arrow-bw.png) no-repeat;}
+#save-icon:hover{background:transparent url(../images/fugue/disk--arrow.png) no-repeat;}
 .child-track-icon{background:url('../images/fugue/arrow-000-small-bw.png') no-repeat;width:30px;cursor:move;}
 .track-resize{background:white url('../images/visualization/draggable_vertical.png') no-repeat top center;position:absolute;right:3px;bottom:-4px;width:14px;height:7px;border:solid #999 1px;z-index:100;}
 .bookmark{background:white;border:solid #999 1px;border-right:none;margin:0.5em;margin-right:0;padding:0.5em;}
@@ -85,4 +87,4 @@ input{font:10px verdana;}
 .icon.more-across{background:url('../images/fugue/arrow-transition-bw.png') no-repeat 0px 0px;}
 .intro{padding:1em;}
 .intro > .action-button{background-color:#CCC;padding:1em;}
-.feature-popup{background-color:#DDD;position:absolute;z-index:1000}
+.feature-popup{background-color:#DDD;position:absolute;z-index:1000;}
diff --git a/static/june_2007_style/panel_layout.css.tmpl b/static/june_2007_style/panel_layout.css.tmpl
index 614079a91a4..292501dda9c 100644
--- a/static/june_2007_style/panel_layout.css.tmpl
+++ b/static/june_2007_style/panel_layout.css.tmpl
@@ -161,6 +161,10 @@ div.unified-panel-body {
     z-index: 20000;
 }
 
+#overlay.modal #overlay-background {
+	background: rgba(0,0,0,0.5);
+}
+
 .dialog-box-container {
     position: relative;
     margin-top: 80px;
@@ -182,6 +186,10 @@ div.unified-panel-body {
     z-index: 80000;
 }
 
+#overlay.modal .dialog-box .body {
+	min-width: 600px;
+}
+
 .dialog-box .body {
     padding: 5px;
     overflow: auto;
diff --git a/static/june_2007_style/trackster.css.tmpl b/static/june_2007_style/trackster.css.tmpl
index 16e92729a7c..2d051579f83 100644
--- a/static/june_2007_style/trackster.css.tmpl
+++ b/static/june_2007_style/trackster.css.tmpl
@@ -405,8 +405,8 @@ input {
     background-color: #CCC;
     padding: 1em;
 }
-.feature-popup{ 
+.feature-popup { 
     background-color: #DDD;
     position: absolute;
-    z-index: 1000
+    z-index: 1000;
 }
diff --git a/static/scripts/galaxy.panels.js b/static/scripts/galaxy.panels.js
index be187d8fb57..37adce6b7e2 100644
--- a/static/scripts/galaxy.panels.js
+++ b/static/scripts/galaxy.panels.js
@@ -163,13 +163,23 @@ function make_right_panel( panel_el, center_el, border_el ) {
 // Modal dialog boxes
 
 function hide_modal() {
-    $(".dialog-box-container" ).fadeOut( function() {
+    $(".dialog-box-container" ).hide( 0, function() {
         $("#overlay").hide();
+		$("#overlay").removeClass( "modal" );
         $( ".dialog-box" ).find( ".body" ).children().remove();
     } );
 };
 
-function show_modal( title, body, buttons, extra_buttons, init_fn ) {
+function show_modal() {
+	$("#overlay").addClass( "modal" );
+	_show_modal.apply( this, arguments );
+}
+
+function show_message() {
+	_show_modal.apply( this, arguments );
+}
+
+function _show_modal( title, body, buttons, extra_buttons, init_fn ) {
     if ( title ) {
         $( ".dialog-box" ).find( ".title" ).html( title );
         $( ".dialog-box" ).find( ".unified-panel-header" ).show(); 
@@ -205,7 +215,7 @@ function show_modal( title, body, buttons, extra_buttons, init_fn ) {
     $( ".dialog-box" ).find( ".body" ).html( body );
     if ( ! $(".dialog-box-container").is( ":visible" ) ) {
         $("#overlay").show();
-        $(".dialog-box-container").fadeIn();
+        $(".dialog-box-container").show();
     }
     // Fix min-width so that modal cannot shrink considerably if 
     // new content is loaded.
diff --git a/templates/workflow/editor.mako b/templates/workflow/editor.mako
index 27ff852b8dc..af01aecc946 100644
--- a/templates/workflow/editor.mako
+++ b/templates/workflow/editor.mako
@@ -213,7 +213,7 @@
                          show_workflow_parameters();
                      },
                      beforeSubmit: function( data ) {
-                         show_modal( "Loading workflow", "progress" );
+                         show_message( "Loading workflow", "progress" );
                      }
                 });
             }
@@ -650,7 +650,7 @@
     };
 
     var save_current_workflow = function ( eventObj, success_callback ) {
-        show_modal( "Saving workflow", "progress" );
+        show_message( "Saving workflow", "progress" );
         workflow.check_changes_in_active_form();
         if (!workflow.has_changes) {
             hide_modal();

From 37b973097f230cf540cdd830854ee1dfc13d4eb7 Mon Sep 17 00:00:00 2001
From: James Taylor <james@jamestaylor.org>
Date: Sun, 30 Oct 2011 18:59:05 -0400
Subject: [PATCH 115/362] Trackster: fixes for bigwig data -- updated bx-python

---
 eggs.ini                                      |  4 +-
 .../interval_to_summary_tree_converter.py     |  2 +-
 .../visualization/tracks/data_providers.py    | 59 ++++++++++++-------
 lib/galaxy/web/controllers/tracks.py          |  3 +-
 static/scripts/trackster.js                   |  8 +--
 5 files changed, 46 insertions(+), 30 deletions(-)

diff --git a/eggs.ini b/eggs.ini
index 7bec53d8b6f..82c12aad70b 100644
--- a/eggs.ini
+++ b/eggs.ini
@@ -12,7 +12,7 @@ repository = http://eggs.g2.bx.psu.edu
 no_auto = pbs_python DRMAA_python
 
 [eggs:platform]
-bx_python = 0.7.0
+bx_python = 0.7.1
 Cheetah = 2.2.2
 ctypes = 1.0.2
 DRMAA_python = 0.2
@@ -67,7 +67,7 @@ Whoosh = 0.3.18
 psycopg2 = _8.4.2_static
 pysqlite = _3.6.17_static
 MySQL_python = _5.1.41_static
-bx_python = _494c2d1d68b3_rebuild1
+; bx_python = _494c2d1d68b3_rebuild1
 GeneTrack = _dev_48da9e998f0caf01c5be731e926f4b0481f658f0
 SQLAlchemy = _dev_r6498
 pysam = _kanwei_b10f6e722e9a
diff --git a/lib/galaxy/datatypes/converters/interval_to_summary_tree_converter.py b/lib/galaxy/datatypes/converters/interval_to_summary_tree_converter.py
index 2fb73a6e18d..f7f89dbf407 100644
--- a/lib/galaxy/datatypes/converters/interval_to_summary_tree_converter.py
+++ b/lib/galaxy/datatypes/converters/interval_to_summary_tree_converter.py
@@ -50,4 +50,4 @@ def main():
     st.write(out_fname)
 
 if __name__ == "__main__": 
-    main()
\ No newline at end of file
+    main()
diff --git a/lib/galaxy/visualization/tracks/data_providers.py b/lib/galaxy/visualization/tracks/data_providers.py
index eb561b62f74..3c09a8dc7d3 100644
--- a/lib/galaxy/visualization/tracks/data_providers.py
+++ b/lib/galaxy/visualization/tracks/data_providers.py
@@ -434,40 +434,55 @@ class BBIDataProvider( TracksDataProvider ):
         # Bigwig has the possibility of it being a standalone bigwig file, in which case we use
         # original_dataset, or coming from wig->bigwig conversion in which we use converted_dataset
         f, bbi = self._get_dataset()
-        
+       
+        # If the stats kwarg was provide, we compute overall summary data for the entire chromosome,
+        # but no reduced data -- currently only providing min/max which is used by trackster to 
+        # determine the default range
         if 'stats' in kwargs:
-            all_dat = bbi.query(chrom, 0, 2147483647, 1)
+            # FIXME: use actual chromosome size
+            summary = bbi.summarize( chrom, 0, 214783647, 1 )
             f.close()
-            if all_dat is None:
+            if summary is None:
                 return None
-            
-            all_dat = all_dat[0] # only 1 summary
-            return { 'data' : { 'max': float( all_dat['max'] ), \
-                                'min': float( all_dat['min'] ), \
-                                'total_frequency': float( all_dat['coverage'] ) } \
-                    }
-                     
+            else:
+                return dict( data=dict( min=summary.min_val[0], max=summary.max_val[0] ) )
+
         start = int(start)
         end = int(end)
+
+        # The following seems not to work very well, for example it will only return one
+        # data point if the tile is 1280px wide. Not sure what the intent is.
+
         # The first zoom level for BBI files is 640. If too much is requested, it will look at each block instead
         # of summaries. The calculation done is: zoom <> (end-start)/num_points/2.
         # Thus, the optimal number of points is (end-start)/num_points/2 = 640
         # num_points = (end-start) / 1280
-        num_points = (end-start) / 1280
-        if num_points < 1:
-            num_points = end - start
-        else:
-            num_points = min(num_points, 500)
+        #num_points = (end-start) / 1280
+        #if num_points < 1:
+        #    num_points = end - start
+        #else:
+        #    num_points = min(num_points, 500)
 
-        data = bbi.query(chrom, start, end, num_points)
+        # For now, we'll do 1000 data points by default However, the summaries
+        # don't seem to work when a summary pixel corresponds to less than one
+        # datapoint, so we prevent that. 
+        # FIXME: need to switch over to using the full data at high levels of
+        # detail.
+        num_points = min( 1000, end - start )
+
+        summary = bbi.summarize( chrom, start, end, num_points )
         f.close()
-        
-        pos = start
-        step_size = (end - start) / num_points
+
         result = []
-        if data:
-            for dat_dict in data:
-                result.append( (pos, float_nan(dat_dict['mean']) ) )
+
+        if summary:
+            mean = summary.sum_data / summary.valid_count
+        
+            pos = start
+            step_size = (end - start) / num_points
+
+            for value in mean:
+                result.append( (pos, float_nan(value) ) )
                 pos += step_size
             
         return { 'data': result }
diff --git a/lib/galaxy/web/controllers/tracks.py b/lib/galaxy/web/controllers/tracks.py
index a1527438a1f..2fcc1916e3c 100644
--- a/lib/galaxy/web/controllers/tracks.py
+++ b/lib/galaxy/web/controllers/tracks.py
@@ -524,6 +524,7 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
             if not standalone_provider.has_data( chrom ):
                 return messages.NO_DATA
             valid_chroms = standalone_provider.valid_chroms()
+
             
         # Have data if we get here
         return { "status": messages.DATA, "valid_chroms": valid_chroms }
@@ -990,4 +991,4 @@ def _get_highest_priority_msg( message_list ):
                 return_message = message
             elif return_message == None and message == messages.PENDING:
                 return_message = message
-    return return_message
\ No newline at end of file
+    return return_message
diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index ce87c95f0f3..0657c8a8018 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -699,7 +699,7 @@ extend(Drawable.prototype, {
     remove: function() {
         this.container.remove_drawable(this);
         
-        this.container_div.fadeOut('slow', function() { 
+        this.container_div.hide(0, function() { 
             $(this).remove();
             // HACK: is there a better way to update the view?
             view.update_intro_div();
@@ -1253,7 +1253,7 @@ extend( View.prototype, DrawableCollection.prototype, {
         DrawableCollection.prototype.remove_drawable.call(this, drawable);
         if (hide) {
             var view = this;
-            drawable.container_div.fadeOut('slow', function() { 
+            drawable.container_div.hide(0, function() { 
                 $(this).remove();
                 view.update_intro_div(); 
             });
@@ -2699,7 +2699,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
             w_scale = width / range,
             resolution = this.view.resolution,
             parent_element = $("<div style='position: relative;'></div>");
-            
+
         // For overview, adjust high, low, resolution, and w_scale.
         if (this.is_overview) {
             low = this.view.max_low;
@@ -4759,4 +4759,4 @@ exports.VariantPainter = VariantPainter;
     for ( key in modules.trackster ) {
         target[key] = modules.trackster[key];
     }
-})(window);
\ No newline at end of file
+})(window);

From 74c5e42ecdcca50ea603f6c90b6dd6afcfe972f7 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Mon, 31 Oct 2011 09:41:09 -0400
Subject: [PATCH 116/362] GATK tools will now use gatk_picard_indexes data
 table.

---
 tool_data_table_conf.xml.sample            | 5 +++++
 tools/gatk/analyze_covariates.xml          | 1 +
 tools/gatk/count_covariates.xml            | 4 ++--
 tools/gatk/indel_realigner.xml             | 5 +++--
 tools/gatk/realigner_target_creator.xml    | 5 +++--
 tools/gatk/table_recalibration.xml         | 5 +++--
 tools/gatk/unified_genotyper.xml           | 4 ++--
 tools/gatk/variant_annotator.xml           | 4 ++--
 tools/gatk/variant_apply_recalibration.xml | 2 +-
 tools/gatk/variant_combine.xml             | 2 +-
 tools/gatk/variant_eval.xml                | 2 +-
 tools/gatk/variant_filtration.xml          | 2 +-
 tools/gatk/variant_recalibrator.xml        | 2 +-
 tools/gatk/variants_validate.xml           | 3 ++-
 tools/picard/picard_ReorderSam.xml         | 2 +-
 15 files changed, 29 insertions(+), 19 deletions(-)

diff --git a/tool_data_table_conf.xml.sample b/tool_data_table_conf.xml.sample
index 869eb8c52de..a217776b72a 100644
--- a/tool_data_table_conf.xml.sample
+++ b/tool_data_table_conf.xml.sample
@@ -70,6 +70,11 @@
         <columns>value, dbkey, name, path</columns>
         <file path="tool-data/picard_index.loc" />
     </table>
+    <!-- Location of Picard dict files valid for GATK -->
+    <table name="gatk_picard_indexes" comment_char="#">
+        <columns>value, dbkey, name, path, tools_valid_for</columns>
+        <file path="tool-data/picard_index.loc" />
+    </table>
     <!-- Location of SRMA dict file and other files -->
     <table name="srma_indexes" comment_char="#">
         <columns>value, dbkey, name, path</columns>
diff --git a/tools/gatk/analyze_covariates.xml b/tools/gatk/analyze_covariates.xml
index ab62a089cdf..d6efcb5436b 100644
--- a/tools/gatk/analyze_covariates.xml
+++ b/tools/gatk/analyze_covariates.xml
@@ -11,6 +11,7 @@
     -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/AnalyzeCovariates.jar"
     -recalFile "${input_recal}"
     -outputDir "${output_html.files_path}"
+    ##--num_threads 4 ##hard coded, for now
     ##-log "${output_log}"
     ##-Rscript,--path_to_Rscript path_to_Rscript; on path is good enough
     -resources "${GALAXY_DATA_INDEX_DIR}/gatk/R"         
diff --git a/tools/gatk/count_covariates.xml b/tools/gatk/count_covariates.xml
index 0a2366fa09a..dcf712b416b 100644
--- a/tools/gatk/count_covariates.xml
+++ b/tools/gatk/count_covariates.xml
@@ -139,10 +139,10 @@
         <param name="input_bam" type="data" format="bam" label="BAM file">
           <validator type="unspecified_build" />
           <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
-          <validator type="dataset_metadata_in_file" filename="picard_index.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
+          <validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
         </param>
         <param name="ref_file" type="select" label="Using reference genome">
-          <options from_data_table="picard_indexes">
+          <options from_data_table="gatk_picard_indexes">
             <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/>
           </options>
         </param>
diff --git a/tools/gatk/indel_realigner.xml b/tools/gatk/indel_realigner.xml
index 9676467e9c4..69ce9adac18 100644
--- a/tools/gatk/indel_realigner.xml
+++ b/tools/gatk/indel_realigner.xml
@@ -13,6 +13,7 @@
     -T "IndelRealigner"
     -o "${output_bam}"
     -et "NO_ET" ##ET no phone home
+    ##--num_threads 4 ##hard coded, for now
     ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
     #if $reference_source.reference_source_selector != "history":
         -R "${reference_source.ref_file.fields.path}"
@@ -108,10 +109,10 @@
         <param name="input_bam" type="data" format="bam" label="BAM file">
           <validator type="unspecified_build" />
           <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
-          <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
+          <validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
         </param>
         <param name="ref_file" type="select" label="Using reference genome">
-          <options from_data_table="picard_indexes">
+          <options from_data_table="gatk_picard_indexes">
             <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/>
           </options>
         </param>
diff --git a/tools/gatk/realigner_target_creator.xml b/tools/gatk/realigner_target_creator.xml
index 7be101ec472..c9c3172bdcb 100644
--- a/tools/gatk/realigner_target_creator.xml
+++ b/tools/gatk/realigner_target_creator.xml
@@ -13,6 +13,7 @@
     -T "RealignerTargetCreator"
     -o "${output_interval}"
     -et "NO_ET" ##ET no phone home
+    ##--num_threads 4 ##hard coded, for now
     ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
     #if $reference_source.reference_source_selector != "history":
         -R "${reference_source.ref_file.fields.path}"
@@ -104,10 +105,10 @@
         <param name="input_bam" type="data" format="bam" label="BAM file">
           <validator type="unspecified_build" />
           <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
-          <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
+          <validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
         </param>
         <param name="ref_file" type="select" label="Using reference genome">
-          <options from_data_table="picard_indexes">
+          <options from_data_table="gatk_picard_indexes">
             <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/>
           </options>
         </param>
diff --git a/tools/gatk/table_recalibration.xml b/tools/gatk/table_recalibration.xml
index 1e4e6da35f6..3c40af6def1 100644
--- a/tools/gatk/table_recalibration.xml
+++ b/tools/gatk/table_recalibration.xml
@@ -13,6 +13,7 @@
     -T "TableRecalibration"
     -o "${output_bam}"
     -et "NO_ET" ##ET no phone home
+    ##--num_threads 4 ##hard coded, for now
     ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
     #if $reference_source.reference_source_selector != "history":
         -R "${reference_source.ref_file.fields.path}"
@@ -118,10 +119,10 @@
         <param name="input_bam" type="data" format="bam" label="BAM file">
           <validator type="unspecified_build" />
           <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
-          <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
+          <validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
         </param>
         <param name="ref_file" type="select" label="Using reference genome">
-          <options from_data_table="picard_indexes">
+          <options from_data_table="gatk_picard_indexes">
             <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/>
           </options>
         </param>
diff --git a/tools/gatk/unified_genotyper.xml b/tools/gatk/unified_genotyper.xml
index ae2cc08c6d1..c9144233946 100644
--- a/tools/gatk/unified_genotyper.xml
+++ b/tools/gatk/unified_genotyper.xml
@@ -136,11 +136,11 @@
             <param name="input_bam" type="data" format="bam" label="BAM file">
               <validator type="unspecified_build" />
               <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
-              <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
+              <validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
             </param>
         </repeat>
         <param name="ref_file" type="select" label="Using reference genome">
-          <options from_data_table="picard_indexes">
+          <options from_data_table="gatk_picard_indexes">
             <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...--> 
           </options>
         </param>
diff --git a/tools/gatk/variant_annotator.xml b/tools/gatk/variant_annotator.xml
index 55802641b2f..6302a0f69b5 100644
--- a/tools/gatk/variant_annotator.xml
+++ b/tools/gatk/variant_annotator.xml
@@ -146,10 +146,10 @@
         <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" help="Not needed for all annotations." >
           <validator type="unspecified_build" />
           <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
-          <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
+          <validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
         </param>
         <param name="ref_file" type="select" label="Using reference genome">
-          <options from_data_table="picard_indexes">
+          <options from_data_table="gatk_picard_indexes">
             <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/>
           </options>
         </param>
diff --git a/tools/gatk/variant_apply_recalibration.xml b/tools/gatk/variant_apply_recalibration.xml
index b66cbf9290d..308eec009b3 100644
--- a/tools/gatk/variant_apply_recalibration.xml
+++ b/tools/gatk/variant_apply_recalibration.xml
@@ -102,7 +102,7 @@
         <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" />
         <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" />
         <param name="ref_file" type="select" label="Using reference genome">
-          <options from_data_table="picard_indexes">
+          <options from_data_table="gatk_picard_indexes">
             <!-- <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> -->
           </options>
         </param>
diff --git a/tools/gatk/variant_combine.xml b/tools/gatk/variant_combine.xml
index 1b51fe17bd6..69b4f7d76e9 100644
--- a/tools/gatk/variant_combine.xml
+++ b/tools/gatk/variant_combine.xml
@@ -114,7 +114,7 @@
           </param>
         </repeat>
         <param name="ref_file" type="select" label="Using reference genome">
-          <options from_data_table="picard_indexes">
+          <options from_data_table="gatk_picard_indexes">
             <!-- <filter type="data_meta" key="dbkey" ref="input_variants.input_variant" column="dbkey"/> -->
           </options>
         </param>
diff --git a/tools/gatk/variant_eval.xml b/tools/gatk/variant_eval.xml
index 25fcf14214a..9ade980aa94 100644
--- a/tools/gatk/variant_eval.xml
+++ b/tools/gatk/variant_eval.xml
@@ -159,7 +159,7 @@
           <param name="input_variant" type="data" format="vcf" label="Input variant file" />
         </repeat>
         <param name="ref_file" type="select" label="Using reference genome">
-          <options from_data_table="picard_indexes">
+          <options from_data_table="gatk_picard_indexes">
             <!-- <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/> -->
           </options>
         </param>
diff --git a/tools/gatk/variant_filtration.xml b/tools/gatk/variant_filtration.xml
index 1e1a79286aa..679c3210211 100644
--- a/tools/gatk/variant_filtration.xml
+++ b/tools/gatk/variant_filtration.xml
@@ -106,7 +106,7 @@
       <when value="cached">
         <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" />
         <param name="ref_file" type="select" label="Using reference genome">
-          <options from_data_table="picard_indexes">
+          <options from_data_table="gatk_picard_indexes">
             <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/>
           </options>
         </param>
diff --git a/tools/gatk/variant_recalibrator.xml b/tools/gatk/variant_recalibrator.xml
index 98c16d3a809..c7159426829 100644
--- a/tools/gatk/variant_recalibrator.xml
+++ b/tools/gatk/variant_recalibrator.xml
@@ -152,7 +152,7 @@
           <param name="input_variants" type="data" format="vcf" label="Variant file to recalibrate" />
         </repeat>
         <param name="ref_file" type="select" label="Using reference genome">
-          <options from_data_table="picard_indexes">
+          <options from_data_table="gatk_picard_indexes">
           <!--  <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> -->
           </options>
         </param>
diff --git a/tools/gatk/variants_validate.xml b/tools/gatk/variants_validate.xml
index e8acb244817..957d9f4f0fc 100644
--- a/tools/gatk/variants_validate.xml
+++ b/tools/gatk/variants_validate.xml
@@ -12,6 +12,7 @@
     -T "ValidateVariants"
     
     -et "NO_ET" ##ET no phone home
+    --num_threads 4 ##hard coded, for now
     ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
     #if $reference_source.reference_source_selector != "history":
         -R "${reference_source.ref_file.fields.path}"
@@ -91,7 +92,7 @@
       <when value="cached">
         <param name="input_variant" type="data" format="vcf" label="Input variant file" />
         <param name="ref_file" type="select" label="Using reference genome">
-          <options from_data_table="picard_indexes">
+          <options from_data_table="gatk_picard_indexes">
             <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/>
           </options>
         </param>
diff --git a/tools/picard/picard_ReorderSam.xml b/tools/picard/picard_ReorderSam.xml
index 71c0059663d..7fb41a573b3 100644
--- a/tools/picard/picard_ReorderSam.xml
+++ b/tools/picard/picard_ReorderSam.xml
@@ -4,7 +4,7 @@
     picard_wrapper.py
       --input=$inputFile
       #if $source.indexSource == "built-in"
-        --ref="${ filter( lambda x: str( x[0] ) == str( $source.ref ), $__app__.tool_data_tables[ 'picard_indexes' ].get_fields() )[0][-1] }"
+        --ref="${source.ref.fields.path}"
       #else
         --ref-file=$refFile
         --species-name=$source.speciesName

From 8b402babb2821985a4aee6ff2163ee1817357ac3 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Mon, 31 Oct 2011 09:49:51 -0400
Subject: [PATCH 117/362] Update SRMA wrapper to use data tables.

---
 tools/sr_mapping/srma_wrapper.py  | 2 +-
 tools/sr_mapping/srma_wrapper.xml | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/tools/sr_mapping/srma_wrapper.py b/tools/sr_mapping/srma_wrapper.py
index 1c6c3f6e90c..5646756aded 100644
--- a/tools/sr_mapping/srma_wrapper.py
+++ b/tools/sr_mapping/srma_wrapper.py
@@ -29,7 +29,7 @@ def __main__():
     parser = optparse.OptionParser()
     parser.add_option( '-r', '--ref', dest='ref', help='The reference genome to index and use' )
     parser.add_option( '-u', '--refUID', dest='refUID', help='The pre-index reference genome unique Identifier' )
-    parser.add_option( '-L', '--refLocations', dest='refLocations', help='The filepath to the srma indices location file' )
+    #parser.add_option( '-L', '--refLocations', dest='refLocations', help='The filepath to the srma indices location file' )
     parser.add_option( '-i', '--input', dest='input', help='The SAM/BAM input file' )
     parser.add_option( '-I', '--inputIndex', dest='inputIndex', help='The SAM/BAM input index file' )
     parser.add_option( '-o', '--output', dest='output', help='The SAM/BAM output file' )
diff --git a/tools/sr_mapping/srma_wrapper.xml b/tools/sr_mapping/srma_wrapper.xml
index ec12a258411..ccb8ab290bc 100644
--- a/tools/sr_mapping/srma_wrapper.xml
+++ b/tools/sr_mapping/srma_wrapper.xml
@@ -4,9 +4,9 @@
     #if $refGenomeSource.refGenomeSource_type == "history":
       --ref=$refGenomeSource.ownFile
     #else:
-      --ref="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.ref ), $__app__.tool_data_tables[ 'srma_indexes' ].get_fields() )[0][-1] }"
+      --ref="${refGenomeSource.ref.fields.path}"
       --refUID=$refGenomeSource.ref
-      --refLocations=${GALAXY_DATA_INDEX_DIR}/srma_index.loc
+      ##--refLocations=${GALAXY_DATA_INDEX_DIR}/srma_index.loc
     #end if
     --input=$input
     --inputIndex=${input.metadata.bam_index}

From 2e11e30091e24c079769c7517420f964aad6665f Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Mon, 31 Oct 2011 14:27:48 -0400
Subject: [PATCH 118/362] Update GATK command line options for
 gatk/indel_realigner.xml

---
 tools/gatk/indel_realigner.xml | 27 ++++++++++++++++++---------
 1 file changed, 18 insertions(+), 9 deletions(-)

diff --git a/tools/gatk/indel_realigner.xml b/tools/gatk/indel_realigner.xml
index 69ce9adac18..27c0ba4b726 100644
--- a/tools/gatk/indel_realigner.xml
+++ b/tools/gatk/indel_realigner.xml
@@ -51,13 +51,16 @@
             #end for
             '
         #end for
-        #if str( $gatk_param_type.input_intervals ) != "None":
-            -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals"
-        #end if
-        #if str( $gatk_param_type.input_exclude_intervals ) != "None":
-            -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals"
-        #end if
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
+            -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
+        #end for
+        
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
+            -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
+        #end for
+
         -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
             -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
@@ -69,10 +72,16 @@
         --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
+        ${gatk_param_type.disable_experimental_low_memory_sharding}
+        ${gatk_param_type.non_deterministic_random_seed}
         '
-        #if str( $gatk_param_type.read_group_black_list ) != "None":
-            -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list"
-        #end if
+        #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
+            #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
+                -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
+            #else
+                -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
+            #end if
+        #end for
     #end if
     #if $reference_source.reference_source_selector == "history":
         -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"

From 1519abb0c6a4cac4369c5ac4aa6e7edcd2c14684 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Mon, 31 Oct 2011 15:31:59 -0400
Subject: [PATCH 119/362] Enhance Trackster VCF support: (a) use ReadPainter
 rather than VariantPainter and (b) provide support for insertions and
 deletions. Pack scripts.

---
 lib/galaxy/datatypes/tabular.py               |   2 +-
 .../visualization/tracks/data_providers.py    |  75 ++++++++---
 static/scripts/packed/trackster.js            |   2 +-
 static/scripts/packed/trackster_ui.js         |   2 +-
 static/scripts/trackster.js                   | 118 ++++++------------
 static/scripts/trackster_ui.js                |   2 +-
 6 files changed, 104 insertions(+), 97 deletions(-)

diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py
index c35ad2e7ac3..e83ed2ce436 100644
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -498,4 +498,4 @@ class Vcf( Tabular ):
         return out
         
     def get_track_type( self ):
-        return "FeatureTrack", {"data": "tabix", "index": "summary_tree"}
+        return "VcfTrack", {"data": "tabix", "index": "summary_tree"}
diff --git a/lib/galaxy/visualization/tracks/data_providers.py b/lib/galaxy/visualization/tracks/data_providers.py
index eb561b62f74..56cdeee230d 100644
--- a/lib/galaxy/visualization/tracks/data_providers.py
+++ b/lib/galaxy/visualization/tracks/data_providers.py
@@ -661,36 +661,81 @@ class IntervalIndexDataProvider( FilterableMixin, TracksDataProvider ):
                 
 class VcfDataProvider( TabixDataProvider ):
     """
-    VCF data provider for the Galaxy track browser.
-
-    Payload format: 
-    [ uid (offset), start, end, ID, reference base(s), alternate base(s), quality score ]
+    VCF data provider. Payload format uses the read format.
     """
 
     col_name_data_attr_mapping = { 'Qual' : { 'index': 6 , 'name' : 'Qual' } }
 
     def process_data( self, iterator, start_val=0, max_vals=sys.maxint, **kwargs ):
+        """
+        Returns a dict with the following attributes:
+            data - a list of variants with the format 
+                [<guid>, <start>, <end>, <name>, cigar, seq] 
+
+            message - error/informative message
+        """
         rval = []
         message = None
         
+        def get_mapping( ref, alt ):
+            """
+            Returns ( offset, new_seq, cigar ) tuple that defines mapping of 
+            alt to ref. Cigar format is an array of [ op_index, length ] pairs 
+            where op_index is the 0-based index into the string "MIDNSHP=X"
+            """
+            
+            cig_ops = "MIDNSHP=X"
+            
+            ref_len = len( ref )
+            alt_len = len( alt )
+            
+            # Substitutions?
+            if ref_len == alt_len:
+                return 0, alt, [ [ cig_ops.find( "M" ), ref_len ] ]
+            
+            # Deletions?
+            alt_in_ref_index = ref.find( alt )
+            if alt_in_ref_index != -1:
+                return alt_in_ref_index, ref[ alt_in_ref_index + 1: ], [ [ cig_ops.find( "D" ), ref_len - alt_len ] ]
+
+            # Insertions?
+            ref_in_alt_index = alt.find( ref )
+            if ref_in_alt_index != -1:
+                return ref_in_alt_index, alt[ ref_in_alt_index + 1: ], [ [ cig_ops.find( "I" ), alt_len - ref_len ] ]
+            
+        # Pack data.
         for count, line in enumerate( iterator ):
             if count < start_val:
                 continue
             if count-start_val >= max_vals:
                 message = ERROR_MAX_VALS % ( "max_vals", "features" )
                 break
-            
+
             feature = line.split()
-            payload = [ hash(line), int(feature[1])-1, int(feature[1]),
-                        # ID: 
-                        feature[2],
-                        # reference base(s):
-                        feature[3],
-                        # alternative base(s)
-                        feature[4],
-                        # phred quality score
-                        float( feature[5] )]
-            rval.append(payload)
+            start = int( feature[1] ) - 1
+            ref = feature[3]
+            alts = feature[4]
+            
+            # HACK? alts == '.' --> monomorphism.
+            if alts == '.':
+                alts = ref
+
+            # Pack variants.
+            for alt in alts.split(","):
+                offset, new_seq, cigar = get_mapping( ref, alt )
+                start += offset
+                end = start + len( new_seq )
+            
+                # Pack line.
+                payload = [ hash( line ), 
+                            start, 
+                            end,
+                            # ID:
+                            feature[2],
+                            cigar,
+                            new_seq,
+                            float( feature[5] )]
+                rval.append(payload)
 
         return { 'data': rval, 'message': message }
 
diff --git a/static/scripts/packed/trackster.js b/static/scripts/packed/trackster.js
index 8f447b2887e..40b076534cf 100644
--- a/static/scripts/packed/trackster.js
+++ b/static/scripts/packed/trackster.js
@@ -1 +1 @@
-var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var m=function(u,t,s){return((u*299)+(t*587)+(s*114))/1000};var e=function(v,u,w,s,r,t){return(Math.max(v,s)-Math.min(v,s))+(Math.max(u,r)-Math.min(u,r))+(Math.max(w,t)-Math.min(w,t))};var g,n,f,k,p,h,q,c,d,b,o,l=false;do{g=Math.random()*16777215;n=g|16711680;f=g|65280;k=g|255;d=m(n,f,k);l=true;for(var j=0;j<a.length;j++){p=a[j];h=p|16711680;q=p|65280;c=p|255;b=m(h,q,c);o=e(n,f,k,h,q,c);if((Math.abs(d-b)<125)||(o<500)){l=false;break}}}while(!l);return"#"+(16777216+g).toString(16).substr(1,6)};var trackster_module=function(f,Z){var q=f("class").extend,t=f("slotting"),N=f("painters");var ag=function(ah,ai){this.document=ah;this.default_font=ai!==undefined?ai:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};q(ag.prototype,{load_pattern:function(ah,al){var ai=this.patterns,aj=this.dummy_context,ak=new Image();ak.src=image_path+al;ak.onload=function(){ai[ah]=aj.createPattern(ak,"repeat")}},get_pattern:function(ah){return this.patterns[ah]},new_canvas:function(){var ah=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ah)}ah.manager=this;return ah}});var o={};var m=function(ah,ai){o[ah.attr("id")]=ai};var n=function(ah,aj,al,ak){al=".group";var ai={};o[ah.attr("id")]=ak;ah.bind("drag",{handle:"."+aj,relative:true},function(au,av){var at=$(this);var ay=$(this).parent(),ap=ay.children(),ar=o[$(this).attr("id")],ao,an,aw,am,aq;an=$(this).parents(al);if(an.length!==0){aw=an.position().top;am=aw+an.outerHeight();if(av.offsetY<aw){$(this).insertBefore(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable_before(ar,ax);return}else{if(av.offsetY>am){$(this).insertAfter(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable(ar);return}}}an=null;for(aq=0;aq<ap.length;aq++){ao=$(ap.get(aq));aw=ao.position().top;am=aw+ao.outerHeight();if(ao.is(al)&&this!==ao.get(0)&&av.offsetY>=aw&&av.offsetY<=am){if(av.offsetY-aw<am-av.offsetY){ao.find(".content-div").prepend(this)}else{ao.find(".content-div").append(this)}if(ar.container){ar.container.remove_drawable(ar)}o[ao.attr("id")].add_drawable(ar);return}}for(aq=0;aq<ap.length;aq++){if(av.offsetY<$(ap.get(aq)).position().top){break}}if(aq===ap.length){if(this!==ap.get(aq-1)){ay.append(this);o[ay.attr("id")].move_drawable(ar,aq)}}else{if(this!==ap.get(aq)){$(this).insertBefore(ap.get(aq));o[ay.attr("id")].move_drawable(ar,(av.deltaY>0?aq-1:aq))}}}).bind("dragstart",function(){ai["border-top"]=ah.css("border-top");ai["border-bottom"]=ah.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ai)})};Z.moveable=n;var af=16,I=9,F=20,U=I+2,A=100,K=12000,S=200,D=5,w=10,M=5000,x=100,p="There was an error in indexing this dataset. ",L="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",u="Currently indexing... please wait",y="Tool cannot be rerun: ",a="Loading data...",aa="Ready for display",d=10,v=5,C=5;function ab(ai,ah){if(!ah){ah=0}var aj=Math.pow(10,ah);return Math.round(ai*aj)/aj}var c=function(ah){this.num_elements=ah;this.clear()};q(c.prototype,{get:function(ai){var ah=this.key_ary.indexOf(ai);if(ah!==-1){if(this.obj_cache[ai].stale){this.key_ary.splice(ah,1);delete this.obj_cache[ai]}else{this.move_key_to_end(ai,ah)}}return this.obj_cache[ai]},set:function(ai,aj){if(!this.obj_cache[ai]){if(this.key_ary.length>=this.num_elements){var ah=this.key_ary.shift();delete this.obj_cache[ah]}this.key_ary.push(ai)}this.obj_cache[ai]=aj;return aj},move_key_to_end:function(ai,ah){this.key_ary.splice(ah,1);this.key_ary.push(ai)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var T=function(ai,ah,aj){c.call(this,ai);this.track=ah;this.subset=(aj!==undefined?aj:true)};q(T.prototype,c.prototype,{load_data:function(aq,al,ao,ai,an){var ap=this.track.view.chrom,ak={chrom:ap,low:aq,high:al,mode:ao,resolution:ai,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ak,an);if(this.track.filters_manager){var ar=[];var ah=this.track.filters_manager.filters;for(var am=0;am<ah.length;am++){ar[ar.length]=ah[am].name}ak.filter_cols=JSON.stringify(ar)}var aj=this;return $.getJSON(this.track.data_url,ak,function(at){aj.set_data(aq,al,ao,at)})},get_data:function(ah,al,am,ai,ak){var aj=this.get_data_from_cache(ah,al,am);if(aj){return aj}aj=this.load_data(ah,al,am,ai,ak);this.set_data(ah,al,am,aj);return aj},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ap,ak,ao,aj,an,al){var aq=this.get_data_from_cache(ap,ak,ao);if(!aq){console.log("ERROR: no current data for: ",this.track,ap,ak,ao,aj,an);return}aq.stale=true;var ai=ap;if(al===this.DEEP_DATA_REQ){$.extend(an,{start_val:aq.data.length+1})}else{if(al===this.BROAD_DATA_REQ){ai=(aq.max_high?aq.max_high:aq.data[aq.data.length-1][2])+1}}var ah=this,am=this.load_data(ai,ak,ao,aj,an);new_data_available=$.Deferred();this.set_data(ap,ak,ao,new_data_available);$.when(am).then(function(ar){if(ar.data){ar.data=aq.data.concat(ar.data);if(ar.max_low){ar.max_low=aq.max_low}if(ar.message){ar.message=ar.message.replace(/[0-9]+/,ar.data.length)}}ah.set_data(ap,ak,ao,ar);new_data_available.resolve(ar)});return new_data_available},get_data_from_cache:function(ah,ai,aj){return this.get(this.gen_key(ah,ai,aj))},set_data:function(ai,aj,ak,ah){return this.set(this.gen_key(ai,aj,ak),ah)},gen_key:function(ah,aj,ak){var ai=ah+"_"+aj+"_"+ak;return ai},split_key:function(ah){return ah.split("_")}});var J=function(ai,ah,aj){T.call(this,ai,ah,aj)};q(J.prototype,T.prototype,c.prototype,{load_data:function(ah,ak,al,ai,aj){if(ai>1){return{data:null}}return T.prototype.load_data.call(this,ah,ak,al,ai,aj)}});var r=function(ak,ai,ah,aj,al){this.name=ak;this.view=ai;this.container=ah;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak}],saved_values:aj,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=al;this.is_overview=false};q(r.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},update_track_icons:function(){},set_name:function(ah){this.old_name=this.name;this.name=ah;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var z=function(al,ak,ai,ah,aj,am){r.call(this,ak,ai,ah,aj,am);this.obj_type=al;this.drawables=[]};q(z.prototype,r.prototype,{init:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah].init()}},_draw:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah]._draw()}},to_json:function(){var ai=[];for(var ah=0;ah<this.drawables.length;ah++){ai.push(this.drawables[ah].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ai}},add_drawable:function(ah){this.drawables.push(ah);ah.container=this},add_drawable_before:function(aj,ah){var ai=this.drawables.indexOf(ah);if(ai!=-1){this.drawables.splice(ai,0,aj);return true}return false},remove_drawable:function(ai){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);ai.container=null;return true}return false},move_drawable:function(ai,aj){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);this.drawables.splice(aj,0,ai);return true}return false}});var R=function(ak,ai,ah,aj){z.call(this,"DrawableGroup",ak,ai,ah,aj,"group-handle");if(!R.id_counter){R.id_counter=0}var al=R.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+al).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+al+"_content_div").appendTo(this.container_div);m(this.container_div,this);m(this.content_div,this);n(this.container_div,this.drag_handle_class,".group",this);this.update_track_icons()};q(R.prototype,r.prototype,z.prototype,{update_track_icons:function(){var ai=this;var ah={};ah["Edit configuration"]=function(){var al=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aj=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(am){if((am.keyCode||am.which)===27){al()}else{if((am.keyCode||am.which)===13){aj()}}};$(window).bind("keypress.check_enter_esc",ak);show_modal("Configure Group",ai.config.build_form(),{Cancel:al,OK:aj})};ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)}});var ae=function(ah,ak,aj,ai){z.call(this,"View");this.container=ah;this.chrom=null;this.vis_id=aj;this.dbkey=ai;this.title=ak;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ag(ah.get(0).ownerDocument);this.reset()};q(ae.prototype,z.prototype,{init:function(){var aj=this.container,ah=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aj);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;m(this.viewport_container,ah);this.intro_div=$("<div/>").addClass("intro");var ak=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ai=function(al){if(al.type==="focusout"||(al.keyCode||al.which)===13||(al.keyCode||al.which)===27){if((al.keyCode||al.which)!==27){ah.go_to($(this).val())}$(this).hide();$(this).val("");ah.location_span.show();ah.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ai).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ah.location_span.hide();ah.chrom_select.hide();ah.nav_input.val(ah.chrom+":"+ah.low+"-"+ah.high);ah.nav_input.css("display","inline-block");ah.nav_input.select();ah.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ah.zoom_out();ah.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.browser_content_div.click(function(al){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("<div />").css({height:ah.browser_content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,{content_div:this.top_labeltrack}));this.add_label_track(new ad(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new B(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(am,ai,ao){if(!am||am==="None"){return}var aj=this;if(am==="previous"){aj.load_chroms({low:this.chrom_start_index-x});return}if(am==="next"){aj.load_chroms({low:this.chrom_start_index+x});return}var an=$.grep(aj.chrom_data,function(ap,aq){return ap.chrom===am})[0];if(an===undefined){aj.load_chroms({chrom:am},function(){aj.change_chrom(am,ai,ao)});return}else{if(am!==aj.chrom){aj.chrom=am;aj.chrom_select.val(aj.chrom);aj.max_high=an.len-1;aj.reset();aj.request_redraw(true);for(var al=0,ah=aj.drawables.length;al<ah;al++){var ak=aj.drawables[al];if(ak.init){ak.init()}}}if(ai!==undefined&&ao!==undefined){aj.low=Math.max(ai,0);aj.high=Math.min(ao,aj.max_high)}aj.reset_overview();aj.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){z.prototype.add_drawable.call(this,ah);ah.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;ah.init();this.label_tracks.push(ah)},remove_drawable:function(aj,ai){z.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.drawables),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(D,Math.ceil(Math.log((this.high-this.low)/S)/Math.log(D)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(aj){if(this.overview_drawable){if(this.overview_drawable.dataset_id===aj.dataset_id){return}this.overview_viewport.find(".track").remove()}var ai=aj.copy({content_div:this.overview_viewport}),ah=this;ai.header_div.hide();ai.is_overview=true;ah.overview_drawable=ai;this.overview_drawable.postdraw_actions=function(){ah.overview_highlight.show().height(ah.overview_drawable.content_div.height());ah.overview_viewport.height(ah.overview_drawable.content_div.height()+ah.overview_box.outerHeight());ah.overview_close.show();ah.resize_window()};this.overview_drawable.init();ah.has_changes=true},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new P(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},al=this.track,aj=ai.tool_id+al.tool_region_and_parameters_str(ai.chrom,ai.low,ai.high),ah,am;if(al.container===view){var ak=new R(this.name,this.track.view,this.track.container);al.container.add_drawable(ak);al.container.remove_drawable(al);ak.add_drawable(al);al.container_div.appendTo(ak.content_div);ah=ak}else{ah=al.container}if(al instanceof e){am=new W(aj,view,ah,"hda");am.change_mode(al.mode);ah.add_drawable(am)}am.content_div.text("Starting job.");this.run(ai,am,function(an){am.dataset_id=an.dataset_id;am.content_div.text("Running job.");am.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(L)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(y+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var P=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){P.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var X=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};q(X.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=ah[this.index];return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(at,aA){this.track=at;this.filters=[];for(var av=0;av<aA.length;av++){var aw=aA[av],aB=aw.name,ah=aw.type,aj=aw.index,az=aw.tool_id,ay=aw.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[av]=new X(aB,aj,az,ay)}else{console.log("ERROR: unsupported filter: ",aB,ah)}}var ak=function(aC,aD,aE){aC.click(function(){var aF=aD.text();max=parseFloat(aE.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aE.slider("option","values")){input_size=2*input_size+1;multi_value=true}aD.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aF).appendTo(aD).focus().select().click(function(aG){aG.stopPropagation()}).blur(function(){$(this).remove();aD.text(aF)}).keyup(function(aK){if(aK.keyCode===27){$(this).trigger("blur")}else{if(aK.keyCode===13){var aI=aE.slider("option","min"),aG=aE.slider("option","max"),aJ=function(aL){return(isNaN(aL)||aL>aG||aL<aI)},aH=$(this).val();if(!multi_value){aH=parseFloat(aH);if(aJ(aH)){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}else{aH=aH.split("-");aH=[parseFloat(aH[0]),parseFloat(aH[1])];if(aJ(aH[0])||aJ(aH[1])){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}aE.slider((multi_value?"values":"value"),aH)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aC){aC.stopPropagation()}).click(function(aC){aC.stopPropagation()}).bind("dblclick",function(aC){aC.stopPropagation()}).bind("keydown",function(aC){aC.stopPropagation()});var ax=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aF,aH){aH.container=$("<div/>").addClass("filter-row slider-row").appendTo(ax);var aG=$("<div/>").addClass("elt-label").appendTo(aH.container);var aE=$("<span/>").addClass("slider-name").text(aH.name+"  ").appendTo(aG);var aD=$("<span/>");var aJ=$("<span/>").addClass("slider-value").appendTo(aG).append("[").append(aD).append("]");var aC=$("<div/>").addClass("slider").appendTo(aH.container);aH.control_element=$("<div/>").attr("id",aH.name+"-filter-control").appendTo(aC);var aI=[0,0];aH.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aL,aM){var aK=aM.values;aD.text(aK[0]+"-"+aK[1]);aH.low=aK[0];aH.high=aK[1];ap.track.request_draw(true,true)},change:function(aK,aL){aH.control_element.slider("option","slide").call(aH.control_element,aK,aL)}});aH.slider=aH.control_element;aH.slider_label=aD;ak(aJ,aD,aH.control_element);$("<div style='clear: both;'/>").appendTo(aH.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(ax);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var ai=this;ao.click(function(){ai.run_on_dataset()})}var ar=$("<div/>").addClass("display-controls").appendTo(this.parent_div),au,an,aq,al={Transparency:function(aC){ap.alpha_filter=aC},Height:function(aC){ap.height_filter=aC}};$.each(al,function(aE,aD){au=$("<div/>").addClass("filter-row").appendTo(ar),an=$("<span/>").addClass("elt-label").text(aE+":").appendTo(au),aq=$("<select/>").attr("name",aE+"_dropdown").css("float","right").appendTo(au);$("<option/>").attr("value",-1).text("== None ==").appendTo(aq);for(var aC=0;aC<ap.filters.length;aC++){$("<option/>").attr("value",aC).text(ap.filters[aC].name).appendTo(aq)}aq.change(function(){$(this).children("option:selected").each(function(){var aF=parseInt($(this).val());al[aE]((aF>=0?ap.filters[aF]:null));ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(au)});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var E=function(ah,ai){N.Scaler.call(this,ai);this.filter=ah};E.prototype.gen_val=function(ah){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var H=function(ah){this.track=ah.track;this.params=ah.params;this.values={};this.restore_values((ah.saved_values?ah.saved_values:{}));this.onchange=ah.onchange};q(H.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(ah,ak,aj,ai,al){this.track=ah;this.index=ak;this.low=ak*S*aj;this.high=(ak+1)*S*aj;this.resolution=aj;this.canvas=$("<div class='track-tile'/>").append(ai);this.data=al;this.stale=false};b.prototype.predisplay_actions=function(){};var l=function(ah,ak,aj,ai,al,am){b.call(this,ah,ak,aj,ai,al);this.max_val=am};q(l.prototype,b.prototype);var Q=function(ah,al,ak,aj,an,ao,am,ai){b.call(this,ah,al,ak,aj,an);this.mode=ao;this.message=am;this.feature_mapper=ai};q(Q.prototype,b.prototype);Q.prototype.predisplay_actions=function(){var ai=this,ah={};if(ai.mode!=="Pack"){return}$(this.canvas).mousemove(function(au){var ao=$(this).offset(),at=au.pageX-ao.left,ar=au.pageY-ao.top,ay=ai.feature_mapper.get_feature_data(at,ar),ap=(ay?ay[0]:null);$(this).siblings(".feature-popup").each(function(){if(!ap||$(this).attr("id")!==ap.toString()){$(this).remove()}});if(ay){var ak=ah[ap];if(!ak){var ap=ay[0],av={name:ay[3],start:ay[1],end:ay[2],strand:ay[4]},an=ai.track.filters_manager.filters,am;for(var aq=0;aq<an.length;aq++){am=an[aq];av[am.name]=ay[am.index]}var ak=$("<div/>").attr("id",ap).addClass("feature-popup"),ax,aw,az=$("<table/>").appendTo(ak),aA;for(ax in av){aw=av[ax];aA=$("<tr/>").appendTo(az);$("<th/>").appendTo(aA).text(ax);$("<td/>").attr("align","left").appendTo(aA).text(typeof(aw)=="number"?ab(aw,2):aw)}ah[ap]=ak}ak.appendTo($(ai.canvas).parent());var al=at+parseInt(ai.canvas.css("left"))+7,aj=ar+parseInt(ai.canvas.css("top"))+7;ak.css("left",al+"px").css("top",aj+"px")}else{if(!au.isPropagationStopped()){au.stopPropagation();$(this).siblings().each(function(){$(this).trigger(au)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var j=function(ak,at,al,ao,au,aj,ai){r.call(this,ak,at,al,{},"draghandle");this.data_url=(aj?aj:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ai?ai:M);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.id=j.id_counter++;this.container_div=$("<div />").addClass("track").attr("id","track_"+this.id).css("position","relative");if(ao){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div/>").addClass("track-name").appendTo(this.header_div).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());this.icons_div=$("<div/>").css("float","left").appendTo(this.header_div).hide();this.settings_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Edit settings").addClass("icon-button settings-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.overview_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Set as overview").addClass("icon-button overview-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.filters_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Filters").addClass("icon-button filters-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.tools_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Tools").addClass("icon-button tools-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.remove_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Remove").addClass("icon-button remove-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);var am=this;this.header_div.dblclick(function(av){av.stopPropagation()});this.settings_icon.click(function(){var ax=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},av=function(){am.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},aw=function(ay){if((ay.keyCode||ay.which)===27){ax()}else{if((ay.keyCode||ay.which)===13){av()}}};$(window).bind("keypress.check_enter_esc",aw);show_modal("Configure Track",am.config.build_form(),{Cancel:ax,OK:av})});this.overview_icon.click(function(){am.view.set_overview(am)});this.filters_icon.click(function(){am.filters_div.toggle();am.filters_manager.reset_filters()});this.tools_icon.click(function(){am.dynamic_tool_div.toggle();if(am.dynamic_tool_div.is(":visible")){am.set_name(am.name+am.tool_region_and_parameters_str())}else{am.revert_name()}$(".tipsy").remove()});this.remove_icon.click(function(){$(".tipsy").remove();am.remove()});if(am.display_modes!==undefined){if(am.mode_div===undefined){am.mode_div=$("<div class='right-float menubutton popup' />").appendTo(am.header_div);var an=(am.config&&am.config.values.mode?am.config.values.mode:am.display_modes[0]);am.mode=an;am.mode_div.text(an);var ah={};for(var ap=0,ar=am.display_modes.length;ap<ar;ap++){var aq=am.display_modes[ap];ah[aq]=function(av){return function(){am.change_mode(av)}}(aq)}make_popupmenu(am.mode_div,ah)}else{am.mode_div.hide()}this.header_div.append($("<div/>").css("clear","both"));this.container_div.hover(function(){am.icons_div.show()},function(){am.icons_div.hide()})}}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Y){return"ReadTrack"}else{if(this instanceof W){return"ToolDataFeatureTrack"}else{if(this instanceof V){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(L)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(G)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.update_track_icons()}ah.content_div.text(aa);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}});this.update_track_icons()},predraw_init:function(){}});var O=function(ak,aj){var ai=this,ah=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=new ac(this,(ak!==undefined?ak:{}));this.filters_available=false;this.filters_visible=false;this.tool=(aj!==undefined&&obj_length(aj)>0?new s(this,aj):undefined);if(this.header_div){if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}};q(O.prototype,r.prototype,j.prototype,{copy:function(ah){return new this.constructor(this.name,this.view,ah,this.hda_ldda,this.dataset_id,this.prefs,this.filters,this.tool)},to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw();return ah},update_track_icons:function(){var ah=this;if(ah.filters_available>0){ah.filters_icon.show()}else{ah.filters_icon.hide()}if(ah.tool){ah.tools_icon.show()}else{ah.tools_icon.hide()}},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof B)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(this.is_overview){aq=this.view.max_low;an=this.view.max_high;am=Math.pow(D,Math.ceil(Math.log((view.max_high-view.max_low)/S)/Math.log(D)));av=ak/(view.max_high-view.max_low)}if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/S);var ap=true;var at=[];var ah=0;while((ai*S*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",F)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*S*an,ax=ap+S*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);if(aq!==undefined){al.tile_cache.set(at,aq);al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw(false,false,false,al)});return null},show_tile:function(an,ap,aq){var aj=this,ai=an.canvas,am=ai;if(an.message){var ar=$("<div/>"),ao=$("<div/>").addClass("tile-message").text(an.message).css({height:F-1,width:an.canvas.width}).appendTo(ar),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ao),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ao);ar.append(ai);am=ar;al.click(function(){an.stale=true;aj.data_manager.get_more_data(an.low,an.high,aj.mode,an.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(at){at.stopPropagation()});ah.click(function(){an.stale=true;aj.data_manager.get_more_data(an.low,an.high,aj.mode,an.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(at){at.stopPropagation()})}an.predisplay_actions();var ak=(an.low-(this.is_overview?this.view.max_low:this.view.low))*aq;if(this.left_offset){ak-=this.left_offset}am.css({position:"absolute",top:0,left:ak,height:""});ap.append(am);aj.max_height=Math.max(aj.max_height,am.height());aj.content_div.css("height",aj.max_height+"px");ap.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*S*ai,al=S*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ai,ah){j.call(this,"label",ai,ah,false,{});this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{init:function(){this.enabled=true},_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var B=function(ah){j.call(this,"reference",ah,{content_div:ah.top_labeltrack},false,{});O.call(this);ah.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ah.dbkey};this.data_manager=new J(C,this,false);this.tile_cache=new c(v)};q(B.prototype,r.prototype,O.prototype,{init:function(){this.enabled=true},draw_tile:function(ar,an,am,ai,at){var al=this,aj=S*am;if(at>this.view.canvas_manager.char_width_px){if(ar.data===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(al,ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(am,ak,aj,an,ah,al){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,am,ak,aj,al);O.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=an;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new T(C,this);this.tile_cache=new c(v);this.left_offset=0;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:am},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:al,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.dataset_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.dataset_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};q(k.prototype,r.prototype,O.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this;ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(ai){ah.container_div.addClass("line-track");var ak=ai.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=ak.min;ah.prefs.max_value=ak.max;$("#track_"+ah.dataset_id+"_minval").val(ah.prefs.min_value);$("#track_"+ah.dataset_id+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=ak.total_frequency;ah.container_div.find(".yaxislabel").remove();var al=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_minval").text(ab(ah.prefs.min_value,3));var aj=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_maxval").text(ab(ah.prefs.max_value,3));aj.css({position:"absolute",top:"24px",left:"10px"});aj.prependTo(ah.container_div);al.css({position:"absolute",bottom:"2px",left:"10px"});al.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new N.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(this.track,aj,al,ak,au.data)}});var e=function(ah,an,ai,am,ap,ao,ak,al){var aj=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];j.call(this,ah,an,ai,true,ao);O.call(this,ak,al);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){aj.set_name(aj.prefs.name);aj.tile_cache.clear();aj.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=am;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new T(20,this);this.left_offset=200;this.painter=N.LinkedFeaturePainter};q(e.prototype,r.prototype,O.prototype,{postdraw_actions:function(ax,ah,ay,aw){O.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.update_track_icons()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",A,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aD,aH,ar,ak){var aA=this,am=aA._get_tile_bounds(aH,aD),aK=am[0],ai=am[1],ay=ai-aK,aB=Math.ceil(ay*ar),aQ=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"||aA.is_overview){az="no_detail"}else{var aP=aw.data;if(this.view.high-this.view.low>K){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aB+al;aj.height=an+U;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aK,ai,200);if(aw.max){at.max=aw.max}aw=at}var aM=new N.SummaryTreePainter(aw,aK,ai,this.prefs);var aC=aj.getContext("2d");aC.translate(al,U);aM.draw(aC,aB,an);return new l(aA,aH,aD,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aE=0,aG=aw.data.length;aE<aG;aE++){var ao=aw.data[aE];var aF=false;var av;for(var aJ=0,aO=au.length;aJ<aO;aJ++){av=au[aJ];av.update_attrs(ao);if(!av.keep(ao)){aF=true;break}}if(!aF){aq.push(ao)}}}var aN=(this.filters_manager.alpha_filter?new E(this.filters_manager.alpha_filter):null);var aL=(this.filters_manager.height_filter?new E(this.filters_manager.height_filter):null);var aM=new (this.painter)(aq,aK,ai,this.prefs,az,aN,aL,ak);var an=Math.max(af,aM.get_required_height(ap));var aj=this.view.canvas_manager.new_canvas();var aI=null;aj.width=aB+al;aj.height=an;var aC=aj.getContext("2d");aC.fillStyle=this.prefs.block_color;aC.font=aC.canvas.manager.default_font;aC.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aw.data){aC.translate(al,0);aI=aM.draw(aC,aB,an,ax);aI.translation=-al}return new Q(aA,aH,aD,aj,aw.data,az,aw.message,aI)}});var V=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.painter=N.VariantPainter};q(V.prototype,r.prototype,O.prototype,e.prototype);var Y=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ak,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=N.ReadPainter;this.update_track_icons()};q(Y.prototype,r.prototype,O.prototype,e.prototype);var 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O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var 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T=W[0],aj=W[1],ab=W[2],R=W[3],ac=Math.floor(Math.max(0,(aj-P)*al)),O=Math.ceil(Math.min(z,Math.max(0,(ab-P)*al))),aa=ac,am=O,Z=(E==="Dense"?0:(0+I))*an,M,af,S=null,ap=null,C=this.prefs.block_color,ae=this.prefs.label_color;N.globalAlpha=this.alpha_scaler.gen_val(W);if(E=="Dense"){I=1}if(E==="no_detail"){N.fillStyle=C;N.fillRect(ac,Z+5,O-ac,g)}else{var L=W[4],Y=W[5],ad=W[6],D=W[7];if(Y&&ad){S=Math.floor(Math.max(0,(Y-P)*al));ap=Math.ceil(Math.min(z,Math.max(0,(ad-P)*al)))}var ak,U;if(E==="Squish"||E==="Dense"){ak=1;U=f}else{ak=5;U=a}if(!D){if(W.strand){if(W.strand==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand_inv")}else{if(W.strand==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand_inv")}}}else{N.fillStyle=C}N.fillRect(ac,Z,O-ac,U)}else{var K,V;if(E==="Squish"||E==="Dense"){N.fillStyle=h;K=Z+Math.floor(f/2)+1;V=1}else{if(L){var K=Z;var 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+var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var m=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(u,t,v,r,i,s){return(Math.max(u,r)-Math.min(u,r))+(Math.max(t,i)-Math.min(t,i))+(Math.max(v,s)-Math.min(v,s))};var g,n,f,k,p,h,q,c,d,b,o,l=false;do{g=Math.random()*16777215;n=g|16711680;f=g|65280;k=g|255;d=m(n,f,k);l=true;for(var j=0;j<a.length;j++){p=a[j];h=p|16711680;q=p|65280;c=p|255;b=m(h,q,c);o=e(n,f,k,h,q,c);if((Math.abs(d-b)<125)||(o<500)){l=false;break}}}while(!l);return"#"+(16777216+g).toString(16).substr(1,6)};var trackster_module=function(f,Y){var p=f("class").extend,s=f("slotting"),M=f("painters");var af=function(ag,ah){this.document=ag;this.default_font=ah!==undefined?ah:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};p(af.prototype,{load_pattern:function(ag,ak){var ah=this.patterns,ai=this.dummy_context,aj=new Image();aj.src=image_path+ak;aj.onload=function(){ah[ag]=ai.createPattern(aj,"repeat")}},get_pattern:function(ag){return this.patterns[ag]},new_canvas:function(){var ag=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ag)}ag.manager=this;return ag}});var n={};var l=function(ag,ah){n[ag.attr("id")]=ah};var m=function(ag,ai,ak,aj){ak=".group";var ah={};n[ag.attr("id")]=aj;ag.bind("drag",{handle:"."+ai,relative:true},function(at,au){var ar=$(this);var ax=$(this).parent(),ao=ax.children(),aq=n[$(this).attr("id")],an,am,av,al,ap;am=$(this).parents(ak);if(am.length!==0){av=am.position().top;al=av+am.outerHeight();if(au.offsetY<av){$(this).insertBefore(am);var aw=n[am.attr("id")];aw.remove_drawable(aq);aw.container.add_drawable_before(aq,aw);return}else{if(au.offsetY>al){$(this).insertAfter(am);var aw=n[am.attr("id")];aw.remove_drawable(aq);aw.container.add_drawable(aq);return}}}am=null;for(ap=0;ap<ao.length;ap++){an=$(ao.get(ap));av=an.position().top;al=av+an.outerHeight();if(an.is(ak)&&this!==an.get(0)&&au.offsetY>=av&&au.offsetY<=al){if(au.offsetY-av<al-au.offsetY){an.find(".content-div").prepend(this)}else{an.find(".content-div").append(this)}if(aq.container){aq.container.remove_drawable(aq)}n[an.attr("id")].add_drawable(aq);return}}for(ap=0;ap<ao.length;ap++){if(au.offsetY<$(ao.get(ap)).position().top){break}}if(ap===ao.length){if(this!==ao.get(ap-1)){ax.append(this);n[ax.attr("id")].move_drawable(aq,ap)}}else{if(this!==ao.get(ap)){$(this).insertBefore(ao.get(ap));n[ax.attr("id")].move_drawable(aq,(au.deltaY>0?ap-1:ap))}}}).bind("dragstart",function(){ah["border-top"]=ag.css("border-top");ah["border-bottom"]=ag.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ah)})};Y.moveable=m;var ae=16,H=9,E=20,T=H+2,z=100,J=12000,R=200,C=5,v=10,L=5000,w=100,o="There was an error in indexing this dataset. ",K="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",F="No data for this chrom/contig.",t="Currently indexing... please wait",x="Tool cannot be rerun: ",a="Loading data...",Z="Ready for display",d=10,u=5,B=5;function aa(ah,ag){if(!ag){ag=0}var ai=Math.pow(10,ag);return Math.round(ah*ai)/ai}var c=function(ag){this.num_elements=ag;this.clear()};p(c.prototype,{get:function(ah){var ag=this.key_ary.indexOf(ah);if(ag!==-1){if(this.obj_cache[ah].stale){this.key_ary.splice(ag,1);delete this.obj_cache[ah]}else{this.move_key_to_end(ah,ag)}}return this.obj_cache[ah]},set:function(ah,ai){if(!this.obj_cache[ah]){if(this.key_ary.length>=this.num_elements){var ag=this.key_ary.shift();delete this.obj_cache[ag]}this.key_ary.push(ah)}this.obj_cache[ah]=ai;return ai},move_key_to_end:function(ah,ag){this.key_ary.splice(ag,1);this.key_ary.push(ah)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var S=function(ah,ag,ai){c.call(this,ah);this.track=ag;this.subset=(ai!==undefined?ai:true)};p(S.prototype,c.prototype,{load_data:function(ap,ak,an,ah,am){var ao=this.track.view.chrom,aj={chrom:ao,low:ap,high:ak,mode:an,resolution:ah,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(aj,am);if(this.track.filters_manager){var aq=[];var ag=this.track.filters_manager.filters;for(var al=0;al<ag.length;al++){aq[aq.length]=ag[al].name}aj.filter_cols=JSON.stringify(aq)}var ai=this;return $.getJSON(this.track.data_url,aj,function(ar){ai.set_data(ap,ak,an,ar)})},get_data:function(ag,ak,al,ah,aj){var ai=this.get_data_from_cache(ag,ak,al);if(ai){return ai}ai=this.load_data(ag,ak,al,ah,aj);this.set_data(ag,ak,al,ai);return ai},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ao,aj,an,ai,am,ak){var ap=this.get_data_from_cache(ao,aj,an);if(!ap){console.log("ERROR: no current data for: ",this.track,ao,aj,an,ai,am);return}ap.stale=true;var ah=ao;if(ak===this.DEEP_DATA_REQ){$.extend(am,{start_val:ap.data.length+1})}else{if(ak===this.BROAD_DATA_REQ){ah=(ap.max_high?ap.max_high:ap.data[ap.data.length-1][2])+1}}var ag=this,al=this.load_data(ah,aj,an,ai,am);new_data_available=$.Deferred();this.set_data(ao,aj,an,new_data_available);$.when(al).then(function(aq){if(aq.data){aq.data=ap.data.concat(aq.data);if(aq.max_low){aq.max_low=ap.max_low}if(aq.message){aq.message=aq.message.replace(/[0-9]+/,aq.data.length)}}ag.set_data(ao,aj,an,aq);new_data_available.resolve(aq)});return new_data_available},get_data_from_cache:function(ag,ah,ai){return this.get(this.gen_key(ag,ah,ai))},set_data:function(ah,ai,aj,ag){return this.set(this.gen_key(ah,ai,aj),ag)},gen_key:function(ag,ai,aj){var ah=ag+"_"+ai+"_"+aj;return ah},split_key:function(ag){return ag.split("_")}});var I=function(ah,ag,ai){S.call(this,ah,ag,ai)};p(I.prototype,S.prototype,c.prototype,{load_data:function(ag,aj,ak,ah,ai){if(ah>1){return{data:null}}return S.prototype.load_data.call(this,ag,aj,ak,ah,ai)}});var q=function(aj,ah,ag,ai,ak){this.name=aj;this.view=ah;this.container=ag;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:aj}],saved_values:ai,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ak;this.is_overview=false};p(q.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},update_track_icons:function(){},set_name:function(ag){this.old_name=this.name;this.name=ag;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var y=function(ak,aj,ah,ag,ai,al){q.call(this,aj,ah,ag,ai,al);this.obj_type=ak;this.drawables=[]};p(y.prototype,q.prototype,{init:function(){for(var ag=0;ag<this.drawables.length;ag++){this.drawables[ag].init()}},_draw:function(){for(var ag=0;ag<this.drawables.length;ag++){this.drawables[ag]._draw()}},to_json:function(){var ah=[];for(var ag=0;ag<this.drawables.length;ag++){ah.push(this.drawables[ag].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ah}},add_drawable:function(ag){this.drawables.push(ag);ag.container=this},add_drawable_before:function(ai,ag){var ah=this.drawables.indexOf(ag);if(ah!=-1){this.drawables.splice(ah,0,ai);return true}return false},remove_drawable:function(ah){var ag=this.drawables.indexOf(ah);if(ag!=-1){this.drawables.splice(ag,1);ah.container=null;return true}return false},move_drawable:function(ah,ai){var ag=this.drawables.indexOf(ah);if(ag!=-1){this.drawables.splice(ag,1);this.drawables.splice(ai,0,ah);return true}return false}});var Q=function(aj,ah,ag,ai){y.call(this,"DrawableGroup",aj,ah,ag,ai,"group-handle");if(!Q.id_counter){Q.id_counter=0}var ak=Q.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+ak).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+ak+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.update_track_icons()};p(Q.prototype,q.prototype,y.prototype,{update_track_icons:function(){var ah=this;var ag={};ag["Edit configuration"]=function(){var ak=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ai=function(){ah.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},aj=function(al){if((al.keyCode||al.which)===27){ak()}else{if((al.keyCode||al.which)===13){ai()}}};$(window).bind("keypress.check_enter_esc",aj);show_modal("Configure Group",ah.config.build_form(),{Cancel:ak,OK:ai})};ag.Remove=function(){ah.remove()};make_popupmenu(ah.name_div,ag)}});var ad=function(ag,aj,ai,ah){y.call(this,"View");this.container=ag;this.chrom=null;this.vis_id=ai;this.dbkey=ah;this.title=aj;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new af(ag.get(0).ownerDocument);this.reset()};p(ad.prototype,y.prototype,{init:function(){var ai=this.container,ag=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ai);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ai);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ai);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,ag);this.intro_div=$("<div/>").addClass("intro");var aj=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ah=function(ak){if(ak.type==="focusout"||(ak.keyCode||ak.which)===13||(ak.keyCode||ak.which)===27){if((ak.keyCode||ak.which)!==27){ag.go_to($(this).val())}$(this).hide();$(this).val("");ag.location_span.show();ag.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ah).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ag.location_span.hide();ag.chrom_select.hide();ag.nav_input.val(ag.chrom+":"+ag.low+"-"+ag.high);ag.nav_input.css("display","inline-block");ag.nav_input.select();ag.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ag.zoom_out();ag.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ag.zoom_in();ag.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ag.change_chrom(ag.chrom_select.val())});this.browser_content_div.click(function(ak){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ak){ag.zoom_in(ak.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ak,al){this.current_x=al.offsetX}).bind("drag",function(ak,am){var an=am.offsetX-this.current_x;this.current_x=am.offsetX;var al=Math.round(an/ag.viewport_container.width()*(ag.max_high-ag.max_low));ag.move_delta(-al)});this.overview_close.click(function(){ag.reset_overview()});this.viewport_container.bind("draginit",function(ak,al){if(ak.clientX>ag.viewport_container.width()-16){return false}}).bind("dragstart",function(ak,al){al.original_low=ag.low;al.current_height=ak.clientY;al.current_x=al.offsetX}).bind("drag",function(am,ao){var ak=$(this);var ap=ao.offsetX-ao.current_x;var al=ak.scrollTop()-(am.clientY-ao.current_height);ak.scrollTop(al);ao.current_height=am.clientY;ao.current_x=ao.offsetX;var an=Math.round(ap/ag.viewport_container.width()*(ag.high-ag.low));ag.move_delta(an)}).bind("mousewheel",function(am,ao,al,ak){if(al){var an=Math.round(-al/ag.viewport_container.width()*(ag.high-ag.low));ag.move_delta(an)}});this.top_labeltrack.bind("dragstart",function(ak,al){return $("<div />").css({height:ag.browser_content_div.height()+ag.top_labeltrack.height()+ag.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ao,ap){$(ap.proxy).css({left:Math.min(ao.pageX,ap.startX),width:Math.abs(ao.pageX-ap.startX)});var al=Math.min(ao.pageX,ap.startX)-ag.container.offset().left,ak=Math.max(ao.pageX,ap.startX)-ag.container.offset().left,an=(ag.high-ag.low),am=ag.viewport_container.width();ag.update_location(Math.round(al/am*an)+ag.low,Math.round(ak/am*an)+ag.low)}).bind("dragend",function(ap,aq){var al=Math.min(ap.pageX,aq.startX),ak=Math.max(ap.pageX,aq.startX),an=(ag.high-ag.low),am=ag.viewport_container.width(),ao=ag.low;ag.low=Math.round(al/am*an)+ao;ag.high=Math.round(ak/am*an)+ao;$(aq.proxy).remove();ag.request_redraw()});this.add_label_track(new ac(this,{content_div:this.top_labeltrack}));this.add_label_track(new ac(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ag.resize_window()});$(document).bind("redraw",function(){ag.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ag,ah){this.location_span.text(commatize(ag)+" - "+commatize(ah));this.nav_input.val(this.chrom+":"+commatize(ag)+"-"+commatize(ah))},load_chroms:function(ai){ai.num=w;$.extend(ai,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ag=this,ah=$.Deferred();$.ajax({url:chrom_url,data:ai,dataType:"json",success:function(ak){if(ak.chrom_info.length===0){alert("Invalid chromosome: "+ai.chrom);return}if(ak.reference){ag.add_label_track(new A(ag))}ag.chrom_data=ak.chrom_info;var an='<option value="">Select Chrom/Contig</option>';for(var am=0,aj=ag.chrom_data.length;am<aj;am++){var al=ag.chrom_data[am].chrom;an+='<option value="'+al+'">'+al+"</option>"}if(ak.prev_chroms){an+='<option value="previous">Previous '+w+"</option>"}if(ak.next_chroms){an+='<option value="next">Next '+w+"</option>"}ag.chrom_select.html(an);ag.chrom_start_index=ak.start_index;ah.resolve(ak)},error:function(){alert("Could not load chroms for this dbkey:",ag.dbkey)}});return ah},change_chrom:function(al,ah,an){if(!al||al==="None"){return}var ai=this;if(al==="previous"){ai.load_chroms({low:this.chrom_start_index-w});return}if(al==="next"){ai.load_chroms({low:this.chrom_start_index+w});return}var am=$.grep(ai.chrom_data,function(ao,ap){return ao.chrom===al})[0];if(am===undefined){ai.load_chroms({chrom:al},function(){ai.change_chrom(al,ah,an)});return}else{if(al!==ai.chrom){ai.chrom=al;ai.chrom_select.val(ai.chrom);ai.max_high=am.len-1;ai.reset();ai.request_redraw(true);for(var ak=0,ag=ai.drawables.length;ak<ag;ak++){var aj=ai.drawables[ak];if(aj.init){aj.init()}}}if(ah!==undefined&&an!==undefined){ai.low=Math.max(ah,0);ai.high=Math.min(an,ai.max_high)}ai.reset_overview();ai.request_redraw()}},go_to:function(ak){ak=ak.replace(/ |,/g,"");var ao=this,ag,aj,ah=ak.split(":"),am=ah[0],an=ah[1];if(an!==undefined){try{var al=an.split("-");ag=parseInt(al[0],10);aj=parseInt(al[1],10)}catch(ai){return false}}ao.change_chrom(am,ag,aj)},move_fraction:function(ai){var ag=this;var ah=ag.high-ag.low;this.move_delta(ai*ah)},move_delta:function(ai){var ag=this;var ah=ag.high-ag.low;if(ag.low-ai<ag.max_low){ag.low=ag.max_low;ag.high=ag.max_low+ah}else{if(ag.high-ai>ag.max_high){ag.high=ag.max_high;ag.low=ag.max_high-ah}else{ag.high-=ai;ag.low-=ai}}ag.request_redraw()},add_drawable:function(ag){y.prototype.add_drawable.call(this,ag);ag.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ag){ag.view=this;ag.init();this.label_tracks.push(ag)},remove_drawable:function(ai,ah){y.prototype.remove_drawable.call(this,ai);if(ah){var ag=this;ai.container_div.fadeOut("slow",function(){$(this).remove();ag.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ao,ag,an,ah){var am=this,ak=(ah?[ah]:am.drawables),ai;var ah;for(var al=0;al<ak.length;al++){ah=ak[al];ai=-1;for(var aj=0;aj<am.tracks_to_be_redrawn.length;aj++){if(am.tracks_to_be_redrawn[aj][0]===ah){ai=aj;break}}if(ai<0){am.tracks_to_be_redrawn.push([ah,ag,an])}else{am.tracks_to_be_redrawn[al][1]=ag;am.tracks_to_be_redrawn[al][2]=an}}requestAnimationFrame(function(){am._redraw(ao)})},_redraw:function(aq){var an=this.low,aj=this.high;if(an<this.max_low){an=this.max_low}if(aj>this.max_high){aj=this.max_high}var ap=this.high-this.low;if(this.high!==0&&ap<this.min_separation){aj=an+this.min_separation}this.low=Math.floor(an);this.high=Math.ceil(aj);this.resolution=Math.pow(C,Math.ceil(Math.log((this.high-this.low)/R)/Math.log(C)));this.zoom_res=Math.pow(v,Math.max(0,Math.ceil(Math.log(this.resolution,v)/Math.log(v))));var ag=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var am=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ar=13;this.overview_box.css({left:ag,width:Math.max(ar,am)}).show();if(am<ar){this.overview_box.css("left",ag-(ar-am)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ag,width:am})}this.update_location(this.low,this.high);if(!aq){var ai,ah,ao;for(var ak=0,al=this.tracks_to_be_redrawn.length;ak<al;ak++){ai=this.tracks_to_be_redrawn[ak][0];ah=this.tracks_to_be_redrawn[ak][1];ao=this.tracks_to_be_redrawn[ak][2];if(ai){ai._draw(ah,ao)}}this.tracks_to_be_redrawn=[];for(ak=0,al=this.label_tracks.length;ak<al;ak++){this.label_tracks[ak]._draw()}}},zoom_in:function(ah,ai){if(this.max_high===0||this.high-this.low<this.min_separation){return}var aj=this.high-this.low,ak=aj/2+this.low,ag=(aj/this.zoom_factor)/2;if(ah){ak=ah/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ak-ag);this.high=Math.round(ak+ag);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ah=this.high-this.low,ai=ah/2+this.low,ag=(ah*this.zoom_factor)/2;this.low=Math.round(ai-ag);this.high=Math.round(ai+ag);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ai){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ai.dataset_id){return}this.overview_viewport.find(".track").remove()}var ah=ai.copy({content_div:this.overview_viewport}),ag=this;ah.header_div.hide();ah.is_overview=true;ag.overview_drawable=ah;this.overview_drawable.postdraw_actions=function(){ag.overview_highlight.show().height(ag.overview_drawable.content_div.height());ag.overview_viewport.height(ag.overview_drawable.content_div.height()+ag.overview_box.outerHeight());ag.overview_close.show();ag.resize_window()};this.overview_drawable.init();ag.has_changes=true},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var r=function(ai,am){this.track=ai;this.name=am.name;this.params=[];var au=am.params;for(var aj=0;aj<au.length;aj++){var ao=au[aj],ah=ao.name,at=ao.label,ak=unescape(ao.html),av=ao.value,aq=ao.type;if(aq==="number"){this.params[this.params.length]=new g(ah,at,ak,av,ao.min,ao.max)}else{if(aq=="select"){this.params[this.params.length]=new O(ah,at,ak,av)}else{console.log("WARNING: unrecognized tool parameter type:",ah,aq)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ax){ax.stopPropagation()}).click(function(ax){ax.stopPropagation()}).bind("dblclick",function(ax){ax.stopPropagation()});var ar=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ap=this.params;var an=this;$.each(this.params,function(ay,aB){var aA=$("<div>").addClass("param-row").appendTo(an.parent_div);var ax=$("<div>").addClass("param-label").text(aB.label).appendTo(aA);var az=$("<div/>").addClass("slider").html(aB.html).appendTo(aA);az.find(":input").val(aB.value);$("<div style='clear: both;'/>").appendTo(aA)});this.parent_div.find("input").click(function(){$(this).select()});var aw=$("<div>").addClass("param-row").appendTo(this.parent_div);var al=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(aw);var ag=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(aw);var an=this;ag.click(function(){an.run_on_region()});al.click(function(){an.run_on_dataset()})};p(r.prototype,{get_param_values_dict:function(){var ag={};this.parent_div.find(":input").each(function(){var ah=$(this).attr("name"),ai=$(this).val();ag[ah]=JSON.stringify(ai)});return ag},get_param_values:function(){var ah=[];var ag={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();if(ai){ah[ah.length]=aj}});return ah},run_on_dataset:function(){var ag=this;ag.run({dataset_id:this.track.original_dataset_id,tool_id:ag.name},null,function(ah){show_modal(ag.name+" is Running",ag.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ah={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},ak=this.track,ai=ah.tool_id+ak.tool_region_and_parameters_str(ah.chrom,ah.low,ah.high),ag,al;if(ak.container===view){var aj=new Q(this.name,this.track.view,this.track.container);ak.container.add_drawable(aj);ak.container.remove_drawable(ak);aj.add_drawable(ak);ak.container_div.appendTo(aj.content_div);ag=aj}else{ag=ak.container}if(ak instanceof e){al=new V(ai,view,ag,"hda");al.change_mode(ak.mode);ag.add_drawable(al)}al.content_div.text("Starting job.");this.run(ah,al,function(am){al.dataset_id=am.dataset_id;al.content_div.text("Running job.");al.init()})},run:function(ah,ai,aj){$.extend(ah,this.get_param_values_dict());var ag=function(){$.getJSON(rerun_tool_url,ah,function(ak){if(ak==="no converter"){ai.container_div.addClass("error");ai.content_div.text(K)}else{if(ak.error){ai.container_div.addClass("error");ai.content_div.text(x+ak.message)}else{if(ak==="pending"){ai.container_div.addClass("pending");ai.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ag,2000)}else{aj(ak)}}}})};ag()}});var O=function(ah,ag,ai,aj){this.name=ah;this.label=ag;this.html=ai;this.value=aj};var g=function(ai,ah,ak,al,aj,ag){O.call(this,ai,ah,ak,al);this.min=aj;this.max=ag};var h=function(ah,ag,ai,aj){this.name=ah;this.index=ag;this.tool_id=ai;this.tool_exp_name=aj};var W=function(ah,ag,ai,aj){h.call(this,ah,ag,ai,aj);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};p(W.prototype,{applies_to:function(ag){if(ag.length>this.index){return true}return false},keep:function(ag){if(!this.applies_to(ag)){return true}var ah=ag[this.index];return(isNaN(ah)||(ah>=this.low&&ah<=this.high))},update_attrs:function(ah){var ag=false;if(!this.applies_to(ah)){return ag}if(ah[this.index]<this.min){this.min=Math.floor(ah[this.index]);ag=true}if(ah[this.index]>this.max){this.max=Math.ceil(ah[this.index]);ag=true}return ag},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var ai=function(al,aj){var ak=aj-al;return(ak<=2?0.01:1)};var ah=this.slider.slider("option","min"),ag=this.slider.slider("option","max");if(this.min<ah||this.max>ag){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ai(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ab=function(ar,az){this.track=ar;this.filters=[];for(var au=0;au<az.length;au++){var av=az[au],aA=av.name,ag=av.type,ai=av.index,ay=av.tool_id,ax=av.tool_exp_name;if(ag==="int"||ag==="float"){this.filters[au]=new W(aA,ai,ay,ax)}else{console.log("ERROR: unsupported filter: ",aA,ag)}}var aj=function(aB,aC,aD){aB.click(function(){var aE=aC.text();max=parseFloat(aD.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aD.slider("option","values")){input_size=2*input_size+1;multi_value=true}aC.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aE).appendTo(aC).focus().select().click(function(aF){aF.stopPropagation()}).blur(function(){$(this).remove();aC.text(aE)}).keyup(function(aJ){if(aJ.keyCode===27){$(this).trigger("blur")}else{if(aJ.keyCode===13){var aH=aD.slider("option","min"),aF=aD.slider("option","max"),aI=function(aK){return(isNaN(aK)||aK>aF||aK<aH)},aG=$(this).val();if(!multi_value){aG=parseFloat(aG);if(aI(aG)){alert("Parameter value must be in the range ["+aH+"-"+aF+"]");return $(this)}}else{aG=aG.split("-");aG=[parseFloat(aG[0]),parseFloat(aG[1])];if(aI(aG[0])||aI(aG[1])){alert("Parameter value must be in the range ["+aH+"-"+aF+"]");return $(this)}}aD.slider((multi_value?"values":"value"),aG)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aB){aB.stopPropagation()}).click(function(aB){aB.stopPropagation()}).bind("dblclick",function(aB){aB.stopPropagation()}).bind("keydown",function(aB){aB.stopPropagation()});var aw=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ao=this;$.each(this.filters,function(aE,aG){aG.container=$("<div/>").addClass("filter-row slider-row").appendTo(aw);var aF=$("<div/>").addClass("elt-label").appendTo(aG.container);var aD=$("<span/>").addClass("slider-name").text(aG.name+"  ").appendTo(aF);var aC=$("<span/>");var aI=$("<span/>").addClass("slider-value").appendTo(aF).append("[").append(aC).append("]");var aB=$("<div/>").addClass("slider").appendTo(aG.container);aG.control_element=$("<div/>").attr("id",aG.name+"-filter-control").appendTo(aB);var aH=[0,0];aG.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aK,aL){var aJ=aL.values;aC.text(aJ[0]+"-"+aJ[1]);aG.low=aJ[0];aG.high=aJ[1];ao.track.request_draw(true,true)},change:function(aJ,aK){aG.control_element.slider("option","slide").call(aG.control_element,aJ,aK)}});aG.slider=aG.control_element;aG.slider_label=aC;aj(aI,aC,aG.control_element);$("<div style='clear: both;'/>").appendTo(aG.container)});if(this.filters.length!==0){var al=$("<div/>").addClass("param-row").appendTo(aw);var an=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(al);var ah=this;an.click(function(){ah.run_on_dataset()})}var aq=$("<div/>").addClass("display-controls").appendTo(this.parent_div),at,am,ap,ak={Transparency:function(aB){ao.alpha_filter=aB},Height:function(aB){ao.height_filter=aB}};$.each(ak,function(aD,aC){at=$("<div/>").addClass("filter-row").appendTo(aq),am=$("<span/>").addClass("elt-label").text(aD+":").appendTo(at),ap=$("<select/>").attr("name",aD+"_dropdown").css("float","right").appendTo(at);$("<option/>").attr("value",-1).text("== None ==").appendTo(ap);for(var aB=0;aB<ao.filters.length;aB++){$("<option/>").attr("value",aB).text(ao.filters[aB].name).appendTo(ap)}ap.change(function(){$(this).children("option:selected").each(function(){var aE=parseInt($(this).val());ak[aD]((aE>=0?ao.filters[aE]:null));ao.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(at)});$("<div style='clear: both;'/>").appendTo(this.parent_div)};p(ab.prototype,{reset_filters:function(){for(var ag=0;ag<this.filters.length;ag++){filter=this.filters[ag];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var ao=function(at,aq,ar){if(!(aq in at)){at[aq]=ar}return at[aq]};var ai={},ag,ah,aj;for(var ak=0;ak<this.filters.length;ak++){ag=this.filters[ak];if(ag.tool_id){if(ag.min!=ag.low){ah=ao(ai,ag.tool_id,[]);ah[ah.length]=ag.tool_exp_name+" >= "+ag.low}if(ag.max!=ag.high){ah=ao(ai,ag.tool_id,[]);ah[ah.length]=ag.tool_exp_name+" <= "+ag.high}}}var am=[];for(var ap in ai){am[am.length]=[ap,ai[ap]]}var an=am.length;(function al(ax,au){var ar=au[0],at=ar[0],aw=ar[1],av="("+aw.join(") and (")+")",aq={cond:av,input:ax,target_dataset_id:ax,tool_id:at},au=au.slice(1);$.getJSON(run_tool_url,aq,function(ay){if(ay.error){show_modal("Filter Dataset","Error running tool "+at,{Close:hide_modal})}else{if(au.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{al(ay.dataset_id,au)}}})})(this.track.dataset_id,am)}});var D=function(ag,ah){M.Scaler.call(this,ah);this.filter=ag};D.prototype.gen_val=function(ag){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ag[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var G=function(ag){this.track=ag.track;this.params=ag.params;this.values={};this.restore_values((ag.saved_values?ag.saved_values:{}));this.onchange=ag.onchange};p(G.prototype,{restore_values:function(ag){var ah=this;$.each(this.params,function(ai,aj){if(ag[aj.key]!==undefined){ah.values[aj.key]=ag[aj.key]}else{ah.values[aj.key]=aj.default_value}})},build_form:function(){var ah=this;var ag=$("<div />");$.each(this.params,function(al,aj){if(!aj.hidden){var ai="param_"+al;var an=ah.values[aj.key];var aq=$("<div class='form-row' />").appendTo(ag);aq.append($("<label />").attr("for",ai).text(aj.label+":"));if(aj.type==="bool"){aq.append($('<input type="checkbox" />').attr("id",ai).attr("name",ai).attr("checked",an))}else{if(aj.type==="text"){aq.append($('<input type="text"/>').attr("id",ai).val(an).click(function(){$(this).select()}))}else{if(aj.type==="color"){var am=$("<input />").attr("id",ai).attr("name",ai).val(an);var ao=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var ak=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ao);var ap=$("<div/>").appendTo(ak).farbtastic({width:100,height:100,callback:am,color:an});$("<div />").append(am).append(ao).appendTo(aq).bind("click",function(ar){ao.css({left:$(this).position().left+($(am).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ao.hide();$(document).unbind("click.color-picker")});ar.stopPropagation()})}else{aq.append($("<input />").attr("id",ai).attr("name",ai).val(an))}}}}});return ag},update_from_form:function(ag){var ai=this;var ah=false;$.each(this.params,function(aj,al){if(!al.hidden){var am="param_"+aj;var ak=ag.find("#"+am).val();if(al.type==="float"){ak=parseFloat(ak)}else{if(al.type==="int"){ak=parseInt(ak)}else{if(al.type==="bool"){ak=ag.find("#"+am).is(":checked")}}}if(ak!==ai.values[al.key]){ai.values[al.key]=ak;ah=true}}});if(ah){this.onchange()}}});var b=function(ag,aj,ai,ah,ak){this.track=ag;this.index=aj;this.low=aj*R*ai;this.high=(aj+1)*R*ai;this.resolution=ai;this.canvas=$("<div class='track-tile'/>").append(ah);this.data=ak;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(ag,aj,ai,ah,ak,al){b.call(this,ag,aj,ai,ah,ak);this.max_val=al};p(k.prototype,b.prototype);var P=function(ag,ak,aj,ai,am,an,al,ah){b.call(this,ag,ak,aj,ai,am);this.mode=an;this.message=al;this.feature_mapper=ah};p(P.prototype,b.prototype);P.prototype.predisplay_actions=function(){var ah=this,ag={};if(ah.mode!=="Pack"){return}$(this.canvas).mousemove(function(at){var an=$(this).offset(),ar=at.pageX-an.left,aq=at.pageY-an.top,ax=ah.feature_mapper.get_feature_data(ar,aq),ao=(ax?ax[0]:null);$(this).siblings(".feature-popup").each(function(){if(!ao||$(this).attr("id")!==ao.toString()){$(this).remove()}});if(ax){var aj=ag[ao];if(!aj){var ao=ax[0],au={name:ax[3],start:ax[1],end:ax[2],strand:ax[4]},am=ah.track.filters_manager.filters,al;for(var ap=0;ap<am.length;ap++){al=am[ap];au[al.name]=ax[al.index]}var aj=$("<div/>").attr("id",ao).addClass("feature-popup"),aw,av,ay=$("<table/>").appendTo(aj),az;for(aw in au){av=au[aw];az=$("<tr/>").appendTo(ay);$("<th/>").appendTo(az).text(aw);$("<td/>").attr("align","left").appendTo(az).text(typeof(av)=="number"?aa(av,2):av)}ag[ao]=aj}aj.appendTo($(ah.canvas).parent());var ak=ar+parseInt(ah.canvas.css("left"))+7,ai=aq+parseInt(ah.canvas.css("top"))+7;aj.css("left",ak+"px").css("top",ai+"px")}else{if(!at.isPropagationStopped()){at.stopPropagation();$(this).siblings().each(function(){$(this).trigger(at)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var i=function(aj,ar,ak,an,at,ai,ah){q.call(this,aj,ar,ak,{},"draghandle");this.data_url=(ai?ai:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ah?ah:L);this.dataset_check_url=converted_datasets_state_url;if(!i.id_counter){i.id_counter=0}this.id=i.id_counter++;this.container_div=$("<div />").addClass("track").attr("id","track_"+this.id).css("position","relative");if(an){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div/>").addClass("track-name").appendTo(this.header_div).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());this.icons_div=$("<div/>").css("float","left").appendTo(this.header_div).hide();this.settings_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Edit settings").addClass("icon-button settings-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.overview_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Set as overview").addClass("icon-button overview-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.filters_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Filters").addClass("icon-button filters-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.tools_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Tools").addClass("icon-button tools-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.remove_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Remove").addClass("icon-button remove-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);var al=this;this.header_div.dblclick(function(au){au.stopPropagation()});this.settings_icon.click(function(){var aw=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},au=function(){al.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},av=function(ax){if((ax.keyCode||ax.which)===27){aw()}else{if((ax.keyCode||ax.which)===13){au()}}};$(window).bind("keypress.check_enter_esc",av);show_modal("Configure Track",al.config.build_form(),{Cancel:aw,OK:au})});this.overview_icon.click(function(){al.view.set_overview(al)});this.filters_icon.click(function(){al.filters_div.toggle();al.filters_manager.reset_filters()});this.tools_icon.click(function(){al.dynamic_tool_div.toggle();if(al.dynamic_tool_div.is(":visible")){al.set_name(al.name+al.tool_region_and_parameters_str())}else{al.revert_name()}$(".tipsy").remove()});this.remove_icon.click(function(){$(".tipsy").remove();al.remove()});if(al.display_modes!==undefined){if(al.mode_div===undefined){al.mode_div=$("<div class='right-float menubutton popup' />").appendTo(al.header_div);var am=(al.config&&al.config.values.mode?al.config.values.mode:al.display_modes[0]);al.mode=am;al.mode_div.text(am);var ag={};for(var ao=0,aq=al.display_modes.length;ao<aq;ao++){var ap=al.display_modes[ao];ag[ap]=function(au){return function(){al.change_mode(au)}}(ap)}make_popupmenu(al.mode_div,ag)}else{al.mode_div.hide()}this.header_div.append($("<div/>").css("clear","both"));this.container_div.hover(function(){al.icons_div.show()},function(){al.icons_div.hide()})}}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};p(i.prototype,q.prototype,{get_type:function(){if(this instanceof ac){return"LabelTrack"}else{if(this instanceof A){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof X){return"ReadTrack"}else{if(this instanceof V){return"ToolDataFeatureTrack"}else{if(this instanceof U){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ag=this;ag.enabled=false;ag.tile_cache.clear();ag.data_manager.clear();ag.initial_canvas=undefined;ag.content_div.css("height","auto");ag.container_div.removeClass("nodata error pending");if(!ag.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ag.hda_ldda,dataset_id:ag.dataset_id,chrom:ag.view.chrom},function(ah){if(!ah||ah==="error"||ah.kind==="error"){ag.container_div.addClass("error");ag.content_div.text(o);if(ah.message){var ai=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ah.message+"</pre>",{Close:hide_modal})});ag.content_div.append(ai)}}else{if(ah==="no converter"){ag.container_div.addClass("error");ag.content_div.text(K)}else{if(ah==="no data"||(ah.data!==undefined&&(ah.data===null||ah.data.length===0))){ag.container_div.addClass("nodata");ag.content_div.text(F)}else{if(ah==="pending"){ag.container_div.addClass("pending");ag.content_div.text(t);setTimeout(function(){ag.init()},ag.data_query_wait)}else{if(ah.status==="data"){if(ah.valid_chroms){ag.valid_chroms=ah.valid_chroms;ag.update_track_icons()}ag.content_div.text(Z);if(ag.view.chrom){ag.content_div.text("");ag.content_div.css("height",ag.height_px+"px");ag.enabled=true;$.when(ag.predraw_init()).done(function(){ag.container_div.removeClass("nodata error pending");ag.request_draw()})}}}}}}});this.update_track_icons()},predraw_init:function(){}});var N=function(ai,ao,aj,al,ap,an,am,ah,ag){i.call(this,ai,ao,aj,al,ap,ah,ag);var ak=this,ao=ak.view;m(ak.container_div,ak.drag_handle_class,".group",ak);this.filters_manager=new ab(this,(an!==undefined?an:{}));this.filters_available=false;this.filters_visible=false;this.tool=(am!==undefined&&obj_length(am)>0?new r(this,am):undefined);if(this.header_div){if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}};p(N.prototype,q.prototype,i.prototype,{copy:function(ag){return new this.constructor(this.name,this.view,ag,this.hda_ldda,this.dataset_id,this.prefs,this.filters,this.tool)},to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ah){var ag=this;ag.mode_div.text(ah);ag.mode=ah;ag.config.values.mode=ah;ag.tile_cache.clear();ag.request_draw();return ag},update_track_icons:function(){var ag=this;if(ag.filters_available>0){ag.filters_icon.show()}else{ag.filters_icon.hide()}if(ag.tool){ag.tools_icon.show()}else{ag.tools_icon.hide()}},_gen_tile_cache_key:function(ah,ai,ag){return ah+"_"+ai+"_"+ag},request_draw:function(ah,ag){this.view.request_redraw(false,ah,ag,this)},_draw:function(ai,aq){if(!this.enabled){return}if(!(this instanceof A)&&(!this.dataset_id)){return}var ap=this.view.low,am=this.view.high,an=am-ap,aj=this.view.container.width(),au=aj/an,al=this.view.resolution,at=$("<div style='position: relative;'></div>");if(this.is_overview){ap=this.view.max_low;am=this.view.max_high;al=Math.pow(C,Math.ceil(Math.log((view.max_high-view.max_low)/R)/Math.log(C)));au=aj/(view.max_high-view.max_low)}if(!aq){this.content_div.children().remove()}this.content_div.append(at);this.max_height=0;var ah=Math.floor(ap/al/R);var ao=true;var ar=[];var ag=0;while((ah*R*al)<am){tile=this.draw_helper(ai,aj,ah,al,at,au);if(tile){ar.push(tile)}else{ao=false}ah+=1;ag++}var ak=this;if(ao){ak.postdraw_actions(ar,aj,au,aq)}},postdraw_actions:function(ak,al,am,ag){var ai=this;var aj=false;for(var ah=0;ah<ak.length;ah++){if(ak[ah].message){aj=true;break}}if(aj){for(var ah=0;ah<ak.length;ah++){tile=ak[ah];if(!tile.message){tile.canvas.css("padding-top",E)}}}},draw_helper:function(ah,ai,aj,am,at,ax,au,an){var ak=this,ar=this._gen_tile_cache_key(ai,ax,aj),ao=aj*R*am,aw=ao+R*am;var ap=(ah?undefined:ak.tile_cache.get(ar));if(ap){ak.show_tile(ap,at,ax);return ap}var aq=function(ay){return("isResolved" in ay)};var al=true;var ag=ak.data_manager.get_data(ao,aw,ak.mode,am,ak.data_url_extra_params);if(aq(ag)){al=false}var av;if(view.reference_track&&ax>view.canvas_manager.char_width_px){av=view.reference_track.data_manager.get_data(ao,aw,ak.mode,am,view.reference_track.data_url_extra_params);if(aq(av)){al=false}}if(al){p(ag,an);var ap=ak.draw_tile(ag,ak.mode,am,aj,ax,av);if(ap!==undefined){ak.tile_cache.set(ar,ap);ak.show_tile(ap,at,ax)}return ap}$.when(ag,av).then(function(){view.request_redraw(false,false,false,ak)});return null},show_tile:function(am,ao,ap){var ai=this,ah=am.canvas,al=ah;if(am.message){var aq=$("<div/>"),an=$("<div/>").addClass("tile-message").text(am.message).css({height:E-1,width:am.canvas.width}).appendTo(aq),ak=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(an),ag=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(an);aq.append(ah);al=aq;ak.click(function(){am.stale=true;ai.data_manager.get_more_data(am.low,am.high,ai.mode,am.resolution,{},ai.data_manager.DEEP_DATA_REQ);ai.request_draw()}).dblclick(function(ar){ar.stopPropagation()});ag.click(function(){am.stale=true;ai.data_manager.get_more_data(am.low,am.high,ai.mode,am.resolution,{},ai.data_manager.BROAD_DATA_REQ);ai.request_draw()}).dblclick(function(ar){ar.stopPropagation()})}am.predisplay_actions();var aj=(am.low-(this.is_overview?this.view.max_low:this.view.low))*ap;if(this.left_offset){aj-=this.left_offset}al.css({position:"absolute",top:0,left:aj,height:""});ao.append(al);ai.max_height=Math.max(ai.max_height,al.height());ai.content_div.css("height",ai.max_height+"px");ao.children().css("height",ai.max_height+"px")},_get_tile_bounds:function(ag,ah){var aj=ag*R*ah,ak=R*ah,ai=(aj+ak<=this.view.max_high?aj+ak:this.view.max_high);return[aj,ai]},tool_region_and_parameters_str:function(ai,ag,aj){var ah=this,ak=(ai!==undefined&&ag!==undefined&&aj!==undefined?ai+":"+ag+"-"+aj:"all");return" - region=["+ak+"], parameters=["+ah.tool.get_param_values().join(", ")+"]"}});var ac=function(ah,ag){i.call(this,"label",ah,ag,false,{});this.container_div.addClass("label-track")};p(ac.prototype,i.prototype,{init:function(){this.enabled=true},_draw:function(){var ai=this.view,aj=ai.high-ai.low,am=Math.floor(Math.pow(10,Math.floor(Math.log(aj)/Math.log(10)))),ag=Math.floor(ai.low/am)*am,ak=this.view.container.width(),ah=$("<div style='position: relative; height: 1.3em;'></div>");while(ag<ai.high){var al=(ag-ai.low)/aj*ak;ah.append($("<div class='label'>"+commatize(ag)+"</div>").css({position:"absolute",left:al-1}));ag+=am}this.content_div.children(":first").remove();this.content_div.append(ah)}});var A=function(ag){N.call(this,"reference",ag,{content_div:ag.top_labeltrack},false,{});ag.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ag.dbkey};this.data_manager=new I(B,this,false);this.tile_cache=new c(u)};p(A.prototype,q.prototype,N.prototype,{init:function(){this.enabled=true},draw_tile:function(aq,am,al,ah,ar){var ak=this,ai=R*al;if(ar>this.view.canvas_manager.char_width_px){if(aq.data===null){ak.content_div.css("height","0px");return}var aj=this.view.canvas_manager.new_canvas();var ap=aj.getContext("2d");aj.width=Math.ceil(ai*ar+ak.left_offset);aj.height=ak.height_px;ap.font=ap.canvas.manager.default_font;ap.textAlign="center";aq=aq.data;for(var an=0,ao=aq.length;an<ao;an++){var ag=Math.round(an*ar);ap.fillText(aq[an],ag+ak.left_offset,10)}return new b(ak,ah,al,aj,aq)}this.content_div.css("height","0px")}});var j=function(al,aj,ai,am,ag,ak){var ah=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";N.call(this,al,aj,ai,true,ak);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=am;this.dataset_id=ag;this.original_dataset_id=ag;this.data_manager=new S(B,this);this.tile_cache=new c(u);this.left_offset=0;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:ak,onchange:function(){ah.set_name(ah.prefs.name);ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;$("#linetrack_"+ah.dataset_id+"_minval").text(ah.prefs.min_value);$("#linetrack_"+ah.dataset_id+"_maxval").text(ah.prefs.max_value);ah.tile_cache.clear();ah.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};p(j.prototype,q.prototype,N.prototype,{add_resize_handle:function(){var ag=this;var aj=false;var ai=false;var ah=$("<div class='track-resize'>");$(ag.container_div).hover(function(){aj=true;ah.show()},function(){aj=false;if(!ai){ah.hide()}});ah.hide().bind("dragstart",function(ak,al){ai=true;al.original_height=$(ag.content_div).height()}).bind("drag",function(al,am){var ak=Math.min(Math.max(am.original_height+am.deltaY,ag.min_height_px),ag.max_height_px);$(ag.content_div).css("height",ak);ag.height_px=ak;ag.request_draw(true)}).bind("dragend",function(ak,al){ag.tile_cache.clear();ai=false;if(!aj){ah.hide()}ag.config.values.height=ag.height_px}).appendTo(ag.container_div)},predraw_init:function(){var ag=this;ag.vertical_range=undefined;return $.getJSON(ag.data_url,{stats:true,chrom:ag.view.chrom,low:null,high:null,hda_ldda:ag.hda_ldda,dataset_id:ag.dataset_id},function(ah){ag.container_div.addClass("line-track");var aj=ah.data;if(isNaN(parseFloat(ag.prefs.min_value))||isNaN(parseFloat(ag.prefs.max_value))){ag.prefs.min_value=aj.min;ag.prefs.max_value=aj.max;$("#track_"+ag.dataset_id+"_minval").val(ag.prefs.min_value);$("#track_"+ag.dataset_id+"_maxval").val(ag.prefs.max_value)}ag.vertical_range=ag.prefs.max_value-ag.prefs.min_value;ag.total_frequency=aj.total_frequency;ag.container_div.find(".yaxislabel").remove();var ak=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ag.dataset_id+"_minval").text(aa(ag.prefs.min_value,3));var ai=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ag.dataset_id+"_maxval").text(aa(ag.prefs.max_value,3));ai.css({position:"absolute",top:"24px",left:"10px"});ai.prependTo(ag.container_div);ak.css({position:"absolute",bottom:"2px",left:"10px"});ak.prependTo(ag.container_div)})},draw_tile:function(at,al,ak,ai,ar){if(this.vertical_range===undefined){return}var ag=this._get_tile_bounds(ai,ak),am=ag[0],aq=ag[1],ah=Math.ceil((aq-am)*ar),ao=this.height_px;var aj=this.view.canvas_manager.new_canvas();aj.width=ah,aj.height=ao;var ap=aj.getContext("2d");var an=new M.LinePainter(at.data,am,aq,this.prefs,al);an.draw(ap,ah,ao);return new b(this.track,ai,ak,aj,at.data)}});var e=function(ag,am,ah,al,ao,an,aj,ak){var ai=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];N.call(this,ag,am,ah,true,an,aj,ak);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ag},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:an,onchange:function(){ai.set_name(ai.prefs.name);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=al;this.dataset_id=ao;this.original_dataset_id=ao;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new S(20,this);this.left_offset=200;this.painter=M.LinkedFeaturePainter};p(e.prototype,q.prototype,N.prototype,{postdraw_actions:function(aw,ag,ax,av){N.prototype.postdraw_actions.call(this,aw,av);var aj=this;if(av){var al=aj.content_div.children();var am=false;for(var ak=al.length-1,aq=0;ak>=aq;ak--){var ai=$(al[ak]);if(am){ai.remove()}else{if(ai.children().length!==0){am=true}}}}if(aj.mode=="Histogram"){var ap=-1;for(var ak=0;ak<aw.length;ak++){var au=aw[ak].max_val;if(au>ap){ap=au}}for(var ak=0;ak<aw.length;ak++){var at=aw[ak];if(at.max_val!==ap){at.canvas.remove();aj.draw_helper(true,ag,at.index,at.resolution,at.canvas.parent(),ax,[],{max:ap})}}}if(aj.filters_manager){var ah=aj.filters_manager.filters;for(var ao=0;ao<ah.length;ao++){ah[ao].update_ui_elt()}var an=false,ar;for(var ak=0;ak<aw.length;ak++){if(aw[ak].data.length){ar=aw[ak].data[0];for(var ao=0;ao<ah.length;ao++){if(ah[ao].applies_to(ar)){an=true;break}}}}if(aj.filters_available!==an){aj.filters_available=an;if(!aj.filters_available){aj.filters_div.hide()}aj.update_track_icons()}}},update_auto_mode:function(ag){if(this.mode=="Auto"){if(ag=="no_detail"){ag="feature spans"}else{if(ag=="summary_tree"){ag="coverage histogram"}}this.mode_div.text("Auto ("+ag+")")}},incremental_slots:function(ak,ah,aj){var ai=this.view.canvas_manager.dummy_context,ag=this.inc_slots[ak];if(!ag||(ag.mode!==aj)){ag=new (s.FeatureSlotter)(ak,aj==="Pack",z,function(al){return ai.measureText(al)});ag.mode=aj;this.inc_slots[ak]=ag}return ag.slot_features(ah)},get_summary_tree_data:function(ak,an,ai,aw){if(aw>ai-an){aw=ai-an}var ar=Math.floor((ai-an)/aw),av=[],aj=0;var al=0,am=0,aq,au=0,ao=[],at,ap;var ah=function(az,ay,aA,ax){az[0]=ay+aA*ax;az[1]=ay+(aA+1)*ax};while(au<aw&&al!==ak.length){var ag=false;for(;au<aw&&!ag;au++){ah(ao,an,au,ar);for(am=al;am<ak.length;am++){aq=ak[am].slice(1,3);if(is_overlap(aq,ao)){ag=true;break}}if(ag){break}}data_start_index=am;av[av.length]=at=[ao[0],0];for(;am<ak.length;am++){aq=ak[am].slice(1,3);if(is_overlap(aq,ao)){at[1]++}else{break}}if(at[1]>aj){aj=at[1]}au++}return{max:aj,delta:ar,data:av}},draw_tile:function(av,ay,aC,aG,aq,aj){var az=this,al=az._get_tile_bounds(aG,aC),aJ=al[0],ah=al[1],ax=ah-aJ,aA=Math.ceil(ax*aq),aP=25,ak=this.left_offset,aw,am;if(ay==="Auto"){if(av.dataset_type==="summary_tree"){ay=av.dataset_type}else{if(av.extra_info==="no_detail"||az.is_overview){ay="no_detail"}else{var aO=av.data;if(this.view.high-this.view.low>J){ay="Squish"}else{ay="Pack"}}}this.update_auto_mode(ay)}if(ay==="summary_tree"||ay==="Histogram"){am=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ag=$("<div />").addClass("yaxislabel");ag.text(av.max);ag.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ag.prependTo(this.container_div);var ai=this.view.canvas_manager.new_canvas();ai.width=aA+ak;ai.height=am+T;if(av.dataset_type!="summary_tree"){var ar=this.get_summary_tree_data(av.data,aJ,ah,200);if(av.max){ar.max=av.max}av=ar}var aL=new M.SummaryTreePainter(av,aJ,ah,this.prefs);var aB=ai.getContext("2d");aB.translate(ak,T);aL.draw(aB,aA,am);return new k(az,aG,aC,ai,av.data,av.max)}var aw,ao=1;if(ay==="no_detail"||ay==="Squish"||ay==="Pack"){ao=this.incremental_slots(aq,av.data,ay);aw=this.inc_slots[aq].slots}var ap=[];if(av.data){var at=this.filters_manager.filters;for(var aD=0,aF=av.data.length;aD<aF;aD++){var an=av.data[aD];var aE=false;var au;for(var aI=0,aN=at.length;aI<aN;aI++){au=at[aI];au.update_attrs(an);if(!au.keep(an)){aE=true;break}}if(!aE){ap.push(an)}}}var aM=(this.filters_manager.alpha_filter?new D(this.filters_manager.alpha_filter):null);var aK=(this.filters_manager.height_filter?new D(this.filters_manager.height_filter):null);var aL=new (this.painter)(ap,aJ,ah,this.prefs,ay,aM,aK,aj);var am=Math.max(ae,aL.get_required_height(ao));var ai=this.view.canvas_manager.new_canvas();var aH=null;ai.width=aA+ak;ai.height=am;var aB=ai.getContext("2d");aB.fillStyle=this.prefs.block_color;aB.font=aB.canvas.manager.default_font;aB.textAlign="right";this.container_div.find(".yaxislabel").remove();if(av.data){aB.translate(ak,0);aH=aL.draw(aB,aA,am,aw);aH.translation=-ak}return new P(az,aG,aC,ai,av.data,ay,av.message,aH)}});var U=function(ak,ai,ah,am,ag,aj,al){e.call(this,ak,ai,ah,am,ag,aj,al);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:aj,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter};p(U.prototype,q.prototype,N.prototype,e.prototype);var X=function(ak,ai,ah,am,ag,aj,al){e.call(this,ak,ai,ah,am,ag,aj,al);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:aj,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter;this.update_track_icons()};p(X.prototype,q.prototype,N.prototype,e.prototype);var V=function(ak,ai,ah,am,ag,aj,al){e.call(this,ak,ai,ah,am,ag,aj,al,{});this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};p(V.prototype,q.prototype,N.prototype,e.prototype,{predraw_init:function(){var ah=this;var ag=function(){if(ah.data_manager.size()===0){setTimeout(ag,300)}else{ah.data_url=default_data_url;ah.data_query_wait=L;ah.dataset_state_url=converted_datasets_state_url;$.getJSON(ah.dataset_state_url,{dataset_id:ah.dataset_id,hda_ldda:ah.hda_ldda},function(ai){})}};ag()}});Y.View=ad;Y.DrawableGroup=Q;Y.LineTrack=j;Y.FeatureTrack=e;Y.ReadTrack=X;Y.VcfTrack=U};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(F,G){for(var E=0;E<=z;E++){var C=false,H=h[E];if(H!==undefined){for(var B=0,D=H.length;B<D;B++){var i=H[B];if(G>i[0]&&F<i[1]){C=true;break}}}if(!C){return E}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(i,w){var t=i("class").extend;var o=function(H,z,F,y,E,C){if(C===undefined){C=4}var B=y-z;var A=E-F;var D=Math.floor(Math.sqrt(B*B+A*A)/C);var I=B/D;var G=A/D;var x;for(x=0;x<D;x++,z+=I,F+=G){if(x%2!==0){continue}H.fillRect(z,F,C,1)}};var p=function(A,z,x,D){var C=z-D/2,B=z+D/2,E=x-Math.sqrt(D*3/2);A.beginPath();A.moveTo(C,E);A.lineTo(B,E);A.lineTo(z,x);A.lineTo(C,E);A.strokeStyle=this.fillStyle;A.fill();A.stroke();A.closePath()};var d=function(x){this.default_val=(x?x:1)};d.prototype.gen_val=function(x){return this.default_val};var l=function(z,B,x,y,A){this.data=z;this.view_start=B;this.view_end=x;this.prefs=t({},this.default_prefs,y);this.mode=A};l.prototype.default_prefs={};var u=function(z,B,x,y,A){l.call(this,z,B,x,y,A)};u.prototype.default_prefs={show_counts:false};u.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var b=function(x,B,D,E,z){l.call(this,x,B,D,E,z);if(this.prefs.min_value===undefined){var F=Infinity;for(var y=0,A=this.data.length;y<A;y++){F=Math.min(F,this.data[y][1])}this.prefs.min_value=F}if(this.prefs.max_value===undefined){var C=-Infinity;for(var y=0,A=this.data.length;y<A;y++){C=Math.max(C,this.data[y][1])}this.prefs.max_value=C}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(M,L,J){var E=false,G=this.prefs.min_value,C=this.prefs.max_value,I=C-G,x=J,z=this.view_start,K=this.view_end-this.view_start,A=L/K,H=this.mode,S=this.data;M.save();var T=Math.round(J+G/I*J);if(H!=="Intensity"){M.fillStyle="#aaa";M.fillRect(0,T,L,1)}M.beginPath();var Q,D,B;if(S.length>1){B=Math.ceil((S[1][0]-S[0][0])*A)}else{B=10}for(var N=0,O=S.length;N<O;N++){M.fillStyle=this.prefs.color;Q=Math.round((S[N][0]-z)*A);D=S[N][1];var P=false,F=false;if(D===null){if(E&&H==="Filled"){M.lineTo(Q,x)}E=false;continue}if(D<G){F=true;D=G}else{if(D>C){P=true;D=C}}if(H==="Histogram"){D=Math.round(D/I*x);M.fillRect(Q,T,B,-D)}else{if(H==="Intensity"){D=255-Math.floor((D-G)/I*255);M.fillStyle="rgb("+D+","+D+","+D+")";M.fillRect(Q,0,B,x)}else{D=Math.round(x-(D-G)/I*x);if(E){M.lineTo(Q,D)}else{E=true;if(H==="Filled"){M.moveTo(Q,x);M.lineTo(Q,D)}else{M.moveTo(Q,D)}}}}M.fillStyle=this.prefs.overflow_color;if(P||F){var R;if(H==="Histogram"||H==="Intensity"){R=B}else{Q-=2;R=4}if(P){M.fillRect(Q,0,R,3)}if(F){M.fillRect(Q,x-3,R,3)}}M.fillStyle=this.prefs.color}if(H==="Filled"){if(E){M.lineTo(Q,T);M.lineTo(0,T)}M.fill()}else{M.stroke()}M.restore()};var m=function(x){this.feature_positions={};this.slot_height=x;this.translation=0};m.prototype.map_feature_data=function(y,A,x,z){if(!this.feature_positions[A]){this.feature_positions[A]=[]}this.feature_positions[A].push({data:y,x_start:x,x_end:z})};m.prototype.get_feature_data=function(z,D){var C=Math.floor(D/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var n=function(z,C,x,y,B,D,A){l.call(this,z,C,x,y,B);this.alpha_scaler=(D?D:new d());this.height_scaler=(A?A:new d())};n.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};t(n.prototype,{get_required_height:function(y){var x=y_scale=this.get_row_height(),z=this.mode;if(z==="no_detail"||z==="Squish"||z==="Pack"){x=y*y_scale}return x+Math.max(Math.round(y_scale/2),5)},draw:function(J,H,F,E){var P=this.data,C=this.view_start,L=this.view_end;J.save();J.fillStyle=this.prefs.block_color;J.textAlign="right";var G=this.view_end-this.view_start,D=H/G,K=this.get_row_height(),O=new m(K),A;for(var M=0,N=P.length;M<N;M++){var z=P[M],B=z[0],I=z[1],x=z[2],y=(E&&E[B]!==undefined?E[B]:null);if((I<L&&x>C)&&(this.mode=="Dense"||y!==null)){A=this.draw_element(J,this.mode,z,y,C,L,D,K,H);O.map_feature_data(z,y,A[0],A[1])}}J.restore();return O},draw_element:function(D,z,F,B,A,C,E,y,x){console.log("WARNING: Unimplemented function.");return[0,0]}});var c=10,h=3,k=5,v=10,f=1,r=3,e=3,a=9,j=2,g="#ccc";var q=function(z,C,x,y,B,D,A){n.call(this,z,C,x,y,B,D,A)};t(q.prototype,n.prototype,{get_row_height:function(){var y=this.mode,x;if(y==="Dense"){x=c}else{if(y==="no_detail"){x=h}else{if(y==="Squish"){x=k}else{x=v}}}return x},draw_element:function(L,C,U,G,N,af,aj,al,x){var R=U[0],ah=U[1],Z=U[2],P=U[3],aa=Math.floor(Math.max(0,(ah-N)*aj)),M=Math.ceil(Math.min(x,Math.max(0,(Z-N)*aj))),Y=aa,ak=M,X=(C==="Dense"?0:(0+G))*al,K,ad,Q=null,an=null,A=this.prefs.block_color,ac=this.prefs.label_color;L.globalAlpha=this.alpha_scaler.gen_val(U);if(C==="Dense"){G=1}if(C==="no_detail"){L.fillStyle=A;L.fillRect(aa,X+5,M-aa,f)}else{var J=U[4],W=U[5],ab=U[6],B=U[7];if(W&&ab){Q=Math.floor(Math.max(0,(W-N)*aj));an=Math.ceil(Math.min(x,Math.max(0,(ab-N)*aj)))}var ai,S;if(C==="Squish"||C==="Dense"){ai=1;S=e}else{ai=5;S=a}if(!B){if(U.strand){if(U.strand==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand_inv")}else{if(U.strand==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand_inv")}}}else{L.fillStyle=A}L.fillRect(aa,X,M-aa,S)}else{var I,T;if(C==="Squish"||C==="Dense"){L.fillStyle=g;I=X+Math.floor(e/2)+1;T=1}else{if(J){var I=X;var T=S;if(J==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand")}else{if(J==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand")}}}else{L.fillStyle=g;I+=(e/2)+1;T=1}}L.fillRect(aa,I,M-aa,T);var D;for(var ag=0,z=B.length;ag<z;ag++){var E=B[ag],y=Math.floor(Math.max(0,(E[0]-N)*aj)),V=Math.ceil(Math.min(x,Math.max((E[1]-N)*aj)));if(y>V){continue}L.fillStyle=A;L.fillRect(y,X+(S-ai)/2+1,V-y,ai);if(Q!==undefined&&ab>W&&!(y>an||V<Q)){var ae=Math.max(y,Q),H=Math.min(V,an);L.fillRect(ae,X+1,H-ae,S);if(B.length==1&&C=="Pack"){if(J==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand_inv")}else{if(J==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand_inv")}}if(ae+14<H){ae+=2;H-=2}L.fillRect(ae,X+1,H-ae,S)}}}if(C==="Pack"){L.globalAlpha=1;L.fillStyle="white";var F=this.height_scaler.gen_val(U),O=Math.ceil(S*F),am=Math.round((S-O)/2);if(F!==1){L.fillRect(aa,I+1,M-aa,am);L.fillRect(aa,I+S-am+1,M-aa,am)}}}L.globalAlpha=1;if(C==="Pack"&&ah>N){L.fillStyle=ac;if(N===0&&aa-L.measureText(P).width<0){L.textAlign="left";L.fillText(P,M+j,X+8);ak+=L.measureText(P).width+j}else{L.textAlign="right";L.fillText(P,aa-j,X+8);Y-=L.measureText(P).width+j}}}L.globalAlpha=1;return[Y,ak]}});var s=function(A,D,x,z,C,E,B,y){n.call(this,A,D,x,z,C,E,B);this.ref_seq=(y?y.data:null)};s.prototype.default_prefs=t({},n.prototype.default_prefs,{show_insertions:false});t(s.prototype,n.prototype,{get_row_height:function(){var x,y=this.mode;if(y==="Dense"){x=c}else{if(y==="Squish"){x=k}else{x=v;if(this.prefs.show_insertions){x*=2}}}return x},draw_read:function(U,P,L,Z,A,T,I,F,E){U.textAlign="center";var S=this,z=[Z,A],O=0,V=0,R=0,x=U.canvas.manager.char_width_px;var ae=[];if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>x){R=Math.round(L/2)}if(!I){I=[[0,F.length]]}for(var M=0,X=I.length;M<X;M++){var J=I[M],B="MIDNSHP=X"[J[0]],N=J[1];if(B==="H"||B==="S"){O-=N}var G=T+O,ad=Math.floor(Math.max(0,(G-Z)*L)),H=Math.floor(Math.max(0,(G+N-Z)*L));if(ad===H){H+=1}switch(B){case"H":break;case"S":case"M":case"=":if(is_overlap([G,G+N],z)){var Q=F.slice(V,V+N);if(R>0){U.fillStyle=this.prefs.block_color;U.fillRect(ad-R,E+1,H-ad,9);U.fillStyle=g;for(var ab=0,y=Q.length;ab<y;ab++){if(this.prefs.show_differences&&this.ref_seq){var K=this.ref_seq[G-Z+ab];if(!K||K.toLowerCase()===Q[ab].toLowerCase()){continue}}if(G+ab>=Z&&G+ab<=A){var ac=Math.floor(Math.max(0,(G+ab-Z)*L));U.fillText(Q[ab],ac,E+9)}}}else{U.fillStyle=this.prefs.block_color;U.fillRect(ad,E+4,H-ad,e)}}V+=N;O+=N;break;case"N":U.fillStyle=g;U.fillRect(ad-R,E+5,H-ad,1);O+=N;break;case"D":U.fillStyle="red";U.fillRect(ad-R,E+4,H-ad,3);O+=N;break;case"P":break;case"I":var Y=ad-R;if(is_overlap([G,G+N],z)){var Q=F.slice(V,V+N);if(this.prefs.show_insertions){var D=ad-(H-ad)/2;if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>x){U.fillStyle="yellow";U.fillRect(D-R,E-9,H-ad,9);ae[ae.length]={type:"triangle",data:[Y,E+4,5]};U.fillStyle=g;switch(compute_overlap([G,G+N],z)){case (OVERLAP_START):Q=Q.slice(Z-G);break;case (OVERLAP_END):Q=Q.slice(0,G-A);break;case (CONTAINED_BY):break;case (CONTAINS):Q=Q.slice(Z-G,G-A);break}for(var ab=0,y=Q.length;ab<y;ab++){var ac=Math.floor(Math.max(0,(G+ab-Z)*L));U.fillText(Q[ab],ac-(H-ad)/2,E)}}else{U.fillStyle="yellow";U.fillRect(D,E+(this.mode!=="Dense"?2:5),H-ad,(P!=="Dense"?e:r))}}else{if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>x){ae.push({type:"text",data:[Q.length,Y,E+9]})}else{}}}V+=N;break;case"X":V+=N;break}}U.fillStyle="yellow";var aa,C,af;for(var W=0;W<ae.length;W++){aa=ae[W];C=aa.type;af=aa.data;if(C==="text"){U.save();U.font="bold "+U.font;U.fillText(af[0],af[1],af[2]);U.restore()}else{if(C=="triangle"){p(U,af[0],af[1],af[2])}}}},draw_element:function(Q,L,D,A,T,y,H,R,O){var G=D[0],P=D[1],z=D[2],I=D[3],C=Math.floor(Math.max(0,(P-T)*H)),E=Math.ceil(Math.min(O,Math.max(0,(z-T)*H))),B=(L==="Dense"?0:(0+A))*R,U=this.prefs.block_color,F=this.prefs.label_color,N=0;if((L==="Pack"||this.mode==="Auto")&&H>Q.canvas.manager.char_width_px){var N=Math.round(H/2)}Q.fillStyle=U;if(D[5] instanceof Array){var M=Math.floor(Math.max(0,(D[4][0]-T)*H)),K=Math.ceil(Math.min(O,Math.max(0,(D[4][1]-T)*H))),J=Math.floor(Math.max(0,(D[5][0]-T)*H)),x=Math.ceil(Math.min(O,Math.max(0,(D[5][1]-T)*H)));if(D[4][1]>=T&&D[4][0]<=y&&D[4][2]){this.draw_read(Q,L,H,T,y,D[4][0],D[4][2],D[4][3],B)}if(D[5][1]>=T&&D[5][0]<=y&&D[5][2]){this.draw_read(Q,L,H,T,y,D[5][0],D[5][2],D[5][3],B)}if(J>K){Q.fillStyle=g;o(Q,K-N,B+5,J-N,B+5)}}else{Q.fillStyle=U;this.draw_read(Q,L,H,T,y,P,D[4],D[5],B)}if(L==="Pack"&&P>T&&I!=="."){Q.fillStyle=this.prefs.label_color;var S=1;if(S===0&&C-Q.measureText(I).width<0){Q.textAlign="left";Q.fillText(I,E+j-N,B+8)}else{Q.textAlign="right";Q.fillText(I,C-j-N,B+8)}Q.fillStyle=U}return[0,0]}});w.Scaler=d;w.SummaryTreePainter=u;w.LinePainter=b;w.LinkedFeaturePainter=q;w.ReadPainter=s};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window);
\ No newline at end of file
diff --git a/static/scripts/packed/trackster_ui.js b/static/scripts/packed/trackster_ui.js
index 0915be0fc30..f9e907210f0 100644
--- a/static/scripts/packed/trackster_ui.js
+++ b/static/scripts/packed/trackster_ui.js
@@ -1 +1 @@
-var add_bookmark=function(b,a){var g=$("#bookmarks-container"),d=$("<div/>").addClass("bookmark").appendTo(g),c=$("<div/>").addClass("delete-icon-container").appendTo(d).click(function(){d.slideUp("fast");d.remove();view.has_changes=true;return false}),e=$("<a href=''/>").addClass("icon-button delete").appendTo(c),f=$("<div/>").addClass("position").appendTo(d),h=$("<a href=''/>").text(b).appendTo(f).click(function(){view.go_to(b);return false});annotation_div=get_editable_text_elt(a,true).addClass("annotation").appendTo(d);view.has_changes=true;return d};var addable_objects={LineTrack:LineTrack,FeatureTrack:FeatureTrack,ReadTrack:ReadTrack,DrawableGroup:DrawableGroup};var track_from_dict=function(c,b){var a=new addable_objects[c.track_type](c.name,view,b,c.hda_ldda,c.dataset_id,c.prefs,c.filters,c.tool);if(c.mode){a.change_mode(c.mode)}return a};var drawable_collection_from_dict=function(f,a){var e=new addable_objects[f.obj_type](f.name,view,a,f.prefs,view.viewport_container,view);for(var d=0;d<f.drawables.length;d++){var b=f.drawables[d],c;if(b.track_type){c=track_from_dict(b,e)}else{c=drawable_collection_from_dict(b)}e.add_drawable(c);e.content_div.append(c.container_div)}return e};var drawable_from_dict=function(b,a){return(b.track_type?track_from_dict(b,a):drawable_collection_from_dict(b,a))};var create_visualization=function(b,e,g,c,a,d,f){view=new View(b,e,g,c);view.editor=true;$.when(view.load_chroms_deferred).then(function(){if(a){var k=a.chrom,p=a.start,h=a.end,m=a.overview;if(k&&(p!==undefined)&&h){view.change_chrom(k,p,h)}}if(d){var o;for(var j=0;j<d.length;j++){o=d[j];view.add_drawable(drawable_from_dict(o,view))}}var n;for(var j=0;j<view.drawables.length;j++){if(view.drawables[j].name===m){view.set_overview(view.drawables[j]);break}}if(f){var l;for(var j=0;j<f.length;j++){l=f[j];add_bookmark(l.position,l.annotation)}}view.has_changes=false});return view};var init_keyboard_nav=function(a){$(document).keydown(function(b){if($(b.srcElement).is(":input")){return}switch(b.which){case 37:a.move_fraction(0.25);break;case 38:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("-="+c+"px");break;case 39:a.move_fraction(-0.25);break;case 40:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("+="+c+"px");break}})};
\ No newline at end of file
+var add_bookmark=function(b,a){var g=$("#bookmarks-container"),d=$("<div/>").addClass("bookmark").appendTo(g),c=$("<div/>").addClass("delete-icon-container").appendTo(d).click(function(){d.slideUp("fast");d.remove();view.has_changes=true;return false}),e=$("<a href=''/>").addClass("icon-button delete").appendTo(c),f=$("<div/>").addClass("position").appendTo(d),h=$("<a href=''/>").text(b).appendTo(f).click(function(){view.go_to(b);return false});annotation_div=get_editable_text_elt(a,true).addClass("annotation").appendTo(d);view.has_changes=true;return d};var addable_objects={LineTrack:LineTrack,FeatureTrack:FeatureTrack,VcfTrack:VcfTrack,ReadTrack:ReadTrack,DrawableGroup:DrawableGroup};var track_from_dict=function(c,b){var a=new addable_objects[c.track_type](c.name,view,b,c.hda_ldda,c.dataset_id,c.prefs,c.filters,c.tool);if(c.mode){a.change_mode(c.mode)}return a};var drawable_collection_from_dict=function(f,a){var e=new addable_objects[f.obj_type](f.name,view,a,f.prefs,view.viewport_container,view);for(var d=0;d<f.drawables.length;d++){var b=f.drawables[d],c;if(b.track_type){c=track_from_dict(b,e)}else{c=drawable_collection_from_dict(b)}e.add_drawable(c);e.content_div.append(c.container_div)}return e};var drawable_from_dict=function(b,a){return(b.track_type?track_from_dict(b,a):drawable_collection_from_dict(b,a))};var create_visualization=function(b,e,g,c,a,d,f){view=new View(b,e,g,c);view.editor=true;$.when(view.load_chroms_deferred).then(function(){if(a){var k=a.chrom,p=a.start,h=a.end,m=a.overview;if(k&&(p!==undefined)&&h){view.change_chrom(k,p,h)}}if(d){var o;for(var j=0;j<d.length;j++){o=d[j];view.add_drawable(drawable_from_dict(o,view))}}var n;for(var j=0;j<view.drawables.length;j++){if(view.drawables[j].name===m){view.set_overview(view.drawables[j]);break}}if(f){var l;for(var j=0;j<f.length;j++){l=f[j];add_bookmark(l.position,l.annotation)}}view.has_changes=false});return view};var init_keyboard_nav=function(a){$(document).keydown(function(b){if($(b.srcElement).is(":input")){return}switch(b.which){case 37:a.move_fraction(0.25);break;case 38:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("-="+c+"px");break;case 39:a.move_fraction(-0.25);break;case 40:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("+="+c+"px");break}})};
\ No newline at end of file
diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index ce87c95f0f3..d09aa17f024 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -3526,7 +3526,28 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
 
 var VcfTrack = function(name, view, container, hda_ldda, dataset_id, prefs, filters) {
     FeatureTrack.call(this, name, view, container, hda_ldda, dataset_id, prefs, filters);
-    this.painter = painters.VariantPainter;
+    
+    this.config = new DrawableConfig( {
+        track: this,
+        params: [
+            { key: 'name', label: 'Name', type: 'text', default_value: name },
+            { key: 'block_color', label: 'Block color', type: 'color', default_value: get_random_color() },
+            { key: 'label_color', label: 'Label color', type: 'color', default_value: 'black' },
+            { key: 'show_insertions', label: 'Show insertions', type: 'bool', default_value: false },
+            { key: 'show_counts', label: 'Show summary counts', type: 'bool', default_value: true },
+            { key: 'mode', type: 'string', default_value: this.mode, hidden: true },
+        ], 
+        saved_values: prefs,
+        onchange: function() {
+            this.track.set_name(this.track.prefs.name);
+            this.track.tile_cache.clear();
+            this.track.request_draw();
+        }
+    });
+    this.prefs = this.config.values;
+    
+    
+    this.painter = painters.ReadPainter;
 };
 
 extend(VcfTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype);
@@ -3605,6 +3626,7 @@ exports.DrawableGroup = DrawableGroup;
 exports.LineTrack = LineTrack;
 exports.FeatureTrack = FeatureTrack;
 exports.ReadTrack = ReadTrack;
+exports.VcfTrack = VcfTrack;
 
 // End trackster_module encapsulation
 };
@@ -4173,20 +4195,20 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
      * Height of a single row, depends on mode
      */
     get_row_height: function() {
-        var mode = this.mode, y_scale;
+        var mode = this.mode, height;
            if (mode === "Dense") {
-            y_scale = DENSE_TRACK_HEIGHT;            
+            height = DENSE_TRACK_HEIGHT;            
         }
         else if (mode === "no_detail") {
-            y_scale = NO_DETAIL_TRACK_HEIGHT;
+            height = NO_DETAIL_TRACK_HEIGHT;
         }
         else if (mode === "Squish") {
-            y_scale = SQUISH_TRACK_HEIGHT;
+            height = SQUISH_TRACK_HEIGHT;
         }
         else { // mode === "Pack"
-            y_scale = PACK_TRACK_HEIGHT;
+            height = PACK_TRACK_HEIGHT;
         }
-        return y_scale;
+        return height;
     },
 
     /**
@@ -4212,7 +4234,7 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
         ctx.globalAlpha = this.alpha_scaler.gen_val(feature);
         
         // In dense mode, put all data in top slot.
-        if (mode == "Dense") {
+        if (mode === "Dense") {
             slot = 1;
         }
         
@@ -4375,65 +4397,6 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
     }
 });
 
-
-var VariantPainter = function(data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler) {
-    FeaturePainter.call(this, data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler);
-}
-
-extend(VariantPainter.prototype, FeaturePainter.prototype, {
-    draw_element: function(ctx, mode, feature, slot, tile_low, tile_high, w_scale, y_scale, width) {
-        var feature = data[i],
-            feature_uid = feature[0],
-            feature_start = feature[1],
-            feature_end = feature[2],
-            feature_name = feature[3],
-            // All features need a start, end, and vertical center.
-            f_start = Math.floor( Math.max(0, (feature_start - tile_low) * w_scale) ),
-            f_end   = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low) * w_scale)) ),
-            y_center = (mode === "Dense" ? 0 : (0 + slot)) * y_scale,
-            thickness, y_start, thick_start = null, thick_end = null;
-        
-        if (no_label) {
-            ctx.fillStyle = block_color;
-            ctx.fillRect(f_start + left_offset, y_center + 5, f_end - f_start, 1);
-        } 
-        else { // Show blocks, labels, etc.                        
-            // Unpack.
-            var ref_base = feature[4], alt_base = feature[5], qual = feature[6];
-        
-            // Draw block for entry.
-            thickness = 9;
-            y_start = 1;
-            ctx.fillRect(f_start + left_offset, y_center, f_end - f_start, thickness);
-        
-            // Add label for entry.
-            if (mode !== "Dense" && feature_name !== undefined && feature_start > tile_low) {
-                // Draw label
-                ctx.fillStyle = label_color;
-                if (tile_low === 0 && f_start - ctx.measureText(feature_name).width < 0) {
-                    ctx.textAlign = "left";
-                    ctx.fillText(feature_name, f_end + 2 + left_offset, y_center + 8);
-                } else {
-                    ctx.textAlign = "right";
-                    ctx.fillText(feature_name, f_start - 2 + left_offset, y_center + 8);
-                }
-                ctx.fillStyle = block_color;
-            }
-        
-            // Show additional data on block.
-            var vcf_label = ref_base + " / " + alt_base;
-            if (feature_start > tile_low && ctx.measureText(vcf_label).width < (f_end - f_start)) {
-                ctx.fillStyle = "white";
-                ctx.textAlign = "center";
-                ctx.fillText(vcf_label, left_offset + f_start + (f_end-f_start)/2, y_center + 8);
-                ctx.fillStyle = block_color;
-            }
-        }
-        
-        return [f_start, f_end];
-    }
-});
-
 var ReadPainter = function(data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler, ref_seq) {
     FeaturePainter.call(this, data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler);
     this.ref_seq = (ref_seq ? ref_seq.data : null);
@@ -4443,23 +4406,23 @@ ReadPainter.prototype.default_prefs = extend({}, FeaturePainter.prototype.defaul
 
 extend(ReadPainter.prototype, FeaturePainter.prototype, {
     /**
-     * Returns y_scale based on mode.
+     * Returns height based on mode.
      */
     get_row_height: function() {
-        var y_scale, mode = this.mode;
+        var height, mode = this.mode;
         if (mode === "Dense") {
-            y_scale = DENSE_TRACK_HEIGHT;            
+            height = DENSE_TRACK_HEIGHT;            
         }
         else if (mode === "Squish") {
-            y_scale = SQUISH_TRACK_HEIGHT;
+            height = SQUISH_TRACK_HEIGHT;
         }
         else { // mode === "Pack"
-            y_scale = PACK_TRACK_HEIGHT;
+            height = PACK_TRACK_HEIGHT;
             if (this.prefs.show_insertions) {
-                y_scale *= 2;
+                height *= 2;
             }
         }
-        return y_scale;
+        return height;
     },
     
     /**
@@ -4585,7 +4548,7 @@ extend(ReadPainter.prototype, FeaturePainter.prototype, {
                                 draw_last[draw_last.length] = {type: "triangle", data: [insert_x_coord, y_center + 4, 5]};
                                 ctx.fillStyle = CONNECTOR_COLOR;
                                 // Based on overlap b/t sequence and tile, get sequence to be drawn.
-                                switch(seq_tile_overlap) {
+                                switch( compute_overlap( [seq_start, seq_start + cig_len], tile_region ) ) {
                                     case(OVERLAP_START):
                                         seq = seq.slice(tile_low-seq_start);
                                         break;
@@ -4616,7 +4579,7 @@ extend(ReadPainter.prototype, FeaturePainter.prototype, {
                         else {
                             if ( (mode === "Pack" || this.mode === "Auto") && orig_seq !== undefined && w_scale > char_width_px) {
                                 // Show insertions with a single number at the insertion point.
-                                draw_last[draw_last.length] = {type: "text", data: [seq.length, insert_x_coord, y_center + 9]};
+                                draw_last.push( { type: "text", data: [seq.length, insert_x_coord, y_center + 9] } );
                             }
                             else {
                                 // TODO: probably can merge this case with code above.
@@ -4703,7 +4666,7 @@ extend(ReadPainter.prototype, FeaturePainter.prototype, {
             ctx.fillStyle = block_color;
             this.draw_read(ctx, mode, w_scale, tile_low, tile_high, feature_start, feature[4], feature[5], y_center);
         }
-        if (mode === "Pack" && feature_start > tile_low) {
+        if (mode === "Pack" && feature_start > tile_low && feature_name !== ".") {
             // Draw label.
             ctx.fillStyle = this.prefs.label_color;
             // FIXME: eliminate tile_index
@@ -4728,7 +4691,6 @@ exports.SummaryTreePainter = SummaryTreePainter;
 exports.LinePainter = LinePainter;
 exports.LinkedFeaturePainter = LinkedFeaturePainter;
 exports.ReadPainter = ReadPainter;
-exports.VariantPainter = VariantPainter;
 
 // End painters_module encapsulation
 };
diff --git a/static/scripts/trackster_ui.js b/static/scripts/trackster_ui.js
index 87b0f68e2b7..1f69df5c46a 100644
--- a/static/scripts/trackster_ui.js
+++ b/static/scripts/trackster_ui.js
@@ -31,7 +31,7 @@ var add_bookmark = function(position, annotation) {
 /**
  * Objects that can be added to a view.
  */
-var addable_objects = { "LineTrack": LineTrack, "FeatureTrack": FeatureTrack, "ReadTrack": ReadTrack, "DrawableGroup": DrawableGroup };
+var addable_objects = { "LineTrack": LineTrack, "FeatureTrack": FeatureTrack, "VcfTrack": VcfTrack, "ReadTrack": ReadTrack, "DrawableGroup": DrawableGroup };
 
 /**
  * Decode a track from a dictionary.

From 463c2d34ebc687566ad5863dbdb0690f60e4f524 Mon Sep 17 00:00:00 2001
From: John Duddy <jduddy@illumina.com>
Date: Mon, 31 Oct 2011 13:13:12 -0700
Subject: [PATCH 120/362] Fix copy/paste errors in histry contents API

---
 lib/galaxy/web/api/history_contents.py | 4 +++-
 lib/galaxy/web/base/controller.py      | 8 +++++---
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/web/api/history_contents.py b/lib/galaxy/web/api/history_contents.py
index 7c4808fd78e..c583e46410d 100644
--- a/lib/galaxy/web/api/history_contents.py
+++ b/lib/galaxy/web/api/history_contents.py
@@ -50,7 +50,9 @@ class HistoryContentsController( BaseAPIController, UsesHistoryDatasetAssociatio
         """
         content_id = id
         try:
-            content = self.get_history_dataset_association( trans, content_id, check_ownership=True, check_accessible=True )
+            # get the history just for the access checks
+            history = self.get_history( trans, history_id, check_ownership=True, check_accessible=True, deleted=False )
+            content = self.get_history_dataset_association( trans, history, content_id, check_ownership=True, check_accessible=True )
         except Exception, e:
             return str( e )
         try:
diff --git a/lib/galaxy/web/base/controller.py b/lib/galaxy/web/base/controller.py
index aac24eca02e..b4cbec7a497 100644
--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -233,16 +233,18 @@ class UsesHistoryDatasetAssociation:
             else:
                 error( "You are not allowed to access this dataset" )
         return data
-    def get_history_dataset_association( self, trans, dataset_id, check_ownership=True, check_accessible=False ):
+    def get_history_dataset_association( self, trans, history, dataset_id, check_ownership=True, check_accessible=False ):
         """Get a HistoryDatasetAssociation from the database by id, verifying ownership."""
-        hda = self.get_object( trans, id, 'HistoryDatasetAssociation', check_ownership=check_ownership, check_accessible=check_accessible, deleted=deleted )
-        self.security_check( trans, history, check_ownership=check_ownership, check_accessible=False ) # check accessibility here
+        self.security_check( trans, history, check_ownership=check_ownership, check_accessible=check_accessible )
+        hda = self.get_object( trans, dataset_id, 'HistoryDatasetAssociation', check_ownership=False, check_accessible=False, deleted=False )
+        
         if check_accessible:
             if trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ):
                 if hda.state == trans.model.Dataset.states.UPLOAD:
                     error( "Please wait until this dataset finishes uploading before attempting to view it." )
             else:
                 error( "You are not allowed to access this dataset" )
+        return hda
     def get_data( self, dataset, preview=True ):
         """ Gets a dataset's data. """
         # Get data from file, truncating if necessary.

From adccc7539d93c655e3e3b607b55d1287f1f6955d Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Mon, 31 Oct 2011 16:20:55 -0400
Subject: [PATCH 121/362] Clean up for some GATK tools.

---
 tools/gatk/count_covariates.xml     | 4 ++--
 tools/gatk/unified_genotyper.xml    | 8 ++++----
 tools/gatk/variant_annotator.xml    | 4 ++--
 tools/gatk/variant_recalibrator.xml | 2 +-
 4 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/tools/gatk/count_covariates.xml b/tools/gatk/count_covariates.xml
index dcf712b416b..5a9da7a6e82 100644
--- a/tools/gatk/count_covariates.xml
+++ b/tools/gatk/count_covariates.xml
@@ -19,8 +19,8 @@
     #end if
     --recal_file "${output_recal}"
     ${standard_covs}
-    #if $covariates.value:
-        #for $cov in $covariates.value:
+    #if str( $covariates ) != "None":
+        #for $cov in str( $covariates ).split( ',' ):
             -cov "${cov}"
         #end for
     #end if
diff --git a/tools/gatk/unified_genotyper.xml b/tools/gatk/unified_genotyper.xml
index c9144233946..263187c44ca 100644
--- a/tools/gatk/unified_genotyper.xml
+++ b/tools/gatk/unified_genotyper.xml
@@ -112,13 +112,13 @@
         --indelGapOpenPenalty "${analysis_param_type.indelGapOpenPenalty}"
         --indelHaplotypeSize "${analysis_param_type.indelHaplotypeSize}"
         ${analysis_param_type.doContextDependentGapPenalties}
-        #if $analysis_param_type.annotation.value:
-            #for $annotation in $analysis_param_type.annotation.value:
+        #if str( $analysis_param_type.annotation ) != "None":
+            #for $annotation in str( $analysis_param_type.annotation ).split( ','):
                 --annotation "${annotation}"
             #end for
         #end if
-        #if $analysis_param_type.group.value:
-            #for $group in $analysis_param_type.group.value:
+        #if str( $analysis_param_type.group ) != "None":
+            #for $group in str( $analysis_param_type.group ).split( ','):
                 --group "${group}"
             #end for
         #end if
diff --git a/tools/gatk/variant_annotator.xml b/tools/gatk/variant_annotator.xml
index 6302a0f69b5..3dc654c151b 100644
--- a/tools/gatk/variant_annotator.xml
+++ b/tools/gatk/variant_annotator.xml
@@ -24,7 +24,7 @@
     #if str( $annotations_type.annotations_type_selector ) == "use_all_annotations":
         --useAllAnnotations
     #else:
-        #if $annotations_type.annotations.value:
+        #if str( $annotations_type.annotations ) != "None":
             #for $annotation in str( $annotations_type.annotations ).split( ',' ):
                 --annotation "${annotation}"
             #end for
@@ -127,7 +127,7 @@
     ##end standard gatk options
     
     -p '
-    #if $annotation_group.value:
+    #if str( $annotation_group ) != "None":
         #for $group in str( $annotation_group ).split( ',' ):
             --group "${group}"
         #end for
diff --git a/tools/gatk/variant_recalibrator.xml b/tools/gatk/variant_recalibrator.xml
index c7159426829..35400ff2713 100644
--- a/tools/gatk/variant_recalibrator.xml
+++ b/tools/gatk/variant_recalibrator.xml
@@ -98,7 +98,7 @@
     
     ##start analysis specific options
     -p '
-    #if $annotations.value:
+    #if str( $annotations ) != "None":
         #for $annotation in str( $annotations ).split( ',' ):
             --use_annotation "${annotation}"
         #end for

From 7633e2c3b4609f6aa37c156098c8b294ffb9d71e Mon Sep 17 00:00:00 2001
From: Richard Burhans <burhans@bx.psu.edu>
Date: Mon, 31 Oct 2011 17:05:24 -0400
Subject: [PATCH 122/362] refactored Tabular.make_html_table()

---
 lib/galaxy/datatypes/tabular.py | 81 +++++++++++++--------------------
 1 file changed, 32 insertions(+), 49 deletions(-)

diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py
index e83ed2ce436..dcd60cc4f00 100644
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -164,64 +164,47 @@ class Tabular( data.Text ):
         dataset.metadata.comment_lines = comment_lines
         dataset.metadata.column_types = column_types
         dataset.metadata.columns = len( column_types )
-    def make_html_table( self, dataset, skipchars=[] ):
+    def make_html_table( self, dataset, **kwargs ):
         """Create HTML table, used for displaying peek"""
         out = ['<table cellspacing="0" cellpadding="3">']
         try:
-            out.append( '<tr>' )
-            # Generate column header
-            for i in range( 1, dataset.metadata.columns+1 ):
-                out.append( '<th>%s</th>' % str( i ) )
-            out.append( '</tr>' )
-            out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) )
+            out.append( self.make_html_peek_header( dataset, kwargs ) )
+            out.append( self.make_html_peek_rows( dataset, kwargs ) )
             out.append( '</table>' )
             out = "".join( out )
         except Exception, exc:
             out = "Can't create peek %s" % str( exc )
         return out
-    def make_html_peek_rows( self, dataset, skipchars=[] ):
-        out = [""]
-        comments = []
-        if not dataset.peek:
-            dataset.set_peek()
-        data = dataset.peek
-        lines =  data.splitlines()
-        for line in lines:
-            line = line.rstrip( '\r\n' )
-            if not line:
-                continue
-            comment = False
-            for skipchar in skipchars:
-                if line.startswith( skipchar ):
-                    comments.append( line )
-                    comment = True
-                    break
-            if comment:
-                continue
-            elems = line.split( '\t' )
-            if len( elems ) != dataset.metadata.columns:
-                # We may have an invalid comment line or invalid data
-                comments.append( line )
-                comment = True
-                continue
-            while len( comments ) > 0: # Keep comments
-                try:
-                    out.append( '<tr><td colspan="100%">' )
-                except:
-                    out.append( '<tr><td>' )
-                out.append( '%s</td></tr>'  % escape( comments.pop(0) ) )
+    def make_html_peek_header( self, dataset, skipchars=[] ):
+        out = []
+        try:
             out.append( '<tr>' )
-            for elem in elems: # valid data
-                elem = escape( elem )
-                out.append( '<td>%s</td>' % elem )
+            for i in range( 1, dataset.metadata.columns+1 ):
+                out.append( '<th>%s</th>' % str( i ) )
             out.append( '</tr>' )
-        # Peek may consist only of comments
-        while len( comments ) > 0:
-            try:
-                out.append( '<tr><td colspan="100%">' )
-            except:
-                out.append( '<tr><td>' )
-            out.append( '%s</td></tr>'  % escape( comments.pop(0) ) )
+        except Exception, exc:
+            raise Exception, "Can't create peek header %s" % str( exc )
+        return "".join( out )
+    def make_html_peek_rows( self, dataset, skipchars=[] ):
+        out = []
+        try:
+            if not dataset.peek:
+                dataset.set_peek()
+            for line in dataset.peek.splitlines():
+                if line.startswith( tuple( skipchars ) ):
+                    out.append( '<tr><td colspan="100%%">%s</td></tr>' % escape( line ) )
+                elif line:
+                    elems = line.split( '\t' )
+                    # we may have an invalid comment line or invalid data
+                    if len( elems ) != dataset.metadata.columns:
+                        out.append( '<tr><td colspan="100%%">%s</td></tr>' % escape( line ) )
+                    else:
+                        out.append( '<tr>' )
+                        for elem in elems:
+                            out.append( '<td>%s</td>' % escape( elem ) )
+                        out.append( '</tr>' )
+        except Exception, exc:
+            raise Exception, "Can't create peek rows %s" % str( exc )
         return "".join( out )
     def set_peek( self, dataset, line_count=None, is_multi_byte=False):
         super(Tabular, self).set_peek( dataset, line_count=line_count, is_multi_byte=is_multi_byte)
@@ -498,4 +481,4 @@ class Vcf( Tabular ):
         return out
         
     def get_track_type( self ):
-        return "VcfTrack", {"data": "tabix", "index": "summary_tree"}
+        return "FeatureTrack", {"data": "tabix", "index": "summary_tree"}

From 9c902705ea37c36dae8951690ae360e7bd69eb20 Mon Sep 17 00:00:00 2001
From: Richard Burhans <burhans@bx.psu.edu>
Date: Mon, 31 Oct 2011 17:13:24 -0400
Subject: [PATCH 123/362] I had an older tabular.py, fixed one line that got
 changed by mistake

---
 lib/galaxy/datatypes/tabular.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py
index dcd60cc4f00..0e393bf3558 100644
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -481,4 +481,4 @@ class Vcf( Tabular ):
         return out
         
     def get_track_type( self ):
-        return "FeatureTrack", {"data": "tabix", "index": "summary_tree"}
+        return "VcfTrack", {"data": "tabix", "index": "summary_tree"}

From 725f613e30783f6c0f31fa370a1d5d909a5ce0fb Mon Sep 17 00:00:00 2001
From: James Taylor <james@jamestaylor.org>
Date: Mon, 31 Oct 2011 18:06:30 -0400
Subject: [PATCH 124/362] Trackster: for line tracks, compute default range
 using +/- two standard deviations around mean, for feature tracks, make
 feature popup look more like other tooltips

---
 .../visualization/tracks/data_providers.py    | 25 ++++++++++++++-----
 static/june_2007_style/blue/trackster.css     |  3 ++-
 static/june_2007_style/trackster.css.tmpl     | 15 +++++++++--
 static/scripts/trackster.js                   | 22 ++++++++++++----
 4 files changed, 51 insertions(+), 14 deletions(-)

diff --git a/lib/galaxy/visualization/tracks/data_providers.py b/lib/galaxy/visualization/tracks/data_providers.py
index 3c09a8dc7d3..30bcb726e36 100644
--- a/lib/galaxy/visualization/tracks/data_providers.py
+++ b/lib/galaxy/visualization/tracks/data_providers.py
@@ -2,8 +2,8 @@
 Data providers for tracks visualizations.
 """
 
-import sys
-from math import ceil, log
+import sys, time
+from math import ceil, log, sqrt
 import pkg_resources
 pkg_resources.require( "bx-python" )
 if sys.version_info[:2] == (2, 4):
@@ -435,9 +435,9 @@ class BBIDataProvider( TracksDataProvider ):
         # original_dataset, or coming from wig->bigwig conversion in which we use converted_dataset
         f, bbi = self._get_dataset()
        
-        # If the stats kwarg was provide, we compute overall summary data for the entire chromosome,
-        # but no reduced data -- currently only providing min/max which is used by trackster to 
-        # determine the default range
+        # If the stats kwarg was provide, we compute overall summary data for
+        # the entire chromosome, but no reduced data -- currently only
+        # providing values used by trackster to determine the default range
         if 'stats' in kwargs:
             # FIXME: use actual chromosome size
             summary = bbi.summarize( chrom, 0, 214783647, 1 )
@@ -445,7 +445,20 @@ class BBIDataProvider( TracksDataProvider ):
             if summary is None:
                 return None
             else:
-                return dict( data=dict( min=summary.min_val[0], max=summary.max_val[0] ) )
+                # Does the summary contain any defined values?
+                valid_count = summary.valid_count[0]
+                if summary.valid_count < 1:
+                    return None
+
+                # Compute $\mu \pm 2\sigma$ to provide an estimate for upper and lower
+                # bounds that contain ~95% of the data.
+                mean = summary.sum_data[0] / valid_count
+                var = summary.sum_squares[0] - mean
+                if valid_count > 1:
+                    var /= valid_count - 1
+                sd = sqrt( var )
+
+                return dict( data=dict( min=summary.min_val[0], max=summary.max_val[0], mean=mean, sd=sd ) )
 
         start = int(start)
         end = int(end)
diff --git a/static/june_2007_style/blue/trackster.css b/static/june_2007_style/blue/trackster.css
index e4f2aad9f4b..a9ba82ae395 100644
--- a/static/june_2007_style/blue/trackster.css
+++ b/static/june_2007_style/blue/trackster.css
@@ -87,4 +87,5 @@ input{font:10px verdana;}
 .icon.more-across{background:url('../images/fugue/arrow-transition-bw.png') no-repeat 0px 0px;}
 .intro{padding:1em;}
 .intro > .action-button{background-color:#CCC;padding:1em;}
-.feature-popup{background-color:#DDD;position:absolute;z-index:1000;}
+.feature-popup{position:absolute;z-index:1000;padding:5px;font-size:10px;filter:alpha(opacity=80);background-repeat:no-repeat;background-image:url(../images/tipsy.gif);background-position:top center;}
+.feature-popup-inner{padding:5px 8px 4px 8px;background-color:black;color:white;}
diff --git a/static/june_2007_style/trackster.css.tmpl b/static/june_2007_style/trackster.css.tmpl
index 2d051579f83..a902ec965d0 100644
--- a/static/june_2007_style/trackster.css.tmpl
+++ b/static/june_2007_style/trackster.css.tmpl
@@ -405,8 +405,19 @@ input {
     background-color: #CCC;
     padding: 1em;
 }
-.feature-popup { 
-    background-color: #DDD;
+
+.feature-popup {
     position: absolute;
     z-index: 1000;
+    padding: 5px;
+    font-size: 10px;
+    filter: alpha(opacity=80);
+    background-repeat: no-repeat;
+    background-image: url(../images/tipsy.gif);
+    background-position: top center;
+}
+.feature-popup-inner {
+    padding: 5px 8px 4px 8px;
+    background-color: black;
+    color: white;
 }
diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index 0657c8a8018..49006daba95 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -2268,8 +2268,8 @@ FeatureTrackTile.prototype.predisplay_actions = function() {
                 // Build popup.
                 
                 var popup = $("<div/>").attr("id", feature_uid).addClass("feature-popup"),
-                    key, value, 
-                    table = $("<table/>").appendTo(popup), row;
+                    table = $("<table/>"),
+                    key, value, row;
                 for (key in feature_dict) {
                     value = feature_dict[key];
                     row = $("<tr/>").appendTo(table);
@@ -2277,6 +2277,7 @@ FeatureTrackTile.prototype.predisplay_actions = function() {
                     $("<td/>").attr("align", "left").appendTo(row)
                               .text(typeof(value) == 'number' ? round(value, 2) : value);
                 }
+                popup.append( $("<div class='feature-popup-inner'>").append( table ) ); 
                 popups[feature_uid] = popup;
             }
             
@@ -2287,7 +2288,7 @@ FeatureTrackTile.prototype.predisplay_actions = function() {
             // parseInt strips "px" from left, top measurements. +7 so that mouse pointer does not
             // overlap popup.
             var 
-                popupX = offsetX + parseInt( tile.canvas.css("left") ) + 7,
+                popupX = offsetX + parseInt( tile.canvas.css("left") ) - popup.width() / 2,
                 popupY = offsetY + parseInt( tile.canvas.css("top") ) + 7;
             popup.css("left", popupX + "px").css("top", popupY + "px")
         }
@@ -3080,9 +3081,20 @@ extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
             track.container_div.addClass( "line-track" );
             var data = result.data;
             if ( isNaN(parseFloat(track.prefs.min_value)) || isNaN(parseFloat(track.prefs.max_value)) ) {
-                track.prefs.min_value = data.min;
-                track.prefs.max_value = data.max;
+                // Compute default minimum and maximum values
+                var min_value = data.min
+                var max_value = data.max
+                // If mean and sd are present, use them to compute a ~95% window
+                // but only if it would shrink the range on one side
+                min_value = Math.floor( Math.min( 0, Math.max( min_value, data.mean - 2 * data.sd ) ) )
+                max_value = Math.ceil( Math.max( 0, Math.min( max_value, data.mean + 2 * data.sd ) ) )
+                // Update the prefs
+                track.prefs.min_value = min_value;
+                track.prefs.max_value = max_value;
                 // Update the config
+                // FIXME: we should probably only save this when the user explicately sets it
+                //        since we lose the ability to compute it on the fly (when changing 
+                //        chromosomes for example).
                 $('#track_' + track.dataset_id + '_minval').val(track.prefs.min_value);
                 $('#track_' + track.dataset_id + '_maxval').val(track.prefs.max_value);
             }

From 97eee3d2ea0edc0440440828fb4f83b1d91a20d0 Mon Sep 17 00:00:00 2001
From: James Taylor <james@jamestaylor.org>
Date: Mon, 31 Oct 2011 18:31:15 -0400
Subject: [PATCH 125/362] Trackster: faster x axis drag/wheel scrolling, seems
 to work across browsers, but hard to tell across platforms, report your
 experiences

---
 static/scripts/trackster.js | 1 +
 1 file changed, 1 insertion(+)

diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index ddf5b8c6eda..8c94fde7fc3 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -1024,6 +1024,7 @@ extend( View.prototype, DrawableCollection.prototype, {
             // Only act on x axis scrolling if we see if, y will be i
             // handled by the browser when the event bubbles up
             if ( dx ) {
+                dx *= 50;
                 var delta_chrom = Math.round( - dx / view.viewport_container.width() * (view.high - view.low) );
                 view.move_delta( delta_chrom );
             }

From d590988ab2c6baed55a6cb9a2dcfb0f8ebf7a403 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Tue, 1 Nov 2011 08:56:07 -0400
Subject: [PATCH 126/362] Fix label for 'How to specify bad variants' in
 variant_recalibrator.xml

---
 tools/gatk/variant_recalibrator.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/gatk/variant_recalibrator.xml b/tools/gatk/variant_recalibrator.xml
index 35400ff2713..65a26f47ada 100644
--- a/tools/gatk/variant_recalibrator.xml
+++ b/tools/gatk/variant_recalibrator.xml
@@ -515,7 +515,7 @@
         <param name="dirichlet" type="float" label="dirichlet parameter in variational Bayes algorithm" value="0.001"/>
         <param name="prior_counts" type="float" label="number of prior counts to use in variational Bayes algorithm" value="20.0"/>
         <conditional name="bad_variant_selector">
-          <param name="bad_variant_selector_type" type="select" label="Basic or Advanced Analysis options">
+          <param name="bad_variant_selector_type" type="select" label="How to specify bad variants">
             <option value="percent" selected="True">Percent</option>
             <option value="min_num">Number</option>
           </param>

From 0fddc97e94a5493d336d0c5b9fccb531f34cb13a Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Tue, 1 Nov 2011 10:49:34 -0400
Subject: [PATCH 127/362] Trackster: (a) refactor tool data functionality into
 TiledTrack class so that it is generally available; (b) enable VcfTracks to
 work with tools; and (c) more robust parameter setting. Enable Unified
 Genotyper to work with Trackster.

---
 .../visualization/tracks/data_providers.py    | 513 ++++++++++--------
 lib/galaxy/web/controllers/tracks.py          |  61 ++-
 static/scripts/packed/trackster.js            |   2 +-
 static/scripts/trackster.js                   |  99 ++--
 templates/tracks/browser.mako                 |   2 +-
 tools/gatk/unified_genotyper.xml              |   2 +-
 6 files changed, 396 insertions(+), 283 deletions(-)

diff --git a/lib/galaxy/visualization/tracks/data_providers.py b/lib/galaxy/visualization/tracks/data_providers.py
index 56cdeee230d..ee15ef1969a 100644
--- a/lib/galaxy/visualization/tracks/data_providers.py
+++ b/lib/galaxy/visualization/tracks/data_providers.py
@@ -135,10 +135,137 @@ class TracksDataProvider( object ):
                     { 'name' : attrs[ 'name' ], 'type' : column_types[viz_col_index], \
                     'index' : attrs[ 'index' ] } )
         return filters
+        
+#
+# -- Base mixins and providers --
+#
+
+class FilterableMixin:
+    def get_filters( self ):
+        """ Returns a dataset's filters. """
+        
+        # is_ functions taken from Tabular.set_meta
+        def is_int( column_text ):
+            try:
+                int( column_text )
+                return True
+            except: 
+                return False
+        def is_float( column_text ):
+            try:
+                float( column_text )
+                return True
+            except: 
+                if column_text.strip().lower() == 'na':
+                    return True #na is special cased to be a float
+                return False
+        
+        #
+        # Get filters.
+        # TODOs: 
+        # (a) might be useful to move this into each datatype's set_meta method;
+        # (b) could look at first N lines to ensure GTF attribute types are consistent.
+        #
+        filters = []
+        # HACK: first 8 fields are for drawing, so start filter column index at 9.
+        filter_col = 8
+        if isinstance( self.original_dataset.datatype, Gff ):
+            # Can filter by score and GTF attributes.
+            filters = [ { 'name': 'Score', 
+                          'type': 'int', 
+                          'index': filter_col, 
+                          'tool_id': 'Filter1',
+                          'tool_exp_name': 'c6' } ]
+            filter_col += 1
+            if isinstance( self.original_dataset.datatype, Gtf ):
+                # Create filters based on dataset metadata.
+                for name, a_type in self.original_dataset.metadata.attribute_types.items():
+                    if a_type in [ 'int', 'float' ]:
+                        filters.append( 
+                            { 'name': name,
+                              'type': a_type, 
+                              'index': filter_col, 
+                              'tool_id': 'gff_filter_by_attribute',
+                              'tool_exp_name': name } )
+                        filter_col += 1
+
+                '''
+                # Old code: use first line in dataset to find attributes.
+                for i, line in enumerate( open(self.original_dataset.file_name) ):
+                    if not line.startswith('#'):
+                        # Look at first line for attributes and types.
+                        attributes = parse_gff_attributes( line.split('\t')[8] )
+                        for attr, value in attributes.items():
+                            # Get attribute type.
+                            if is_int( value ):
+                                attr_type = 'int'
+                            elif is_float( value ):
+                                attr_type = 'float'
+                            else:
+                                attr_type = 'str'
+                            # Add to filters.
+                            if attr_type is not 'str':
+                                filters.append( { 'name': attr, 'type': attr_type, 'index': filter_col } )
+                                filter_col += 1
+                        break
+                '''
+        elif isinstance( self.original_dataset.datatype, Bed ):
+            # Can filter by score column only.
+            filters = [ { 'name': 'Score', 
+                          'type': 'int', 
+                          'index': filter_col, 
+                          'tool_id': 'Filter1',
+                          'tool_exp_name': 'c5'
+                           } ]
+
+        return filters
+
+
+class TabixDataProvider( FilterableMixin, TracksDataProvider ):
+    """
+    Tabix index data provider for the Galaxy track browser.
+    """
+    
+    col_name_data_attr_mapping = { 4 : { 'index': 4 , 'name' : 'Score' } }
+        
+    def get_iterator( self, chrom, start, end ):
+        start, end = int(start), int(end)
+        if end >= (2<<29):
+            end = (2<<29 - 1) # Tabix-enforced maximum
+                    
+        bgzip_fname = self.dependencies['bgzip'].file_name
+        
+        # if os.path.getsize(self.converted_dataset.file_name) == 0:
+            # return { 'kind': messages.ERROR, 'message': "Tabix converted size was 0, meaning the input file had invalid values." }
+        tabix = ctabix.Tabixfile(bgzip_fname, index_filename=self.converted_dataset.file_name)
+        
+        # If chrom is not found in indexes, try removing the first three 
+        # characters (e.g. 'chr') and see if that works. This enables the
+        # provider to handle chrome names defined as chrXXX and as XXX.
+        chrom = str(chrom)
+        if chrom not in tabix.contigs and chrom.startswith("chr") and (chrom[3:] in tabix.contigs):
+            chrom = chrom[3:]
+        
+        return tabix.fetch(reference=chrom, start=start, end=end)
+        
+    def get_data( self, chrom, start, end, start_val=0, max_vals=None, **kwargs ):
+        iterator = self.get_iterator( chrom, start, end )
+        return self.process_data( iterator, start_val, max_vals, **kwargs )
+        
+    def write_data_to_file( self, chrom, start, end, filename ):
+        iterator = self.get_iterator( chrom, start, end )
+        out = open( filename, "w" )
+        for line in iterator:
+            out.write( "%s\n" % line )
+        out.close()
+
+#
+# -- BED data providers --
+#
 
 class BedDataProvider( TracksDataProvider ):
     """
-    Abstract class that processes BED data from text format to payload format.
+    Abstract class that processes BED data from native format to payload format.
     
     Payload format: [ uid (offset), start, end, name, strand, thick_start, thick_end, blocks ]
     """
@@ -220,7 +347,166 @@ class BedDataProvider( TracksDataProvider ):
         for line in iterator:
             out.write( "%s\n" % line )
         out.close()
-            
+        
+class BedTabixDataProvider( TabixDataProvider, BedDataProvider ):
+    """
+    Provides data from a BED file indexed via tabix.
+    """
+    pass
+
+class RawBedDataProvider( BedDataProvider ):
+    """
+    Provide data from BED file.
+
+    NOTE: this data provider does not use indices, and hence will be very slow
+    for large datasets.
+    """
+
+    def get_iterator( self, chrom, start, end ):
+        def line_filter_iter():
+            for line in open( self.original_dataset.file_name ):
+                feature = line.split()
+                feature_chrom = feature[0]
+                feature_start = int( feature[1] )
+                feature_end = int( feature[2] )
+                if feature_chrom != chrom or feature_start > int( end ) or feature_end < int( start ):
+                    continue
+                yield line
+        return line_filter_iter()
+
+#
+# -- VCF data providers --
+#
+
+class VcfDataProvider( TracksDataProvider ):
+    """
+    Abstract class that processes VCF data from native format to payload format.
+
+    Payload format: TODO
+    """
+    
+    col_name_data_attr_mapping = { 'Qual' : { 'index': 6 , 'name' : 'Qual' } }
+    
+
+    def get_iterator( self, chrom, start, end ):
+        raise "Unimplemented Method"
+
+    def get_data( self, chrom, start, end, start_val=0, max_vals=None, **kwargs ):
+        iterator = self.get_iterator( chrom, start, end )
+        return self.process_data( iterator, start_val, max_vals, **kwargs )
+
+    def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ):
+        """
+        Returns a dict with the following attributes:
+            data - a list of variants with the format 
+                [<guid>, <start>, <end>, <name>, cigar, seq] 
+
+            message - error/informative message
+        """
+        rval = []
+        message = None
+
+        def get_mapping( ref, alt ):
+            """
+            Returns ( offset, new_seq, cigar ) tuple that defines mapping of 
+            alt to ref. Cigar format is an array of [ op_index, length ] pairs 
+            where op_index is the 0-based index into the string "MIDNSHP=X"
+            """
+
+            cig_ops = "MIDNSHP=X"
+
+            ref_len = len( ref )
+            alt_len = len( alt )
+
+            # Substitutions?
+            if ref_len == alt_len:
+                return 0, alt, [ [ cig_ops.find( "M" ), ref_len ] ]
+
+            # Deletions?
+            alt_in_ref_index = ref.find( alt )
+            if alt_in_ref_index != -1:
+                return alt_in_ref_index, ref[ alt_in_ref_index + 1: ], [ [ cig_ops.find( "D" ), ref_len - alt_len ] ]
+
+            # Insertions?
+            ref_in_alt_index = alt.find( ref )
+            if ref_in_alt_index != -1:
+                return ref_in_alt_index, alt[ ref_in_alt_index + 1: ], [ [ cig_ops.find( "I" ), alt_len - ref_len ] ]
+
+        # Pack data.
+        for count, line in enumerate( iterator ):
+            if count < start_val:
+                continue
+            if max_vals and count-start_val >= max_vals:
+                message = ERROR_MAX_VALS % ( max_vals, "features" )
+                break
+
+            feature = line.split()
+            start = int( feature[1] ) - 1
+            ref = feature[3]
+            alts = feature[4]
+
+            # HACK? alts == '.' --> monomorphism.
+            if alts == '.':
+                alts = ref
+
+            # Pack variants.
+            for alt in alts.split(","):
+                offset, new_seq, cigar = get_mapping( ref, alt )
+                start += offset
+                end = start + len( new_seq )
+
+                # Pack line.
+                payload = [ hash( line ), 
+                            start, 
+                            end,
+                            # ID:
+                            feature[2],
+                            cigar,
+                            new_seq,
+                            float( feature[5] )]
+                rval.append(payload)
+
+        return { 'data': rval, 'message': message }
+
+    def write_data_to_file( self, chrom, start, end, filename ):
+        iterator = self.get_iterator( chrom, start, end )
+        out = open( filename, "w" )
+        for line in iterator:
+            out.write( "%s\n" % line )
+        out.close()
+
+class VcfTabixDataProvider( TabixDataProvider, VcfDataProvider ):
+    """
+    Provides data from a VCF file indexed via tabix.
+    """
+    pass
+
+class RawVcfDataProvider( VcfDataProvider ):
+    """
+    Provide data from VCF file.
+
+    NOTE: this data provider does not use indices, and hence will be very slow
+    for large datasets.
+    """
+
+    def get_iterator( self, chrom, start, end ):
+        def line_filter_iter():
+            for line in open( self.original_dataset.file_name ):
+                if line.startswith("#"):
+                    continue
+                variant = line.split()
+                variant_chrom, variant_start, id, ref, alts = variant[ 0:5 ]
+                variant_start = int( variant_start )
+                longest_alt = -1
+                for alt in alts:
+                    if len( alt ) > longest_alt:
+                        longest_alt = len( alt )
+                variant_end = variant_start + abs( len( ref ) - longest_alt )
+                if variant_chrom != chrom or variant_start > int( end ) or variant_end < int( start ):
+                    continue
+                yield line
+        return line_filter_iter()
+
 class SummaryTreeDataProvider( TracksDataProvider ):
     """
     Summary tree data provider for the Galaxy track browser. 
@@ -485,118 +771,7 @@ class BigWigDataProvider (BBIDataProvider ):
         else:
             f = open( self.original_dataset.file_name )
         return f, BigWigFile(file=f)
-
-class FilterableMixin:
-    def get_filters( self ):
-        """ Returns a dataset's filters. """
-        
-        # is_ functions taken from Tabular.set_meta
-        def is_int( column_text ):
-            try:
-                int( column_text )
-                return True
-            except: 
-                return False
-        def is_float( column_text ):
-            try:
-                float( column_text )
-                return True
-            except: 
-                if column_text.strip().lower() == 'na':
-                    return True #na is special cased to be a float
-                return False
-        
-        #
-        # Get filters.
-        # TODOs: 
-        # (a) might be useful to move this into each datatype's set_meta method;
-        # (b) could look at first N lines to ensure GTF attribute types are consistent.
-        #
-        filters = []
-        # HACK: first 8 fields are for drawing, so start filter column index at 9.
-        filter_col = 8
-        if isinstance( self.original_dataset.datatype, Gff ):
-            # Can filter by score and GTF attributes.
-            filters = [ { 'name': 'Score', 
-                          'type': 'int', 
-                          'index': filter_col, 
-                          'tool_id': 'Filter1',
-                          'tool_exp_name': 'c6' } ]
-            filter_col += 1
-            if isinstance( self.original_dataset.datatype, Gtf ):
-                # Create filters based on dataset metadata.
-                for name, a_type in self.original_dataset.metadata.attribute_types.items():
-                    if a_type in [ 'int', 'float' ]:
-                        filters.append( 
-                            { 'name': name,
-                              'type': a_type, 
-                              'index': filter_col, 
-                              'tool_id': 'gff_filter_by_attribute',
-                              'tool_exp_name': name } )
-                        filter_col += 1
-
-                '''
-                # Old code: use first line in dataset to find attributes.
-                for i, line in enumerate( open(self.original_dataset.file_name) ):
-                    if not line.startswith('#'):
-                        # Look at first line for attributes and types.
-                        attributes = parse_gff_attributes( line.split('\t')[8] )
-                        for attr, value in attributes.items():
-                            # Get attribute type.
-                            if is_int( value ):
-                                attr_type = 'int'
-                            elif is_float( value ):
-                                attr_type = 'float'
-                            else:
-                                attr_type = 'str'
-                            # Add to filters.
-                            if attr_type is not 'str':
-                                filters.append( { 'name': attr, 'type': attr_type, 'index': filter_col } )
-                                filter_col += 1
-                        break
-                '''
-        elif isinstance( self.original_dataset.datatype, Bed ):
-            # Can filter by score column only.
-            filters = [ { 'name': 'Score', 
-                          'type': 'int', 
-                          'index': filter_col, 
-                          'tool_id': 'Filter1',
-                          'tool_exp_name': 'c5'
-                           } ]
-
-        return filters
-    
-class TabixDataProvider( FilterableMixin, TracksDataProvider ):
-    """
-    Tabix index data provider for the Galaxy track browser.
-    """
-    
-    col_name_data_attr_mapping = { 4 : { 'index': 4 , 'name' : 'Score' } }
-        
-    def get_iterator( self, chrom, start, end ):
-        start, end = int(start), int(end)
-        if end >= (2<<29):
-            end = (2<<29 - 1) # Tabix-enforced maximum
-                    
-        bgzip_fname = self.dependencies['bgzip'].file_name
-        
-        # if os.path.getsize(self.converted_dataset.file_name) == 0:
-            # return { 'kind': messages.ERROR, 'message': "Tabix converted size was 0, meaning the input file had invalid values." }
-        tabix = ctabix.Tabixfile(bgzip_fname, index_filename=self.converted_dataset.file_name)
-        
-        # If chrom is not found in indexes, try removing the first three 
-        # characters (e.g. 'chr') and see if that works. This enables the
-        # provider to handle chrome names defined as chrXXX and as XXX.
-        chrom = str(chrom)
-        if chrom not in tabix.contigs and chrom.startswith("chr") and (chrom[3:] in tabix.contigs):
-            chrom = chrom[3:]
-        
-        return tabix.fetch(reference=chrom, start=start, end=end)
-        
-    def get_data( self, chrom, start, end, start_val=0, max_vals=None, **kwargs ):
-        iterator = self.get_iterator( chrom, start, end )
-        return self.process_data( iterator, start_val, max_vals, **kwargs )
-    
+            
 class IntervalIndexDataProvider( FilterableMixin, TracksDataProvider ):
     """
     Interval index files used only for GFF files.
@@ -658,86 +833,6 @@ class IntervalIndexDataProvider( FilterableMixin, TracksDataProvider ):
             results.append( payload )
 
         return { 'data': results, 'message': message }
-                
-class VcfDataProvider( TabixDataProvider ):
-    """
-    VCF data provider. Payload format uses the read format.
-    """
-
-    col_name_data_attr_mapping = { 'Qual' : { 'index': 6 , 'name' : 'Qual' } }
-
-    def process_data( self, iterator, start_val=0, max_vals=sys.maxint, **kwargs ):
-        """
-        Returns a dict with the following attributes:
-            data - a list of variants with the format 
-                [<guid>, <start>, <end>, <name>, cigar, seq] 
-
-            message - error/informative message
-        """
-        rval = []
-        message = None
-        
-        def get_mapping( ref, alt ):
-            """
-            Returns ( offset, new_seq, cigar ) tuple that defines mapping of 
-            alt to ref. Cigar format is an array of [ op_index, length ] pairs 
-            where op_index is the 0-based index into the string "MIDNSHP=X"
-            """
-            
-            cig_ops = "MIDNSHP=X"
-            
-            ref_len = len( ref )
-            alt_len = len( alt )
-            
-            # Substitutions?
-            if ref_len == alt_len:
-                return 0, alt, [ [ cig_ops.find( "M" ), ref_len ] ]
-            
-            # Deletions?
-            alt_in_ref_index = ref.find( alt )
-            if alt_in_ref_index != -1:
-                return alt_in_ref_index, ref[ alt_in_ref_index + 1: ], [ [ cig_ops.find( "D" ), ref_len - alt_len ] ]
-
-            # Insertions?
-            ref_in_alt_index = alt.find( ref )
-            if ref_in_alt_index != -1:
-                return ref_in_alt_index, alt[ ref_in_alt_index + 1: ], [ [ cig_ops.find( "I" ), alt_len - ref_len ] ]
-            
-        # Pack data.
-        for count, line in enumerate( iterator ):
-            if count < start_val:
-                continue
-            if count-start_val >= max_vals:
-                message = ERROR_MAX_VALS % ( "max_vals", "features" )
-                break
-
-            feature = line.split()
-            start = int( feature[1] ) - 1
-            ref = feature[3]
-            alts = feature[4]
-            
-            # HACK? alts == '.' --> monomorphism.
-            if alts == '.':
-                alts = ref
-
-            # Pack variants.
-            for alt in alts.split(","):
-                offset, new_seq, cigar = get_mapping( ref, alt )
-                start += offset
-                end = start + len( new_seq )
-            
-                # Pack line.
-                payload = [ hash( line ), 
-                            start, 
-                            end,
-                            # ID:
-                            feature[2],
-                            cigar,
-                            new_seq,
-                            float( feature[5] )]
-                rval.append(payload)
-
-        return { 'data': rval, 'message': message }
 
 class GFFDataProvider( TracksDataProvider ):
     """
@@ -769,40 +864,16 @@ class GFFDataProvider( TracksDataProvider ):
             offset += feature.raw_size
             
         return { 'data': results, 'message': message }
-        
-class BedTabixDataProvider( TabixDataProvider, BedDataProvider ):
-    """
-    Provides data from a BED file indexed via tabix.
-    """
-    pass
-    
-class RawBedDataProvider( BedDataProvider ):
-    """
-    Provide data from BED file.
-
-    NOTE: this data provider does not use indices, and hence will be very slow
-    for large datasets.
-    """
-    
-    def get_iterator( self, chrom, start, end ):
-        def line_filter_iter():
-            for line in open( self.original_dataset.file_name ):
-                feature = line.split()
-                feature_chrom, feature_start, feature_end = feature[ 0:3 ]
-                if feature_chrom != chrom or feature_start > end or feature_end < start:
-                    continue
-                yield line
-        return line_filter_iter()
-       
+               
 #        
-# Helper methods.
+# -- Helper methods. --
 #
 
 # Mapping from dataset type name to a class that can fetch data from a file of that
 # type. First key is converted dataset type; if result is another dict, second key
 # is original dataset type. TODO: This needs to be more flexible.
 dataset_type_name_to_data_provider = {
-    "tabix": { Vcf: VcfDataProvider, Bed: BedTabixDataProvider, "default" : TabixDataProvider },
+    "tabix": { Vcf: VcfTabixDataProvider, Bed: BedTabixDataProvider, "default" : TabixDataProvider },
     "interval_index": IntervalIndexDataProvider,
     "bai": BamDataProvider,
     "summary_tree": SummaryTreeDataProvider,
diff --git a/lib/galaxy/web/controllers/tracks.py b/lib/galaxy/web/controllers/tracks.py
index a1527438a1f..416fa6e4057 100644
--- a/lib/galaxy/web/controllers/tracks.py
+++ b/lib/galaxy/web/controllers/tracks.py
@@ -465,10 +465,14 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
             data = GFFDataProvider( original_dataset=dataset ).get_data( chrom, low, high, **kwargs )
             data[ 'dataset_type' ] = 'interval_index'
             data[ 'extra_info' ] = None
-        if isinstance( dataset.datatype, Bed ):
+        elif isinstance( dataset.datatype, Bed ):
             data = RawBedDataProvider( original_dataset=dataset ).get_data( chrom, low, high, **kwargs )
             data[ 'dataset_type' ] = 'interval_index'
             data[ 'extra_info' ] = None
+        elif isinstance( dataset.datatype, Vcf ):
+            data = RawVcfDataProvider( original_dataset=dataset ).get_data( chrom, low, high, **kwargs )
+            data[ 'dataset_type' ] = 'tabix'
+            data[ 'extra_info' ] = None
         return data
         
     @web.json
@@ -586,7 +590,7 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
             data_provider = data_provider_class( converted_dataset=converted_dataset, original_dataset=dataset, dependencies=deps )
         
         # Get and return data from data_provider.
-        result = data_provider.get_data( chrom, low, high, int(start_val), int(max_vals), **kwargs )
+        result = data_provider.get_data( chrom, low, high, int( start_val ), int( max_vals ), **kwargs )
         result.update( { 'dataset_type': tracks_dataset_type, 'extra_info': extra_info } )
         return result
         
@@ -840,6 +844,45 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
         # Set input datasets for tool. If running on region, extract and use subset
         # when possible.
         #
+        
+        def set_param_value( param_dict, param_name, param_value ):
+            """
+            Set new parameter value in a parameter dictionary.
+            """
+            
+            # Recursive function to set param value.
+            def set_value( param_dict, group_name, group_index, param_name, param_value ):
+                print "searching", param_dict
+                if group_name in param_dict:
+                    param_dict[ group_name ][ group_index ][ param_name ] = param_value
+                    return True
+                elif param_name in param_dict:
+                    param_dict[ param_name ] = param_value
+                    return True
+                else:
+                    # Recursive search.
+                    return_val = False
+                    for name, value in param_dict.items():
+                        if isinstance( value, dict ):
+                            return_val = set_value( value, group_name, group_index, param_name, param_value)
+                            if return_val:
+                                print "setting parameter", param_dict
+                                return return_val
+                    return False
+            
+            # Parse parameter name if necessary.
+            if param_name.find( "|" ) == -1:
+                # Non-grouping parameter.
+                group_name = group_index = None
+            else:
+                # Grouping parameter.
+                group, param_name = param_name.split( "|" )
+                index = group.rfind( "_" )
+                group_name = group[ :index ]
+                group_index = int( group[ index + 1: ] )
+            
+            return set_value( param_dict, group_name, group_index, param_name, param_value )
+            
         for jida in original_job.input_datasets:
             input_dataset = jida.dataset
             if input_dataset is None: #optional dataset and dataset wasn't selected
@@ -875,10 +918,20 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
                 new_dataset.set_size()
                 new_dataset.info = "Data subset for trackster"
                 new_dataset.set_dataset_state( trans.app.model.Dataset.states.OK )
+                
+                # Set metadata.
+                if trans.app.config.set_metadata_externally:
+                    trans.app.datatypes_registry.set_external_metadata_tool.tool_action.execute( trans.app.datatypes_registry.set_external_metadata_tool, trans, incoming = { 'input1':new_dataset } )
+                else:
+                    message = 'Attributes updated'
+                    new_dataset.set_meta()
+                    new_dataset.datatype.after_setting_metadata( data )
+                    
                 trans.sa_session.flush()
-            
+                
                 # Add dataset to tool's parameters.
-                tool_params[ jida.name ] = new_dataset
+                if not set_param_value( tool_params, jida.name, new_dataset ):
+                    return to_json_string( { "error" : True, "message" : "error setting parameter %s" % jida.name } )
         
         #        
         # Execute tool and handle outputs.
diff --git a/static/scripts/packed/trackster.js b/static/scripts/packed/trackster.js
index 40b076534cf..a0af2f6d9db 100644
--- a/static/scripts/packed/trackster.js
+++ b/static/scripts/packed/trackster.js
@@ -1 +1 @@
-var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var m=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(u,t,v,r,i,s){return(Math.max(u,r)-Math.min(u,r))+(Math.max(t,i)-Math.min(t,i))+(Math.max(v,s)-Math.min(v,s))};var g,n,f,k,p,h,q,c,d,b,o,l=false;do{g=Math.random()*16777215;n=g|16711680;f=g|65280;k=g|255;d=m(n,f,k);l=true;for(var j=0;j<a.length;j++){p=a[j];h=p|16711680;q=p|65280;c=p|255;b=m(h,q,c);o=e(n,f,k,h,q,c);if((Math.abs(d-b)<125)||(o<500)){l=false;break}}}while(!l);return"#"+(16777216+g).toString(16).substr(1,6)};var trackster_module=function(f,Y){var p=f("class").extend,s=f("slotting"),M=f("painters");var af=function(ag,ah){this.document=ag;this.default_font=ah!==undefined?ah:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};p(af.prototype,{load_pattern:function(ag,ak){var ah=this.patterns,ai=this.dummy_context,aj=new Image();aj.src=image_path+ak;aj.onload=function(){ah[ag]=ai.createPattern(aj,"repeat")}},get_pattern:function(ag){return this.patterns[ag]},new_canvas:function(){var ag=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ag)}ag.manager=this;return ag}});var n={};var l=function(ag,ah){n[ag.attr("id")]=ah};var m=function(ag,ai,ak,aj){ak=".group";var ah={};n[ag.attr("id")]=aj;ag.bind("drag",{handle:"."+ai,relative:true},function(at,au){var ar=$(this);var ax=$(this).parent(),ao=ax.children(),aq=n[$(this).attr("id")],an,am,av,al,ap;am=$(this).parents(ak);if(am.length!==0){av=am.position().top;al=av+am.outerHeight();if(au.offsetY<av){$(this).insertBefore(am);var aw=n[am.attr("id")];aw.remove_drawable(aq);aw.container.add_drawable_before(aq,aw);return}else{if(au.offsetY>al){$(this).insertAfter(am);var aw=n[am.attr("id")];aw.remove_drawable(aq);aw.container.add_drawable(aq);return}}}am=null;for(ap=0;ap<ao.length;ap++){an=$(ao.get(ap));av=an.position().top;al=av+an.outerHeight();if(an.is(ak)&&this!==an.get(0)&&au.offsetY>=av&&au.offsetY<=al){if(au.offsetY-av<al-au.offsetY){an.find(".content-div").prepend(this)}else{an.find(".content-div").append(this)}if(aq.container){aq.container.remove_drawable(aq)}n[an.attr("id")].add_drawable(aq);return}}for(ap=0;ap<ao.length;ap++){if(au.offsetY<$(ao.get(ap)).position().top){break}}if(ap===ao.length){if(this!==ao.get(ap-1)){ax.append(this);n[ax.attr("id")].move_drawable(aq,ap)}}else{if(this!==ao.get(ap)){$(this).insertBefore(ao.get(ap));n[ax.attr("id")].move_drawable(aq,(au.deltaY>0?ap-1:ap))}}}).bind("dragstart",function(){ah["border-top"]=ag.css("border-top");ah["border-bottom"]=ag.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ah)})};Y.moveable=m;var ae=16,H=9,E=20,T=H+2,z=100,J=12000,R=200,C=5,v=10,L=5000,w=100,o="There was an error in indexing this dataset. 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S=function(ah,ag,ai){c.call(this,ah);this.track=ag;this.subset=(ai!==undefined?ai:true)};p(S.prototype,c.prototype,{load_data:function(ap,ak,an,ah,am){var ao=this.track.view.chrom,aj={chrom:ao,low:ap,high:ak,mode:an,resolution:ah,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(aj,am);if(this.track.filters_manager){var aq=[];var ag=this.track.filters_manager.filters;for(var al=0;al<ag.length;al++){aq[aq.length]=ag[al].name}aj.filter_cols=JSON.stringify(aq)}var ai=this;return $.getJSON(this.track.data_url,aj,function(ar){ai.set_data(ap,ak,an,ar)})},get_data:function(ag,ak,al,ah,aj){var ai=this.get_data_from_cache(ag,ak,al);if(ai){return ai}ai=this.load_data(ag,ak,al,ah,aj);this.set_data(ag,ak,al,ai);return ai},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ao,aj,an,ai,am,ak){var ap=this.get_data_from_cache(ao,aj,an);if(!ap){console.log("ERROR: no current data for: ",this.track,ao,aj,an,ai,am);return}ap.stale=true;var ah=ao;if(ak===this.DEEP_DATA_REQ){$.extend(am,{start_val:ap.data.length+1})}else{if(ak===this.BROAD_DATA_REQ){ah=(ap.max_high?ap.max_high:ap.data[ap.data.length-1][2])+1}}var ag=this,al=this.load_data(ah,aj,an,ai,am);new_data_available=$.Deferred();this.set_data(ao,aj,an,new_data_available);$.when(al).then(function(aq){if(aq.data){aq.data=ap.data.concat(aq.data);if(aq.max_low){aq.max_low=ap.max_low}if(aq.message){aq.message=aq.message.replace(/[0-9]+/,aq.data.length)}}ag.set_data(ao,aj,an,aq);new_data_available.resolve(aq)});return new_data_available},get_data_from_cache:function(ag,ah,ai){return this.get(this.gen_key(ag,ah,ai))},set_data:function(ah,ai,aj,ag){return this.set(this.gen_key(ah,ai,aj),ag)},gen_key:function(ag,ai,aj){var ah=ag+"_"+ai+"_"+aj;return ah},split_key:function(ag){return ag.split("_")}});var I=function(ah,ag,ai){S.call(this,ah,ag,ai)};p(I.prototype,S.prototype,c.prototype,{load_data:function(ag,aj,ak,ah,ai){if(ah>1){return{data:null}}return S.prototype.load_data.call(this,ag,aj,ak,ah,ai)}});var q=function(aj,ah,ag,ai,ak){this.name=aj;this.view=ah;this.container=ag;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:aj}],saved_values:ai,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ak;this.is_overview=false};p(q.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},update_track_icons:function(){},set_name:function(ag){this.old_name=this.name;this.name=ag;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var y=function(ak,aj,ah,ag,ai,al){q.call(this,aj,ah,ag,ai,al);this.obj_type=ak;this.drawables=[]};p(y.prototype,q.prototype,{init:function(){for(var ag=0;ag<this.drawables.length;ag++){this.drawables[ag].init()}},_draw:function(){for(var ag=0;ag<this.drawables.length;ag++){this.drawables[ag]._draw()}},to_json:function(){var ah=[];for(var ag=0;ag<this.drawables.length;ag++){ah.push(this.drawables[ag].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ah}},add_drawable:function(ag){this.drawables.push(ag);ag.container=this},add_drawable_before:function(ai,ag){var ah=this.drawables.indexOf(ag);if(ah!=-1){this.drawables.splice(ah,0,ai);return true}return false},remove_drawable:function(ah){var ag=this.drawables.indexOf(ah);if(ag!=-1){this.drawables.splice(ag,1);ah.container=null;return true}return false},move_drawable:function(ah,ai){var ag=this.drawables.indexOf(ah);if(ag!=-1){this.drawables.splice(ag,1);this.drawables.splice(ai,0,ah);return true}return false}});var Q=function(aj,ah,ag,ai){y.call(this,"DrawableGroup",aj,ah,ag,ai,"group-handle");if(!Q.id_counter){Q.id_counter=0}var ak=Q.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+ak).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+ak+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.update_track_icons()};p(Q.prototype,q.prototype,y.prototype,{update_track_icons:function(){var ah=this;var ag={};ag["Edit configuration"]=function(){var ak=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ai=function(){ah.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},aj=function(al){if((al.keyCode||al.which)===27){ak()}else{if((al.keyCode||al.which)===13){ai()}}};$(window).bind("keypress.check_enter_esc",aj);show_modal("Configure Group",ah.config.build_form(),{Cancel:ak,OK:ai})};ag.Remove=function(){ah.remove()};make_popupmenu(ah.name_div,ag)}});var ad=function(ag,aj,ai,ah){y.call(this,"View");this.container=ag;this.chrom=null;this.vis_id=ai;this.dbkey=ah;this.title=aj;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new af(ag.get(0).ownerDocument);this.reset()};p(ad.prototype,y.prototype,{init:function(){var ai=this.container,ag=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ai);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ai);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ai);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,ag);this.intro_div=$("<div/>").addClass("intro");var aj=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ah=function(ak){if(ak.type==="focusout"||(ak.keyCode||ak.which)===13||(ak.keyCode||ak.which)===27){if((ak.keyCode||ak.which)!==27){ag.go_to($(this).val())}$(this).hide();$(this).val("");ag.location_span.show();ag.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ah).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ag.location_span.hide();ag.chrom_select.hide();ag.nav_input.val(ag.chrom+":"+ag.low+"-"+ag.high);ag.nav_input.css("display","inline-block");ag.nav_input.select();ag.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ag.zoom_out();ag.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ag.zoom_in();ag.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ag.change_chrom(ag.chrom_select.val())});this.browser_content_div.click(function(ak){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ak){ag.zoom_in(ak.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ak,al){this.current_x=al.offsetX}).bind("drag",function(ak,am){var an=am.offsetX-this.current_x;this.current_x=am.offsetX;var al=Math.round(an/ag.viewport_container.width()*(ag.max_high-ag.max_low));ag.move_delta(-al)});this.overview_close.click(function(){ag.reset_overview()});this.viewport_container.bind("draginit",function(ak,al){if(ak.clientX>ag.viewport_container.width()-16){return false}}).bind("dragstart",function(ak,al){al.original_low=ag.low;al.current_height=ak.clientY;al.current_x=al.offsetX}).bind("drag",function(am,ao){var ak=$(this);var ap=ao.offsetX-ao.current_x;var al=ak.scrollTop()-(am.clientY-ao.current_height);ak.scrollTop(al);ao.current_height=am.clientY;ao.current_x=ao.offsetX;var an=Math.round(ap/ag.viewport_container.width()*(ag.high-ag.low));ag.move_delta(an)}).bind("mousewheel",function(am,ao,al,ak){if(al){var an=Math.round(-al/ag.viewport_container.width()*(ag.high-ag.low));ag.move_delta(an)}});this.top_labeltrack.bind("dragstart",function(ak,al){return $("<div />").css({height:ag.browser_content_div.height()+ag.top_labeltrack.height()+ag.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ao,ap){$(ap.proxy).css({left:Math.min(ao.pageX,ap.startX),width:Math.abs(ao.pageX-ap.startX)});var al=Math.min(ao.pageX,ap.startX)-ag.container.offset().left,ak=Math.max(ao.pageX,ap.startX)-ag.container.offset().left,an=(ag.high-ag.low),am=ag.viewport_container.width();ag.update_location(Math.round(al/am*an)+ag.low,Math.round(ak/am*an)+ag.low)}).bind("dragend",function(ap,aq){var al=Math.min(ap.pageX,aq.startX),ak=Math.max(ap.pageX,aq.startX),an=(ag.high-ag.low),am=ag.viewport_container.width(),ao=ag.low;ag.low=Math.round(al/am*an)+ao;ag.high=Math.round(ak/am*an)+ao;$(aq.proxy).remove();ag.request_redraw()});this.add_label_track(new ac(this,{content_div:this.top_labeltrack}));this.add_label_track(new ac(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ag.resize_window()});$(document).bind("redraw",function(){ag.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ag,ah){this.location_span.text(commatize(ag)+" - "+commatize(ah));this.nav_input.val(this.chrom+":"+commatize(ag)+"-"+commatize(ah))},load_chroms:function(ai){ai.num=w;$.extend(ai,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ag=this,ah=$.Deferred();$.ajax({url:chrom_url,data:ai,dataType:"json",success:function(ak){if(ak.chrom_info.length===0){alert("Invalid chromosome: "+ai.chrom);return}if(ak.reference){ag.add_label_track(new A(ag))}ag.chrom_data=ak.chrom_info;var an='<option value="">Select Chrom/Contig</option>';for(var am=0,aj=ag.chrom_data.length;am<aj;am++){var al=ag.chrom_data[am].chrom;an+='<option value="'+al+'">'+al+"</option>"}if(ak.prev_chroms){an+='<option value="previous">Previous '+w+"</option>"}if(ak.next_chroms){an+='<option value="next">Next '+w+"</option>"}ag.chrom_select.html(an);ag.chrom_start_index=ak.start_index;ah.resolve(ak)},error:function(){alert("Could not load chroms for this dbkey:",ag.dbkey)}});return ah},change_chrom:function(al,ah,an){if(!al||al==="None"){return}var ai=this;if(al==="previous"){ai.load_chroms({low:this.chrom_start_index-w});return}if(al==="next"){ai.load_chroms({low:this.chrom_start_index+w});return}var am=$.grep(ai.chrom_data,function(ao,ap){return ao.chrom===al})[0];if(am===undefined){ai.load_chroms({chrom:al},function(){ai.change_chrom(al,ah,an)});return}else{if(al!==ai.chrom){ai.chrom=al;ai.chrom_select.val(ai.chrom);ai.max_high=am.len-1;ai.reset();ai.request_redraw(true);for(var ak=0,ag=ai.drawables.length;ak<ag;ak++){var aj=ai.drawables[ak];if(aj.init){aj.init()}}}if(ah!==undefined&&an!==undefined){ai.low=Math.max(ah,0);ai.high=Math.min(an,ai.max_high)}ai.reset_overview();ai.request_redraw()}},go_to:function(ak){ak=ak.replace(/ |,/g,"");var ao=this,ag,aj,ah=ak.split(":"),am=ah[0],an=ah[1];if(an!==undefined){try{var al=an.split("-");ag=parseInt(al[0],10);aj=parseInt(al[1],10)}catch(ai){return false}}ao.change_chrom(am,ag,aj)},move_fraction:function(ai){var ag=this;var ah=ag.high-ag.low;this.move_delta(ai*ah)},move_delta:function(ai){var ag=this;var ah=ag.high-ag.low;if(ag.low-ai<ag.max_low){ag.low=ag.max_low;ag.high=ag.max_low+ah}else{if(ag.high-ai>ag.max_high){ag.high=ag.max_high;ag.low=ag.max_high-ah}else{ag.high-=ai;ag.low-=ai}}ag.request_redraw()},add_drawable:function(ag){y.prototype.add_drawable.call(this,ag);ag.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ag){ag.view=this;ag.init();this.label_tracks.push(ag)},remove_drawable:function(ai,ah){y.prototype.remove_drawable.call(this,ai);if(ah){var ag=this;ai.container_div.fadeOut("slow",function(){$(this).remove();ag.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ao,ag,an,ah){var am=this,ak=(ah?[ah]:am.drawables),ai;var ah;for(var al=0;al<ak.length;al++){ah=ak[al];ai=-1;for(var aj=0;aj<am.tracks_to_be_redrawn.length;aj++){if(am.tracks_to_be_redrawn[aj][0]===ah){ai=aj;break}}if(ai<0){am.tracks_to_be_redrawn.push([ah,ag,an])}else{am.tracks_to_be_redrawn[al][1]=ag;am.tracks_to_be_redrawn[al][2]=an}}requestAnimationFrame(function(){am._redraw(ao)})},_redraw:function(aq){var an=this.low,aj=this.high;if(an<this.max_low){an=this.max_low}if(aj>this.max_high){aj=this.max_high}var ap=this.high-this.low;if(this.high!==0&&ap<this.min_separation){aj=an+this.min_separation}this.low=Math.floor(an);this.high=Math.ceil(aj);this.resolution=Math.pow(C,Math.ceil(Math.log((this.high-this.low)/R)/Math.log(C)));this.zoom_res=Math.pow(v,Math.max(0,Math.ceil(Math.log(this.resolution,v)/Math.log(v))));var ag=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var am=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ar=13;this.overview_box.css({left:ag,width:Math.max(ar,am)}).show();if(am<ar){this.overview_box.css("left",ag-(ar-am)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ag,width:am})}this.update_location(this.low,this.high);if(!aq){var ai,ah,ao;for(var ak=0,al=this.tracks_to_be_redrawn.length;ak<al;ak++){ai=this.tracks_to_be_redrawn[ak][0];ah=this.tracks_to_be_redrawn[ak][1];ao=this.tracks_to_be_redrawn[ak][2];if(ai){ai._draw(ah,ao)}}this.tracks_to_be_redrawn=[];for(ak=0,al=this.label_tracks.length;ak<al;ak++){this.label_tracks[ak]._draw()}}},zoom_in:function(ah,ai){if(this.max_high===0||this.high-this.low<this.min_separation){return}var aj=this.high-this.low,ak=aj/2+this.low,ag=(aj/this.zoom_factor)/2;if(ah){ak=ah/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ak-ag);this.high=Math.round(ak+ag);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ah=this.high-this.low,ai=ah/2+this.low,ag=(ah*this.zoom_factor)/2;this.low=Math.round(ai-ag);this.high=Math.round(ai+ag);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ai){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ai.dataset_id){return}this.overview_viewport.find(".track").remove()}var ah=ai.copy({content_div:this.overview_viewport}),ag=this;ah.header_div.hide();ah.is_overview=true;ag.overview_drawable=ah;this.overview_drawable.postdraw_actions=function(){ag.overview_highlight.show().height(ag.overview_drawable.content_div.height());ag.overview_viewport.height(ag.overview_drawable.content_div.height()+ag.overview_box.outerHeight());ag.overview_close.show();ag.resize_window()};this.overview_drawable.init();ag.has_changes=true},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var r=function(ai,am){this.track=ai;this.name=am.name;this.params=[];var au=am.params;for(var aj=0;aj<au.length;aj++){var ao=au[aj],ah=ao.name,at=ao.label,ak=unescape(ao.html),av=ao.value,aq=ao.type;if(aq==="number"){this.params[this.params.length]=new g(ah,at,ak,av,ao.min,ao.max)}else{if(aq=="select"){this.params[this.params.length]=new O(ah,at,ak,av)}else{console.log("WARNING: unrecognized tool parameter type:",ah,aq)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ax){ax.stopPropagation()}).click(function(ax){ax.stopPropagation()}).bind("dblclick",function(ax){ax.stopPropagation()});var ar=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ap=this.params;var an=this;$.each(this.params,function(ay,aB){var aA=$("<div>").addClass("param-row").appendTo(an.parent_div);var ax=$("<div>").addClass("param-label").text(aB.label).appendTo(aA);var az=$("<div/>").addClass("slider").html(aB.html).appendTo(aA);az.find(":input").val(aB.value);$("<div style='clear: both;'/>").appendTo(aA)});this.parent_div.find("input").click(function(){$(this).select()});var aw=$("<div>").addClass("param-row").appendTo(this.parent_div);var al=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(aw);var ag=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(aw);var an=this;ag.click(function(){an.run_on_region()});al.click(function(){an.run_on_dataset()})};p(r.prototype,{get_param_values_dict:function(){var ag={};this.parent_div.find(":input").each(function(){var ah=$(this).attr("name"),ai=$(this).val();ag[ah]=JSON.stringify(ai)});return ag},get_param_values:function(){var ah=[];var ag={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();if(ai){ah[ah.length]=aj}});return ah},run_on_dataset:function(){var ag=this;ag.run({dataset_id:this.track.original_dataset_id,tool_id:ag.name},null,function(ah){show_modal(ag.name+" is Running",ag.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ah={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},ak=this.track,ai=ah.tool_id+ak.tool_region_and_parameters_str(ah.chrom,ah.low,ah.high),ag,al;if(ak.container===view){var aj=new Q(this.name,this.track.view,this.track.container);ak.container.add_drawable(aj);ak.container.remove_drawable(ak);aj.add_drawable(ak);ak.container_div.appendTo(aj.content_div);ag=aj}else{ag=ak.container}if(ak instanceof e){al=new V(ai,view,ag,"hda");al.change_mode(ak.mode);ag.add_drawable(al)}al.content_div.text("Starting job.");this.run(ah,al,function(am){al.dataset_id=am.dataset_id;al.content_div.text("Running job.");al.init()})},run:function(ah,ai,aj){$.extend(ah,this.get_param_values_dict());var ag=function(){$.getJSON(rerun_tool_url,ah,function(ak){if(ak==="no converter"){ai.container_div.addClass("error");ai.content_div.text(K)}else{if(ak.error){ai.container_div.addClass("error");ai.content_div.text(x+ak.message)}else{if(ak==="pending"){ai.container_div.addClass("pending");ai.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ag,2000)}else{aj(ak)}}}})};ag()}});var O=function(ah,ag,ai,aj){this.name=ah;this.label=ag;this.html=ai;this.value=aj};var g=function(ai,ah,ak,al,aj,ag){O.call(this,ai,ah,ak,al);this.min=aj;this.max=ag};var h=function(ah,ag,ai,aj){this.name=ah;this.index=ag;this.tool_id=ai;this.tool_exp_name=aj};var W=function(ah,ag,ai,aj){h.call(this,ah,ag,ai,aj);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};p(W.prototype,{applies_to:function(ag){if(ag.length>this.index){return true}return false},keep:function(ag){if(!this.applies_to(ag)){return true}var ah=ag[this.index];return(isNaN(ah)||(ah>=this.low&&ah<=this.high))},update_attrs:function(ah){var ag=false;if(!this.applies_to(ah)){return ag}if(ah[this.index]<this.min){this.min=Math.floor(ah[this.index]);ag=true}if(ah[this.index]>this.max){this.max=Math.ceil(ah[this.index]);ag=true}return ag},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var ai=function(al,aj){var ak=aj-al;return(ak<=2?0.01:1)};var ah=this.slider.slider("option","min"),ag=this.slider.slider("option","max");if(this.min<ah||this.max>ag){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ai(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ab=function(ar,az){this.track=ar;this.filters=[];for(var au=0;au<az.length;au++){var av=az[au],aA=av.name,ag=av.type,ai=av.index,ay=av.tool_id,ax=av.tool_exp_name;if(ag==="int"||ag==="float"){this.filters[au]=new W(aA,ai,ay,ax)}else{console.log("ERROR: unsupported filter: ",aA,ag)}}var aj=function(aB,aC,aD){aB.click(function(){var aE=aC.text();max=parseFloat(aD.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aD.slider("option","values")){input_size=2*input_size+1;multi_value=true}aC.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aE).appendTo(aC).focus().select().click(function(aF){aF.stopPropagation()}).blur(function(){$(this).remove();aC.text(aE)}).keyup(function(aJ){if(aJ.keyCode===27){$(this).trigger("blur")}else{if(aJ.keyCode===13){var aH=aD.slider("option","min"),aF=aD.slider("option","max"),aI=function(aK){return(isNaN(aK)||aK>aF||aK<aH)},aG=$(this).val();if(!multi_value){aG=parseFloat(aG);if(aI(aG)){alert("Parameter value must be in the range ["+aH+"-"+aF+"]");return $(this)}}else{aG=aG.split("-");aG=[parseFloat(aG[0]),parseFloat(aG[1])];if(aI(aG[0])||aI(aG[1])){alert("Parameter value must be in the range ["+aH+"-"+aF+"]");return $(this)}}aD.slider((multi_value?"values":"value"),aG)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aB){aB.stopPropagation()}).click(function(aB){aB.stopPropagation()}).bind("dblclick",function(aB){aB.stopPropagation()}).bind("keydown",function(aB){aB.stopPropagation()});var aw=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ao=this;$.each(this.filters,function(aE,aG){aG.container=$("<div/>").addClass("filter-row slider-row").appendTo(aw);var aF=$("<div/>").addClass("elt-label").appendTo(aG.container);var aD=$("<span/>").addClass("slider-name").text(aG.name+"  ").appendTo(aF);var aC=$("<span/>");var aI=$("<span/>").addClass("slider-value").appendTo(aF).append("[").append(aC).append("]");var aB=$("<div/>").addClass("slider").appendTo(aG.container);aG.control_element=$("<div/>").attr("id",aG.name+"-filter-control").appendTo(aB);var aH=[0,0];aG.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aK,aL){var aJ=aL.values;aC.text(aJ[0]+"-"+aJ[1]);aG.low=aJ[0];aG.high=aJ[1];ao.track.request_draw(true,true)},change:function(aJ,aK){aG.control_element.slider("option","slide").call(aG.control_element,aJ,aK)}});aG.slider=aG.control_element;aG.slider_label=aC;aj(aI,aC,aG.control_element);$("<div style='clear: both;'/>").appendTo(aG.container)});if(this.filters.length!==0){var al=$("<div/>").addClass("param-row").appendTo(aw);var an=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(al);var ah=this;an.click(function(){ah.run_on_dataset()})}var aq=$("<div/>").addClass("display-controls").appendTo(this.parent_div),at,am,ap,ak={Transparency:function(aB){ao.alpha_filter=aB},Height:function(aB){ao.height_filter=aB}};$.each(ak,function(aD,aC){at=$("<div/>").addClass("filter-row").appendTo(aq),am=$("<span/>").addClass("elt-label").text(aD+":").appendTo(at),ap=$("<select/>").attr("name",aD+"_dropdown").css("float","right").appendTo(at);$("<option/>").attr("value",-1).text("== None ==").appendTo(ap);for(var aB=0;aB<ao.filters.length;aB++){$("<option/>").attr("value",aB).text(ao.filters[aB].name).appendTo(ap)}ap.change(function(){$(this).children("option:selected").each(function(){var aE=parseInt($(this).val());ak[aD]((aE>=0?ao.filters[aE]:null));ao.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(at)});$("<div style='clear: both;'/>").appendTo(this.parent_div)};p(ab.prototype,{reset_filters:function(){for(var ag=0;ag<this.filters.length;ag++){filter=this.filters[ag];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var ao=function(at,aq,ar){if(!(aq in at)){at[aq]=ar}return at[aq]};var ai={},ag,ah,aj;for(var ak=0;ak<this.filters.length;ak++){ag=this.filters[ak];if(ag.tool_id){if(ag.min!=ag.low){ah=ao(ai,ag.tool_id,[]);ah[ah.length]=ag.tool_exp_name+" >= "+ag.low}if(ag.max!=ag.high){ah=ao(ai,ag.tool_id,[]);ah[ah.length]=ag.tool_exp_name+" <= "+ag.high}}}var am=[];for(var ap in ai){am[am.length]=[ap,ai[ap]]}var an=am.length;(function al(ax,au){var ar=au[0],at=ar[0],aw=ar[1],av="("+aw.join(") and (")+")",aq={cond:av,input:ax,target_dataset_id:ax,tool_id:at},au=au.slice(1);$.getJSON(run_tool_url,aq,function(ay){if(ay.error){show_modal("Filter Dataset","Error running tool "+at,{Close:hide_modal})}else{if(au.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{al(ay.dataset_id,au)}}})})(this.track.dataset_id,am)}});var D=function(ag,ah){M.Scaler.call(this,ah);this.filter=ag};D.prototype.gen_val=function(ag){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ag[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var G=function(ag){this.track=ag.track;this.params=ag.params;this.values={};this.restore_values((ag.saved_values?ag.saved_values:{}));this.onchange=ag.onchange};p(G.prototype,{restore_values:function(ag){var ah=this;$.each(this.params,function(ai,aj){if(ag[aj.key]!==undefined){ah.values[aj.key]=ag[aj.key]}else{ah.values[aj.key]=aj.default_value}})},build_form:function(){var ah=this;var ag=$("<div />");$.each(this.params,function(al,aj){if(!aj.hidden){var ai="param_"+al;var an=ah.values[aj.key];var aq=$("<div class='form-row' />").appendTo(ag);aq.append($("<label />").attr("for",ai).text(aj.label+":"));if(aj.type==="bool"){aq.append($('<input type="checkbox" />').attr("id",ai).attr("name",ai).attr("checked",an))}else{if(aj.type==="text"){aq.append($('<input type="text"/>').attr("id",ai).val(an).click(function(){$(this).select()}))}else{if(aj.type==="color"){var am=$("<input />").attr("id",ai).attr("name",ai).val(an);var ao=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var ak=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ao);var ap=$("<div/>").appendTo(ak).farbtastic({width:100,height:100,callback:am,color:an});$("<div />").append(am).append(ao).appendTo(aq).bind("click",function(ar){ao.css({left:$(this).position().left+($(am).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ao.hide();$(document).unbind("click.color-picker")});ar.stopPropagation()})}else{aq.append($("<input />").attr("id",ai).attr("name",ai).val(an))}}}}});return ag},update_from_form:function(ag){var ai=this;var ah=false;$.each(this.params,function(aj,al){if(!al.hidden){var am="param_"+aj;var ak=ag.find("#"+am).val();if(al.type==="float"){ak=parseFloat(ak)}else{if(al.type==="int"){ak=parseInt(ak)}else{if(al.type==="bool"){ak=ag.find("#"+am).is(":checked")}}}if(ak!==ai.values[al.key]){ai.values[al.key]=ak;ah=true}}});if(ah){this.onchange()}}});var b=function(ag,aj,ai,ah,ak){this.track=ag;this.index=aj;this.low=aj*R*ai;this.high=(aj+1)*R*ai;this.resolution=ai;this.canvas=$("<div class='track-tile'/>").append(ah);this.data=ak;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(ag,aj,ai,ah,ak,al){b.call(this,ag,aj,ai,ah,ak);this.max_val=al};p(k.prototype,b.prototype);var P=function(ag,ak,aj,ai,am,an,al,ah){b.call(this,ag,ak,aj,ai,am);this.mode=an;this.message=al;this.feature_mapper=ah};p(P.prototype,b.prototype);P.prototype.predisplay_actions=function(){var ah=this,ag={};if(ah.mode!=="Pack"){return}$(this.canvas).mousemove(function(at){var an=$(this).offset(),ar=at.pageX-an.left,aq=at.pageY-an.top,ax=ah.feature_mapper.get_feature_data(ar,aq),ao=(ax?ax[0]:null);$(this).siblings(".feature-popup").each(function(){if(!ao||$(this).attr("id")!==ao.toString()){$(this).remove()}});if(ax){var aj=ag[ao];if(!aj){var ao=ax[0],au={name:ax[3],start:ax[1],end:ax[2],strand:ax[4]},am=ah.track.filters_manager.filters,al;for(var ap=0;ap<am.length;ap++){al=am[ap];au[al.name]=ax[al.index]}var aj=$("<div/>").attr("id",ao).addClass("feature-popup"),aw,av,ay=$("<table/>").appendTo(aj),az;for(aw in au){av=au[aw];az=$("<tr/>").appendTo(ay);$("<th/>").appendTo(az).text(aw);$("<td/>").attr("align","left").appendTo(az).text(typeof(av)=="number"?aa(av,2):av)}ag[ao]=aj}aj.appendTo($(ah.canvas).parent());var ak=ar+parseInt(ah.canvas.css("left"))+7,ai=aq+parseInt(ah.canvas.css("top"))+7;aj.css("left",ak+"px").css("top",ai+"px")}else{if(!at.isPropagationStopped()){at.stopPropagation();$(this).siblings().each(function(){$(this).trigger(at)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var i=function(aj,ar,ak,an,at,ai,ah){q.call(this,aj,ar,ak,{},"draghandle");this.data_url=(ai?ai:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ah?ah:L);this.dataset_check_url=converted_datasets_state_url;if(!i.id_counter){i.id_counter=0}this.id=i.id_counter++;this.container_div=$("<div />").addClass("track").attr("id","track_"+this.id).css("position","relative");if(an){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div/>").addClass("track-name").appendTo(this.header_div).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());this.icons_div=$("<div/>").css("float","left").appendTo(this.header_div).hide();this.settings_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Edit settings").addClass("icon-button settings-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.overview_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Set as overview").addClass("icon-button overview-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.filters_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Filters").addClass("icon-button filters-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.tools_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Tools").addClass("icon-button tools-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.remove_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Remove").addClass("icon-button remove-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);var al=this;this.header_div.dblclick(function(au){au.stopPropagation()});this.settings_icon.click(function(){var aw=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},au=function(){al.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},av=function(ax){if((ax.keyCode||ax.which)===27){aw()}else{if((ax.keyCode||ax.which)===13){au()}}};$(window).bind("keypress.check_enter_esc",av);show_modal("Configure Track",al.config.build_form(),{Cancel:aw,OK:au})});this.overview_icon.click(function(){al.view.set_overview(al)});this.filters_icon.click(function(){al.filters_div.toggle();al.filters_manager.reset_filters()});this.tools_icon.click(function(){al.dynamic_tool_div.toggle();if(al.dynamic_tool_div.is(":visible")){al.set_name(al.name+al.tool_region_and_parameters_str())}else{al.revert_name()}$(".tipsy").remove()});this.remove_icon.click(function(){$(".tipsy").remove();al.remove()});if(al.display_modes!==undefined){if(al.mode_div===undefined){al.mode_div=$("<div class='right-float menubutton popup' />").appendTo(al.header_div);var am=(al.config&&al.config.values.mode?al.config.values.mode:al.display_modes[0]);al.mode=am;al.mode_div.text(am);var ag={};for(var ao=0,aq=al.display_modes.length;ao<aq;ao++){var ap=al.display_modes[ao];ag[ap]=function(au){return function(){al.change_mode(au)}}(ap)}make_popupmenu(al.mode_div,ag)}else{al.mode_div.hide()}this.header_div.append($("<div/>").css("clear","both"));this.container_div.hover(function(){al.icons_div.show()},function(){al.icons_div.hide()})}}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};p(i.prototype,q.prototype,{get_type:function(){if(this instanceof ac){return"LabelTrack"}else{if(this instanceof A){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof X){return"ReadTrack"}else{if(this instanceof V){return"ToolDataFeatureTrack"}else{if(this instanceof U){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ag=this;ag.enabled=false;ag.tile_cache.clear();ag.data_manager.clear();ag.initial_canvas=undefined;ag.content_div.css("height","auto");ag.container_div.removeClass("nodata error pending");if(!ag.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ag.hda_ldda,dataset_id:ag.dataset_id,chrom:ag.view.chrom},function(ah){if(!ah||ah==="error"||ah.kind==="error"){ag.container_div.addClass("error");ag.content_div.text(o);if(ah.message){var ai=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ah.message+"</pre>",{Close:hide_modal})});ag.content_div.append(ai)}}else{if(ah==="no converter"){ag.container_div.addClass("error");ag.content_div.text(K)}else{if(ah==="no data"||(ah.data!==undefined&&(ah.data===null||ah.data.length===0))){ag.container_div.addClass("nodata");ag.content_div.text(F)}else{if(ah==="pending"){ag.container_div.addClass("pending");ag.content_div.text(t);setTimeout(function(){ag.init()},ag.data_query_wait)}else{if(ah.status==="data"){if(ah.valid_chroms){ag.valid_chroms=ah.valid_chroms;ag.update_track_icons()}ag.content_div.text(Z);if(ag.view.chrom){ag.content_div.text("");ag.content_div.css("height",ag.height_px+"px");ag.enabled=true;$.when(ag.predraw_init()).done(function(){ag.container_div.removeClass("nodata error pending");ag.request_draw()})}}}}}}});this.update_track_icons()},predraw_init:function(){}});var N=function(ai,ao,aj,al,ap,an,am,ah,ag){i.call(this,ai,ao,aj,al,ap,ah,ag);var ak=this,ao=ak.view;m(ak.container_div,ak.drag_handle_class,".group",ak);this.filters_manager=new ab(this,(an!==undefined?an:{}));this.filters_available=false;this.filters_visible=false;this.tool=(am!==undefined&&obj_length(am)>0?new r(this,am):undefined);if(this.header_div){if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}};p(N.prototype,q.prototype,i.prototype,{copy:function(ag){return new this.constructor(this.name,this.view,ag,this.hda_ldda,this.dataset_id,this.prefs,this.filters,this.tool)},to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ah){var ag=this;ag.mode_div.text(ah);ag.mode=ah;ag.config.values.mode=ah;ag.tile_cache.clear();ag.request_draw();return ag},update_track_icons:function(){var ag=this;if(ag.filters_available>0){ag.filters_icon.show()}else{ag.filters_icon.hide()}if(ag.tool){ag.tools_icon.show()}else{ag.tools_icon.hide()}},_gen_tile_cache_key:function(ah,ai,ag){return ah+"_"+ai+"_"+ag},request_draw:function(ah,ag){this.view.request_redraw(false,ah,ag,this)},_draw:function(ai,aq){if(!this.enabled){return}if(!(this instanceof A)&&(!this.dataset_id)){return}var ap=this.view.low,am=this.view.high,an=am-ap,aj=this.view.container.width(),au=aj/an,al=this.view.resolution,at=$("<div style='position: relative;'></div>");if(this.is_overview){ap=this.view.max_low;am=this.view.max_high;al=Math.pow(C,Math.ceil(Math.log((view.max_high-view.max_low)/R)/Math.log(C)));au=aj/(view.max_high-view.max_low)}if(!aq){this.content_div.children().remove()}this.content_div.append(at);this.max_height=0;var ah=Math.floor(ap/al/R);var ao=true;var ar=[];var ag=0;while((ah*R*al)<am){tile=this.draw_helper(ai,aj,ah,al,at,au);if(tile){ar.push(tile)}else{ao=false}ah+=1;ag++}var ak=this;if(ao){ak.postdraw_actions(ar,aj,au,aq)}},postdraw_actions:function(ak,al,am,ag){var ai=this;var aj=false;for(var ah=0;ah<ak.length;ah++){if(ak[ah].message){aj=true;break}}if(aj){for(var ah=0;ah<ak.length;ah++){tile=ak[ah];if(!tile.message){tile.canvas.css("padding-top",E)}}}},draw_helper:function(ah,ai,aj,am,at,ax,au,an){var ak=this,ar=this._gen_tile_cache_key(ai,ax,aj),ao=aj*R*am,aw=ao+R*am;var ap=(ah?undefined:ak.tile_cache.get(ar));if(ap){ak.show_tile(ap,at,ax);return ap}var aq=function(ay){return("isResolved" in ay)};var al=true;var ag=ak.data_manager.get_data(ao,aw,ak.mode,am,ak.data_url_extra_params);if(aq(ag)){al=false}var av;if(view.reference_track&&ax>view.canvas_manager.char_width_px){av=view.reference_track.data_manager.get_data(ao,aw,ak.mode,am,view.reference_track.data_url_extra_params);if(aq(av)){al=false}}if(al){p(ag,an);var ap=ak.draw_tile(ag,ak.mode,am,aj,ax,av);if(ap!==undefined){ak.tile_cache.set(ar,ap);ak.show_tile(ap,at,ax)}return ap}$.when(ag,av).then(function(){view.request_redraw(false,false,false,ak)});return null},show_tile:function(am,ao,ap){var ai=this,ah=am.canvas,al=ah;if(am.message){var aq=$("<div/>"),an=$("<div/>").addClass("tile-message").text(am.message).css({height:E-1,width:am.canvas.width}).appendTo(aq),ak=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(an),ag=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(an);aq.append(ah);al=aq;ak.click(function(){am.stale=true;ai.data_manager.get_more_data(am.low,am.high,ai.mode,am.resolution,{},ai.data_manager.DEEP_DATA_REQ);ai.request_draw()}).dblclick(function(ar){ar.stopPropagation()});ag.click(function(){am.stale=true;ai.data_manager.get_more_data(am.low,am.high,ai.mode,am.resolution,{},ai.data_manager.BROAD_DATA_REQ);ai.request_draw()}).dblclick(function(ar){ar.stopPropagation()})}am.predisplay_actions();var aj=(am.low-(this.is_overview?this.view.max_low:this.view.low))*ap;if(this.left_offset){aj-=this.left_offset}al.css({position:"absolute",top:0,left:aj,height:""});ao.append(al);ai.max_height=Math.max(ai.max_height,al.height());ai.content_div.css("height",ai.max_height+"px");ao.children().css("height",ai.max_height+"px")},_get_tile_bounds:function(ag,ah){var aj=ag*R*ah,ak=R*ah,ai=(aj+ak<=this.view.max_high?aj+ak:this.view.max_high);return[aj,ai]},tool_region_and_parameters_str:function(ai,ag,aj){var ah=this,ak=(ai!==undefined&&ag!==undefined&&aj!==undefined?ai+":"+ag+"-"+aj:"all");return" - region=["+ak+"], parameters=["+ah.tool.get_param_values().join(", ")+"]"}});var ac=function(ah,ag){i.call(this,"label",ah,ag,false,{});this.container_div.addClass("label-track")};p(ac.prototype,i.prototype,{init:function(){this.enabled=true},_draw:function(){var ai=this.view,aj=ai.high-ai.low,am=Math.floor(Math.pow(10,Math.floor(Math.log(aj)/Math.log(10)))),ag=Math.floor(ai.low/am)*am,ak=this.view.container.width(),ah=$("<div style='position: relative; height: 1.3em;'></div>");while(ag<ai.high){var al=(ag-ai.low)/aj*ak;ah.append($("<div class='label'>"+commatize(ag)+"</div>").css({position:"absolute",left:al-1}));ag+=am}this.content_div.children(":first").remove();this.content_div.append(ah)}});var A=function(ag){N.call(this,"reference",ag,{content_div:ag.top_labeltrack},false,{});ag.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ag.dbkey};this.data_manager=new I(B,this,false);this.tile_cache=new c(u)};p(A.prototype,q.prototype,N.prototype,{init:function(){this.enabled=true},draw_tile:function(aq,am,al,ah,ar){var ak=this,ai=R*al;if(ar>this.view.canvas_manager.char_width_px){if(aq.data===null){ak.content_div.css("height","0px");return}var aj=this.view.canvas_manager.new_canvas();var ap=aj.getContext("2d");aj.width=Math.ceil(ai*ar+ak.left_offset);aj.height=ak.height_px;ap.font=ap.canvas.manager.default_font;ap.textAlign="center";aq=aq.data;for(var an=0,ao=aq.length;an<ao;an++){var ag=Math.round(an*ar);ap.fillText(aq[an],ag+ak.left_offset,10)}return new b(ak,ah,al,aj,aq)}this.content_div.css("height","0px")}});var j=function(al,aj,ai,am,ag,ak){var ah=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";N.call(this,al,aj,ai,true,ak);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=am;this.dataset_id=ag;this.original_dataset_id=ag;this.data_manager=new S(B,this);this.tile_cache=new c(u);this.left_offset=0;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:ak,onchange:function(){ah.set_name(ah.prefs.name);ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;$("#linetrack_"+ah.dataset_id+"_minval").text(ah.prefs.min_value);$("#linetrack_"+ah.dataset_id+"_maxval").text(ah.prefs.max_value);ah.tile_cache.clear();ah.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};p(j.prototype,q.prototype,N.prototype,{add_resize_handle:function(){var ag=this;var aj=false;var ai=false;var ah=$("<div class='track-resize'>");$(ag.container_div).hover(function(){aj=true;ah.show()},function(){aj=false;if(!ai){ah.hide()}});ah.hide().bind("dragstart",function(ak,al){ai=true;al.original_height=$(ag.content_div).height()}).bind("drag",function(al,am){var ak=Math.min(Math.max(am.original_height+am.deltaY,ag.min_height_px),ag.max_height_px);$(ag.content_div).css("height",ak);ag.height_px=ak;ag.request_draw(true)}).bind("dragend",function(ak,al){ag.tile_cache.clear();ai=false;if(!aj){ah.hide()}ag.config.values.height=ag.height_px}).appendTo(ag.container_div)},predraw_init:function(){var ag=this;ag.vertical_range=undefined;return $.getJSON(ag.data_url,{stats:true,chrom:ag.view.chrom,low:null,high:null,hda_ldda:ag.hda_ldda,dataset_id:ag.dataset_id},function(ah){ag.container_div.addClass("line-track");var aj=ah.data;if(isNaN(parseFloat(ag.prefs.min_value))||isNaN(parseFloat(ag.prefs.max_value))){ag.prefs.min_value=aj.min;ag.prefs.max_value=aj.max;$("#track_"+ag.dataset_id+"_minval").val(ag.prefs.min_value);$("#track_"+ag.dataset_id+"_maxval").val(ag.prefs.max_value)}ag.vertical_range=ag.prefs.max_value-ag.prefs.min_value;ag.total_frequency=aj.total_frequency;ag.container_div.find(".yaxislabel").remove();var ak=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ag.dataset_id+"_minval").text(aa(ag.prefs.min_value,3));var ai=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ag.dataset_id+"_maxval").text(aa(ag.prefs.max_value,3));ai.css({position:"absolute",top:"24px",left:"10px"});ai.prependTo(ag.container_div);ak.css({position:"absolute",bottom:"2px",left:"10px"});ak.prependTo(ag.container_div)})},draw_tile:function(at,al,ak,ai,ar){if(this.vertical_range===undefined){return}var ag=this._get_tile_bounds(ai,ak),am=ag[0],aq=ag[1],ah=Math.ceil((aq-am)*ar),ao=this.height_px;var aj=this.view.canvas_manager.new_canvas();aj.width=ah,aj.height=ao;var ap=aj.getContext("2d");var an=new M.LinePainter(at.data,am,aq,this.prefs,al);an.draw(ap,ah,ao);return new b(this.track,ai,ak,aj,at.data)}});var e=function(ag,am,ah,al,ao,an,aj,ak){var ai=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];N.call(this,ag,am,ah,true,an,aj,ak);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ag},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:an,onchange:function(){ai.set_name(ai.prefs.name);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=al;this.dataset_id=ao;this.original_dataset_id=ao;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new S(20,this);this.left_offset=200;this.painter=M.LinkedFeaturePainter};p(e.prototype,q.prototype,N.prototype,{postdraw_actions:function(aw,ag,ax,av){N.prototype.postdraw_actions.call(this,aw,av);var aj=this;if(av){var al=aj.content_div.children();var am=false;for(var ak=al.length-1,aq=0;ak>=aq;ak--){var ai=$(al[ak]);if(am){ai.remove()}else{if(ai.children().length!==0){am=true}}}}if(aj.mode=="Histogram"){var ap=-1;for(var ak=0;ak<aw.length;ak++){var au=aw[ak].max_val;if(au>ap){ap=au}}for(var ak=0;ak<aw.length;ak++){var at=aw[ak];if(at.max_val!==ap){at.canvas.remove();aj.draw_helper(true,ag,at.index,at.resolution,at.canvas.parent(),ax,[],{max:ap})}}}if(aj.filters_manager){var ah=aj.filters_manager.filters;for(var ao=0;ao<ah.length;ao++){ah[ao].update_ui_elt()}var an=false,ar;for(var ak=0;ak<aw.length;ak++){if(aw[ak].data.length){ar=aw[ak].data[0];for(var ao=0;ao<ah.length;ao++){if(ah[ao].applies_to(ar)){an=true;break}}}}if(aj.filters_available!==an){aj.filters_available=an;if(!aj.filters_available){aj.filters_div.hide()}aj.update_track_icons()}}},update_auto_mode:function(ag){if(this.mode=="Auto"){if(ag=="no_detail"){ag="feature spans"}else{if(ag=="summary_tree"){ag="coverage histogram"}}this.mode_div.text("Auto ("+ag+")")}},incremental_slots:function(ak,ah,aj){var ai=this.view.canvas_manager.dummy_context,ag=this.inc_slots[ak];if(!ag||(ag.mode!==aj)){ag=new (s.FeatureSlotter)(ak,aj==="Pack",z,function(al){return ai.measureText(al)});ag.mode=aj;this.inc_slots[ak]=ag}return ag.slot_features(ah)},get_summary_tree_data:function(ak,an,ai,aw){if(aw>ai-an){aw=ai-an}var ar=Math.floor((ai-an)/aw),av=[],aj=0;var al=0,am=0,aq,au=0,ao=[],at,ap;var ah=function(az,ay,aA,ax){az[0]=ay+aA*ax;az[1]=ay+(aA+1)*ax};while(au<aw&&al!==ak.length){var ag=false;for(;au<aw&&!ag;au++){ah(ao,an,au,ar);for(am=al;am<ak.length;am++){aq=ak[am].slice(1,3);if(is_overlap(aq,ao)){ag=true;break}}if(ag){break}}data_start_index=am;av[av.length]=at=[ao[0],0];for(;am<ak.length;am++){aq=ak[am].slice(1,3);if(is_overlap(aq,ao)){at[1]++}else{break}}if(at[1]>aj){aj=at[1]}au++}return{max:aj,delta:ar,data:av}},draw_tile:function(av,ay,aC,aG,aq,aj){var az=this,al=az._get_tile_bounds(aG,aC),aJ=al[0],ah=al[1],ax=ah-aJ,aA=Math.ceil(ax*aq),aP=25,ak=this.left_offset,aw,am;if(ay==="Auto"){if(av.dataset_type==="summary_tree"){ay=av.dataset_type}else{if(av.extra_info==="no_detail"||az.is_overview){ay="no_detail"}else{var aO=av.data;if(this.view.high-this.view.low>J){ay="Squish"}else{ay="Pack"}}}this.update_auto_mode(ay)}if(ay==="summary_tree"||ay==="Histogram"){am=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ag=$("<div />").addClass("yaxislabel");ag.text(av.max);ag.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ag.prependTo(this.container_div);var ai=this.view.canvas_manager.new_canvas();ai.width=aA+ak;ai.height=am+T;if(av.dataset_type!="summary_tree"){var ar=this.get_summary_tree_data(av.data,aJ,ah,200);if(av.max){ar.max=av.max}av=ar}var aL=new M.SummaryTreePainter(av,aJ,ah,this.prefs);var aB=ai.getContext("2d");aB.translate(ak,T);aL.draw(aB,aA,am);return new k(az,aG,aC,ai,av.data,av.max)}var aw,ao=1;if(ay==="no_detail"||ay==="Squish"||ay==="Pack"){ao=this.incremental_slots(aq,av.data,ay);aw=this.inc_slots[aq].slots}var ap=[];if(av.data){var at=this.filters_manager.filters;for(var aD=0,aF=av.data.length;aD<aF;aD++){var an=av.data[aD];var aE=false;var au;for(var aI=0,aN=at.length;aI<aN;aI++){au=at[aI];au.update_attrs(an);if(!au.keep(an)){aE=true;break}}if(!aE){ap.push(an)}}}var aM=(this.filters_manager.alpha_filter?new D(this.filters_manager.alpha_filter):null);var aK=(this.filters_manager.height_filter?new D(this.filters_manager.height_filter):null);var aL=new (this.painter)(ap,aJ,ah,this.prefs,ay,aM,aK,aj);var am=Math.max(ae,aL.get_required_height(ao));var ai=this.view.canvas_manager.new_canvas();var aH=null;ai.width=aA+ak;ai.height=am;var aB=ai.getContext("2d");aB.fillStyle=this.prefs.block_color;aB.font=aB.canvas.manager.default_font;aB.textAlign="right";this.container_div.find(".yaxislabel").remove();if(av.data){aB.translate(ak,0);aH=aL.draw(aB,aA,am,aw);aH.translation=-ak}return new P(az,aG,aC,ai,av.data,ay,av.message,aH)}});var U=function(ak,ai,ah,am,ag,aj,al){e.call(this,ak,ai,ah,am,ag,aj,al);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:aj,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter};p(U.prototype,q.prototype,N.prototype,e.prototype);var X=function(ak,ai,ah,am,ag,aj,al){e.call(this,ak,ai,ah,am,ag,aj,al);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:aj,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter;this.update_track_icons()};p(X.prototype,q.prototype,N.prototype,e.prototype);var V=function(ak,ai,ah,am,ag,aj,al){e.call(this,ak,ai,ah,am,ag,aj,al,{});this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};p(V.prototype,q.prototype,N.prototype,e.prototype,{predraw_init:function(){var ah=this;var ag=function(){if(ah.data_manager.size()===0){setTimeout(ag,300)}else{ah.data_url=default_data_url;ah.data_query_wait=L;ah.dataset_state_url=converted_datasets_state_url;$.getJSON(ah.dataset_state_url,{dataset_id:ah.dataset_id,hda_ldda:ah.hda_ldda},function(ai){})}};ag()}});Y.View=ad;Y.DrawableGroup=Q;Y.LineTrack=j;Y.FeatureTrack=e;Y.ReadTrack=X;Y.VcfTrack=U};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(F,G){for(var E=0;E<=z;E++){var C=false,H=h[E];if(H!==undefined){for(var B=0,D=H.length;B<D;B++){var i=H[B];if(G>i[0]&&F<i[1]){C=true;break}}}if(!C){return E}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(i,w){var t=i("class").extend;var o=function(H,z,F,y,E,C){if(C===undefined){C=4}var B=y-z;var A=E-F;var D=Math.floor(Math.sqrt(B*B+A*A)/C);var I=B/D;var G=A/D;var x;for(x=0;x<D;x++,z+=I,F+=G){if(x%2!==0){continue}H.fillRect(z,F,C,1)}};var p=function(A,z,x,D){var C=z-D/2,B=z+D/2,E=x-Math.sqrt(D*3/2);A.beginPath();A.moveTo(C,E);A.lineTo(B,E);A.lineTo(z,x);A.lineTo(C,E);A.strokeStyle=this.fillStyle;A.fill();A.stroke();A.closePath()};var d=function(x){this.default_val=(x?x:1)};d.prototype.gen_val=function(x){return this.default_val};var l=function(z,B,x,y,A){this.data=z;this.view_start=B;this.view_end=x;this.prefs=t({},this.default_prefs,y);this.mode=A};l.prototype.default_prefs={};var u=function(z,B,x,y,A){l.call(this,z,B,x,y,A)};u.prototype.default_prefs={show_counts:false};u.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var b=function(x,B,D,E,z){l.call(this,x,B,D,E,z);if(this.prefs.min_value===undefined){var F=Infinity;for(var y=0,A=this.data.length;y<A;y++){F=Math.min(F,this.data[y][1])}this.prefs.min_value=F}if(this.prefs.max_value===undefined){var C=-Infinity;for(var y=0,A=this.data.length;y<A;y++){C=Math.max(C,this.data[y][1])}this.prefs.max_value=C}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(M,L,J){var E=false,G=this.prefs.min_value,C=this.prefs.max_value,I=C-G,x=J,z=this.view_start,K=this.view_end-this.view_start,A=L/K,H=this.mode,S=this.data;M.save();var T=Math.round(J+G/I*J);if(H!=="Intensity"){M.fillStyle="#aaa";M.fillRect(0,T,L,1)}M.beginPath();var Q,D,B;if(S.length>1){B=Math.ceil((S[1][0]-S[0][0])*A)}else{B=10}for(var N=0,O=S.length;N<O;N++){M.fillStyle=this.prefs.color;Q=Math.round((S[N][0]-z)*A);D=S[N][1];var P=false,F=false;if(D===null){if(E&&H==="Filled"){M.lineTo(Q,x)}E=false;continue}if(D<G){F=true;D=G}else{if(D>C){P=true;D=C}}if(H==="Histogram"){D=Math.round(D/I*x);M.fillRect(Q,T,B,-D)}else{if(H==="Intensity"){D=255-Math.floor((D-G)/I*255);M.fillStyle="rgb("+D+","+D+","+D+")";M.fillRect(Q,0,B,x)}else{D=Math.round(x-(D-G)/I*x);if(E){M.lineTo(Q,D)}else{E=true;if(H==="Filled"){M.moveTo(Q,x);M.lineTo(Q,D)}else{M.moveTo(Q,D)}}}}M.fillStyle=this.prefs.overflow_color;if(P||F){var R;if(H==="Histogram"||H==="Intensity"){R=B}else{Q-=2;R=4}if(P){M.fillRect(Q,0,R,3)}if(F){M.fillRect(Q,x-3,R,3)}}M.fillStyle=this.prefs.color}if(H==="Filled"){if(E){M.lineTo(Q,T);M.lineTo(0,T)}M.fill()}else{M.stroke()}M.restore()};var 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ag=an;if(aj===this.DEEP_DATA_REQ){$.extend(al,{start_val:ao.data.length+1})}else{if(aj===this.BROAD_DATA_REQ){ag=(ao.max_high?ao.max_high:ao.data[ao.data.length-1][2])+1}}var af=this,ak=this.load_data(ag,ai,am,ah,al);new_data_available=$.Deferred();this.set_data(an,ai,am,new_data_available);$.when(ak).then(function(ap){if(ap.data){ap.data=ao.data.concat(ap.data);if(ap.max_low){ap.max_low=ao.max_low}if(ap.message){ap.message=ap.message.replace(/[0-9]+/,ap.data.length)}}af.set_data(an,ai,am,ap);new_data_available.resolve(ap)});return new_data_available},get_data_from_cache:function(af,ag,ah){return this.get(this.gen_key(af,ag,ah))},set_data:function(ag,ah,ai,af){return this.set(this.gen_key(ag,ah,ai),af)},gen_key:function(af,ah,ai){var ag=af+"_"+ah+"_"+ai;return ag},split_key:function(af){return af.split("_")}});var I=function(ag,af,ah){S.call(this,ag,af,ah)};p(I.prototype,S.prototype,c.prototype,{load_data:function(af,ai,aj,ag,ah){if(ag>1){return{data:null}}return S.prototype.load_data.call(this,af,ai,aj,ag,ah)}});var q=function(ai,ag,af,ah,aj){this.name=ai;this.view=ag;this.container=af;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ai}],saved_values:ah,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=aj;this.is_overview=false};p(q.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},update_track_icons:function(){},set_name:function(af){this.old_name=this.name;this.name=af;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var y=function(aj,ai,ag,af,ah,ak){q.call(this,ai,ag,af,ah,ak);this.obj_type=aj;this.drawables=[]};p(y.prototype,q.prototype,{init:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af].init()}},_draw:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af]._draw()}},to_json:function(){var ag=[];for(var af=0;af<this.drawables.length;af++){ag.push(this.drawables[af].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ag}},add_drawable:function(af){this.drawables.push(af);af.container=this},add_drawable_before:function(ah,af){var ag=this.drawables.indexOf(af);if(ag!=-1){this.drawables.splice(ag,0,ah);return true}return false},remove_drawable:function(ag){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);ag.container=null;return true}return false},move_drawable:function(ag,ah){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);this.drawables.splice(ah,0,ag);return true}return false}});var Q=function(ai,ag,af,ah){y.call(this,"DrawableGroup",ai,ag,af,ah,"group-handle");if(!Q.id_counter){Q.id_counter=0}var aj=Q.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+aj).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+aj+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.update_track_icons()};p(Q.prototype,q.prototype,y.prototype,{update_track_icons:function(){var ag=this;var af={};af["Edit configuration"]=function(){var aj=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ah=function(){ag.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ai=function(ak){if((ak.keyCode||ak.which)===27){aj()}else{if((ak.keyCode||ak.which)===13){ah()}}};$(window).bind("keypress.check_enter_esc",ai);show_modal("Configure Group",ag.config.build_form(),{Cancel:aj,OK:ah})};af.Remove=function(){ag.remove()};make_popupmenu(ag.name_div,af)}});var ac=function(af,ai,ah,ag){y.call(this,"View");this.container=af;this.chrom=null;this.vis_id=ah;this.dbkey=ag;this.title=ai;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ae(af.get(0).ownerDocument);this.reset()};p(ac.prototype,y.prototype,{init:function(){var ah=this.container,af=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ah);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ah);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ah);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,af);this.intro_div=$("<div/>").addClass("intro");var ai=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ag=function(aj){if(aj.type==="focusout"||(aj.keyCode||aj.which)===13||(aj.keyCode||aj.which)===27){if((aj.keyCode||aj.which)!==27){af.go_to($(this).val())}$(this).hide();$(this).val("");af.location_span.show();af.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ag).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){af.location_span.hide();af.chrom_select.hide();af.nav_input.val(af.chrom+":"+af.low+"-"+af.high);af.nav_input.css("display","inline-block");af.nav_input.select();af.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){af.zoom_out();af.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){af.zoom_in();af.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){af.change_chrom(af.chrom_select.val())});this.browser_content_div.click(function(aj){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(aj){af.zoom_in(aj.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(aj,ak){this.current_x=ak.offsetX}).bind("drag",function(aj,al){var am=al.offsetX-this.current_x;this.current_x=al.offsetX;var ak=Math.round(am/af.viewport_container.width()*(af.max_high-af.max_low));af.move_delta(-ak)});this.overview_close.click(function(){af.reset_overview()});this.viewport_container.bind("draginit",function(aj,ak){if(aj.clientX>af.viewport_container.width()-16){return false}}).bind("dragstart",function(aj,ak){ak.original_low=af.low;ak.current_height=aj.clientY;ak.current_x=ak.offsetX}).bind("drag",function(al,an){var aj=$(this);var ao=an.offsetX-an.current_x;var ak=aj.scrollTop()-(al.clientY-an.current_height);aj.scrollTop(ak);an.current_height=al.clientY;an.current_x=an.offsetX;var am=Math.round(ao/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}).bind("mousewheel",function(al,an,ak,aj){if(ak){var am=Math.round(-ak/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}});this.top_labeltrack.bind("dragstart",function(aj,ak){return $("<div />").css({height:af.browser_content_div.height()+af.top_labeltrack.height()+af.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(an,ao){$(ao.proxy).css({left:Math.min(an.pageX,ao.startX),width:Math.abs(an.pageX-ao.startX)});var ak=Math.min(an.pageX,ao.startX)-af.container.offset().left,aj=Math.max(an.pageX,ao.startX)-af.container.offset().left,am=(af.high-af.low),al=af.viewport_container.width();af.update_location(Math.round(ak/al*am)+af.low,Math.round(aj/al*am)+af.low)}).bind("dragend",function(ao,ap){var ak=Math.min(ao.pageX,ap.startX),aj=Math.max(ao.pageX,ap.startX),am=(af.high-af.low),al=af.viewport_container.width(),an=af.low;af.low=Math.round(ak/al*am)+an;af.high=Math.round(aj/al*am)+an;$(ap.proxy).remove();af.request_redraw()});this.add_label_track(new ab(this,{content_div:this.top_labeltrack}));this.add_label_track(new ab(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){af.resize_window()});$(document).bind("redraw",function(){af.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(af,ag){this.location_span.text(commatize(af)+" - "+commatize(ag));this.nav_input.val(this.chrom+":"+commatize(af)+"-"+commatize(ag))},load_chroms:function(ah){ah.num=w;$.extend(ah,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var af=this,ag=$.Deferred();$.ajax({url:chrom_url,data:ah,dataType:"json",success:function(aj){if(aj.chrom_info.length===0){alert("Invalid chromosome: "+ah.chrom);return}if(aj.reference){af.add_label_track(new A(af))}af.chrom_data=aj.chrom_info;var am='<option value="">Select Chrom/Contig</option>';for(var al=0,ai=af.chrom_data.length;al<ai;al++){var ak=af.chrom_data[al].chrom;am+='<option value="'+ak+'">'+ak+"</option>"}if(aj.prev_chroms){am+='<option value="previous">Previous '+w+"</option>"}if(aj.next_chroms){am+='<option value="next">Next '+w+"</option>"}af.chrom_select.html(am);af.chrom_start_index=aj.start_index;ag.resolve(aj)},error:function(){alert("Could not load chroms for this dbkey:",af.dbkey)}});return ag},change_chrom:function(ak,ag,am){if(!ak||ak==="None"){return}var ah=this;if(ak==="previous"){ah.load_chroms({low:this.chrom_start_index-w});return}if(ak==="next"){ah.load_chroms({low:this.chrom_start_index+w});return}var al=$.grep(ah.chrom_data,function(an,ao){return an.chrom===ak})[0];if(al===undefined){ah.load_chroms({chrom:ak},function(){ah.change_chrom(ak,ag,am)});return}else{if(ak!==ah.chrom){ah.chrom=ak;ah.chrom_select.val(ah.chrom);ah.max_high=al.len-1;ah.reset();ah.request_redraw(true);for(var aj=0,af=ah.drawables.length;aj<af;aj++){var ai=ah.drawables[aj];if(ai.init){ai.init()}}}if(ag!==undefined&&am!==undefined){ah.low=Math.max(ag,0);ah.high=Math.min(am,ah.max_high)}ah.reset_overview();ah.request_redraw()}},go_to:function(aj){aj=aj.replace(/ |,/g,"");var an=this,af,ai,ag=aj.split(":"),al=ag[0],am=ag[1];if(am!==undefined){try{var ak=am.split("-");af=parseInt(ak[0],10);ai=parseInt(ak[1],10)}catch(ah){return false}}an.change_chrom(al,af,ai)},move_fraction:function(ah){var af=this;var ag=af.high-af.low;this.move_delta(ah*ag)},move_delta:function(ah){var af=this;var ag=af.high-af.low;if(af.low-ah<af.max_low){af.low=af.max_low;af.high=af.max_low+ag}else{if(af.high-ah>af.max_high){af.high=af.max_high;af.low=af.max_high-ag}else{af.high-=ah;af.low-=ah}}af.request_redraw()},add_drawable:function(af){y.prototype.add_drawable.call(this,af);af.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(af){af.view=this;af.init();this.label_tracks.push(af)},remove_drawable:function(ah,ag){y.prototype.remove_drawable.call(this,ah);if(ag){var af=this;ah.container_div.fadeOut("slow",function(){$(this).remove();af.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(an,af,am,ag){var al=this,aj=(ag?[ag]:al.drawables),ah;var ag;for(var ak=0;ak<aj.length;ak++){ag=aj[ak];ah=-1;for(var ai=0;ai<al.tracks_to_be_redrawn.length;ai++){if(al.tracks_to_be_redrawn[ai][0]===ag){ah=ai;break}}if(ah<0){al.tracks_to_be_redrawn.push([ag,af,am])}else{al.tracks_to_be_redrawn[ak][1]=af;al.tracks_to_be_redrawn[ak][2]=am}}requestAnimationFrame(function(){al._redraw(an)})},_redraw:function(ap){var am=this.low,ai=this.high;if(am<this.max_low){am=this.max_low}if(ai>this.max_high){ai=this.max_high}var ao=this.high-this.low;if(this.high!==0&&ao<this.min_separation){ai=am+this.min_separation}this.low=Math.floor(am);this.high=Math.ceil(ai);this.resolution=Math.pow(C,Math.ceil(Math.log((this.high-this.low)/R)/Math.log(C)));this.zoom_res=Math.pow(v,Math.max(0,Math.ceil(Math.log(this.resolution,v)/Math.log(v))));var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var al=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var aq=13;this.overview_box.css({left:af,width:Math.max(aq,al)}).show();if(al<aq){this.overview_box.css("left",af-(aq-al)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:al})}this.update_location(this.low,this.high);if(!ap){var ah,ag,an;for(var aj=0,ak=this.tracks_to_be_redrawn.length;aj<ak;aj++){ah=this.tracks_to_be_redrawn[aj][0];ag=this.tracks_to_be_redrawn[aj][1];an=this.tracks_to_be_redrawn[aj][2];if(ah){ah._draw(ag,an)}}this.tracks_to_be_redrawn=[];for(aj=0,ak=this.label_tracks.length;aj<ak;aj++){this.label_tracks[aj]._draw()}}},zoom_in:function(ag,ah){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ai=this.high-this.low,aj=ai/2+this.low,af=(ai/this.zoom_factor)/2;if(ag){aj=ag/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(aj-af);this.high=Math.round(aj+af);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ag=this.high-this.low,ah=ag/2+this.low,af=(ag*this.zoom_factor)/2;this.low=Math.round(ah-af);this.high=Math.round(ah+af);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ah.dataset_id){return}this.overview_viewport.find(".track").remove()}var ag=ah.copy({content_div:this.overview_viewport}),af=this;ag.header_div.hide();ag.is_overview=true;af.overview_drawable=ag;this.overview_drawable.postdraw_actions=function(){af.overview_highlight.show().height(af.overview_drawable.content_div.height());af.overview_viewport.height(af.overview_drawable.content_div.height()+af.overview_box.outerHeight());af.overview_close.show();af.resize_window()};this.overview_drawable.init();af.has_changes=true},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var r=function(ah,al){this.track=ah;this.name=al.name;this.params=[];var at=al.params;for(var ai=0;ai<at.length;ai++){var an=at[ai],ag=an.name,ar=an.label,aj=unescape(an.html),au=an.value,ap=an.type;if(ap==="number"){this.params[this.params.length]=new g(ag,ar,aj,au,an.min,an.max)}else{if(ap=="select"){this.params[this.params.length]=new O(ag,ar,aj,au)}else{console.log("WARNING: unrecognized tool parameter type:",ag,ap)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aw){aw.stopPropagation()}).click(function(aw){aw.stopPropagation()}).bind("dblclick",function(aw){aw.stopPropagation()});var aq=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ao=this.params;var am=this;$.each(this.params,function(ax,aA){var az=$("<div>").addClass("param-row").appendTo(am.parent_div);var aw=$("<div>").addClass("param-label").text(aA.label).appendTo(az);var ay=$("<div/>").addClass("slider").html(aA.html).appendTo(az);ay.find(":input").val(aA.value);$("<div style='clear: both;'/>").appendTo(az)});this.parent_div.find("input").click(function(){$(this).select()});var av=$("<div>").addClass("param-row").appendTo(this.parent_div);var ak=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(av);var af=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(av);var am=this;af.click(function(){am.run_on_region()});ak.click(function(){am.run_on_dataset()})};p(r.prototype,{get_param_values_dict:function(){var af={};this.parent_div.find(":input").each(function(){var ag=$(this).attr("name"),ah=$(this).val();af[ag]=JSON.stringify(ah)});return af},get_param_values:function(){var ag=[];var af={};this.parent_div.find(":input").each(function(){var ah=$(this).attr("name"),ai=$(this).val();if(ah){ag[ag.length]=ai}});return ag},run_on_dataset:function(){var af=this;af.run({dataset_id:this.track.original_dataset_id,tool_id:af.name},null,function(ag){show_modal(af.name+" is Running",af.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ag={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},aj=this.track,ah=ag.tool_id+aj.tool_region_and_parameters_str(ag.chrom,ag.low,ag.high),af;if(aj.container===view){var ai=new Q(this.name,this.track.view,this.track.container);aj.container.add_drawable(ai);aj.container.remove_drawable(aj);ai.add_drawable(aj);aj.container_div.appendTo(ai.content_div);af=ai}else{af=aj.container}var ak=new aj.constructor(ah,view,af,"hda");ak.init_for_tool_data();ak.change_mode(aj.mode);af.add_drawable(ak);ak.content_div.text("Starting job.");this.run(ag,ak,function(al){ak.dataset_id=al.dataset_id;ak.content_div.text("Running job.");ak.init()})},run:function(ag,ah,ai){$.extend(ag,this.get_param_values_dict());var af=function(){$.getJSON(rerun_tool_url,ag,function(aj){if(aj==="no converter"){ah.container_div.addClass("error");ah.content_div.text(K)}else{if(aj.error){ah.container_div.addClass("error");ah.content_div.text(x+aj.message)}else{if(aj==="pending"){ah.container_div.addClass("pending");ah.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(af,2000)}else{ai(aj)}}}})};af()}});var O=function(ag,af,ah,ai){this.name=ag;this.label=af;this.html=ah;this.value=ai};var g=function(ah,ag,aj,ak,ai,af){O.call(this,ah,ag,aj,ak);this.min=ai;this.max=af};var h=function(ag,af,ah,ai){this.name=ag;this.index=af;this.tool_id=ah;this.tool_exp_name=ai};var V=function(ag,af,ah,ai){h.call(this,ag,af,ah,ai);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};p(V.prototype,{applies_to:function(af){if(af.length>this.index){return true}return false},keep:function(af){if(!this.applies_to(af)){return true}var ag=af[this.index];return(isNaN(ag)||(ag>=this.low&&ag<=this.high))},update_attrs:function(ag){var af=false;if(!this.applies_to(ag)){return af}if(ag[this.index]<this.min){this.min=Math.floor(ag[this.index]);af=true}if(ag[this.index]>this.max){this.max=Math.ceil(ag[this.index]);af=true}return af},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var ah=function(ak,ai){var aj=ai-ak;return(aj<=2?0.01:1)};var ag=this.slider.slider("option","min"),af=this.slider.slider("option","max");if(this.min<ag||this.max>af){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ah(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var aa=function(aq,ay){this.track=aq;this.filters=[];for(var at=0;at<ay.length;at++){var au=ay[at],az=au.name,af=au.type,ah=au.index,ax=au.tool_id,aw=au.tool_exp_name;if(af==="int"||af==="float"){this.filters[at]=new V(az,ah,ax,aw)}else{console.log("ERROR: unsupported filter: ",az,af)}}var ai=function(aA,aB,aC){aA.click(function(){var aD=aB.text();max=parseFloat(aC.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aC.slider("option","values")){input_size=2*input_size+1;multi_value=true}aB.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aD).appendTo(aB).focus().select().click(function(aE){aE.stopPropagation()}).blur(function(){$(this).remove();aB.text(aD)}).keyup(function(aI){if(aI.keyCode===27){$(this).trigger("blur")}else{if(aI.keyCode===13){var aG=aC.slider("option","min"),aE=aC.slider("option","max"),aH=function(aJ){return(isNaN(aJ)||aJ>aE||aJ<aG)},aF=$(this).val();if(!multi_value){aF=parseFloat(aF);if(aH(aF)){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}else{aF=aF.split("-");aF=[parseFloat(aF[0]),parseFloat(aF[1])];if(aH(aF[0])||aH(aF[1])){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}aC.slider((multi_value?"values":"value"),aF)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aA){aA.stopPropagation()}).click(function(aA){aA.stopPropagation()}).bind("dblclick",function(aA){aA.stopPropagation()}).bind("keydown",function(aA){aA.stopPropagation()});var av=$("<div/>").addClass("sliders").appendTo(this.parent_div);var an=this;$.each(this.filters,function(aD,aF){aF.container=$("<div/>").addClass("filter-row slider-row").appendTo(av);var aE=$("<div/>").addClass("elt-label").appendTo(aF.container);var aC=$("<span/>").addClass("slider-name").text(aF.name+"  ").appendTo(aE);var aB=$("<span/>");var aH=$("<span/>").addClass("slider-value").appendTo(aE).append("[").append(aB).append("]");var aA=$("<div/>").addClass("slider").appendTo(aF.container);aF.control_element=$("<div/>").attr("id",aF.name+"-filter-control").appendTo(aA);var aG=[0,0];aF.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aJ,aK){var aI=aK.values;aB.text(aI[0]+"-"+aI[1]);aF.low=aI[0];aF.high=aI[1];an.track.request_draw(true,true)},change:function(aI,aJ){aF.control_element.slider("option","slide").call(aF.control_element,aI,aJ)}});aF.slider=aF.control_element;aF.slider_label=aB;ai(aH,aB,aF.control_element);$("<div style='clear: both;'/>").appendTo(aF.container)});if(this.filters.length!==0){var ak=$("<div/>").addClass("param-row").appendTo(av);var am=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ak);var ag=this;am.click(function(){ag.run_on_dataset()})}var ap=$("<div/>").addClass("display-controls").appendTo(this.parent_div),ar,al,ao,aj={Transparency:function(aA){an.alpha_filter=aA},Height:function(aA){an.height_filter=aA}};$.each(aj,function(aC,aB){ar=$("<div/>").addClass("filter-row").appendTo(ap),al=$("<span/>").addClass("elt-label").text(aC+":").appendTo(ar),ao=$("<select/>").attr("name",aC+"_dropdown").css("float","right").appendTo(ar);$("<option/>").attr("value",-1).text("== None ==").appendTo(ao);for(var aA=0;aA<an.filters.length;aA++){$("<option/>").attr("value",aA).text(an.filters[aA].name).appendTo(ao)}ao.change(function(){$(this).children("option:selected").each(function(){var aD=parseInt($(this).val());aj[aC]((aD>=0?an.filters[aD]:null));an.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(ar)});$("<div style='clear: both;'/>").appendTo(this.parent_div)};p(aa.prototype,{reset_filters:function(){for(var af=0;af<this.filters.length;af++){filter=this.filters[af];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var an=function(ar,ap,aq){if(!(ap in ar)){ar[ap]=aq}return ar[ap]};var ah={},af,ag,ai;for(var aj=0;aj<this.filters.length;aj++){af=this.filters[aj];if(af.tool_id){if(af.min!=af.low){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" >= "+af.low}if(af.max!=af.high){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" <= "+af.high}}}var al=[];for(var ao in ah){al[al.length]=[ao,ah[ao]]}var am=al.length;(function ak(aw,at){var aq=at[0],ar=aq[0],av=aq[1],au="("+av.join(") and (")+")",ap={cond:au,input:aw,target_dataset_id:aw,tool_id:ar},at=at.slice(1);$.getJSON(run_tool_url,ap,function(ax){if(ax.error){show_modal("Filter Dataset","Error running tool "+ar,{Close:hide_modal})}else{if(at.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ak(ax.dataset_id,at)}}})})(this.track.dataset_id,al)}});var D=function(af,ag){M.Scaler.call(this,ag);this.filter=af};D.prototype.gen_val=function(af){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(af[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var G=function(af){this.track=af.track;this.params=af.params;this.values={};this.restore_values((af.saved_values?af.saved_values:{}));this.onchange=af.onchange};p(G.prototype,{restore_values:function(af){var ag=this;$.each(this.params,function(ah,ai){if(af[ai.key]!==undefined){ag.values[ai.key]=af[ai.key]}else{ag.values[ai.key]=ai.default_value}})},build_form:function(){var ag=this;var af=$("<div />");$.each(this.params,function(ak,ai){if(!ai.hidden){var ah="param_"+ak;var am=ag.values[ai.key];var ap=$("<div class='form-row' />").appendTo(af);ap.append($("<label />").attr("for",ah).text(ai.label+":"));if(ai.type==="bool"){ap.append($('<input type="checkbox" />').attr("id",ah).attr("name",ah).attr("checked",am))}else{if(ai.type==="text"){ap.append($('<input type="text"/>').attr("id",ah).val(am).click(function(){$(this).select()}))}else{if(ai.type==="color"){var al=$("<input />").attr("id",ah).attr("name",ah).val(am);var an=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var aj=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(an);var ao=$("<div/>").appendTo(aj).farbtastic({width:100,height:100,callback:al,color:am});$("<div />").append(al).append(an).appendTo(ap).bind("click",function(aq){an.css({left:$(this).position().left+($(al).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){an.hide();$(document).unbind("click.color-picker")});aq.stopPropagation()})}else{ap.append($("<input />").attr("id",ah).attr("name",ah).val(am))}}}}});return af},update_from_form:function(af){var ah=this;var ag=false;$.each(this.params,function(ai,ak){if(!ak.hidden){var al="param_"+ai;var aj=af.find("#"+al).val();if(ak.type==="float"){aj=parseFloat(aj)}else{if(ak.type==="int"){aj=parseInt(aj)}else{if(ak.type==="bool"){aj=af.find("#"+al).is(":checked")}}}if(aj!==ah.values[ak.key]){ah.values[ak.key]=aj;ag=true}}});if(ag){this.onchange()}}});var b=function(af,ai,ah,ag,aj){this.track=af;this.index=ai;this.low=ai*R*ah;this.high=(ai+1)*R*ah;this.resolution=ah;this.canvas=$("<div class='track-tile'/>").append(ag);this.data=aj;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(af,ai,ah,ag,aj,ak){b.call(this,af,ai,ah,ag,aj);this.max_val=ak};p(k.prototype,b.prototype);var P=function(af,aj,ai,ah,al,am,ak,ag){b.call(this,af,aj,ai,ah,al);this.mode=am;this.message=ak;this.feature_mapper=ag};p(P.prototype,b.prototype);P.prototype.predisplay_actions=function(){var ag=this,af={};if(ag.mode!=="Pack"){return}$(this.canvas).mousemove(function(ar){var am=$(this).offset(),aq=ar.pageX-am.left,ap=ar.pageY-am.top,aw=ag.feature_mapper.get_feature_data(aq,ap),an=(aw?aw[0]:null);$(this).siblings(".feature-popup").each(function(){if(!an||$(this).attr("id")!==an.toString()){$(this).remove()}});if(aw){var ai=af[an];if(!ai){var an=aw[0],at={name:aw[3],start:aw[1],end:aw[2],strand:aw[4]},al=ag.track.filters_manager.filters,ak;for(var ao=0;ao<al.length;ao++){ak=al[ao];at[ak.name]=aw[ak.index]}var ai=$("<div/>").attr("id",an).addClass("feature-popup"),av,au,ax=$("<table/>").appendTo(ai),ay;for(av in at){au=at[av];ay=$("<tr/>").appendTo(ax);$("<th/>").appendTo(ay).text(av);$("<td/>").attr("align","left").appendTo(ay).text(typeof(au)=="number"?Z(au,2):au)}af[an]=ai}ai.appendTo($(ag.canvas).parent());var aj=aq+parseInt(ag.canvas.css("left"))+7,ah=ap+parseInt(ag.canvas.css("top"))+7;ai.css("left",aj+"px").css("top",ah+"px")}else{if(!ar.isPropagationStopped()){ar.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ar)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var i=function(ai,aq,aj,am,ar,ah,ag){q.call(this,ai,aq,aj,{},"draghandle");this.data_url=(ah?ah:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ag?ag:L);this.dataset_check_url=converted_datasets_state_url;if(!i.id_counter){i.id_counter=0}this.id=i.id_counter++;this.container_div=$("<div />").addClass("track").attr("id","track_"+this.id).css("position","relative");if(am){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div/>").addClass("track-name").appendTo(this.header_div).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());this.icons_div=$("<div/>").css("float","left").appendTo(this.header_div).hide();this.settings_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Edit settings").addClass("icon-button settings-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.overview_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Set as overview").addClass("icon-button overview-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.filters_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Filters").addClass("icon-button filters-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.tools_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Tools").addClass("icon-button tools-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.remove_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Remove").addClass("icon-button remove-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);var ak=this;this.header_div.dblclick(function(at){at.stopPropagation()});this.settings_icon.click(function(){var av=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},at=function(){ak.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},au=function(aw){if((aw.keyCode||aw.which)===27){av()}else{if((aw.keyCode||aw.which)===13){at()}}};$(window).bind("keypress.check_enter_esc",au);show_modal("Configure Track",ak.config.build_form(),{Cancel:av,OK:at})});this.overview_icon.click(function(){ak.view.set_overview(ak)});this.filters_icon.click(function(){ak.filters_div.toggle();ak.filters_manager.reset_filters()});this.tools_icon.click(function(){ak.dynamic_tool_div.toggle();if(ak.dynamic_tool_div.is(":visible")){ak.set_name(ak.name+ak.tool_region_and_parameters_str())}else{ak.revert_name()}$(".tipsy").remove()});this.remove_icon.click(function(){$(".tipsy").remove();ak.remove()});if(ak.display_modes!==undefined){if(ak.mode_div===undefined){ak.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ak.header_div);var al=(ak.config&&ak.config.values.mode?ak.config.values.mode:ak.display_modes[0]);ak.mode=al;ak.mode_div.text(al);var af={};for(var an=0,ap=ak.display_modes.length;an<ap;an++){var ao=ak.display_modes[an];af[ao]=function(at){return function(){ak.change_mode(at)}}(ao)}make_popupmenu(ak.mode_div,af)}else{ak.mode_div.hide()}this.header_div.append($("<div/>").css("clear","both"));this.container_div.hover(function(){ak.icons_div.show()},function(){ak.icons_div.hide()})}}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};p(i.prototype,q.prototype,{get_type:function(){if(this instanceof ab){return"LabelTrack"}else{if(this instanceof A){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof W){return"ReadTrack"}else{if(this instanceof U){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}return""},init:function(){var af=this;af.enabled=false;af.tile_cache.clear();af.data_manager.clear();af.initial_canvas=undefined;af.content_div.css("height","auto");af.container_div.removeClass("nodata error pending");if(!af.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:af.hda_ldda,dataset_id:af.dataset_id,chrom:af.view.chrom},function(ag){if(!ag||ag==="error"||ag.kind==="error"){af.container_div.addClass("error");af.content_div.text(o);if(ag.message){var ah=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})});af.content_div.append(ah)}}else{if(ag==="no converter"){af.container_div.addClass("error");af.content_div.text(K)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){af.container_div.addClass("nodata");af.content_div.text(F)}else{if(ag==="pending"){af.container_div.addClass("pending");af.content_div.text(t);setTimeout(function(){af.init()},af.data_query_wait)}else{if(ag.status==="data"){if(ag.valid_chroms){af.valid_chroms=ag.valid_chroms;af.update_track_icons()}af.content_div.text(Y);if(af.view.chrom){af.content_div.text("");af.content_div.css("height",af.height_px+"px");af.enabled=true;$.when(af.predraw_init()).done(function(){af.container_div.removeClass("nodata error pending");af.request_draw()})}}}}}}});this.update_track_icons()},predraw_init:function(){}});var N=function(aj,ah,ag,am,ai,al,ak){i.call(this,aj,ah,ag,am,ai);var af=this,ah=af.view;m(af.container_div,af.drag_handle_class,".group",af);this.filters_manager=new aa(this,(al!==undefined?al:{}));this.filters_available=false;this.filters_visible=false;this.tool=(ak!==undefined&&obj_length(ak)>0?new r(this,ak):undefined);if(this.header_div){if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}};p(N.prototype,q.prototype,i.prototype,{copy:function(af){return new this.constructor(this.name,this.view,af,this.hda_ldda,this.dataset_id,this.prefs,this.filters,this.tool)},to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ag){var af=this;af.mode_div.text(ag);af.mode=ag;af.config.values.mode=ag;af.tile_cache.clear();af.request_draw();return af},update_track_icons:function(){var af=this;if(af.filters_available>0){af.filters_icon.show()}else{af.filters_icon.hide()}if(af.tool){af.tools_icon.show()}else{af.tools_icon.hide()}},_gen_tile_cache_key:function(ag,ah,af){return ag+"_"+ah+"_"+af},request_draw:function(ag,af){this.view.request_redraw(false,ag,af,this)},_draw:function(ah,ap){if(!this.enabled){return}if(!(this instanceof A)&&(!this.dataset_id)){return}var ao=this.view.low,al=this.view.high,am=al-ao,ai=this.view.container.width(),at=ai/am,ak=this.view.resolution,ar=$("<div style='position: relative;'></div>");if(this.is_overview){ao=this.view.max_low;al=this.view.max_high;ak=Math.pow(C,Math.ceil(Math.log((view.max_high-view.max_low)/R)/Math.log(C)));at=ai/(view.max_high-view.max_low)}if(!ap){this.content_div.children().remove()}this.content_div.append(ar);this.max_height=0;var ag=Math.floor(ao/ak/R);var an=true;var aq=[];var af=0;while((ag*R*ak)<al){tile=this.draw_helper(ah,ai,ag,ak,ar,at);if(tile){aq.push(tile)}else{an=false}ag+=1;af++}var aj=this;if(an){aj.postdraw_actions(aq,ai,at,ap)}},postdraw_actions:function(aj,ak,al,af){var ah=this;var ai=false;for(var ag=0;ag<aj.length;ag++){if(aj[ag].message){ai=true;break}}if(ai){for(var ag=0;ag<aj.length;ag++){tile=aj[ag];if(!tile.message){tile.canvas.css("padding-top",E)}}}},draw_helper:function(ag,ah,ai,al,ar,aw,at,am){var aj=this,aq=this._gen_tile_cache_key(ah,aw,ai),an=ai*R*al,av=an+R*al;var ao=(ag?undefined:aj.tile_cache.get(aq));if(ao){aj.show_tile(ao,ar,aw);return ao}var ap=function(ax){return("isResolved" in ax)};var ak=true;var af=aj.data_manager.get_data(an,av,aj.mode,al,aj.data_url_extra_params);if(ap(af)){ak=false}var au;if(view.reference_track&&aw>view.canvas_manager.char_width_px){au=view.reference_track.data_manager.get_data(an,av,aj.mode,al,view.reference_track.data_url_extra_params);if(ap(au)){ak=false}}if(ak){p(af,am);var ao=aj.draw_tile(af,aj.mode,al,ai,aw,au);if(ao!==undefined){aj.tile_cache.set(aq,ao);aj.show_tile(ao,ar,aw)}return ao}$.when(af,au).then(function(){view.request_redraw(false,false,false,aj)});return null},show_tile:function(al,an,ao){var ah=this,ag=al.canvas,ak=ag;if(al.message){var ap=$("<div/>"),am=$("<div/>").addClass("tile-message").text(al.message).css({height:E-1,width:al.canvas.width}).appendTo(ap),aj=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(am),af=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(am);ap.append(ag);ak=ap;aj.click(function(){al.stale=true;ah.data_manager.get_more_data(al.low,al.high,ah.mode,al.resolution,{},ah.data_manager.DEEP_DATA_REQ);ah.request_draw()}).dblclick(function(aq){aq.stopPropagation()});af.click(function(){al.stale=true;ah.data_manager.get_more_data(al.low,al.high,ah.mode,al.resolution,{},ah.data_manager.BROAD_DATA_REQ);ah.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}al.predisplay_actions();var ai=(al.low-(this.is_overview?this.view.max_low:this.view.low))*ao;if(this.left_offset){ai-=this.left_offset}ak.css({position:"absolute",top:0,left:ai,height:""});an.append(ak);ah.max_height=Math.max(ah.max_height,ak.height());ah.content_div.css("height",ah.max_height+"px");an.children().css("height",ah.max_height+"px")},_get_tile_bounds:function(af,ag){var ai=af*R*ag,aj=R*ag,ah=(ai+aj<=this.view.max_high?ai+aj:this.view.max_high);return[ai,ah]},tool_region_and_parameters_str:function(ah,af,ai){var ag=this,aj=(ah!==undefined&&af!==undefined&&ai!==undefined?ah+":"+af+"-"+ai:"all");return" - region=["+aj+"], parameters=["+ag.tool.get_param_values().join(", ")+"]"},init_for_tool_data:function(){this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.predraw_init=function(){var ag=this;var af=function(){if(ag.data_manager.size()===0){setTimeout(af,300)}else{ag.data_url=default_data_url;ag.data_query_wait=L;ag.dataset_state_url=converted_datasets_state_url;$.getJSON(ag.dataset_state_url,{dataset_id:ag.dataset_id,hda_ldda:ag.hda_ldda},function(ah){})}};af()}}});var ab=function(ag,af){i.call(this,"label",ag,af,false,{});this.container_div.addClass("label-track")};p(ab.prototype,i.prototype,{init:function(){this.enabled=true},_draw:function(){var ah=this.view,ai=ah.high-ah.low,al=Math.floor(Math.pow(10,Math.floor(Math.log(ai)/Math.log(10)))),af=Math.floor(ah.low/al)*al,aj=this.view.container.width(),ag=$("<div style='position: relative; height: 1.3em;'></div>");while(af<ah.high){var ak=(af-ah.low)/ai*aj;ag.append($("<div class='label'>"+commatize(af)+"</div>").css({position:"absolute",left:ak-1}));af+=al}this.content_div.children(":first").remove();this.content_div.append(ag)}});var A=function(af){N.call(this,"reference",af,{content_div:af.top_labeltrack},false,{});af.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:af.dbkey};this.data_manager=new I(B,this,false);this.tile_cache=new c(u)};p(A.prototype,q.prototype,N.prototype,{init:function(){this.enabled=true},draw_tile:function(ap,al,ak,ag,aq){var aj=this,ah=R*ak;if(aq>this.view.canvas_manager.char_width_px){if(ap.data===null){aj.content_div.css("height","0px");return}var ai=this.view.canvas_manager.new_canvas();var ao=ai.getContext("2d");ai.width=Math.ceil(ah*aq+aj.left_offset);ai.height=aj.height_px;ao.font=ao.canvas.manager.default_font;ao.textAlign="center";ap=ap.data;for(var am=0,an=ap.length;am<an;am++){var af=Math.round(am*aq);ao.fillText(ap[am],af+aj.left_offset,10)}return new b(aj,ag,ak,ai,ap)}this.content_div.css("height","0px")}});var j=function(ak,ai,ah,al,af,aj){var ag=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";N.call(this,ak,ai,ah,true,aj);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=al;this.dataset_id=af;this.original_dataset_id=af;this.data_manager=new S(B,this);this.tile_cache=new c(u);this.left_offset=0;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:aj,onchange:function(){ag.set_name(ag.prefs.name);ag.vertical_range=ag.prefs.max_value-ag.prefs.min_value;$("#linetrack_"+ag.dataset_id+"_minval").text(ag.prefs.min_value);$("#linetrack_"+ag.dataset_id+"_maxval").text(ag.prefs.max_value);ag.tile_cache.clear();ag.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};p(j.prototype,q.prototype,N.prototype,{add_resize_handle:function(){var af=this;var ai=false;var ah=false;var ag=$("<div class='track-resize'>");$(af.container_div).hover(function(){ai=true;ag.show()},function(){ai=false;if(!ah){ag.hide()}});ag.hide().bind("dragstart",function(aj,ak){ah=true;ak.original_height=$(af.content_div).height()}).bind("drag",function(ak,al){var aj=Math.min(Math.max(al.original_height+al.deltaY,af.min_height_px),af.max_height_px);$(af.content_div).css("height",aj);af.height_px=aj;af.request_draw(true)}).bind("dragend",function(aj,ak){af.tile_cache.clear();ah=false;if(!ai){ag.hide()}af.config.values.height=af.height_px}).appendTo(af.container_div)},predraw_init:function(){var af=this;af.vertical_range=undefined;return $.getJSON(af.data_url,{stats:true,chrom:af.view.chrom,low:null,high:null,hda_ldda:af.hda_ldda,dataset_id:af.dataset_id},function(ag){af.container_div.addClass("line-track");var ai=ag.data;if(isNaN(parseFloat(af.prefs.min_value))||isNaN(parseFloat(af.prefs.max_value))){af.prefs.min_value=ai.min;af.prefs.max_value=ai.max;$("#track_"+af.dataset_id+"_minval").val(af.prefs.min_value);$("#track_"+af.dataset_id+"_maxval").val(af.prefs.max_value)}af.vertical_range=af.prefs.max_value-af.prefs.min_value;af.total_frequency=ai.total_frequency;af.container_div.find(".yaxislabel").remove();var aj=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_minval").text(Z(af.prefs.min_value,3));var ah=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_maxval").text(Z(af.prefs.max_value,3));ah.css({position:"absolute",top:"24px",left:"10px"});ah.prependTo(af.container_div);aj.css({position:"absolute",bottom:"2px",left:"10px"});aj.prependTo(af.container_div)})},draw_tile:function(ar,ak,aj,ah,aq){if(this.vertical_range===undefined){return}var af=this._get_tile_bounds(ah,aj),al=af[0],ap=af[1],ag=Math.ceil((ap-al)*aq),an=this.height_px;var ai=this.view.canvas_manager.new_canvas();ai.width=ag,ai.height=an;var ao=ai.getContext("2d");var am=new M.LinePainter(ar.data,al,ap,this.prefs,ak);am.draw(ao,ag,an);return new b(this.track,ah,aj,ai,ar.data)}});var e=function(af,al,ag,ak,an,am,ai,aj){var ah=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];N.call(this,af,al,ag,true,am,ai,aj);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:am,onchange:function(){ah.set_name(ah.prefs.name);ah.tile_cache.clear();ah.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=ak;this.dataset_id=an;this.original_dataset_id=an;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new S(20,this);this.left_offset=200;this.painter=M.LinkedFeaturePainter};p(e.prototype,q.prototype,N.prototype,{postdraw_actions:function(av,af,aw,au){N.prototype.postdraw_actions.call(this,av,au);var ai=this;if(au){var ak=ai.content_div.children();var al=false;for(var aj=ak.length-1,ap=0;aj>=ap;aj--){var ah=$(ak[aj]);if(al){ah.remove()}else{if(ah.children().length!==0){al=true}}}}if(ai.mode=="Histogram"){var ao=-1;for(var aj=0;aj<av.length;aj++){var at=av[aj].max_val;if(at>ao){ao=at}}for(var aj=0;aj<av.length;aj++){var ar=av[aj];if(ar.max_val!==ao){ar.canvas.remove();ai.draw_helper(true,af,ar.index,ar.resolution,ar.canvas.parent(),aw,[],{max:ao})}}}if(ai.filters_manager){var ag=ai.filters_manager.filters;for(var an=0;an<ag.length;an++){ag[an].update_ui_elt()}var am=false,aq;for(var aj=0;aj<av.length;aj++){if(av[aj].data.length){aq=av[aj].data[0];for(var an=0;an<ag.length;an++){if(ag[an].applies_to(aq)){am=true;break}}}}if(ai.filters_available!==am){ai.filters_available=am;if(!ai.filters_available){ai.filters_div.hide()}ai.update_track_icons()}}},update_auto_mode:function(af){if(this.mode=="Auto"){if(af=="no_detail"){af="feature spans"}else{if(af=="summary_tree"){af="coverage histogram"}}this.mode_div.text("Auto ("+af+")")}},incremental_slots:function(aj,ag,ai){var ah=this.view.canvas_manager.dummy_context,af=this.inc_slots[aj];if(!af||(af.mode!==ai)){af=new (s.FeatureSlotter)(aj,ai==="Pack",z,function(ak){return ah.measureText(ak)});af.mode=ai;this.inc_slots[aj]=af}return af.slot_features(ag)},get_summary_tree_data:function(aj,am,ah,av){if(av>ah-am){av=ah-am}var aq=Math.floor((ah-am)/av),au=[],ai=0;var ak=0,al=0,ap,at=0,an=[],ar,ao;var ag=function(ay,ax,az,aw){ay[0]=ax+az*aw;ay[1]=ax+(az+1)*aw};while(at<av&&ak!==aj.length){var af=false;for(;at<av&&!af;at++){ag(an,am,at,aq);for(al=ak;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){af=true;break}}if(af){break}}data_start_index=al;au[au.length]=ar=[an[0],0];for(;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){ar[1]++}else{break}}if(ar[1]>ai){ai=ar[1]}at++}return{max:ai,delta:aq,data:au}},draw_tile:function(au,ax,aB,aF,ap,ai){var ay=this,ak=ay._get_tile_bounds(aF,aB),aI=ak[0],ag=ak[1],aw=ag-aI,az=Math.ceil(aw*ap),aO=25,aj=this.left_offset,av,al;if(ax==="Auto"){if(au.dataset_type==="summary_tree"){ax=au.dataset_type}else{if(au.extra_info==="no_detail"||ay.is_overview){ax="no_detail"}else{var aN=au.data;if(this.view.high-this.view.low>J){ax="Squish"}else{ax="Pack"}}}this.update_auto_mode(ax)}if(ax==="summary_tree"||ax==="Histogram"){al=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var af=$("<div />").addClass("yaxislabel");af.text(au.max);af.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});af.prependTo(this.container_div);var ah=this.view.canvas_manager.new_canvas();ah.width=az+aj;ah.height=al+T;if(au.dataset_type!="summary_tree"){var aq=this.get_summary_tree_data(au.data,aI,ag,200);if(au.max){aq.max=au.max}au=aq}var aK=new M.SummaryTreePainter(au,aI,ag,this.prefs);var aA=ah.getContext("2d");aA.translate(aj,T);aK.draw(aA,az,al);return new k(ay,aF,aB,ah,au.data,au.max)}var av,an=1;if(ax==="no_detail"||ax==="Squish"||ax==="Pack"){an=this.incremental_slots(ap,au.data,ax);av=this.inc_slots[ap].slots}var ao=[];if(au.data){var ar=this.filters_manager.filters;for(var aC=0,aE=au.data.length;aC<aE;aC++){var am=au.data[aC];var aD=false;var at;for(var aH=0,aM=ar.length;aH<aM;aH++){at=ar[aH];at.update_attrs(am);if(!at.keep(am)){aD=true;break}}if(!aD){ao.push(am)}}}var aL=(this.filters_manager.alpha_filter?new D(this.filters_manager.alpha_filter):null);var aJ=(this.filters_manager.height_filter?new D(this.filters_manager.height_filter):null);var aK=new (this.painter)(ao,aI,ag,this.prefs,ax,aL,aJ,ai);var al=Math.max(ad,aK.get_required_height(an));var ah=this.view.canvas_manager.new_canvas();var aG=null;ah.width=az+aj;ah.height=al;var aA=ah.getContext("2d");aA.fillStyle=this.prefs.block_color;aA.font=aA.canvas.manager.default_font;aA.textAlign="right";this.container_div.find(".yaxislabel").remove();if(au.data){aA.translate(aj,0);aG=aK.draw(aA,az,al,av);aG.translation=-aj}return new P(ay,aF,aB,ah,au.data,ax,au.message,aG)}});var U=function(ak,ah,ag,am,af,aj,al,ai){e.call(this,ak,ah,ag,am,af,aj,al,ai);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:aj,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter};p(U.prototype,q.prototype,N.prototype,e.prototype);var W=function(aj,ah,ag,al,af,ai,ak){e.call(this,aj,ah,ag,al,af,ai,ak);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:aj},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ai,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter;this.update_track_icons()};p(W.prototype,q.prototype,N.prototype,e.prototype);X.View=ac;X.DrawableGroup=Q;X.LineTrack=j;X.FeatureTrack=e;X.ReadTrack=W;X.VcfTrack=U};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(F,G){for(var E=0;E<=z;E++){var C=false,H=h[E];if(H!==undefined){for(var B=0,D=H.length;B<D;B++){var i=H[B];if(G>i[0]&&F<i[1]){C=true;break}}}if(!C){return E}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(i,w){var t=i("class").extend;var o=function(H,z,F,y,E,C){if(C===undefined){C=4}var B=y-z;var A=E-F;var D=Math.floor(Math.sqrt(B*B+A*A)/C);var I=B/D;var G=A/D;var x;for(x=0;x<D;x++,z+=I,F+=G){if(x%2!==0){continue}H.fillRect(z,F,C,1)}};var p=function(A,z,x,D){var C=z-D/2,B=z+D/2,E=x-Math.sqrt(D*3/2);A.beginPath();A.moveTo(C,E);A.lineTo(B,E);A.lineTo(z,x);A.lineTo(C,E);A.strokeStyle=this.fillStyle;A.fill();A.stroke();A.closePath()};var d=function(x){this.default_val=(x?x:1)};d.prototype.gen_val=function(x){return this.default_val};var l=function(z,B,x,y,A){this.data=z;this.view_start=B;this.view_end=x;this.prefs=t({},this.default_prefs,y);this.mode=A};l.prototype.default_prefs={};var u=function(z,B,x,y,A){l.call(this,z,B,x,y,A)};u.prototype.default_prefs={show_counts:false};u.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var b=function(x,B,D,E,z){l.call(this,x,B,D,E,z);if(this.prefs.min_value===undefined){var F=Infinity;for(var y=0,A=this.data.length;y<A;y++){F=Math.min(F,this.data[y][1])}this.prefs.min_value=F}if(this.prefs.max_value===undefined){var C=-Infinity;for(var y=0,A=this.data.length;y<A;y++){C=Math.max(C,this.data[y][1])}this.prefs.max_value=C}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(M,L,J){var E=false,G=this.prefs.min_value,C=this.prefs.max_value,I=C-G,x=J,z=this.view_start,K=this.view_end-this.view_start,A=L/K,H=this.mode,S=this.data;M.save();var T=Math.round(J+G/I*J);if(H!=="Intensity"){M.fillStyle="#aaa";M.fillRect(0,T,L,1)}M.beginPath();var Q,D,B;if(S.length>1){B=Math.ceil((S[1][0]-S[0][0])*A)}else{B=10}for(var N=0,O=S.length;N<O;N++){M.fillStyle=this.prefs.color;Q=Math.round((S[N][0]-z)*A);D=S[N][1];var P=false,F=false;if(D===null){if(E&&H==="Filled"){M.lineTo(Q,x)}E=false;continue}if(D<G){F=true;D=G}else{if(D>C){P=true;D=C}}if(H==="Histogram"){D=Math.round(D/I*x);M.fillRect(Q,T,B,-D)}else{if(H==="Intensity"){D=255-Math.floor((D-G)/I*255);M.fillStyle="rgb("+D+","+D+","+D+")";M.fillRect(Q,0,B,x)}else{D=Math.round(x-(D-G)/I*x);if(E){M.lineTo(Q,D)}else{E=true;if(H==="Filled"){M.moveTo(Q,x);M.lineTo(Q,D)}else{M.moveTo(Q,D)}}}}M.fillStyle=this.prefs.overflow_color;if(P||F){var R;if(H==="Histogram"||H==="Intensity"){R=B}else{Q-=2;R=4}if(P){M.fillRect(Q,0,R,3)}if(F){M.fillRect(Q,x-3,R,3)}}M.fillStyle=this.prefs.color}if(H==="Filled"){if(E){M.lineTo(Q,T);M.lineTo(0,T)}M.fill()}else{M.stroke()}M.restore()};var m=function(x){this.feature_positions={};this.slot_height=x;this.translation=0};m.prototype.map_feature_data=function(y,A,x,z){if(!this.feature_positions[A]){this.feature_positions[A]=[]}this.feature_positions[A].push({data:y,x_start:x,x_end:z})};m.prototype.get_feature_data=function(z,D){var C=Math.floor(D/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var n=function(z,C,x,y,B,D,A){l.call(this,z,C,x,y,B);this.alpha_scaler=(D?D:new d());this.height_scaler=(A?A:new d())};n.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};t(n.prototype,{get_required_height:function(y){var x=y_scale=this.get_row_height(),z=this.mode;if(z==="no_detail"||z==="Squish"||z==="Pack"){x=y*y_scale}return x+Math.max(Math.round(y_scale/2),5)},draw:function(J,H,F,E){var P=this.data,C=this.view_start,L=this.view_end;J.save();J.fillStyle=this.prefs.block_color;J.textAlign="right";var G=this.view_end-this.view_start,D=H/G,K=this.get_row_height(),O=new m(K),A;for(var M=0,N=P.length;M<N;M++){var z=P[M],B=z[0],I=z[1],x=z[2],y=(E&&E[B]!==undefined?E[B]:null);if((I<L&&x>C)&&(this.mode=="Dense"||y!==null)){A=this.draw_element(J,this.mode,z,y,C,L,D,K,H);O.map_feature_data(z,y,A[0],A[1])}}J.restore();return O},draw_element:function(D,z,F,B,A,C,E,y,x){console.log("WARNING: Unimplemented function.");return[0,0]}});var c=10,h=3,k=5,v=10,f=1,r=3,e=3,a=9,j=2,g="#ccc";var q=function(z,C,x,y,B,D,A){n.call(this,z,C,x,y,B,D,A)};t(q.prototype,n.prototype,{get_row_height:function(){var y=this.mode,x;if(y==="Dense"){x=c}else{if(y==="no_detail"){x=h}else{if(y==="Squish"){x=k}else{x=v}}}return x},draw_element:function(L,C,U,G,N,af,aj,al,x){var R=U[0],ah=U[1],Z=U[2],P=U[3],aa=Math.floor(Math.max(0,(ah-N)*aj)),M=Math.ceil(Math.min(x,Math.max(0,(Z-N)*aj))),Y=aa,ak=M,X=(C==="Dense"?0:(0+G))*al,K,ad,Q=null,an=null,A=this.prefs.block_color,ac=this.prefs.label_color;L.globalAlpha=this.alpha_scaler.gen_val(U);if(C==="Dense"){G=1}if(C==="no_detail"){L.fillStyle=A;L.fillRect(aa,X+5,M-aa,f)}else{var J=U[4],W=U[5],ab=U[6],B=U[7];if(W&&ab){Q=Math.floor(Math.max(0,(W-N)*aj));an=Math.ceil(Math.min(x,Math.max(0,(ab-N)*aj)))}var ai,S;if(C==="Squish"||C==="Dense"){ai=1;S=e}else{ai=5;S=a}if(!B){if(U.strand){if(U.strand==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand_inv")}else{if(U.strand==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand_inv")}}}else{L.fillStyle=A}L.fillRect(aa,X,M-aa,S)}else{var I,T;if(C==="Squish"||C==="Dense"){L.fillStyle=g;I=X+Math.floor(e/2)+1;T=1}else{if(J){var I=X;var T=S;if(J==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand")}else{if(J==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand")}}}else{L.fillStyle=g;I+=(e/2)+1;T=1}}L.fillRect(aa,I,M-aa,T);var D;for(var ag=0,z=B.length;ag<z;ag++){var E=B[ag],y=Math.floor(Math.max(0,(E[0]-N)*aj)),V=Math.ceil(Math.min(x,Math.max((E[1]-N)*aj)));if(y>V){continue}L.fillStyle=A;L.fillRect(y,X+(S-ai)/2+1,V-y,ai);if(Q!==undefined&&ab>W&&!(y>an||V<Q)){var ae=Math.max(y,Q),H=Math.min(V,an);L.fillRect(ae,X+1,H-ae,S);if(B.length==1&&C=="Pack"){if(J==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand_inv")}else{if(J==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand_inv")}}if(ae+14<H){ae+=2;H-=2}L.fillRect(ae,X+1,H-ae,S)}}}if(C==="Pack"){L.globalAlpha=1;L.fillStyle="white";var F=this.height_scaler.gen_val(U),O=Math.ceil(S*F),am=Math.round((S-O)/2);if(F!==1){L.fillRect(aa,I+1,M-aa,am);L.fillRect(aa,I+S-am+1,M-aa,am)}}}L.globalAlpha=1;if(C==="Pack"&&ah>N){L.fillStyle=ac;if(N===0&&aa-L.measureText(P).width<0){L.textAlign="left";L.fillText(P,M+j,X+8);ak+=L.measureText(P).width+j}else{L.textAlign="right";L.fillText(P,aa-j,X+8);Y-=L.measureText(P).width+j}}}L.globalAlpha=1;return[Y,ak]}});var s=function(A,D,x,z,C,E,B,y){n.call(this,A,D,x,z,C,E,B);this.ref_seq=(y?y.data:null)};s.prototype.default_prefs=t({},n.prototype.default_prefs,{show_insertions:false});t(s.prototype,n.prototype,{get_row_height:function(){var x,y=this.mode;if(y==="Dense"){x=c}else{if(y==="Squish"){x=k}else{x=v;if(this.prefs.show_insertions){x*=2}}}return x},draw_read:function(U,P,L,Z,A,T,I,F,E){U.textAlign="center";var S=this,z=[Z,A],O=0,V=0,R=0,x=U.canvas.manager.char_width_px;var ae=[];if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>x){R=Math.round(L/2)}if(!I){I=[[0,F.length]]}for(var M=0,X=I.length;M<X;M++){var J=I[M],B="MIDNSHP=X"[J[0]],N=J[1];if(B==="H"||B==="S"){O-=N}var G=T+O,ad=Math.floor(Math.max(0,(G-Z)*L)),H=Math.floor(Math.max(0,(G+N-Z)*L));if(ad===H){H+=1}switch(B){case"H":break;case"S":case"M":case"=":if(is_overlap([G,G+N],z)){var Q=F.slice(V,V+N);if(R>0){U.fillStyle=this.prefs.block_color;U.fillRect(ad-R,E+1,H-ad,9);U.fillStyle=g;for(var ab=0,y=Q.length;ab<y;ab++){if(this.prefs.show_differences&&this.ref_seq){var K=this.ref_seq[G-Z+ab];if(!K||K.toLowerCase()===Q[ab].toLowerCase()){continue}}if(G+ab>=Z&&G+ab<=A){var ac=Math.floor(Math.max(0,(G+ab-Z)*L));U.fillText(Q[ab],ac,E+9)}}}else{U.fillStyle=this.prefs.block_color;U.fillRect(ad,E+4,H-ad,e)}}V+=N;O+=N;break;case"N":U.fillStyle=g;U.fillRect(ad-R,E+5,H-ad,1);O+=N;break;case"D":U.fillStyle="red";U.fillRect(ad-R,E+4,H-ad,3);O+=N;break;case"P":break;case"I":var Y=ad-R;if(is_overlap([G,G+N],z)){var Q=F.slice(V,V+N);if(this.prefs.show_insertions){var D=ad-(H-ad)/2;if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>x){U.fillStyle="yellow";U.fillRect(D-R,E-9,H-ad,9);ae[ae.length]={type:"triangle",data:[Y,E+4,5]};U.fillStyle=g;switch(compute_overlap([G,G+N],z)){case (OVERLAP_START):Q=Q.slice(Z-G);break;case (OVERLAP_END):Q=Q.slice(0,G-A);break;case (CONTAINED_BY):break;case (CONTAINS):Q=Q.slice(Z-G,G-A);break}for(var ab=0,y=Q.length;ab<y;ab++){var ac=Math.floor(Math.max(0,(G+ab-Z)*L));U.fillText(Q[ab],ac-(H-ad)/2,E)}}else{U.fillStyle="yellow";U.fillRect(D,E+(this.mode!=="Dense"?2:5),H-ad,(P!=="Dense"?e:r))}}else{if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>x){ae.push({type:"text",data:[Q.length,Y,E+9]})}else{}}}V+=N;break;case"X":V+=N;break}}U.fillStyle="yellow";var aa,C,af;for(var W=0;W<ae.length;W++){aa=ae[W];C=aa.type;af=aa.data;if(C==="text"){U.save();U.font="bold "+U.font;U.fillText(af[0],af[1],af[2]);U.restore()}else{if(C=="triangle"){p(U,af[0],af[1],af[2])}}}},draw_element:function(Q,L,D,A,T,y,H,R,O){var G=D[0],P=D[1],z=D[2],I=D[3],C=Math.floor(Math.max(0,(P-T)*H)),E=Math.ceil(Math.min(O,Math.max(0,(z-T)*H))),B=(L==="Dense"?0:(0+A))*R,U=this.prefs.block_color,F=this.prefs.label_color,N=0;if((L==="Pack"||this.mode==="Auto")&&H>Q.canvas.manager.char_width_px){var N=Math.round(H/2)}Q.fillStyle=U;if(D[5] instanceof Array){var M=Math.floor(Math.max(0,(D[4][0]-T)*H)),K=Math.ceil(Math.min(O,Math.max(0,(D[4][1]-T)*H))),J=Math.floor(Math.max(0,(D[5][0]-T)*H)),x=Math.ceil(Math.min(O,Math.max(0,(D[5][1]-T)*H)));if(D[4][1]>=T&&D[4][0]<=y&&D[4][2]){this.draw_read(Q,L,H,T,y,D[4][0],D[4][2],D[4][3],B)}if(D[5][1]>=T&&D[5][0]<=y&&D[5][2]){this.draw_read(Q,L,H,T,y,D[5][0],D[5][2],D[5][3],B)}if(J>K){Q.fillStyle=g;o(Q,K-N,B+5,J-N,B+5)}}else{Q.fillStyle=U;this.draw_read(Q,L,H,T,y,P,D[4],D[5],B)}if(L==="Pack"&&P>T&&I!=="."){Q.fillStyle=this.prefs.label_color;var S=1;if(S===0&&C-Q.measureText(I).width<0){Q.textAlign="left";Q.fillText(I,E+j-N,B+8)}else{Q.textAlign="right";Q.fillText(I,C-j-N,B+8)}Q.fillStyle=U}return[0,0]}});w.Scaler=d;w.SummaryTreePainter=u;w.LinePainter=b;w.LinkedFeaturePainter=q;w.ReadPainter=s};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window);
\ No newline at end of file
diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index d09aa17f024..ddbc4a28cf0 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -1577,8 +1577,7 @@ extend(Tool.prototype, {
             // Set name of track to include tool name, parameters, and region used.
             track_name = url_params.tool_id +
                          current_track.tool_region_and_parameters_str(url_params.chrom, url_params.low, url_params.high),
-            container,
-            new_track;
+            container;
             
         // If track not in a group, create a group for it and add new track to group. If track 
         // already in group, add track to group.
@@ -1595,11 +1594,12 @@ extend(Tool.prototype, {
         else {
             container = current_track.container;
         }
-        if (current_track instanceof FeatureTrack) {
-            new_track = new ToolDataFeatureTrack(track_name, view, container, "hda");
-            new_track.change_mode(current_track.mode);
-            container.add_drawable(new_track);
-        }
+        
+        // Create and init new track.
+        var new_track = new current_track.constructor(track_name, view, container, "hda");
+        new_track.init_for_tool_data();
+        new_track.change_mode(current_track.mode);
+        container.add_drawable(new_track);
         new_track.content_div.text("Starting job.");
         
         // Run tool.
@@ -2316,7 +2316,6 @@ FeatureTrackTile.prototype.predisplay_actions = function() {
  * ----> ReferenceTrack
  * ----> FeatureTrack
  * -------> ReadTrack
- * -------> ToolDataFeatureTrack
  * -------> VcfTrack
  */
 var Track = function(name, view, container, show_header, prefs, data_url, data_query_wait) {
@@ -2476,9 +2475,6 @@ extend(Track.prototype, Drawable.prototype, {
         else if (this instanceof ReadTrack) {
             return "ReadTrack";
         }
-        else if (this instanceof ToolDataFeatureTrack) {
-            return "ToolDataFeatureTrack";
-        }
         else if (this instanceof VcfTrack) {
             return "VcfTrack";
         }
@@ -2562,8 +2558,8 @@ extend(Track.prototype, Drawable.prototype, {
     predraw_init: function() {}
 });
 
-var TiledTrack = function(name, view, container, show_header, prefs, filters_list, tool_dict, data_url, data_query_wait) {
-    Track.call(this, name, view, container, show_header, prefs, data_url, data_query_wait);
+var TiledTrack = function(name, view, container, show_header, prefs, filters_list, tool_dict) {
+    Track.call(this, name, view, container, show_header, prefs);
 
     var track = this,
         view = track.view;
@@ -2910,6 +2906,39 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
             region = (chrom !== undefined && low !== undefined && high !== undefined ?
                       chrom + ":" + low + "-" + high : "all");
         return " - region=[" + region + "], parameters=[" + track.tool.get_param_values().join(", ") + "]";
+    },
+    /**
+     * Set up track to receive tool data.
+     */
+    init_for_tool_data: function() {
+        // Set up track to fetch initial data from raw data URL when the dataset--not the converted datasets--
+        // is ready.
+        this.data_url = raw_data_url;
+        this.data_query_wait = 1000;
+        this.dataset_check_url = dataset_state_url;
+        
+        /**
+         * Predraw init sets up postdraw init.
+         */
+        this.predraw_init = function() {
+            // Postdraw init: once data has been fetched, reset data url, wait time and start indexing.
+            var track = this; 
+            var post_init = function() {
+                if (track.data_manager.size() === 0) {
+                    // Track still drawing initial data, so do nothing.
+                    setTimeout(post_init, 300);
+                }
+                else {
+                    // Track drawing done: reset dataset check, data URL, wait time and get dataset state to start
+                    // indexing.
+                    track.data_url = default_data_url;
+                    track.data_query_wait = DEFAULT_DATA_QUERY_WAIT;
+                    track.dataset_state_url = converted_datasets_state_url;
+                    $.getJSON(track.dataset_state_url, {dataset_id : track.dataset_id, hda_ldda: track.hda_ldda}, function(track_data) {});
+                }
+            };
+            post_init();
+        }
     }
 });
 
@@ -3524,8 +3553,8 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
     }
 });
 
-var VcfTrack = function(name, view, container, hda_ldda, dataset_id, prefs, filters) {
-    FeatureTrack.call(this, name, view, container, hda_ldda, dataset_id, prefs, filters);
+var VcfTrack = function(name, view, container, hda_ldda, dataset_id, prefs, filters, tool) {
+    FeatureTrack.call(this, name, view, container, hda_ldda, dataset_id, prefs, filters, tool);
     
     this.config = new DrawableConfig( {
         track: this,
@@ -3546,13 +3575,11 @@ var VcfTrack = function(name, view, container, hda_ldda, dataset_id, prefs, filt
     });
     this.prefs = this.config.values;
     
-    
     this.painter = painters.ReadPainter;
 };
 
 extend(VcfTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype);
 
-
 var ReadTrack = function (name, view, container, hda_ldda, dataset_id, prefs, filters) {
     FeatureTrack.call(this, name, view, container, hda_ldda, dataset_id, prefs, filters);
     
@@ -3581,44 +3608,6 @@ var ReadTrack = function (name, view, container, hda_ldda, dataset_id, prefs, fi
 };
 extend(ReadTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype);
 
-/**
- * Feature track that displays data generated from tool.
- */
-var ToolDataFeatureTrack = function(name, view, container, hda_ldda, dataset_id, prefs, filters) {
-    FeatureTrack.call(this, name, view, container, hda_ldda, dataset_id, prefs, filters, {});
-    
-    // Set up track to fetch initial data from raw data URL when the dataset--not the converted datasets--
-    // is ready.
-    this.data_url = raw_data_url;
-    this.data_query_wait = 1000;
-    this.dataset_check_url = dataset_state_url;
-};
-
-extend(ToolDataFeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype, {
-    /**
-     * For this track type, the predraw init sets up postdraw init. 
-     */
-    predraw_init: function() {        
-        // Postdraw init: once data has been fetched, reset data url, wait time and start indexing.
-        var track = this; 
-        var post_init = function() {
-            if (track.data_manager.size() === 0) {
-                // Track still drawing initial data, so do nothing.
-                setTimeout(post_init, 300);
-            }
-            else {
-                // Track drawing done: reset dataset check, data URL, wait time and get dataset state to start
-                // indexing.
-                track.data_url = default_data_url;
-                track.data_query_wait = DEFAULT_DATA_QUERY_WAIT;
-                track.dataset_state_url = converted_datasets_state_url;
-                $.getJSON(track.dataset_state_url, {dataset_id : track.dataset_id, hda_ldda: track.hda_ldda}, function(track_data) {});
-            }
-        };
-        post_init();
-    }
-});
-
 // Exports
 
 exports.View = View;
diff --git a/templates/tracks/browser.mako b/templates/tracks/browser.mako
index 1dc017fc469..1799b085f00 100644
--- a/templates/tracks/browser.mako
+++ b/templates/tracks/browser.mako
@@ -125,7 +125,7 @@ ${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.e
             view = create_visualization( $("#browser-container"), "${config.get('title') | h}", 
                                          "${config.get('vis_id')}", "${config.get('dbkey')}", 
                                          JSON.parse('${ h.to_json_string( config.get( 'viewport', dict() ) ) }'),
-                                         JSON.parse('${ h.to_json_string( config['tracks'] ) }'),
+                                         JSON.parse('${ h.to_json_string( config['tracks'] ).replace("'", "\\'") }'),
                                          JSON.parse('${ h.to_json_string( config['bookmarks'] ) }')
                                          );
             init_editor();
diff --git a/tools/gatk/unified_genotyper.xml b/tools/gatk/unified_genotyper.xml
index 263187c44ca..08490b17cff 100644
--- a/tools/gatk/unified_genotyper.xml
+++ b/tools/gatk/unified_genotyper.xml
@@ -396,7 +396,7 @@
     <data format="txt" name="output_metrics" label="${tool.name} on ${on_string} (metrics)" />
     <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
   </outputs>
-  <!-- FIXME! <trackster_conf/> -->
+  <trackster_conf/>
   <tests>
       <test>
           <param name="reference_source_selector" value="history" />

From a2722d1ba78bdffc896ea45c106aaf6bf1ecc8c5 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Tue, 1 Nov 2011 13:40:21 -0400
Subject: [PATCH 128/362] Fix bug introduced in f34a17e508e5.

---
 lib/galaxy/web/controllers/tracks.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/web/controllers/tracks.py b/lib/galaxy/web/controllers/tracks.py
index 416fa6e4057..8286ddddfe0 100644
--- a/lib/galaxy/web/controllers/tracks.py
+++ b/lib/galaxy/web/controllers/tracks.py
@@ -925,7 +925,7 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
                 else:
                     message = 'Attributes updated'
                     new_dataset.set_meta()
-                    new_dataset.datatype.after_setting_metadata( data )
+                    new_dataset.datatype.after_setting_metadata( new_dataset )
                     
                 trans.sa_session.flush()
                 

From 6a4b39b97c1f1d6c5d67e5cf18448d0ea9b131a5 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Tue, 1 Nov 2011 13:43:10 -0400
Subject: [PATCH 129/362] Remove debugging statements from f34a17e508e5.

---
 lib/galaxy/web/controllers/tracks.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/lib/galaxy/web/controllers/tracks.py b/lib/galaxy/web/controllers/tracks.py
index 8286ddddfe0..68397d6a3be 100644
--- a/lib/galaxy/web/controllers/tracks.py
+++ b/lib/galaxy/web/controllers/tracks.py
@@ -852,7 +852,6 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
             
             # Recursive function to set param value.
             def set_value( param_dict, group_name, group_index, param_name, param_value ):
-                print "searching", param_dict
                 if group_name in param_dict:
                     param_dict[ group_name ][ group_index ][ param_name ] = param_value
                     return True
@@ -866,7 +865,6 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
                         if isinstance( value, dict ):
                             return_val = set_value( value, group_name, group_index, param_name, param_value)
                             if return_val:
-                                print "setting parameter", param_dict
                                 return return_val
                     return False
             

From 501bd68cd16039355ba9876b79a42de39953f3f8 Mon Sep 17 00:00:00 2001
From: James Taylor <james@jamestaylor.org>
Date: Tue, 1 Nov 2011 14:54:11 -0400
Subject: [PATCH 130/362] Trackster: set min/max values for wiggle tracks using
 standard deviation. Add a new FeaturePainter that uses Arcs to connect
 blocks. Allow FeaturePainters to provide (computed) top and bottom padding
 around the rows where features are drawn.

---
 .../visualization/tracks/data_providers.py    |  10 +-
 static/scripts/trackster.js                   | 112 +++++++++++++++---
 2 files changed, 102 insertions(+), 20 deletions(-)

diff --git a/lib/galaxy/visualization/tracks/data_providers.py b/lib/galaxy/visualization/tracks/data_providers.py
index 8b3a705203a..9f83e698cab 100644
--- a/lib/galaxy/visualization/tracks/data_providers.py
+++ b/lib/galaxy/visualization/tracks/data_providers.py
@@ -10,6 +10,7 @@ if sys.version_info[:2] == (2, 4):
     pkg_resources.require( "ctypes" )
 pkg_resources.require( "pysam" )
 pkg_resources.require( "numpy" )
+from numpy import *
 from galaxy.datatypes.util.gff_util import *
 from galaxy.util.json import from_json_string
 from bx.interval_index_file import Indexes
@@ -490,12 +491,17 @@ class BBIDataProvider( TracksDataProvider ):
 
         if summary:
             mean = summary.sum_data / summary.valid_count
+
+            ## Standard deviation by bin, not yet used
+            ## var = summary.sum_squares - mean
+            ## var /= minimum( valid_count - 1, 1 )
+            ## sd = sqrt( var )
         
             pos = start
             step_size = (end - start) / num_points
 
-            for value in mean:
-                result.append( (pos, float_nan(value) ) )
+            for i in range( num_points ):
+                result.append( (pos, float_nan( mean[i] ) ) )
                 pos += step_size
             
         return { 'data': result }
diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index 8c94fde7fc3..b6c190781ca 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -3512,7 +3512,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
         var filter_height_scaler = (this.filters_manager.height_filter ? new FilterScaler(this.filters_manager.height_filter) : null);
         // HACK: ref_seq will only be defined for ReadTracks, and only the ReadPainter accepts that argument
         var painter = new (this.painter)(filtered, tile_low, tile_high, this.prefs, mode, filter_alpha_scaler, filter_height_scaler, ref_seq);
-        var required_height = Math.max(MIN_TRACK_HEIGHT, painter.get_required_height(slots_required));
+        var required_height = Math.max(MIN_TRACK_HEIGHT, painter.get_required_height(slots_required,width));
         var canvas = this.view.canvas_manager.new_canvas();
         var feature_mapper = null;
         
@@ -4078,6 +4078,7 @@ var FeaturePositionMapper = function(slot_height) {
     this.feature_positions = {};
     this.slot_height = slot_height;
     this.translation = 0;
+    this.y_translation = 0;
 };
 
 /**
@@ -4099,7 +4100,7 @@ FeaturePositionMapper.prototype.map_feature_data = function(feature_data, slot,
  */
 FeaturePositionMapper.prototype.get_feature_data = function(x, y) {
     // Find slot using Y.
-    var slot = Math.floor( y/this.slot_height ),
+    var slot = Math.floor( (y-this.y_translation)/this.slot_height ),
         feature_dict;
 
     // May not be over a slot due to padding, margin, etc.
@@ -4129,15 +4130,23 @@ var FeaturePainter = function(data, view_start, view_end, prefs, mode, alpha_sca
 FeaturePainter.prototype.default_prefs = { block_color: "#FFF", connector_color: "#FFF" };
 
 extend(FeaturePainter.prototype, {
-    get_required_height: function(rows_required) {
+    get_required_height: function(rows_required, width) {
         // y_scale is the height per row
         var required_height = y_scale = this.get_row_height(), mode = this.mode;
         // If using a packing mode, need to multiply by the number of slots used
         if (mode === "no_detail" || mode === "Squish" || mode === "Pack") {
             required_height = rows_required * y_scale;
         }
+        return required_height + this.get_top_padding(width) + this.get_bottom_padding(width);
+    },
+    /** Extra padding before first row of features */
+    get_top_padding: function(width) {
+        return 0;
+    },
+    /** Extra padding after last row of features */
+    get_bottom_padding: function(width) {
         // Pad bottom by half a row, at least 5 px
-        return required_height + Math.max( Math.round( y_scale / 2 ), 5 );
+        return Math.max( Math.round( this.get_row_height() / 2 ), 5 ) 
     },
     /**
      * Draw data on ctx using slots and within the rectangle defined by width and height. Returns
@@ -4174,6 +4183,7 @@ extend(FeaturePainter.prototype, {
         }
 
         ctx.restore();
+        feature_mapper.y_translation = this.get_top_padding(width);
         return feature_mapper;
     },
     /** 
@@ -4200,6 +4210,10 @@ var DENSE_TRACK_HEIGHT = 10,
 
 var LinkedFeaturePainter = function(data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler) {
     FeaturePainter.call(this, data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler);
+    // Whether to draw a single connector in the background that spans the entire feature (the intron fishbone)
+    this.draw_background_connector = true;
+    // Whether to call draw_connector for every pair of blocks
+    this.draw_individual_connectors = false;
 };
 
 extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
@@ -4237,7 +4251,7 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
             f_end   = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low) * w_scale)) ),
             draw_start = f_start,
             draw_end = f_end,
-            y_center = (mode === "Dense" ? 0 : (0 + slot)) * y_scale,
+            y_center = (mode === "Dense" ? 0 : (0 + slot)) * y_scale + this.get_top_padding(width),
             thickness, y_start, thick_start = null, thick_end = null,
             // TODO: is there any reason why block, label color cannot be set at the Painter level?
             block_color = this.prefs.block_color,
@@ -4300,38 +4314,51 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
                 // needed. This ensures that whole feature, regardless of whether it starts with
                 // a block, is visible.
                 //
-                
-                // Draw whole feature as connector/intron.
+               
+                // Compute y axis center position and height
                 var cur_y_center, cur_height;
                 if (mode === "Squish" || mode === "Dense") {
-                    ctx.fillStyle = CONNECTOR_COLOR;
                     cur_y_center = y_center + Math.floor(SQUISH_FEATURE_HEIGHT/2) + 1;
                     cur_height = 1;
                 }
                 else { // mode === "Pack"
                     if (feature_strand) {
-                        var cur_y_center = y_center;
-                        var cur_height = thick_height;
-                        if (feature_strand === "+") {
-                            ctx.fillStyle = ctx.canvas.manager.get_pattern( 'right_strand' );
-                        } else if (feature_strand === "-") {
-                            ctx.fillStyle = ctx.canvas.manager.get_pattern( 'left_strand' );
-                        }
+                        cur_y_center = y_center;
+                        cur_height = thick_height;
                     }
                     else {
-                        ctx.fillStyle = CONNECTOR_COLOR;
                         cur_y_center += (SQUISH_FEATURE_HEIGHT/2) + 1;
                         cur_height = 1;
                     }
                 }
-                ctx.fillRect(f_start, cur_y_center, f_end - f_start, cur_height);
+
+                // Draw whole feature as connector/intron.
+                if ( this.draw_background_connector ) {
+                    if (mode === "Squish" || mode === "Dense") {
+                        ctx.fillStyle = CONNECTOR_COLOR;
+                    }
+                    else { // mode === "Pack"
+                        if (feature_strand) {
+                            if (feature_strand === "+") {
+                                ctx.fillStyle = ctx.canvas.manager.get_pattern( 'right_strand' );
+                            } else if (feature_strand === "-") {
+                                ctx.fillStyle = ctx.canvas.manager.get_pattern( 'left_strand' );
+                            }
+                        }
+                        else {
+                            ctx.fillStyle = CONNECTOR_COLOR;
+                        }
+                    }
+                    ctx.fillRect(f_start, cur_y_center, f_end - f_start, cur_height);
+                }
                 
                 // Draw blocks.
                 var start_and_height;
                 for (var k = 0, k_len = feature_blocks.length; k < k_len; k++) {
                     var block = feature_blocks[k],
                         block_start = Math.floor( Math.max(0, (block[0] - tile_low) * w_scale) ),
-                        block_end = Math.ceil( Math.min(width, Math.max((block[1] - tile_low) * w_scale)) );
+                        block_end = Math.ceil( Math.min(width, Math.max((block[1] - tile_low) * w_scale)) ),
+                        last_block_start, last_block_end;
 
                     // Skip drawing if block not on tile.    
                     if (block_start > block_end) { continue; }
@@ -4362,6 +4389,12 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
                             ctx.fillRect(block_thick_start, y_center + 1, block_thick_end - block_thick_start, thick_height );
                         }   
                     }
+                    // Draw individual connectors if required
+                    if ( this.draw_individual_connectors && last_block_start ) {
+                        this.draw_connector( ctx, last_block_start, last_block_end, block_start, block_end, y_center );
+                    }
+                    last_block_start = block_start;
+                    last_block_end = block_end;
                 }
                                 
                 // FIXME: Height scaling only works in Pack mode right now.
@@ -4699,11 +4732,54 @@ extend(ReadPainter.prototype, FeaturePainter.prototype, {
     }
 });
 
+var ArcLinkedFeaturePainter = function(data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler) {
+    LinkedFeaturePainter.call(this, data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler);
+    // Need to know the longest feature length for adding spacing
+    this.longest_feature_length = this.calculate_longest_feature_length();
+    this.draw_background_connector = false;
+    this.draw_individual_connectors = true;
+};
+
+extend(ArcLinkedFeaturePainter.prototype, FeaturePainter.prototype, LinkedFeaturePainter.prototype, {
+
+    calculate_longest_feature_length: function () {
+        var longest_feature_length = 0;
+        for (var i = 0, len = this.data.length; i < len; i++) {
+            var feature = this.data[i], feature_start = feature[1], feature_end = feature[2];
+            longest_feature_length = Math.max( longest_feature_length, feature_end - feature_start );
+        }
+        return longest_feature_length;
+    },
+
+    get_top_padding: function( width ) { 
+        var view_range = this.view_end - this.view_start,
+            w_scale = width / view_range;
+        return Math.min( 128, Math.ceil( ( this.longest_feature_length / 2 ) * w_scale ) );
+    },
+
+    draw_connector: function( ctx, block1_start, block1_end, block2_start, block2_end, y_center ) {
+        // Arc drawing -- from closest endpoints
+        var x_center = ( block1_end + block2_start ) / 2,
+            radius = block2_start - x_center; 
+        // For full half circles
+        var angle1 = Math.PI, angle2 = 0;
+        if ( radius > 0 ) {
+            ctx.beginPath();
+            ctx.arc( x_center, y_center, block2_start - x_center, Math.PI, 0 );
+            ctx.stroke();
+        }
+    }
+});
+
+
+
+
 exports.Scaler = Scaler;
 exports.SummaryTreePainter = SummaryTreePainter;
 exports.LinePainter = LinePainter;
 exports.LinkedFeaturePainter = LinkedFeaturePainter;
 exports.ReadPainter = ReadPainter;
+exports.ArcLinkedFeaturePainter = ArcLinkedFeaturePainter;
 
 // End painters_module encapsulation
 };

From 5b131454263567f124b30555d8209d9b36b3df3a Mon Sep 17 00:00:00 2001
From: Richard Burhans <burhans@bx.psu.edu>
Date: Tue, 1 Nov 2011 15:52:53 -0400
Subject: [PATCH 131/362] consolidated make_html_table for tabular datatypes

---
 lib/galaxy/datatypes/genetics.py |  24 +-----
 lib/galaxy/datatypes/interval.py |  51 ++-----------
 lib/galaxy/datatypes/tabular.py  | 124 ++++++++++---------------------
 3 files changed, 52 insertions(+), 147 deletions(-)

diff --git a/lib/galaxy/datatypes/genetics.py b/lib/galaxy/datatypes/genetics.py
index 48fafada24a..98b4dabeb86 100644
--- a/lib/galaxy/datatypes/genetics.py
+++ b/lib/galaxy/datatypes/genetics.py
@@ -192,27 +192,9 @@ class rgTabList(Tabular):
         Tabular.__init__( self, **kwd )
         self.column_names = []
 
-    def make_html_table( self, dataset, skipchars=[] ):
-        """
-        Create HTML table, used for displaying peek
-        """
-        out = ['<table cellspacing="0" cellpadding="3">']
-        comments = []
-        try:
-            # Generate column header
-            out.append( '<tr>' )
-            for i, name in enumerate( self.column_names ):
-                out.append( '<th>%s.%s</th>' % ( str( i+1 ), name ) )
-            if dataset.metadata.columns - len( self.column_names ) > 0:
-                for i in range( len( self.column_names ), dataset.metadata.columns ):
-                    out.append( '<th>%s</th>' % str( i+1 ) )
-                out.append( '</tr>' )
-            out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) )
-            out.append( '</table>' )
-            out = "".join( out )
-        except Exception, exc:
-            out = "Can't create peek %s" % exc
-        return out
+    def display_peek( self, dataset ):
+        """Returns formated html of peek"""
+        return Tabular.make_html_table( self, dataset, column_names=self.column_names )
 
     def get_mime(self):
         """Returns the mime type of the datatype"""
diff --git a/lib/galaxy/datatypes/interval.py b/lib/galaxy/datatypes/interval.py
index 0c7693e6c5b..0d2ccc4cd3d 100644
--- a/lib/galaxy/datatypes/interval.py
+++ b/lib/galaxy/datatypes/interval.py
@@ -219,33 +219,9 @@ class Interval( Tabular ):
                 os.write(fd, '%s\n' % '\t'.join(tmp) )    
         os.close(fd)
         return open(temp_name)
-    def make_html_table( self, dataset, skipchars=[] ):
-        """Create HTML table, used for displaying peek"""
-        out = ['<table cellspacing="0" cellpadding="3">']
-        comments = []
-        try:
-            # Generate column header
-            out.append('<tr>')
-            for i in range( 1, dataset.metadata.columns+1 ):
-                if i == dataset.metadata.chromCol:
-                    out.append( '<th>%s.Chrom</th>' % i )
-                elif i == dataset.metadata.startCol:
-                    out.append( '<th>%s.Start</th>' % i )
-                elif i == dataset.metadata.endCol:
-                    out.append( '<th>%s.End</th>' % i )
-                elif dataset.metadata.strandCol and i == dataset.metadata.strandCol:
-                    out.append( '<th>%s.Strand</th>' % i )
-                elif dataset.metadata.nameCol and i == dataset.metadata.nameCol:
-                    out.append( '<th>%s.Name</th>' % i )
-                else:
-                    out.append( '<th>%s</th>' % i )
-            out.append('</tr>')
-            out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) )
-            out.append( '</table>' )
-            out = "".join( out )
-        except Exception, exc:
-            out = "Can't create peek %s" % str( exc )
-        return out
+    def display_peek( self, dataset ):
+        """Returns formated html of peek"""
+        return Tabular.make_html_table( self, dataset, column_parameter_alias={'chromCol':'Chrom', 'startCol':'Start', 'endCol':'End', 'strandCol':'Strand', 'nameCol':'Name'} )
     def ucsc_links( self, dataset, type, app, base_url ):
         """
         Generate links to UCSC genome browser sites based on the dbkey
@@ -617,21 +593,9 @@ class Gff( Tabular, _RemoteCallMixin ):
                     except:
                         pass
         Tabular.set_meta( self, dataset, overwrite = overwrite, skip = i )
-    def make_html_table( self, dataset, skipchars=[] ):
-        """Create HTML table, used for displaying peek"""
-        out = ['<table cellspacing="0" cellpadding="3">']
-        comments = []
-        try:
-            # Generate column header
-            out.append( '<tr>' )
-            for i, name in enumerate( self.column_names ):
-                out.append( '<th>%s.%s</th>' % ( str( i+1 ), name ) )
-            out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) )
-            out.append( '</table>' )
-            out = "".join( out )
-        except Exception, exc:
-            out = "Can't create peek %s" % exc
-        return out
+    def display_peek( self, dataset ):
+        """Returns formated html of peek"""
+        return Tabular.make_html_table( self, dataset, column_names=self.column_names )
     def get_estimated_display_viewport( self, dataset ):
         """
         Return a chrom, start, stop tuple for viewing a file.  There are slight differences between gff 2 and gff 3
@@ -1081,7 +1045,8 @@ class Wiggle( Tabular, _RemoteCallMixin ):
                     link = self._get_remote_call_url( redirect_url, site_name, dataset, type, app, base_url )
                     ret_val.append( ( site_name, link ) )
         return ret_val
-    def make_html_table( self, dataset ):
+    def display_peek( self, dataset ):
+        """Returns formated html of peek"""
         return Tabular.make_html_table( self, dataset, skipchars=['track', '#'] )
     def set_meta( self, dataset, overwrite = True, **kwd ):
         max_data_lines = None
diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py
index 0e393bf3558..7b1d3fccb4f 100644
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -168,24 +168,46 @@ class Tabular( data.Text ):
         """Create HTML table, used for displaying peek"""
         out = ['<table cellspacing="0" cellpadding="3">']
         try:
-            out.append( self.make_html_peek_header( dataset, kwargs ) )
-            out.append( self.make_html_peek_rows( dataset, kwargs ) )
+            out.append( self.make_html_peek_header( dataset, **kwargs ) )
+            out.append( self.make_html_peek_rows( dataset, **kwargs ) )
             out.append( '</table>' )
             out = "".join( out )
         except Exception, exc:
             out = "Can't create peek %s" % str( exc )
         return out
-    def make_html_peek_header( self, dataset, skipchars=[] ):
+    def make_html_peek_header( self, dataset, skipchars=[], column_names=[], column_number_format='%s', column_parameter_alias={}, **kwargs ):
         out = []
         try:
+            column_headers = [None] * dataset.metadata.columns
+
+            # fill in empty headers with data from column_names
+            for i in range( min( dataset.metadata.columns, len( column_names ) ) ):
+                if column_headers[i] is None and column_names[i] is not None:
+                    column_headers[i] = column_names[i]
+
+            # fill in empty headers from ColumnParameters set in the metadata
+            for name, spec in dataset.metadata.spec.items():
+                if isinstance( spec.param, metadata.ColumnParameter ):
+                    try:
+                        i = int( getattr( dataset.metadata, name ) ) - 1
+                    except:
+                        i = -1
+                    if 0 <= i < dataset.metadata.columns and column_headers[i] is None:
+                        column_headers[i] = column_parameter_alias.get(name, name)
+
             out.append( '<tr>' )
-            for i in range( 1, dataset.metadata.columns+1 ):
-                out.append( '<th>%s</th>' % str( i ) )
+            for i, header in enumerate( column_headers ):
+                out.append( '<th>' )
+                if header is None:
+                    out.append( column_number_format % str( i + 1 ) )
+                else:
+                    out.append( '%s.%s' % ( str( i + 1 ), escape( header ) ) )
+                out.append( '</th>' )
             out.append( '</tr>' )
         except Exception, exc:
             raise Exception, "Can't create peek header %s" % str( exc )
         return "".join( out )
-    def make_html_peek_rows( self, dataset, skipchars=[] ):
+    def make_html_peek_rows( self, dataset, skipchars=[], **kwargs ):
         out = []
         try:
             if not dataset.peek:
@@ -235,26 +257,9 @@ class Taxonomy( Tabular ):
                              'Superorder', 'Order', 'Suborder', 'Superfamily', 'Family', 'Subfamily',
                              'Tribe', 'Subtribe', 'Genus', 'Subgenus', 'Species', 'Subspecies'
                              ]
-    def make_html_table( self, dataset, skipchars=[] ):
-        """Create HTML table, used for displaying peek"""
-        out = ['<table cellspacing="0" cellpadding="3">']
-        comments = []
-        try:
-            # Generate column header
-            out.append( '<tr>' )
-            for i, name in enumerate( self.column_names ):
-                out.append( '<th>%s.%s</th>' % ( str( i+1 ), name ) )
-            # This data type requires at least 24 columns in the data
-            if dataset.metadata.columns - len( self.column_names ) > 0:
-                for i in range( len( self.column_names ), dataset.metadata.columns ):
-                    out.append( '<th>%s</th>' % str( i+1 ) )
-                out.append( '</tr>' )
-            out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) )
-            out.append( '</table>' )
-            out = "".join( out )
-        except Exception, exc:
-            out = "Can't create peek %s" % exc
-        return out
+    def display_peek( self, dataset ):
+        """Returns formated html of peek"""
+        return Tabular.make_html_table( self, dataset, column_names=self.column_names )
 
 class Sam( Tabular ):
     file_ext = 'sam'
@@ -264,25 +269,10 @@ class Sam( Tabular ):
         self.column_names = ['QNAME', 'FLAG', 'RNAME', 'POS', 'MAPQ', 'CIGAR',
                              'MRNM', 'MPOS', 'ISIZE', 'SEQ', 'QUAL', 'OPT'
                              ]
-    def make_html_table( self, dataset, skipchars=[] ):
-        """Create HTML table, used for displaying peek"""
-        out = ['<table cellspacing="0" cellpadding="3">']
-        try:
-            # Generate column header
-            out.append( '<tr>' )
-            for i, name in enumerate( self.column_names ):
-                out.append( '<th>%s.%s</th>' % ( str( i+1 ), name ) )
-            # This data type requires at least 11 columns in the data
-            if dataset.metadata.columns - len( self.column_names ) > 0:
-                for i in range( len( self.column_names ), dataset.metadata.columns ):
-                    out.append( '<th>%s</th>' % str( i+1 ) )
-                out.append( '</tr>' )
-            out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) )
-            out.append( '</table>' )
-            out = "".join( out )
-        except Exception, exc:
-            out = "Can't create peek %s" % exc
-        return out
+    def display_peek( self, dataset ):
+        """Returns formated html of peek"""
+        return Tabular.make_html_table( self, dataset, column_names=self.column_names )
+
     def sniff( self, filename ):
         """
         Determines whether the file is in SAM format
@@ -376,29 +366,9 @@ class Pileup( Tabular ):
     def init_meta( self, dataset, copy_from=None ):
         Tabular.init_meta( self, dataset, copy_from=copy_from )
 
-    def make_html_table( self, dataset, skipchars=[] ):
-        """Create HTML table, used for displaying peek"""
-        out = ['<table cellspacing="0" cellpadding="3">']
-        comments = []
-        try:
-            # Generate column header
-            out.append('<tr>')
-            for i in range( 1, dataset.metadata.columns+1 ):
-                if i == dataset.metadata.chromCol:
-                    out.append( '<th>%s.Chrom</th>' % i )
-                elif i == dataset.metadata.startCol:
-                    out.append( '<th>%s.Start</th>' % i )
-                elif i == dataset.metadata.baseCol:
-                    out.append( '<th>%s.Base</th>' % i )
-                else:
-                    out.append( '<th>%s</th>' % i )
-            out.append('</tr>')
-            out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) )
-            out.append( '</table>' )
-            out = "".join( out )
-        except Exception, exc:
-            out = "Can't create peek %s" % str( exc )
-        return out
+    def display_peek( self, dataset ):
+        """Returns formated html of peek"""
+        return Tabular.make_html_table( self, dataset, column_parameter_alias={'chromCol':'Chrom', 'startCol':'Start', 'baseCol':'Base'} )
 
     def repair_methods( self, dataset ):
         """Return options for removing errors along with a description"""
@@ -464,21 +434,9 @@ class Vcf( Tabular ):
     def sniff( self, filename ):
         headers = get_headers( filename, '\n', count=1 )
         return headers[0][0].startswith("##fileformat=VCF")
+    def display_peek( self, dataset ):
+        """Returns formated html of peek"""
+        return Tabular.make_html_table( self, dataset, column_names=self.column_names )
             
-    def make_html_table( self, dataset, skipchars=[] ):
-        """Create HTML table, used for displaying peek"""
-        out = ['<table cellspacing="0" cellpadding="3">']
-        try:
-            # Generate column header
-            out.append( '<tr>' )
-            for i, name in enumerate( self.column_names ):
-                out.append( '<th>%s.%s</th>' % ( str( i+1 ), name ) )
-            out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) )
-            out.append( '</table>' )
-            out = "".join( out )
-        except Exception, exc:
-            out = "Can't create peek %s" % exc
-        return out
-        
     def get_track_type( self ):
         return "VcfTrack", {"data": "tabix", "index": "summary_tree"}

From b6d64f6a52df6d1210a573746f057019410a53b3 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Tue, 1 Nov 2011 17:51:53 -0400
Subject: [PATCH 132/362] Fix vertical scrolling via keyboard in Trackster.

---
 static/scripts/jquery.scrollTo.js        | 215 -----------------------
 static/scripts/packed/jquery.scrollTo.js |   1 -
 static/scripts/trackster_ui.js           |   4 +-
 3 files changed, 2 insertions(+), 218 deletions(-)
 delete mode 100644 static/scripts/jquery.scrollTo.js
 delete mode 100644 static/scripts/packed/jquery.scrollTo.js

diff --git a/static/scripts/jquery.scrollTo.js b/static/scripts/jquery.scrollTo.js
deleted file mode 100644
index eec31e191cb..00000000000
--- a/static/scripts/jquery.scrollTo.js
+++ /dev/null
@@ -1,215 +0,0 @@
-/**
- * jQuery.ScrollTo
- * Copyright (c) 2007-2009 Ariel Flesler - aflesler(at)gmail(dot)com | http://flesler.blogspot.com
- * Dual licensed under MIT and GPL.
- * Date: 5/25/2009
- *
- * @projectDescription Easy element scrolling using jQuery.
- * http://flesler.blogspot.com/2007/10/jqueryscrollto.html
- * Works with jQuery +1.2.6. Tested on FF 2/3, IE 6/7/8, Opera 9.5/6, Safari 3, Chrome 1 on WinXP.
- *
- * @author Ariel Flesler
- * @version 1.4.2
- *
- * @id jQuery.scrollTo
- * @id jQuery.fn.scrollTo
- * @param {String, Number, DOMElement, jQuery, Object} target Where to scroll the matched elements.
- *	  The different options for target are:
- *		- A number position (will be applied to all axes).
- *		- A string position ('44', '100px', '+=90', etc ) will be applied to all axes
- *		- A jQuery/DOM element ( logically, child of the element to scroll )
- *		- A string selector, that will be relative to the element to scroll ( 'li:eq(2)', etc )
- *		- A hash { top:x, left:y }, x and y can be any kind of number/string like above.
-*		- A percentage of the container's dimension/s, for example: 50% to go to the middle.
- *		- The string 'max' for go-to-end. 
- * @param {Number} duration The OVERALL length of the animation, this argument can be the settings object instead.
- * @param {Object,Function} settings Optional set of settings or the onAfter callback.
- *	 @option {String} axis Which axis must be scrolled, use 'x', 'y', 'xy' or 'yx'.
- *	 @option {Number} duration The OVERALL length of the animation.
- *	 @option {String} easing The easing method for the animation.
- *	 @option {Boolean} margin If true, the margin of the target element will be deducted from the final position.
- *	 @option {Object, Number} offset Add/deduct from the end position. One number for both axes or { top:x, left:y }.
- *	 @option {Object, Number} over Add/deduct the height/width multiplied by 'over', can be { top:x, left:y } when using both axes.
- *	 @option {Boolean} queue If true, and both axis are given, the 2nd axis will only be animated after the first one ends.
- *	 @option {Function} onAfter Function to be called after the scrolling ends. 
- *	 @option {Function} onAfterFirst If queuing is activated, this function will be called after the first scrolling ends.
- * @return {jQuery} Returns the same jQuery object, for chaining.
- *
- * @desc Scroll to a fixed position
- * @example $('div').scrollTo( 340 );
- *
- * @desc Scroll relatively to the actual position
- * @example $('div').scrollTo( '+=340px', { axis:'y' } );
- *
- * @dec Scroll using a selector (relative to the scrolled element)
- * @example $('div').scrollTo( 'p.paragraph:eq(2)', 500, { easing:'swing', queue:true, axis:'xy' } );
- *
- * @ Scroll to a DOM element (same for jQuery object)
- * @example var second_child = document.getElementById('container').firstChild.nextSibling;
- *			$('#container').scrollTo( second_child, { duration:500, axis:'x', onAfter:function(){
- *				alert('scrolled!!');																   
- *			}});
- *
- * @desc Scroll on both axes, to different values
- * @example $('div').scrollTo( { top: 300, left:'+=200' }, { axis:'xy', offset:-20 } );
- */
-;(function( $ ){
-	
-	var $scrollTo = $.scrollTo = function( target, duration, settings ){
-		$(window).scrollTo( target, duration, settings );
-	};
-
-	$scrollTo.defaults = {
-		axis:'xy',
-		duration: parseFloat($.fn.jquery) >= 1.3 ? 0 : 1
-	};
-
-	// Returns the element that needs to be animated to scroll the window.
-	// Kept for backwards compatibility (specially for localScroll & serialScroll)
-	$scrollTo.window = function( scope ){
-		return $(window)._scrollable();
-	};
-
-	// Hack, hack, hack :)
-	// Returns the real elements to scroll (supports window/iframes, documents and regular nodes)
-	$.fn._scrollable = function(){
-		return this.map(function(){
-			var elem = this,
-				isWin = !elem.nodeName || $.inArray( elem.nodeName.toLowerCase(), ['iframe','#document','html','body'] ) != -1;
-
-				if( !isWin )
-					return elem;
-
-			var doc = (elem.contentWindow || elem).document || elem.ownerDocument || elem;
-			
-			return $.browser.safari || doc.compatMode == 'BackCompat' ?
-				doc.body : 
-				doc.documentElement;
-		});
-	};
-
-	$.fn.scrollTo = function( target, duration, settings ){
-		if( typeof duration == 'object' ){
-			settings = duration;
-			duration = 0;
-		}
-		if( typeof settings == 'function' )
-			settings = { onAfter:settings };
-			
-		if( target == 'max' )
-			target = 9e9;
-			
-		settings = $.extend( {}, $scrollTo.defaults, settings );
-		// Speed is still recognized for backwards compatibility
-		duration = duration || settings.speed || settings.duration;
-		// Make sure the settings are given right
-		settings.queue = settings.queue && settings.axis.length > 1;
-		
-		if( settings.queue )
-			// Let's keep the overall duration
-			duration /= 2;
-		settings.offset = both( settings.offset );
-		settings.over = both( settings.over );
-
-		return this._scrollable().each(function(){
-			var elem = this,
-				$elem = $(elem),
-				targ = target, toff, attr = {},
-				win = $elem.is('html,body');
-
-			switch( typeof targ ){
-				// A number will pass the regex
-				case 'number':
-				case 'string':
-					if( /^([+-]=)?\d+(\.\d+)?(px|%)?$/.test(targ) ){
-						targ = both( targ );
-						// We are done
-						break;
-					}
-					// Relative selector, no break!
-					targ = $(targ,this);
-				case 'object':
-					// DOMElement / jQuery
-					if( targ.is || targ.style )
-						// Get the real position of the target 
-						toff = (targ = $(targ)).offset();
-			}
-			$.each( settings.axis.split(''), function( i, axis ){
-				var Pos	= axis == 'x' ? 'Left' : 'Top',
-					pos = Pos.toLowerCase(),
-					key = 'scroll' + Pos,
-					old = elem[key],
-					max = $scrollTo.max(elem, axis);
-
-				if( toff ){// jQuery / DOMElement
-					attr[key] = toff[pos] + ( win ? 0 : old - $elem.offset()[pos] );
-
-					// If it's a dom element, reduce the margin
-					if( settings.margin ){
-						attr[key] -= parseInt(targ.css('margin'+Pos)) || 0;
-						attr[key] -= parseInt(targ.css('border'+Pos+'Width')) || 0;
-					}
-					
-					attr[key] += settings.offset[pos] || 0;
-					
-					if( settings.over[pos] )
-						// Scroll to a fraction of its width/height
-						attr[key] += targ[axis=='x'?'width':'height']() * settings.over[pos];
-				}else{ 
-					var val = targ[pos];
-					// Handle percentage values
-					attr[key] = val.slice && val.slice(-1) == '%' ? 
-						parseFloat(val) / 100 * max
-						: val;
-				}
-
-				// Number or 'number'
-				if( /^\d+$/.test(attr[key]) )
-					// Check the limits
-					attr[key] = attr[key] <= 0 ? 0 : Math.min( attr[key], max );
-
-				// Queueing axes
-				if( !i && settings.queue ){
-					// Don't waste time animating, if there's no need.
-					if( old != attr[key] )
-						// Intermediate animation
-						animate( settings.onAfterFirst );
-					// Don't animate this axis again in the next iteration.
-					delete attr[key];
-				}
-			});
-
-			animate( settings.onAfter );			
-
-			function animate( callback ){
-				$elem.animate( attr, duration, settings.easing, callback && function(){
-					callback.call(this, target, settings);
-				});
-			};
-
-		}).end();
-	};
-	
-	// Max scrolling position, works on quirks mode
-	// It only fails (not too badly) on IE, quirks mode.
-	$scrollTo.max = function( elem, axis ){
-		var Dim = axis == 'x' ? 'Width' : 'Height',
-			scroll = 'scroll'+Dim;
-		
-		if( !$(elem).is('html,body') )
-			return elem[scroll] - $(elem)[Dim.toLowerCase()]();
-		
-		var size = 'client' + Dim,
-			html = elem.ownerDocument.documentElement,
-			body = elem.ownerDocument.body;
-
-		return Math.max( html[scroll], body[scroll] ) 
-			 - Math.min( html[size]  , body[size]   );
-			
-	};
-
-	function both( val ){
-		return typeof val == 'object' ? val : { top:val, left:val };
-	};
-
-})( jQuery );
\ No newline at end of file
diff --git a/static/scripts/packed/jquery.scrollTo.js b/static/scripts/packed/jquery.scrollTo.js
deleted file mode 100644
index 97e5843fbb0..00000000000
--- a/static/scripts/packed/jquery.scrollTo.js
+++ /dev/null
@@ -1 +0,0 @@
-(function(c){var a=c.scrollTo=function(f,e,d){c(window).scrollTo(f,e,d)};a.defaults={axis:"xy",duration:parseFloat(c.fn.jquery)>=1.3?0:1};a.window=function(d){return c(window)._scrollable()};c.fn._scrollable=function(){return this.map(function(){var e=this,d=!e.nodeName||c.inArray(e.nodeName.toLowerCase(),["iframe","#document","html","body"])!=-1;if(!d){return e}var f=(e.contentWindow||e).document||e.ownerDocument||e;return c.browser.safari||f.compatMode=="BackCompat"?f.body:f.documentElement})};c.fn.scrollTo=function(f,e,d){if(typeof e=="object"){d=e;e=0}if(typeof d=="function"){d={onAfter:d}}if(f=="max"){f=9000000000}d=c.extend({},a.defaults,d);e=e||d.speed||d.duration;d.queue=d.queue&&d.axis.length>1;if(d.queue){e/=2}d.offset=b(d.offset);d.over=b(d.over);return this._scrollable().each(function(){var l=this,j=c(l),k=f,i,g={},m=j.is("html,body");switch(typeof k){case"number":case"string":if(/^([+-]=)?\d+(\.\d+)?(px|%)?$/.test(k)){k=b(k);break}k=c(k,this);case"object":if(k.is||k.style){i=(k=c(k)).offset()}}c.each(d.axis.split(""),function(q,r){var s=r=="x"?"Left":"Top",u=s.toLowerCase(),p="scroll"+s,o=l[p],n=a.max(l,r);if(i){g[p]=i[u]+(m?0:o-j.offset()[u]);if(d.margin){g[p]-=parseInt(k.css("margin"+s))||0;g[p]-=parseInt(k.css("border"+s+"Width"))||0}g[p]+=d.offset[u]||0;if(d.over[u]){g[p]+=k[r=="x"?"width":"height"]()*d.over[u]}}else{var t=k[u];g[p]=t.slice&&t.slice(-1)=="%"?parseFloat(t)/100*n:t}if(/^\d+$/.test(g[p])){g[p]=g[p]<=0?0:Math.min(g[p],n)}if(!q&&d.queue){if(o!=g[p]){h(d.onAfterFirst)}delete g[p]}});h(d.onAfter);function h(n){j.animate(g,e,d.easing,n&&function(){n.call(this,f,d)})}}).end()};a.max=function(j,i){var h=i=="x"?"Width":"Height",e="scroll"+h;if(!c(j).is("html,body")){return j[e]-c(j)[h.toLowerCase()]()}var g="client"+h,f=j.ownerDocument.documentElement,d=j.ownerDocument.body;return Math.max(f[e],d[e])-Math.min(f[g],d[g])};function b(d){return typeof d=="object"?d:{top:d,left:d}}})(jQuery);
\ No newline at end of file
diff --git a/static/scripts/trackster_ui.js b/static/scripts/trackster_ui.js
index 1f69df5c46a..05c53eaf30f 100644
--- a/static/scripts/trackster_ui.js
+++ b/static/scripts/trackster_ui.js
@@ -154,14 +154,14 @@ var init_keyboard_nav = function(view) {
                 break
             case 38:
                 var change = Math.round(view.viewport_container.height()/15.0);
-                view.viewport_container.scrollTo('-=' + change + 'px');
+                view.viewport_container.scrollTop( view.viewport_container.scrollTop() - 20);
                 break;
             case 39:
                 view.move_fraction(-0.25);
                 break;
             case 40:
                 var change = Math.round(view.viewport_container.height()/15.0);
-                view.viewport_container.scrollTo('+=' + change + 'px');
+                view.viewport_container.scrollTop( view.viewport_container.scrollTop() + 20);
                 break;
         }
     });

From 4464b804e25471edf621980abde77a9fb36b7748 Mon Sep 17 00:00:00 2001
From: James Taylor <james@jamestaylor.org>
Date: Tue, 1 Nov 2011 18:56:34 -0400
Subject: [PATCH 133/362] Make default height for LineTracks smaller, 32px
 seems more reasonable. Possibly it should be larger if there is both positive
 and negative data?

---
 static/scripts/trackster.js | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index ac36d65d95c..daf3b11dd92 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -3031,7 +3031,8 @@ var LineTrack = function (name, view, container, hda_ldda, dataset_id, prefs) {
    
     this.min_height_px = 16; 
     this.max_height_px = 400; 
-    this.height_px = 80;
+    // Default height for new tracks, should be a defined constant?
+    this.height_px = 32;
     this.hda_ldda = hda_ldda;
     this.dataset_id = dataset_id;
     this.original_dataset_id = dataset_id;

From 5d38edf14e6691cfb0440964541536d08e70695f Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Wed, 2 Nov 2011 13:28:43 -0400
Subject: [PATCH 134/362] Fix a typo in tasks.

---
 lib/galaxy/jobs/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index a8ffb49512f..b1bb8549eb7 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -1123,7 +1123,7 @@ class DefaultJobDispatcher( object ):
 
     def __get_runner_name( self, job_wrapper ):
         if self.app.config.use_tasked_jobs and job_wrapper.tool.parallelism is not None and not isinstance(job_wrapper, TaskWrapper):
-            runnner_name = "tasks"
+            runner_name = "tasks"
         else:
             runner_name = ( job_wrapper.get_job_runner().split(":", 1) )[0]
         return runner_name

From dc24de99a32e1eb018b6c73682901ca9a533d5c1 Mon Sep 17 00:00:00 2001
From: James Taylor <james@jamestaylor.org>
Date: Wed, 2 Nov 2011 13:29:26 -0400
Subject: [PATCH 135/362] Trackster: don't import all of numpy in data provider
 (problem with numpy's log un summary tree handling)

---
 lib/galaxy/visualization/tracks/data_providers.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/visualization/tracks/data_providers.py b/lib/galaxy/visualization/tracks/data_providers.py
index ec4a63723a6..612809e569a 100644
--- a/lib/galaxy/visualization/tracks/data_providers.py
+++ b/lib/galaxy/visualization/tracks/data_providers.py
@@ -10,7 +10,7 @@ if sys.version_info[:2] == (2, 4):
     pkg_resources.require( "ctypes" )
 pkg_resources.require( "pysam" )
 pkg_resources.require( "numpy" )
-from numpy import *
+import numpy
 from galaxy.datatypes.util.gff_util import *
 from galaxy.util.json import from_json_string
 from bx.interval_index_file import Indexes
@@ -743,7 +743,7 @@ class BBIDataProvider( TracksDataProvider ):
                 var = summary.sum_squares[0] - mean
                 if valid_count > 1:
                     var /= valid_count - 1
-                sd = sqrt( var )
+                sd = numpy.sqrt( var )
 
                 return dict( data=dict( min=summary.min_val[0], max=summary.max_val[0], mean=mean, sd=sd ) )
 

From 2ca322c0e2208a6997876fbb921e809ba730625f Mon Sep 17 00:00:00 2001
From: James Taylor <james@jamestaylor.org>
Date: Wed, 2 Nov 2011 13:37:24 -0400
Subject: [PATCH 136/362] Trackster: allow configuration elements to have help
 text

---
 static/june_2007_style/base.css.tmpl | 4 ++++
 static/june_2007_style/blue/base.css | 1 +
 static/scripts/trackster.js          | 7 ++++++-
 3 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/static/june_2007_style/base.css.tmpl b/static/june_2007_style/base.css.tmpl
index 998165bb0d7..d53be3086af 100644
--- a/static/june_2007_style/base.css.tmpl
+++ b/static/june_2007_style/base.css.tmpl
@@ -231,6 +231,10 @@ div.form-row-error-message {
     padding: 3px 0 0 1em;
 }
 
+.form-row .help {
+    color: #666;
+}
+
 select, input, textarea {
     font: inherit;
 }
diff --git a/static/june_2007_style/blue/base.css b/static/june_2007_style/blue/base.css
index a6caed06955..70bc7fede74 100644
--- a/static/june_2007_style/blue/base.css
+++ b/static/june_2007_style/blue/base.css
@@ -43,6 +43,7 @@ div.form-row label.inline{display:inline;}
 div.form-row-input{float:left;}
 div.form-row-input label{font-weight:normal;display:inline;}
 div.form-row-error-message{width:300px;float:left;color:red;font-weight:bold;padding:3px 0 0 1em;}
+.form-row .help{color:#666;}
 select,input,textarea{font:inherit;}
 select,textarea,input[type="text"],input[type="file"],input[type="password"]{-webkit-box-sizing:border-box;max-width:300px;}
 .errormessagelarge,.warningmessagelarge,.donemessagelarge,.infomessagelarge{padding:10px;padding-left:52px;min-height:32px;border:1px solid #AA6666;background-color:#FFCCCC;background-image:url(error_message_icon.png);background-repeat:no-repeat;background-position:10px 10px;}
diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index daf3b11dd92..ce186cbd681 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -2149,6 +2149,10 @@ extend(DrawableConfig.prototype, {
                 else {
                     row.append( $('<input />').attr("id", id ).attr("name", id ).val( value ) ); 
                 }
+                // Help text
+                if ( param.help ) {
+                    row.append( $("<div class='help'/>").text( param.help ) );
+                }
             }
         });
         return container;
@@ -3194,7 +3198,8 @@ var FeatureTrack = function(name, view, container, hda_ldda, dataset_id, prefs,
             { key: 'name', label: 'Name', type: 'text', default_value: name },
             { key: 'block_color', label: 'Block color', type: 'color', default_value: get_random_color() },
             { key: 'label_color', label: 'Label color', type: 'color', default_value: 'black' },
-            { key: 'show_counts', label: 'Show summary counts', type: 'bool', default_value: true },
+            { key: 'show_counts', label: 'Show summary counts', type: 'bool', default_value: true, 
+              help: 'Show the number of items in each bin when drawing summary histogram' },
             { key: 'mode', type: 'string', default_value: this.mode, hidden: true },
         ], 
         saved_values: prefs,

From 5940b1a7b6fdfe910ae1dc959ac6f711ce67e4d4 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Wed, 2 Nov 2011 13:37:33 -0400
Subject: [PATCH 137/362] Allow administrators to impersonate other users. 
 Useful for debugging, but be aware that this gives said administrator a full
 session as the user, with the ability to do anything as that user (the user
 does not gain the administrator's privileges, however).

---
 lib/galaxy/config.py                      |  1 +
 lib/galaxy/web/controllers/admin.py       | 21 +++++++++++++++++++++
 templates/webapps/galaxy/admin/index.mako |  3 +++
 universe_wsgi.ini.sample                  |  3 +++
 4 files changed, 28 insertions(+)

diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py
index a5369a3256a..f291b7c3d51 100644
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -71,6 +71,7 @@ class Configuration( object ):
         self.allow_user_creation = string_as_bool( kwargs.get( "allow_user_creation", "True" ) )
         self.allow_user_deletion = string_as_bool( kwargs.get( "allow_user_deletion", "False" ) )
         self.allow_user_dataset_purge = string_as_bool( kwargs.get( "allow_user_dataset_purge", "False" ) )
+        self.allow_user_impersonation = string_as_bool( kwargs.get( "allow_user_impersonation", "False" ) )
         self.new_user_dataset_access_role_default_private = string_as_bool( kwargs.get( "new_user_dataset_access_role_default_private", "False" ) )
         self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root )
         self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates" ), self.root )
diff --git a/lib/galaxy/web/controllers/admin.py b/lib/galaxy/web/controllers/admin.py
index 3c0335120e1..c07cf6ac4ed 100644
--- a/lib/galaxy/web/controllers/admin.py
+++ b/lib/galaxy/web/controllers/admin.py
@@ -1029,6 +1029,27 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
                                                           id=trans.security.encode_id( repository.id ),
                                                           message=message,
                                                           status=status ) )
+    @web.expose
+    @web.require_admin
+    def impersonate( self, trans, email=None, **kwd ):
+        if not trans.app.config.allow_user_impersonation:
+            return trans.show_error_message( "User impersonation is not enabled in this instance of Galaxy." )
+        message = ''
+        status = 'done'
+        emails = None
+        if email is not None:
+            user = trans.sa_session.query( trans.app.model.User ).filter_by( email=email ).first()
+            if user:
+                trans.set_user( user )
+                message = 'You are now logged in as %s, <a target="_top" href="%s">return to the home page</a>' % ( email, url_for( controller='root' ) )
+                emails = []
+            else:
+                message = 'Invalid user selected'
+                status = 'error'
+        if emails is None:
+            emails = [ u.email for u in trans.sa_session.query( trans.app.model.User ).enable_eagerloads( False ).all() ]
+        return trans.fill_template( 'admin/impersonate.mako', emails=emails, message=message, status=status )
+
     def __get_relative_install_dir( self, trans, repository ):
         # Get the directory where the repository is install.
         tool_shed = self.__clean_tool_shed_url( repository.tool_shed )
diff --git a/templates/webapps/galaxy/admin/index.mako b/templates/webapps/galaxy/admin/index.mako
index c199df5be0a..ca3e1fc9f0f 100644
--- a/templates/webapps/galaxy/admin/index.mako
+++ b/templates/webapps/galaxy/admin/index.mako
@@ -46,6 +46,9 @@
                         <div class="toolTitle"><a href="${h.url_for( controller='admin', action='users', webapp=webapp )}" target="galaxy_main">Manage users</a></div>
                         <div class="toolTitle"><a href="${h.url_for( controller='admin', action='groups', webapp=webapp )}" target="galaxy_main">Manage groups</a></div>
                         <div class="toolTitle"><a href="${h.url_for( controller='admin', action='roles', webapp=webapp )}" target="galaxy_main">Manage roles</a></div>
+                        %if trans.app.config.allow_user_impersonation:
+                            <div class="toolTitle"><a href="${h.url_for( controller='admin', action='impersonate', webapp=webapp )}" target="galaxy_main">Impersonate a user</a></div>
+                        %endif
                     </div>
                 </div>
                 <div class="toolSectionPad"></div>
diff --git a/universe_wsgi.ini.sample b/universe_wsgi.ini.sample
index 1cadd24543b..ffe82277e35 100644
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -405,6 +405,9 @@ use_interactive = True
 # Allow administrators to delete accounts.
 #allow_user_deletion = False
 
+# Allow administrators to log in as other users (useful for debugging)
+#allow_user_impersonation = False
+
 # Allow users to remove their datasets from disk immediately (otherwise,
 # datasets will be removed after a time period specified by an administrator in
 # the cleanup scripts run via cron)

From 0102b1d0d89aa9789d094baacf89f8d44e0be292 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Wed, 2 Nov 2011 16:39:08 -0400
Subject: [PATCH 138/362] The "How to Cite Galaxy" link was being read from
 screencasts_url, not citation_url.

---
 extract_dataset_parts.sh                  | 0
 templates/webapps/galaxy/base_panels.mako | 2 +-
 2 files changed, 1 insertion(+), 1 deletion(-)
 mode change 100644 => 100755 extract_dataset_parts.sh

diff --git a/extract_dataset_parts.sh b/extract_dataset_parts.sh
old mode 100644
new mode 100755
diff --git a/templates/webapps/galaxy/base_panels.mako b/templates/webapps/galaxy/base_panels.mako
index 425b60d1b5f..50ef7be93bc 100644
--- a/templates/webapps/galaxy/base_panels.mako
+++ b/templates/webapps/galaxy/base_panels.mako
@@ -114,7 +114,7 @@
                             ['Support', app.config.get( "support_url", "http://wiki.g2.bx.psu.edu/Support" ), "_blank" ],
                             ['Galaxy Wiki', app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/" ), "_blank" ],
                             ['Video tutorials (screencasts)', app.config.get( "screencasts_url", "http://galaxycast.org" ), "_blank" ],
-                            ['How to Cite Galaxy', app.config.get( "screencasts_url", "http://wiki.g2.bx.psu.edu/Citing%20Galaxy" ), "_blank" ]
+                            ['How to Cite Galaxy', app.config.get( "citation_url", "http://wiki.g2.bx.psu.edu/Citing%20Galaxy" ), "_blank" ]
                         ]
         tab( "help", "Help", None, menu_options=menu_options)
     %>

From a69f2eac7056bd93472a424bfe47623823d103a9 Mon Sep 17 00:00:00 2001
From: John Duddy <jduddy@illumina.com>
Date: Wed, 2 Nov 2011 14:15:08 -0700
Subject: [PATCH 139/362] Fix signature of slit method

---
 lib/galaxy/datatypes/data.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/datatypes/data.py b/lib/galaxy/datatypes/data.py
index 6172713a54a..56c054ee262 100644
--- a/lib/galaxy/datatypes/data.py
+++ b/lib/galaxy/datatypes/data.py
@@ -462,15 +462,16 @@ class Text( Data ):
             dataset.peek = 'file does not exist'
             dataset.blurb = 'file purged from disk'
 
-    def split( input_files, subdir_generator_function, split_params): 
+    def split( cls, input_datasets, subdir_generator_function, split_params):
         """
         Split the input files by line.
         """
         if split_params is None:
             return
             
-        if len(input_files) > 1:
+        if len(input_datasets) > 1:
             raise Exception("Text file splitting does not support multiple files")
+        input_files = [ds.file_name for ds in input_datasets]
         
         lines_per_file = None
         chunk_size = None
@@ -534,7 +535,7 @@ class Text( Data ):
                 part_file.close()
             raise
         f.close()
-    split = staticmethod(split)
+    split = classmethod(split)
 
 class LineCount( Text ):
     """

From cefa76b491ccd96e4d7c433eaddf23489c0651eb Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Wed, 2 Nov 2011 17:48:22 -0400
Subject: [PATCH 140/362] Trackster: (a) give every Drawable unique id and (b)
 remove unused reference to jquery.scrollTo.

---
 static/scripts/trackster.js   | 11 ++++-------
 templates/tracks/browser.mako |  2 +-
 2 files changed, 5 insertions(+), 8 deletions(-)

diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index ddbc4a28cf0..f31698af2ed 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -654,6 +654,8 @@ extend(ReferenceTrackDataManager.prototype, DataManager.prototype, Cache.prototy
  * associated with a view and container. They optionally have a drag handle class. 
  */
 var Drawable = function(name, view, container, prefs, drag_handle_class) {
+    if (!Drawable.id_counter) { Drawable.id_counter = 0; }
+    this.id = Drawable.id_counter++;
     this.name = name;
     this.view = view;
     this.container = container;
@@ -804,13 +806,11 @@ var DrawableGroup = function(name, view, container, prefs) {
     DrawableCollection.call(this, "DrawableGroup", name, view, container, prefs, "group-handle");
         
     // HTML elements.
-    if (!DrawableGroup.id_counter) { DrawableGroup.id_counter = 0; }
-    var group_id = DrawableGroup.id_counter++
-    this.container_div = $("<div/>").addClass("group").attr("id", "group_" + group_id).appendTo(this.container.content_div);
+    this.container_div = $("<div/>").addClass("group").attr("id", "group_" + this.id).appendTo(this.container.content_div);
     this.header_div = $("<div/>").addClass("track-header").appendTo(this.container_div);
     this.header_div.append($("<div/>").addClass(this.drag_handle_class));
     this.name_div = $("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);    
-    this.content_div = $("<div/>").addClass("content-div").attr("id", "group_" + group_id + "_content_div").appendTo(this.container_div);
+    this.content_div = $("<div/>").addClass("content-div").attr("id", "group_" + this.id + "_content_div").appendTo(this.container_div);
     
     // Set up containers/moving for group: register both container_div and content div as container
     // because both are used as containers (container div to recognize container, content_div to 
@@ -2329,9 +2329,6 @@ var Track = function(name, view, container, show_header, prefs, data_url, data_q
     this.data_url_extra_params = {}
     this.data_query_wait = (data_query_wait ? data_query_wait : DEFAULT_DATA_QUERY_WAIT);
     this.dataset_check_url = converted_datasets_state_url;
-
-    if (!Track.id_counter) { Track.id_counter = 0; }
-    this.id = Track.id_counter++;
     
     //
     // Create HTML element structure for track.
diff --git a/templates/tracks/browser.mako b/templates/tracks/browser.mako
index 1799b085f00..7c929625742 100644
--- a/templates/tracks/browser.mako
+++ b/templates/tracks/browser.mako
@@ -42,7 +42,7 @@ ${parent.javascripts()}
   <script type='text/javascript' src="${h.url_for('/static/scripts/excanvas.js')}"></script>
 <![endif]-->
 
-${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.event.drag", "jquery.mousewheel", "jquery.autocomplete", "trackster", "trackster_ui", "jquery.ui.sortable.slider", "jquery.scrollTo", "farbtastic", "jquery.tipsy" )}
+${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.event.drag", "jquery.mousewheel", "jquery.autocomplete", "trackster", "trackster_ui", "jquery.ui.sortable.slider", "farbtastic", "jquery.tipsy" )}
 
 <script type="text/javascript">
     //

From 96cfea923d9f7552d5364afabc8f017ea70d1a7e Mon Sep 17 00:00:00 2001
From: James Taylor <james@jamestaylor.org>
Date: Wed, 2 Nov 2011 17:53:00 -0400
Subject: [PATCH 141/362] Trackster: allow track contents to be hidden without
 removing track. Hidden tracks are condensed and not drawn. TODO: whether a
 track is hidden is not currently saved. No easy way to inherit prefs right
 now.

---
 static/scripts/trackster.js | 51 +++++++++++++++++++++++++++++++++++--
 1 file changed, 49 insertions(+), 2 deletions(-)

diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index ce186cbd681..98c52c4cde8 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -2335,6 +2335,8 @@ var Track = function(name, view, container, show_header, prefs, data_url, data_q
     this.data_url_extra_params = {}
     this.data_query_wait = (data_query_wait ? data_query_wait : DEFAULT_DATA_QUERY_WAIT);
     this.dataset_check_url = converted_datasets_state_url;
+    // FIXME: this should be a saved setting
+    this.content_visible = true;
 
     if (!Track.id_counter) { Track.id_counter = 0; }
     this.id = Track.id_counter++;
@@ -2353,6 +2355,9 @@ var Track = function(name, view, container, show_header, prefs, data_url, data_q
         this.icons_div = $("<div/>").css("float", "left").appendTo(this.header_div).hide();
     
         // Track icons.
+        this.toggle_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Hide/show track content")
+                                      .addClass("icon-button toggle").tipsy( {gravity: 's'} )
+                                      .appendTo(this.icons_div);
         this.settings_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Edit settings")
                                       .addClass("icon-button settings-icon").tipsy( {gravity: 's'} )
                                       .appendTo(this.icons_div);
@@ -2372,6 +2377,21 @@ var Track = function(name, view, container, show_header, prefs, data_url, data_q
             
         // Suppress double clicks in header so that they do not impact viz.
         this.header_div.dblclick( function(e) { e.stopPropagation(); } );
+
+        // Toggle icon hides or shows the track content
+        this.toggle_icon.click( function() {
+            if ( track.content_visible ) {
+                track.toggle_icon.addClass("toggle-expand").removeClass("toggle");
+                track.hide_contents();
+                track.mode_div.hide();
+                track.content_visible = false;
+            } else {
+                track.toggle_icon.addClass("toggle").removeClass("toggle-expand");
+                track.content_visible = true;
+                track.mode_div.show();
+                track.show_contents();
+            }
+        });
         
         // Clicking on settings icon opens track config.
         this.settings_icon.click( function() {
@@ -2558,6 +2578,26 @@ extend(Track.prototype, Drawable.prototype, {
         
         this.update_track_icons();
     },
+    /**
+     * Hide any elements that are part of the tracks contents area. Should
+     * remove as approprite, the track will be redrawn by show_contents.
+     */
+    hide_contents : function () {
+        // Clear contents by removing any elements that are contained in
+        // the tracks content_div
+        this.content_div.children().remove();
+        // Hide the content div
+        this.content_div.hide();
+        // And any y axis labels (common to several track types)
+        this.container_div.find(".yaxislabel, .track-resize").hide()
+    },
+    show_contents : function() {
+        // Show the contents div and labels (if present)
+        this.content_div.show();
+        this.container_div.find(".yaxislabel, .track-resize").show()
+        // Request a redraw of the content
+        this.request_draw();
+    },
     /**
      * Additional initialization required before drawing track for the first time.
      */
@@ -2689,6 +2729,11 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
      */
     _draw: function(force, clear_after) {
         if (!this.enabled) { return; }
+
+        // TODO: There should probably be a general way to disable content drawing 
+        //       for all drawables. However the button to toggle this is currently
+        //       only present for Track instances.
+        if (!this.content_visible) { return; }
         
         // HACK: ReferenceTrack can draw without dataset ID, but other tracks cannot.
         if ( !(this instanceof ReferenceTrack) && (!this.dataset_id) ) { return; }
@@ -3084,8 +3129,10 @@ extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
         var drag_control = $( "<div class='track-resize'>" )
         // Control shows on hover over track, stays while dragging
         $(track.container_div).hover( function() { 
-            in_handle = true;
-            drag_control.show(); 
+            if ( track.content_visible ) {
+                in_handle = true;
+                drag_control.show(); 
+            }
         }, function() { 
             in_handle = false;
             if ( ! in_drag ) { drag_control.hide(); }

From 93dbdc044af5bfc6c415cf308a2a3fb3ee13a3e2 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Wed, 2 Nov 2011 18:05:38 -0400
Subject: [PATCH 142/362] Trackster: fix bug in showing 'add datasets' button
 and rename update_track_icons to update_icons for clarity.

---
 static/scripts/trackster.js | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index f31698af2ed..b83a78e7024 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -679,7 +679,7 @@ extend(Drawable.prototype, {
     request_draw: function() {},
     _draw: function() {},
     to_json: function() {},
-    update_track_icons: function() {},
+    update_icons: function() {},
     /**
      * Set drawable name.
      */ 
@@ -819,14 +819,14 @@ var DrawableGroup = function(name, view, container, prefs) {
     is_container(this.content_div, this);
     moveable(this.container_div, this.drag_handle_class, ".group", this);
     
-    this.update_track_icons();
+    this.update_icons();
 };
 
 extend(DrawableGroup.prototype, Drawable.prototype, DrawableCollection.prototype, {
     /**
      * Make popup menu for group.
      */
-    update_track_icons: function() {
+    update_icons: function() {
         var group = this;
         
         var group_dropdown = {};
@@ -1073,7 +1073,7 @@ extend( View.prototype, DrawableCollection.prototype, {
     },
     /** Add or remove intro div depending on view state. */
     update_intro_div: function() {
-        if (this.num_tracks === 0) {
+        if (this.drawables.length === 0) {
             this.intro_div.appendTo(this.viewport_container);
         }
         else {
@@ -2531,7 +2531,7 @@ extend(Track.prototype, Drawable.prototype, {
             } else if (result['status'] === "data") {
                 if (result['valid_chroms']) {
                     track.valid_chroms = result['valid_chroms'];
-                    track.update_track_icons();
+                    track.update_icons();
                 }
                 track.content_div.text(DATA_OK);
                 if (track.view.chrom) {
@@ -2547,7 +2547,7 @@ extend(Track.prototype, Drawable.prototype, {
             }
         });
         
-        this.update_track_icons();
+        this.update_icons();
     },
     /**
      * Additional initialization required before drawing track for the first time.
@@ -2625,7 +2625,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
     /**
      * Update track's buttons.
      */
-    update_track_icons: function() {
+    update_icons: function() {
         var track = this;
         
         //
@@ -3287,7 +3287,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
                 if (!track.filters_available) {
                     track.filters_div.hide();
                 }
-                track.update_track_icons();
+                track.update_icons();
             }
         }
     },
@@ -3601,7 +3601,7 @@ var ReadTrack = function (name, view, container, hda_ldda, dataset_id, prefs, fi
     this.prefs = this.config.values;
     
     this.painter = painters.ReadPainter;
-    this.update_track_icons();
+    this.update_icons();
 };
 extend(ReadTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype);
 

From 5ea4590857f077c7e88d2c29135bfc828276ec90 Mon Sep 17 00:00:00 2001
From: James Taylor <james@jamestaylor.org>
Date: Wed, 2 Nov 2011 18:07:28 -0400
Subject: [PATCH 143/362] Trackster: show color pickers to left of input rather
 than underneath

---
 static/scripts/trackster.js | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index 98c52c4cde8..77c5a61d71a 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -2126,7 +2126,7 @@ extend(DrawableConfig.prototype, {
                 } else if ( param.type === 'color' ) {
                     var input = $('<input />').attr("id", id ).attr("name", id ).val( value );
                     // Color picker in tool tip style float
-                    var tip = $( "<div class='tipsy tipsy-north' style='position: absolute;' />" ).hide();
+                    var tip = $( "<div class='tipsy tipsy-west' style='position: absolute;' />" ).hide();
                     // Inner div for padding purposes
                     var tip_inner = $("<div style='background-color: black; padding: 10px;'></div>").appendTo(tip);
                     var farb_container = $("<div/>")
@@ -2136,8 +2136,10 @@ extend(DrawableConfig.prototype, {
                     // Outer div container input and tip for hover to work
                     $("<div />").append( input ).append( tip ).appendTo( row ).bind( "click", function ( e ) { 
                         tip.css( { 
-                            left: $(this).position().left + ( $(input).width() / 2 ) - 60,
-                            top: $(this).position().top + $(this.height) 
+                            // left: $(this).position().left + ( $(input).width() / 2 ) - 60,
+                            // top: $(this).position().top + $(this.height) 
+                            left: $(this).position().left + $(input).width() + 5,
+                            top: $(this).position().top - ( $(tip).height() / 2 ) + ( $(input).height() / 2 )
                             } ).show();
                         $(document).bind( "click.color-picker", function() {
                             tip.hide();

From aaaa431b2b8119021ecb7561efdd7ebab79c49f3 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Thu, 3 Nov 2011 09:47:29 -0400
Subject: [PATCH 144/362] Fix bug I introduced when I made changes to eliminate
 the User Type select field if no real options exist because there are no
 required form definitions.

---
 templates/user/register.mako            | 2 +-
 templates/webapps/galaxy/user/info.mako | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/templates/user/register.mako b/templates/user/register.mako
index ba420c9e4aa..8b49ed559ce 100644
--- a/templates/user/register.mako
+++ b/templates/user/register.mako
@@ -65,7 +65,7 @@
                     ${subscribe_check_box.get_html()}
                 </div>
             %endif
-            %if len( user_type_fd_id_select_field.options ) > 1:
+            %if user_type_fd_id_select_field and len( user_type_fd_id_select_field.options ) > 1:
                 <div class="form-row">
                     <label>User type</label>
                     ${user_type_fd_id_select_field.get_html()}
diff --git a/templates/webapps/galaxy/user/info.mako b/templates/webapps/galaxy/user/info.mako
index a78e77e2cdd..fd1a4519aba 100644
--- a/templates/webapps/galaxy/user/info.mako
+++ b/templates/webapps/galaxy/user/info.mako
@@ -13,7 +13,7 @@ ${render_user_info()}
     <div class="toolForm">
         <form name="user_info" id="user_info" action="${h.url_for( controller='user', action='edit_info', cntrller=cntrller, user_id=trans.security.encode_id( user.id ) )}" method="post" >
             <div class="toolFormTitle">User information</div>
-            %if len( user_type_fd_id_select_field.options ) > 1:
+            %if user_type_fd_id_select_field and len( user_type_fd_id_select_field.options ) > 1:
                 <div class="form-row">
                     <label>User type:</label>
                     ${user_type_fd_id_select_field.get_html()}

From 08185087a75e8159a6f6565d8e5ad0e3a8d4105c Mon Sep 17 00:00:00 2001
From: Guruprasad Anada <gua110@bx.psu.edu>
Date: Thu, 3 Nov 2011 10:49:45 -0400
Subject: [PATCH 145/362] Added 3 tools: 1) to compute weighted average values
 based on interval intersections (under Regional variation), 2) to perform
 logistic regression (under Multiple regression), 3) to compute partial
 R-squared  (under Multiple regression).

---
 tool_conf.xml.sample                          |   3 +
 tools/regVariation/WeightedAverage.py         | 103 ++++++++++
 tools/regVariation/WeightedAverage.xml        |  71 +++++++
 tools/regVariation/logistic_regression_vif.py | 185 ++++++++++++++++++
 .../regVariation/logistic_regression_vif.xml  |  74 +++++++
 tools/regVariation/partialR_square.py         | 146 ++++++++++++++
 tools/regVariation/partialR_square.xml        |  68 +++++++
 7 files changed, 650 insertions(+)
 create mode 100755 tools/regVariation/WeightedAverage.py
 create mode 100755 tools/regVariation/WeightedAverage.xml
 create mode 100755 tools/regVariation/logistic_regression_vif.py
 create mode 100755 tools/regVariation/logistic_regression_vif.xml
 create mode 100755 tools/regVariation/partialR_square.py
 create mode 100755 tools/regVariation/partialR_square.xml

diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index d309da3e364..d189a3b2319 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -175,6 +175,7 @@
   <section name="Regional Variation" id="regVar">
     <tool file="regVariation/windowSplitter.xml" />
     <tool file="regVariation/featureCounter.xml" />
+    <tool file="regVariation/WeightedAverage.xml" />
     <tool file="regVariation/quality_filter.xml" />
     <tool file="regVariation/maf_cpg_filter.xml" />
     <tool file="regVariation/getIndels_2way.xml" />
@@ -194,8 +195,10 @@
   </section>
   <section name="Multiple regression" id="multReg">
     <tool file="regVariation/linear_regression.xml" />
+    <tool file="regVariation/logistic_regression_vif.xml" />
     <tool file="regVariation/best_regression_subsets.xml" />
     <tool file="regVariation/rcve.xml" />
+    <tool file="regVariation/partialR_square.xml" />
   </section>
   <section name="Multivariate Analysis" id="multVar">
     <tool file="multivariate_stats/pca.xml" />
diff --git a/tools/regVariation/WeightedAverage.py b/tools/regVariation/WeightedAverage.py
new file mode 100755
index 00000000000..d0299dd18ed
--- /dev/null
+++ b/tools/regVariation/WeightedAverage.py
@@ -0,0 +1,103 @@
+#!/usr/bin/env python
+"""
+
+usage: %prog bed_file_1 bed_file_2 out_file
+    -1, --cols1=N,N,N,N: Columns for chr, start, end, strand in first file
+    -2, --cols2=N,N,N,N,N: Columns for chr, start, end, strand, name/value in second file
+"""
+from galaxy import eggs
+
+import collections
+import sys, string
+#import numpy
+from galaxy import eggs
+import pkg_resources
+pkg_resources.require( "bx-python" )
+import sys, traceback, fileinput
+from warnings import warn
+from galaxy.tools.util.galaxyops import *
+from bx.cookbook import doc_optparse
+
+
+#export PYTHONPATH=~/galaxy/lib/
+#running command python WeightedAverage.py interval_interpolate.bed value_interpolate.bed interpolate_result.bed
+
+def stop_err(msg):
+    sys.stderr.write(msg)
+    sys.exit()
+
+
+def FindRate(chromosome,start_stop,dictType):
+    OverlapList=[]
+    for tempO in dictType[chromosome]:
+        DatabaseInterval=[tempO[0],tempO[1]]
+        Overlap=GetOverlap(start_stop,DatabaseInterval)
+        if Overlap>0:
+            OverlapList.append([Overlap,tempO[2]])
+                                 
+    if len(OverlapList)>0:
+   
+        SumRecomb=0
+        SumOverlap=0
+        for member in OverlapList:
+            SumRecomb+=member[0]*member[1]
+            SumOverlap+=member[0]    
+        averageRate=SumRecomb/SumOverlap
+                               
+        return averageRate
+                               
+    else:
+        return 'NA'
+                                                       
+                           
+    
+def GetOverlap(a,b):
+    return min(a[1],b[1])-max(a[0],b[0])
+
+options, args = doc_optparse.parse( __doc__ )
+
+try:
+    chr_col_1, start_col_1, end_col_1, strand_col1 = parse_cols_arg( options.cols1 )
+    chr_col_2, start_col_2, end_col_2, strand_col2, name_col_2 = parse_cols_arg( options.cols2 )      
+    input1, input2, input3 = args
+except Exception, eee:
+    print eee
+    stop_err( "Data issue: click the pencil icon in the history item to correct the metadata attributes." )
+    
+
+
+fd2=open(input2)
+lines2=fd2.readlines()
+RecombChrDict=collections.defaultdict(list)
+
+skipped=0
+for line in lines2:
+    temp=line.strip().split()
+    try:
+        assert float(temp[int(name_col_2)])
+    except:
+        skipped+=1
+        continue
+    tempIndex=[int(temp[int(start_col_2)]),int(temp[int(end_col_2)]),float(temp[int(name_col_2)])]
+    RecombChrDict[temp[int(chr_col_2)]].append(tempIndex)
+
+print "Skipped %d features with invalid values" %(skipped)
+
+fd1=open(input1)
+lines=fd1.readlines()
+finalProduct=''
+for line in lines:
+    temp=line.strip().split('\t')
+    chromosome=temp[int(chr_col_1)]
+    start=int(temp[int(start_col_1)])
+    stop=int(temp[int(end_col_1)])
+    start_stop=[start,stop]
+    RecombRate=FindRate(chromosome,start_stop,RecombChrDict)
+    try:
+        RecombRate="%.4f" %(float(RecombRate))
+    except:
+        RecombRate=RecombRate
+    finalProduct+=line.strip()+'\t'+str(RecombRate)+'\n'
+fdd=open(input3,'w')
+fdd.writelines(finalProduct)
+fdd.close()
diff --git a/tools/regVariation/WeightedAverage.xml b/tools/regVariation/WeightedAverage.xml
new file mode 100755
index 00000000000..9e9406985d2
--- /dev/null
+++ b/tools/regVariation/WeightedAverage.xml
@@ -0,0 +1,71 @@
+<tool id="wtavg" name="Assign weighted-average" version="1.0.0">
+  <description> of the values of features overlapping an interval </description>
+  <command interpreter="python">WeightedAverage.py  $genomic_interval $genomic_feature $out_file1 -1 ${genomic_interval.metadata.chromCol},${genomic_interval.metadata.startCol},${genomic_interval.metadata.endCol},${genomic_interval.metadata.strandCol} -2 ${genomic_feature.metadata.chromCol},${genomic_feature.metadata.startCol},${genomic_feature.metadata.endCol},${genomic_feature.metadata.strandCol},${genomic_feature.metadata.nameCol}</command>
+
+  <inputs>
+    <param format="interval" name="genomic_interval" type="data" label="Genomic intervals (first dataset)" help="Dataset missing? See Note below."/>
+    <param format="interval" name="genomic_feature" label="Genomic features (second dataset)" type="data" help="Make sure the value column is specified. See Note below." />
+  </inputs>
+  <outputs>
+    <data format="input" name="out_file1" metadata_source="genomic_interval" />
+  </outputs>
+  <tests>
+    <!-- Test data with valid values -->
+    <test>
+      <param name="genomic_interval" value="interval_interpolate.bed"/>
+      <param name="genomic_feature" value="value_interpolate.bed"/>
+      <output name="out_file1" file="interpolate_result.bed"/>
+    </test>
+    
+  </tests>
+  <help>
+
+
+.. class:: infomark
+
+**What it does**
+
+For each interval in your first dataset, this tool calculates the weighted average value of the overlapping features in your second dataset.
+
+- When a genomic interval partially or totally overlaps a single genomic feature, the value of that genomic feature is assigned to the genomic interval.
+- When a genomic interval partially or totally overlaps with more than one genomic features, the average of the values of the overlapping genomic features weighted by the corresponding number of overlapping bases is assigned to the genomic interval.
+- When a genomic interval does not overlap with any genomic feature, 'NA' will be assigned as it's value.
+
+-----
+
+.. class:: warningmark
+
+**Note**
+
+The input datasets should be in **bed** or **interval** format. Please use "edit attributes"/pencil icon to specify the column containing the values for the features in the second dataset as **name/identifier** column.
+
+The output will contain all the columns in the first input plus a new column containing the assigned value for each interval.
+
+-----
+
+**Example**
+
+- Suppose our first dataset contains the following **genomic intervals**::
+    
+    chr  start stop
+    chr1 1000  2000
+    chr1 3000  5000
+    chr1 8000  9000
+  
+- and our second dataset contains the following **genomic features** each having an associated value (in fourth column) ::
+
+    chr  start stop name
+    chr1 900   1200 0.5
+    chr1 2900  3100 0.2
+    chr1 4800  5100 0.8
+  
+- For each **genomic interval** in our first dataset, this tool calculates the weighted average value of the overlapping **genomic features** in our second dataset ::
+
+    chr1 1000  2000 0.5
+    chr1 3000  5000 0.6
+    chr1 8000  9000 NA
+  
+
+
+</help>
+</tool>
\ No newline at end of file
diff --git a/tools/regVariation/logistic_regression_vif.py b/tools/regVariation/logistic_regression_vif.py
new file mode 100755
index 00000000000..b4198c6588f
--- /dev/null
+++ b/tools/regVariation/logistic_regression_vif.py
@@ -0,0 +1,185 @@
+#!/usr/bin/env python
+
+from galaxy import eggs
+import sys, string
+from rpy import *
+import numpy
+
+#export PYTHONPATH=~/galaxy/lib/
+
+def stop_err(msg):
+    sys.stderr.write(msg)
+    sys.exit()
+#infile = 'logreg_inp.tab'
+#y_col=3
+#x_cols=[1,2,3]
+#outfile='logreg_out.txt'
+#python logistic_regression_vif.py logreg_inp.tab 4 1,2,3 logreg_out2.tabular   # running test
+infile = sys.argv[1]
+y_col = int(sys.argv[2])-1
+x_cols = sys.argv[3].split(',')
+outfile = sys.argv[4]
+
+
+print "Predictor columns: %s; Response column: %d" %(x_cols,y_col+1)
+fout = open(outfile,'w')
+elems = []
+for i, line in enumerate( file ( infile )):
+    line = line.rstrip('\r\n')
+    if len( line )>0 and not line.startswith( '#' ):
+        elems = line.split( '\t' )
+        break 
+    if i == 30:
+        break # Hopefully we'll never get here...
+
+if len( elems )<1:
+    stop_err( "The data in your input dataset is either missing or not formatted properly." )
+
+y_vals = []
+x_vals = []
+
+for k,col in enumerate(x_cols):
+    x_cols[k] = int(col)-1
+    x_vals.append([])
+
+NA = 'NA'
+for ind,line in enumerate( file( infile )):
+    if line and not line.startswith( '#' ):
+        try:
+            fields = line.split("\t")
+            try:
+                yval = float(fields[y_col])
+            except:
+                yval = r('NA')
+            y_vals.append(yval)
+            for k,col in enumerate(x_cols):
+                try:
+                    xval = float(fields[col])
+                except:
+                    xval = r('NA')
+                x_vals[k].append(xval)
+        except:
+            pass
+
+x_vals1 = numpy.asarray(x_vals).transpose()
+
+check1=0
+check0=0
+for i in y_vals:
+    if i == 1:
+        check1=1
+    if i == 0:
+        check0=1
+if check1==0 or check0==0:
+    sys.exit("Warning: logistic regression must have at least two classes")
+
+for i in y_vals:
+    if i not in [1,0,r('NA')]:
+        print >>fout, str(i)
+        sys.exit("Warning: the current version of this tool can run only with two classes and need to be labeled as 0 and 1.")
+    
+    
+dat= r.list(x=array(x_vals1), y=y_vals)
+novif=0
+set_default_mode(NO_CONVERSION)
+try:
+    linear_model = r.glm(r("y ~ x"), data = r.na_exclude(dat),family="binomial")
+    #r('library(car)')
+    #r.assign('dat',dat)
+    #r.assign('ncols',len(x_cols))
+    #r.vif(r('glm(dat$y ~ ., data = na.exclude(data.frame(as.matrix(dat$x,ncol=ncols))->datx),family="binomial")')).as_py()
+    
+except RException, rex:
+    stop_err("Error performing logistic regression on the input data.\nEither the response column or one of the predictor columns contain only non-numeric or invalid values.")
+if len(x_cols)>1:
+    try:
+    
+        r('library(car)')
+        r.assign('dat',dat)
+        r.assign('ncols',len(x_cols))
+        vif=r.vif(r('glm(dat$y ~ ., data = na.exclude(data.frame(as.matrix(dat$x,ncol=ncols))->datx),family="binomial")'))
+    except RException, rex:
+        print rex
+else:
+    novif=1
+    
+set_default_mode(BASIC_CONVERSION)
+
+coeffs=linear_model.as_py()['coefficients']
+null_deviance=linear_model.as_py()['null.deviance']
+residual_deviance=linear_model.as_py()['deviance']
+yintercept= coeffs['(Intercept)']
+summary = r.summary(linear_model)
+co = summary.get('coefficients', 'NA')
+"""
+if len(co) != len(x_vals)+1:
+    stop_err("Stopped performing logistic regression on the input data, since one of the predictor columns contains only non-numeric or invalid values.")
+"""
+
+try:
+    yintercept = r.round(float(yintercept), digits=10)
+    pvaly = r.round(float(co[0][3]), digits=10)
+except:
+    pass
+print >>fout, "response column\tc%d" %(y_col+1)
+tempP=[]
+for i in x_cols:
+    tempP.append('c'+str(i+1))
+tempP=','.join(tempP)
+print >>fout, "predictor column(s)\t%s" %(tempP)
+print >>fout, "Y-intercept\t%s" %(yintercept)
+print >>fout, "p-value (Y-intercept)\t%s" %(pvaly)
+
+if len(x_vals) == 1:    #Simple linear  regression case with 1 predictor variable
+    try:
+        slope = r.round(float(coeffs['x']), digits=10)
+    except:
+        slope = 'NA'
+    try:
+        pval = r.round(float(co[1][3]), digits=10)
+    except:
+        pval = 'NA'
+    print >>fout, "Slope (c%d)\t%s" %(x_cols[0]+1,slope)
+    print >>fout, "p-value (c%d)\t%s" %(x_cols[0]+1,pval)
+else:    #Multiple regression case with >1 predictors
+    ind=1
+    while ind < len(coeffs.keys()):
+        try:
+            slope = r.round(float(coeffs['x'+str(ind)]), digits=10)
+        except:
+            slope = 'NA'
+        print >>fout, "Slope (c%d)\t%s" %(x_cols[ind-1]+1,slope)
+        try:
+            pval = r.round(float(co[ind][3]), digits=10)
+        except:
+            pval = 'NA'
+        print >>fout, "p-value (c%d)\t%s" %(x_cols[ind-1]+1,pval)
+        ind+=1
+
+rsq = summary.get('r.squared','NA')
+
+
+try:
+    rsq= r.round(float((null_deviance-residual_deviance)/null_deviance), digits=5)
+    null_deviance= r.round(float(null_deviance), digits=5)
+    residual_deviance= r.round(float(residual_deviance), digits=5)
+
+    #rsq = r.round(float(rsq), digits=5)
+
+except:
+    pass
+
+print >>fout, "Null deviance\t%s" %(null_deviance)
+print >>fout, "Residual deviance\t%s" %(residual_deviance)
+print >>fout, "pseudo R-squared\t%s" %(rsq)
+print >>fout, "\n"
+print >>fout, 'vif'
+
+if novif==0:
+    py_vif=vif.as_py()
+    count=0
+    for i in sorted(py_vif.keys()):
+        print >>fout,'c'+str(x_cols[count]+1) ,str(py_vif[i])
+        count+=1
+elif novif==1:
+    print >>fout, "vif can calculate only when model have more than 1 predictor"
diff --git a/tools/regVariation/logistic_regression_vif.xml b/tools/regVariation/logistic_regression_vif.xml
new file mode 100755
index 00000000000..2b491bd1aac
--- /dev/null
+++ b/tools/regVariation/logistic_regression_vif.xml
@@ -0,0 +1,74 @@
+<tool id="LogisticRegression" name="Perform Logistic Regression with vif" version="1.0.1">
+  <description> </description>
+  <command interpreter="python">
+    logistic_regression_vif.py 
+      $input1
+      $response_col
+      $predictor_cols
+      $out_file1
+      1>/dev/null
+  </command>
+  <inputs>
+    <param format="tabular" name="input1" type="data" label="Select data" help="Dataset missing? See TIP below."/>
+    <param name="response_col" label="Response column (Y)" type="data_column" data_ref="input1" numerical="True"/>
+    <param name="predictor_cols" label="Predictor columns (X)" type="data_column" data_ref="input1" numerical="True" multiple="true" >
+        <validator type="no_options" message="Please select at least one column."/>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="input" name="out_file1" metadata_source="input1" />
+
+  </outputs>
+  <requirements>
+    <requirement type="python-module">rpy</requirement>
+  </requirements>
+  <tests>
+    <test>
+        <param name="input1" value="logreg_inp.tabular"/>
+        <param name="response_col" value="4"/>
+        <param name="predictor_cols" value="1,2,3"/>
+        <output name="out_file1" file="logreg_out2.tabular"/>
+
+    </test>
+  </tests>
+  <help>
+
+
+.. class:: infomark
+
+**TIP:** If your data is not TAB delimited, use *Edit Datasets-&gt;Convert characters*
+
+-----
+
+.. class:: infomark
+
+**What it does**
+
+This tool uses the **'glm'** function from R statistical package to perform logistic regression on the input data. It outputs one file containing the summary statistics of the performed regression. Also, it calculates VIF(Variance Inflation Factor) with **'vif'** function from library (car) in R.
+
+
+*R Development Core Team (2010). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org.*
+
+-----
+
+.. class:: warningmark
+
+**Note**
+
+- This tool currently treats all predictor variables as continuous numeric variables and response variable as categorical variable. Currently, the response variable can have only two classes, namely 0 and 1. The program will take 0 as base class.
+
+- Rows containing non-numeric (or missing) data in any of the chosen columns will be skipped from the analysis.
+
+- The summary statistics in the output are described below:
+
+- Pseudo R-squared: the proportion of model improvement from null model
+- p-value: p-value for the z-test of the null hypothesis that the corresponding slope is equal to zero against the two-sided alternative.
+- Coefficient indicates log ratio of (probability to be class 1 / probability to be class 0)
+
+- This tool also provides **Variance Inflation Factor or VIF** which quantifies the level of multicollinearity. The tool will automatic generate VIF if the model has more than one predictor. The higher the VIF, the higher is the multicollinearity. Multicollinearity will inflate  standard error and reduce level of significance of the predictor. In the worst case, it can reverse direction of slope for highly correlated predictors if one of them is significant. A general thumb-rule is to use those predictors having VIF lower than 10 or 5.
+- **vif** is calculated by 
+    - First, regressing each predictor over all other predictors, and recording R-squared for each regression.
+    - Second, computing vif as 1/(1- R_squared)
+
+  </help>
+</tool>
diff --git a/tools/regVariation/partialR_square.py b/tools/regVariation/partialR_square.py
new file mode 100755
index 00000000000..326a7bef41a
--- /dev/null
+++ b/tools/regVariation/partialR_square.py
@@ -0,0 +1,146 @@
+#!/usr/bin/env python
+
+from galaxy import eggs
+
+import sys, string
+from rpy import *
+import numpy
+
+#export PYTHONPATH=~/galaxy/lib/
+#running command python partialR_square.py reg_inp.tab 4 1,2,3 partialR_result.tabular
+
+def stop_err(msg):
+    sys.stderr.write(msg)
+    sys.exit()
+
+def sscombs(s):
+    if len(s) == 1:
+        return [s]
+    else:
+        ssc = sscombs(s[1:])
+        return [s[0]] + [s[0]+comb for comb in ssc] + ssc
+
+
+infile = sys.argv[1]
+y_col = int(sys.argv[2])-1
+x_cols = sys.argv[3].split(',')
+outfile = sys.argv[4]
+
+print "Predictor columns: %s; Response column: %d" %(x_cols,y_col+1)
+fout = open(outfile,'w')
+
+for i, line in enumerate( file ( infile )):
+    line = line.rstrip('\r\n')
+    if len( line )>0 and not line.startswith( '#' ):
+        elems = line.split( '\t' )
+        break 
+    if i == 30:
+        break # Hopefully we'll never get here...
+
+if len( elems )<1:
+    stop_err( "The data in your input dataset is either missing or not formatted properly." )
+
+y_vals = []
+x_vals = []
+
+for k,col in enumerate(x_cols):
+    x_cols[k] = int(col)-1
+    x_vals.append([])
+    """
+    try:
+        float( elems[x_cols[k]] )
+    except:
+        try:
+            msg = "This operation cannot be performed on non-numeric column %d containing value '%s'." %( col, elems[x_cols[k]] )
+        except:
+            msg = "This operation cannot be performed on non-numeric data."
+        stop_err( msg )
+    """
+NA = 'NA'
+for ind,line in enumerate( file( infile )):
+    if line and not line.startswith( '#' ):
+        try:
+            fields = line.split("\t")
+            try:
+                yval = float(fields[y_col])
+            except Exception, ey:
+                yval = r('NA')
+                #print >>sys.stderr, "ey = %s" %ey
+            y_vals.append(yval)
+            for k,col in enumerate(x_cols):
+                try:
+                    xval = float(fields[col])
+                except Exception, ex:
+                    xval = r('NA')
+                    #print >>sys.stderr, "ex = %s" %ex
+                x_vals[k].append(xval)
+        except:
+            pass
+
+x_vals1 = numpy.asarray(x_vals).transpose()
+dat= r.list(x=array(x_vals1), y=y_vals)
+
+set_default_mode(NO_CONVERSION)
+try:
+    full = r.lm(r("y ~ x"), data= r.na_exclude(dat))    #full model includes all the predictor variables specified by the user
+except RException, rex:
+    stop_err("Error performing linear regression on the input data.\nEither the response column or one of the predictor columns contain no numeric values.")
+set_default_mode(BASIC_CONVERSION)
+
+summary = r.summary(full)
+fullr2 = summary.get('r.squared','NA')
+
+if fullr2 == 'NA':
+    stop_error("Error in linear regression")
+
+if len(x_vals) < 10:
+    s = ""
+    for ch in range(len(x_vals)):
+        s += str(ch)
+else:
+    stop_err("This tool only works with less than 10 predictors.")
+
+print >>fout, "#Model\tR-sq\tpartial_R_Terms\tpartial_R_Value"
+all_combos = sorted(sscombs(s), key=len)
+all_combos.reverse()
+for j,cols in enumerate(all_combos):
+    #if len(cols) == len(s):    #Same as the full model above
+    #    continue
+    if len(cols) == 1:
+        x_vals1 = x_vals[int(cols)]
+    else:
+        x_v = []
+        for col in cols:
+            x_v.append(x_vals[int(col)])
+        x_vals1 = numpy.asarray(x_v).transpose()
+    dat= r.list(x=array(x_vals1), y=y_vals)
+    set_default_mode(NO_CONVERSION)
+    red = r.lm(r("y ~ x"), data= dat)    #Reduced model
+    set_default_mode(BASIC_CONVERSION)
+    summary = r.summary(red)
+    redr2 = summary.get('r.squared','NA')
+    try:
+        partial_R = (float(fullr2)-float(redr2))/(1-float(redr2))
+    except:
+        partial_R = 'NA'
+    col_str = ""
+    for col in cols:
+        col_str = col_str + str(int(x_cols[int(col)]) + 1) + " "
+    col_str.strip()
+    partial_R_col_str = ""
+    for col in s:
+        if col not in cols:
+            partial_R_col_str = partial_R_col_str + str(int(x_cols[int(col)]) + 1) + " "
+    partial_R_col_str.strip()
+    if len(cols) == len(s):    #full model
+        partial_R_col_str = "-"
+        partial_R = "-"
+    try:
+        redr2 = "%.4f" %(float(redr2))
+    except:
+        pass
+    try:
+        partial_R = "%.4f" %(float(partial_R))
+    except:
+        pass
+    print >>fout, "%s\t%s\t%s\t%s" %(col_str,redr2,partial_R_col_str,partial_R)
diff --git a/tools/regVariation/partialR_square.xml b/tools/regVariation/partialR_square.xml
new file mode 100755
index 00000000000..4068a07a374
--- /dev/null
+++ b/tools/regVariation/partialR_square.xml
@@ -0,0 +1,68 @@
+<tool id="partialRsq" name="Compute partial R square" version="1.0.0">
+  <description> </description>
+  <command interpreter="python">
+    partialR_square.py 
+      $input1
+      $response_col
+      $predictor_cols
+      $out_file1
+      1>/dev/null
+  </command>
+  <inputs>
+    <param format="tabular" name="input1" type="data" label="Select data" help="Dataset missing? See TIP below."/>
+    <param name="response_col" label="Response column (Y)" type="data_column" data_ref="input1" />
+    <param name="predictor_cols" label="Predictor columns (X)" type="data_column" data_ref="input1" multiple="true">
+        <validator type="no_options" message="Please select at least one column."/>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="input" name="out_file1" metadata_source="input1" />
+  </outputs>
+  <requirements>
+    <requirement type="python-module">rpy</requirement>
+  </requirements>
+  <tests>
+    <!-- Test data with vlid values -->
+  	<test>
+      <param name="input1" value="regr_inp.tabular"/>
+      <param name="response_col" value="3"/>
+      <param name="predictor_cols" value="1,2"/>
+      <output name="out_file1" file="partialR_result.tabular"/>
+    </test>
+    
+  </tests>
+  <help>
+
+.. class:: infomark
+
+**TIP:** If your data is not TAB delimited, use *Edit Datasets-&gt;Convert characters*
+
+-----
+
+.. class:: infomark
+
+**What it does**
+
+This tool computes the Partial R squared for all possible variable subsets using the following formula:
+
+**Partial R squared = [SSE(without i: 1,2,...,p-1) - SSE (full: 1,2,..,i..,p-1) / SSE(without i: 1,2,...,p-1)]**, which denotes the case where the 'i'th predictor is dropped. 
+
+
+
+In general, **Partial R squared = [SSE(without i: 1,2,...,p-1) - SSE (full: 1,2,..,i..,p-1) / SSE(without i: 1,2,...,p-1)]**, where,
+
+- SSE (full: 1,2,..,i..,p-1) = Sum of Squares left out by the full set of predictors SSE(X1, X2 … Xp)
+- SSE (full: 1,2,..,i..,p-1) = Sum of Squares left out by the set of predictors excluding; for example, if we omit the first predictor, it will be SSE(X2 … Xp).
+
+
+The 4 columns in the output are described below:
+
+- Column 1 (Model): denotes the variables present in the model
+- Column 2 (R-sq): denotes the R-squared value corresponding to the model in Column 1
+- Column 3 (Partial R squared_Terms): denotes the variable/s for which Partial R squared is computed. These are the variables that are absent in the reduced model in Column 1. A '-' in this column indicates that the model in Column 1 is the Full model.
+- Column 4 (Partial R squared): denotes the Partial R squared value corresponding to the variable/s in Column 3. A '-' in this column indicates that the model in Column 1 is the Full model.
+
+*R Development Core Team (2010). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org.*  
+  
+  </help>
+</tool>

From 454a062eecbd6e3f5f860ef47eabcbbce3037829 Mon Sep 17 00:00:00 2001
From: Jim Johnson <jj@umn.edu>
Date: Thu, 3 Nov 2011 10:30:36 -0500
Subject: [PATCH 146/362] Tophat - update tool wrappers for Tophat version
 1.3.1+

---
 tools/ngs_rna/tophat_color_wrapper.xml | 12 ++++++++++--
 tools/ngs_rna/tophat_wrapper.py        | 20 ++++++++++++++------
 tools/ngs_rna/tophat_wrapper.xml       | 12 ++++++++++--
 3 files changed, 34 insertions(+), 10 deletions(-)

diff --git a/tools/ngs_rna/tophat_color_wrapper.xml b/tools/ngs_rna/tophat_color_wrapper.xml
index 762e267730d..00a3f25defc 100644
--- a/tools/ngs_rna/tophat_color_wrapper.xml
+++ b/tools/ngs_rna/tophat_color_wrapper.xml
@@ -40,15 +40,18 @@
                     -g $singlePaired.sParams.max_multihits
                     --min-segment-intron $singlePaired.sParams.min_segment_intron
                     --max-segment-intron $singlePaired.sParams.max_segment_intron
+                    --initial-read-mismatches=$singlePaired.sParams.initial_read_mismatches
                     --seg-mismatches=$singlePaired.sParams.seg_mismatches
                     --seg-length=$singlePaired.sParams.seg_length
                     --library-type=$singlePaired.sParams.library_type
                     
                     ## Indel search.
                     #if $singlePaired.sParams.indel_search.allow_indel_search == "Yes":
-                        --allow-indels
+                        ## --allow-indels
                         --max-insertion-length $singlePaired.sParams.indel_search.max_insertion_length
                         --max-deletion-length $singlePaired.sParams.indel_search.max_deletion_length
+                    #else:
+                        --no-novel-indels
                     #end if
 
                     ## Supplying junctions parameters.
@@ -99,15 +102,18 @@
                     -g $singlePaired.pParams.max_multihits
                     --min-segment-intron $singlePaired.pParams.min_segment_intron
                     --max-segment-intron $singlePaired.pParams.max_segment_intron
+                    --initial-read-mismatches=$singlePaired.pParams.initial_read_mismatches
                     --seg-mismatches=$singlePaired.pParams.seg_mismatches
                     --seg-length=$singlePaired.pParams.seg_length
                     --library-type=$singlePaired.pParams.library_type
                     
                     ## Indel search.
                     #if $singlePaired.pParams.indel_search.allow_indel_search == "Yes":
-                        --allow-indels
+                        ## --allow-indels
                         --max-insertion-length $singlePaired.pParams.indel_search.max_insertion_length
                         --max-deletion-length $singlePaired.pParams.indel_search.max_deletion_length
+                    #else:
+                        --no-novel-indels
                     #end if
 
                     ## Supplying junctions parameters.
@@ -203,6 +209,7 @@
                   <param name="max_multihits" type="integer" value="40" label="Maximum number of alignments to be allowed" />
                   <param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" />
                   <param name="max_segment_intron" type="integer" value="500000" label="Maximum intron length that may be found during split-segment (default) search" />
+                  <param name="initial_read_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in the initial read mapping" />
                   <param name="seg_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in each segment alignment for reads mapped independently" />
                   <param name="seg_length" type="integer" value="25" label="Minimum length of read segments" />
                   
@@ -309,6 +316,7 @@
                   <param name="max_multihits" type="integer" value="40" label="Maximum number of alignments to be allowed" />
                   <param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" />
                   <param name="max_segment_intron" type="integer" value="500000" label="Maximum intron length that may be found during split-segment (default) search" />
+                  <param name="initial_read_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in the initial read mapping" />
                   <param name="seg_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in each segment alignment for reads mapped independently" />
                   <param name="seg_length" type="integer" value="25" label="Minimum length of read segments" />
                   <!-- Options for supplying own junctions. -->
diff --git a/tools/ngs_rna/tophat_wrapper.py b/tools/ngs_rna/tophat_wrapper.py
index 1ce05ac65f9..13682cedec5 100644
--- a/tools/ngs_rna/tophat_wrapper.py
+++ b/tools/ngs_rna/tophat_wrapper.py
@@ -29,10 +29,11 @@ def __main__():
                         help='The maximum intron length. When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read.' )
     parser.add_option( '-F', '--junction_filter', dest='junction_filter', help='Filter out junctions supported by too few alignments (number of reads divided by average depth of coverage)' )
     parser.add_option( '-g', '--max_multihits', dest='max_multihits', help='Maximum number of alignments to be allowed' )
+    parser.add_option( '', '--initial-read-mismatches', dest='initial_read_mismatches', help='Number of mismatches allowed in the initial read mapping' )
     parser.add_option( '', '--seg-mismatches', dest='seg_mismatches', help='Number of mismatches allowed in each segment alignment for reads mapped independently' )
     parser.add_option( '', '--seg-length', dest='seg_length', help='Minimum length of read segments' )
     parser.add_option( '', '--library-type', dest='library_type', help='TopHat will treat the reads as strand specific. Every read alignment will have an XS attribute tag. Consider supplying library type options below to select the correct RNA-seq protocol.' )
-    parser.add_option( '', '--allow-indels', action="store_true", help='Allow indel search. Indel search is disabled by default.' )
+    parser.add_option( '', '--allow-indels', action="store_true", help='Allow indel search. Indel search is disabled by default.(Not used since version 1.3.0)' )
     parser.add_option( '', '--max-insertion-length', dest='max_insertion_length', help='The maximum insertion length. The default is 3.' )
     parser.add_option( '', '--max-deletion-length', dest='max_deletion_length', help='The maximum deletion length. The default is 3.' )
 
@@ -50,6 +51,7 @@ def __main__():
                                                                     sequence, inclusive.')
     parser.add_option( '', '--no-novel-juncs', action="store_true", dest='no_novel_juncs', help="Only look for junctions indicated in the \
                                                                                             supplied GFF file. (ignored without -G)")
+    parser.add_option( '', '--no-novel-indels', action="store_true", dest='no_novel_indels', help="Skip indel search. Indel search is enabled by default.")
     # Types of search.
     parser.add_option( '', '--microexon-search', action="store_true", dest='microexon_search', help='With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer.')
     parser.add_option( '', '--closure-search', action="store_true", dest='closure_search', help='Enables the mate pair closure-based search for junctions. Closure-based search should only be used when the expected inner distance between mates is small (<= 50bp)')
@@ -160,12 +162,16 @@ def __main__():
                 opts += ' --no-novel-juncs'
             if options.library_type:
                 opts += ' --library-type %s' % options.library_type
-            if options.allow_indels:
-                # Max options do not work for Tophat v1.2.0, despite documentation to the contrary.
-                opts += ' --allow-indels'
-                #opts += ' --max-insertion-length %i --max-deletion-length %i' % ( int( options.max_insertion_length ), int( options.max_deletion_length ) )
+            if options.no_novel_indels:
+                opts += ' --no-novel-indels'
+            else:
+                if options.max_insertion_length:
+                    opts += ' --max-insertion-length %i' % int( options.max_insertion_length )
+                if options..max_deletion_length:
+                    opts += ' --max-deletion-length %i' % int( options.max_deletion_length )
+                # Max options do not work for Tophat v1.2.0, despite documentation to the contrary. (Fixed in version 1.3.1)
                 # need to warn user of this fact
-                sys.stdout.write( "Max insertion length and max deletion length options don't work in Tophat v1.2.0\n" )
+                #sys.stdout.write( "Max insertion length and max deletion length options don't work in Tophat v1.2.0\n" )
 
             # Search type options.
             if options.coverage_search:
@@ -180,6 +186,8 @@ def __main__():
                 opts += ' --microexon-search'
             if options.single_paired == 'paired':
                 opts += ' --mate-std-dev %s' % options.mate_std_dev
+            if options.initial_read_mismatches:
+                opts += ' --initial-read-mismatches %d' % int( options.initial_read_mismatches )
             if options.seg_mismatches:
                 opts += ' --segment-mismatches %d' % int( options.seg_mismatches )
             if options.seg_length:
diff --git a/tools/ngs_rna/tophat_wrapper.xml b/tools/ngs_rna/tophat_wrapper.xml
index 3b30afdbc43..690b07ffaa3 100644
--- a/tools/ngs_rna/tophat_wrapper.xml
+++ b/tools/ngs_rna/tophat_wrapper.xml
@@ -38,15 +38,18 @@
                     -g $singlePaired.sParams.max_multihits
                     --min-segment-intron $singlePaired.sParams.min_segment_intron
                     --max-segment-intron $singlePaired.sParams.max_segment_intron
+                    --initial-read-mismatches=$singlePaired.sParams.initial_read_mismatches
                     --seg-mismatches=$singlePaired.sParams.seg_mismatches
                     --seg-length=$singlePaired.sParams.seg_length
                     --library-type=$singlePaired.sParams.library_type
                     
                     ## Indel search.
                     #if $singlePaired.sParams.indel_search.allow_indel_search == "Yes":
-                        --allow-indels
+                        ## --allow-indels
                         --max-insertion-length $singlePaired.sParams.indel_search.max_insertion_length
                         --max-deletion-length $singlePaired.sParams.indel_search.max_deletion_length
+                    #else:
+                        --no-novel-indels
                     #end if
 
                     ## Supplying junctions parameters.
@@ -97,15 +100,18 @@
                     -g $singlePaired.pParams.max_multihits
                     --min-segment-intron $singlePaired.pParams.min_segment_intron
                     --max-segment-intron $singlePaired.pParams.max_segment_intron
+                    --initial-read-mismatches=$singlePaired.pParams.initial_read_mismatches
                     --seg-mismatches=$singlePaired.pParams.seg_mismatches
                     --seg-length=$singlePaired.pParams.seg_length
                     --library-type=$singlePaired.pParams.library_type
                     
                     ## Indel search.
                     #if $singlePaired.pParams.indel_search.allow_indel_search == "Yes":
-                        --allow-indels
+                        ## --allow-indels
                         --max-insertion-length $singlePaired.pParams.indel_search.max_insertion_length
                         --max-deletion-length $singlePaired.pParams.indel_search.max_deletion_length
+                    #else:
+                        --no-novel-indels
                     #end if
 
                     ## Supplying junctions parameters.
@@ -201,6 +207,7 @@
                   <param name="max_multihits" type="integer" value="40" label="Maximum number of alignments to be allowed" />
                   <param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" />
                   <param name="max_segment_intron" type="integer" value="500000" label="Maximum intron length that may be found during split-segment (default) search" />
+                  <param name="initial_read_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in the initial read mapping" />
                   <param name="seg_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in each segment alignment for reads mapped independently" />
                   <param name="seg_length" type="integer" value="25" label="Minimum length of read segments" />
                   
@@ -307,6 +314,7 @@
                   <param name="max_multihits" type="integer" value="40" label="Maximum number of alignments to be allowed" />
                   <param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" />
                   <param name="max_segment_intron" type="integer" value="500000" label="Maximum intron length that may be found during split-segment (default) search" />
+                  <param name="initial_read_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in the initial read mapping" />
                   <param name="seg_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in each segment alignment for reads mapped independently" />
                   <param name="seg_length" type="integer" value="25" label="Minimum length of read segments" />
                   <!-- Options for supplying own junctions. -->

From 65101a5f2ff0594130f2b9d7f2d451900393fac1 Mon Sep 17 00:00:00 2001
From: Jim Johnson <jj@umn.edu>
Date: Thu, 3 Nov 2011 10:40:49 -0500
Subject: [PATCH 147/362] Tophat - Indel search should be default option

---
 tools/ngs_rna/tophat_color_wrapper.xml | 4 ++--
 tools/ngs_rna/tophat_wrapper.xml       | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/tools/ngs_rna/tophat_color_wrapper.xml b/tools/ngs_rna/tophat_color_wrapper.xml
index 00a3f25defc..f162ec959bb 100644
--- a/tools/ngs_rna/tophat_color_wrapper.xml
+++ b/tools/ngs_rna/tophat_color_wrapper.xml
@@ -196,8 +196,8 @@
                   <param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." />
                   <conditional name="indel_search">
                       <param name="allow_indel_search" type="select" label="Allow indel search">
-                          <option value="No">No</option>
                           <option value="Yes">Yes</option>
+                          <option value="No">No</option>
                       </param>
                       <when value="No"/>
                       <when value="Yes">
@@ -303,8 +303,8 @@
                   <param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." />
                   <conditional name="indel_search">
                       <param name="allow_indel_search" type="select" label="Allow indel search">
-                          <option value="No">No</option>
                           <option value="Yes">Yes</option>
+                          <option value="No">No</option>
                       </param>
                       <when value="No"/>
                       <when value="Yes">
diff --git a/tools/ngs_rna/tophat_wrapper.xml b/tools/ngs_rna/tophat_wrapper.xml
index 690b07ffaa3..5f7ec9b56c4 100644
--- a/tools/ngs_rna/tophat_wrapper.xml
+++ b/tools/ngs_rna/tophat_wrapper.xml
@@ -194,8 +194,8 @@
                   <param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." />
                   <conditional name="indel_search">
                       <param name="allow_indel_search" type="select" label="Allow indel search">
-                          <option value="No">No</option>
                           <option value="Yes">Yes</option>
+                          <option value="No">No</option>
                       </param>
                       <when value="No"/>
                       <when value="Yes">
@@ -301,8 +301,8 @@
                   <param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." />
                   <conditional name="indel_search">
                       <param name="allow_indel_search" type="select" label="Allow indel search">
-                          <option value="No">No</option>
                           <option value="Yes">Yes</option>
+                          <option value="No">No</option>
                       </param>
                       <when value="No"/>
                       <when value="Yes">

From 9b8f11585702c7d3ac951cbe3a446fb531f42bfb Mon Sep 17 00:00:00 2001
From: Jim Johnson <jj@umn.edu>
Date: Thu, 3 Nov 2011 11:09:35 -0500
Subject: [PATCH 148/362] Tophat - fix typo in code.

---
 tools/ngs_rna/tophat_wrapper.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/ngs_rna/tophat_wrapper.py b/tools/ngs_rna/tophat_wrapper.py
index 13682cedec5..603ca561112 100644
--- a/tools/ngs_rna/tophat_wrapper.py
+++ b/tools/ngs_rna/tophat_wrapper.py
@@ -167,7 +167,7 @@ def __main__():
             else:
                 if options.max_insertion_length:
                     opts += ' --max-insertion-length %i' % int( options.max_insertion_length )
-                if options..max_deletion_length:
+                if options.max_deletion_length:
                     opts += ' --max-deletion-length %i' % int( options.max_deletion_length )
                 # Max options do not work for Tophat v1.2.0, despite documentation to the contrary. (Fixed in version 1.3.1)
                 # need to warn user of this fact

From d7652ea0627456de64a1b872a16e8739f2cb26fe Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Thu, 3 Nov 2011 16:23:59 -0400
Subject: [PATCH 149/362] Temporary work-arounds for dealing with Galaxy panels
 when switching from workflow UI and Galaxy UI.

---
 lib/galaxy/web/controllers/admin.py    |  2 +-
 lib/galaxy/web/controllers/workflow.py | 31 +++++++++++++++++---------
 2 files changed, 22 insertions(+), 11 deletions(-)

diff --git a/lib/galaxy/web/controllers/admin.py b/lib/galaxy/web/controllers/admin.py
index c07cf6ac4ed..131343d8ffa 100644
--- a/lib/galaxy/web/controllers/admin.py
+++ b/lib/galaxy/web/controllers/admin.py
@@ -800,7 +800,7 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
             message += 'directory in order to automatically install tools from a Galaxy tool shed (e.g., the file name <b>shed_tool_conf.xml</b> whose '
             message += '<b>&lt;toolbox&gt;</b> tag is <b>&lt;toolbox tool_path="../shed_tools"&gt;</b>).<p/>See the '
             message += '<a href="http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance" '
-            message += 'target=_blank">Automatic installation of Galaxy tool shed repository tools into a local Galaxy instance</a> section of the '
+            message += 'target="_blank">Automatic installation of Galaxy tool shed repository tools into a local Galaxy instance</a> section of the '
             message += '<a href="http://wiki.g2.bx.psu.edu/Tool%20Shed" target="_blank">Galaxy tool shed wiki</a> for all of the details.'
             return trans.show_error_message( message )
         message = kwd.get( 'message', ''  )
diff --git a/lib/galaxy/web/controllers/workflow.py b/lib/galaxy/web/controllers/workflow.py
index f1efc758a36..700ecdf7d47 100644
--- a/lib/galaxy/web/controllers/workflow.py
+++ b/lib/galaxy/web/controllers/workflow.py
@@ -1193,20 +1193,31 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
                             # the Galaxy panels displayed whenever in Galaxy.
                             message += "The workflow requires the following tools that are not available in this Galaxy instance."
                             message += "You can likely install the required tools from one of the Galaxy tool sheds listed below.<br/><br/>"
-                            for tool_shed_name, tool_shed_url in trans.app.tool_shed_registry.tool_sheds.items():
-                                if tool_shed_url.endswith( '/' ):
-                                    tool_shed_url = tool_shed_url.rstrip( '/' )
-                                    url = '%s/repository/find_tools?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, trans.request.host )
+                            for shed_name, shed_url in trans.app.tool_shed_registry.tool_sheds.items():
+                                if shed_url.endswith( '/' ):
+                                    shed_url = shed_url.rstrip( '/' )
+                                    url = '%s/repository/find_tools?galaxy_url=%s&webapp=%s' % ( shed_url, trans.request.host, webapp )
                                     for missing_tool_tup in missing_tool_tups:
                                         missing_tool_id = missing_tool_tup[0]
                                         url += '&tool_id=%s' % missing_tool_id
-                                message += '<a href="%s">%s</a><br/>' % ( url, tool_shed_name )
+                                message += '<a href="%s">%s</a><br/>' % ( url, shed_name )
                                 status = 'error'
-                            return trans.response.send_redirect( web.url_for( controller='admin',
-                                                                              action='index',
-                                                                              webapp='galaxy',
-                                                                              message=message,
-                                                                              status=status ) )
+                            if local_file or tool_shed_url:
+                                # Another Galaxy panels Hack: The request did not originate from the Galaxy 
+                                # workflow view, so we don't need to render the Galaxy panels.
+                                return trans.response.send_redirect( web.url_for( controller='admin',
+                                                                                  action='center',
+                                                                                  webapp='galaxy',
+                                                                                  message=message,
+                                                                                  status=status ) )
+                            else:
+                                # Another Galaxy panels hack: The request originated from the Galaxy
+                                # workflow view, so we need to render the Galaxy panels.
+                                return trans.response.send_redirect( web.url_for( controller='admin',
+                                                                                  action='index',
+                                                                                  webapp='galaxy',
+                                                                                  message=message,
+                                                                                  status=status ) )
                         else:
                             # TODO: Figure out what to do here...
                             pass

From 9a3b5dca067211392fb40969f0972a8239273c9a Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Thu, 3 Nov 2011 16:45:44 -0400
Subject: [PATCH 150/362] Improve Cufflinks' documentation for gene annotation
 dataset parameters.

---
 tools/ngs_rna/cufflinks_wrapper.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/ngs_rna/cufflinks_wrapper.xml b/tools/ngs_rna/cufflinks_wrapper.xml
index 59c4f122ee6..34caf3681b7 100644
--- a/tools/ngs_rna/cufflinks_wrapper.xml
+++ b/tools/ngs_rna/cufflinks_wrapper.xml
@@ -61,10 +61,10 @@
             </param>
             <when value="No"></when>
             <when value="Use reference annotation">
-                <param format="gff3,gtf" name="reference_annotation_file" type="data" label="Reference Annotation" help="Make sure your annotation file is in GTF format and that Galaxy knows that your file is GTF--not GFF."/>
+                <param format="gff3,gtf" name="reference_annotation_file" type="data" label="Reference Annotation" help="Gene annotation dataset in GTF or GFF3 format."/>
             	</when>
 	        <when value="Use reference annotation guide">
-                <param format="gff3,gtf" name="reference_annotation_guide_file" type="data" label="Reference Annotation" help="Make sure your annotation file is in GTF format and that Galaxy knows that your file is GTF--not GFF."/>
+                <param format="gff3,gtf" name="reference_annotation_guide_file" type="data" label="Reference Annotation" help="Gene annotation dataset in GTF or GFF3 format."/>
                 </when>
         </conditional>
         <conditional name="bias_correction">

From b5bdbf6e44eb81db56a04de62dac3a6d7198e9a5 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Thu, 3 Nov 2011 16:54:45 -0400
Subject: [PATCH 151/362] Use panels when adding a build from a new track
 browser.

---
 templates/tracks/new_browser.mako | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/templates/tracks/new_browser.mako b/templates/tracks/new_browser.mako
index cc9a5bf396c..4d67ff896c0 100644
--- a/templates/tracks/new_browser.mako
+++ b/templates/tracks/new_browser.mako
@@ -19,7 +19,7 @@
     </div>
     <div class="form-row">
         Is the build not listed here? 
-        <a href="${h.url_for( controller='user', action='dbkeys', panels=True )}">Add a Custom Build</a>
+        <a href="${h.url_for( controller='user', action='dbkeys', use_panels=True )}">Add a Custom Build</a>
     </div>
     %if default_dbkey is not None:
         <script type="text/javascript">

From e669a876aa910a8022d9424c7db47d9646d46763 Mon Sep 17 00:00:00 2001
From: James Taylor <james@jamestaylor.org>
Date: Sat, 5 Nov 2011 14:55:11 -0400
Subject: [PATCH 152/362] Trackster: making config form generation for
 parameters a function so it can be used recursively (for conditional
 configuration, not yet implemented)

---
 static/scripts/trackster.js | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index 77c5a61d71a..89a13f06f71 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -2113,8 +2113,14 @@ extend(DrawableConfig.prototype, {
     build_form: function() {
         var track_config = this;
         var container = $("<div />");
-        $.each( this.params, function( index, param ) {
-            if ( ! param.hidden ) {
+        var param;
+        // Function to process parameters recursively
+        function handle_params( params, container ) {
+            for ( var index = 0; index < params.length; index++ ) {
+                param = params[index];
+                // Hidden params have no representation in the form
+                if ( param.hidden ) { continue; }
+                // Build row for param
                 var id = 'param_' + index;
                 var value = track_config.values[ param.key ];
                 var row = $("<div class='form-row' />").appendTo( container );
@@ -2132,7 +2138,6 @@ extend(DrawableConfig.prototype, {
                     var farb_container = $("<div/>")
                             .appendTo(tip_inner)
                             .farbtastic( { width: 100, height: 100, callback: input, color: value });
-                            
                     // Outer div container input and tip for hover to work
                     $("<div />").append( input ).append( tip ).appendTo( row ).bind( "click", function ( e ) { 
                         tip.css( { 
@@ -2156,7 +2161,10 @@ extend(DrawableConfig.prototype, {
                     row.append( $("<div class='help'/>").text( param.help ) );
                 }
             }
-        });
+        }
+        // Handle top level parameters in order
+        handle_params( this.params, container );
+        // Return element containing constructed form
         return container;
     },
     update_from_form: function( container ) {

From 901fdbb6133de9ddae24fd70da2ef3b14a19ec5f Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Sat, 5 Nov 2011 18:21:38 -0400
Subject: [PATCH 153/362] Trackster: color reads based on strand aligned to.

---
 .../visualization/tracks/data_providers.py    | 42 ++++++++++++++-----
 static/scripts/trackster.js                   | 29 +++++++------
 2 files changed, 45 insertions(+), 26 deletions(-)

diff --git a/lib/galaxy/visualization/tracks/data_providers.py b/lib/galaxy/visualization/tracks/data_providers.py
index ee15ef1969a..29cb08dece9 100644
--- a/lib/galaxy/visualization/tracks/data_providers.py
+++ b/lib/galaxy/visualization/tracks/data_providers.py
@@ -462,8 +462,10 @@ class VcfDataProvider( TracksDataProvider ):
                             # ID:
                             feature[2],
                             cigar,
+                            # TODO? VCF does not have strand, so default to positive.
+                            "+",
                             new_seq,
-                            float( feature[5] )]
+                            float( feature[5] ) ]
                 rval.append(payload)
 
         return { 'data': rval, 'message': message }
@@ -609,11 +611,11 @@ class BamDataProvider( TracksDataProvider ):
             data - a list of reads with the format 
                     [<guid>, <start>, <end>, <name>, <read_1>, <read_2>] 
                 where <read_1> has the format
-                    [<start>, <end>, <cigar>, ?<read_seq>?]
+                    [<start>, <end>, <cigar>, <strand>, ?<read_seq>?]
                 and <read_2> has the format
-                    [<start>, <end>, <cigar>, ?<read_seq>?]
+                    [<start>, <end>, <cigar>, <strand>, ?<read_seq>?]
                 For single-end reads, read has format:
-                    [<guid>, <start>, <end>, <name>, cigar, seq] 
+                    [<guid>, <start>, <end>, <name>, <cigar>, <strand>, <seq>] 
                 NOTE: read end and sequence data are not valid for reads outside of
                 requested region and should not be used.
             
@@ -641,17 +643,34 @@ class BamDataProvider( TracksDataProvider ):
             else:
                 return None
                 
+        # Decode strand from read flag.
+        def decode_strand( read_flag, mask ):
+            strand_flag = ( read_flag & mask == 0 )
+            if strand_flag:
+                return "+"
+            else:
+                return "-"
+                
         # Encode reads as list of lists.
         results = []
         paired_pending = {}
+        unmapped = 0
         for count, read in enumerate( data ):
             if count < start_val:
                 continue
-            if count-start_val >= max_vals:
+            if ( count - start_val - unmapped ) >= max_vals:
                 message = ERROR_MAX_VALS % ( max_vals, "reads" )
                 break
+                
+            # If not mapped, skip read.
+            is_mapped = ( read.flag & 0x0004 == 0 )
+            if not is_mapped:
+                unmapped += 1
+                continue
+                            
             qname = read.qname
             seq = read.seq
+            strand = decode_strand( read.flag, 0x0010 )
             if read.cigar is not None:
                 read_len = sum( [cig[1] for cig in read.cigar] ) # Use cigar to determine length
             else:
@@ -664,14 +683,15 @@ class BamDataProvider( TracksDataProvider ):
                                       pair['start'], 
                                       read.pos + read_len, 
                                       qname, 
-                                      [ pair['start'], pair['end'], pair['cigar'], pair['seq'] ], 
-                                      [ read.pos, read.pos + read_len, read.cigar, seq ] 
+                                      [ pair['start'], pair['end'], pair['cigar'], pair['strand'], pair['seq'] ], 
+                                      [ read.pos, read.pos + read_len, read.cigar, strand, seq ] 
                                      ] )
                     del paired_pending[qname]
                 else:
-                    paired_pending[qname] = { 'start': read.pos, 'end': read.pos + read_len, 'seq': seq, 'mate_start': read.mpos, 'rlen': read_len, 'cigar': read.cigar }
+                    paired_pending[qname] = { 'start': read.pos, 'end': read.pos + read_len, 'seq': seq, 'mate_start': read.mpos,
+                                              'rlen': read_len, 'strand': strand, 'cigar': read.cigar }
             else:
-                results.append( [ "%i_%s" % ( read.pos, qname ), read.pos, read.pos + read_len, qname, read.cigar, read.seq] )
+                results.append( [ "%i_%s" % ( read.pos, qname ), read.pos, read.pos + read_len, qname, read.cigar, strand, read.seq] )
                 
         # Take care of reads whose mates are out of range.
         # TODO: count paired reads when adhering to max_vals?
@@ -683,14 +703,14 @@ class BamDataProvider( TracksDataProvider ):
                 # Make read_1 start=end so that length is 0 b/c we don't know
                 # read length.
                 r1 = [ read['mate_start'], read['mate_start'] ]
-                r2 = [ read['start'], read['end'], read['cigar'], read['seq'] ]
+                r2 = [ read['start'], read['end'], read['cigar'], read['strand'], read['seq'] ]
             else:
                 # Mate is after read.
                 read_start = read['start']
                 # Make read_2 start=end so that length is 0 b/c we don't know
                 # read length. Hence, end of read is start of read_2.
                 read_end = read['mate_start']
-                r1 = [ read['start'], read['end'], read['cigar'], read['seq'] ]
+                r1 = [ read['start'], read['end'], read['cigar'], read['strand'], read['seq'] ]
                 r2 = [ read['mate_start'], read['mate_start'] ]
 
             results.append( [ "%i_%s" % ( read_start, qname ), read_start, read_end, qname, r1, r2 ] )
diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index b83a78e7024..75356dadb93 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -3580,11 +3580,15 @@ extend(VcfTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrac
 var ReadTrack = function (name, view, container, hda_ldda, dataset_id, prefs, filters) {
     FeatureTrack.call(this, name, view, container, hda_ldda, dataset_id, prefs, filters);
     
+    var 
+        block_color = get_random_color(),
+        reverse_strand_color = get_random_color( [ block_color, "#ffffff" ] );
     this.config = new DrawableConfig( {
         track: this,
         params: [
             { key: 'name', label: 'Name', type: 'text', default_value: name },
-            { key: 'block_color', label: 'Block color', type: 'color', default_value: get_random_color() },
+            { key: 'block_color', label: 'Block and sense strand color', type: 'color', default_value: block_color },
+            { key: 'reverse_strand_color', label: 'Antisense strand color', type: 'color', default_value: reverse_strand_color },
             { key: 'label_color', label: 'Label color', type: 'color', default_value: 'black' },
             { key: 'show_insertions', label: 'Show insertions', type: 'bool', default_value: false },
             { key: 'show_differences', label: 'Show differences only', type: 'bool', default_value: true },
@@ -4388,8 +4392,6 @@ var ReadPainter = function(data, view_start, view_end, prefs, mode, alpha_scaler
     this.ref_seq = (ref_seq ? ref_seq.data : null);
 };
 
-ReadPainter.prototype.default_prefs = extend({}, FeaturePainter.prototype.default_prefs, { show_insertions: false });
-
 extend(ReadPainter.prototype, FeaturePainter.prototype, {
     /**
      * Returns height based on mode.
@@ -4414,14 +4416,15 @@ extend(ReadPainter.prototype, FeaturePainter.prototype, {
     /**
      * Draw a single read.
      */
-    draw_read: function(ctx, mode, w_scale, tile_low, tile_high, feature_start, cigar, orig_seq, y_center) {
+    draw_read: function(ctx, mode, w_scale, y_center, tile_low, tile_high, feature_start, cigar, strand, orig_seq) {
         ctx.textAlign = "center";
         var track = this,
             tile_region = [tile_low, tile_high],
             base_offset = 0,
             seq_offset = 0,
             gap = 0,
-            char_width_px = ctx.canvas.manager.char_width_px;
+            char_width_px = ctx.canvas.manager.char_width_px,
+            block_color = (strand === "+" ? this.prefs.block_color : this.prefs.reverse_strand_color);
             
         // Keep list of items that need to be drawn on top of initial drawing layer.
         var draw_last = [];
@@ -4468,7 +4471,7 @@ extend(ReadPainter.prototype, FeaturePainter.prototype, {
                         // Draw.
                         var seq = orig_seq.slice(seq_offset, seq_offset + cig_len);
                         if (gap > 0) {
-                            ctx.fillStyle = this.prefs.block_color;
+                            ctx.fillStyle = block_color;
                             ctx.fillRect(s_start - gap, y_center + 1, s_end - s_start, 9);
                             ctx.fillStyle = CONNECTOR_COLOR;
                             // TODO: this can be made much more efficient by computing the complete sequence
@@ -4486,7 +4489,7 @@ extend(ReadPainter.prototype, FeaturePainter.prototype, {
                                 }
                             }
                         } else {
-                            ctx.fillStyle = this.prefs.block_color;
+                            ctx.fillStyle = block_color;
                             // TODO: This is a pretty hack-ish way to fill rectangle based on mode.
                             ctx.fillRect(s_start, y_center + 4, s_end - s_start, SQUISH_FEATURE_HEIGHT);
                         }
@@ -4615,7 +4618,6 @@ extend(ReadPainter.prototype, FeaturePainter.prototype, {
             f_start = Math.floor( Math.max(0, (feature_start - tile_low) * w_scale) ),
             f_end   = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low) * w_scale)) ),
             y_center = (mode === "Dense" ? 0 : (0 + slot)) * y_scale,
-            block_color = this.prefs.block_color,
             label_color = this.prefs.label_color,
             // Left-gap for label text since we align chrom text to the position tick.
             gap = 0;
@@ -4626,7 +4628,6 @@ extend(ReadPainter.prototype, FeaturePainter.prototype, {
         }
         
         // Draw read.
-        ctx.fillStyle = block_color;
         if (feature[5] instanceof Array) {
             // Read is paired.
             var b1_start = Math.floor( Math.max(0, (feature[4][0] - tile_low) * w_scale) ),
@@ -4635,12 +4636,12 @@ extend(ReadPainter.prototype, FeaturePainter.prototype, {
                 b2_end   = Math.ceil( Math.min(width, Math.max(0, (feature[5][1] - tile_low) * w_scale)) );
 
             // Draw left/forward read.
-            if (feature[4][1] >= tile_low && feature[4][0] <= tile_high && feature[4][2]) {
-                this.draw_read(ctx, mode, w_scale, tile_low, tile_high, feature[4][0], feature[4][2], feature[4][3], y_center);
+            if (feature[4][1] >= tile_low && feature[4][0] <= tile_high && feature[4][2]) {                
+                this.draw_read(ctx, mode, w_scale, y_center, tile_low, tile_high, feature[4][0], feature[4][2], feature[4][3], feature[4][4]);
             }
             // Draw right/reverse read.
             if (feature[5][1] >= tile_low && feature[5][0] <= tile_high && feature[5][2]) {
-                this.draw_read(ctx, mode, w_scale, tile_low, tile_high, feature[5][0], feature[5][2], feature[5][3], y_center);
+                this.draw_read(ctx, mode, w_scale, y_center, tile_low, tile_high, feature[5][0], feature[5][2], feature[5][3], feature[5][4]);
             }
             // Draw connector.
             if (b2_start > b1_end) {
@@ -4649,8 +4650,7 @@ extend(ReadPainter.prototype, FeaturePainter.prototype, {
             }
         } else {
             // Read is single.
-            ctx.fillStyle = block_color;
-            this.draw_read(ctx, mode, w_scale, tile_low, tile_high, feature_start, feature[4], feature[5], y_center);
+            this.draw_read(ctx, mode, w_scale, y_center, tile_low, tile_high, feature_start, feature[4], feature[5], feature[6]);
         }
         if (mode === "Pack" && feature_start > tile_low && feature_name !== ".") {
             // Draw label.
@@ -4664,7 +4664,6 @@ extend(ReadPainter.prototype, FeaturePainter.prototype, {
                 ctx.textAlign = "right";
                 ctx.fillText(feature_name, f_start - LABEL_SPACING - gap, y_center + 8);
             }
-            ctx.fillStyle = block_color;
         }
         
         // FIXME: provide actual coordinates for drawn read.

From 7e001829db5758ee3052d4a80f148461c0a80d21 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Sat, 5 Nov 2011 19:12:07 -0400
Subject: [PATCH 154/362] Trackster: tooltips for navigational elements and
 better showing/hiding of add tracks button.

---
 static/scripts/trackster.js    | 10 ++++++----
 static/scripts/trackster_ui.js |  3 +++
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index 75356dadb93..bf57da53f95 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -941,7 +941,7 @@ extend( View.prototype, DrawableCollection.prototype, {
             }
         };
         this.nav_input = $("<input/>").addClass("nav-input").hide().bind("keyup focusout", submit_nav).appendTo(this.nav_controls);
-        this.location_span = $("<span/>").addClass("location").appendTo(this.nav_controls);
+        this.location_span = $("<span/>").addClass("location").attr('original-title', 'Click to change location').tipsy( { gravity: 'n' } ).appendTo(this.nav_controls);
         this.location_span.click(function() {
             view.location_span.hide();
             view.chrom_select.hide();
@@ -953,8 +953,11 @@ extend( View.prototype, DrawableCollection.prototype, {
         if (this.vis_id !== undefined) {
             this.hidden_input = $("<input/>").attr("type", "hidden").val(this.vis_id).appendTo(this.nav_controls);
         }
-        this.zo_link = $("<a id='zoom-out' />").click(function() { view.zoom_out(); view.request_redraw(); }).appendTo(this.nav_controls);
-        this.zi_link = $("<a id='zoom-in' />").click(function() { view.zoom_in(); view.request_redraw(); }).appendTo(this.nav_controls);        
+        
+        this.zo_link = $("<a/>").attr("id", "zoom-out").attr("title", "Zoom out").tipsy( {gravity: 'n'} )
+                                .click(function() { view.zoom_out(); view.request_redraw(); }).appendTo(this.nav_controls);
+        this.zi_link = $("<a/>").attr("id", "zoom-in").attr("title", "Zoom in").tipsy( {gravity: 'n'} )
+                                .click(function() { view.zoom_in(); view.request_redraw(); }).appendTo(this.nav_controls);      
         
         // Get initial set of chroms.
         this.load_chroms_deferred = this.load_chroms({low: 0});
@@ -1069,7 +1072,6 @@ extend( View.prototype, DrawableCollection.prototype, {
         
         this.reset();
         $(window).trigger("resize");
-        this.update_intro_div();
     },
     /** Add or remove intro div depending on view state. */
     update_intro_div: function() {
diff --git a/static/scripts/trackster_ui.js b/static/scripts/trackster_ui.js
index 05c53eaf30f..1183a377f5e 100644
--- a/static/scripts/trackster_ui.js
+++ b/static/scripts/trackster_ui.js
@@ -111,6 +111,9 @@ var create_visualization = function(parent_elt, title, id, dbkey, viewport_confi
             }
         }
         
+        // Need to update intro div after drawables have been added.
+        view.update_intro_div();
+        
         // Set overview.
         var overview_track;
         for (var i = 0; i < view.drawables.length; i++) {

From 43ec3def31bc341eb3c673ca2655e5fdf40168d4 Mon Sep 17 00:00:00 2001
From: James Taylor <james@jamestaylor.org>
Date: Mon, 7 Nov 2011 10:21:17 -0500
Subject: [PATCH 155/362] Trackster: use hover event for feature track popups

---
 eggs.ini                      |  4 ++--
 static/scripts/trackster.js   | 11 ++++++++++-
 templates/tracks/browser.mako |  2 +-
 3 files changed, 13 insertions(+), 4 deletions(-)

diff --git a/eggs.ini b/eggs.ini
index 82c12aad70b..7bec53d8b6f 100644
--- a/eggs.ini
+++ b/eggs.ini
@@ -12,7 +12,7 @@ repository = http://eggs.g2.bx.psu.edu
 no_auto = pbs_python DRMAA_python
 
 [eggs:platform]
-bx_python = 0.7.1
+bx_python = 0.7.0
 Cheetah = 2.2.2
 ctypes = 1.0.2
 DRMAA_python = 0.2
@@ -67,7 +67,7 @@ Whoosh = 0.3.18
 psycopg2 = _8.4.2_static
 pysqlite = _3.6.17_static
 MySQL_python = _5.1.41_static
-; bx_python = _494c2d1d68b3_rebuild1
+bx_python = _494c2d1d68b3_rebuild1
 GeneTrack = _dev_48da9e998f0caf01c5be731e926f4b0481f658f0
 SQLAlchemy = _dev_r6498
 pysam = _kanwei_b10f6e722e9a
diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index 89a13f06f71..71185763fa1 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -2242,7 +2242,16 @@ FeatureTrackTile.prototype.predisplay_actions = function() {
     // Only show popups in Pack mode.
     if (tile.mode !== "Pack") { return; }
     
-    $(this.canvas).mousemove(function (e) {
+    $(this.canvas).hover( function() { 
+        this.hovered = true; 
+        $(this).mousemove();
+    }, function() { 
+        this.hovered = false; 
+        // Clear popup if it is still hanging around (this is probably not needed) 
+        $(this).siblings(".feature-popup").remove();
+    } ).mousemove(function (e) {
+        // Use the hover plugin to get a delay before showing popup
+        if ( !this.hovered ) { return; }
         // Get feature data for position.
         var 
             this_offset = $(this).offset(),
diff --git a/templates/tracks/browser.mako b/templates/tracks/browser.mako
index 1799b085f00..fa7cc535a01 100644
--- a/templates/tracks/browser.mako
+++ b/templates/tracks/browser.mako
@@ -42,7 +42,7 @@ ${parent.javascripts()}
   <script type='text/javascript' src="${h.url_for('/static/scripts/excanvas.js')}"></script>
 <![endif]-->
 
-${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.event.drag", "jquery.mousewheel", "jquery.autocomplete", "trackster", "trackster_ui", "jquery.ui.sortable.slider", "jquery.scrollTo", "farbtastic", "jquery.tipsy" )}
+${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.event.drag", "jquery.event.hover", "jquery.event.hover", "jquery.mousewheel", "jquery.autocomplete", "trackster", "trackster_ui", "jquery.ui.sortable.slider", "jquery.scrollTo", "farbtastic", "jquery.tipsy" )}
 
 <script type="text/javascript">
     //

From cae7a6ffc2de5d00456b2493a63eab5d4b2cd63c Mon Sep 17 00:00:00 2001
From: James Taylor <james@jamestaylor.org>
Date: Mon, 7 Nov 2011 10:32:18 -0500
Subject: [PATCH 156/362] Move bx-python version to 0.7.1 (again)

---
 eggs.ini | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/eggs.ini b/eggs.ini
index 7bec53d8b6f..82c12aad70b 100644
--- a/eggs.ini
+++ b/eggs.ini
@@ -12,7 +12,7 @@ repository = http://eggs.g2.bx.psu.edu
 no_auto = pbs_python DRMAA_python
 
 [eggs:platform]
-bx_python = 0.7.0
+bx_python = 0.7.1
 Cheetah = 2.2.2
 ctypes = 1.0.2
 DRMAA_python = 0.2
@@ -67,7 +67,7 @@ Whoosh = 0.3.18
 psycopg2 = _8.4.2_static
 pysqlite = _3.6.17_static
 MySQL_python = _5.1.41_static
-bx_python = _494c2d1d68b3_rebuild1
+; bx_python = _494c2d1d68b3_rebuild1
 GeneTrack = _dev_48da9e998f0caf01c5be731e926f4b0481f658f0
 SQLAlchemy = _dev_r6498
 pysam = _kanwei_b10f6e722e9a

From 949ce6552d00c35d44a3e7fa4a716af1471a945b Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Mon, 7 Nov 2011 11:19:07 -0500
Subject: [PATCH 157/362] Fix for implicit dataset conversion that was broken
 in 1827729ed37e.

---
 lib/galaxy/datatypes/display_applications/parameters.py | 4 +---
 lib/galaxy/tools/actions/__init__.py                    | 4 +---
 2 files changed, 2 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/datatypes/display_applications/parameters.py b/lib/galaxy/datatypes/display_applications/parameters.py
index a22af845bcf..a9fad370243 100644
--- a/lib/galaxy/datatypes/display_applications/parameters.py
+++ b/lib/galaxy/datatypes/display_applications/parameters.py
@@ -94,13 +94,11 @@ class DisplayApplicationDataParameter( DisplayApplicationParameter ):
             if target_ext and not converted_dataset:
                 if isinstance( data, DisplayDataValueWrapper ):
                     data = data.value
-                assoc = trans.app.model.ImplicitlyConvertedDatasetAssociation( parent = data, file_type = target_ext, metadata_safe = False )
                 new_data = data.datatype.convert_dataset( trans, data, target_ext, return_output = True, visible = False ).values()[0]
                 new_data.hid = data.hid
                 new_data.name = data.name
                 trans.sa_session.add( new_data )
-                trans.sa_session.flush()
-                assoc.dataset = new_data
+                assoc = trans.app.model.ImplicitlyConvertedDatasetAssociation( parent = data, file_type = target_ext, dataset = new_data, metadata_safe = False )
                 trans.sa_session.add( assoc )
                 trans.sa_session.flush()
             elif converted_dataset and converted_dataset.state == converted_dataset.states.ERROR:
diff --git a/lib/galaxy/tools/actions/__init__.py b/lib/galaxy/tools/actions/__init__.py
index 000b6980716..33ac4968fca 100644
--- a/lib/galaxy/tools/actions/__init__.py
+++ b/lib/galaxy/tools/actions/__init__.py
@@ -43,13 +43,11 @@ class DefaultToolAction( object ):
                             data = converted_dataset
                         else:
                             #run converter here
-                            assoc = trans.app.model.ImplicitlyConvertedDatasetAssociation( parent = data, file_type = target_ext, metadata_safe = False )
                             new_data = data.datatype.convert_dataset( trans, data, target_ext, return_output = True, visible = False ).values()[0]
                             new_data.hid = data.hid
                             new_data.name = data.name
                             trans.sa_session.add( new_data )
-                            trans.sa_session.flush()
-                            assoc.dataset = new_data
+                            assoc = trans.app.model.ImplicitlyConvertedDatasetAssociation( parent = data, file_type = target_ext, dataset = new_data, metadata_safe = False )
                             trans.sa_session.add( assoc )
                             trans.sa_session.flush()
                             data = new_data

From 609f6acaa0b87b2631312e3a1ce12215a926cd3a Mon Sep 17 00:00:00 2001
From: James Taylor <james@jamestaylor.org>
Date: Mon, 7 Nov 2011 15:31:32 -0500
Subject: [PATCH 158/362] Eggs: add revision string for new bx-python

---
 eggs.ini | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/eggs.ini b/eggs.ini
index 82c12aad70b..06dca8b1bac 100644
--- a/eggs.ini
+++ b/eggs.ini
@@ -67,7 +67,7 @@ Whoosh = 0.3.18
 psycopg2 = _8.4.2_static
 pysqlite = _3.6.17_static
 MySQL_python = _5.1.41_static
-; bx_python = _494c2d1d68b3_rebuild1
+bx_python = _7b95ff194725
 GeneTrack = _dev_48da9e998f0caf01c5be731e926f4b0481f658f0
 SQLAlchemy = _dev_r6498
 pysam = _kanwei_b10f6e722e9a

From 583799bea90b4d0f3f5efef91b4331d33e58d800 Mon Sep 17 00:00:00 2001
From: James Taylor <james@jamestaylor.org>
Date: Mon, 7 Nov 2011 12:34:23 -0500
Subject: [PATCH 159/362] Trackster: allow selecting the arc connector style
 for feature tracks, add support for select config parameter type

---
 static/scripts/trackster.js | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index 5875baee4e9..8a30353398e 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -2127,10 +2127,21 @@ extend(DrawableConfig.prototype, {
                 var value = track_config.values[ param.key ];
                 var row = $("<div class='form-row' />").appendTo( container );
                 row.append( $('<label />').attr("for", id ).text( param.label + ":" ) );
+                // Draw parameter as checkbox
                 if ( param.type === 'bool' ) {
                     row.append( $('<input type="checkbox" />').attr("id", id ).attr("name", id ).attr( 'checked', value ) );
+                // Draw parameter as textbox
                 } else if ( param.type === 'text' ) {
                     row.append( $('<input type="text"/>').attr("id", id ).val(value).click( function() { $(this).select() }));
+                // Draw paramter as select area
+                } else if ( param.type == 'select' ) {
+                    var select = $('<select />').attr("id", id);
+                    for ( var i = 0; i < param.options.length; i++ ) {
+                        $("<option/>").text( param.options[i].label ).attr( "value", param.options[i].value ).appendTo( select );
+                    }
+                    select.val( value );
+                    row.append( select );
+                // Draw parameter as color picker
                 } else if ( param.type === 'color' ) {
                     var input = $('<input />').attr("id", id ).attr("name", id ).val( value );
                     // Color picker in tool tip style float
@@ -3269,12 +3280,15 @@ var FeatureTrack = function(name, view, container, hda_ldda, dataset_id, prefs,
             { key: 'label_color', label: 'Label color', type: 'color', default_value: 'black' },
             { key: 'show_counts', label: 'Show summary counts', type: 'bool', default_value: true, 
               help: 'Show the number of items in each bin when drawing summary histogram' },
+            { key: 'connector_style', label: 'Connector style', type: 'select', default_value: 'fishbones',
+                options: [ { label: 'Line with arrows', value: 'fishbone' }, { label: 'Arcs', value: 'arcs' } ] },
             { key: 'mode', type: 'string', default_value: this.mode, hidden: true },
         ], 
         saved_values: prefs,
         onchange: function() {
             track.set_name(track.prefs.name);
             track.tile_cache.clear();
+            track.set_painter_from_config();
             track.request_draw();
         }
     });
@@ -3297,6 +3311,14 @@ var FeatureTrack = function(name, view, container, hda_ldda, dataset_id, prefs,
     this.painter = painters.LinkedFeaturePainter;
 };
 extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
+    set_painter_from_config: function() {
+        console.log( this, this.config );
+        if ( this.config.values['connector_style'] == 'arcs' ) {
+            this.painter = painters.ArcLinkedFeaturePainter;
+        } else {
+            this.painter = painters.LinkedFeaturePainter;
+        }
+    },
     /**
      * Actions to be taken after draw has been completed. Draw is completed when all tiles have been 
      * drawn/fetched and shown.

From e9e0a5e859ac1a4bfadb7d13da19015111c56650 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 7 Nov 2011 12:46:14 -0500
Subject: [PATCH 160/362] Fix bug introduced in 0ba260ea43c4 for displaying
 workflows.

---
 templates/workflow/display.mako | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/templates/workflow/display.mako b/templates/workflow/display.mako
index 969ccdb62ef..871aed75fac 100644
--- a/templates/workflow/display.mako
+++ b/templates/workflow/display.mako
@@ -1,8 +1,8 @@
 <%inherit file="/display_base.mako"/>
 <%namespace file="/display_common.mako" import="render_message" />
 
-<%
-    from galaxy.tools.parameters import DataToolParameter, RuntimeValue 
+<%!
+    from galaxy.tools.parameters import DataToolParameter, RuntimeValue
     from galaxy.web import form_builder
 %>
 
@@ -118,4 +118,4 @@
             </tr>
         %endfor
     </table>
-</%def>
\ No newline at end of file
+</%def>

From 174e93cb25ef30c967bfa1bc3fafe8e5d6035077 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Mon, 7 Nov 2011 15:27:43 -0500
Subject: [PATCH 161/362] Actually send error reports to the creator instead of
 lying and saying that we did.

---
 lib/galaxy/util/__init__.py | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/util/__init__.py b/lib/galaxy/util/__init__.py
index 893e9bcc408..daad6cc04ec 100644
--- a/lib/galaxy/util/__init__.py
+++ b/lib/galaxy/util/__init__.py
@@ -574,11 +574,9 @@ def send_mail( frm, to, subject, body, config ):
     """
     Sends an email.
     """
-    header_to = to
-    if isinstance( to, list ):
-        header_to = ', '.join( to )
+    to = listify( to )
     msg = MIMEText( body )
-    msg[ 'To' ] = header_to
+    msg[ 'To' ] = ', '.join( to )
     msg[ 'From' ] = frm
     msg[ 'Subject' ] = subject
     if config.smtp_server is None:
@@ -613,8 +611,6 @@ def send_mail( frm, to, subject, body, config ):
             log.error( "No suitable authentication method was found: %s" % e )
             s.close()
             raise
-    if isinstance( to, basestring ):
-        to = [ to ]
     s.sendmail( frm, to, msg.as_string() )
     s.quit()
 

From 75b4737ea2949adfc96dec8fa0f64777296740d2 Mon Sep 17 00:00:00 2001
From: James Taylor <james@jamestaylor.org>
Date: Mon, 7 Nov 2011 15:36:46 -0500
Subject: [PATCH 162/362] Trackster: fix loading of track connector style when
 initializing from saved

---
 static/scripts/trackster.js | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index 8a30353398e..b0874d450b9 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -3308,7 +3308,8 @@ var FeatureTrack = function(name, view, container, hda_ldda, dataset_id, prefs,
     this.data_manager = new DataManager(20, this);
     this.left_offset = 200;
 
-    this.painter = painters.LinkedFeaturePainter;
+    // this.painter = painters.LinkedFeaturePainter;
+    this.set_painter_from_config();
 };
 extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
     set_painter_from_config: function() {

From c4cb89efc2c1da88eab2c8f894a26d766672086f Mon Sep 17 00:00:00 2001
From: James Taylor <james@jamestaylor.org>
Date: Mon, 7 Nov 2011 16:59:15 -0500
Subject: [PATCH 163/362] Trackster: code for adding multiple bookmarks from a
 dataset. Currently the button is commented out until this can be made more
 usable

---
 .../visualization/tracks/data_providers.py    |   8 ++-
 lib/galaxy/web/controllers/tracks.py          |  23 ++++++-
 static/june_2007_style/base.css.tmpl          |   8 +++
 static/june_2007_style/blue/base.css          |   4 +-
 static/june_2007_style/blue/fugue.png         | Bin 6563 -> 7566 bytes
 static/scripts/trackster.js                   |   1 -
 templates/tracks/browser.mako                 |  61 ++++++++++++++++--
 7 files changed, 96 insertions(+), 9 deletions(-)

diff --git a/lib/galaxy/visualization/tracks/data_providers.py b/lib/galaxy/visualization/tracks/data_providers.py
index 30792835d2d..a909699ab69 100644
--- a/lib/galaxy/visualization/tracks/data_providers.py
+++ b/lib/galaxy/visualization/tracks/data_providers.py
@@ -363,14 +363,18 @@ class RawBedDataProvider( BedDataProvider ):
     for large datasets.
     """
 
-    def get_iterator( self, chrom, start, end ):
+    def get_iterator( self, chrom=None, start=None, end=None ):
         def line_filter_iter():
             for line in open( self.original_dataset.file_name ):
+                if line.startswith( "track" ) or line.startswith( "browser" ):
+                    continue
                 feature = line.split()
                 feature_chrom = feature[0]
                 feature_start = int( feature[1] )
                 feature_end = int( feature[2] )
-                if feature_chrom != chrom or feature_start > int( end ) or feature_end < int( start ):
+                if ( chrom is not None and feature_chrom != chrom ) \
+                    or ( start is not None and feature_start > int( end ) ) \
+                    or ( end is not None and feature_end < int( start ) ):
                     continue
                 yield line
         return line_filter_iter()
diff --git a/lib/galaxy/web/controllers/tracks.py b/lib/galaxy/web/controllers/tracks.py
index 3ae6cea5063..8dd0d3fa22f 100644
--- a/lib/galaxy/web/controllers/tracks.py
+++ b/lib/galaxy/web/controllers/tracks.py
@@ -13,7 +13,7 @@ from galaxy.web.controllers.library import LibraryListGrid
 from galaxy.web.framework import simplejson
 from galaxy.web.framework.helpers import time_ago, grids
 from galaxy.util.bunch import Bunch
-from galaxy.datatypes.interval import Gff
+from galaxy.datatypes.interval import Gff, Bed
 from galaxy.model import NoConverterException, ConverterDependencyException
 from galaxy.visualization.tracks.data_providers import *
 from galaxy.visualization.tracks.visual_analytics import get_tool_def, get_dataset_job
@@ -246,6 +246,27 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
             "tool": get_tool_def( trans, dataset )
         }
         return track
+
+    @web.json
+    def bookmarks_from_dataset( self, trans, hda_id=None, ldda_id=None ):
+        if hda_id:
+            hda_ldda = "hda"
+            dataset = self.get_dataset( trans, hda_id, check_ownership=False, check_accessible=True )
+        elif ldda_id:
+            hda_ldda = "ldda"
+            dataset = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( ldda_id ) )
+        rows = []
+        if isinstance( dataset.datatype, Bed ):
+            data = RawBedDataProvider( original_dataset=dataset ).get_iterator()
+            for i, line in enumerate( data ):
+                if ( i > 500 ): break
+                fields = line.split()
+                location = name = "%s:%s-%s" % ( fields[0], fields[1], fields[2] )
+                if len( fields ) > 3:
+                    name = fields[4]
+                rows.append( [location, name] )
+        return { 'data': rows }
+
         
     @web.expose
     @web.require_login()
diff --git a/static/june_2007_style/base.css.tmpl b/static/june_2007_style/base.css.tmpl
index d53be3086af..2e2f1e4c4d9 100644
--- a/static/june_2007_style/base.css.tmpl
+++ b/static/june_2007_style/base.css.tmpl
@@ -909,6 +909,14 @@ div.permissionContainer {
     -sprite-group: fugue;
     -sprite-image: fugue/plus-circle.png;
 }
+.icon-button.plus-button {
+    -sprite-group: fugue;
+    -sprite-image: fugue/plus-button.png;
+}
+.icon-button.gear {
+    -sprite-group: fugue;
+    -sprite-image: fugue/gear.png;
+}
 
 .tipsy {
     padding: 5px;
diff --git a/static/june_2007_style/blue/base.css b/static/june_2007_style/blue/base.css
index 70bc7fede74..432582606d5 100644
--- a/static/june_2007_style/blue/base.css
+++ b/static/june_2007_style/blue/base.css
@@ -163,6 +163,8 @@ div.permissionContainer{padding-left:20px;}
 .icon-button.vis-chart{background:url(fugue.png) no-repeat 0px -286px;}
 .icon-button.go-to-full-screen{background:url(fugue.png) no-repeat 0px -312px;}
 .icon-button.import{background:url(fugue.png) no-repeat 0px -338px;}
+.icon-button.plus-button{background:url(fugue.png) no-repeat 0px -364px;}
+.icon-button.gear{background:url(fugue.png) no-repeat 0px -390px;}
 .tipsy{padding:5px;font-size:10px;filter:alpha(opacity=80);background-repeat:no-repeat;background-image:url(../images/tipsy.gif);}
 .tipsy-inner{padding:5px 8px 4px 8px;background-color:black;color:white;max-width:200px;text-align:center;}
 .tipsy-north{background-position:top center;}
@@ -171,7 +173,7 @@ div.permissionContainer{padding-left:20px;}
 .tipsy-west{background-position:left center;}
 .editable-text{cursor:pointer;}
 .editable-text:hover{cursor:text;border:dotted #999999 1px;}
-.text-and-autocomplete-select{background:url(fugue.png) no-repeat right -364px;}
+.text-and-autocomplete-select{background:url(fugue.png) no-repeat right -416px;}
 .icon-button.multiinput{background:url(../images/documents-stack.png) no-repeat;cursor:pointer;float:none;display:inline-block;margin-left:10px;}
 .icon-button.multiinput.disabled{background:url(../images/documents-stack-faded.png) no-repeat;cursor:auto;}
 .workflow-invocation-complete{border:solid 1px #6A6;border-left-width:5px;margin:10px 0;padding-left:5px;}
diff --git a/static/june_2007_style/blue/fugue.png b/static/june_2007_style/blue/fugue.png
index d6212bec398de01cdd52fe403a8445bfe9831878..393ca9daedb4cecd5e5f37a2bc925cf991809338 100644
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diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index b0874d450b9..40bae40def9 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -3313,7 +3313,6 @@ var FeatureTrack = function(name, view, container, hda_ldda, dataset_id, prefs,
 };
 extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
     set_painter_from_config: function() {
-        console.log( this, this.config );
         if ( this.config.values['connector_style'] == 'arcs' ) {
             this.painter = painters.ArcLinkedFeaturePainter;
         } else {
diff --git a/templates/tracks/browser.mako b/templates/tracks/browser.mako
index 8b9b7069714..113bc5e1129 100644
--- a/templates/tracks/browser.mako
+++ b/templates/tracks/browser.mako
@@ -110,6 +110,52 @@ ${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.e
             }
         });
     };
+
+    /**
+     * Use a popup grid to bookmarks from a dataset.
+     */
+    var add_bookmarks = function() {
+        show_modal( "Select dataset for new bookmarks", "progress" );
+        $.ajax({
+            url: "${h.url_for( action='list_histories' )}",
+            data: { "f-dbkey": view.dbkey },
+            error: function() { alert( "Grid failed" ); },
+            success: function(table_html) {
+                show_modal(
+                    "Select dataset for new bookmarks",
+                    table_html, {
+                        "Cancel": function() {
+                            hide_modal();
+                        },
+                        "Insert": function() {
+                            // Just use the first selected
+                            $('input[name=id]:checked,input[name=ldda_ids]:checked').first().each(function(){
+                                var data, id = $(this).val();
+                                    if ($(this).attr("name") === "id") {
+                                        data = { hda_id: id };
+                                    } else {
+                                        data = { ldda_id: id};
+                                    }
+
+                                    $.ajax({
+                                        url: "${h.url_for( action='bookmarks_from_dataset' )}",
+                                        data: data,
+                                        dataType: "json",
+                                    }).then( function(data) {
+                                        for( i = 0; i < data.data.length; i++ ) {
+                                            var row = data.data[i];
+                                            console.log( row[0], row[1] );
+                                            add_bookmark( row[0], row[1] );
+                                        }
+                                    });
+                            });
+                            hide_modal();
+                        }
+                    }
+                );
+            }
+        });
+    };
     
     $(function() {
         // Manual tipsy config because default gravity is S and cannot be changed.
@@ -240,7 +286,13 @@ ${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.e
                     annotation = "Bookmark description";
                 return add_bookmark(position, annotation);
             });
-            
+
+            // make_popupmenu( $("#bookmarks-more-button"), {
+            //     "Add from BED dataset": function() {
+            //         add_bookmarks();    
+            //     }
+            // });
+
             init_keyboard_nav(view);
         };
         
@@ -271,14 +323,15 @@ ${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.e
 
 <div class="unified-panel-header" unselectable="on">
     <div class="unified-panel-header-inner">
+        <div style="float: right">
+            <a id="add-bookmark-button" class='icon-button menu-button plus-button' href="javascript:void(0);" title="Add bookmark"></a>
+            ## <a id="bookmarks-more-button" class='icon-button menu-button gear popup' href="javascript:void(0);" title="More actions"></a>
+        </div>
         Bookmarks
     </div>
 </div>
 <div class="unified-panel-body" style="overflow: auto;">
     <div id="bookmarks-container"></div>
-    <div>
-        <a class="icon-button import" style="margin-left: .5em; width: 100%" original-title="Add Bookmark" id="add-bookmark-button" href="javascript:void(0);">Add Bookmark</a>
-    </div>
 </div>
 
 </%def>

From 98513d7e2f283dc330ad5b55515ac8b48fb99796 Mon Sep 17 00:00:00 2001
From: James Taylor <james@jamestaylor.org>
Date: Mon, 7 Nov 2011 18:22:47 -0500
Subject: [PATCH 164/362] Trackster: fix strand drawing for single blocks with
 no thin/thick part

---
 static/scripts/trackster.js | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index 40bae40def9..ba5a12d7410 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -4385,17 +4385,17 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
             // Draw feature/feature blocks + connectors.
             if (!feature_blocks) {
                 // If there are no blocks, treat the feature as one big exon.
-                if ( feature.strand ) {
-                    if (feature.strand === "+") {
+                ctx.fillStyle = block_color;
+                ctx.fillRect(f_start, y_center + 1, f_end - f_start, thick_height);
+                // If strand is specified, draw arrows over feature
+                if ( feature_strand ) {
+                    if (feature_strand === "+") {
                         ctx.fillStyle = ctx.canvas.manager.get_pattern( 'right_strand_inv' );
-                    } else if (feature.strand === "-") {
+                    } else if (feature_strand === "-") {
                         ctx.fillStyle = ctx.canvas.manager.get_pattern( 'left_strand_inv' );
                     }
+                    ctx.fillRect(f_start, y_center + 1, f_end - f_start, thick_height);
                 }
-                else { // No strand.
-                    ctx.fillStyle = block_color;
-                }                            
-                ctx.fillRect(f_start, y_center, f_end - f_start, thick_height);
             } else { 
                 //
                 // There are feature blocks and mode is either Squish or Pack.

From 8a1585a4bb2bed3f46ea59b60c9dc8610d8aa163 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Tue, 8 Nov 2011 10:23:52 -0500
Subject: [PATCH 165/362] Invalidate other Galaxy sessions upon password
 change.  Thanks Bob Harris!

---
 lib/galaxy/web/controllers/user.py | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/web/controllers/user.py b/lib/galaxy/web/controllers/user.py
index 0c6c3ed40b1..00426878c03 100644
--- a/lib/galaxy/web/controllers/user.py
+++ b/lib/galaxy/web/controllers/user.py
@@ -753,7 +753,7 @@ class User( BaseUIController, UsesFormDefinitions ):
             password = kwd.get( 'password', '' )
             confirm = kwd.get( 'confirm', '' )
             ok = True
-            if not webapp == 'galaxy' and not is_admin:
+            if not is_admin:
                 # If the current user is changing their own password, validate their current password
                 current = kwd.get( 'current', '' )
                 if not trans.user.check_password( current ):
@@ -768,10 +768,17 @@ class User( BaseUIController, UsesFormDefinitions ):
                 else:
                     # Save new password
                     user.set_password_cleartext( password )
+                    # Invalidate all other sessions
+                    for other_galaxy_session in trans.sa_session.query( trans.app.model.GalaxySession ) \
+                                                     .filter( and_( trans.app.model.GalaxySession.table.c.user_id==trans.user.id,
+                                                                    trans.app.model.GalaxySession.table.c.is_valid==True,
+                                                                    trans.app.model.GalaxySession.table.c.id!=trans.galaxy_session.id ) ):
+                        other_galaxy_session.is_valid = False
+                        trans.sa_session.add( other_galaxy_session )
                     trans.sa_session.add( user )
                     trans.sa_session.flush()
                     trans.log_event( "User change password" )
-                    message = 'The password has been changed.'
+                    message = 'The password has been changed and any other existing Galaxy sessions have been logged out (but jobs in histories in those sessions will not be interrupted).'
         elif user and params.get( 'edit_user_info_button', False ):
             # Edit user information - webapp MUST BE 'galaxy'
             user_type_fd_id = params.get( 'user_type_fd_id', 'none' )

From 1284227acdd2c99295c49726d3c208f47fa138c7 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Tue, 8 Nov 2011 10:59:27 -0500
Subject: [PATCH 166/362] Squash SAMTools stderr chatter when using FreeBayes
 which would cause error state. FreeBayes should be updated to e.g. have
 access to built-in reference genomes, etc.

---
 tools/human_genome_variation/freebayes.xml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tools/human_genome_variation/freebayes.xml b/tools/human_genome_variation/freebayes.xml
index a5d579ee19f..50a906d0992 100644
--- a/tools/human_genome_variation/freebayes.xml
+++ b/tools/human_genome_variation/freebayes.xml
@@ -5,11 +5,11 @@
   </requirements>
   <description>Bayesian genetic variant detector</description>
   <command>
-    ln -s $reference localref.fa;
-    ln -s $bamfile localbam.bam;
-    samtools faidx localref.fa;
-    samtools sort localbam.bam localbam.bam;
-    samtools index localbam.bam;
+    ln -s $reference localref.fa &amp;&amp;
+    ln -s $bamfile localbam.bam &amp;&amp;
+    samtools faidx localref.fa 2&gt;&amp;1 || echo "Error running samtools faidx for FreeBayes" &gt;&amp;2 &amp;&amp;
+    samtools sort localbam.bam localbam.bam 2&gt;&amp;1 || echo "Error running samtools sort for FreeBayes" &gt;&amp;2 &amp;&amp;
+    samtools index localbam.bam 2&gt;&amp;1 || echo "Error running samtools index for FreeBayes" &gt;&amp;2 &amp;&amp;
     freebayes --fasta-reference localref.fa localbam.bam --vcf $output
             #if $params.source_select == "full":
                 $params.showRefRepeats

From a5224d49e9a5932f88d50ce9c3bca25ca6493cfa Mon Sep 17 00:00:00 2001
From: James Taylor <james@jamestaylor.org>
Date: Tue, 8 Nov 2011 11:37:12 -0500
Subject: [PATCH 167/362] Trackster: dense mode features are full height again,
 don't draw strand indicators when drawing squished features.

---
 static/scripts/trackster.js | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index ba5a12d7410..00d2a080774 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -4292,7 +4292,7 @@ var DENSE_TRACK_HEIGHT = 10,
     SQUISH_TRACK_HEIGHT = 5,
     PACK_TRACK_HEIGHT = 10,
     NO_DETAIL_FEATURE_HEIGHT = 1,
-    DENSE_FEATURE_HEIGHT = 3,
+    DENSE_FEATURE_HEIGHT = 9,
     SQUISH_FEATURE_HEIGHT = 3,
     PACK_FEATURE_HEIGHT = 9,
     LABEL_SPACING = 2,
@@ -4365,7 +4365,9 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
             var feature_strand = feature[4],
                 feature_ts = feature[5],
                 feature_te = feature[6],
-                feature_blocks = feature[7];
+                feature_blocks = feature[7],
+                // Whether we are drawing full height or squished features
+                full_height = true;
             
             if (feature_ts && feature_te) {
                 thick_start = Math.floor( Math.max(0, (feature_ts - tile_low) * w_scale) );
@@ -4374,9 +4376,13 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
             
             // Set vars that depend on mode.
             var thin_height, thick_height;
-            if (mode === "Squish" || mode === "Dense" ) {
+            if (mode === "Squish" ) {
                 thin_height = 1;
                 thick_height = SQUISH_FEATURE_HEIGHT;
+                full_height = false;
+            } else if ( mode === "Dense" ) {
+                thin_height = 5;
+                thick_height = DENSE_FEATURE_HEIGHT;
             } else { // mode === "Pack"
                 thin_height = 5;
                 thick_height = PACK_FEATURE_HEIGHT;
@@ -4388,7 +4394,7 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
                 ctx.fillStyle = block_color;
                 ctx.fillRect(f_start, y_center + 1, f_end - f_start, thick_height);
                 // If strand is specified, draw arrows over feature
-                if ( feature_strand ) {
+                if ( feature_strand && full_height ) {
                     if (feature_strand === "+") {
                         ctx.fillStyle = ctx.canvas.manager.get_pattern( 'right_strand_inv' );
                     } else if (feature_strand === "-") {

From 5d9e946ef3bdaa794097e52d8bbd56060a09fb9c Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Tue, 8 Nov 2011 11:59:36 -0500
Subject: [PATCH 168/362] Fix importing library datasets into multiple
 histories - library datasets will now only be imported into those checked.

---
 lib/galaxy/web/controllers/library_common.py          | 11 ++++++-----
 .../webapps/community/controllers/repository.py       |  8 ++++----
 .../library/common/import_datasets_to_histories.mako  |  6 +++---
 3 files changed, 13 insertions(+), 12 deletions(-)

diff --git a/lib/galaxy/web/controllers/library_common.py b/lib/galaxy/web/controllers/library_common.py
index fcda23aa4e1..1c2b2e61e15 100644
--- a/lib/galaxy/web/controllers/library_common.py
+++ b/lib/galaxy/web/controllers/library_common.py
@@ -1855,7 +1855,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitions ):
                                         status=status )
             
     @web.expose
-    def import_datasets_to_histories( self, trans, cntrller, library_id='', folder_id='', ldda_ids='', target_history_ids='', new_history_name='', **kwd ):
+    def import_datasets_to_histories( self, trans, cntrller, library_id='', folder_id='', ldda_ids='', target_history_id='', target_history_ids='', new_history_name='', **kwd ):
         # This method is called from one of the following places:
         # - a menu option for a library dataset ( ldda_ids is a single ldda id )
         # - a menu option for a library folder ( folder_id has a value )
@@ -1870,7 +1870,6 @@ class LibraryCommon( BaseUIController, UsesFormDefinitions ):
         action = params.get( 'do_action', None )
         user = trans.get_user()
         current_history = trans.get_history()
-        selected_history_id = params.get( 'selected_history_id', trans.security.encode_id( current_history.id ) )
         if library_id:
             library = trans.sa_session.query( trans.model.Library ).get( trans.security.decode_id( library_id ) )
         else:
@@ -1882,9 +1881,11 @@ class LibraryCommon( BaseUIController, UsesFormDefinitions ):
         ldda_ids = util.listify( ldda_ids )
         if ldda_ids:
             ldda_ids = map( trans.security.decode_id, ldda_ids )
-        target_history_ids = util.listify( target_history_ids )
         if target_history_ids:
-            target_history_ids = [ trans.security.decode_id( target_history_id ) for target_history_id in target_history_ids if target_history_id ]
+            target_history_ids = util.listify( target_history_ids )
+            target_history_ids = set( [ trans.security.decode_id( target_history_id ) for target_history_id in target_history_ids if target_history_id ] )
+        elif target_history_id:
+            target_history_ids = [ trans.security.decode_id( target_history_id ) ]
         if params.get( 'import_datasets_to_histories_button', False ):
             invalid_datasets = 0
             if not ldda_ids or not ( target_history_ids or new_history_name ):
@@ -1965,7 +1966,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitions ):
                                     library=library,
                                     current_history=current_history,
                                     ldda_ids=ldda_ids,
-                                    selected_history_id=selected_history_id,
+                                    target_history_id=target_history_id,
                                     target_history_ids=target_history_ids,
                                     source_lddas=source_lddas,
                                     target_histories=target_histories,
diff --git a/lib/galaxy/webapps/community/controllers/repository.py b/lib/galaxy/webapps/community/controllers/repository.py
index a41b734c140..140bc636f2d 100644
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -236,7 +236,7 @@ class MatchedRepositoryListGrid( grids.Grid ):
     template='/webapps/community/repository/grid.mako'
     default_sort_key = "Repository.name"
     columns = [
-        NameColumn( "Name",
+        NameColumn( "Repository name",
                     link=( lambda item: dict( operation="view_or_manage_repository",
                                               id=item.id,
                                               webapp="community" ) ),
@@ -588,17 +588,17 @@ class RepositoryController( BaseUIController, ItemRatings ):
                                     match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
                         else:
                             ok = False
-            if workflow_names:
+            elif workflow_names:
                 if 'workflows' in metadata:
                     workflows = metadata[ 'workflows' ]
                 else:
                     workflows = []
                 for workflow_dict in workflows:
                     for workflow_name in workflow_names:
-                        if self.__in_workflow_dict( workflow_dict, exact_matches_checked, workflow_name=workflow_name ):
+                        if self.__in_workflow_dict( workflow_dict, exact_matches_checked, workflow_name ):
                             match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) )
         return ok, match_tuples
-    def __in_workflow_dict( self, workflow_dict, exact_matches_checked, workflow_name=None ):
+    def __in_workflow_dict( self, workflow_dict, exact_matches_checked, workflow_name ):
         workflow_dict_workflow_name = workflow_dict[ 'name' ].lower()
         return ( workflow_name == workflow_dict_workflow_name ) or \
                ( not exact_matches_checked and workflow_dict_workflow_name.find( workflow_name ) >= 0 )
diff --git a/templates/library/common/import_datasets_to_histories.mako b/templates/library/common/import_datasets_to_histories.mako
index a6bff3e0559..d3a5bb15d44 100644
--- a/templates/library/common/import_datasets_to_histories.mako
+++ b/templates/library/common/import_datasets_to_histories.mako
@@ -49,12 +49,12 @@
         <div class="toolFormTitle">Destination Histories:</div>
         <div class="toolFormBody">
             <div class="form-row" id="single-destination">
-                <select id="single-dest-select" name="target_history_ids">
+                <select id="single-dest-select" name="target_history_id">
                     %for i, target_history in enumerate( target_histories ):
                         <%
                             encoded_id = trans.security.encode_id( target_history.id )
-                            if encoded_id == selected_history_id:
-                                selected_text = " selected"
+                            if encoded_id == target_history_id:
+                                selected_text = " selected='selected'"
                             else:
                                 selected_text = ""
                             if target_history == current_history:

From 10add085ca7ade54a1d05f6f0c51620d92846789 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Tue, 8 Nov 2011 15:18:24 -0500
Subject: [PATCH 169/362] Fix for generating metadata in tool shed repositories
 for a tool that does not use a tool_data_table entry for a dynamic
 SelectField input parameter.

---
 lib/galaxy/web/controllers/admin.py           | 21 +++++++++----------
 .../webapps/community/controllers/common.py   | 15 +++++++------
 2 files changed, 19 insertions(+), 17 deletions(-)

diff --git a/lib/galaxy/web/controllers/admin.py b/lib/galaxy/web/controllers/admin.py
index 131343d8ffa..2080571fda0 100644
--- a/lib/galaxy/web/controllers/admin.py
+++ b/lib/galaxy/web/controllers/admin.py
@@ -1147,21 +1147,20 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
     def __get_repository_tools_and_sample_files( self, trans, tool_path, repo_files_dir ):
         # The sample_files list contains all files whose name ends in .sample
         sample_files = []
-        # The repository_tools_tups list contains tuples of ( relative_path_to_tool_config, tool ) pairs
-        repository_tools_tups = []
+        # Find all special .sample files first.
         for root, dirs, files in os.walk( repo_files_dir ):
-            if not root.find( '.hg' ) >= 0 and not root.find( 'hgrc' ) >= 0:
-                if '.hg' in dirs:
-                    # Don't visit .hg directories - should be impossible since we don't
-                    # allow uploaded archives that contain .hg dirs, but just in case...
-                    dirs.remove( '.hg' )
-                if 'hgrc' in files:
-                     # Don't include hgrc files in commit.
-                    files.remove( 'hgrc' )
-                # Find all special .sample files first.
+            if root.find( '.hg' ) < 0:
                 for name in files:
                     if name.endswith( '.sample' ):
                         sample_files.append( os.path.abspath( os.path.join( root, name ) ) )
+        # The repository_tools_tups list contains tuples of ( relative_path_to_tool_config, tool ) pairs
+        repository_tools_tups = []
+        for root, dirs, files in os.walk( repo_files_dir ):
+            if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0:
+                if '.hg' in dirs:
+                    dirs.remove( '.hg' )
+                if 'hgrc' in files:
+                    files.remove( 'hgrc' )
                 for name in files:
                     # Find all tool configs.
                     if name.endswith( '.xml' ):
diff --git a/lib/galaxy/webapps/community/controllers/common.py b/lib/galaxy/webapps/community/controllers/common.py
index 2faabb031bf..a493713d4b4 100644
--- a/lib/galaxy/webapps/community/controllers/common.py
+++ b/lib/galaxy/webapps/community/controllers/common.py
@@ -214,7 +214,8 @@ def check_tool_input_params( trans, name, tool, sample_files, invalid_files ):
                             copy_sample_loc_file( trans, sample_file )
                             options.index_file = index_tail
                             options.missing_index_file = None
-                            options.tool_data_table.missing_index_file = None
+                            if options.tool_data_table:
+                                options.tool_data_table.missing_index_file = None
                             sample_found = True
                             break
                     if not sample_found:
@@ -325,8 +326,14 @@ def set_repository_metadata( trans, id, changeset_revision, **kwd ):
     if ctx is not None:
         metadata_dict = {}
         if changeset_revision == repository.tip:
+            # Find all special .sample files first.
             for root, dirs, files in os.walk( repo_dir ):
-                if not root.find( '.hg' ) >= 0 and not root.find( 'hgrc' ) >= 0:
+                if root.find( '.hg' ) < 0:
+                    for name in files:
+                        if name.endswith( '.sample' ):
+                            sample_files.append( os.path.abspath( os.path.join( root, name ) ) )
+            for root, dirs, files in os.walk( repo_dir ):
+                if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0:
                     if '.hg' in dirs:
                         # Don't visit .hg directories - should be impossible since we don't
                         # allow uploaded archives that contain .hg dirs, but just in case...
@@ -334,10 +341,6 @@ def set_repository_metadata( trans, id, changeset_revision, **kwd ):
                     if 'hgrc' in files:
                          # Don't include hgrc files in commit.
                         files.remove( 'hgrc' )
-                    # Find all special .sample files first.
-                    for name in files:
-                        if name.endswith( '.sample' ):
-                            sample_files.append( os.path.abspath( os.path.join( root, name ) ) )
                     for name in files:
                         # Find all tool configs.
                         if name.endswith( '.xml' ):

From edf615b3594920fc956a3a3009d601451c3cff4d Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Tue, 8 Nov 2011 16:35:48 -0500
Subject: [PATCH 170/362] Add locale files for Chinese provided by hanfeisun.

---
 locale/zh/LC_MESSAGES/ginga.mo | Bin 0 -> 9248 bytes
 locale/zh/LC_MESSAGES/ginga.po | 597 +++++++++++++++++++++++++++++++++
 locale/zh/LC_MESSAGES/tools.mo | Bin 0 -> 498 bytes
 locale/zh/LC_MESSAGES/tools.po |  84 +++++
 4 files changed, 681 insertions(+)
 create mode 100644 locale/zh/LC_MESSAGES/ginga.mo
 create mode 100644 locale/zh/LC_MESSAGES/ginga.po
 create mode 100644 locale/zh/LC_MESSAGES/tools.mo
 create mode 100644 locale/zh/LC_MESSAGES/tools.po

diff --git a/locale/zh/LC_MESSAGES/ginga.mo b/locale/zh/LC_MESSAGES/ginga.mo
new file mode 100644
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GIT binary patch
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diff --git a/locale/zh/LC_MESSAGES/ginga.po b/locale/zh/LC_MESSAGES/ginga.po
new file mode 100644
index 00000000000..f7f7721a399
--- /dev/null
+++ b/locale/zh/LC_MESSAGES/ginga.po
@@ -0,0 +1,597 @@
+# SOME DESCRIPTIVE TITLE.
+# Copyright (C) YEAR THE PACKAGE'S COPYRIGHT HOLDER
+# This file is distributed under the same license as the PACKAGE package.
+# FIRST AUTHOR <EMAIL@ADDRESS>, YEAR.
+#
+msgid ""
+msgstr ""
+"Project-Id-Version: yinhe 1.0\n"
+"Report-Msgid-Bugs-To: \n"
+"POT-Creation-Date: 2011-10-15 13:58+0800\n"
+"PO-Revision-Date: 2011-11-04 19:13+0900\n"
+"Last-Translator: Hanfei Sun <hfsun.tju@gmail.com> Juan Wang <jinling8@gmail.com>\n"
+"Language-Team: Chinese\n"
+"MIME-Version: 1.0\n"
+"Content-Type: text/plain; charset=UTF-8\n"
+"Content-Transfer-Encoding: 8bit\n"
+"Plural-Forms: nplurals=1; plural=0;\n"
+
+#:
+msgid "iso-8859-1"
+msgstr "utf-8"
+
+#:
+msgid "lang=\"en\""
+msgstr "lang=\"zh\""
+
+
+#: templates/base_panels.mako:5
+msgid "Galaxy"
+msgstr "Galaxy"
+
+#: templates/history/options.mako:24
+msgid "Are you sure you want to delete the current history?"
+msgstr "确认要删除当前的历史记录吗？"
+
+
+#: templates/root/history.mako:38
+msgid "collapse all"
+msgstr "全部收缩"
+
+
+#: templates/root/index.mako:5
+msgid "Tools"
+msgstr "工具"
+ 
+
+#: tools/**.xml
+msgid "Get Data"
+msgstr "获取数据"
+
+msgid "Get ENCODE Data"
+msgstr "获取ENCODE数据"
+
+msgid "ENCODE Tools"
+msgstr "ENCODE工具"
+
+msgid "Lift-Over"
+msgstr "版本转换"
+
+
+msgid "Text Manipulation"
+msgstr "文本操作"
+
+msgid "Filter and Sort"
+msgstr "过滤和排序"
+
+msgid "Join, Subtract and Group"
+msgstr "结合，差集与分组"
+
+msgid "Convert Formats"
+msgstr "格式转换"
+
+msgid "Extract Features"
+msgstr "特征提取"
+
+msgid "Fetch Sequences"
+msgstr "获取序列"
+
+msgid "Fetch Alignments"
+msgstr "获取比对上的序列"
+
+msgid "Get Genomic Scores"
+msgstr "获得基因组分数"
+
+msgid "Operate on Genomic Intervals"
+msgstr "基因组区间操作"
+
+msgid "Statistics"
+msgstr "统计量"
+
+msgid "Graph/Display Data"
+msgstr "图形／数据"
+
+msgid "Regional Variation"
+msgstr "区域多态性"
+
+msgid "Evolution: HyPhy"
+msgstr "进化: HyPhy"
+
+msgid "Taxonomy manipulation"
+msgstr "分类处理"
+
+msgid "Solexa tools"
+msgstr "Solexa工具"
+
+msgid "FASTA manipulation"
+msgstr "FASTA处理"
+
+msgid "Short Read QC and Manipulation"
+msgstr "短片段数据质量控制及处理"
+
+msgid "Short Read Mapping"
+msgstr "短片段回贴"
+
+
+#: templates/admin_main.mako:3 templates/admin_main.mako:8
+msgid "Galaxy Administration"
+msgstr "Galaxy 管理"
+
+#: templates/admin_main.mako:17
+msgid "Admin password: "
+msgstr "管理员密码: "
+
+#: templates/admin_main.mako:19
+msgid "Reload tool: "
+msgstr "重新载入工具"
+
+#: templates/admin_main.mako:35
+msgid "Reload"
+msgstr "重新载入"
+
+#: templates/dataset/edit_attributes.mako:2
+msgid "History Item Attributes"
+msgstr "历史项目属性"
+
+#: templates/dataset/edit_attributes.mako:19
+msgid "Edit Attributes"
+msgstr "编辑属性"
+
+#: templates/dataset/edit_attributes.mako:64
+msgid ""
+"This will inspect the dataset and attempt to correct the above column values "
+"if they are not accurate."
+msgstr "数据集检查，若有错误，更正上述栏中的值。"
+
+#: templates/dataset/edit_attributes.mako:68
+msgid ""
+"Required metadata values are missing. Some of these values may not be "
+"editable by the user. Selecting \"Auto-detect\" will attempt to fix these "
+"values."
+msgstr "所需元数据值缺失。其中一些值可能无法被用户编辑。选择“自动检测”将修正这些值。"
+
+#: templates/dataset/edit_attributes.mako:78
+msgid "Convert to new format"
+msgstr "转换成新格式"
+
+#: templates/dataset/edit_attributes.mako:84
+msgid "Convert to"
+msgstr "转换"
+
+#: templates/dataset/edit_attributes.mako:95
+msgid ""
+"This will create a new dataset with the contents of this dataset converted "
+"to a new format."
+msgstr "这将创建一个新的数据集，内容是转换后的数据集。"
+
+#: templates/dataset/edit_attributes.mako:111
+msgid "Change data type"
+msgstr "改变数据类型"
+
+#: templates/dataset/edit_attributes.mako:117
+msgid "New Type"
+msgstr "新类型"
+
+#: templates/dataset/edit_attributes.mako:124
+msgid ""
+"This will change the datatype of the existing dataset but <i>not</i> modify "
+"its contents. Use this if Galaxy has incorrectly guessed the type of your "
+"dataset."
+msgstr "这将改变已有数据集的数据类型，但是<i>不</i>改变其内容。当Galaxy不能正确判断你的数据类型时，设置该参数。"
+
+#: templates/dataset/edit_attributes.mako:137
+msgid "Copy History Item"
+msgstr "复制历史记录项"
+
+#: templates/history/list.mako:3
+msgid "Saved Histories"
+msgstr "保存的历史记录"
+
+#: templates/history/list.mako:19
+msgid "Stored Histories"
+msgstr "存储的历史记录"
+
+#: templates/history/list.mako:21 templates/root/history.mako:239
+msgid "hide deleted"
+msgstr "隐藏已删除"
+
+#: templates/history/list.mako:23
+msgid "show deleted"
+msgstr "显示已删除"
+
+#: templates/history/list.mako:27
+msgid "Name"
+msgstr "名称"
+
+#: templates/history/list.mako:27
+msgid "Size"
+msgstr "大小"
+
+#: templates/history/list.mako:27
+msgid "Last modified"
+msgstr "最后修改"
+
+#: templates/history/list.mako:27
+msgid "Actions"
+msgstr "操作"
+
+#: templates/history/list.mako:45
+msgid "rename"
+msgstr "重命名"
+
+#: templates/history/list.mako:46
+msgid "switch to"
+msgstr "切换到"
+
+#: templates/history/list.mako:47
+msgid "delete"
+msgstr "删除"
+
+#: templates/history/list.mako:49
+msgid "undelete"
+msgstr "取消删除"
+
+#: templates/history/list.mako:55
+msgid "Action"
+msgstr "操作"
+
+#: templates/history/list.mako:56 templates/history/options.mako:21
+msgid "Share"
+msgstr "共享"
+
+#: templates/history/list.mako:56 templates/history/options.mako:15
+msgid "Rename"
+msgstr "重命名"
+
+#: templates/history/list.mako:56 templates/history/options.mako:24
+msgid "Delete"
+msgstr "删除"
+
+#: templates/history/list.mako:58
+msgid "Undelete"
+msgstr "取消删除"
+
+#: templates/history/list.mako:65
+msgid "You have no stored histories"
+msgstr "没有存储的历史记录"
+
+#: templates/history/options.mako:5
+msgid "History Options"
+msgstr "历史记录选项"
+
+#: templates/history/options.mako:9
+msgid "You must be "
+msgstr "你必须"
+
+#: templates/history/options.mako:9
+msgid "logged in"
+msgstr "登录"
+
+#: templates/history/options.mako:9
+msgid " to store or switch histories."
+msgstr "以存储或切换历史记录"
+
+#: templates/history/options.mako:15
+#, python-format
+msgid " current history (stored as \"%s\")"
+msgstr " 当前历史（以\"%s\"形式存储）"
+
+#: templates/history/options.mako:16
+msgid "List"
+msgstr "列表"
+
+#: templates/history/options.mako:16
+msgid " previously stored histories"
+msgstr " 以前存储的历史记录"
+
+#: templates/history/options.mako:18
+msgid "Create"
+msgstr "创建"
+
+#: templates/history/options.mako:18
+msgid " a new empty history"
+msgstr " 一个新的空历史记录"
+
+#: templates/history/options.mako:20
+msgid "Construct workflow"
+msgstr "构建工作流程"
+
+#: templates/history/options.mako:20
+msgid " from the current history"
+msgstr " 来源于当前历史"
+
+#: templates/history/options.mako:21 templates/history/options.mako:24
+msgid " current history"
+msgstr " 当前历史"
+
+#: templates/history/options.mako:23
+msgid "Show deleted"
+msgstr "显示已删除"
+
+#: templates/history/options.mako:23
+msgid " datasets in history"
+msgstr " 历史中的数据集"
+
+#: templates/history/rename.mako:3 templates/history/rename.mako:6
+msgid "Rename History"
+msgstr "重命名历史"
+
+
+msgid "Rename Histories"
+msgstr "重命名历史记录"
+
+msgid "Perform Action"
+msgstr "运行操作"
+
+msgid "Submit"
+msgstr "提交"
+
+
+
+#: templates/history/rename.mako:10
+msgid "Current Name"
+msgstr "当前名称"
+
+#: templates/history/rename.mako:10
+msgid "New Name"
+msgstr "新名称"
+
+#: templates/history/share.mako:3
+msgid "Share histories"
+msgstr "共享历史记录"
+
+#: templates/history/share.mako:6
+msgid "Share Histories"
+msgstr "共享历史记录"
+
+#: templates/history/share.mako:9
+msgid "History Name:"
+msgstr "历史名称"
+
+#: templates/history/share.mako:9
+msgid "Number of Datasets:"
+msgstr "数据集数量"
+
+#: templates/history/share.mako:9
+msgid "Share Link"
+msgstr "共享链接"
+
+#: templates/history/share.mako:15
+msgid "This history contains no data."
+msgstr "这项历史中没有数据"
+
+#: templates/history/share.mako:21
+msgid "copy link to share"
+msgstr "复制链接以共享"
+
+#: templates/history/share.mako:24
+msgid "Email of User to share with:"
+msgstr "发送到这些Email地址进行分享"
+
+#: templates/root/history.mako:7
+msgid "Galaxy History"
+msgstr "Galaxy 历史"
+
+#: templates/root/history.mako:237
+msgid "refresh"
+msgstr "刷新"
+
+#: templates/root/history.mako:245
+msgid "You are currently viewing a deleted history!"
+msgstr "正在查看已删除的历史"
+
+#: templates/root/history.mako:289
+msgid "Your history is empty. Click 'Get Data' on the left pane to start"
+msgstr "历史已空，请单击左边窗格中‘获取数据’"
+
+#: templates/root/history_common.mako:41
+msgid "Job is waiting to run"
+msgstr "等待运行的进程"
+
+#: templates/root/history_common.mako:43
+msgid "Job is currently running"
+msgstr "正在运行的进程"
+
+#: templates/root/history_common.mako:46
+msgid "An error occurred running this job: "
+msgstr "进程运行时出错 "
+
+#: templates/root/history_common.mako:47
+msgid "report this error"
+msgstr "报告错误"
+
+#: templates/root/history_common.mako:54
+msgid "No data: "
+msgstr "没有数据： "
+
+#: templates/root/history_common.mako:58
+msgid "format: "
+msgstr "格式： "
+
+#: templates/root/history_common.mako:59
+msgid "database: "
+msgstr "数据库： "
+
+#: templates/root/history_common.mako:66 templates/root/masthead.mako:20
+msgid "Info: "
+msgstr "信息： "
+
+#: templates/root/history_common.mako:85
+#, python-format
+msgid "Error: unknown dataset state \"%s\"."
+msgstr "错误：未知的数据集状态 \"%s\"。"
+
+
+msgid "Options"
+msgstr "选项"
+
+msgid "History"
+msgstr "历史"
+
+#: templates/root/masthead.mako:20
+msgid "report bugs"
+msgstr "错误报告"
+
+#: templates/root/masthead.mako:21
+msgid "wiki"
+msgstr "wiki"
+
+#: templates/root/masthead.mako:22
+msgid "screencasts"
+msgstr "演示视频"
+
+
+#: templates/root/masthead.mako:23
+msgid "blog"
+msgstr "博客"
+
+#: templates/root/masthead.mako:31
+#, python-format
+msgid "Logged in as %s: "
+msgstr "以%s的身份登录: "
+
+#: templates/root/masthead.mako:31
+msgid "manage"
+msgstr "管理"
+
+#: templates/root/masthead.mako:32
+msgid "logout"
+msgstr "注销"
+
+#: templates/root/masthead.mako:34
+msgid "Account: "
+msgstr "帐户: "
+
+#: templates/root/masthead.mako:34
+msgid "create"
+msgstr "创建"
+
+#: templates/root/masthead.mako:35
+msgid "login"
+msgstr "登录"
+
+#: templates/root/tool_menu.mako:52
+msgid "Galaxy Tools"
+msgstr "Galaxy 工具"
+
+#: templates/root/tool_menu.mako:129
+msgid "Workflow"
+msgstr "工作流程"
+
+#: templates/root/tool_menu.mako:134
+msgid "Manage"
+msgstr "管理"
+
+#: templates/root/tool_menu.mako:134
+msgid "workflows"
+msgstr "工作流程"
+
+#: templates/user/index.mako:2 templates/user/index.mako:4
+msgid "Account settings"
+msgstr "帐户设置"
+
+#: templates/user/index.mako:7
+#, python-format
+msgid "You are currently logged in as %s."
+msgstr "当前以%s的身份登录"
+
+#: templates/user/index.mako:9
+msgid "Change your password"
+msgstr "修改密码"
+
+#: templates/user/index.mako:10
+msgid "Update your email address"
+msgstr "更新电子邮件地址"
+
+#: templates/user/index.mako:11
+msgid "Logout"
+msgstr "注销"
+
+#: templates/user/index.mako:16
+msgid "Login"
+msgstr "登录"
+
+#: templates/user/index.mako:17
+msgid "Create new account"
+msgstr "创建新帐户"
+
+msgid "Show Tool Search"
+msgstr "显示工具搜索"
+
+msgid "Analyze Data"
+msgstr "分析数据"
+
+msgid "analysis"
+msgstr "分析"
+
+msgid "History Lists"
+msgstr "历史记录清单"
+
+msgid "Histories Shared with Me"
+msgstr "共享的数据"
+
+msgid "Current History"
+msgstr "当前历史记录"
+
+msgid "Create New"
+msgstr "创建"
+
+msgid "Clone"
+msgstr "复制"
+
+msgid "Share or Publish"
+msgstr "共享或发布"
+
+msgid "Extract Workflow"
+msgstr "提取工作流程"
+
+msgid "Dataset Security"
+msgstr "数据安全性"
+
+
+msgid "Show Deleted Datasets"
+msgstr "显示已删除数据"
+
+msgid "Show Hidden Datasets"
+msgstr "显示隐藏数据"
+
+msgid "Show Structure"
+msgstr "显示结构"
+
+msgid "Export to File"
+msgstr "导出为文件"
+
+msgid "Other Actions"
+msgstr "其他"
+
+msgid "Import from File"
+msgstr "导入文件"
+
+msgid "Shared Data"
+msgstr "数据共享"
+
+msgid "Data Libraries" 
+msgstr "数据仓库"
+
+msgid "Published Histories"
+msgstr "已发布的历史记录"
+
+msgid "Published Workflows"
+msgstr "已发布的工作流程"
+
+msgid "Published Pages"
+msgstr "已发布的页面"
+
+msgid "Help"
+msgstr "帮助"
+
+msgid "Email comments, bug reports, or suggestions"
+msgstr "发邮件进行意见反馈或错误报告"
+
+
+msgid "User"
+msgstr "用户"
+
+
+msgid "Register"
+msgstr "注册"
\ No newline at end of file
diff --git a/locale/zh/LC_MESSAGES/tools.mo b/locale/zh/LC_MESSAGES/tools.mo
new file mode 100644
index 0000000000000000000000000000000000000000..41ed000d840b744b5f71dec64104a8289a1b53de
GIT binary patch
literal 498
zcmaKo!A=4(5QbNyiP?Da?4b`}*P=wFh*4lg49L1{ICv{CENhmQv|S@Uf{A*<$1vV}
z8*dOF!$A{0>7Rb-H2FK7{_h(rQwOz-Y$998DsqS{6d-HJC33&yI9Ir@BQvaVeQ9y`
zM>VjdDy(n<t*)VGX}wQ7piQDACqdXc_bU<U_+h)=x^P1nD{X1h#7Uo)v)Ir`apE^m
z>W$-*YBluRZ8vB|w4y;+>_D+IaI(W#fwEni+b1l~*&bzi#?VMZxJec-{p)K8V`-#?
zG^wykb8;r+020#9Bsm-oOeQ^hogK#`k)&QvjgH)gkZ~qrpb>}>CwId?d_kINk<wG8
zM}`wQ{yLgcu1LPi5_6mNrvIBq&SP#xNedDunvC&l7H;kKI2DO3lHO2g1Gbde0X_Kj
zEhZm;roQZ{ej;N|4!VhTYal^mJQ(DJld|YSN|;yh@~-po_%?fbo=;!r4=>IqN6?N)

literal 0
HcmV?d00001

diff --git a/locale/zh/LC_MESSAGES/tools.po b/locale/zh/LC_MESSAGES/tools.po
new file mode 100644
index 00000000000..17466fe187a
--- /dev/null
+++ b/locale/zh/LC_MESSAGES/tools.po
@@ -0,0 +1,84 @@
+# Japanese translations for PROJECT.
+# Copyright (C) 2009 ORGANIZATION
+# This file is distributed under the same license as the PROJECT project.
+# FIRST AUTHOR <EMAIL@ADDRESS>, 2009.
+#
+msgid ""
+msgstr ""
+"Project-Id-Version: PROJECT VERSION\n"
+"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
+"POT-Creation-Date: 2009-03-17 04:06-0400\n"
+"PO-Revision-Date: 2009-03-17 04:06-0400\n"
+"Last-Translator: Hanfei Sun <hfsun.tju@gmail.com>\n"
+"Language-Team: zh <hfsun.tju@gmail.com>\n"
+"Plural-Forms: nplurals=1; plural=0\n"
+"MIME-Version: 1.0\n"
+"Content-Type: text/plain; charset=utf-8\n"
+"Content-Transfer-Encoding: 8bit\n"
+"Generated-By: Babel 0.9.4\n"
+
+msgid "Get Data"
+msgstr "获取数据"
+
+msgid "Get ENCODE Data"
+msgstr ""
+
+msgid "ENCODE Tools"
+msgstr ""
+
+msgid "Lift-Over"
+msgstr ""
+
+msgid "Text Manipulation"
+msgstr ""
+
+msgid "Filter and Sort"
+msgstr ""
+
+msgid "Join, Subtract and Group"
+msgstr ""
+
+msgid "Convert Formats"
+msgstr ""
+
+msgid "Extract Features"
+msgstr ""
+
+msgid "Fetch Sequences"
+msgstr ""
+
+msgid "Fetch Alignments"
+msgstr ""
+
+msgid "Get Genomic Scores"
+msgstr ""
+
+msgid "Operate on Genomic Intervals"
+msgstr ""
+
+msgid "Statistics"
+msgstr ""
+
+msgid "Graph/Display Data"
+msgstr ""
+
+msgid "Regional Variation"
+msgstr ""
+
+msgid "Evolution: HyPhy"
+msgstr ""
+
+msgid "Taxonomy manipulation"
+msgstr ""
+
+msgid "Solexa tools"
+msgstr ""
+
+msgid "FASTA manipulation"
+msgstr ""
+
+msgid "Short Read QC and Manipulation"
+msgstr ""
+
+msgid "Short Read Mapping"
+msgstr ""

From 46ece42f6e59bf47f26c853ddf44c1675176cb59 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Tue, 8 Nov 2011 16:53:19 -0500
Subject: [PATCH 171/362] Update FASTQ Groomer tool help to indicate that
 Illumina 1.8+ is Sanger encoded.

---
 tools/fastq/fastq_groomer.xml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/tools/fastq/fastq_groomer.xml b/tools/fastq/fastq_groomer.xml
index 5a3738eb08d..10a4adeb453 100644
--- a/tools/fastq/fastq_groomer.xml
+++ b/tools/fastq/fastq_groomer.xml
@@ -16,7 +16,7 @@
     <param name="input_file" type="data" format="fastq" label="File to groom" />
     <param name="input_type" type="select" label="Input FASTQ quality scores type">
       <option value="solexa">Solexa</option>
-      <option value="illumina">Illumina 1.3+</option>
+      <option value="illumina">Illumina 1.3-1.7</option>
       <option value="sanger" selected="True">Sanger</option>
       <option value="cssanger">Color Space Sanger</option>
     </param>
@@ -358,6 +358,10 @@ When converting between color space (csSanger) and base/sequence space (Sanger,
 
 Diagram adapted from http://en.wikipedia.org/wiki/FASTQ_format
 
+.. class:: infomark
+
+Output from Illumina 1.8+ pipelines are Sanger encoded.
+
 ------
 
 **Citation**

From 1e93e633fbba0b401a9a1137c5c755b65e4ca6ed Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Wed, 9 Nov 2011 09:41:12 -0500
Subject: [PATCH 172/362] Remove "-targetNotSorted" argument from GATK indel
 realigner: vanished without warning or notice.

---
 tools/gatk/indel_realigner.xml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/tools/gatk/indel_realigner.xml b/tools/gatk/indel_realigner.xml
index 27c0ba4b726..0e8c4635f93 100644
--- a/tools/gatk/indel_realigner.xml
+++ b/tools/gatk/indel_realigner.xml
@@ -1,4 +1,4 @@
-<tool id="gatk_indel_realigner" name="Indel Realigner" version="0.0.3">
+<tool id="gatk_indel_realigner" name="Indel Realigner" version="0.0.4">
   <description>- perform local realignment</description>
   <requirements>
       <requirement type="package" version="1.2">gatk</requirement>
@@ -90,7 +90,6 @@
     ##start analysis specific options
     -d "-targetIntervals" "${target_intervals}" "${target_intervals.ext}" "gatk_target_intervals"
     -p '
-    -targetNotSorted ##always resort input intervals
     --disable_bam_indexing
     '
     #if $analysis_param_type.analysis_param_type_selector == "advanced":

From 8c4f54ff77cacc1034e54d4f6b1214f1f5e45dbf Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 10 Nov 2011 08:54:23 -0500
Subject: [PATCH 173/362] Repack of .js

---
 static/scripts/packed/galaxy.panels.js | 2 +-
 static/scripts/packed/trackster.js     | 2 +-
 static/scripts/packed/trackster_ui.js  | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/static/scripts/packed/galaxy.panels.js b/static/scripts/packed/galaxy.panels.js
index e21108b1627..e289002e659 100644
--- a/static/scripts/packed/galaxy.panels.js
+++ b/static/scripts/packed/galaxy.panels.js
@@ -1 +1 @@
-function ensure_dd_helper(){if($("#DD-helper").length==0){$("<div id='DD-helper'/>").css({background:"white",opacity:0,zIndex:9000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}var MIN_PANEL_WIDTH=100,MAX_PANEL_WIDTH=1000;function make_left_panel(h,c,e){var g=false;var f=null;var d=function(i){var j=i;if(i<0){i=0}$(h).css("width",i);$(e).css("left",j);$(c).css("left",i+7);if(document.recalc){document.recalc()}};var a=function(){if(g){$(e).removeClass("hover");$(e).animate({left:f},"fast");$(h).css("left",-f).show().animate({left:0},"fast",function(){d(f);$(e).removeClass("hidden")});g=false}else{f=$(e).position().left;$(c).css("left",$(e).innerWidth());if(document.recalc){document.recalc()}$(e).removeClass("hover");$(h).animate({left:-f},"fast");$(e).animate({left:-1},"fast",function(){$(this).addClass("hidden")});g=true}};$(e).bind("dragstart",function(){$("#DD-helper").show()}).bind("dragend",function(){$("#DD-helper").hide()}).bind("drag",function(i,j){x=j.offsetX;x=Math.min(MAX_PANEL_WIDTH,Math.max(MIN_PANEL_WIDTH,x));if(g){$(h).css("left",0);$(e).removeClass("hidden");g=false}d(x)}).bind("dragclickonly",function(){a()}).find("div").show();var b=function(i){if((g&&i=="show")||(!g&&i=="hide")){a()}};return{force_panel:b}}function make_right_panel(a,e,h){var j=false,g=false,c=null;var d=function(k){$(a).css("width",k);$(e).css("right",k+9);$(h).css("right",k).css("left","");if(document.recalc){document.recalc()}};var i=function(){if(j){$(h).removeClass("hover");$(h).animate({right:c},"fast");$(a).css("right",-c).show().animate({right:0},"fast",function(){d(c);$(h).removeClass("hidden")});j=false}else{c=$(document).width()-$(h).position().left-$(h).outerWidth();$(e).css("right",$(h).innerWidth()+1);if(document.recalc){document.recalc()}$(h).removeClass("hover");$(a).animate({right:-c},"fast");$(h).animate({right:-1},"fast",function(){$(this).addClass("hidden")});j=true}g=false};var b=function(k){var l=$(e).width()-(j?c:0);if(l<k){if(!j){i();g=true}}else{if(g){i();g=false}}};$(h).hover(function(){$(this).addClass("hover")},function(){$(this).removeClass("hover")}).bind("dragstart",function(){$("#DD-helper").show()}).bind("dragend",function(){$("#DD-helper").hide()}).bind("drag",function(k,l){x=l.offsetX;w=$(window).width();x=Math.min(w-MIN_PANEL_WIDTH,x);x=Math.max(w-MAX_PANEL_WIDTH,x);if(j){$(a).css("right",0);$(h).removeClass("hidden");j=false}d(w-x-$(this).outerWidth())}).bind("dragclickonly",function(){i()}).find("div").show();var f=function(k){if((j&&k=="show")||(!j&&k=="hide")){i()}};return{handle_minwidth_hint:b,force_panel:f}}function hide_modal(){$(".dialog-box-container").fadeOut(function(){$("#overlay").hide();$(".dialog-box").find(".body").children().remove()})}function show_modal(h,c,f,d,g){if(h){$(".dialog-box").find(".title").html(h);$(".dialog-box").find(".unified-panel-header").show()}else{$(".dialog-box").find(".unified-panel-header").hide()}var a=$(".dialog-box").find(".buttons").html("");if(f){$.each(f,function(b,i){a.append($("<button/>").text(b).click(i));a.append(" ")});a.show()}else{a.hide()}var a=$(".dialog-box").find(".extra_buttons").html("");if(d){$.each(d,function(b,i){a.append($("<button/>").text(b).click(i));a.append(" ")});a.show()}else{a.hide()}if(c=="progress"){c=$("<img/>").attr("src",image_path+"/yui/rel_interstitial_loading.gif")}var e=$(".dialog-box").find(".body");e.css("min-width","");$(".dialog-box").find(".body").html(c);if(!$(".dialog-box-container").is(":visible")){$("#overlay").show();$(".dialog-box-container").fadeIn()}e.css("min-width",e.width());if(g){g()}}function show_in_overlay(c){var d=c.width||"600";var b=c.height||"400";var a=c.scroll||"auto";$("#overlay-background").bind("click.overlay",function(){hide_modal();$("#overlay-background").unbind("click.overlay")});show_modal(null,$("<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-17px;top:-15px;src='"+image_path+"/closebox.png'><iframe style='margin: 0; padding: 0;' src='"+c.url+"' width='"+d+"' height='"+b+"' scrolling='"+a+"' frameborder='0'></iframe></div>"));$("#close_button").bind("click",function(){hide_modal()})}$(function(){$(".tab").each(function(){var a=$(this).children(".submenu");if(a.length>0){if($.browser.msie){a.prepend("<iframe style=\"position: absolute; top: 0; left: 0; width: 100%; height: 100%; z-index: -1; filter:Alpha(Opacity='0');\"></iframe>")}$(this).hover(function(){a.show()},function(){a.hide()});a.click(function(){a.hide()})}})});function user_changed(a,b){if(a){$(".loggedin-only").show();$(".loggedout-only").hide();$("#user-email").text(a);if(b){$(".admin-only").show()}}else{$(".loggedin-only").hide();$(".loggedout-only").show();$(".admin-only").hide()}};
\ No newline at end of file
+function ensure_dd_helper(){if($("#DD-helper").length==0){$("<div id='DD-helper'/>").css({background:"white",opacity:0,zIndex:9000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}var MIN_PANEL_WIDTH=100,MAX_PANEL_WIDTH=1000;function make_left_panel(h,c,e){var g=false;var f=null;var d=function(i){var j=i;if(i<0){i=0}$(h).css("width",i);$(e).css("left",j);$(c).css("left",i+7);if(document.recalc){document.recalc()}};var a=function(){if(g){$(e).removeClass("hover");$(e).animate({left:f},"fast");$(h).css("left",-f).show().animate({left:0},"fast",function(){d(f);$(e).removeClass("hidden")});g=false}else{f=$(e).position().left;$(c).css("left",$(e).innerWidth());if(document.recalc){document.recalc()}$(e).removeClass("hover");$(h).animate({left:-f},"fast");$(e).animate({left:-1},"fast",function(){$(this).addClass("hidden")});g=true}};$(e).bind("dragstart",function(){$("#DD-helper").show()}).bind("dragend",function(){$("#DD-helper").hide()}).bind("drag",function(i,j){x=j.offsetX;x=Math.min(MAX_PANEL_WIDTH,Math.max(MIN_PANEL_WIDTH,x));if(g){$(h).css("left",0);$(e).removeClass("hidden");g=false}d(x)}).bind("dragclickonly",function(){a()}).find("div").show();var b=function(i){if((g&&i=="show")||(!g&&i=="hide")){a()}};return{force_panel:b}}function make_right_panel(a,e,h){var j=false,g=false,c=null;var d=function(k){$(a).css("width",k);$(e).css("right",k+9);$(h).css("right",k).css("left","");if(document.recalc){document.recalc()}};var i=function(){if(j){$(h).removeClass("hover");$(h).animate({right:c},"fast");$(a).css("right",-c).show().animate({right:0},"fast",function(){d(c);$(h).removeClass("hidden")});j=false}else{c=$(document).width()-$(h).position().left-$(h).outerWidth();$(e).css("right",$(h).innerWidth()+1);if(document.recalc){document.recalc()}$(h).removeClass("hover");$(a).animate({right:-c},"fast");$(h).animate({right:-1},"fast",function(){$(this).addClass("hidden")});j=true}g=false};var b=function(k){var l=$(e).width()-(j?c:0);if(l<k){if(!j){i();g=true}}else{if(g){i();g=false}}};$(h).hover(function(){$(this).addClass("hover")},function(){$(this).removeClass("hover")}).bind("dragstart",function(){$("#DD-helper").show()}).bind("dragend",function(){$("#DD-helper").hide()}).bind("drag",function(k,l){x=l.offsetX;w=$(window).width();x=Math.min(w-MIN_PANEL_WIDTH,x);x=Math.max(w-MAX_PANEL_WIDTH,x);if(j){$(a).css("right",0);$(h).removeClass("hidden");j=false}d(w-x-$(this).outerWidth())}).bind("dragclickonly",function(){i()}).find("div").show();var f=function(k){if((j&&k=="show")||(!j&&k=="hide")){i()}};return{handle_minwidth_hint:b,force_panel:f}}function hide_modal(){$(".dialog-box-container").hide(0,function(){$("#overlay").hide();$("#overlay").removeClass("modal");$(".dialog-box").find(".body").children().remove()})}function show_modal(){$("#overlay").addClass("modal");_show_modal.apply(this,arguments)}function show_message(){_show_modal.apply(this,arguments)}function _show_modal(h,c,f,d,g){if(h){$(".dialog-box").find(".title").html(h);$(".dialog-box").find(".unified-panel-header").show()}else{$(".dialog-box").find(".unified-panel-header").hide()}var a=$(".dialog-box").find(".buttons").html("");if(f){$.each(f,function(b,i){a.append($("<button/>").text(b).click(i));a.append(" ")});a.show()}else{a.hide()}var a=$(".dialog-box").find(".extra_buttons").html("");if(d){$.each(d,function(b,i){a.append($("<button/>").text(b).click(i));a.append(" ")});a.show()}else{a.hide()}if(c=="progress"){c=$("<img/>").attr("src",image_path+"/yui/rel_interstitial_loading.gif")}var e=$(".dialog-box").find(".body");e.css("min-width","");$(".dialog-box").find(".body").html(c);if(!$(".dialog-box-container").is(":visible")){$("#overlay").show();$(".dialog-box-container").show()}e.css("min-width",e.width());if(g){g()}}function show_in_overlay(c){var d=c.width||"600";var b=c.height||"400";var a=c.scroll||"auto";$("#overlay-background").bind("click.overlay",function(){hide_modal();$("#overlay-background").unbind("click.overlay")});show_modal(null,$("<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-17px;top:-15px;src='"+image_path+"/closebox.png'><iframe style='margin: 0; padding: 0;' src='"+c.url+"' width='"+d+"' height='"+b+"' scrolling='"+a+"' frameborder='0'></iframe></div>"));$("#close_button").bind("click",function(){hide_modal()})}$(function(){$(".tab").each(function(){var a=$(this).children(".submenu");if(a.length>0){if($.browser.msie){a.prepend("<iframe style=\"position: absolute; top: 0; left: 0; width: 100%; height: 100%; z-index: -1; filter:Alpha(Opacity='0');\"></iframe>")}$(this).hover(function(){a.show()},function(){a.hide()});a.click(function(){a.hide()})}})});function user_changed(a,b){if(a){$(".loggedin-only").show();$(".loggedout-only").hide();$("#user-email").text(a);if(b){$(".admin-only").show()}}else{$(".loggedin-only").hide();$(".loggedout-only").show();$(".admin-only").hide()}};
\ No newline at end of file
diff --git a/static/scripts/packed/trackster.js b/static/scripts/packed/trackster.js
index a0af2f6d9db..c8edfa0975b 100644
--- a/static/scripts/packed/trackster.js
+++ b/static/scripts/packed/trackster.js
@@ -1 +1 @@
-var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var m=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(u,t,v,r,i,s){return(Math.max(u,r)-Math.min(u,r))+(Math.max(t,i)-Math.min(t,i))+(Math.max(v,s)-Math.min(v,s))};var g,n,f,k,p,h,q,c,d,b,o,l=false;do{g=Math.random()*16777215;n=g|16711680;f=g|65280;k=g|255;d=m(n,f,k);l=true;for(var j=0;j<a.length;j++){p=a[j];h=p|16711680;q=p|65280;c=p|255;b=m(h,q,c);o=e(n,f,k,h,q,c);if((Math.abs(d-b)<125)||(o<500)){l=false;break}}}while(!l);return"#"+(16777216+g).toString(16).substr(1,6)};var trackster_module=function(f,X){var p=f("class").extend,s=f("slotting"),M=f("painters");var ae=function(af,ag){this.document=af;this.default_font=ag!==undefined?ag:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};p(ae.prototype,{load_pattern:function(af,aj){var ag=this.patterns,ah=this.dummy_context,ai=new Image();ai.src=image_path+aj;ai.onload=function(){ag[af]=ah.createPattern(ai,"repeat")}},get_pattern:function(af){return this.patterns[af]},new_canvas:function(){var af=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(af)}af.manager=this;return af}});var n={};var l=function(af,ag){n[af.attr("id")]=ag};var m=function(af,ah,aj,ai){aj=".group";var ag={};n[af.attr("id")]=ai;af.bind("drag",{handle:"."+ah,relative:true},function(ar,at){var aq=$(this);var aw=$(this).parent(),an=aw.children(),ap=n[$(this).attr("id")],am,al,au,ak,ao;al=$(this).parents(aj);if(al.length!==0){au=al.position().top;ak=au+al.outerHeight();if(at.offsetY<au){$(this).insertBefore(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable_before(ap,av);return}else{if(at.offsetY>ak){$(this).insertAfter(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable(ap);return}}}al=null;for(ao=0;ao<an.length;ao++){am=$(an.get(ao));au=am.position().top;ak=au+am.outerHeight();if(am.is(aj)&&this!==am.get(0)&&at.offsetY>=au&&at.offsetY<=ak){if(at.offsetY-au<ak-at.offsetY){am.find(".content-div").prepend(this)}else{am.find(".content-div").append(this)}if(ap.container){ap.container.remove_drawable(ap)}n[am.attr("id")].add_drawable(ap);return}}for(ao=0;ao<an.length;ao++){if(at.offsetY<$(an.get(ao)).position().top){break}}if(ao===an.length){if(this!==an.get(ao-1)){aw.append(this);n[aw.attr("id")].move_drawable(ap,ao)}}else{if(this!==an.get(ao)){$(this).insertBefore(an.get(ao));n[aw.attr("id")].move_drawable(ap,(at.deltaY>0?ao-1:ao))}}}).bind("dragstart",function(){ag["border-top"]=af.css("border-top");ag["border-bottom"]=af.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ag)})};X.moveable=m;var ad=16,H=9,E=20,T=H+2,z=100,J=12000,R=200,C=5,v=10,L=5000,w=100,o="There was an error in indexing this dataset. ",K="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",F="No data for this chrom/contig.",t="Currently indexing... please wait",x="Tool cannot be rerun: ",a="Loading data...",Y="Ready for display",d=10,u=5,B=5;function Z(ag,af){if(!af){af=0}var ah=Math.pow(10,af);return Math.round(ag*ah)/ah}var c=function(af){this.num_elements=af;this.clear()};p(c.prototype,{get:function(ag){var af=this.key_ary.indexOf(ag);if(af!==-1){if(this.obj_cache[ag].stale){this.key_ary.splice(af,1);delete this.obj_cache[ag]}else{this.move_key_to_end(ag,af)}}return this.obj_cache[ag]},set:function(ag,ah){if(!this.obj_cache[ag]){if(this.key_ary.length>=this.num_elements){var af=this.key_ary.shift();delete this.obj_cache[af]}this.key_ary.push(ag)}this.obj_cache[ag]=ah;return ah},move_key_to_end:function(ag,af){this.key_ary.splice(af,1);this.key_ary.push(ag)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var S=function(ag,af,ah){c.call(this,ag);this.track=af;this.subset=(ah!==undefined?ah:true)};p(S.prototype,c.prototype,{load_data:function(ao,aj,am,ag,al){var an=this.track.view.chrom,ai={chrom:an,low:ao,high:aj,mode:am,resolution:ag,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ai,al);if(this.track.filters_manager){var ap=[];var af=this.track.filters_manager.filters;for(var ak=0;ak<af.length;ak++){ap[ap.length]=af[ak].name}ai.filter_cols=JSON.stringify(ap)}var ah=this;return $.getJSON(this.track.data_url,ai,function(aq){ah.set_data(ao,aj,am,aq)})},get_data:function(af,aj,ak,ag,ai){var ah=this.get_data_from_cache(af,aj,ak);if(ah){return ah}ah=this.load_data(af,aj,ak,ag,ai);this.set_data(af,aj,ak,ah);return ah},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(an,ai,am,ah,al,aj){var ao=this.get_data_from_cache(an,ai,am);if(!ao){console.log("ERROR: no current data for: ",this.track,an,ai,am,ah,al);return}ao.stale=true;var ag=an;if(aj===this.DEEP_DATA_REQ){$.extend(al,{start_val:ao.data.length+1})}else{if(aj===this.BROAD_DATA_REQ){ag=(ao.max_high?ao.max_high:ao.data[ao.data.length-1][2])+1}}var af=this,ak=this.load_data(ag,ai,am,ah,al);new_data_available=$.Deferred();this.set_data(an,ai,am,new_data_available);$.when(ak).then(function(ap){if(ap.data){ap.data=ao.data.concat(ap.data);if(ap.max_low){ap.max_low=ao.max_low}if(ap.message){ap.message=ap.message.replace(/[0-9]+/,ap.data.length)}}af.set_data(an,ai,am,ap);new_data_available.resolve(ap)});return new_data_available},get_data_from_cache:function(af,ag,ah){return this.get(this.gen_key(af,ag,ah))},set_data:function(ag,ah,ai,af){return this.set(this.gen_key(ag,ah,ai),af)},gen_key:function(af,ah,ai){var ag=af+"_"+ah+"_"+ai;return ag},split_key:function(af){return af.split("_")}});var I=function(ag,af,ah){S.call(this,ag,af,ah)};p(I.prototype,S.prototype,c.prototype,{load_data:function(af,ai,aj,ag,ah){if(ag>1){return{data:null}}return S.prototype.load_data.call(this,af,ai,aj,ag,ah)}});var q=function(ai,ag,af,ah,aj){this.name=ai;this.view=ag;this.container=af;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ai}],saved_values:ah,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=aj;this.is_overview=false};p(q.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},update_track_icons:function(){},set_name:function(af){this.old_name=this.name;this.name=af;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var y=function(aj,ai,ag,af,ah,ak){q.call(this,ai,ag,af,ah,ak);this.obj_type=aj;this.drawables=[]};p(y.prototype,q.prototype,{init:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af].init()}},_draw:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af]._draw()}},to_json:function(){var ag=[];for(var af=0;af<this.drawables.length;af++){ag.push(this.drawables[af].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ag}},add_drawable:function(af){this.drawables.push(af);af.container=this},add_drawable_before:function(ah,af){var ag=this.drawables.indexOf(af);if(ag!=-1){this.drawables.splice(ag,0,ah);return true}return false},remove_drawable:function(ag){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);ag.container=null;return true}return false},move_drawable:function(ag,ah){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);this.drawables.splice(ah,0,ag);return true}return false}});var Q=function(ai,ag,af,ah){y.call(this,"DrawableGroup",ai,ag,af,ah,"group-handle");if(!Q.id_counter){Q.id_counter=0}var aj=Q.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+aj).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+aj+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.update_track_icons()};p(Q.prototype,q.prototype,y.prototype,{update_track_icons:function(){var ag=this;var af={};af["Edit configuration"]=function(){var aj=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ah=function(){ag.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ai=function(ak){if((ak.keyCode||ak.which)===27){aj()}else{if((ak.keyCode||ak.which)===13){ah()}}};$(window).bind("keypress.check_enter_esc",ai);show_modal("Configure Group",ag.config.build_form(),{Cancel:aj,OK:ah})};af.Remove=function(){ag.remove()};make_popupmenu(ag.name_div,af)}});var ac=function(af,ai,ah,ag){y.call(this,"View");this.container=af;this.chrom=null;this.vis_id=ah;this.dbkey=ag;this.title=ai;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ae(af.get(0).ownerDocument);this.reset()};p(ac.prototype,y.prototype,{init:function(){var ah=this.container,af=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ah);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ah);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ah);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,af);this.intro_div=$("<div/>").addClass("intro");var ai=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ag=function(aj){if(aj.type==="focusout"||(aj.keyCode||aj.which)===13||(aj.keyCode||aj.which)===27){if((aj.keyCode||aj.which)!==27){af.go_to($(this).val())}$(this).hide();$(this).val("");af.location_span.show();af.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ag).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){af.location_span.hide();af.chrom_select.hide();af.nav_input.val(af.chrom+":"+af.low+"-"+af.high);af.nav_input.css("display","inline-block");af.nav_input.select();af.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){af.zoom_out();af.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){af.zoom_in();af.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){af.change_chrom(af.chrom_select.val())});this.browser_content_div.click(function(aj){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(aj){af.zoom_in(aj.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(aj,ak){this.current_x=ak.offsetX}).bind("drag",function(aj,al){var am=al.offsetX-this.current_x;this.current_x=al.offsetX;var ak=Math.round(am/af.viewport_container.width()*(af.max_high-af.max_low));af.move_delta(-ak)});this.overview_close.click(function(){af.reset_overview()});this.viewport_container.bind("draginit",function(aj,ak){if(aj.clientX>af.viewport_container.width()-16){return false}}).bind("dragstart",function(aj,ak){ak.original_low=af.low;ak.current_height=aj.clientY;ak.current_x=ak.offsetX}).bind("drag",function(al,an){var aj=$(this);var ao=an.offsetX-an.current_x;var ak=aj.scrollTop()-(al.clientY-an.current_height);aj.scrollTop(ak);an.current_height=al.clientY;an.current_x=an.offsetX;var am=Math.round(ao/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}).bind("mousewheel",function(al,an,ak,aj){if(ak){var am=Math.round(-ak/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}});this.top_labeltrack.bind("dragstart",function(aj,ak){return $("<div />").css({height:af.browser_content_div.height()+af.top_labeltrack.height()+af.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(an,ao){$(ao.proxy).css({left:Math.min(an.pageX,ao.startX),width:Math.abs(an.pageX-ao.startX)});var ak=Math.min(an.pageX,ao.startX)-af.container.offset().left,aj=Math.max(an.pageX,ao.startX)-af.container.offset().left,am=(af.high-af.low),al=af.viewport_container.width();af.update_location(Math.round(ak/al*am)+af.low,Math.round(aj/al*am)+af.low)}).bind("dragend",function(ao,ap){var ak=Math.min(ao.pageX,ap.startX),aj=Math.max(ao.pageX,ap.startX),am=(af.high-af.low),al=af.viewport_container.width(),an=af.low;af.low=Math.round(ak/al*am)+an;af.high=Math.round(aj/al*am)+an;$(ap.proxy).remove();af.request_redraw()});this.add_label_track(new ab(this,{content_div:this.top_labeltrack}));this.add_label_track(new ab(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){af.resize_window()});$(document).bind("redraw",function(){af.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(af,ag){this.location_span.text(commatize(af)+" - "+commatize(ag));this.nav_input.val(this.chrom+":"+commatize(af)+"-"+commatize(ag))},load_chroms:function(ah){ah.num=w;$.extend(ah,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var af=this,ag=$.Deferred();$.ajax({url:chrom_url,data:ah,dataType:"json",success:function(aj){if(aj.chrom_info.length===0){alert("Invalid chromosome: "+ah.chrom);return}if(aj.reference){af.add_label_track(new A(af))}af.chrom_data=aj.chrom_info;var am='<option value="">Select Chrom/Contig</option>';for(var al=0,ai=af.chrom_data.length;al<ai;al++){var ak=af.chrom_data[al].chrom;am+='<option value="'+ak+'">'+ak+"</option>"}if(aj.prev_chroms){am+='<option value="previous">Previous '+w+"</option>"}if(aj.next_chroms){am+='<option value="next">Next '+w+"</option>"}af.chrom_select.html(am);af.chrom_start_index=aj.start_index;ag.resolve(aj)},error:function(){alert("Could not load chroms for this dbkey:",af.dbkey)}});return ag},change_chrom:function(ak,ag,am){if(!ak||ak==="None"){return}var ah=this;if(ak==="previous"){ah.load_chroms({low:this.chrom_start_index-w});return}if(ak==="next"){ah.load_chroms({low:this.chrom_start_index+w});return}var al=$.grep(ah.chrom_data,function(an,ao){return an.chrom===ak})[0];if(al===undefined){ah.load_chroms({chrom:ak},function(){ah.change_chrom(ak,ag,am)});return}else{if(ak!==ah.chrom){ah.chrom=ak;ah.chrom_select.val(ah.chrom);ah.max_high=al.len-1;ah.reset();ah.request_redraw(true);for(var aj=0,af=ah.drawables.length;aj<af;aj++){var ai=ah.drawables[aj];if(ai.init){ai.init()}}}if(ag!==undefined&&am!==undefined){ah.low=Math.max(ag,0);ah.high=Math.min(am,ah.max_high)}ah.reset_overview();ah.request_redraw()}},go_to:function(aj){aj=aj.replace(/ |,/g,"");var an=this,af,ai,ag=aj.split(":"),al=ag[0],am=ag[1];if(am!==undefined){try{var ak=am.split("-");af=parseInt(ak[0],10);ai=parseInt(ak[1],10)}catch(ah){return false}}an.change_chrom(al,af,ai)},move_fraction:function(ah){var af=this;var ag=af.high-af.low;this.move_delta(ah*ag)},move_delta:function(ah){var af=this;var ag=af.high-af.low;if(af.low-ah<af.max_low){af.low=af.max_low;af.high=af.max_low+ag}else{if(af.high-ah>af.max_high){af.high=af.max_high;af.low=af.max_high-ag}else{af.high-=ah;af.low-=ah}}af.request_redraw()},add_drawable:function(af){y.prototype.add_drawable.call(this,af);af.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(af){af.view=this;af.init();this.label_tracks.push(af)},remove_drawable:function(ah,ag){y.prototype.remove_drawable.call(this,ah);if(ag){var af=this;ah.container_div.fadeOut("slow",function(){$(this).remove();af.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(an,af,am,ag){var al=this,aj=(ag?[ag]:al.drawables),ah;var ag;for(var ak=0;ak<aj.length;ak++){ag=aj[ak];ah=-1;for(var ai=0;ai<al.tracks_to_be_redrawn.length;ai++){if(al.tracks_to_be_redrawn[ai][0]===ag){ah=ai;break}}if(ah<0){al.tracks_to_be_redrawn.push([ag,af,am])}else{al.tracks_to_be_redrawn[ak][1]=af;al.tracks_to_be_redrawn[ak][2]=am}}requestAnimationFrame(function(){al._redraw(an)})},_redraw:function(ap){var am=this.low,ai=this.high;if(am<this.max_low){am=this.max_low}if(ai>this.max_high){ai=this.max_high}var ao=this.high-this.low;if(this.high!==0&&ao<this.min_separation){ai=am+this.min_separation}this.low=Math.floor(am);this.high=Math.ceil(ai);this.resolution=Math.pow(C,Math.ceil(Math.log((this.high-this.low)/R)/Math.log(C)));this.zoom_res=Math.pow(v,Math.max(0,Math.ceil(Math.log(this.resolution,v)/Math.log(v))));var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var al=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var aq=13;this.overview_box.css({left:af,width:Math.max(aq,al)}).show();if(al<aq){this.overview_box.css("left",af-(aq-al)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:al})}this.update_location(this.low,this.high);if(!ap){var ah,ag,an;for(var aj=0,ak=this.tracks_to_be_redrawn.length;aj<ak;aj++){ah=this.tracks_to_be_redrawn[aj][0];ag=this.tracks_to_be_redrawn[aj][1];an=this.tracks_to_be_redrawn[aj][2];if(ah){ah._draw(ag,an)}}this.tracks_to_be_redrawn=[];for(aj=0,ak=this.label_tracks.length;aj<ak;aj++){this.label_tracks[aj]._draw()}}},zoom_in:function(ag,ah){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ai=this.high-this.low,aj=ai/2+this.low,af=(ai/this.zoom_factor)/2;if(ag){aj=ag/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(aj-af);this.high=Math.round(aj+af);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ag=this.high-this.low,ah=ag/2+this.low,af=(ag*this.zoom_factor)/2;this.low=Math.round(ah-af);this.high=Math.round(ah+af);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ah.dataset_id){return}this.overview_viewport.find(".track").remove()}var ag=ah.copy({content_div:this.overview_viewport}),af=this;ag.header_div.hide();ag.is_overview=true;af.overview_drawable=ag;this.overview_drawable.postdraw_actions=function(){af.overview_highlight.show().height(af.overview_drawable.content_div.height());af.overview_viewport.height(af.overview_drawable.content_div.height()+af.overview_box.outerHeight());af.overview_close.show();af.resize_window()};this.overview_drawable.init();af.has_changes=true},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var r=function(ah,al){this.track=ah;this.name=al.name;this.params=[];var at=al.params;for(var ai=0;ai<at.length;ai++){var an=at[ai],ag=an.name,ar=an.label,aj=unescape(an.html),au=an.value,ap=an.type;if(ap==="number"){this.params[this.params.length]=new g(ag,ar,aj,au,an.min,an.max)}else{if(ap=="select"){this.params[this.params.length]=new O(ag,ar,aj,au)}else{console.log("WARNING: unrecognized tool parameter type:",ag,ap)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aw){aw.stopPropagation()}).click(function(aw){aw.stopPropagation()}).bind("dblclick",function(aw){aw.stopPropagation()});var aq=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ao=this.params;var am=this;$.each(this.params,function(ax,aA){var az=$("<div>").addClass("param-row").appendTo(am.parent_div);var aw=$("<div>").addClass("param-label").text(aA.label).appendTo(az);var ay=$("<div/>").addClass("slider").html(aA.html).appendTo(az);ay.find(":input").val(aA.value);$("<div style='clear: both;'/>").appendTo(az)});this.parent_div.find("input").click(function(){$(this).select()});var av=$("<div>").addClass("param-row").appendTo(this.parent_div);var ak=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(av);var af=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(av);var am=this;af.click(function(){am.run_on_region()});ak.click(function(){am.run_on_dataset()})};p(r.prototype,{get_param_values_dict:function(){var af={};this.parent_div.find(":input").each(function(){var ag=$(this).attr("name"),ah=$(this).val();af[ag]=JSON.stringify(ah)});return af},get_param_values:function(){var ag=[];var af={};this.parent_div.find(":input").each(function(){var ah=$(this).attr("name"),ai=$(this).val();if(ah){ag[ag.length]=ai}});return ag},run_on_dataset:function(){var af=this;af.run({dataset_id:this.track.original_dataset_id,tool_id:af.name},null,function(ag){show_modal(af.name+" is Running",af.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ag={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},aj=this.track,ah=ag.tool_id+aj.tool_region_and_parameters_str(ag.chrom,ag.low,ag.high),af;if(aj.container===view){var ai=new Q(this.name,this.track.view,this.track.container);aj.container.add_drawable(ai);aj.container.remove_drawable(aj);ai.add_drawable(aj);aj.container_div.appendTo(ai.content_div);af=ai}else{af=aj.container}var ak=new aj.constructor(ah,view,af,"hda");ak.init_for_tool_data();ak.change_mode(aj.mode);af.add_drawable(ak);ak.content_div.text("Starting job.");this.run(ag,ak,function(al){ak.dataset_id=al.dataset_id;ak.content_div.text("Running job.");ak.init()})},run:function(ag,ah,ai){$.extend(ag,this.get_param_values_dict());var af=function(){$.getJSON(rerun_tool_url,ag,function(aj){if(aj==="no converter"){ah.container_div.addClass("error");ah.content_div.text(K)}else{if(aj.error){ah.container_div.addClass("error");ah.content_div.text(x+aj.message)}else{if(aj==="pending"){ah.container_div.addClass("pending");ah.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(af,2000)}else{ai(aj)}}}})};af()}});var O=function(ag,af,ah,ai){this.name=ag;this.label=af;this.html=ah;this.value=ai};var g=function(ah,ag,aj,ak,ai,af){O.call(this,ah,ag,aj,ak);this.min=ai;this.max=af};var h=function(ag,af,ah,ai){this.name=ag;this.index=af;this.tool_id=ah;this.tool_exp_name=ai};var V=function(ag,af,ah,ai){h.call(this,ag,af,ah,ai);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};p(V.prototype,{applies_to:function(af){if(af.length>this.index){return true}return false},keep:function(af){if(!this.applies_to(af)){return true}var ag=af[this.index];return(isNaN(ag)||(ag>=this.low&&ag<=this.high))},update_attrs:function(ag){var af=false;if(!this.applies_to(ag)){return af}if(ag[this.index]<this.min){this.min=Math.floor(ag[this.index]);af=true}if(ag[this.index]>this.max){this.max=Math.ceil(ag[this.index]);af=true}return af},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var ah=function(ak,ai){var aj=ai-ak;return(aj<=2?0.01:1)};var ag=this.slider.slider("option","min"),af=this.slider.slider("option","max");if(this.min<ag||this.max>af){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ah(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var aa=function(aq,ay){this.track=aq;this.filters=[];for(var at=0;at<ay.length;at++){var au=ay[at],az=au.name,af=au.type,ah=au.index,ax=au.tool_id,aw=au.tool_exp_name;if(af==="int"||af==="float"){this.filters[at]=new V(az,ah,ax,aw)}else{console.log("ERROR: unsupported filter: ",az,af)}}var ai=function(aA,aB,aC){aA.click(function(){var aD=aB.text();max=parseFloat(aC.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aC.slider("option","values")){input_size=2*input_size+1;multi_value=true}aB.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aD).appendTo(aB).focus().select().click(function(aE){aE.stopPropagation()}).blur(function(){$(this).remove();aB.text(aD)}).keyup(function(aI){if(aI.keyCode===27){$(this).trigger("blur")}else{if(aI.keyCode===13){var aG=aC.slider("option","min"),aE=aC.slider("option","max"),aH=function(aJ){return(isNaN(aJ)||aJ>aE||aJ<aG)},aF=$(this).val();if(!multi_value){aF=parseFloat(aF);if(aH(aF)){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}else{aF=aF.split("-");aF=[parseFloat(aF[0]),parseFloat(aF[1])];if(aH(aF[0])||aH(aF[1])){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}aC.slider((multi_value?"values":"value"),aF)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aA){aA.stopPropagation()}).click(function(aA){aA.stopPropagation()}).bind("dblclick",function(aA){aA.stopPropagation()}).bind("keydown",function(aA){aA.stopPropagation()});var av=$("<div/>").addClass("sliders").appendTo(this.parent_div);var an=this;$.each(this.filters,function(aD,aF){aF.container=$("<div/>").addClass("filter-row slider-row").appendTo(av);var aE=$("<div/>").addClass("elt-label").appendTo(aF.container);var aC=$("<span/>").addClass("slider-name").text(aF.name+"  ").appendTo(aE);var aB=$("<span/>");var aH=$("<span/>").addClass("slider-value").appendTo(aE).append("[").append(aB).append("]");var aA=$("<div/>").addClass("slider").appendTo(aF.container);aF.control_element=$("<div/>").attr("id",aF.name+"-filter-control").appendTo(aA);var aG=[0,0];aF.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aJ,aK){var aI=aK.values;aB.text(aI[0]+"-"+aI[1]);aF.low=aI[0];aF.high=aI[1];an.track.request_draw(true,true)},change:function(aI,aJ){aF.control_element.slider("option","slide").call(aF.control_element,aI,aJ)}});aF.slider=aF.control_element;aF.slider_label=aB;ai(aH,aB,aF.control_element);$("<div style='clear: both;'/>").appendTo(aF.container)});if(this.filters.length!==0){var ak=$("<div/>").addClass("param-row").appendTo(av);var am=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ak);var ag=this;am.click(function(){ag.run_on_dataset()})}var ap=$("<div/>").addClass("display-controls").appendTo(this.parent_div),ar,al,ao,aj={Transparency:function(aA){an.alpha_filter=aA},Height:function(aA){an.height_filter=aA}};$.each(aj,function(aC,aB){ar=$("<div/>").addClass("filter-row").appendTo(ap),al=$("<span/>").addClass("elt-label").text(aC+":").appendTo(ar),ao=$("<select/>").attr("name",aC+"_dropdown").css("float","right").appendTo(ar);$("<option/>").attr("value",-1).text("== None ==").appendTo(ao);for(var aA=0;aA<an.filters.length;aA++){$("<option/>").attr("value",aA).text(an.filters[aA].name).appendTo(ao)}ao.change(function(){$(this).children("option:selected").each(function(){var aD=parseInt($(this).val());aj[aC]((aD>=0?an.filters[aD]:null));an.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(ar)});$("<div style='clear: both;'/>").appendTo(this.parent_div)};p(aa.prototype,{reset_filters:function(){for(var af=0;af<this.filters.length;af++){filter=this.filters[af];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var an=function(ar,ap,aq){if(!(ap in ar)){ar[ap]=aq}return ar[ap]};var ah={},af,ag,ai;for(var aj=0;aj<this.filters.length;aj++){af=this.filters[aj];if(af.tool_id){if(af.min!=af.low){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" >= "+af.low}if(af.max!=af.high){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" <= "+af.high}}}var al=[];for(var ao in ah){al[al.length]=[ao,ah[ao]]}var am=al.length;(function ak(aw,at){var aq=at[0],ar=aq[0],av=aq[1],au="("+av.join(") and (")+")",ap={cond:au,input:aw,target_dataset_id:aw,tool_id:ar},at=at.slice(1);$.getJSON(run_tool_url,ap,function(ax){if(ax.error){show_modal("Filter Dataset","Error running tool "+ar,{Close:hide_modal})}else{if(at.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ak(ax.dataset_id,at)}}})})(this.track.dataset_id,al)}});var D=function(af,ag){M.Scaler.call(this,ag);this.filter=af};D.prototype.gen_val=function(af){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(af[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var G=function(af){this.track=af.track;this.params=af.params;this.values={};this.restore_values((af.saved_values?af.saved_values:{}));this.onchange=af.onchange};p(G.prototype,{restore_values:function(af){var ag=this;$.each(this.params,function(ah,ai){if(af[ai.key]!==undefined){ag.values[ai.key]=af[ai.key]}else{ag.values[ai.key]=ai.default_value}})},build_form:function(){var ag=this;var af=$("<div />");$.each(this.params,function(ak,ai){if(!ai.hidden){var ah="param_"+ak;var am=ag.values[ai.key];var ap=$("<div class='form-row' />").appendTo(af);ap.append($("<label />").attr("for",ah).text(ai.label+":"));if(ai.type==="bool"){ap.append($('<input type="checkbox" />').attr("id",ah).attr("name",ah).attr("checked",am))}else{if(ai.type==="text"){ap.append($('<input type="text"/>').attr("id",ah).val(am).click(function(){$(this).select()}))}else{if(ai.type==="color"){var al=$("<input />").attr("id",ah).attr("name",ah).val(am);var an=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var aj=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(an);var ao=$("<div/>").appendTo(aj).farbtastic({width:100,height:100,callback:al,color:am});$("<div />").append(al).append(an).appendTo(ap).bind("click",function(aq){an.css({left:$(this).position().left+($(al).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){an.hide();$(document).unbind("click.color-picker")});aq.stopPropagation()})}else{ap.append($("<input />").attr("id",ah).attr("name",ah).val(am))}}}}});return af},update_from_form:function(af){var ah=this;var ag=false;$.each(this.params,function(ai,ak){if(!ak.hidden){var al="param_"+ai;var aj=af.find("#"+al).val();if(ak.type==="float"){aj=parseFloat(aj)}else{if(ak.type==="int"){aj=parseInt(aj)}else{if(ak.type==="bool"){aj=af.find("#"+al).is(":checked")}}}if(aj!==ah.values[ak.key]){ah.values[ak.key]=aj;ag=true}}});if(ag){this.onchange()}}});var b=function(af,ai,ah,ag,aj){this.track=af;this.index=ai;this.low=ai*R*ah;this.high=(ai+1)*R*ah;this.resolution=ah;this.canvas=$("<div class='track-tile'/>").append(ag);this.data=aj;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(af,ai,ah,ag,aj,ak){b.call(this,af,ai,ah,ag,aj);this.max_val=ak};p(k.prototype,b.prototype);var P=function(af,aj,ai,ah,al,am,ak,ag){b.call(this,af,aj,ai,ah,al);this.mode=am;this.message=ak;this.feature_mapper=ag};p(P.prototype,b.prototype);P.prototype.predisplay_actions=function(){var ag=this,af={};if(ag.mode!=="Pack"){return}$(this.canvas).mousemove(function(ar){var am=$(this).offset(),aq=ar.pageX-am.left,ap=ar.pageY-am.top,aw=ag.feature_mapper.get_feature_data(aq,ap),an=(aw?aw[0]:null);$(this).siblings(".feature-popup").each(function(){if(!an||$(this).attr("id")!==an.toString()){$(this).remove()}});if(aw){var ai=af[an];if(!ai){var an=aw[0],at={name:aw[3],start:aw[1],end:aw[2],strand:aw[4]},al=ag.track.filters_manager.filters,ak;for(var ao=0;ao<al.length;ao++){ak=al[ao];at[ak.name]=aw[ak.index]}var ai=$("<div/>").attr("id",an).addClass("feature-popup"),av,au,ax=$("<table/>").appendTo(ai),ay;for(av in at){au=at[av];ay=$("<tr/>").appendTo(ax);$("<th/>").appendTo(ay).text(av);$("<td/>").attr("align","left").appendTo(ay).text(typeof(au)=="number"?Z(au,2):au)}af[an]=ai}ai.appendTo($(ag.canvas).parent());var aj=aq+parseInt(ag.canvas.css("left"))+7,ah=ap+parseInt(ag.canvas.css("top"))+7;ai.css("left",aj+"px").css("top",ah+"px")}else{if(!ar.isPropagationStopped()){ar.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ar)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var i=function(ai,aq,aj,am,ar,ah,ag){q.call(this,ai,aq,aj,{},"draghandle");this.data_url=(ah?ah:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ag?ag:L);this.dataset_check_url=converted_datasets_state_url;if(!i.id_counter){i.id_counter=0}this.id=i.id_counter++;this.container_div=$("<div />").addClass("track").attr("id","track_"+this.id).css("position","relative");if(am){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div/>").addClass("track-name").appendTo(this.header_div).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());this.icons_div=$("<div/>").css("float","left").appendTo(this.header_div).hide();this.settings_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Edit settings").addClass("icon-button settings-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.overview_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Set as overview").addClass("icon-button overview-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.filters_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Filters").addClass("icon-button filters-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.tools_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Tools").addClass("icon-button tools-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.remove_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Remove").addClass("icon-button remove-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);var ak=this;this.header_div.dblclick(function(at){at.stopPropagation()});this.settings_icon.click(function(){var av=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},at=function(){ak.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},au=function(aw){if((aw.keyCode||aw.which)===27){av()}else{if((aw.keyCode||aw.which)===13){at()}}};$(window).bind("keypress.check_enter_esc",au);show_modal("Configure Track",ak.config.build_form(),{Cancel:av,OK:at})});this.overview_icon.click(function(){ak.view.set_overview(ak)});this.filters_icon.click(function(){ak.filters_div.toggle();ak.filters_manager.reset_filters()});this.tools_icon.click(function(){ak.dynamic_tool_div.toggle();if(ak.dynamic_tool_div.is(":visible")){ak.set_name(ak.name+ak.tool_region_and_parameters_str())}else{ak.revert_name()}$(".tipsy").remove()});this.remove_icon.click(function(){$(".tipsy").remove();ak.remove()});if(ak.display_modes!==undefined){if(ak.mode_div===undefined){ak.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ak.header_div);var al=(ak.config&&ak.config.values.mode?ak.config.values.mode:ak.display_modes[0]);ak.mode=al;ak.mode_div.text(al);var af={};for(var an=0,ap=ak.display_modes.length;an<ap;an++){var ao=ak.display_modes[an];af[ao]=function(at){return function(){ak.change_mode(at)}}(ao)}make_popupmenu(ak.mode_div,af)}else{ak.mode_div.hide()}this.header_div.append($("<div/>").css("clear","both"));this.container_div.hover(function(){ak.icons_div.show()},function(){ak.icons_div.hide()})}}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};p(i.prototype,q.prototype,{get_type:function(){if(this instanceof ab){return"LabelTrack"}else{if(this instanceof A){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof W){return"ReadTrack"}else{if(this instanceof U){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}return""},init:function(){var af=this;af.enabled=false;af.tile_cache.clear();af.data_manager.clear();af.initial_canvas=undefined;af.content_div.css("height","auto");af.container_div.removeClass("nodata error pending");if(!af.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:af.hda_ldda,dataset_id:af.dataset_id,chrom:af.view.chrom},function(ag){if(!ag||ag==="error"||ag.kind==="error"){af.container_div.addClass("error");af.content_div.text(o);if(ag.message){var ah=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})});af.content_div.append(ah)}}else{if(ag==="no converter"){af.container_div.addClass("error");af.content_div.text(K)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){af.container_div.addClass("nodata");af.content_div.text(F)}else{if(ag==="pending"){af.container_div.addClass("pending");af.content_div.text(t);setTimeout(function(){af.init()},af.data_query_wait)}else{if(ag.status==="data"){if(ag.valid_chroms){af.valid_chroms=ag.valid_chroms;af.update_track_icons()}af.content_div.text(Y);if(af.view.chrom){af.content_div.text("");af.content_div.css("height",af.height_px+"px");af.enabled=true;$.when(af.predraw_init()).done(function(){af.container_div.removeClass("nodata error pending");af.request_draw()})}}}}}}});this.update_track_icons()},predraw_init:function(){}});var N=function(aj,ah,ag,am,ai,al,ak){i.call(this,aj,ah,ag,am,ai);var af=this,ah=af.view;m(af.container_div,af.drag_handle_class,".group",af);this.filters_manager=new aa(this,(al!==undefined?al:{}));this.filters_available=false;this.filters_visible=false;this.tool=(ak!==undefined&&obj_length(ak)>0?new r(this,ak):undefined);if(this.header_div){if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}};p(N.prototype,q.prototype,i.prototype,{copy:function(af){return new this.constructor(this.name,this.view,af,this.hda_ldda,this.dataset_id,this.prefs,this.filters,this.tool)},to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ag){var af=this;af.mode_div.text(ag);af.mode=ag;af.config.values.mode=ag;af.tile_cache.clear();af.request_draw();return af},update_track_icons:function(){var af=this;if(af.filters_available>0){af.filters_icon.show()}else{af.filters_icon.hide()}if(af.tool){af.tools_icon.show()}else{af.tools_icon.hide()}},_gen_tile_cache_key:function(ag,ah,af){return ag+"_"+ah+"_"+af},request_draw:function(ag,af){this.view.request_redraw(false,ag,af,this)},_draw:function(ah,ap){if(!this.enabled){return}if(!(this instanceof A)&&(!this.dataset_id)){return}var ao=this.view.low,al=this.view.high,am=al-ao,ai=this.view.container.width(),at=ai/am,ak=this.view.resolution,ar=$("<div style='position: relative;'></div>");if(this.is_overview){ao=this.view.max_low;al=this.view.max_high;ak=Math.pow(C,Math.ceil(Math.log((view.max_high-view.max_low)/R)/Math.log(C)));at=ai/(view.max_high-view.max_low)}if(!ap){this.content_div.children().remove()}this.content_div.append(ar);this.max_height=0;var ag=Math.floor(ao/ak/R);var an=true;var aq=[];var af=0;while((ag*R*ak)<al){tile=this.draw_helper(ah,ai,ag,ak,ar,at);if(tile){aq.push(tile)}else{an=false}ag+=1;af++}var aj=this;if(an){aj.postdraw_actions(aq,ai,at,ap)}},postdraw_actions:function(aj,ak,al,af){var ah=this;var ai=false;for(var ag=0;ag<aj.length;ag++){if(aj[ag].message){ai=true;break}}if(ai){for(var ag=0;ag<aj.length;ag++){tile=aj[ag];if(!tile.message){tile.canvas.css("padding-top",E)}}}},draw_helper:function(ag,ah,ai,al,ar,aw,at,am){var aj=this,aq=this._gen_tile_cache_key(ah,aw,ai),an=ai*R*al,av=an+R*al;var ao=(ag?undefined:aj.tile_cache.get(aq));if(ao){aj.show_tile(ao,ar,aw);return ao}var ap=function(ax){return("isResolved" in ax)};var ak=true;var af=aj.data_manager.get_data(an,av,aj.mode,al,aj.data_url_extra_params);if(ap(af)){ak=false}var au;if(view.reference_track&&aw>view.canvas_manager.char_width_px){au=view.reference_track.data_manager.get_data(an,av,aj.mode,al,view.reference_track.data_url_extra_params);if(ap(au)){ak=false}}if(ak){p(af,am);var ao=aj.draw_tile(af,aj.mode,al,ai,aw,au);if(ao!==undefined){aj.tile_cache.set(aq,ao);aj.show_tile(ao,ar,aw)}return ao}$.when(af,au).then(function(){view.request_redraw(false,false,false,aj)});return null},show_tile:function(al,an,ao){var ah=this,ag=al.canvas,ak=ag;if(al.message){var ap=$("<div/>"),am=$("<div/>").addClass("tile-message").text(al.message).css({height:E-1,width:al.canvas.width}).appendTo(ap),aj=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(am),af=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(am);ap.append(ag);ak=ap;aj.click(function(){al.stale=true;ah.data_manager.get_more_data(al.low,al.high,ah.mode,al.resolution,{},ah.data_manager.DEEP_DATA_REQ);ah.request_draw()}).dblclick(function(aq){aq.stopPropagation()});af.click(function(){al.stale=true;ah.data_manager.get_more_data(al.low,al.high,ah.mode,al.resolution,{},ah.data_manager.BROAD_DATA_REQ);ah.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}al.predisplay_actions();var ai=(al.low-(this.is_overview?this.view.max_low:this.view.low))*ao;if(this.left_offset){ai-=this.left_offset}ak.css({position:"absolute",top:0,left:ai,height:""});an.append(ak);ah.max_height=Math.max(ah.max_height,ak.height());ah.content_div.css("height",ah.max_height+"px");an.children().css("height",ah.max_height+"px")},_get_tile_bounds:function(af,ag){var ai=af*R*ag,aj=R*ag,ah=(ai+aj<=this.view.max_high?ai+aj:this.view.max_high);return[ai,ah]},tool_region_and_parameters_str:function(ah,af,ai){var ag=this,aj=(ah!==undefined&&af!==undefined&&ai!==undefined?ah+":"+af+"-"+ai:"all");return" - region=["+aj+"], parameters=["+ag.tool.get_param_values().join(", ")+"]"},init_for_tool_data:function(){this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.predraw_init=function(){var ag=this;var af=function(){if(ag.data_manager.size()===0){setTimeout(af,300)}else{ag.data_url=default_data_url;ag.data_query_wait=L;ag.dataset_state_url=converted_datasets_state_url;$.getJSON(ag.dataset_state_url,{dataset_id:ag.dataset_id,hda_ldda:ag.hda_ldda},function(ah){})}};af()}}});var ab=function(ag,af){i.call(this,"label",ag,af,false,{});this.container_div.addClass("label-track")};p(ab.prototype,i.prototype,{init:function(){this.enabled=true},_draw:function(){var ah=this.view,ai=ah.high-ah.low,al=Math.floor(Math.pow(10,Math.floor(Math.log(ai)/Math.log(10)))),af=Math.floor(ah.low/al)*al,aj=this.view.container.width(),ag=$("<div style='position: relative; height: 1.3em;'></div>");while(af<ah.high){var ak=(af-ah.low)/ai*aj;ag.append($("<div class='label'>"+commatize(af)+"</div>").css({position:"absolute",left:ak-1}));af+=al}this.content_div.children(":first").remove();this.content_div.append(ag)}});var A=function(af){N.call(this,"reference",af,{content_div:af.top_labeltrack},false,{});af.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:af.dbkey};this.data_manager=new I(B,this,false);this.tile_cache=new c(u)};p(A.prototype,q.prototype,N.prototype,{init:function(){this.enabled=true},draw_tile:function(ap,al,ak,ag,aq){var aj=this,ah=R*ak;if(aq>this.view.canvas_manager.char_width_px){if(ap.data===null){aj.content_div.css("height","0px");return}var ai=this.view.canvas_manager.new_canvas();var ao=ai.getContext("2d");ai.width=Math.ceil(ah*aq+aj.left_offset);ai.height=aj.height_px;ao.font=ao.canvas.manager.default_font;ao.textAlign="center";ap=ap.data;for(var am=0,an=ap.length;am<an;am++){var af=Math.round(am*aq);ao.fillText(ap[am],af+aj.left_offset,10)}return new b(aj,ag,ak,ai,ap)}this.content_div.css("height","0px")}});var j=function(ak,ai,ah,al,af,aj){var ag=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";N.call(this,ak,ai,ah,true,aj);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=al;this.dataset_id=af;this.original_dataset_id=af;this.data_manager=new S(B,this);this.tile_cache=new c(u);this.left_offset=0;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:aj,onchange:function(){ag.set_name(ag.prefs.name);ag.vertical_range=ag.prefs.max_value-ag.prefs.min_value;$("#linetrack_"+ag.dataset_id+"_minval").text(ag.prefs.min_value);$("#linetrack_"+ag.dataset_id+"_maxval").text(ag.prefs.max_value);ag.tile_cache.clear();ag.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};p(j.prototype,q.prototype,N.prototype,{add_resize_handle:function(){var af=this;var ai=false;var ah=false;var ag=$("<div class='track-resize'>");$(af.container_div).hover(function(){ai=true;ag.show()},function(){ai=false;if(!ah){ag.hide()}});ag.hide().bind("dragstart",function(aj,ak){ah=true;ak.original_height=$(af.content_div).height()}).bind("drag",function(ak,al){var aj=Math.min(Math.max(al.original_height+al.deltaY,af.min_height_px),af.max_height_px);$(af.content_div).css("height",aj);af.height_px=aj;af.request_draw(true)}).bind("dragend",function(aj,ak){af.tile_cache.clear();ah=false;if(!ai){ag.hide()}af.config.values.height=af.height_px}).appendTo(af.container_div)},predraw_init:function(){var af=this;af.vertical_range=undefined;return $.getJSON(af.data_url,{stats:true,chrom:af.view.chrom,low:null,high:null,hda_ldda:af.hda_ldda,dataset_id:af.dataset_id},function(ag){af.container_div.addClass("line-track");var ai=ag.data;if(isNaN(parseFloat(af.prefs.min_value))||isNaN(parseFloat(af.prefs.max_value))){af.prefs.min_value=ai.min;af.prefs.max_value=ai.max;$("#track_"+af.dataset_id+"_minval").val(af.prefs.min_value);$("#track_"+af.dataset_id+"_maxval").val(af.prefs.max_value)}af.vertical_range=af.prefs.max_value-af.prefs.min_value;af.total_frequency=ai.total_frequency;af.container_div.find(".yaxislabel").remove();var aj=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_minval").text(Z(af.prefs.min_value,3));var ah=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_maxval").text(Z(af.prefs.max_value,3));ah.css({position:"absolute",top:"24px",left:"10px"});ah.prependTo(af.container_div);aj.css({position:"absolute",bottom:"2px",left:"10px"});aj.prependTo(af.container_div)})},draw_tile:function(ar,ak,aj,ah,aq){if(this.vertical_range===undefined){return}var af=this._get_tile_bounds(ah,aj),al=af[0],ap=af[1],ag=Math.ceil((ap-al)*aq),an=this.height_px;var ai=this.view.canvas_manager.new_canvas();ai.width=ag,ai.height=an;var ao=ai.getContext("2d");var am=new M.LinePainter(ar.data,al,ap,this.prefs,ak);am.draw(ao,ag,an);return new b(this.track,ah,aj,ai,ar.data)}});var e=function(af,al,ag,ak,an,am,ai,aj){var ah=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];N.call(this,af,al,ag,true,am,ai,aj);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:am,onchange:function(){ah.set_name(ah.prefs.name);ah.tile_cache.clear();ah.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=ak;this.dataset_id=an;this.original_dataset_id=an;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new S(20,this);this.left_offset=200;this.painter=M.LinkedFeaturePainter};p(e.prototype,q.prototype,N.prototype,{postdraw_actions:function(av,af,aw,au){N.prototype.postdraw_actions.call(this,av,au);var ai=this;if(au){var ak=ai.content_div.children();var al=false;for(var aj=ak.length-1,ap=0;aj>=ap;aj--){var ah=$(ak[aj]);if(al){ah.remove()}else{if(ah.children().length!==0){al=true}}}}if(ai.mode=="Histogram"){var ao=-1;for(var aj=0;aj<av.length;aj++){var at=av[aj].max_val;if(at>ao){ao=at}}for(var aj=0;aj<av.length;aj++){var ar=av[aj];if(ar.max_val!==ao){ar.canvas.remove();ai.draw_helper(true,af,ar.index,ar.resolution,ar.canvas.parent(),aw,[],{max:ao})}}}if(ai.filters_manager){var ag=ai.filters_manager.filters;for(var an=0;an<ag.length;an++){ag[an].update_ui_elt()}var am=false,aq;for(var aj=0;aj<av.length;aj++){if(av[aj].data.length){aq=av[aj].data[0];for(var an=0;an<ag.length;an++){if(ag[an].applies_to(aq)){am=true;break}}}}if(ai.filters_available!==am){ai.filters_available=am;if(!ai.filters_available){ai.filters_div.hide()}ai.update_track_icons()}}},update_auto_mode:function(af){if(this.mode=="Auto"){if(af=="no_detail"){af="feature spans"}else{if(af=="summary_tree"){af="coverage histogram"}}this.mode_div.text("Auto ("+af+")")}},incremental_slots:function(aj,ag,ai){var ah=this.view.canvas_manager.dummy_context,af=this.inc_slots[aj];if(!af||(af.mode!==ai)){af=new (s.FeatureSlotter)(aj,ai==="Pack",z,function(ak){return ah.measureText(ak)});af.mode=ai;this.inc_slots[aj]=af}return af.slot_features(ag)},get_summary_tree_data:function(aj,am,ah,av){if(av>ah-am){av=ah-am}var aq=Math.floor((ah-am)/av),au=[],ai=0;var ak=0,al=0,ap,at=0,an=[],ar,ao;var ag=function(ay,ax,az,aw){ay[0]=ax+az*aw;ay[1]=ax+(az+1)*aw};while(at<av&&ak!==aj.length){var af=false;for(;at<av&&!af;at++){ag(an,am,at,aq);for(al=ak;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){af=true;break}}if(af){break}}data_start_index=al;au[au.length]=ar=[an[0],0];for(;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){ar[1]++}else{break}}if(ar[1]>ai){ai=ar[1]}at++}return{max:ai,delta:aq,data:au}},draw_tile:function(au,ax,aB,aF,ap,ai){var ay=this,ak=ay._get_tile_bounds(aF,aB),aI=ak[0],ag=ak[1],aw=ag-aI,az=Math.ceil(aw*ap),aO=25,aj=this.left_offset,av,al;if(ax==="Auto"){if(au.dataset_type==="summary_tree"){ax=au.dataset_type}else{if(au.extra_info==="no_detail"||ay.is_overview){ax="no_detail"}else{var aN=au.data;if(this.view.high-this.view.low>J){ax="Squish"}else{ax="Pack"}}}this.update_auto_mode(ax)}if(ax==="summary_tree"||ax==="Histogram"){al=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var af=$("<div />").addClass("yaxislabel");af.text(au.max);af.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});af.prependTo(this.container_div);var ah=this.view.canvas_manager.new_canvas();ah.width=az+aj;ah.height=al+T;if(au.dataset_type!="summary_tree"){var aq=this.get_summary_tree_data(au.data,aI,ag,200);if(au.max){aq.max=au.max}au=aq}var aK=new M.SummaryTreePainter(au,aI,ag,this.prefs);var aA=ah.getContext("2d");aA.translate(aj,T);aK.draw(aA,az,al);return new k(ay,aF,aB,ah,au.data,au.max)}var av,an=1;if(ax==="no_detail"||ax==="Squish"||ax==="Pack"){an=this.incremental_slots(ap,au.data,ax);av=this.inc_slots[ap].slots}var ao=[];if(au.data){var ar=this.filters_manager.filters;for(var aC=0,aE=au.data.length;aC<aE;aC++){var am=au.data[aC];var aD=false;var at;for(var aH=0,aM=ar.length;aH<aM;aH++){at=ar[aH];at.update_attrs(am);if(!at.keep(am)){aD=true;break}}if(!aD){ao.push(am)}}}var aL=(this.filters_manager.alpha_filter?new D(this.filters_manager.alpha_filter):null);var aJ=(this.filters_manager.height_filter?new D(this.filters_manager.height_filter):null);var aK=new (this.painter)(ao,aI,ag,this.prefs,ax,aL,aJ,ai);var al=Math.max(ad,aK.get_required_height(an));var ah=this.view.canvas_manager.new_canvas();var aG=null;ah.width=az+aj;ah.height=al;var aA=ah.getContext("2d");aA.fillStyle=this.prefs.block_color;aA.font=aA.canvas.manager.default_font;aA.textAlign="right";this.container_div.find(".yaxislabel").remove();if(au.data){aA.translate(aj,0);aG=aK.draw(aA,az,al,av);aG.translation=-aj}return new P(ay,aF,aB,ah,au.data,ax,au.message,aG)}});var U=function(ak,ah,ag,am,af,aj,al,ai){e.call(this,ak,ah,ag,am,af,aj,al,ai);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:aj,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter};p(U.prototype,q.prototype,N.prototype,e.prototype);var W=function(aj,ah,ag,al,af,ai,ak){e.call(this,aj,ah,ag,al,af,ai,ak);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:aj},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ai,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter;this.update_track_icons()};p(W.prototype,q.prototype,N.prototype,e.prototype);X.View=ac;X.DrawableGroup=Q;X.LineTrack=j;X.FeatureTrack=e;X.ReadTrack=W;X.VcfTrack=U};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(F,G){for(var E=0;E<=z;E++){var C=false,H=h[E];if(H!==undefined){for(var B=0,D=H.length;B<D;B++){var i=H[B];if(G>i[0]&&F<i[1]){C=true;break}}}if(!C){return E}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(i,w){var t=i("class").extend;var o=function(H,z,F,y,E,C){if(C===undefined){C=4}var B=y-z;var A=E-F;var D=Math.floor(Math.sqrt(B*B+A*A)/C);var I=B/D;var G=A/D;var x;for(x=0;x<D;x++,z+=I,F+=G){if(x%2!==0){continue}H.fillRect(z,F,C,1)}};var p=function(A,z,x,D){var C=z-D/2,B=z+D/2,E=x-Math.sqrt(D*3/2);A.beginPath();A.moveTo(C,E);A.lineTo(B,E);A.lineTo(z,x);A.lineTo(C,E);A.strokeStyle=this.fillStyle;A.fill();A.stroke();A.closePath()};var d=function(x){this.default_val=(x?x:1)};d.prototype.gen_val=function(x){return this.default_val};var l=function(z,B,x,y,A){this.data=z;this.view_start=B;this.view_end=x;this.prefs=t({},this.default_prefs,y);this.mode=A};l.prototype.default_prefs={};var u=function(z,B,x,y,A){l.call(this,z,B,x,y,A)};u.prototype.default_prefs={show_counts:false};u.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var b=function(x,B,D,E,z){l.call(this,x,B,D,E,z);if(this.prefs.min_value===undefined){var F=Infinity;for(var y=0,A=this.data.length;y<A;y++){F=Math.min(F,this.data[y][1])}this.prefs.min_value=F}if(this.prefs.max_value===undefined){var C=-Infinity;for(var y=0,A=this.data.length;y<A;y++){C=Math.max(C,this.data[y][1])}this.prefs.max_value=C}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(M,L,J){var E=false,G=this.prefs.min_value,C=this.prefs.max_value,I=C-G,x=J,z=this.view_start,K=this.view_end-this.view_start,A=L/K,H=this.mode,S=this.data;M.save();var T=Math.round(J+G/I*J);if(H!=="Intensity"){M.fillStyle="#aaa";M.fillRect(0,T,L,1)}M.beginPath();var Q,D,B;if(S.length>1){B=Math.ceil((S[1][0]-S[0][0])*A)}else{B=10}for(var N=0,O=S.length;N<O;N++){M.fillStyle=this.prefs.color;Q=Math.round((S[N][0]-z)*A);D=S[N][1];var P=false,F=false;if(D===null){if(E&&H==="Filled"){M.lineTo(Q,x)}E=false;continue}if(D<G){F=true;D=G}else{if(D>C){P=true;D=C}}if(H==="Histogram"){D=Math.round(D/I*x);M.fillRect(Q,T,B,-D)}else{if(H==="Intensity"){D=255-Math.floor((D-G)/I*255);M.fillStyle="rgb("+D+","+D+","+D+")";M.fillRect(Q,0,B,x)}else{D=Math.round(x-(D-G)/I*x);if(E){M.lineTo(Q,D)}else{E=true;if(H==="Filled"){M.moveTo(Q,x);M.lineTo(Q,D)}else{M.moveTo(Q,D)}}}}M.fillStyle=this.prefs.overflow_color;if(P||F){var R;if(H==="Histogram"||H==="Intensity"){R=B}else{Q-=2;R=4}if(P){M.fillRect(Q,0,R,3)}if(F){M.fillRect(Q,x-3,R,3)}}M.fillStyle=this.prefs.color}if(H==="Filled"){if(E){M.lineTo(Q,T);M.lineTo(0,T)}M.fill()}else{M.stroke()}M.restore()};var m=function(x){this.feature_positions={};this.slot_height=x;this.translation=0};m.prototype.map_feature_data=function(y,A,x,z){if(!this.feature_positions[A]){this.feature_positions[A]=[]}this.feature_positions[A].push({data:y,x_start:x,x_end:z})};m.prototype.get_feature_data=function(z,D){var C=Math.floor(D/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var n=function(z,C,x,y,B,D,A){l.call(this,z,C,x,y,B);this.alpha_scaler=(D?D:new d());this.height_scaler=(A?A:new d())};n.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};t(n.prototype,{get_required_height:function(y){var x=y_scale=this.get_row_height(),z=this.mode;if(z==="no_detail"||z==="Squish"||z==="Pack"){x=y*y_scale}return x+Math.max(Math.round(y_scale/2),5)},draw:function(J,H,F,E){var P=this.data,C=this.view_start,L=this.view_end;J.save();J.fillStyle=this.prefs.block_color;J.textAlign="right";var G=this.view_end-this.view_start,D=H/G,K=this.get_row_height(),O=new m(K),A;for(var M=0,N=P.length;M<N;M++){var z=P[M],B=z[0],I=z[1],x=z[2],y=(E&&E[B]!==undefined?E[B]:null);if((I<L&&x>C)&&(this.mode=="Dense"||y!==null)){A=this.draw_element(J,this.mode,z,y,C,L,D,K,H);O.map_feature_data(z,y,A[0],A[1])}}J.restore();return O},draw_element:function(D,z,F,B,A,C,E,y,x){console.log("WARNING: Unimplemented function.");return[0,0]}});var c=10,h=3,k=5,v=10,f=1,r=3,e=3,a=9,j=2,g="#ccc";var q=function(z,C,x,y,B,D,A){n.call(this,z,C,x,y,B,D,A)};t(q.prototype,n.prototype,{get_row_height:function(){var y=this.mode,x;if(y==="Dense"){x=c}else{if(y==="no_detail"){x=h}else{if(y==="Squish"){x=k}else{x=v}}}return x},draw_element:function(L,C,U,G,N,af,aj,al,x){var R=U[0],ah=U[1],Z=U[2],P=U[3],aa=Math.floor(Math.max(0,(ah-N)*aj)),M=Math.ceil(Math.min(x,Math.max(0,(Z-N)*aj))),Y=aa,ak=M,X=(C==="Dense"?0:(0+G))*al,K,ad,Q=null,an=null,A=this.prefs.block_color,ac=this.prefs.label_color;L.globalAlpha=this.alpha_scaler.gen_val(U);if(C==="Dense"){G=1}if(C==="no_detail"){L.fillStyle=A;L.fillRect(aa,X+5,M-aa,f)}else{var J=U[4],W=U[5],ab=U[6],B=U[7];if(W&&ab){Q=Math.floor(Math.max(0,(W-N)*aj));an=Math.ceil(Math.min(x,Math.max(0,(ab-N)*aj)))}var ai,S;if(C==="Squish"||C==="Dense"){ai=1;S=e}else{ai=5;S=a}if(!B){if(U.strand){if(U.strand==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand_inv")}else{if(U.strand==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand_inv")}}}else{L.fillStyle=A}L.fillRect(aa,X,M-aa,S)}else{var I,T;if(C==="Squish"||C==="Dense"){L.fillStyle=g;I=X+Math.floor(e/2)+1;T=1}else{if(J){var I=X;var T=S;if(J==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand")}else{if(J==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand")}}}else{L.fillStyle=g;I+=(e/2)+1;T=1}}L.fillRect(aa,I,M-aa,T);var D;for(var ag=0,z=B.length;ag<z;ag++){var E=B[ag],y=Math.floor(Math.max(0,(E[0]-N)*aj)),V=Math.ceil(Math.min(x,Math.max((E[1]-N)*aj)));if(y>V){continue}L.fillStyle=A;L.fillRect(y,X+(S-ai)/2+1,V-y,ai);if(Q!==undefined&&ab>W&&!(y>an||V<Q)){var ae=Math.max(y,Q),H=Math.min(V,an);L.fillRect(ae,X+1,H-ae,S);if(B.length==1&&C=="Pack"){if(J==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand_inv")}else{if(J==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand_inv")}}if(ae+14<H){ae+=2;H-=2}L.fillRect(ae,X+1,H-ae,S)}}}if(C==="Pack"){L.globalAlpha=1;L.fillStyle="white";var F=this.height_scaler.gen_val(U),O=Math.ceil(S*F),am=Math.round((S-O)/2);if(F!==1){L.fillRect(aa,I+1,M-aa,am);L.fillRect(aa,I+S-am+1,M-aa,am)}}}L.globalAlpha=1;if(C==="Pack"&&ah>N){L.fillStyle=ac;if(N===0&&aa-L.measureText(P).width<0){L.textAlign="left";L.fillText(P,M+j,X+8);ak+=L.measureText(P).width+j}else{L.textAlign="right";L.fillText(P,aa-j,X+8);Y-=L.measureText(P).width+j}}}L.globalAlpha=1;return[Y,ak]}});var s=function(A,D,x,z,C,E,B,y){n.call(this,A,D,x,z,C,E,B);this.ref_seq=(y?y.data:null)};s.prototype.default_prefs=t({},n.prototype.default_prefs,{show_insertions:false});t(s.prototype,n.prototype,{get_row_height:function(){var x,y=this.mode;if(y==="Dense"){x=c}else{if(y==="Squish"){x=k}else{x=v;if(this.prefs.show_insertions){x*=2}}}return x},draw_read:function(U,P,L,Z,A,T,I,F,E){U.textAlign="center";var S=this,z=[Z,A],O=0,V=0,R=0,x=U.canvas.manager.char_width_px;var ae=[];if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>x){R=Math.round(L/2)}if(!I){I=[[0,F.length]]}for(var M=0,X=I.length;M<X;M++){var J=I[M],B="MIDNSHP=X"[J[0]],N=J[1];if(B==="H"||B==="S"){O-=N}var G=T+O,ad=Math.floor(Math.max(0,(G-Z)*L)),H=Math.floor(Math.max(0,(G+N-Z)*L));if(ad===H){H+=1}switch(B){case"H":break;case"S":case"M":case"=":if(is_overlap([G,G+N],z)){var Q=F.slice(V,V+N);if(R>0){U.fillStyle=this.prefs.block_color;U.fillRect(ad-R,E+1,H-ad,9);U.fillStyle=g;for(var ab=0,y=Q.length;ab<y;ab++){if(this.prefs.show_differences&&this.ref_seq){var K=this.ref_seq[G-Z+ab];if(!K||K.toLowerCase()===Q[ab].toLowerCase()){continue}}if(G+ab>=Z&&G+ab<=A){var ac=Math.floor(Math.max(0,(G+ab-Z)*L));U.fillText(Q[ab],ac,E+9)}}}else{U.fillStyle=this.prefs.block_color;U.fillRect(ad,E+4,H-ad,e)}}V+=N;O+=N;break;case"N":U.fillStyle=g;U.fillRect(ad-R,E+5,H-ad,1);O+=N;break;case"D":U.fillStyle="red";U.fillRect(ad-R,E+4,H-ad,3);O+=N;break;case"P":break;case"I":var Y=ad-R;if(is_overlap([G,G+N],z)){var Q=F.slice(V,V+N);if(this.prefs.show_insertions){var D=ad-(H-ad)/2;if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>x){U.fillStyle="yellow";U.fillRect(D-R,E-9,H-ad,9);ae[ae.length]={type:"triangle",data:[Y,E+4,5]};U.fillStyle=g;switch(compute_overlap([G,G+N],z)){case (OVERLAP_START):Q=Q.slice(Z-G);break;case (OVERLAP_END):Q=Q.slice(0,G-A);break;case (CONTAINED_BY):break;case (CONTAINS):Q=Q.slice(Z-G,G-A);break}for(var ab=0,y=Q.length;ab<y;ab++){var ac=Math.floor(Math.max(0,(G+ab-Z)*L));U.fillText(Q[ab],ac-(H-ad)/2,E)}}else{U.fillStyle="yellow";U.fillRect(D,E+(this.mode!=="Dense"?2:5),H-ad,(P!=="Dense"?e:r))}}else{if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>x){ae.push({type:"text",data:[Q.length,Y,E+9]})}else{}}}V+=N;break;case"X":V+=N;break}}U.fillStyle="yellow";var aa,C,af;for(var W=0;W<ae.length;W++){aa=ae[W];C=aa.type;af=aa.data;if(C==="text"){U.save();U.font="bold "+U.font;U.fillText(af[0],af[1],af[2]);U.restore()}else{if(C=="triangle"){p(U,af[0],af[1],af[2])}}}},draw_element:function(Q,L,D,A,T,y,H,R,O){var G=D[0],P=D[1],z=D[2],I=D[3],C=Math.floor(Math.max(0,(P-T)*H)),E=Math.ceil(Math.min(O,Math.max(0,(z-T)*H))),B=(L==="Dense"?0:(0+A))*R,U=this.prefs.block_color,F=this.prefs.label_color,N=0;if((L==="Pack"||this.mode==="Auto")&&H>Q.canvas.manager.char_width_px){var N=Math.round(H/2)}Q.fillStyle=U;if(D[5] instanceof Array){var M=Math.floor(Math.max(0,(D[4][0]-T)*H)),K=Math.ceil(Math.min(O,Math.max(0,(D[4][1]-T)*H))),J=Math.floor(Math.max(0,(D[5][0]-T)*H)),x=Math.ceil(Math.min(O,Math.max(0,(D[5][1]-T)*H)));if(D[4][1]>=T&&D[4][0]<=y&&D[4][2]){this.draw_read(Q,L,H,T,y,D[4][0],D[4][2],D[4][3],B)}if(D[5][1]>=T&&D[5][0]<=y&&D[5][2]){this.draw_read(Q,L,H,T,y,D[5][0],D[5][2],D[5][3],B)}if(J>K){Q.fillStyle=g;o(Q,K-N,B+5,J-N,B+5)}}else{Q.fillStyle=U;this.draw_read(Q,L,H,T,y,P,D[4],D[5],B)}if(L==="Pack"&&P>T&&I!=="."){Q.fillStyle=this.prefs.label_color;var S=1;if(S===0&&C-Q.measureText(I).width<0){Q.textAlign="left";Q.fillText(I,E+j-N,B+8)}else{Q.textAlign="right";Q.fillText(I,C-j-N,B+8)}Q.fillStyle=U}return[0,0]}});w.Scaler=d;w.SummaryTreePainter=u;w.LinePainter=b;w.LinkedFeaturePainter=q;w.ReadPainter=s};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window);
\ No newline at end of file
+var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var m=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(u,t,v,r,i,s){return(Math.max(u,r)-Math.min(u,r))+(Math.max(t,i)-Math.min(t,i))+(Math.max(v,s)-Math.min(v,s))};var g,n,f,k,p,h,q,c,d,b,o,l=false;do{g=Math.random()*16777215;n=g|16711680;f=g|65280;k=g|255;d=m(n,f,k);l=true;for(var j=0;j<a.length;j++){p=a[j];h=p|16711680;q=p|65280;c=p|255;b=m(h,q,c);o=e(n,f,k,h,q,c);if((Math.abs(d-b)<125)||(o<500)){l=false;break}}}while(!l);return"#"+(16777216+g).toString(16).substr(1,6)};var trackster_module=function(f,X){var p=f("class").extend,s=f("slotting"),M=f("painters");var ae=function(af,ag){this.document=af;this.default_font=ag!==undefined?ag:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};p(ae.prototype,{load_pattern:function(af,aj){var ag=this.patterns,ah=this.dummy_context,ai=new Image();ai.src=image_path+aj;ai.onload=function(){ag[af]=ah.createPattern(ai,"repeat")}},get_pattern:function(af){return this.patterns[af]},new_canvas:function(){var af=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(af)}af.manager=this;return af}});var n={};var l=function(af,ag){n[af.attr("id")]=ag};var m=function(af,ah,aj,ai){aj=".group";var ag={};n[af.attr("id")]=ai;af.bind("drag",{handle:"."+ah,relative:true},function(ar,at){var aq=$(this);var aw=$(this).parent(),an=aw.children(),ap=n[$(this).attr("id")],am,al,au,ak,ao;al=$(this).parents(aj);if(al.length!==0){au=al.position().top;ak=au+al.outerHeight();if(at.offsetY<au){$(this).insertBefore(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable_before(ap,av);return}else{if(at.offsetY>ak){$(this).insertAfter(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable(ap);return}}}al=null;for(ao=0;ao<an.length;ao++){am=$(an.get(ao));au=am.position().top;ak=au+am.outerHeight();if(am.is(aj)&&this!==am.get(0)&&at.offsetY>=au&&at.offsetY<=ak){if(at.offsetY-au<ak-at.offsetY){am.find(".content-div").prepend(this)}else{am.find(".content-div").append(this)}if(ap.container){ap.container.remove_drawable(ap)}n[am.attr("id")].add_drawable(ap);return}}for(ao=0;ao<an.length;ao++){if(at.offsetY<$(an.get(ao)).position().top){break}}if(ao===an.length){if(this!==an.get(ao-1)){aw.append(this);n[aw.attr("id")].move_drawable(ap,ao)}}else{if(this!==an.get(ao)){$(this).insertBefore(an.get(ao));n[aw.attr("id")].move_drawable(ap,(at.deltaY>0?ao-1:ao))}}}).bind("dragstart",function(){ag["border-top"]=af.css("border-top");ag["border-bottom"]=af.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ag)})};X.moveable=m;var ad=16,H=9,E=20,T=H+2,z=100,J=12000,R=200,C=5,v=10,L=5000,w=100,o="There was an error in indexing this dataset. ",K="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",F="No data for this chrom/contig.",t="Currently indexing... please wait",x="Tool cannot be rerun: ",a="Loading data...",Y="Ready for display",d=10,u=5,B=5;function Z(ag,af){if(!af){af=0}var ah=Math.pow(10,af);return Math.round(ag*ah)/ah}var c=function(af){this.num_elements=af;this.clear()};p(c.prototype,{get:function(ag){var af=this.key_ary.indexOf(ag);if(af!==-1){if(this.obj_cache[ag].stale){this.key_ary.splice(af,1);delete this.obj_cache[ag]}else{this.move_key_to_end(ag,af)}}return this.obj_cache[ag]},set:function(ag,ah){if(!this.obj_cache[ag]){if(this.key_ary.length>=this.num_elements){var af=this.key_ary.shift();delete this.obj_cache[af]}this.key_ary.push(ag)}this.obj_cache[ag]=ah;return ah},move_key_to_end:function(ag,af){this.key_ary.splice(af,1);this.key_ary.push(ag)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var S=function(ag,af,ah){c.call(this,ag);this.track=af;this.subset=(ah!==undefined?ah:true)};p(S.prototype,c.prototype,{load_data:function(ao,aj,am,ag,al){var an=this.track.view.chrom,ai={chrom:an,low:ao,high:aj,mode:am,resolution:ag,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ai,al);if(this.track.filters_manager){var ap=[];var af=this.track.filters_manager.filters;for(var ak=0;ak<af.length;ak++){ap[ap.length]=af[ak].name}ai.filter_cols=JSON.stringify(ap)}var ah=this;return $.getJSON(this.track.data_url,ai,function(aq){ah.set_data(ao,aj,am,aq)})},get_data:function(af,aj,ak,ag,ai){var ah=this.get_data_from_cache(af,aj,ak);if(ah){return ah}ah=this.load_data(af,aj,ak,ag,ai);this.set_data(af,aj,ak,ah);return ah},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(an,ai,am,ah,al,aj){var ao=this.get_data_from_cache(an,ai,am);if(!ao){console.log("ERROR: no current data for: ",this.track,an,ai,am,ah,al);return}ao.stale=true;var ag=an;if(aj===this.DEEP_DATA_REQ){$.extend(al,{start_val:ao.data.length+1})}else{if(aj===this.BROAD_DATA_REQ){ag=(ao.max_high?ao.max_high:ao.data[ao.data.length-1][2])+1}}var af=this,ak=this.load_data(ag,ai,am,ah,al);new_data_available=$.Deferred();this.set_data(an,ai,am,new_data_available);$.when(ak).then(function(ap){if(ap.data){ap.data=ao.data.concat(ap.data);if(ap.max_low){ap.max_low=ao.max_low}if(ap.message){ap.message=ap.message.replace(/[0-9]+/,ap.data.length)}}af.set_data(an,ai,am,ap);new_data_available.resolve(ap)});return new_data_available},get_data_from_cache:function(af,ag,ah){return this.get(this.gen_key(af,ag,ah))},set_data:function(ag,ah,ai,af){return this.set(this.gen_key(ag,ah,ai),af)},gen_key:function(af,ah,ai){var ag=af+"_"+ah+"_"+ai;return ag},split_key:function(af){return af.split("_")}});var I=function(ag,af,ah){S.call(this,ag,af,ah)};p(I.prototype,S.prototype,c.prototype,{load_data:function(af,ai,aj,ag,ah){if(ag>1){return{data:null}}return S.prototype.load_data.call(this,af,ai,aj,ag,ah)}});var q=function(ai,ag,af,ah,aj){if(!q.id_counter){q.id_counter=0}this.id=q.id_counter++;this.name=ai;this.view=ag;this.container=af;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ai}],saved_values:ah,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=aj;this.is_overview=false};p(q.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},update_icons:function(){},set_name:function(af){this.old_name=this.name;this.name=af;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.hide(0,function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var y=function(aj,ai,ag,af,ah,ak){q.call(this,ai,ag,af,ah,ak);this.obj_type=aj;this.drawables=[]};p(y.prototype,q.prototype,{init:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af].init()}},_draw:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af]._draw()}},to_json:function(){var ag=[];for(var af=0;af<this.drawables.length;af++){ag.push(this.drawables[af].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ag}},add_drawable:function(af){this.drawables.push(af);af.container=this},add_drawable_before:function(ah,af){var ag=this.drawables.indexOf(af);if(ag!=-1){this.drawables.splice(ag,0,ah);return true}return false},remove_drawable:function(ag){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);ag.container=null;return true}return false},move_drawable:function(ag,ah){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);this.drawables.splice(ah,0,ag);return true}return false}});var Q=function(ai,ag,af,ah){y.call(this,"DrawableGroup",ai,ag,af,ah,"group-handle");this.container_div=$("<div/>").addClass("group").attr("id","group_"+this.id).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.update_icons()};p(Q.prototype,q.prototype,y.prototype,{update_icons:function(){var ag=this;var af={};af["Edit configuration"]=function(){var aj=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ah=function(){ag.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ai=function(ak){if((ak.keyCode||ak.which)===27){aj()}else{if((ak.keyCode||ak.which)===13){ah()}}};$(window).bind("keypress.check_enter_esc",ai);show_modal("Configure Group",ag.config.build_form(),{Cancel:aj,OK:ah})};af.Remove=function(){ag.remove()};make_popupmenu(ag.name_div,af)}});var ac=function(af,ai,ah,ag){y.call(this,"View");this.container=af;this.chrom=null;this.vis_id=ah;this.dbkey=ag;this.title=ai;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ae(af.get(0).ownerDocument);this.reset()};p(ac.prototype,y.prototype,{init:function(){var ah=this.container,af=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ah);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ah);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ah);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,af);this.intro_div=$("<div/>").addClass("intro");var ai=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ag=function(aj){if(aj.type==="focusout"||(aj.keyCode||aj.which)===13||(aj.keyCode||aj.which)===27){if((aj.keyCode||aj.which)!==27){af.go_to($(this).val())}$(this).hide();$(this).val("");af.location_span.show();af.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ag).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tipsy({gravity:"n"}).appendTo(this.nav_controls);this.location_span.click(function(){af.location_span.hide();af.chrom_select.hide();af.nav_input.val(af.chrom+":"+af.low+"-"+af.high);af.nav_input.css("display","inline-block");af.nav_input.select();af.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tipsy({gravity:"n"}).click(function(){af.zoom_out();af.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tipsy({gravity:"n"}).click(function(){af.zoom_in();af.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){af.change_chrom(af.chrom_select.val())});this.browser_content_div.click(function(aj){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(aj){af.zoom_in(aj.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(aj,ak){this.current_x=ak.offsetX}).bind("drag",function(aj,al){var am=al.offsetX-this.current_x;this.current_x=al.offsetX;var ak=Math.round(am/af.viewport_container.width()*(af.max_high-af.max_low));af.move_delta(-ak)});this.overview_close.click(function(){af.reset_overview()});this.viewport_container.bind("draginit",function(aj,ak){if(aj.clientX>af.viewport_container.width()-16){return false}}).bind("dragstart",function(aj,ak){ak.original_low=af.low;ak.current_height=aj.clientY;ak.current_x=ak.offsetX}).bind("drag",function(al,an){var aj=$(this);var ao=an.offsetX-an.current_x;var ak=aj.scrollTop()-(al.clientY-an.current_height);aj.scrollTop(ak);an.current_height=al.clientY;an.current_x=an.offsetX;var am=Math.round(ao/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}).bind("mousewheel",function(al,an,ak,aj){if(ak){ak*=50;var am=Math.round(-ak/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}});this.top_labeltrack.bind("dragstart",function(aj,ak){return $("<div />").css({height:af.browser_content_div.height()+af.top_labeltrack.height()+af.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(an,ao){$(ao.proxy).css({left:Math.min(an.pageX,ao.startX),width:Math.abs(an.pageX-ao.startX)});var ak=Math.min(an.pageX,ao.startX)-af.container.offset().left,aj=Math.max(an.pageX,ao.startX)-af.container.offset().left,am=(af.high-af.low),al=af.viewport_container.width();af.update_location(Math.round(ak/al*am)+af.low,Math.round(aj/al*am)+af.low)}).bind("dragend",function(ao,ap){var ak=Math.min(ao.pageX,ap.startX),aj=Math.max(ao.pageX,ap.startX),am=(af.high-af.low),al=af.viewport_container.width(),an=af.low;af.low=Math.round(ak/al*am)+an;af.high=Math.round(aj/al*am)+an;$(ap.proxy).remove();af.request_redraw()});this.add_label_track(new ab(this,{content_div:this.top_labeltrack}));this.add_label_track(new ab(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){af.resize_window()});$(document).bind("redraw",function(){af.redraw()});this.reset();$(window).trigger("resize")},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(af,ag){this.location_span.text(commatize(af)+" - "+commatize(ag));this.nav_input.val(this.chrom+":"+commatize(af)+"-"+commatize(ag))},load_chroms:function(ah){ah.num=w;$.extend(ah,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var af=this,ag=$.Deferred();$.ajax({url:chrom_url,data:ah,dataType:"json",success:function(aj){if(aj.chrom_info.length===0){alert("Invalid chromosome: "+ah.chrom);return}if(aj.reference){af.add_label_track(new A(af))}af.chrom_data=aj.chrom_info;var am='<option value="">Select Chrom/Contig</option>';for(var al=0,ai=af.chrom_data.length;al<ai;al++){var ak=af.chrom_data[al].chrom;am+='<option value="'+ak+'">'+ak+"</option>"}if(aj.prev_chroms){am+='<option value="previous">Previous '+w+"</option>"}if(aj.next_chroms){am+='<option value="next">Next '+w+"</option>"}af.chrom_select.html(am);af.chrom_start_index=aj.start_index;ag.resolve(aj)},error:function(){alert("Could not load chroms for this dbkey:",af.dbkey)}});return ag},change_chrom:function(ak,ag,am){if(!ak||ak==="None"){return}var ah=this;if(ak==="previous"){ah.load_chroms({low:this.chrom_start_index-w});return}if(ak==="next"){ah.load_chroms({low:this.chrom_start_index+w});return}var al=$.grep(ah.chrom_data,function(an,ao){return an.chrom===ak})[0];if(al===undefined){ah.load_chroms({chrom:ak},function(){ah.change_chrom(ak,ag,am)});return}else{if(ak!==ah.chrom){ah.chrom=ak;ah.chrom_select.val(ah.chrom);ah.max_high=al.len-1;ah.reset();ah.request_redraw(true);for(var aj=0,af=ah.drawables.length;aj<af;aj++){var ai=ah.drawables[aj];if(ai.init){ai.init()}}}if(ag!==undefined&&am!==undefined){ah.low=Math.max(ag,0);ah.high=Math.min(am,ah.max_high)}ah.reset_overview();ah.request_redraw()}},go_to:function(aj){aj=aj.replace(/ |,/g,"");var an=this,af,ai,ag=aj.split(":"),al=ag[0],am=ag[1];if(am!==undefined){try{var ak=am.split("-");af=parseInt(ak[0],10);ai=parseInt(ak[1],10)}catch(ah){return false}}an.change_chrom(al,af,ai)},move_fraction:function(ah){var af=this;var ag=af.high-af.low;this.move_delta(ah*ag)},move_delta:function(ah){var af=this;var ag=af.high-af.low;if(af.low-ah<af.max_low){af.low=af.max_low;af.high=af.max_low+ag}else{if(af.high-ah>af.max_high){af.high=af.max_high;af.low=af.max_high-ag}else{af.high-=ah;af.low-=ah}}af.request_redraw()},add_drawable:function(af){y.prototype.add_drawable.call(this,af);af.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(af){af.view=this;af.init();this.label_tracks.push(af)},remove_drawable:function(ah,ag){y.prototype.remove_drawable.call(this,ah);if(ag){var af=this;ah.container_div.hide(0,function(){$(this).remove();af.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(an,af,am,ag){var al=this,aj=(ag?[ag]:al.drawables),ah;var ag;for(var ak=0;ak<aj.length;ak++){ag=aj[ak];ah=-1;for(var ai=0;ai<al.tracks_to_be_redrawn.length;ai++){if(al.tracks_to_be_redrawn[ai][0]===ag){ah=ai;break}}if(ah<0){al.tracks_to_be_redrawn.push([ag,af,am])}else{al.tracks_to_be_redrawn[ak][1]=af;al.tracks_to_be_redrawn[ak][2]=am}}requestAnimationFrame(function(){al._redraw(an)})},_redraw:function(ap){var am=this.low,ai=this.high;if(am<this.max_low){am=this.max_low}if(ai>this.max_high){ai=this.max_high}var ao=this.high-this.low;if(this.high!==0&&ao<this.min_separation){ai=am+this.min_separation}this.low=Math.floor(am);this.high=Math.ceil(ai);this.resolution=Math.pow(C,Math.ceil(Math.log((this.high-this.low)/R)/Math.log(C)));this.zoom_res=Math.pow(v,Math.max(0,Math.ceil(Math.log(this.resolution,v)/Math.log(v))));var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var al=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var aq=13;this.overview_box.css({left:af,width:Math.max(aq,al)}).show();if(al<aq){this.overview_box.css("left",af-(aq-al)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:al})}this.update_location(this.low,this.high);if(!ap){var ah,ag,an;for(var aj=0,ak=this.tracks_to_be_redrawn.length;aj<ak;aj++){ah=this.tracks_to_be_redrawn[aj][0];ag=this.tracks_to_be_redrawn[aj][1];an=this.tracks_to_be_redrawn[aj][2];if(ah){ah._draw(ag,an)}}this.tracks_to_be_redrawn=[];for(aj=0,ak=this.label_tracks.length;aj<ak;aj++){this.label_tracks[aj]._draw()}}},zoom_in:function(ag,ah){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ai=this.high-this.low,aj=ai/2+this.low,af=(ai/this.zoom_factor)/2;if(ag){aj=ag/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(aj-af);this.high=Math.round(aj+af);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ag=this.high-this.low,ah=ag/2+this.low,af=(ag*this.zoom_factor)/2;this.low=Math.round(ah-af);this.high=Math.round(ah+af);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ah.dataset_id){return}this.overview_viewport.find(".track").remove()}var ag=ah.copy({content_div:this.overview_viewport}),af=this;ag.header_div.hide();ag.is_overview=true;af.overview_drawable=ag;this.overview_drawable.postdraw_actions=function(){af.overview_highlight.show().height(af.overview_drawable.content_div.height());af.overview_viewport.height(af.overview_drawable.content_div.height()+af.overview_box.outerHeight());af.overview_close.show();af.resize_window()};this.overview_drawable.init();af.has_changes=true},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var r=function(ah,al){this.track=ah;this.name=al.name;this.params=[];var at=al.params;for(var ai=0;ai<at.length;ai++){var an=at[ai],ag=an.name,ar=an.label,aj=unescape(an.html),au=an.value,ap=an.type;if(ap==="number"){this.params[this.params.length]=new g(ag,ar,aj,au,an.min,an.max)}else{if(ap=="select"){this.params[this.params.length]=new O(ag,ar,aj,au)}else{console.log("WARNING: unrecognized tool parameter type:",ag,ap)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aw){aw.stopPropagation()}).click(function(aw){aw.stopPropagation()}).bind("dblclick",function(aw){aw.stopPropagation()});var aq=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ao=this.params;var am=this;$.each(this.params,function(ax,aA){var az=$("<div>").addClass("param-row").appendTo(am.parent_div);var aw=$("<div>").addClass("param-label").text(aA.label).appendTo(az);var ay=$("<div/>").addClass("slider").html(aA.html).appendTo(az);ay.find(":input").val(aA.value);$("<div style='clear: both;'/>").appendTo(az)});this.parent_div.find("input").click(function(){$(this).select()});var av=$("<div>").addClass("param-row").appendTo(this.parent_div);var ak=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(av);var af=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(av);var am=this;af.click(function(){am.run_on_region()});ak.click(function(){am.run_on_dataset()})};p(r.prototype,{get_param_values_dict:function(){var af={};this.parent_div.find(":input").each(function(){var ag=$(this).attr("name"),ah=$(this).val();af[ag]=JSON.stringify(ah)});return af},get_param_values:function(){var ag=[];var af={};this.parent_div.find(":input").each(function(){var ah=$(this).attr("name"),ai=$(this).val();if(ah){ag[ag.length]=ai}});return ag},run_on_dataset:function(){var af=this;af.run({dataset_id:this.track.original_dataset_id,tool_id:af.name},null,function(ag){show_modal(af.name+" is Running",af.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ag={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},aj=this.track,ah=ag.tool_id+aj.tool_region_and_parameters_str(ag.chrom,ag.low,ag.high),af;if(aj.container===view){var ai=new Q(this.name,this.track.view,this.track.container);aj.container.add_drawable(ai);aj.container.remove_drawable(aj);ai.add_drawable(aj);aj.container_div.appendTo(ai.content_div);af=ai}else{af=aj.container}var ak=new aj.constructor(ah,view,af,"hda");ak.init_for_tool_data();ak.change_mode(aj.mode);af.add_drawable(ak);ak.content_div.text("Starting job.");this.run(ag,ak,function(al){ak.dataset_id=al.dataset_id;ak.content_div.text("Running job.");ak.init()})},run:function(ag,ah,ai){$.extend(ag,this.get_param_values_dict());var af=function(){$.getJSON(rerun_tool_url,ag,function(aj){if(aj==="no converter"){ah.container_div.addClass("error");ah.content_div.text(K)}else{if(aj.error){ah.container_div.addClass("error");ah.content_div.text(x+aj.message)}else{if(aj==="pending"){ah.container_div.addClass("pending");ah.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(af,2000)}else{ai(aj)}}}})};af()}});var O=function(ag,af,ah,ai){this.name=ag;this.label=af;this.html=ah;this.value=ai};var g=function(ah,ag,aj,ak,ai,af){O.call(this,ah,ag,aj,ak);this.min=ai;this.max=af};var h=function(ag,af,ah,ai){this.name=ag;this.index=af;this.tool_id=ah;this.tool_exp_name=ai};var V=function(ag,af,ah,ai){h.call(this,ag,af,ah,ai);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};p(V.prototype,{applies_to:function(af){if(af.length>this.index){return true}return false},keep:function(af){if(!this.applies_to(af)){return true}var ag=af[this.index];return(isNaN(ag)||(ag>=this.low&&ag<=this.high))},update_attrs:function(ag){var af=false;if(!this.applies_to(ag)){return af}if(ag[this.index]<this.min){this.min=Math.floor(ag[this.index]);af=true}if(ag[this.index]>this.max){this.max=Math.ceil(ag[this.index]);af=true}return af},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var ah=function(ak,ai){var aj=ai-ak;return(aj<=2?0.01:1)};var ag=this.slider.slider("option","min"),af=this.slider.slider("option","max");if(this.min<ag||this.max>af){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ah(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var aa=function(aq,ay){this.track=aq;this.filters=[];for(var at=0;at<ay.length;at++){var au=ay[at],az=au.name,af=au.type,ah=au.index,ax=au.tool_id,aw=au.tool_exp_name;if(af==="int"||af==="float"){this.filters[at]=new V(az,ah,ax,aw)}else{console.log("ERROR: unsupported filter: ",az,af)}}var ai=function(aA,aB,aC){aA.click(function(){var aD=aB.text();max=parseFloat(aC.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aC.slider("option","values")){input_size=2*input_size+1;multi_value=true}aB.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aD).appendTo(aB).focus().select().click(function(aE){aE.stopPropagation()}).blur(function(){$(this).remove();aB.text(aD)}).keyup(function(aI){if(aI.keyCode===27){$(this).trigger("blur")}else{if(aI.keyCode===13){var aG=aC.slider("option","min"),aE=aC.slider("option","max"),aH=function(aJ){return(isNaN(aJ)||aJ>aE||aJ<aG)},aF=$(this).val();if(!multi_value){aF=parseFloat(aF);if(aH(aF)){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}else{aF=aF.split("-");aF=[parseFloat(aF[0]),parseFloat(aF[1])];if(aH(aF[0])||aH(aF[1])){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}aC.slider((multi_value?"values":"value"),aF)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aA){aA.stopPropagation()}).click(function(aA){aA.stopPropagation()}).bind("dblclick",function(aA){aA.stopPropagation()}).bind("keydown",function(aA){aA.stopPropagation()});var av=$("<div/>").addClass("sliders").appendTo(this.parent_div);var an=this;$.each(this.filters,function(aD,aF){aF.container=$("<div/>").addClass("filter-row slider-row").appendTo(av);var aE=$("<div/>").addClass("elt-label").appendTo(aF.container);var aC=$("<span/>").addClass("slider-name").text(aF.name+"  ").appendTo(aE);var aB=$("<span/>");var aH=$("<span/>").addClass("slider-value").appendTo(aE).append("[").append(aB).append("]");var aA=$("<div/>").addClass("slider").appendTo(aF.container);aF.control_element=$("<div/>").attr("id",aF.name+"-filter-control").appendTo(aA);var aG=[0,0];aF.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aJ,aK){var aI=aK.values;aB.text(aI[0]+"-"+aI[1]);aF.low=aI[0];aF.high=aI[1];an.track.request_draw(true,true)},change:function(aI,aJ){aF.control_element.slider("option","slide").call(aF.control_element,aI,aJ)}});aF.slider=aF.control_element;aF.slider_label=aB;ai(aH,aB,aF.control_element);$("<div style='clear: both;'/>").appendTo(aF.container)});if(this.filters.length!==0){var ak=$("<div/>").addClass("param-row").appendTo(av);var am=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ak);var ag=this;am.click(function(){ag.run_on_dataset()})}var ap=$("<div/>").addClass("display-controls").appendTo(this.parent_div),ar,al,ao,aj={Transparency:function(aA){an.alpha_filter=aA},Height:function(aA){an.height_filter=aA}};$.each(aj,function(aC,aB){ar=$("<div/>").addClass("filter-row").appendTo(ap),al=$("<span/>").addClass("elt-label").text(aC+":").appendTo(ar),ao=$("<select/>").attr("name",aC+"_dropdown").css("float","right").appendTo(ar);$("<option/>").attr("value",-1).text("== None ==").appendTo(ao);for(var aA=0;aA<an.filters.length;aA++){$("<option/>").attr("value",aA).text(an.filters[aA].name).appendTo(ao)}ao.change(function(){$(this).children("option:selected").each(function(){var aD=parseInt($(this).val());aj[aC]((aD>=0?an.filters[aD]:null));an.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(ar)});$("<div style='clear: both;'/>").appendTo(this.parent_div)};p(aa.prototype,{reset_filters:function(){for(var af=0;af<this.filters.length;af++){filter=this.filters[af];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var an=function(ar,ap,aq){if(!(ap in ar)){ar[ap]=aq}return ar[ap]};var ah={},af,ag,ai;for(var aj=0;aj<this.filters.length;aj++){af=this.filters[aj];if(af.tool_id){if(af.min!=af.low){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" >= "+af.low}if(af.max!=af.high){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" <= "+af.high}}}var al=[];for(var ao in ah){al[al.length]=[ao,ah[ao]]}var am=al.length;(function ak(aw,at){var aq=at[0],ar=aq[0],av=aq[1],au="("+av.join(") and (")+")",ap={cond:au,input:aw,target_dataset_id:aw,tool_id:ar},at=at.slice(1);$.getJSON(run_tool_url,ap,function(ax){if(ax.error){show_modal("Filter Dataset","Error running tool "+ar,{Close:hide_modal})}else{if(at.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ak(ax.dataset_id,at)}}})})(this.track.dataset_id,al)}});var D=function(af,ag){M.Scaler.call(this,ag);this.filter=af};D.prototype.gen_val=function(af){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(af[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var G=function(af){this.track=af.track;this.params=af.params;this.values={};this.restore_values((af.saved_values?af.saved_values:{}));this.onchange=af.onchange};p(G.prototype,{restore_values:function(af){var ag=this;$.each(this.params,function(ah,ai){if(af[ai.key]!==undefined){ag.values[ai.key]=af[ai.key]}else{ag.values[ai.key]=ai.default_value}})},build_form:function(){var ai=this;var af=$("<div />");var ah;function ag(am,aj){for(var ao=0;ao<am.length;ao++){ah=am[ao];if(ah.hidden){continue}var ak="param_"+ao;var at=ai.values[ah.key];var av=$("<div class='form-row' />").appendTo(aj);av.append($("<label />").attr("for",ak).text(ah.label+":"));if(ah.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ak).attr("name",ak).attr("checked",at))}else{if(ah.type==="text"){av.append($('<input type="text"/>').attr("id",ak).val(at).click(function(){$(this).select()}))}else{if(ah.type=="select"){var aq=$("<select />").attr("id",ak);for(var an=0;an<ah.options.length;an++){$("<option/>").text(ah.options[an].label).attr("value",ah.options[an].value).appendTo(aq)}aq.val(at);av.append(aq)}else{if(ah.type==="color"){var ap=$("<input />").attr("id",ak).attr("name",ak).val(at);var ar=$("<div class='tipsy tipsy-west' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ar);var au=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:ap,color:at});$("<div />").append(ap).append(ar).appendTo(av).bind("click",function(aw){ar.css({left:$(this).position().left+$(ap).width()+5,top:$(this).position().top-($(ar).height()/2)+($(ap).height()/2)}).show();$(document).bind("click.color-picker",function(){ar.hide();$(document).unbind("click.color-picker")});aw.stopPropagation()})}else{av.append($("<input />").attr("id",ak).attr("name",ak).val(at))}}}}if(ah.help){av.append($("<div class='help'/>").text(ah.help))}}}ag(this.params,af);return af},update_from_form:function(af){var ah=this;var ag=false;$.each(this.params,function(ai,ak){if(!ak.hidden){var al="param_"+ai;var aj=af.find("#"+al).val();if(ak.type==="float"){aj=parseFloat(aj)}else{if(ak.type==="int"){aj=parseInt(aj)}else{if(ak.type==="bool"){aj=af.find("#"+al).is(":checked")}}}if(aj!==ah.values[ak.key]){ah.values[ak.key]=aj;ag=true}}});if(ag){this.onchange()}}});var b=function(af,ai,ah,ag,aj){this.track=af;this.index=ai;this.low=ai*R*ah;this.high=(ai+1)*R*ah;this.resolution=ah;this.canvas=$("<div class='track-tile'/>").append(ag);this.data=aj;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(af,ai,ah,ag,aj,ak){b.call(this,af,ai,ah,ag,aj);this.max_val=ak};p(k.prototype,b.prototype);var P=function(af,aj,ai,ah,al,am,ak,ag){b.call(this,af,aj,ai,ah,al);this.mode=am;this.message=ak;this.feature_mapper=ag};p(P.prototype,b.prototype);P.prototype.predisplay_actions=function(){var ag=this,af={};if(ag.mode!=="Pack"){return}$(this.canvas).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).siblings(".feature-popup").remove()}).mousemove(function(ar){if(!this.hovered){return}var am=$(this).offset(),aq=ar.pageX-am.left,ap=ar.pageY-am.top,aw=ag.feature_mapper.get_feature_data(aq,ap),an=(aw?aw[0]:null);$(this).siblings(".feature-popup").each(function(){if(!an||$(this).attr("id")!==an.toString()){$(this).remove()}});if(aw){var ai=af[an];if(!ai){var an=aw[0],at={name:aw[3],start:aw[1],end:aw[2],strand:aw[4]},al=ag.track.filters_manager.filters,ak;for(var ao=0;ao<al.length;ao++){ak=al[ao];at[ak.name]=aw[ak.index]}var ai=$("<div/>").attr("id",an).addClass("feature-popup"),ax=$("<table/>"),av,au,ay;for(av in at){au=at[av];ay=$("<tr/>").appendTo(ax);$("<th/>").appendTo(ay).text(av);$("<td/>").attr("align","left").appendTo(ay).text(typeof(au)=="number"?Z(au,2):au)}ai.append($("<div class='feature-popup-inner'>").append(ax));af[an]=ai}ai.appendTo($(ag.canvas).parent());var aj=aq+parseInt(ag.canvas.css("left"))-ai.width()/2,ah=ap+parseInt(ag.canvas.css("top"))+7;ai.css("left",aj+"px").css("top",ah+"px")}else{if(!ar.isPropagationStopped()){ar.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ar)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var i=function(ai,aq,aj,am,ar,ah,ag){q.call(this,ai,aq,aj,{},"draghandle");this.data_url=(ah?ah:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ag?ag:L);this.dataset_check_url=converted_datasets_state_url;this.content_visible=true;if(!i.id_counter){i.id_counter=0}this.id=i.id_counter++;this.container_div=$("<div />").addClass("track").attr("id","track_"+this.id).css("position","relative");if(am){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div/>").addClass("track-name").appendTo(this.header_div).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());this.icons_div=$("<div/>").css("float","left").appendTo(this.header_div).hide();this.toggle_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Hide/show track content").addClass("icon-button toggle").tipsy({gravity:"s"}).appendTo(this.icons_div);this.settings_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Edit settings").addClass("icon-button settings-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.overview_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Set as overview").addClass("icon-button overview-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.filters_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Filters").addClass("icon-button filters-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.tools_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Tools").addClass("icon-button tools-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.remove_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Remove").addClass("icon-button remove-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);var ak=this;this.header_div.dblclick(function(at){at.stopPropagation()});this.toggle_icon.click(function(){if(ak.content_visible){ak.toggle_icon.addClass("toggle-expand").removeClass("toggle");ak.hide_contents();ak.mode_div.hide();ak.content_visible=false}else{ak.toggle_icon.addClass("toggle").removeClass("toggle-expand");ak.content_visible=true;ak.mode_div.show();ak.show_contents()}});this.settings_icon.click(function(){var av=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},at=function(){ak.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},au=function(aw){if((aw.keyCode||aw.which)===27){av()}else{if((aw.keyCode||aw.which)===13){at()}}};$(window).bind("keypress.check_enter_esc",au);show_modal("Configure Track",ak.config.build_form(),{Cancel:av,OK:at})});this.overview_icon.click(function(){ak.view.set_overview(ak)});this.filters_icon.click(function(){ak.filters_div.toggle();ak.filters_manager.reset_filters()});this.tools_icon.click(function(){ak.dynamic_tool_div.toggle();if(ak.dynamic_tool_div.is(":visible")){ak.set_name(ak.name+ak.tool_region_and_parameters_str())}else{ak.revert_name()}$(".tipsy").remove()});this.remove_icon.click(function(){$(".tipsy").remove();ak.remove()});if(ak.display_modes!==undefined){if(ak.mode_div===undefined){ak.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ak.header_div);var al=(ak.config&&ak.config.values.mode?ak.config.values.mode:ak.display_modes[0]);ak.mode=al;ak.mode_div.text(al);var af={};for(var an=0,ap=ak.display_modes.length;an<ap;an++){var ao=ak.display_modes[an];af[ao]=function(at){return function(){ak.change_mode(at)}}(ao)}make_popupmenu(ak.mode_div,af)}else{ak.mode_div.hide()}this.header_div.append($("<div/>").css("clear","both"));this.container_div.hover(function(){ak.icons_div.show()},function(){ak.icons_div.hide()})}}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};p(i.prototype,q.prototype,{get_type:function(){if(this instanceof ab){return"LabelTrack"}else{if(this instanceof A){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof W){return"ReadTrack"}else{if(this instanceof U){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}return""},init:function(){var af=this;af.enabled=false;af.tile_cache.clear();af.data_manager.clear();af.initial_canvas=undefined;af.content_div.css("height","auto");af.container_div.removeClass("nodata error pending");if(!af.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:af.hda_ldda,dataset_id:af.dataset_id,chrom:af.view.chrom},function(ag){if(!ag||ag==="error"||ag.kind==="error"){af.container_div.addClass("error");af.content_div.text(o);if(ag.message){var ah=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})});af.content_div.append(ah)}}else{if(ag==="no converter"){af.container_div.addClass("error");af.content_div.text(K)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){af.container_div.addClass("nodata");af.content_div.text(F)}else{if(ag==="pending"){af.container_div.addClass("pending");af.content_div.text(t);setTimeout(function(){af.init()},af.data_query_wait)}else{if(ag.status==="data"){if(ag.valid_chroms){af.valid_chroms=ag.valid_chroms;af.update_icons()}af.content_div.text(Y);if(af.view.chrom){af.content_div.text("");af.content_div.css("height",af.height_px+"px");af.enabled=true;$.when(af.predraw_init()).done(function(){af.container_div.removeClass("nodata error pending");af.request_draw()})}}}}}}});this.update_icons()},hide_contents:function(){this.content_div.children().remove();this.content_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.content_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},predraw_init:function(){}});var N=function(aj,ah,ag,am,ai,al,ak){i.call(this,aj,ah,ag,am,ai);var af=this,ah=af.view;m(af.container_div,af.drag_handle_class,".group",af);this.filters_manager=new aa(this,(al!==undefined?al:{}));this.filters_available=false;this.filters_visible=false;this.tool=(ak!==undefined&&obj_length(ak)>0?new r(this,ak):undefined);if(this.header_div){if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}};p(N.prototype,q.prototype,i.prototype,{copy:function(af){return new this.constructor(this.name,this.view,af,this.hda_ldda,this.dataset_id,this.prefs,this.filters,this.tool)},to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ag){var af=this;af.mode_div.text(ag);af.mode=ag;af.config.values.mode=ag;af.tile_cache.clear();af.request_draw();return af},update_icons:function(){var af=this;if(af.filters_available>0){af.filters_icon.show()}else{af.filters_icon.hide()}if(af.tool){af.tools_icon.show()}else{af.tools_icon.hide()}},_gen_tile_cache_key:function(ag,ah,af){return ag+"_"+ah+"_"+af},request_draw:function(ag,af){this.view.request_redraw(false,ag,af,this)},_draw:function(ah,ap){if(!this.enabled){return}if(!this.content_visible){return}if(!(this instanceof A)&&(!this.dataset_id)){return}var ao=this.view.low,al=this.view.high,am=al-ao,ai=this.view.container.width(),at=ai/am,ak=this.view.resolution,ar=$("<div style='position: relative;'></div>");if(this.is_overview){ao=this.view.max_low;al=this.view.max_high;ak=Math.pow(C,Math.ceil(Math.log((view.max_high-view.max_low)/R)/Math.log(C)));at=ai/(view.max_high-view.max_low)}if(!ap){this.content_div.children().remove()}this.content_div.append(ar);this.max_height=0;var ag=Math.floor(ao/ak/R);var an=true;var aq=[];var af=0;while((ag*R*ak)<al){tile=this.draw_helper(ah,ai,ag,ak,ar,at);if(tile){aq.push(tile)}else{an=false}ag+=1;af++}var aj=this;if(an){aj.postdraw_actions(aq,ai,at,ap)}},postdraw_actions:function(aj,ak,al,af){var ah=this;var ai=false;for(var ag=0;ag<aj.length;ag++){if(aj[ag].message){ai=true;break}}if(ai){for(var ag=0;ag<aj.length;ag++){tile=aj[ag];if(!tile.message){tile.canvas.css("padding-top",E)}}}},draw_helper:function(ag,ah,ai,al,ar,aw,at,am){var aj=this,aq=this._gen_tile_cache_key(ah,aw,ai),an=ai*R*al,av=an+R*al;var ao=(ag?undefined:aj.tile_cache.get(aq));if(ao){aj.show_tile(ao,ar,aw);return ao}var ap=function(ax){return("isResolved" in ax)};var ak=true;var af=aj.data_manager.get_data(an,av,aj.mode,al,aj.data_url_extra_params);if(ap(af)){ak=false}var au;if(view.reference_track&&aw>view.canvas_manager.char_width_px){au=view.reference_track.data_manager.get_data(an,av,aj.mode,al,view.reference_track.data_url_extra_params);if(ap(au)){ak=false}}if(ak){p(af,am);var ao=aj.draw_tile(af,aj.mode,al,ai,aw,au);if(ao!==undefined){aj.tile_cache.set(aq,ao);aj.show_tile(ao,ar,aw)}return ao}$.when(af,au).then(function(){view.request_redraw(false,false,false,aj)});return null},show_tile:function(al,an,ao){var ah=this,ag=al.canvas,ak=ag;if(al.message){var ap=$("<div/>"),am=$("<div/>").addClass("tile-message").text(al.message).css({height:E-1,width:al.canvas.width}).appendTo(ap),aj=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(am),af=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(am);ap.append(ag);ak=ap;aj.click(function(){al.stale=true;ah.data_manager.get_more_data(al.low,al.high,ah.mode,al.resolution,{},ah.data_manager.DEEP_DATA_REQ);ah.request_draw()}).dblclick(function(aq){aq.stopPropagation()});af.click(function(){al.stale=true;ah.data_manager.get_more_data(al.low,al.high,ah.mode,al.resolution,{},ah.data_manager.BROAD_DATA_REQ);ah.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}al.predisplay_actions();var ai=(al.low-(this.is_overview?this.view.max_low:this.view.low))*ao;if(this.left_offset){ai-=this.left_offset}ak.css({position:"absolute",top:0,left:ai,height:""});an.append(ak);ah.max_height=Math.max(ah.max_height,ak.height());ah.content_div.css("height",ah.max_height+"px");an.children().css("height",ah.max_height+"px")},_get_tile_bounds:function(af,ag){var ai=af*R*ag,aj=R*ag,ah=(ai+aj<=this.view.max_high?ai+aj:this.view.max_high);return[ai,ah]},tool_region_and_parameters_str:function(ah,af,ai){var ag=this,aj=(ah!==undefined&&af!==undefined&&ai!==undefined?ah+":"+af+"-"+ai:"all");return" - region=["+aj+"], parameters=["+ag.tool.get_param_values().join(", ")+"]"},init_for_tool_data:function(){this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.predraw_init=function(){var ag=this;var af=function(){if(ag.data_manager.size()===0){setTimeout(af,300)}else{ag.data_url=default_data_url;ag.data_query_wait=L;ag.dataset_state_url=converted_datasets_state_url;$.getJSON(ag.dataset_state_url,{dataset_id:ag.dataset_id,hda_ldda:ag.hda_ldda},function(ah){})}};af()}}});var ab=function(ag,af){i.call(this,"label",ag,af,false,{});this.container_div.addClass("label-track")};p(ab.prototype,i.prototype,{init:function(){this.enabled=true},_draw:function(){var ah=this.view,ai=ah.high-ah.low,al=Math.floor(Math.pow(10,Math.floor(Math.log(ai)/Math.log(10)))),af=Math.floor(ah.low/al)*al,aj=this.view.container.width(),ag=$("<div style='position: relative; height: 1.3em;'></div>");while(af<ah.high){var ak=(af-ah.low)/ai*aj;ag.append($("<div class='label'>"+commatize(af)+"</div>").css({position:"absolute",left:ak-1}));af+=al}this.content_div.children(":first").remove();this.content_div.append(ag)}});var A=function(af){N.call(this,"reference",af,{content_div:af.top_labeltrack},false,{});af.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:af.dbkey};this.data_manager=new I(B,this,false);this.tile_cache=new c(u)};p(A.prototype,q.prototype,N.prototype,{init:function(){this.enabled=true},draw_tile:function(ap,al,ak,ag,aq){var aj=this,ah=R*ak;if(aq>this.view.canvas_manager.char_width_px){if(ap.data===null){aj.content_div.css("height","0px");return}var ai=this.view.canvas_manager.new_canvas();var ao=ai.getContext("2d");ai.width=Math.ceil(ah*aq+aj.left_offset);ai.height=aj.height_px;ao.font=ao.canvas.manager.default_font;ao.textAlign="center";ap=ap.data;for(var am=0,an=ap.length;am<an;am++){var af=Math.round(am*aq);ao.fillText(ap[am],af+aj.left_offset,10)}return new b(aj,ag,ak,ai,ap)}this.content_div.css("height","0px")}});var j=function(ak,ai,ah,al,af,aj){var ag=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";N.call(this,ak,ai,ah,true,aj);this.min_height_px=16;this.max_height_px=400;this.height_px=32;this.hda_ldda=al;this.dataset_id=af;this.original_dataset_id=af;this.data_manager=new S(B,this);this.tile_cache=new c(u);this.left_offset=0;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:aj,onchange:function(){ag.set_name(ag.prefs.name);ag.vertical_range=ag.prefs.max_value-ag.prefs.min_value;$("#linetrack_"+ag.dataset_id+"_minval").text(ag.prefs.min_value);$("#linetrack_"+ag.dataset_id+"_maxval").text(ag.prefs.max_value);ag.tile_cache.clear();ag.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};p(j.prototype,q.prototype,N.prototype,{add_resize_handle:function(){var af=this;var ai=false;var ah=false;var ag=$("<div class='track-resize'>");$(af.container_div).hover(function(){if(af.content_visible){ai=true;ag.show()}},function(){ai=false;if(!ah){ag.hide()}});ag.hide().bind("dragstart",function(aj,ak){ah=true;ak.original_height=$(af.content_div).height()}).bind("drag",function(ak,al){var aj=Math.min(Math.max(al.original_height+al.deltaY,af.min_height_px),af.max_height_px);$(af.content_div).css("height",aj);af.height_px=aj;af.request_draw(true)}).bind("dragend",function(aj,ak){af.tile_cache.clear();ah=false;if(!ai){ag.hide()}af.config.values.height=af.height_px}).appendTo(af.container_div)},predraw_init:function(){var af=this;af.vertical_range=undefined;return $.getJSON(af.data_url,{stats:true,chrom:af.view.chrom,low:null,high:null,hda_ldda:af.hda_ldda,dataset_id:af.dataset_id},function(ag){af.container_div.addClass("line-track");var aj=ag.data;if(isNaN(parseFloat(af.prefs.min_value))||isNaN(parseFloat(af.prefs.max_value))){var ah=aj.min;var al=aj.max;ah=Math.floor(Math.min(0,Math.max(ah,aj.mean-2*aj.sd)));al=Math.ceil(Math.max(0,Math.min(al,aj.mean+2*aj.sd)));af.prefs.min_value=ah;af.prefs.max_value=al;$("#track_"+af.dataset_id+"_minval").val(af.prefs.min_value);$("#track_"+af.dataset_id+"_maxval").val(af.prefs.max_value)}af.vertical_range=af.prefs.max_value-af.prefs.min_value;af.total_frequency=aj.total_frequency;af.container_div.find(".yaxislabel").remove();var ak=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_minval").text(Z(af.prefs.min_value,3));var ai=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_maxval").text(Z(af.prefs.max_value,3));ai.css({position:"absolute",top:"24px",left:"10px"});ai.prependTo(af.container_div);ak.css({position:"absolute",bottom:"2px",left:"10px"});ak.prependTo(af.container_div)})},draw_tile:function(ar,ak,aj,ah,aq){if(this.vertical_range===undefined){return}var af=this._get_tile_bounds(ah,aj),al=af[0],ap=af[1],ag=Math.ceil((ap-al)*aq),an=this.height_px;var ai=this.view.canvas_manager.new_canvas();ai.width=ag,ai.height=an;var ao=ai.getContext("2d");var am=new M.LinePainter(ar.data,al,ap,this.prefs,ak);am.draw(ao,ag,an);return new b(this.track,ah,aj,ai,ar.data)}});var e=function(af,al,ag,ak,an,am,ai,aj){var ah=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];N.call(this,af,al,ag,true,am,ai,aj);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:am,onchange:function(){ah.set_name(ah.prefs.name);ah.tile_cache.clear();ah.set_painter_from_config();ah.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=ak;this.dataset_id=an;this.original_dataset_id=an;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new S(20,this);this.left_offset=200;this.set_painter_from_config()};p(e.prototype,q.prototype,N.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style=="arcs"){this.painter=M.ArcLinkedFeaturePainter}else{this.painter=M.LinkedFeaturePainter}},postdraw_actions:function(av,af,aw,au){N.prototype.postdraw_actions.call(this,av,au);var ai=this;if(au){var ak=ai.content_div.children();var al=false;for(var aj=ak.length-1,ap=0;aj>=ap;aj--){var ah=$(ak[aj]);if(al){ah.remove()}else{if(ah.children().length!==0){al=true}}}}if(ai.mode=="Histogram"){var ao=-1;for(var aj=0;aj<av.length;aj++){var at=av[aj].max_val;if(at>ao){ao=at}}for(var aj=0;aj<av.length;aj++){var ar=av[aj];if(ar.max_val!==ao){ar.canvas.remove();ai.draw_helper(true,af,ar.index,ar.resolution,ar.canvas.parent(),aw,[],{max:ao})}}}if(ai.filters_manager){var ag=ai.filters_manager.filters;for(var an=0;an<ag.length;an++){ag[an].update_ui_elt()}var am=false,aq;for(var aj=0;aj<av.length;aj++){if(av[aj].data.length){aq=av[aj].data[0];for(var an=0;an<ag.length;an++){if(ag[an].applies_to(aq)){am=true;break}}}}if(ai.filters_available!==am){ai.filters_available=am;if(!ai.filters_available){ai.filters_div.hide()}ai.update_icons()}}},update_auto_mode:function(af){if(this.mode=="Auto"){if(af=="no_detail"){af="feature spans"}else{if(af=="summary_tree"){af="coverage histogram"}}this.mode_div.text("Auto ("+af+")")}},incremental_slots:function(aj,ag,ai){var ah=this.view.canvas_manager.dummy_context,af=this.inc_slots[aj];if(!af||(af.mode!==ai)){af=new (s.FeatureSlotter)(aj,ai==="Pack",z,function(ak){return ah.measureText(ak)});af.mode=ai;this.inc_slots[aj]=af}return af.slot_features(ag)},get_summary_tree_data:function(aj,am,ah,av){if(av>ah-am){av=ah-am}var aq=Math.floor((ah-am)/av),au=[],ai=0;var ak=0,al=0,ap,at=0,an=[],ar,ao;var ag=function(ay,ax,az,aw){ay[0]=ax+az*aw;ay[1]=ax+(az+1)*aw};while(at<av&&ak!==aj.length){var af=false;for(;at<av&&!af;at++){ag(an,am,at,aq);for(al=ak;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){af=true;break}}if(af){break}}data_start_index=al;au[au.length]=ar=[an[0],0];for(;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){ar[1]++}else{break}}if(ar[1]>ai){ai=ar[1]}at++}return{max:ai,delta:aq,data:au}},draw_tile:function(au,ax,aB,aF,ap,ai){var ay=this,ak=ay._get_tile_bounds(aF,aB),aI=ak[0],ag=ak[1],aw=ag-aI,az=Math.ceil(aw*ap),aO=25,aj=this.left_offset,av,al;if(ax==="Auto"){if(au.dataset_type==="summary_tree"){ax=au.dataset_type}else{if(au.extra_info==="no_detail"||ay.is_overview){ax="no_detail"}else{var aN=au.data;if(this.view.high-this.view.low>J){ax="Squish"}else{ax="Pack"}}}this.update_auto_mode(ax)}if(ax==="summary_tree"||ax==="Histogram"){al=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var af=$("<div />").addClass("yaxislabel");af.text(au.max);af.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});af.prependTo(this.container_div);var ah=this.view.canvas_manager.new_canvas();ah.width=az+aj;ah.height=al+T;if(au.dataset_type!="summary_tree"){var aq=this.get_summary_tree_data(au.data,aI,ag,200);if(au.max){aq.max=au.max}au=aq}var aK=new M.SummaryTreePainter(au,aI,ag,this.prefs);var aA=ah.getContext("2d");aA.translate(aj,T);aK.draw(aA,az,al);return new k(ay,aF,aB,ah,au.data,au.max)}var av,an=1;if(ax==="no_detail"||ax==="Squish"||ax==="Pack"){an=this.incremental_slots(ap,au.data,ax);av=this.inc_slots[ap].slots}var ao=[];if(au.data){var ar=this.filters_manager.filters;for(var aC=0,aE=au.data.length;aC<aE;aC++){var am=au.data[aC];var aD=false;var at;for(var aH=0,aM=ar.length;aH<aM;aH++){at=ar[aH];at.update_attrs(am);if(!at.keep(am)){aD=true;break}}if(!aD){ao.push(am)}}}var aL=(this.filters_manager.alpha_filter?new D(this.filters_manager.alpha_filter):null);var aJ=(this.filters_manager.height_filter?new D(this.filters_manager.height_filter):null);var aK=new (this.painter)(ao,aI,ag,this.prefs,ax,aL,aJ,ai);var al=Math.max(ad,aK.get_required_height(an,az));var ah=this.view.canvas_manager.new_canvas();var aG=null;ah.width=az+aj;ah.height=al;var aA=ah.getContext("2d");aA.fillStyle=this.prefs.block_color;aA.font=aA.canvas.manager.default_font;aA.textAlign="right";this.container_div.find(".yaxislabel").remove();if(au.data){aA.translate(aj,0);aG=aK.draw(aA,az,al,av);aG.translation=-aj}return new P(ay,aF,aB,ah,au.data,ax,au.message,aG)}});var U=function(ak,ah,ag,am,af,aj,al,ai){e.call(this,ak,ah,ag,am,af,aj,al,ai);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:aj,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter};p(U.prototype,q.prototype,N.prototype,e.prototype);var W=function(af,ak,ag,aj,an,am,ah){e.call(this,af,ak,ag,aj,an,am,ah);var ai=get_random_color(),al=get_random_color([ai,"#ffffff"]);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ai},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:al},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:am,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter;this.update_icons()};p(W.prototype,q.prototype,N.prototype,e.prototype);X.View=ac;X.DrawableGroup=Q;X.LineTrack=j;X.FeatureTrack=e;X.ReadTrack=W;X.VcfTrack=U};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(F,G){for(var E=0;E<=z;E++){var C=false,H=h[E];if(H!==undefined){for(var B=0,D=H.length;B<D;B++){var i=H[B];if(G>i[0]&&F<i[1]){C=true;break}}}if(!C){return E}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(i,x){var u=i("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y<E;y++,A+=J,G+=H){if(y%2!==0){continue}I.fillRect(A,G,D,1)}};var q=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var d=function(y){this.default_val=(y?y:1)};d.prototype.gen_val=function(y){return this.default_val};var l=function(A,C,y,z,B){this.data=A;this.view_start=C;this.view_end=y;this.prefs=u({},this.default_prefs,z);this.mode=B};l.prototype.default_prefs={};var v=function(A,C,y,z,B){l.call(this,A,C,y,z,B)};v.prototype.default_prefs={show_counts:false};v.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var b=function(y,C,E,F,A){l.call(this,y,C,E,F,A);if(this.prefs.min_value===undefined){var G=Infinity;for(var z=0,B=this.data.length;z<B;z++){G=Math.min(G,this.data[z][1])}this.prefs.min_value=G}if(this.prefs.max_value===undefined){var D=-Infinity;for(var z=0,B=this.data.length;z<B;z++){D=Math.max(D,this.data[z][1])}this.prefs.max_value=D}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var m=function(y){this.feature_positions={};this.slot_height=y;this.translation=0;this.y_translation=0};m.prototype.map_feature_data=function(z,B,y,A){if(!this.feature_positions[B]){this.feature_positions[B]=[]}this.feature_positions[B].push({data:z,x_start:y,x_end:A})};m.prototype.get_feature_data=function(z,D){var C=Math.floor((D-this.y_translation)/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var o=function(A,D,y,z,C,E,B){l.call(this,A,D,y,z,C);this.alpha_scaler=(E?E:new d());this.height_scaler=(B?B:new d())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(A,z){var y=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){y=A*y_scale}return y+this.get_top_padding(z)+this.get_bottom_padding(z)},get_top_padding:function(y){return 0},get_bottom_padding:function(y){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(K,I,G,F){var Q=this.data,D=this.view_start,M=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var H=this.view_end-this.view_start,E=I/H,L=this.get_row_height(),P=new m(L),B;for(var N=0,O=Q.length;N<O;N++){var A=Q[N],C=A[0],J=A[1],y=A[2],z=(F&&F[C]!==undefined?F[C]:null);if((J<M&&y>D)&&(this.mode=="Dense"||z!==null)){B=this.draw_element(K,this.mode,A,z,D,M,E,L,I);P.map_feature_data(A,z,B[0],B[1])}}K.restore();P.y_translation=this.get_top_padding(I);return P},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.");return[0,0]}});var c=10,h=3,k=5,w=10,f=1,s=9,e=3,a=9,j=2,g="#ccc";var r=function(A,D,y,z,C,E,B){o.call(this,A,D,y,z,C,E,B);this.draw_background_connector=true;this.draw_individual_connectors=false};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=c}else{if(z==="no_detail"){y=h}else{if(z==="Squish"){y=k}else{y=w}}}return y},draw_element:function(M,D,X,H,O,aj,an,ap,y){var T=X[0],al=X[1],ad=X[2],Q=X[3],ae=Math.floor(Math.max(0,(al-O)*an)),N=Math.ceil(Math.min(y,Math.max(0,(ad-O)*an))),ac=ae,ao=N,aa=(D==="Dense"?0:(0+H))*ap+this.get_top_padding(y),L,ah,R=null,ar=null,B=this.prefs.block_color,ag=this.prefs.label_color;M.globalAlpha=this.alpha_scaler.gen_val(X);if(D==="Dense"){H=1}if(D==="no_detail"){M.fillStyle=B;M.fillRect(ae,aa+5,N-ae,f)}else{var K=X[4],Z=X[5],af=X[6],C=X[7],V=true;if(Z&&af){R=Math.floor(Math.max(0,(Z-O)*an));ar=Math.ceil(Math.min(y,Math.max(0,(af-O)*an)))}var am,U;if(D==="Squish"){am=1;U=e;V=false}else{if(D==="Dense"){am=5;U=s}else{am=5;U=a}}if(!C){M.fillStyle=B;M.fillRect(ae,aa+1,N-ae,U);if(K&&V){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}M.fillRect(ae,aa+1,N-ae,U)}}else{var J,W;if(D==="Squish"||D==="Dense"){J=aa+Math.floor(e/2)+1;W=1}else{if(K){J=aa;W=U}else{J+=(e/2)+1;W=1}}if(this.draw_background_connector){if(D==="Squish"||D==="Dense"){M.fillStyle=g}else{if(K){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand")}}}else{M.fillStyle=g}}M.fillRect(ae,J,N-ae,W)}var E;for(var ak=0,A=C.length;ak<A;ak++){var F=C[ak],z=Math.floor(Math.max(0,(F[0]-O)*an)),Y=Math.ceil(Math.min(y,Math.max((F[1]-O)*an))),S,ab;if(z>Y){continue}M.fillStyle=B;M.fillRect(z,aa+(U-am)/2+1,Y-z,am);if(R!==undefined&&af>Z&&!(z>ar||Y<R)){var ai=Math.max(z,R),I=Math.min(Y,ar);M.fillRect(ai,aa+1,I-ai,U);if(C.length==1&&D=="Pack"){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}if(ai+14<I){ai+=2;I-=2}M.fillRect(ai,aa+1,I-ai,U)}}if(this.draw_individual_connectors&&S){this.draw_connector(M,S,ab,z,Y,aa)}S=z;ab=Y}if(D==="Pack"){M.globalAlpha=1;M.fillStyle="white";var G=this.height_scaler.gen_val(X),P=Math.ceil(U*G),aq=Math.round((U-P)/2);if(G!==1){M.fillRect(ae,J+1,N-ae,aq);M.fillRect(ae,J+U-aq+1,N-ae,aq)}}}M.globalAlpha=1;if(D==="Pack"&&al>O){M.fillStyle=ag;if(O===0&&ae-M.measureText(Q).width<0){M.textAlign="left";M.fillText(Q,N+j,aa+8);ao+=M.measureText(Q).width+j}else{M.textAlign="right";M.fillText(Q,ae-j,aa+8);ac-=M.measureText(Q).width+j}}}M.globalAlpha=1;return[ac,ao]}});var t=function(B,E,y,A,D,F,C,z){o.call(this,B,E,y,A,D,F,C);this.ref_seq=(z?z.data:null)};u(t.prototype,o.prototype,{get_row_height:function(){var y,z=this.mode;if(z==="Dense"){y=c}else{if(z==="Squish"){y=k}else{y=w;if(this.prefs.show_insertions){y*=2}}}return y},draw_read:function(K,A,ag,V,L,aa,ad,C,B,M){K.textAlign="center";var J=this,R=[L,aa],Z=0,W=0,D=0,F=K.canvas.manager.char_width_px,y=(B==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var O=[];if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){D=Math.round(ag/2)}if(!C){C=[[0,M.length]]}for(var G=0,I=C.length;G<I;G++){var z=C[G],E="MIDNSHP=X"[z[0]],S=z[1];if(E==="H"||E==="S"){Z-=S}var U=ad+Z,Y=Math.floor(Math.max(0,(U-L)*ag)),ab=Math.floor(Math.max(0,(U+S-L)*ag));if(Y===ab){ab+=1}switch(E){case"H":break;case"S":case"M":case"=":if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(D>0){K.fillStyle=y;K.fillRect(Y-D,V+1,ab-Y,9);K.fillStyle=g;for(var af=0,H=N.length;af<H;af++){if(this.prefs.show_differences&&this.ref_seq){var P=this.ref_seq[U-L+af];if(!P||P.toLowerCase()===N[af].toLowerCase()){continue}}if(U+af>=L&&U+af<=aa){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X,V+9)}}}else{K.fillStyle=y;K.fillRect(Y,V+4,ab-Y,e)}}W+=S;Z+=S;break;case"N":K.fillStyle=g;K.fillRect(Y-D,V+5,ab-Y,1);Z+=S;break;case"D":K.fillStyle="red";K.fillRect(Y-D,V+4,ab-Y,3);Z+=S;break;case"P":break;case"I":var ah=Y-D;if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(this.prefs.show_insertions){var T=Y-(ab-Y)/2;if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){K.fillStyle="yellow";K.fillRect(T-D,V-9,ab-Y,9);O[O.length]={type:"triangle",data:[ah,V+4,5]};K.fillStyle=g;switch(compute_overlap([U,U+S],R)){case (OVERLAP_START):N=N.slice(L-U);break;case (OVERLAP_END):N=N.slice(0,U-aa);break;case (CONTAINED_BY):break;case (CONTAINS):N=N.slice(L-U,U-aa);break}for(var af=0,H=N.length;af<H;af++){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X-(ab-Y)/2,V)}}else{K.fillStyle="yellow";K.fillRect(T,V+(this.mode!=="Dense"?2:5),ab-Y,(A!=="Dense"?e:s))}}else{if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){O.push({type:"text",data:[N.length,ah,V+9]})}else{}}}W+=S;break;case"X":W+=S;break}}K.fillStyle="yellow";var Q,ai,ae;for(var ac=0;ac<O.length;ac++){Q=O[ac];ai=Q.type;ae=Q.data;if(ai==="text"){K.save();K.font="bold "+K.font;K.fillText(ae[0],ae[1],ae[2]);K.restore()}else{if(ai=="triangle"){q(K,ae[0],ae[1],ae[2])}}}},draw_element:function(R,M,E,B,U,z,I,S,P){var H=E[0],Q=E[1],A=E[2],J=E[3],D=Math.floor(Math.max(0,(Q-U)*I)),F=Math.ceil(Math.min(P,Math.max(0,(A-U)*I))),C=(M==="Dense"?0:(0+B))*S,G=this.prefs.label_color,O=0;if((M==="Pack"||this.mode==="Auto")&&I>R.canvas.manager.char_width_px){var O=Math.round(I/2)}if(E[5] instanceof Array){var N=Math.floor(Math.max(0,(E[4][0]-U)*I)),L=Math.ceil(Math.min(P,Math.max(0,(E[4][1]-U)*I))),K=Math.floor(Math.max(0,(E[5][0]-U)*I)),y=Math.ceil(Math.min(P,Math.max(0,(E[5][1]-U)*I)));if(E[4][1]>=U&&E[4][0]<=z&&E[4][2]){this.draw_read(R,M,I,C,U,z,E[4][0],E[4][2],E[4][3],E[4][4])}if(E[5][1]>=U&&E[5][0]<=z&&E[5][2]){this.draw_read(R,M,I,C,U,z,E[5][0],E[5][2],E[5][3],E[5][4])}if(K>L){R.fillStyle=g;p(R,L-O,C+5,K-O,C+5)}}else{this.draw_read(R,M,I,C,U,z,Q,E[4],E[5],E[6])}if(M==="Pack"&&Q>U&&J!=="."){R.fillStyle=this.prefs.label_color;var T=1;if(T===0&&D-R.measureText(J).width<0){R.textAlign="left";R.fillText(J,F+j-O,C+8)}else{R.textAlign="right";R.fillText(J,D-j-O,C+8)}}return[0,0]}});var n=function(A,D,y,z,C,E,B){r.call(this,A,D,y,z,C,E,B);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};u(n.prototype,o.prototype,r.prototype,{calculate_longest_feature_length:function(){var z=0;for(var C=0,y=this.data.length;C<y;C++){var B=this.data[C],A=B[1],D=B[2];z=Math.max(z,D-A)}return z},get_top_padding:function(z){var y=this.view_end-this.view_start,A=z/y;return Math.min(128,Math.ceil((this.longest_feature_length/2)*A))},draw_connector:function(G,B,F,H,E,D){var y=(F+H)/2,C=H-y;var A=Math.PI,z=0;if(C>0){G.beginPath();G.arc(y,D,H-y,Math.PI,0);G.stroke()}}});x.Scaler=d;x.SummaryTreePainter=v;x.LinePainter=b;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.ArcLinkedFeaturePainter=n};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window);
\ No newline at end of file
diff --git a/static/scripts/packed/trackster_ui.js b/static/scripts/packed/trackster_ui.js
index f9e907210f0..ce85fac69fc 100644
--- a/static/scripts/packed/trackster_ui.js
+++ b/static/scripts/packed/trackster_ui.js
@@ -1 +1 @@
-var add_bookmark=function(b,a){var g=$("#bookmarks-container"),d=$("<div/>").addClass("bookmark").appendTo(g),c=$("<div/>").addClass("delete-icon-container").appendTo(d).click(function(){d.slideUp("fast");d.remove();view.has_changes=true;return false}),e=$("<a href=''/>").addClass("icon-button delete").appendTo(c),f=$("<div/>").addClass("position").appendTo(d),h=$("<a href=''/>").text(b).appendTo(f).click(function(){view.go_to(b);return false});annotation_div=get_editable_text_elt(a,true).addClass("annotation").appendTo(d);view.has_changes=true;return d};var addable_objects={LineTrack:LineTrack,FeatureTrack:FeatureTrack,VcfTrack:VcfTrack,ReadTrack:ReadTrack,DrawableGroup:DrawableGroup};var track_from_dict=function(c,b){var a=new addable_objects[c.track_type](c.name,view,b,c.hda_ldda,c.dataset_id,c.prefs,c.filters,c.tool);if(c.mode){a.change_mode(c.mode)}return a};var drawable_collection_from_dict=function(f,a){var e=new addable_objects[f.obj_type](f.name,view,a,f.prefs,view.viewport_container,view);for(var d=0;d<f.drawables.length;d++){var b=f.drawables[d],c;if(b.track_type){c=track_from_dict(b,e)}else{c=drawable_collection_from_dict(b)}e.add_drawable(c);e.content_div.append(c.container_div)}return e};var drawable_from_dict=function(b,a){return(b.track_type?track_from_dict(b,a):drawable_collection_from_dict(b,a))};var create_visualization=function(b,e,g,c,a,d,f){view=new View(b,e,g,c);view.editor=true;$.when(view.load_chroms_deferred).then(function(){if(a){var k=a.chrom,p=a.start,h=a.end,m=a.overview;if(k&&(p!==undefined)&&h){view.change_chrom(k,p,h)}}if(d){var o;for(var j=0;j<d.length;j++){o=d[j];view.add_drawable(drawable_from_dict(o,view))}}var n;for(var j=0;j<view.drawables.length;j++){if(view.drawables[j].name===m){view.set_overview(view.drawables[j]);break}}if(f){var l;for(var j=0;j<f.length;j++){l=f[j];add_bookmark(l.position,l.annotation)}}view.has_changes=false});return view};var init_keyboard_nav=function(a){$(document).keydown(function(b){if($(b.srcElement).is(":input")){return}switch(b.which){case 37:a.move_fraction(0.25);break;case 38:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("-="+c+"px");break;case 39:a.move_fraction(-0.25);break;case 40:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("+="+c+"px");break}})};
\ No newline at end of file
+var add_bookmark=function(b,a){var g=$("#bookmarks-container"),d=$("<div/>").addClass("bookmark").appendTo(g),c=$("<div/>").addClass("delete-icon-container").appendTo(d).click(function(){d.slideUp("fast");d.remove();view.has_changes=true;return false}),e=$("<a href=''/>").addClass("icon-button delete").appendTo(c),f=$("<div/>").addClass("position").appendTo(d),h=$("<a href=''/>").text(b).appendTo(f).click(function(){view.go_to(b);return false});annotation_div=get_editable_text_elt(a,true).addClass("annotation").appendTo(d);view.has_changes=true;return d};var addable_objects={LineTrack:LineTrack,FeatureTrack:FeatureTrack,VcfTrack:VcfTrack,ReadTrack:ReadTrack,DrawableGroup:DrawableGroup};var track_from_dict=function(c,b){var a=new addable_objects[c.track_type](c.name,view,b,c.hda_ldda,c.dataset_id,c.prefs,c.filters,c.tool);if(c.mode){a.change_mode(c.mode)}return a};var drawable_collection_from_dict=function(f,a){var e=new addable_objects[f.obj_type](f.name,view,a,f.prefs,view.viewport_container,view);for(var d=0;d<f.drawables.length;d++){var b=f.drawables[d],c;if(b.track_type){c=track_from_dict(b,e)}else{c=drawable_collection_from_dict(b)}e.add_drawable(c);e.content_div.append(c.container_div)}return e};var drawable_from_dict=function(b,a){return(b.track_type?track_from_dict(b,a):drawable_collection_from_dict(b,a))};var create_visualization=function(b,e,g,c,a,d,f){view=new View(b,e,g,c);view.editor=true;$.when(view.load_chroms_deferred).then(function(){if(a){var k=a.chrom,p=a.start,h=a.end,m=a.overview;if(k&&(p!==undefined)&&h){view.change_chrom(k,p,h)}}if(d){var o;for(var j=0;j<d.length;j++){o=d[j];view.add_drawable(drawable_from_dict(o,view))}}view.update_intro_div();var n;for(var j=0;j<view.drawables.length;j++){if(view.drawables[j].name===m){view.set_overview(view.drawables[j]);break}}if(f){var l;for(var j=0;j<f.length;j++){l=f[j];add_bookmark(l.position,l.annotation)}}view.has_changes=false});return view};var init_keyboard_nav=function(a){$(document).keydown(function(b){if($(b.srcElement).is(":input")){return}switch(b.which){case 37:a.move_fraction(0.25);break;case 38:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTop(a.viewport_container.scrollTop()-20);break;case 39:a.move_fraction(-0.25);break;case 40:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTop(a.viewport_container.scrollTop()+20);break}})};
\ No newline at end of file

From 12e6400183a6a13dffa1a01d290b0a1271a95501 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Thu, 10 Nov 2011 10:57:39 -0500
Subject: [PATCH 174/362] Add the ability to enter a new tool panel section
 label when installing repositories with tools from a tool shed in addition to
 being able to choose an existing tool panel section for containing the tools.
  Also clean up code related to message displayed when a local Galaxy instance
 is missing tools required by an imported workflow.

---
 lib/galaxy/web/base/controller.py             |  1 +
 lib/galaxy/web/controllers/admin.py           | 51 +++++++++++++++----
 lib/galaxy/web/controllers/workflow.py        | 31 ++++++-----
 .../admin/select_tool_panel_section.mako      | 13 +++--
 .../browse_repository.mako                    |  2 +-
 5 files changed, 67 insertions(+), 31 deletions(-)

diff --git a/lib/galaxy/web/base/controller.py b/lib/galaxy/web/base/controller.py
index b4cbec7a497..2cb1db6ce55 100644
--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -22,6 +22,7 @@ from Cheetah.Template import Template
 
 pkg_resources.require( 'elementtree' )
 from elementtree import ElementTree, ElementInclude
+from elementtree.ElementTree import Element
 
 log = logging.getLogger( __name__ )
 
diff --git a/lib/galaxy/web/controllers/admin.py b/lib/galaxy/web/controllers/admin.py
index 2080571fda0..bde9352111b 100644
--- a/lib/galaxy/web/controllers/admin.py
+++ b/lib/galaxy/web/controllers/admin.py
@@ -3,7 +3,7 @@ from galaxy import model
 from galaxy.model.orm import *
 from galaxy.web.framework.helpers import time_ago, iff, grids
 from galaxy.tools.search import ToolBoxSearch
-from galaxy.tools import json_fix
+from galaxy.tools import ToolSection, json_fix
 import logging
 log = logging.getLogger( __name__ )
 
@@ -403,7 +403,7 @@ class RepositoryListGrid( grids.Grid ):
         def get_value( self, trans, grid, tool_shed_repository ):
             return tool_shed_repository.tool_shed
     # Grid definition
-    title = "Tool shed repositories"
+    title = "Installed tool shed repositories"
     model_class = model.ToolShedRepository
     template='/admin/tool_shed_repository/grid.mako'
     default_sort_key = "name"
@@ -807,28 +807,45 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
         status = kwd.get( 'status', 'done' )
         tool_shed_url = kwd[ 'tool_shed_url' ]
         repo_info_dict = kwd[ 'repo_info_dict' ]
+        new_tool_panel_section = kwd.get( 'new_tool_panel_section', '' )
+        tool_panel_section = kwd.get( 'tool_panel_section', '' )
         if kwd.get( 'select_tool_panel_section_button', False ):
             shed_tool_conf = kwd[ 'shed_tool_conf' ]
             # Get the tool path.
             for k, tool_path in trans.app.toolbox.shed_tool_confs.items():
                 if k == shed_tool_conf:
                     break
-            if 'tool_panel_section' in kwd:
-                section_key = 'section_%s' % kwd[ 'tool_panel_section' ]
-                tool_section = trans.app.toolbox.tool_panel[ section_key ]
+            if new_tool_panel_section or tool_panel_section:
+                if new_tool_panel_section:
+                    section_id = new_tool_panel_section.lower().replace( ' ', '_' )
+                    new_section_key = 'section_%s' % str( section_id )
+                    if new_section_key in trans.app.toolbox.tool_panel:
+                        # Appending a tool to an existing section in trans.app.toolbox.tool_panel
+                        log.debug( "Appending to tool panel section: %s" % new_tool_panel_section )
+                        tool_section = trans.app.toolbox.tool_panel[ new_section_key ]
+                    else:
+                        # Appending a new section to trans.app.toolbox.tool_panel
+                        log.debug( "Loading new tool panel section: %s" % new_tool_panel_section )
+                        elem = Element( 'section' )
+                        elem.attrib[ 'name' ] = new_tool_panel_section
+                        elem.attrib[ 'id' ] = section_id
+                        tool_section = ToolSection( elem )
+                        trans.app.toolbox.tool_panel[ new_section_key ] = tool_section
+                else:
+                    section_key = 'section_%s' % tool_panel_section
+                    tool_section = trans.app.toolbox.tool_panel[ section_key ]
                 # Decode the encoded repo_info_dict param value.
                 repo_info_dict = tool_shed_decode( repo_info_dict )
                 # Clone the repository to the configured location.
                 current_working_dir = os.getcwd()
+                installed_repository_names = []
                 for name, repo_info_tuple in repo_info_dict.items():
                     description, repository_clone_url, changeset_revision = repo_info_tuple
                     clone_dir = os.path.join( tool_path, self.__generate_tool_path( repository_clone_url, changeset_revision ) )
                     if os.path.exists( clone_dir ):
                         # Repository and revision has already been cloned.
                         # TODO: implement the ability to re-install or revert an existing repository.
-                        message += 'Revision <b>%s</b> of repository <b>%s</b> has already been installed.  Updating an existing repository is not yet supported.<br/>' % \
-                        ( changeset_revision, name )
-                        status = 'error'
+                        message += 'Revision <b>%s</b> of repository <b>%s</b> was previously installed.<br/>' % ( changeset_revision, name )
                     else:
                         os.makedirs( clone_dir )
                         log.debug( 'Cloning %s...' % repository_clone_url )
@@ -892,9 +909,7 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
                                     if trans.app.toolbox_search.enabled:
                                         # If search support for tools is enabled, index the new installed tools.
                                         trans.app.toolbox_search = ToolBoxSearch( trans.app.toolbox )
-                                message += 'Revision <b>%s</b> of repository <b>%s</b> has been loaded into tool panel section <b>%s</b>.<br/>' % \
-                                    ( changeset_revision, name, tool_section.name )
-                                #return trans.show_ok_message( message )
+                                installed_repository_names.append( name )
                             else:
                                 tmp_stderr = open( tmp_name, 'rb' )
                                 message += '%s<br/>' % tmp_stderr.read()
@@ -905,6 +920,19 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
                             message += '%s<br/>' % tmp_stderr.read()
                             tmp_stderr.close()
                             status = 'error'
+                if installed_repository_names:
+                    installed_repository_names.sort()
+                    message += 'These %d repositories were installed and all tools were loaded into tool panel section <b>%s</b>:<br/>' % \
+                        ( len( installed_repository_names ), tool_section.name )
+                    for i, repo_name in enumerate( installed_repository_names ):
+                        if i == len( installed_repository_names ) -1:
+                            message += '%s.<br/>' % repo_name
+                        else:
+                            message += '%s, ' % repo_name
+                return trans.response.send_redirect( web.url_for( controller='admin',
+                                                                  action='browse_tool_shed_repositories',
+                                                                  message=message,
+                                                                  status=status ) )
             else:
                 message = 'Choose the section in your tool panel to contain the installed tools.'
                 status = 'error'
@@ -921,6 +949,7 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
                                     shed_tool_conf=shed_tool_conf,
                                     shed_tool_conf_select_field=shed_tool_conf_select_field,
                                     tool_panel_section_select_field=tool_panel_section_select_field,
+                                    new_tool_panel_section=new_tool_panel_section,
                                     message=message,
                                     status=status )
     @web.expose
diff --git a/lib/galaxy/web/controllers/workflow.py b/lib/galaxy/web/controllers/workflow.py
index 700ecdf7d47..f15d8a6b1f4 100644
--- a/lib/galaxy/web/controllers/workflow.py
+++ b/lib/galaxy/web/controllers/workflow.py
@@ -1115,10 +1115,10 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
             workflow_name = tool_shed_decode( workflow_name )
         # The following parameters will have a value only if the import originated
         # from a tool shed repository installed locally.
-        local_file = kwd.get( 'local_file', '' )
+        installed_repository_file = kwd.get( 'installed_repository_file', '' )
         repository_id = kwd.get( 'repository_id', '' )
-        if local_file and not import_button:
-            workflow_file = open( local_file, 'rb' )
+        if installed_repository_file and not import_button:
+            workflow_file = open( installed_repository_file, 'rb' )
             workflow_text = workflow_file.read()
             workflow_file.close()
             import_button = True
@@ -1197,27 +1197,26 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
                                 if shed_url.endswith( '/' ):
                                     shed_url = shed_url.rstrip( '/' )
                                     url = '%s/repository/find_tools?galaxy_url=%s&webapp=%s' % ( shed_url, trans.request.host, webapp )
+                                    if missing_tool_tups:
+                                        url += '&tool_id='
                                     for missing_tool_tup in missing_tool_tups:
                                         missing_tool_id = missing_tool_tup[0]
-                                        url += '&tool_id=%s' % missing_tool_id
+                                        url += '%s,' % missing_tool_id
                                 message += '<a href="%s">%s</a><br/>' % ( url, shed_name )
                                 status = 'error'
-                            if local_file or tool_shed_url:
+                            if installed_repository_file or tool_shed_url:
                                 # Another Galaxy panels Hack: The request did not originate from the Galaxy 
                                 # workflow view, so we don't need to render the Galaxy panels.
-                                return trans.response.send_redirect( web.url_for( controller='admin',
-                                                                                  action='center',
-                                                                                  webapp='galaxy',
-                                                                                  message=message,
-                                                                                  status=status ) )
+                                action = 'center'
                             else:
                                 # Another Galaxy panels hack: The request originated from the Galaxy
                                 # workflow view, so we need to render the Galaxy panels.
-                                return trans.response.send_redirect( web.url_for( controller='admin',
-                                                                                  action='index',
-                                                                                  webapp='galaxy',
-                                                                                  message=message,
-                                                                                  status=status ) )
+                                action = 'index'
+                            return trans.response.send_redirect( web.url_for( controller='admin',
+                                                                              action=action,
+                                                                              webapp='galaxy',
+                                                                              message=message,
+                                                                              status=status ) )
                         else:
                             # TODO: Figure out what to do here...
                             pass
@@ -1228,7 +1227,7 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
                         url = 'http://%s/workflow/view_workflow?repository_metadata_id=%s&workflow_name=%s&webapp=%s&message=%s' % \
                             ( tool_shed_url, repository_metadata_id, tool_shed_encode( workflow_name ), webapp, message )
                         return trans.response.send_redirect( url )
-                    elif local_file:
+                    elif installed_repository_file:
                         # The workflow was read from a file included with an installed tool shed repository.
                         message = "Workflow <b>%s</b> imported successfully." % workflow.name
                         return trans.response.send_redirect( web.url_for( controller='admin',
diff --git a/templates/admin/select_tool_panel_section.mako b/templates/admin/select_tool_panel_section.mako
index 045c418143a..1a0b90058db 100644
--- a/templates/admin/select_tool_panel_section.mako
+++ b/templates/admin/select_tool_panel_section.mako
@@ -23,7 +23,7 @@
 <br/>
 
 <div class="toolForm">
-    <div class="toolFormTitle">Load tools into tool panel</div>
+    <div class="toolFormTitle">Choose section to load tools into tool panel</div>
     <div class="toolFormBody">
     <form name="select_tool_panel_section" id="select_tool_panel_section" action="${h.url_for( controller='admin', action='install_tool_shed_repository', tool_shed_url=tool_shed_url, repo_info_dict=repo_info_dict )}" method="post" >
         %if shed_tool_conf_select_field:
@@ -40,10 +40,17 @@
             <input type="hidden" name="shed_tool_conf" value="${shed_tool_conf}"/>
         %endif
         <div class="form-row">
-            <label>Tool panel section:</label>
+            <label>Add new tool panel section:</label>
+            <input name="new_tool_panel_section" type="textfield" value="${new_tool_panel_section}" size="40"/>
+            <div class="toolParamHelp" style="clear: both;">
+                Add a new tool panel section or choose an existing section in your tool panel below to contain the installed tools.
+            </div>
+        </div>
+        <div class="form-row">
+            <label>Select existing tool panel section:</label>
             ${tool_panel_section_select_field.get_html()}
             <div class="toolParamHelp" style="clear: both;">
-                Choose the section in your tool panel to contain the installed tools.
+                Choose an existing section in your tool panel to contain the installed tools.
             </div>
         </div>
         <div class="form-row">
diff --git a/templates/admin/tool_shed_repository/browse_repository.mako b/templates/admin/tool_shed_repository/browse_repository.mako
index b8d9ea5a7a7..10f3a95a8b3 100644
--- a/templates/admin/tool_shed_repository/browse_repository.mako
+++ b/templates/admin/tool_shed_repository/browse_repository.mako
@@ -103,7 +103,7 @@
                                 <div class="menubutton" style="float: left;" id="workflow-${index}-popup">
                                     ${workflow_name}
                                     <div popupmenu="workflow-${index}-popup">
-                                        <a class="action-button" href="${h.url_for( controller='workflow', action='import_workflow', local_file=full_path, repository_id=trans.security.encode_id( repository.id ) )}">Import to Galaxy</a>
+                                        <a class="action-button" href="${h.url_for( controller='workflow', action='import_workflow', installed_repository_file=full_path, repository_id=trans.security.encode_id( repository.id ) )}">Import to Galaxy</a>
                                     </div>
                                 </div>
                             </td>

From 5cebc27913a78f60064991a44dba4823c31d82f8 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Thu, 10 Nov 2011 11:54:50 -0500
Subject: [PATCH 175/362] Update GeneTrack help.

---
 tools/genetrack/genetrack_indexer.xml         | 4 ++++
 tools/genetrack/genetrack_peak_prediction.xml | 4 ++++
 2 files changed, 8 insertions(+)

diff --git a/tools/genetrack/genetrack_indexer.xml b/tools/genetrack/genetrack_indexer.xml
index d603cba9466..fbd22d472e5 100644
--- a/tools/genetrack/genetrack_indexer.xml
+++ b/tools/genetrack/genetrack_indexer.xml
@@ -49,10 +49,14 @@ This tool will create a visualization of the bed file that is selected.
   When shifting the averaging process in GeneTrack is able correct for longer or shorter
   than expected fragment sizes as long as the errors are reasonably random.
 
+See http://genetrack.bx.psu.edu/ for more information on GeneTrack.
+
 ------
 
 **Citation**
 
+For the underlying tool, please cite `Albert I, Wachi S, Jiang C, Pugh BF. GeneTrack--a genomic data processing and visualization framework. Bioinformatics. 2008 May 15;24(10):1305-6. &lt;http://www.ncbi.nlm.nih.gov/pubmed/18388141&gt;`_
+
 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
 
 </help>
diff --git a/tools/genetrack/genetrack_peak_prediction.xml b/tools/genetrack/genetrack_peak_prediction.xml
index 68e11a1fd5a..92a86582434 100644
--- a/tools/genetrack/genetrack_peak_prediction.xml
+++ b/tools/genetrack/genetrack_peak_prediction.xml
@@ -54,10 +54,14 @@ This tool will generate genome wide peak prediction from an index file.
 
 - **Prediction method** the function used to average nearby values
 
+See http://genetrack.bx.psu.edu/ for more information on GeneTrack.
+
 ------
 
 **Citation**
 
+For the underlying tool, please cite `Albert I, Wachi S, Jiang C, Pugh BF. GeneTrack--a genomic data processing and visualization framework. Bioinformatics. 2008 May 15;24(10):1305-6. &lt;http://www.ncbi.nlm.nih.gov/pubmed/18388141&gt;`_
+
 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
 
 </help>

From 4553be64604734d85cf8450950b360f70893862e Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Thu, 10 Nov 2011 12:09:45 -0500
Subject: [PATCH 176/362] Eliminate the non-functional PacBio tools from the
 distribution and the sample tool config.

---
 tool_conf.xml.sample                  |  11 --
 tools/ilmn_pacbio/abyss.xml           |  30 ---
 tools/ilmn_pacbio/assembly_stats.py   |  83 --------
 tools/ilmn_pacbio/assembly_stats.xml  |  54 ------
 tools/ilmn_pacbio/cov_model.py        | 238 -----------------------
 tools/ilmn_pacbio/quake.py            | 136 -------------
 tools/ilmn_pacbio/quake.xml           |  44 -----
 tools/ilmn_pacbio/quake_pe.xml        |  53 ------
 tools/ilmn_pacbio/quake_wrapper.py    | 132 -------------
 tools/ilmn_pacbio/smrtpipe.py         |   5 -
 tools/ilmn_pacbio/smrtpipe_filter.xml |  67 -------
 tools/ilmn_pacbio/smrtpipe_galaxy.py  | 265 --------------------------
 tools/ilmn_pacbio/smrtpipe_hybrid.xml |  59 ------
 tools/ilmn_pacbio/soap_denovo.xml     |  73 -------
 14 files changed, 1250 deletions(-)
 delete mode 100644 tools/ilmn_pacbio/abyss.xml
 delete mode 100644 tools/ilmn_pacbio/assembly_stats.py
 delete mode 100644 tools/ilmn_pacbio/assembly_stats.xml
 delete mode 100644 tools/ilmn_pacbio/cov_model.py
 delete mode 100644 tools/ilmn_pacbio/quake.py
 delete mode 100644 tools/ilmn_pacbio/quake.xml
 delete mode 100644 tools/ilmn_pacbio/quake_pe.xml
 delete mode 100644 tools/ilmn_pacbio/quake_wrapper.py
 delete mode 100644 tools/ilmn_pacbio/smrtpipe.py
 delete mode 100644 tools/ilmn_pacbio/smrtpipe_filter.xml
 delete mode 100644 tools/ilmn_pacbio/smrtpipe_galaxy.py
 delete mode 100644 tools/ilmn_pacbio/smrtpipe_hybrid.xml
 delete mode 100644 tools/ilmn_pacbio/soap_denovo.xml

diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index d189a3b2319..93f171d1a28 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -477,17 +477,6 @@
     <tool file="vcf_tools/filter.xml" />
     <tool file="vcf_tools/extract.xml" />
   </section>
-  <section name="PacBio/Illumina Assembly" id="hybrid">
-    <tool file="ilmn_pacbio/quake.xml"/>
-    <tool file="ilmn_pacbio/quake_pe.xml"/>
-    <tool file="ilmn_pacbio/soap_denovo.xml"/>
-    <!--
-    Uncomment this tool when we support the HDF5 format
-    <tool file="ilmn_pacbio/smrtpipe_filter.xml"/>
-    -->
-    <tool file="ilmn_pacbio/smrtpipe_hybrid.xml"/>
-    <tool file="ilmn_pacbio/assembly_stats.xml"/>
-  </section>
   <!--
   TODO: uncomment the following EMBOSS section whenever
   moving to test, but comment it in .sample to eliminate
diff --git a/tools/ilmn_pacbio/abyss.xml b/tools/ilmn_pacbio/abyss.xml
deleted file mode 100644
index d9ae4b805da..00000000000
--- a/tools/ilmn_pacbio/abyss.xml
+++ /dev/null
@@ -1,30 +0,0 @@
-<tool id="abyss" name="ABySS" version="1.0.0">
-  <description>Short-read de Bruijn assembly</description>
-  <command interpreter="python">
-    quake_wrapper.py -k $k -r $input1 -p 8 > $output1
-  </command>
-  <inputs>
-    <param name="input1" format="fastq" type="data" label="Select FASTQ file to correct" />
-    <param name="k" type="integer" value="16" label="Size of k-mers to correct" />
-  </inputs>
-  <outputs>
-    <data format="fastq" name="output1" label="Error-corrected reads from ${on_string}" />
-  </outputs>
-  <help>
-
-**What it does**
-
-TBD.  Calls ABySS assembler
-
-**Parameter list**
-
-k
-
-**Output**
-
-Corrected reads
-
-  </help>
-</tool>
-
-
diff --git a/tools/ilmn_pacbio/assembly_stats.py b/tools/ilmn_pacbio/assembly_stats.py
deleted file mode 100644
index 2fe5e2aad62..00000000000
--- a/tools/ilmn_pacbio/assembly_stats.py
+++ /dev/null
@@ -1,83 +0,0 @@
-#!/usr/bin/env python
-#
-#Copyright (c) 2011, Pacific Biosciences of California, Inc.
-#
-#All rights reserved.
-#
-#Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
-#    * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
-#    * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
-#    * Neither the name of Pacific Biosciences nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
-#
-#THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-#WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS CONTRIBUTORS BE LIABLE FOR ANY
-#DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-#LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-#(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-#
-import sys, os
-from optparse import OptionParser
-from galaxy import eggs
-import pkg_resources
-pkg_resources.require( 'bx-python' )
-from bx.seq.fasta import FastaReader
-
-def getStats( fastaFile, genomeLength, minContigLength ):
-    lengths = []
-    stats = { "Num" : 0,
-              "Sum" : 0, 
-              "Max" : 0, 
-              "Avg" : 0,
-              "N50" : 0,
-              "99%" : 0 }
-    fasta_reader = FastaReader( open( fastaFile, 'rb' ) )
-    while True:
-        seq = fasta_reader.next()
-        if not seq:
-            break
-        if seq.length < minContigLength:
-            continue
-        lengths.append( seq.length )
-    if lengths:
-        stats[ 'Num' ] = len( lengths )
-        stats[ 'Sum' ] = sum( lengths )
-        stats[ 'Max' ] = max( lengths )
-        stats[ 'Avg' ] = int( sum( lengths ) / float( len( lengths ) ) )
-        stats[ 'N50' ] = 0
-        stats[ '99%' ] = 0
-        if genomeLength == 0:
-            genomeLength = sum( lengths )
-        lengths.sort()
-        lengths.reverse()
-        lenSum = 0
-        stats[ "99%" ] = len( lengths )
-        for idx, length in enumerate( lengths ):
-            lenSum += length
-            if ( lenSum > genomeLength / 2 ):
-                stats[ "N50" ] = length
-                break
-        lenSum = 0
-        for idx, length in enumerate( lengths ):
-            lenSum += length
-            if lenSum > genomeLength * 0.99:
-                stats[ "99%" ] = idx + 1
-                break
-    return stats
-
-def __main__():
-    #Parse Command Line
-    usage = 'Usage: %prog input output --minContigLength'
-    parser = OptionParser( usage=usage )
-    parser.add_option( "--minContigLength", dest="minContigLength", help="Minimum length of contigs to analyze" )
-    parser.add_option( "--genomeLength", dest="genomeLength", help="Length of genome for which to calculate N50s" )
-    parser.set_defaults( minContigLength=0, genomeLength=0 )
-    options, args = parser.parse_args()
-    input_fasta_file = args[ 0 ]
-    output_tabular_file = args[ 1 ]
-    statKeys = "Num Sum Max Avg N50 99%".split( " " )
-    stats = getStats( input_fasta_file, int( options.genomeLength ), int( options.minContigLength ) )
-    fout = open( output_tabular_file, "w" )
-    fout.write( "%s\n" % "\t".join( map( lambda key: str( stats[ key ] ), statKeys ) ) )
-    fout.close()
-
-if __name__=="__main__": __main__()
diff --git a/tools/ilmn_pacbio/assembly_stats.xml b/tools/ilmn_pacbio/assembly_stats.xml
deleted file mode 100644
index cf8bd090f1f..00000000000
--- a/tools/ilmn_pacbio/assembly_stats.xml
+++ /dev/null
@@ -1,54 +0,0 @@
-<tool id="assembly_stats" name="Assembly Statistics" version="1.0.0">
-    <description>Calculate common measures of assembly quality</description>
-    <command interpreter="python">
-        assembly_stats.py $input1 $output1 --minContigLength=${minLength}
-    </command>
-    <inputs>
-        <param name="input1" format="fasta" type="data" label="Select FASTA file containing contigs"/>
-        <param name="minLength" type="integer" value="0" label="Minimum length of contigs to consider"/>
-    </inputs>
-    <outputs>
-        <data name="output1" format="tabular" label="Assembly statistics for ${on_string}"/>
-    </outputs>
-    <tests>
-        <test>
-            <param name="input1" value="3.fasta" ftype="fasta"/>
-            <param name="minLength" value="100"/>
-            <output name="output1" ftype="tabular" file="assembly_stats.tabular" />
-        </test>
-    </tests>
-    <help>
-
-**What it does**
-
-Reports standard measures of *de novo* assembly quality such as number of contigs, sum of contigs, mean contig length, and N50.
-
-**Parameter list**
-
-Minimum length
-    Only include contigs of this size or greater for calculating statistics.
-
-**Output**
-
-Num contigs
-    Total number of contigs in the assembly
-
-Sum of contig lengths
-    Total sum of contig lengths
-
-Maximum contig length
-    Maximum of the contig lengths
-
-Mean contig length
-    Average contig length
-
-N50
-    Contig length at which 50% of the assembly is contained in contigs of this size or greater.
-
-99%
-    Number of contigs accounting for 99% of the observed assembly.
-
-    </help>
-</tool>
-
-
diff --git a/tools/ilmn_pacbio/cov_model.py b/tools/ilmn_pacbio/cov_model.py
deleted file mode 100644
index 71fc04e964a..00000000000
--- a/tools/ilmn_pacbio/cov_model.py
+++ /dev/null
@@ -1,238 +0,0 @@
-#!/usr/bin/env python
-from optparse import OptionParser, SUPPRESS_HELP
-import os, random, quake
-
-############################################################
-# cov_model.py
-#
-# Given a file of kmer counts, reports the cutoff to use
-# to separate trusted/untrusted kmers.
-############################################################
-
-############################################################
-# main
-############################################################
-def main():
-    usage = 'usage: %prog [options] <counts file>'
-    parser = OptionParser(usage)
-    parser.add_option('--int', dest='count_kmers', action='store_true', default=False, help='Kmers were counted as integers w/o the use of quality values [default: %default]')
-    parser.add_option('--ratio', dest='ratio', type='int', default=200, help='Likelihood ratio to set trusted/untrusted cutoff [default: %default]')
-    parser.add_option('--no_sample', dest='no_sample', action='store_true', default=False, help='Do not sample kmer coverages into kmers.txt because its already done [default: %default]')
-    # help='Model kmer coverage as a function of GC content of kmers [default: %default]'
-    parser.add_option('--gc', dest='model_gc', action='store_true', default=False, help=SUPPRESS_HELP)
-    (options, args) = parser.parse_args()
-
-    if len(args) != 1:
-        parser.error('Must provide kmers counts file')
-    else:
-        ctsf = args[0]
-
-    if options.count_kmers:
-        model_cutoff(ctsf, options.ratio)
-        print 'Cutoff: %s' % open('cutoff.txt').readline().rstrip()
-        
-    else:
-        if options.model_gc:
-            model_q_gc_cutoffs(ctsf, 25000, options.ratio)
-        else:
-            model_q_cutoff(ctsf, 50000, options.ratio, options.no_sample)
-            print 'Cutoff: %s' % open('cutoff.txt').readline().rstrip()
-
-
-############################################################
-# model_cutoff
-#
-# Make a histogram of kmers to give to R to learn the cutoff
-############################################################
-def model_cutoff(ctsf, ratio):
-    # make kmer histogram
-    cov_max = 0
-    for line in open(ctsf):
-        cov = int(line.split()[1])
-        if cov > cov_max:
-            cov_max = cov
-
-    kmer_hist = [0]*cov_max
-    for line in open(ctsf):
-        cov = int(line.split()[1])
-        kmer_hist[cov-1] += 1
-
-    cov_out = open('kmers.hist', 'w')
-    for cov in range(0,cov_max):
-        if kmer_hist[cov]:
-            print >> cov_out, '%d\t%d' % (cov+1,kmer_hist[cov])
-    cov_out.close()
-
-    os.system('R --slave --args %d < %s/cov_model.r 2> r.log' % (ratio,quake.quake_dir))
-
-
-############################################################
-# model_q_cutoff
-#
-# Sample kmers to give to R to learn the cutoff
-# 'div100' is necessary when the number of kmers is too 
-# large for random.sample, so we only consider every 100th
-# kmer.
-############################################################
-def model_q_cutoff(ctsf, sample, ratio, no_sample=False):
-    if not no_sample:
-        # count number of kmer coverages
-        num_covs = 0
-        for line in open(ctsf):
-            num_covs += 1
-
-        # choose random kmer coverages
-        div100 = False
-        if sample >= num_covs:
-            rand_covs = range(num_covs)
-        else:
-            if num_covs > 1000000000:
-                div100 = True
-                rand_covs = random.sample(xrange(num_covs/100), sample)
-            else:
-                rand_covs = random.sample(xrange(num_covs), sample)
-        rand_covs.sort()
-
-        # print to file
-        out = open('kmers.txt', 'w')
-        kmer_i = 0
-        rand_i = 0
-        for line in open(ctsf):
-            if div100:
-                if kmer_i % 100 == 0 and kmer_i/100 == rand_covs[rand_i]:
-                    print >> out, line.split()[1]
-                    rand_i += 1
-                    if rand_i >= sample:
-                        break
-            else:
-                if kmer_i == rand_covs[rand_i]:
-                    print >> out, line.split()[1]
-                    rand_i += 1
-                    if rand_i >= sample:
-                        break
-            kmer_i += 1
-        out.close()
-
-    os.system('R --slave --args %d < %s/cov_model_qmer.r 2> r.log' % (ratio,quake.quake_dir))
-
-
-############################################################
-# model_q_gc_cutoffs
-#
-# Sample kmers to give to R to learn the cutoff for each
-# GC value
-############################################################
-def model_q_gc_cutoffs(ctsf, sample, ratio):
-    # count number of kmer coverages at each at
-    k = len(open(ctsf).readline().split()[0])
-    num_covs_at = [0]*(k+1)
-    for line in open(ctsf):
-        kmer = line.split()[0]
-        num_covs_at[count_at(kmer)] += 1
-
-    # for each AT bin
-    at_cutoffs = []
-    for at in range(1,k):
-        # sample covs
-        if sample >= num_covs_at[at]:
-            rand_covs = range(num_covs_at[at])
-        else:
-            rand_covs = random.sample(xrange(num_covs_at[at]), sample)
-        rand_covs.sort()
-
-        # print to file
-        out = open('kmers.txt', 'w')
-        kmer_i = 0
-        rand_i = 0
-        for line in open(ctsf):
-            (kmer,cov) = line.split()
-            if count_at(kmer) == at:
-                if kmer_i == rand_covs[rand_i]:
-                    print >> out, cov
-                    rand_i += 1
-                    if rand_i >= sample:
-                        break
-                kmer_i += 1
-        out.close()
-        
-        os.system('R --slave --args %d < %s/cov_model_qmer.r 2> r%d.log' % (ratio,quake.quake_dir,at))
-
-        at_cutoffs.append( open('cutoff.txt').readline().rstrip() )
-        if at in [1,k-1]:   # setting extremes to next closests
-            at_cutoffs.append( open('cutoff.txt').readline().rstrip() )
-
-        os.system('mv kmers.txt kmers.at%d.txt' % at)
-        os.system('mv cutoff.txt cutoff.at%d.txt' % at)
-
-    out = open('cutoffs.gc.txt','w')
-    print >> out, '\n'.join(at_cutoffs)
-    out.close()
-
-
-############################################################
-# model_q_gc_cutoffs_bigmem
-#
-# Sample kmers to give to R to learn the cutoff for each
-# GC value
-############################################################
-def model_q_gc_cutoffs_bigmem(ctsf, sample, ratio):
-    # input coverages
-    k = 0
-    for line in open(ctsf):
-        (kmer,cov) = line.split()
-        if k == 0:
-            k = len(kmer)
-            at_covs = ['']*(k+1)
-        else:
-            at = count_at(kmer)
-            if at_covs[at]:
-                at_covs[at].append(cov)
-            else:
-                at_covs[at] = [cov]
-
-    for at in range(1,k):
-        print '%d %d' % (at,len(at_covs[at]))
-
-    # for each AT bin
-    at_cutoffs = []
-    for at in range(1,k):
-        # sample covs
-        if sample >= len(at_covs[at]):
-            rand_covs = at_covs[at]
-        else:
-            rand_covs = random.sample(at_covs[at], sample)
-
-        # print to file
-        out = open('kmers.txt', 'w')
-        for rc in rand_covs:
-            print >> out, rc
-        out.close()
-
-        os.system('R --slave --args %d < %s/cov_model_qmer.r 2> r%d.log' % (ratio,quake.quake_dir,at))
-
-        at_cutoffs.append( open('cutoff.txt').readline().rstrip() )
-        if at in [1,k-1]:   # setting extremes to next closests
-            at_cutoffs.append( open('cutoff.txt').readline().rstrip() )
-
-        os.system('mv kmers.txt kmers.at%d.txt' % at)
-        os.system('mv cutoff.txt cutoff.at%d.txt' % at)
-
-    out = open('cutoffs.gc.txt','w')
-    print >> out, '\n'.join(at_cutoffs)
-    out.close()
-        
-    
-############################################################
-# count_at
-#
-# Count A's and T's in the given sequence
-############################################################
-def count_at(seq):
-    return len([nt for nt in seq if nt in ['A','T']])
-
-
-############################################################
-# __main__
-############################################################
-if __name__ == '__main__':
-    main()
diff --git a/tools/ilmn_pacbio/quake.py b/tools/ilmn_pacbio/quake.py
deleted file mode 100644
index b6ba7b03643..00000000000
--- a/tools/ilmn_pacbio/quake.py
+++ /dev/null
@@ -1,136 +0,0 @@
-#!/usr/bin/env python
-from optparse import OptionParser, SUPPRESS_HELP
-import os, random, sys
-import cov_model
-
-############################################################
-# quake.py
-#
-# Launch pipeline to correct errors in Illumina sequencing
-# reads.
-############################################################
-
-#r_dir = '/nfshomes/dakelley/research/error_correction/bin'
-quake_dir = os.path.abspath(os.path.dirname(sys.argv[0]))
-
-############################################################
-# main
-############################################################
-def main():
-    usage = 'usage: %prog [options]'
-    parser = OptionParser(usage)
-    parser.add_option('-r', dest='readsf', help='Fastq file of reads')
-    parser.add_option('-f', dest='reads_listf', help='File containing fastq file names, one per line or two per line for paired end reads.')
-    parser.add_option('-k', dest='k', type='int', help='Size of k-mers to correct')
-    parser.add_option('-p', dest='proc', type='int', default=4, help='Number of processes [default: %default]')
-    parser.add_option('-q', dest='quality_scale', type='int', default=-1, help='Quality value ascii scale, generally 64 or 33. If not specified, it will guess.')
-    parser.add_option('--no_count', dest='no_count', action='store_true', default=False, help='Kmers are already counted and in expected file [reads file].qcts or [reads file].cts [default: %default]')
-    parser.add_option('--no_cut', dest='no_cut', action='store_true', default=False, help='Coverage model is optimized and cutoff was printed to expected file cutoff.txt [default: %default]')
-    parser.add_option('--int', dest='counted_kmers', action='store_true', default=False, help='Kmers were counted as integers w/o the use of quality values [default: %default]')
-    parser.add_option('--ratio', dest='ratio', type='int', default=200, help='Likelihood ratio to set trusted/untrusted cutoff.  Generally set between 10-1000 with lower numbers suggesting a lower threshold. [default: %default]')
-    # help='Model kmer coverage as a function of GC content of kmers [default: %default]'
-    parser.add_option('--gc', dest='model_gc', action='store_true', default=False, help=SUPPRESS_HELP)
-    parser.add_option('--headers', action='store_true', default=False, help='Output original read headers (i.e. pass --headers to correct)' )
-    (options, args) = parser.parse_args()
-
-    if not options.readsf and not options.reads_listf:
-        parser.error('Must provide fastq file of reads with -r or file with list of fastq files of reads with -f')
-    if not options.k:
-        parser.error('Must provide k-mer size with -k')
-    if options.quality_scale == -1:
-        options.quality_scale = guess_quality_scale(options.readsf, options.reads_listf)
-
-    if options.counted_kmers:
-        cts_suf = 'cts'
-    else:
-        cts_suf = 'qcts'
-    if options.readsf:
-        ctsf = '%s.%s' % (os.path.splitext( os.path.split(options.readsf)[1] )[0], cts_suf)
-        reads_str = '-r %s' % options.readsf
-    else:
-        ctsf = '%s.%s' % (os.path.split(options.reads_listf)[1], cts_suf)
-        reads_str = '-f %s' % options.reads_listf
-
-    if not options.no_count and not options.no_cut:
-        count_kmers(options.readsf, options.reads_listf, options.k, ctsf, options.quality_scale)
-
-    if not options.no_cut:
-        # model coverage
-        if options.counted_kmers:
-            cov_model.model_cutoff(ctsf, options.ratio)
-        else:
-            if options.model_gc:
-                cov_model.model_q_gc_cutoffs(ctsf, 10000, options.ratio)
-            else:
-                cov_model.model_q_cutoff(ctsf, 25000, options.ratio)
-
-
-    if options.model_gc:
-        # run correct C++ code
-        os.system('%s/correct %s -k %d -m %s -a cutoffs.gc.txt -p %d -q %d' % (quake_dir,reads_str, options.k, ctsf, options.proc, options.quality_scale))
-
-    else:
-        cutoff = open('cutoff.txt').readline().rstrip()
-
-        # run correct C++ code
-        headers = '--headers' if options.headers else ''
-        os.system('%s/correct %s %s -k %d -m %s -c %s -p %d -q %d' % (quake_dir,headers, reads_str, options.k, ctsf, cutoff, options.proc, options.quality_scale))
-
-
-################################################################################
-# guess_quality_scale
-# Guess at ascii scale of quality values by examining
-# a bunch of reads and looking for quality values < 64,
-# in which case we set it to 33.
-################################################################################
-def guess_quality_scale(readsf, reads_listf):
-    reads_to_check = 1000
-    if not readsf:
-        readsf = open(reads_listf).readline().split()[0]
-
-    fqf = open(readsf)
-    reads_checked = 0
-    header = fqf.readline()
-    while header and reads_checked < reads_to_check:
-        seq = fqf.readline()
-        mid = fqf.readline()
-        qual = fqf.readline().rstrip()
-        reads_checked += 1
-        for q in qual:
-            if ord(q) < 64:
-                print 'Guessing quality values are on ascii 33 scale'
-                return 33
-        header = fqf.readline()
-
-    print 'Guessing quality values are on ascii 64 scale'
-    return 64
-        
-
-
-############################################################
-# count_kmers
-#
-# Count kmers in the reads file using AMOS count-kmers or
-# count-qmers
-############################################################
-def count_kmers(readsf, reads_listf, k, ctsf, quality_scale):
-    # find files
-    fq_files = []
-    if readsf:
-        fq_files.append(readsf)
-    else:
-        for line in open(reads_listf):
-            for fqf in line.split():
-                fq_files.append(fqf)
-
-    if ctsf[-4:] == 'qcts':
-        os.system('cat %s | %s/count-qmers -k %d -q %d > %s' % (' '.join(fq_files), quake_dir, k, quality_scale, ctsf))
-    else:
-        os.system('cat %s | %s/count-kmers -k %d > %s' % (' '.join(fq_files), quake_dir, k, ctsf))
-    
-            
-############################################################
-# __main__
-############################################################
-if __name__ == '__main__':
-    main()
diff --git a/tools/ilmn_pacbio/quake.xml b/tools/ilmn_pacbio/quake.xml
deleted file mode 100644
index 0098749f45e..00000000000
--- a/tools/ilmn_pacbio/quake.xml
+++ /dev/null
@@ -1,44 +0,0 @@
-<tool id="quake" name="Quake" version="1.0.0">
-  <description>Quality-aware error correction</description>
-  <command interpreter="python">
-    quake_wrapper.py --default_cutoff=10 --headers -k $k -f $fofnfile -p 12 > $output1
-  </command>
-  <inputs>
-    <param name="input1" format="fastq" type="data" label="Select FASTQ file to correct" />
-    <param name="k" type="integer" value="16" label="Size of k-mers to correct" />
-  </inputs>
-  <configfiles>
-    <configfile name="fofnfile">
-${input1.file_name}
-    </configfile>
-  </configfiles>
-  <outputs>
-    <data format="fastq" name="output1" label="Error-corrected reads from ${on_string}" />
-  </outputs>
-  <help>
-
-**What it does**
-
-Applies the Quake_ algorithm for quality-aware correction of
-substitution error in short reads.
-
-Kelley DR, Schatz MC, Salzberg SL.
-"Quake: quality-aware detection and correction of sequencing errors."
-*Genome Biol.* 2010;11(11):R116.
-
-.. _Quake: http://www.cbcb.umd.edu/software/quake
-
-**Parameter list**
-
-k
-    k-mer size for detecting spurious k-mers versus true k-mers from
-    the genome.  Recommendations for choosing a value of k can be found
-    here_.
-
-.. _here: http://www.cbcb.umd.edu/software/quake/faq.html
-
-**Output**
-
-A FASTQ file of corrected and trimmed reads.
-  </help>
-</tool>
diff --git a/tools/ilmn_pacbio/quake_pe.xml b/tools/ilmn_pacbio/quake_pe.xml
deleted file mode 100644
index af5d7b6f0e2..00000000000
--- a/tools/ilmn_pacbio/quake_pe.xml
+++ /dev/null
@@ -1,53 +0,0 @@
-<tool id="quake_pe" name="Quake PE" version="1.0.0">
-  <description>Quality-aware error correction for paired-end reads</description>
-  <command interpreter="python">
-    quake_wrapper.py --default_cutoff=$cutoff --headers -k $k -f $fofnfile -p 12 --output=$output1,$output2
-  </command>
-  <inputs>
-    <param name="input1" format="fastq" type="data" label="FASTQ file for forward reads" />
-    <param name="input2" format="fastq" type="data" label="FASTQ file for reverse reads" />
-    <param name="k" type="integer" value="16" label="Size of k-mers to correct" />
-    <param name="cutoff" type="integer" value="0" label="Default coverage cutoff if estimation fails"/>
-  </inputs>
-  <configfiles>
-    <configfile name="fofnfile">${input1.file_name} ${input2.file_name}
-    </configfile>
-  </configfiles>
-  <outputs>
-    <data format="fastq" name="output1" label="Error-corrected forward reads from ${on_string}" />
-    <data format="fastq" name="output2" label="Error-corrected reverse reads from ${on_string}" />
-  </outputs>
-  <help>
-
-**What it does**
-
-Applies the Quake_ algorithm for quality-aware correction of
-substitution error in short reads.  This form of the tool is customized
-for correcting paired-end reads.
-
-Kelley DR, Schatz MC, Salzberg SL.
-"Quake: quality-aware detection and correction of sequencing errors."
-*Genome Biol.* 2010;11(11):R116.
-
-.. _Quake: http://www.cbcb.umd.edu/software/quake
-
-**Parameter list**
-
-K-mer size
-    k-mer size for detecting spurious k-mers versus true k-mers from
-    the genome.  Recommendations for choosing a value of k can be found
-    here_.
-
-Default coverage cutoff
-    If the appropriate coverage cutoff can not be found then Quake can be
-    forced to proceed anyways with the supplied cutoff.  In this case, 
-    the optimal cutoff can be estimated by examining
-    the k-mer coverage histogram by eye.
-
-.. _here: http://www.cbcb.umd.edu/software/quake/faq.html
-
-**Output**
-
-A FASTQ file of corrected and trimmed reads.
-  </help>
-</tool>
diff --git a/tools/ilmn_pacbio/quake_wrapper.py b/tools/ilmn_pacbio/quake_wrapper.py
deleted file mode 100644
index 4873ca579c9..00000000000
--- a/tools/ilmn_pacbio/quake_wrapper.py
+++ /dev/null
@@ -1,132 +0,0 @@
-#!/usr/bin/python
-#
-# Copyright (c) 2011, Pacific Biosciences of California, Inc.
-#
-# All rights reserved.
-#
-#Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
-#    * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
-#    * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
-#    * Neither the name of Pacific Biosciences nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
-#
-#THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-#WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS CONTRIBUTORS BE LIABLE FOR ANY
-#DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-#LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-#(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-#
-import sys
-import os
-import subprocess
-
-QUAKE_EXE = os.path.join( os.path.dirname(os.path.abspath(sys.argv[0])), 'quake.py' )
-cmdLine = sys.argv
-cmdLine.pop(0)
-
-#
-# horribly not robust, but it was a pain to rewrite everything with
-# optparse
-#
-j = -1
-cut = 0
-for i,arg in enumerate(cmdLine):
-    if '--default_cutoff' in arg:
-        j = i
-        cut = int(arg.split('=')[1])
-if j>=0:
-    cmdLine = cmdLine[:j] + cmdLine[j+1:]
-
-j = -1
-output=''
-for i,arg in enumerate(cmdLine):
-    if '--output' in arg:
-        j = i
-        output = arg.split('=')[1]
-if j>=0:
-    cmdLine = cmdLine[:j] + cmdLine[j+1:]
-
-def backticks( cmd, merge_stderr=True ):
-    """
-    Simulates the perl backticks (``) command with error-handling support
-    Returns ( command output as sequence of strings, error code, error message )
-    """
-    if merge_stderr:
-        _stderr = subprocess.STDOUT
-    else:
-        _stderr = subprocess.PIPE
-
-    p = subprocess.Popen( cmd, shell=True, stdin=subprocess.PIPE,
-                          stdout=subprocess.PIPE, stderr=_stderr,
-                          close_fds=True )
-
-    out = [ l[:-1] for l in p.stdout.readlines() ]
-
-    p.stdout.close()
-    if not merge_stderr:
-        p.stderr.close()
-
-    # need to allow process to terminate
-    p.wait()
-
-    errCode = p.returncode and p.returncode or 0
-    if p.returncode>0:
-        errorMessage = os.linesep.join(out)
-        output = []
-    else:
-        errorMessage = ''
-        output = out
-
-    return output, errCode, errorMessage
-
-def to_stdout():
-    def toCorFastq(f):
-        stem, ext = os.path.splitext( os.path.basename(f) )
-        dir = os.path.dirname(f)
-        corFastq = os.path.join(dir,'%s.cor%s' % (stem,ext) )
-        if not os.path.exists(corFastq):
-            print >>sys.stderr, "Can't find path %s" % corFastq
-            sys.exit(1)
-        return corFastq
-    if '-r' in cmdLine:
-        fastqFile = cmdLine[ cmdLine.index('-r')+1 ]
-        corFastq = toCorFastq(fastqFile)
-        infile = open( corFastq, 'r' )
-        for line in infile:
-            sys.stdout.write( line )
-        infile.close()
-    else:
-        fofnFile = cmdLine[ cmdLine.index('-f')+1 ]
-        infile = open(fofnFile,'r')
-        for line in infile:
-            line = line.strip()
-            if len(line)>0:
-                fastqFiles = line.split()
-                break
-        infile.close()
-        outs = output.split(',')
-        for o,f in zip(outs,fastqFiles):
-            cf = toCorFastq(f)
-            os.system( 'cp %s %s' % ( cf, o ) )
-
-def run():
-    cmd = '%s %s' % ( QUAKE_EXE, " ".join(cmdLine) )
-    output, errCode, errMsg = backticks( cmd )
-
-    if errCode==0:
-        to_stdout()
-    else:
-        # if Quake exits with an error in cutoff determination we  
-        # can force correction if requested
-        if 'cutoff.txt' in errMsg and cut>0:
-            outfile = open( 'cutoff.txt', 'w' )
-            print >>outfile, str(cut)
-            outfile.close()
-            cmd = '%s --no_count --no_cut %s' % ( QUAKE_EXE, " ".join(cmdLine) )
-            output, errCode, errMsg = backticks( cmd )
-        if errCode==0:
-            to_stdout()
-        else:
-            print >>sys.stderr, errMsg
-            sys.exit(1)
-
-if __name__=='__main__': run()
diff --git a/tools/ilmn_pacbio/smrtpipe.py b/tools/ilmn_pacbio/smrtpipe.py
deleted file mode 100644
index 504b95e9835..00000000000
--- a/tools/ilmn_pacbio/smrtpipe.py
+++ /dev/null
@@ -1,5 +0,0 @@
-#!/usr/bin/env python
-# EASY-INSTALL-SCRIPT: 'pbpy==0.1','smrtpipe.py'
-__requires__ = 'pbpy==0.1'
-import pkg_resources
-pkg_resources.run_script('pbpy==0.1', 'smrtpipe.py')
diff --git a/tools/ilmn_pacbio/smrtpipe_filter.xml b/tools/ilmn_pacbio/smrtpipe_filter.xml
deleted file mode 100644
index b487f388c8a..00000000000
--- a/tools/ilmn_pacbio/smrtpipe_filter.xml
+++ /dev/null
@@ -1,67 +0,0 @@
-<tool id="smrtpipe_filter" name="SMRTpipe Filter" version="1.0.0">
-  <description>Produce filtered reads from a set of PacBio primary analysis outputs.</description>
-  <command interpreter="python">
-    smrtpipe_galaxy.py --output=data/filtered_subreads.fasta --galaxy_output=${outfile} ${iniFile}
-  </command>
-  <inputs>
-    <conditional name="source">
-      <param name="input_source" type="select" label="Choose the source for the analysis inputs">
-        <option value="path">Path to fofn or multiple bas.h5 paths</option>
-        <option value="history">History</option>
-      </param>
-      <when value="path">
-        <repeat name="inputFiles" title="Input files">
-          <param name="path" type="text" label="File path" size="75"/>
-        </repeat>
-      </when>
-      <when value="history">
-        <param name="input1" type="data" format="tabular" label="File containing input paths" />
-      </when>
-    </conditional>
-    <param name="minimum_readlength" type="integer" value="50" label="Minimum raw readlength" />
-    <param name="minimum_readscore" type="float" value="0.75" label="Minimum read quality" />
-  </inputs>
-  <configfiles>
-    <configfile name="iniFile">
-[input]
-#if $source.input_source=="history":
-#for $l in open($source.input1.file_name,'r'):
-$l
-#end for
-#else
-#for $p in $source.inputFiles
-${p.path}
-#end for
-#end if
-
-[S_Filter]
-filters=MinRL=${minimum_readlength},MinReadScore=${minimum_readscore}
-    </configfile>
-  </configfiles>
-  <outputs>
-    <data name="outfile" format="fasta" label="Filtered subreads" />
-  </outputs>
-  <help>
-
-**What it does**
-
-Filters PacBio bas.h5 files and produces a FASTA file of filtered subreads.
-
-In PacBio SMRT sequencing, the template format is a SMRTbell: a circular
-molecule with adapters at two locations in the circle.  The subreads are the
-portions of the read between adapters.
-
-**Parameter list**
-
-Minimum readlength
-    Only keep reads from ZMWs that produced this many bases or more.
-
-Minimum read quality
-    Only keep reads with overall quality scores of this value or more.  The read quality score is a *de novo* prediction of the accuracy of the read.
-
-**Output**
-
-FASTA file of filtered reads.
-
-  </help>
-</tool>
diff --git a/tools/ilmn_pacbio/smrtpipe_galaxy.py b/tools/ilmn_pacbio/smrtpipe_galaxy.py
deleted file mode 100644
index 637e9d4f7f0..00000000000
--- a/tools/ilmn_pacbio/smrtpipe_galaxy.py
+++ /dev/null
@@ -1,265 +0,0 @@
-#!/usr/bin/python
-import sys
-import os
-import subprocess
-import optparse as op
-import xml.etree.cElementTree as et
-
-TRACE=False
-#
-# Turn on tracing to dump out __input__.xml and __settings__.xml somewhere
-#
-#TRACE=True
-#TRACE_PATH='/home/UNIXHOME/jsorenson'
-
-class SmrtpipeGalaxy:
-    """Wrapper for running smrtpipe under galaxy"""
-    def __init__( self, argv ):
-        self.__parseOptions( argv )
-
-    def __parseOptions( self, argv ):
-        usage = 'Usage: %prog [--help] [options] smrtpipe.ini'
-        parser = op.OptionParser( usage=usage, description=SmrtpipeGalaxy.__doc__ )
-        parser.add_option( "--output",
-                           help="Designate a file generated by smrtpipe as the expected output for galaxy" )
-        parser.add_option( "--nproc", type="int",
-                           help="Number of processes to use (-D NPROC)" )
-        parser.add_option( "--galaxy_output",
-                           help="File name provided by galaxy where output should be placed" )
-        parser.add_option( "--dry_run", action="store_true", 
-                           help="Create auxiliary XML files and exit" )
-        parser.add_option( "--dat_extension", 
-                           help="Soft link .dat files to have this extension (some pipelines require certain extensions)" ) 
-
-        parser.set_defaults( output=None, dry_run=False, galaxy_output=None,
-            dat_extension=None, nproc=0 )
-        self.options, self.args = parser.parse_args( argv )
-
-        if len(self.args)!=2:
-            parser.error( 'Expected 1 argument' )
-
-        self.configFile = self.args[1]
-
-    def __parseConfig( self ):
-        infile = open( self.configFile, 'r' )
-        section = None
-        sections = []
-        for line in infile:
-            l = line.strip()
-            if len(l)==0 or line.startswith('#'):
-                continue
-            if l.startswith('[') and l.endswith(']'):
-                section = section_factory( l[1:-1] )
-                sections.append(section)
-                continue
-            if section is None:
-                continue
-            if '=' in l:
-                section.addParameterLine(l)
-            else:
-                section.addLine(l)
-        infile.close()
-        return sections
-
-    def transferOutput( self ):
-        if not self.options.output or not self.options.galaxy_output:
-            return True, ''
-        if not os.path.exists(self.options.output):
-            return False, "Can't find file %s (job error?)" % self.options.output
-        os.system( 'cp %s %s' % (self.options.output, self.options.galaxy_output ))
-        return True, ''
-
-    def run( self ):
-        if not os.path.exists( self.configFile ):
-            print >>sys.stderr, "Can't find config file %s" % self.configFile
-            return 1
-
-        sections = self.__parseConfig()
-
-        if len(sections)==0:
-            print >>sys.stderr, "No sections found in %s" % self.configFile
-            return 1
-        if sections[0].name != 'input':
-            print >>sys.stderr, "No [input] section found in %s" % self.configFile
-            return 1
-
-        INPUT_FILE = '__input__.xml'
-        SETTINGS_FILE = '__settings__.xml'
-
-        sections[0].softLinkDats( self.options.dat_extension )
-        inputXml = sections[0].makeXmlElement()
-        write_xml_to_file( INPUT_FILE, inputXml )
-        if TRACE:
-            write_xml_to_file( os.path.join(TRACE_PATH,INPUT_FILE), inputXml )
-
-        settings = et.Element( 'smrtpipeSettings' )
-        for s in sections[1:]:
-            s.makeXmlElement( settings )
-
-        write_xml_to_file( SETTINGS_FILE, settings )
-        if TRACE:
-            write_xml_to_file( os.path.join(TRACE_PATH,SETTINGS_FILE), settings )
-
-        nproc = '-D NPROC=%d' % self.options.nproc if self.options.nproc>0 else ''
-        cmd = 'smrtpipe.py %s --params=%s xml:%s > smrtpipe.err 2>1' % \
-            ( nproc, SETTINGS_FILE, INPUT_FILE )
-
-        if self.options.dry_run:
-            print 'Command to run:'
-            print cmd
-            return 0
-
-        out, errCode, errMsg = backticks( cmd )
-        if errCode!=0:
-            print >>sys.stderr, "error while running: %s" % cmd
-            print >>sys.stderr, errMsg
-            if os.path.exists('log/smrtpipe.log'):
-                print >>sys.stderr, 'Log:'
-                infile = open('log/smrtpipe.log','r')
-                for line in infile: sys.stderr.write(line)
-                infile.close()
-            return errCode
-
-        success, errMsg = self.transferOutput()
-        if not success:
-            print >>sys.stderr, errMsg
-            return 1
-
-        return 0
-
-def write_xml_to_file( fileName, root ):
-    outfile = open( fileName, 'w' )
-    outfile.write( '<?xml version="1.0"?>\n' )
-    outfile.write( et.tostring(root) + '\n' )
-    outfile.close()
-
-def section_factory( name ):
-    if name=='input':
-        return InputSection(name)
-    else:
-        return Section(name)
-
-class Section:
-    def __init__( self, name ):
-        self._name = name
-        self._lines = []        
-        self._vars = {}
-
-    @property
-    def name(self):
-        return self._name
-
-    def addLine( self, line ):
-        self._lines.append(line)
-
-    def addParameterLine( self, line ):
-        self.addLine(line)
-        i = line.find( '=' )
-        key = line[:i].strip()
-        value = line[i+1:].strip()
-        self._vars[key] = value
-
-    def makeXmlElement( self, settings ):
-        if self._name=='global':
-            root = et.SubElement( settings, "protocol", {'name':'generic'} )
-        else:
-            root = et.SubElement( settings, "module", {'name':self._name} )
-        for k,v in self._vars.iteritems():
-            param = et.SubElement( root, 'param', {'name':k} )
-            val = et.SubElement( param, 'value' )
-            val.text = v
-        return None
-
-    def __str__( self ):
-        "for debugging"
-        buffer = [ 'S { name=' ]
-        buffer.append(self._name)
-        buffer.append('; lines=%s' % ','.join(self._lines) )
-        for k,v in self._vars.iteritems():
-            buffer.append('; %s=%s' % (k,v) )
-        buffer.append(' }')
-        return ''.join(buffer)
-
-class InputSection( Section ):
-    def __init__( self, name ):
-        Section.__init__(self,name)
-
-    def softLinkDats( self, newExtension ):
-        if not newExtension:
-            return
-        newLines = []
-        for l in self._lines:
-            if ':' in l:
-                protocol = l[:l.find(':')+1]
-                file = l[l.find(':')+1:]
-            else:
-                protocol = ''
-                file = l
-            if os.path.exists(file) and file.endswith('.dat'):
-                newFile = '%s.%s' % ( file, newExtension )
-                if not os.path.exists(newFile):
-                    os.system( 'ln -s %s %s' % ( file, newFile ) )
-                newLines.append(protocol+newFile)
-            else:
-                newLines.append(l)
-        self._lines = newLines
-
-    def makeXmlElement( self, parent=None ):
-        root = et.Element( "pacbioAnalysisInputs" )
-        data = et.SubElement( root, 'dataReferences' )
-        iRef = 0
-        for l in self._lines:
-            def add(x,iRef):
-                if len(x)==0: return iRef
-                node = et.SubElement( data, 'url' )
-                if ':' in x:
-                    node.attrib[ 'ref' ] = x
-                else:
-                    node.attrib[ 'ref' ] = 'run:0000000-%04d' % iRef
-                    node2 = et.SubElement( node, 'location' )
-                    node2.text = x
-                return iRef+1
-            if l.endswith('fofn') and os.path.exists(l):
-                infile = open(l,'r')
-                for j,line in enumerate(infile): iRef=add(line.strip(),iRef)
-                infile.close()
-            else:
-                iRef=add(l,iRef)
-        return root
-
-def backticks( cmd, merge_stderr=True ):
-    """
-    Simulates the perl backticks (``) command with error-handling support
-    Returns ( command output as sequence of strings, error code, error message )
-    """
-    if merge_stderr:
-        _stderr = subprocess.STDOUT
-    else:
-        _stderr = subprocess.PIPE
-
-    p = subprocess.Popen( cmd, shell=True, stdin=subprocess.PIPE,
-                          stdout=subprocess.PIPE, stderr=_stderr,
-                          close_fds=True )
-
-    out = [ l[:-1] for l in p.stdout.readlines() ]
-
-    p.stdout.close()
-    if not merge_stderr:
-        p.stderr.close()
-
-    # need to allow process to terminate
-    p.wait()
-
-    errCode = p.returncode and p.returncode or 0
-    if p.returncode>0:
-        errorMessage = os.linesep.join(out)
-        output = []
-    else:
-        errorMessage = ''
-        output = out
-        
-    return output, errCode, errorMessage
-
-if __name__=='__main__':
-    app = SmrtpipeGalaxy( sys.argv )
-    sys.exit( app.run() )
diff --git a/tools/ilmn_pacbio/smrtpipe_hybrid.xml b/tools/ilmn_pacbio/smrtpipe_hybrid.xml
deleted file mode 100644
index d0e7d81e752..00000000000
--- a/tools/ilmn_pacbio/smrtpipe_hybrid.xml
+++ /dev/null
@@ -1,59 +0,0 @@
-<tool id="smrtpipe_hybrid" name="AHA" version="1.0.0">
-  <description>Assemble contigs from a set of contigs and PacBio reads.</description>
-  <command interpreter="python">
-    smrtpipe_galaxy.py --nproc=24 --dat_extension=fasta --output=data/scaffold.fasta --galaxy_output=${outfile} ${iniFile}
-  </command>
-  <!--
-  <command>cp ${iniFile} ${outfile}</command>
-  -->
-  <inputs>
-    <param name="contigs" format="fasta" type="data" label="Starting Contigs"/>
-    <param name="reads" format="fasta" type="data" label="PacBio Reads"/>
-    <param name="schedule" type="text" value="6,3,75;6,3,75;5,3,75;5,3,75;6,2,75;6,2,75;5,2,75;5,2,75" label="Parameter Schedule" size="60"/>
-  </inputs>
-  <configfiles>
-    <configfile name="iniFile">
-[input]
-assembled_contigs:${contigs}
-file:${reads}
-
-[HybridAssembly]
-instrumentModel=RS
-cleanup=False
-untangler=pacbio
-#set $schedule2 = $schedule.replace('X',';')
-paramSchedule=${schedule2}
-dontFillin=False
-longReadsAsStrobe=True
-exactQueryIds=True
-rm4Opts=-minMatch 7 -minFrac 0.1 -minPctIdentity 65 -bestn 10 -noSplitSubreads
-numberProcesses=16
-cluster=False
-minRepeatLength=100000
-    </configfile>
-  </configfiles>
-  <outputs>
-    <data name="outfile" format="fasta" label="Hybrid assembly contigs from ${on_string}"/>
-  </outputs>
-  <help>
-
-**What it does**
-
-The AHA assembly algorithm is an AMOS_-based pipeline
-for finishing bacterial-sized
-genomes using draft contigs and PacBio reads.
-
-.. _AMOS: http://sourceforge.net/apps/mediawiki/amos
-
-**Parameter list**
-
-Parameter schedule
-    The parameter schedule is a semi-colon delimited list of triples.  Each triple represents an iteration of hybrid assembly (alignment/scaffolding/gap-filling).  The three paremeters for each iteration are the Z-score, number of reads required to define a link, and the minimum length of subreads used in links.
-
-**Output**
-
-FASTA file containing scaffolded and gap-filled contigs resulting from the 
-hybrid assembly.
-
-  </help>
-</tool>
diff --git a/tools/ilmn_pacbio/soap_denovo.xml b/tools/ilmn_pacbio/soap_denovo.xml
deleted file mode 100644
index 1fb857f9760..00000000000
--- a/tools/ilmn_pacbio/soap_denovo.xml
+++ /dev/null
@@ -1,73 +0,0 @@
-<tool id="soap_denovo" name="SOAPdenovo" version="1.0.0">
-  <description>Short-read de novo assembly</description>
-  <!--
-      # SOAPdenovo-127mer all -s ${soap_config} -o assembly -K ${k} -p 8 -d -D
-      # cat ${soap_config} > ${output1}
-      # cp ${soap_config} ${output1} &amp;&amp;
-  -->
-  <command>
-      SOAPdenovo-127mer all -s ${soap_config} -o assembly -K ${k} -p 24 -d -D -R
-  </command>
-  <inputs>
-    <conditional name="inputs">
-      <param name="read_type" type="select" label="Illumina read type">
-        <option value="single">Single fragment</option>
-        <option value="paired">Paired-end</option>
-      </param>
-      <when value="single">
-        <param name="input1" format="fastq" type="data" label="FASTQ file for reads"/>
-      </when>
-      <when value="paired">
-        <param name="input1" format="fastq" type="data" label="FASTQ file for forward reads"/>
-        <param name="input2" format="fastq" type="data" label="FASTQ file for reverse reads"/>
-        <param name="d" type="integer" value="500" label="Estimated insert size for paired-end reads" />
-      </when>
-    </conditional>
-    <param name="k" type="integer" value="23" label="Size of k for forming the de Bruijn overlap graph" />
-  </inputs>
-  <configfiles>
-    <configfile name="soap_config">max_rd_len=105
-[LIB]
-#if $inputs.read_type == "single"
-q=${inputs.input1.file_name}
-#else
-avg_ins=${inputs.d}
-asm_flags=3
-reverse_seq=0
-q1=${inputs.input1.file_name}
-q2=${inputs.input2.file_name}
-#end if
-    </configfile>
-  </configfiles>
-  <outputs>
-    <data name="assembled_contigs" format="fasta" from_work_dir="assembly.scafSeq" label="Assembled contigs from ${on_string}" />
-  </outputs>
-  <help>
-
-**What it does**
-
-Runs SOAPdenovo_ to generate a genome assembly
-using single-fragment or paired-end short reads.
-
-Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J.
-"De novo assembly of human genomes with massively parallel short read sequencing."
-*Genome Res.* 2010 Feb;20(2):265-72.
-
-.. _SOAPdenovo: http://soap.genomics.org.cn/soapdenovo.html
-
-**Parameter list**
-
-k
-    k-mer size for constructing the de Bruijn graph.  The appropriate size of k is genome and data set dependent, but a good starting choice might be 75% of the read length.
-
-Insert size
-    For paired-end libraries, the expected insert size.
-
-**Output**
-
-assembly
-
-  </help>
-</tool>
-
-

From 4eb1c48536ee1c090255546fda424ee2ea038477 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Thu, 10 Nov 2011 12:49:44 -0500
Subject: [PATCH 177/362] Fix an exception class that doesn't exist.  Thanks
 Oleksandr Moskalenko.

---
 lib/galaxy/util/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/util/__init__.py b/lib/galaxy/util/__init__.py
index daad6cc04ec..5910f6a3d1b 100644
--- a/lib/galaxy/util/__init__.py
+++ b/lib/galaxy/util/__init__.py
@@ -607,7 +607,7 @@ def send_mail( frm, to, subject, body, config ):
             log.error( "The server didn't accept the username/password combination: %s" % e )
             s.close()
             raise
-        except smtplib.SMTPError, e:
+        except smtplib.SMTPException, e:
             log.error( "No suitable authentication method was found: %s" % e )
             s.close()
             raise

From 401e67db6c98d441c039966cb7d0193d751a6f55 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 10 Nov 2011 14:56:35 -0500
Subject: [PATCH 178/362] Fix for slug check flag pointed out by Andrew Warren.

---
 lib/galaxy/web/controllers/workflow.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/web/controllers/workflow.py b/lib/galaxy/web/controllers/workflow.py
index f15d8a6b1f4..8f67fc5b28e 100644
--- a/lib/galaxy/web/controllers/workflow.py
+++ b/lib/galaxy/web/controllers/workflow.py
@@ -149,7 +149,8 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
         # Legacy issue: all shared workflows must have slugs.
         slug_set = False
         for workflow_assoc in shared_by_others:
-            slug_set = self.create_item_slug( trans.sa_session, workflow_assoc.stored_workflow )
+            if self.create_item_slug( trans.sa_session, workflow_assoc.stored_workflow ):
+                slug_set = True
         if slug_set:
             trans.sa_session.flush()
 

From ebdaf62c9071605a8c521a3154e57612603e92fd Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Thu, 10 Nov 2011 16:16:26 -0500
Subject: [PATCH 179/362] Make toggle icons use black and white and color on
 hover to match other Trackster icons.

---
 static/june_2007_style/base.css.tmpl      | 4 ----
 static/june_2007_style/blue/base.css      | 7 ++++---
 static/june_2007_style/blue/trackster.css | 2 +-
 static/june_2007_style/trackster.css.tmpl | 2 +-
 static/scripts/trackster.js               | 6 +++---
 5 files changed, 9 insertions(+), 12 deletions(-)

diff --git a/static/june_2007_style/base.css.tmpl b/static/june_2007_style/base.css.tmpl
index 2e2f1e4c4d9..d135799caad 100644
--- a/static/june_2007_style/base.css.tmpl
+++ b/static/june_2007_style/base.css.tmpl
@@ -865,10 +865,6 @@ div.permissionContainer {
     -sprite-group: fugue;
     -sprite-image: fugue/toggle-expand.png;
 }
-.icon-button.toggle {
-    -sprite-group: fugue;
-    -sprite-image: fugue/toggle.png;
-}
 .icon-button.toggle-contract {
     -sprite-group: fugue;
     -sprite-image: fugue/toggle.png;
diff --git a/static/june_2007_style/blue/base.css b/static/june_2007_style/blue/base.css
index 432582606d5..16d3898bded 100644
--- a/static/june_2007_style/blue/base.css
+++ b/static/june_2007_style/blue/base.css
@@ -151,9 +151,10 @@ div.permissionContainer{padding-left:20px;}
 .icon-button.tag{background:url(fugue.png) no-repeat 0px -0px;}
 .icon-button.tags{background:url(fugue.png) no-repeat 0px -26px;}
 .icon-button.tag--plus{background:url(fugue.png) no-repeat 0px -52px;}
-.icon-button.toggle-expand{background:url(fugue.png) no-repeat 0px -78px;}
-.icon-button.toggle{background:url(fugue.png) no-repeat 0px -104px;}
-.icon-button.toggle-contract{background:url(fugue.png) no-repeat 0px -104px;}
+.icon-button.toggle-expand{background:transparent url(../images/fugue/toggle-expand-bw.png) no-repeat;}
+.icon-button.toggle-expand:hover{background:url(fugue.png) no-repeat 0px -78px;}
+.icon-button.toggle-contract{background:transparent url(../images/fugue/toggle-bw.png) no-repeat;}
+.icon-button.toggle-contract:hover{background:url(fugue.png) no-repeat 0px -104px;}
 .icon-button.arrow-circle{background:url(fugue.png) no-repeat 0px -130px;}
 .icon-button.chevron{background:url(fugue.png) no-repeat 0px -156px;}
 .icon-button.bug{background:url(fugue.png) no-repeat 0px -182px;}
diff --git a/static/june_2007_style/blue/trackster.css b/static/june_2007_style/blue/trackster.css
index a9ba82ae395..2d30f57f93d 100644
--- a/static/june_2007_style/blue/trackster.css
+++ b/static/june_2007_style/blue/trackster.css
@@ -56,7 +56,7 @@ input{font:10px verdana;}
 .tool-name{font-size:110%;font-weight:bold;}
 .param-row{margin-top:0.2em;margin-left:1em;}
 .param-label{float:left;font-weight:bold;padding-top:0.2em;}
-.menu-button{padding:0px 4px 0px 4px;}
+.menu-button{margin:0px 4px 0px 4px;}
 .settings-icon{background:transparent url(../images/fugue/gear-bw.png) no-repeat;}
 .settings-icon:hover{background:transparent url(../images/fugue/gear.png) no-repeat;}
 .overview-icon{background:transparent url(../images/fugue/application-dock-270-bw.png) no-repeat;}
diff --git a/static/june_2007_style/trackster.css.tmpl b/static/june_2007_style/trackster.css.tmpl
index a902ec965d0..4602f49bf01 100644
--- a/static/june_2007_style/trackster.css.tmpl
+++ b/static/june_2007_style/trackster.css.tmpl
@@ -295,7 +295,7 @@ input {
     padding-top: 0.2em;
 }
 .menu-button {
-    padding: 0px 4px 0px 4px;
+    margin: 0px 4px 0px 4px;
 }
 .settings-icon {
     background: transparent url(../images/fugue/gear-bw.png) no-repeat;
diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index 00d2a080774..a4960ad1cd9 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -2389,7 +2389,7 @@ var Track = function(name, view, container, show_header, prefs, data_url, data_q
     
         // Track icons.
         this.toggle_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Hide/show track content")
-                                      .addClass("icon-button toggle").tipsy( {gravity: 's'} )
+                                      .addClass("icon-button toggle-contract").tipsy( {gravity: 's'} )
                                       .appendTo(this.icons_div);
         this.settings_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Edit settings")
                                       .addClass("icon-button settings-icon").tipsy( {gravity: 's'} )
@@ -2414,12 +2414,12 @@ var Track = function(name, view, container, show_header, prefs, data_url, data_q
         // Toggle icon hides or shows the track content
         this.toggle_icon.click( function() {
             if ( track.content_visible ) {
-                track.toggle_icon.addClass("toggle-expand").removeClass("toggle");
+                track.toggle_icon.addClass("toggle-expand").removeClass("toggle-contract");
                 track.hide_contents();
                 track.mode_div.hide();
                 track.content_visible = false;
             } else {
-                track.toggle_icon.addClass("toggle").removeClass("toggle-expand");
+                track.toggle_icon.addClass("toggle-contract").removeClass("toggle-expand");
                 track.content_visible = true;
                 track.mode_div.show();
                 track.show_contents();

From 14057dc5e20b8208286c430ce8c034551b20ee37 Mon Sep 17 00:00:00 2001
From: Ross Lazarus <ross.lazarus@gmail.com>
Date: Fri, 11 Nov 2011 08:23:15 +1100
Subject: [PATCH 180/362] Updates for picard tools 1.56 - they changed the
 params for CollectInsertSizeMetrics.jar - bless them - so you will need to
 update your local picard install in tool-data/shared/jars/picard

Fixes to picard_wrapper.py so if a picard tool returns a non zero exit code, it will raise an error state.
Sadly, this doesn't help the CollectInsertSizeMetrics problem it was meant to address - it will die
with no outputs if given an input containing unpaired reads - but the exit code is still zero.
Talk about irony.
At least it should work right if they ever get around to setting exit codes to indicate a problem.
---
 tools/picard/picard_wrapper.py      | 104 ++++++++++++++++++----------
 tools/picard/rgPicardASMetrics.xml  |   2 +-
 tools/picard/rgPicardInsertSize.xml |  26 ++++---
 3 files changed, 85 insertions(+), 47 deletions(-)

diff --git a/tools/picard/picard_wrapper.py b/tools/picard/picard_wrapper.py
index 5fc6f3903bc..03fbbb90ca3 100644
--- a/tools/picard/picard_wrapper.py
+++ b/tools/picard/picard_wrapper.py
@@ -125,14 +125,15 @@ class PicardBase():
         tef.close()
         stderrs = self.readLarge(temperr)
         stdouts = self.readLarge(templog)        
-        if len(stderrs) > 0:
+        if rval > 0:
             s = '## executing %s returned status %d and stderr: \n%s\n' % (cl,rval,stderrs)
+            stdouts = '%s\n%s' % (stdouts,stderrs)
         else:
             s = '## executing %s returned status %d and nothing on stderr\n' % (cl,rval)
         logging.info(s)
         os.unlink(templog) # always
         os.unlink(temperr) # always
-        return s, stdouts # sometimes this is an output
+        return s, stdouts, rval  # sometimes s is an output
     
     def runPic(self, jar, cl):
         """
@@ -141,8 +142,8 @@ class PicardBase():
         runme = ['java -Xmx%s' % self.opts.maxjheap]
         runme.append('-jar %s' % jar)
         runme += cl
-        s,stdout = self.runCL(cl=runme, output_dir=self.opts.outdir)
-        return stdout
+        s,stdouts,rval = self.runCL(cl=runme, output_dir=self.opts.outdir)
+        return stdouts,rval
 
     def samToBam(self,infile=None,outdir=None):
         """
@@ -150,8 +151,8 @@ class PicardBase():
         """
         fd,tempbam = tempfile.mkstemp(dir=outdir,suffix='rgutilsTemp.bam')
         cl = ['samtools view -h -b -S -o ',tempbam,infile]
-        tlog,stdouts = self.runCL(cl,outdir)
-        return tlog,tempbam
+        tlog,stdouts,rval = self.runCL(cl,outdir)
+        return tlog,tempbam,rval
 
     #def bamToSam(self,infile=None,outdir=None):
     #    """
@@ -167,7 +168,7 @@ class PicardBase():
         """
         print '## sortSam got infile=%s,outfile=%s,outdir=%s' % (infile,outfile,outdir)
         cl = ['samtools sort',infile,outfile]
-        tlog,stdouts = self.runCL(cl,outdir)
+        tlog,stdouts,rval = self.runCL(cl,outdir)
         return tlog
 
     def cleanup(self):
@@ -243,6 +244,9 @@ class PicardBase():
         if len(pdflist) > 0: # assumes all pdfs come with thumbnail .jpgs
             for p in pdflist:
                 imghref = '%s.jpg' % os.path.splitext(p)[0] # removes .pdf
+                mimghref = '%s-0.jpg' % os.path.splitext(p)[0] # multiple pages pdf -> multiple thumbnails without asking!
+                if mimghref in flist:
+                    imghref=mimghref
                 res.append('<table cellpadding="10"><tr><td>\n')
                 res.append('<a href="%s"><img src="%s" title="Click image preview for a print quality PDF version" hspace="10" align="middle"></a>\n' % (p,imghref)) 
                 res.append('</tr></td></table>\n')   
@@ -383,6 +387,8 @@ def __main__():
     op.add_option('', '--taillimit', default="0")
     op.add_option('', '--histwidth', default="0")
     op.add_option('', '--minpct', default="0.01")
+    op.add_option('', '--malevel', default="")
+    op.add_option('', '--deviations', default="0.0")
     # CollectAlignmentSummaryMetrics
     op.add_option('', '--maxinsert', default="20")
     op.add_option('', '--adaptors', action='append', type="string")
@@ -430,7 +436,8 @@ def __main__():
 
     tmp_dir = opts.outdir
     haveTempout = False # we use this where sam output is an option
-
+    rval = 0
+    stdouts = 'Not run yet'
     # set ref and dict files to use (create if necessary)
     ref_file_name = opts.ref
     if opts.ref_file <> None:
@@ -453,7 +460,7 @@ def __main__():
         pic.delme.append(dict_file_name)
         pic.delme.append(ref_file_name)
         pic.delme.append(tmp_ref_name)
-        s = pic.runPic(jarpath, cl)
+        stdouts,rval = pic.runPic(jarpath, cl)
         # run relevant command(s)
 
     # define temporary output
@@ -486,7 +493,7 @@ def __main__():
             cl.append('RGCN="%s"' % opts.rg_seq_center)
         if opts.rg_desc:
             cl.append('RGDS="%s"' % opts.rg_desc)
-        pic.runPic(opts.jar, cl)
+        stdouts,rval = pic.runPic(opts.jar, cl)
         haveTempout = True
 
     elif pic.picname == 'BamIndexStats':
@@ -499,9 +506,9 @@ def __main__():
         pic.delme.append(tmp_bam_name)
         pic.delme.append(tmp_bai_name)
         pic.delme.append(tmp_name)
-        s = pic.runPic( opts.jar, cl )
+        stdouts,rval = pic.runPic( opts.jar, cl )
         f = open(pic.metricsOut,'a')
-        f.write(s) # got this on stdout from runCl
+        f.write(stdouts) # got this on stdout from runCl
         f.write('\n')
         f.close()
         doTranspose = False # but not transposed
@@ -519,7 +526,7 @@ def __main__():
             cl.append('READ_NAME_REGEX="%s"' % opts.readregex)
         if float(opts.optdupdist) > 0:
             cl.append('OPTICAL_DUPLICATE_PIXEL_DISTANCE=%s' % opts.optdupdist)
-        pic.runPic(opts.jar,cl)
+        stdouts,rval = pic.runPic(opts.jar, cl)
 
     elif pic.picname == 'CollectAlignmentSummaryMetrics':
         # Why do we do this fakefasta thing? Because we need NO fai to be available or picard barfs unless it has the same length as the input data.
@@ -532,7 +539,7 @@ def __main__():
             info = s
             shutil.copy(ref_file_name,fakefasta)
         pic.delme.append(fakefasta)
-        cl.append('ASSUME_SORTED=%s' % opts.assumesorted)
+        cl.append('ASSUME_SORTED=true')
         adaptorseqs = ''.join([' ADAPTER_SEQUENCE=%s' % x for x in opts.adaptors])
         cl.append(adaptorseqs)
         cl.append('IS_BISULFITE_SEQUENCED=%s' % opts.bisulphite)
@@ -541,13 +548,24 @@ def __main__():
         cl.append('R=%s' % fakefasta)
         cl.append('TMP_DIR=%s' % opts.tmpdir)
         if not opts.assumesorted.lower() == 'true': # we need to sort input
-            fakeinput = '%s.sorted' % opts.input
-            s = pic.sortSam(opts.input, fakeinput, opts.outdir)
-            pic.delme.append(fakeinput)
-            cl.append('INPUT=%s' % fakeinput)
+            sortedfile = '%s.sorted' % os.path.basename(opts.input)
+            if opts.datatype == 'sam': # need to work with a bam 
+                tlog,tempbam,rval = pic.samToBam(opts.input,opts.outdir)
+                pic.delme.append(tempbam)
+                try:
+                    tlog = pic.sortSam(tempbam,sortedfile,opts.outdir)
+                except:
+                    print '## exception on sorting sam file %s' % opts.input
+            else: # is already bam
+                try:
+                    tlog = pic.sortSam(opts.input,sortedfile,opts.outdir)
+                except: # bug - [bam_sort_core] not being ignored - TODO fixme
+                    print '## exception on sorting bam file %s' % opts.input
+            cl.append('INPUT=%s.bam' % os.path.abspath(os.path.join(opts.outdir,sortedfile)))
+            pic.delme.append(os.path.join(opts.outdir,sortedfile))
         else:
             cl.append('INPUT=%s' % os.path.abspath(opts.input)) 
-        pic.runPic(opts.jar,cl)
+        stdouts,rval = pic.runPic(opts.jar, cl)
        
         
     elif pic.picname == 'CollectGcBiasMetrics':
@@ -575,10 +593,10 @@ def __main__():
         cl.append('TMP_DIR=%s' % opts.tmpdir)
         cl.append('CHART_OUTPUT=%s' % temppdf)
         cl.append('SUMMARY_OUTPUT=%s' % pic.metricsOut)
-        pic.runPic(opts.jar,cl)
+        stdouts,rval = pic.runPic(opts.jar, cl)
         if os.path.isfile(temppdf):
             cl2 = ['convert','-resize x400',temppdf,os.path.join(opts.outdir,jpgname)] # make the jpg for fixPicardOutputs to find
-            s,stdouts = pic.runCL(cl=cl2,output_dir=opts.outdir)
+            s,stdouts,rval = pic.runCL(cl=cl2,output_dir=opts.outdir)
         else:
             s='### runGC: Unable to find pdf %s - please check the log for the causal problem\n' % temppdf
         lf = open(pic.log_filename,'a')
@@ -587,29 +605,39 @@ def __main__():
         lf.close()
         
     elif pic.picname == 'CollectInsertSizeMetrics':
+        """ <command interpreter="python">
+   picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --deviations "$deviations"
+   --histwidth "$histWidth" --minpct "$minPct" --malevel "$malevel"
+   -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/CollectInsertSizeMetrics.jar" -d "$html_file.files_path" -t "$html_file"
+  </command>
+        """
         isPDF = 'InsertSizeHist.pdf'
         pdfpath = os.path.join(opts.outdir,isPDF)
         histpdf = 'InsertSizeHist.pdf'
         cl.append('I=%s' % opts.input)
         cl.append('O=%s' % pic.metricsOut)
         cl.append('HISTOGRAM_FILE=%s' % histpdf)
-        if opts.taillimit <> '0':
-            cl.append('TAIL_LIMIT=%s' % opts.taillimit)
+        #if opts.taillimit <> '0': # this was deprecated although still mentioned in the docs at 1.56
+        #    cl.append('TAIL_LIMIT=%s' % opts.taillimit)
         if  opts.histwidth <> '0':
             cl.append('HISTOGRAM_WIDTH=%s' % opts.histwidth)
         if float( opts.minpct) > 0.0:
             cl.append('MINIMUM_PCT=%s' % opts.minpct)
-        pic.runPic(opts.jar,cl)   
+        if float(opts.deviations) > 0.0:
+            cl.append('DEVIATIONS=%s' % opts.deviations)
+        if opts.malevel.strip():
+            malevels = ['METRIC_ACCUMULATION_LEVEL=%s' % x for x in opts.malevel.split(',')]
+            cl.append(' '.join(malevels))
+        stdouts,rval = pic.runPic(opts.jar, cl)
         if os.path.exists(pdfpath): # automake thumbnail - will be added to html 
             cl2 = ['mogrify', '-format jpg -resize x400 %s' % pdfpath]
-            s,stdouts = pic.runCL(cl=cl2,output_dir=opts.outdir)
+            pic.runCL(cl=cl2,output_dir=opts.outdir)
         else:
             s = 'Unable to find expected pdf file %s<br/>\n' % pdfpath
             s += 'This <b>always happens if single ended data was provided</b> to this tool,\n'
             s += 'so please double check that your input data really is paired-end NGS data.<br/>\n'
             s += 'If your input was paired data this may be a bug worth reporting to the galaxy-bugs list\n<br/>'
-            stdouts = ''
-        logging.info(s)
+            logging.info(s)
         if len(stdouts) > 0:
            logging.info(stdouts)
         
@@ -627,13 +655,13 @@ def __main__():
         cl.append('READ_NAME_REGEX="%s"' % opts.readregex)
         # maximum offset between two duplicate clusters
         cl.append('OPTICAL_DUPLICATE_PIXEL_DISTANCE=%s' % opts.optdupdist)
-        pic.runPic(opts.jar, cl)
+        stdouts,rval = pic.runPic(opts.jar, cl)
 
     elif pic.picname == 'FixMateInformation':
         cl.append('I=%s' % opts.input)
         cl.append('O=%s' % tempout)
         cl.append('SORT_ORDER=%s' % opts.sortorder)
-        pic.runPic(opts.jar,cl)
+        stdouts,rval = pic.runPic(opts.jar,cl)
         haveTempout = True
         
     elif pic.picname == 'ReorderSam':
@@ -649,14 +677,14 @@ def __main__():
         # contig length discordance
         if opts.allow_contig_len_discord == 'true':
             cl.append('ALLOW_CONTIG_LENGTH_DISCORDANCE=true')
-        pic.runPic(opts.jar, cl)
+        stdouts,rval = pic.runPic(opts.jar, cl)
         haveTempout = True
 
     elif pic.picname == 'ReplaceSamHeader':
         cl.append('INPUT=%s' % opts.input)
         cl.append('OUTPUT=%s' % tempout)
         cl.append('HEADER=%s' % opts.header_file)
-        pic.runPic(opts.jar, cl)
+        stdouts,rval = pic.runPic(opts.jar, cl)
         haveTempout = True
 
     elif pic.picname == 'CalculateHsMetrics':
@@ -673,7 +701,7 @@ def __main__():
         cl.append('INPUT=%s' % os.path.abspath(opts.input))
         cl.append('OUTPUT=%s' % pic.metricsOut)
         cl.append('TMP_DIR=%s' % opts.tmpdir)
-        pic.runPic(opts.jar,cl)
+        stdouts,rval = pic.runPic(opts.jar,cl)
            
     elif pic.picname == 'ValidateSamFile':
         import pysam
@@ -682,7 +710,7 @@ def __main__():
         stf = open(pic.log_filename,'w')
         tlog = None
         if opts.datatype == 'sam': # need to work with a bam 
-            tlog,tempbam = pic.samToBam(opts.input,opts.outdir)
+            tlog,tempbam,rval = pic.samToBam(opts.input,opts.outdir)
             try:
                 tlog = pic.sortSam(tempbam,sortedfile,opts.outdir)
             except:
@@ -709,7 +737,7 @@ def __main__():
             cl.append('IS_BISULFITE_SEQUENCED=true')
         if opts.ref <> None or opts.ref_file <> None:
             cl.append('R=%s' %  ref_file_name)
-        pic.runPic(opts.jar,cl)
+        stdouts,rval = pic.runPic(opts.jar,cl)
         if opts.datatype == 'sam':
             pic.delme.append(tempbam)
         newsam = opts.output
@@ -725,10 +753,12 @@ def __main__():
     if haveTempout:
         # Some Picard tools produced a potentially intermediate bam file. 
         # Either just move to final location or create sam
-        shutil.move(tempout, os.path.abspath(opts.output))
-
+        if os.path.exists(tempout):
+            shutil.move(tempout, os.path.abspath(opts.output))
     if opts.htmlout <> None or doFix: # return a pretty html page
         pic.fixPicardOutputs(transpose=doTranspose,maxloglines=maxloglines)
-
+    if rval <> 0:
+        print >> sys.stderr, '## exit code=%d; stdout=%s' % (rval,stdouts)
+        # signal failure
 if __name__=="__main__": __main__()
 
diff --git a/tools/picard/rgPicardASMetrics.xml b/tools/picard/rgPicardASMetrics.xml
index abd3d8fab3d..15381bbfcac 100644
--- a/tools/picard/rgPicardASMetrics.xml
+++ b/tools/picard/rgPicardASMetrics.xml
@@ -1,7 +1,7 @@
 <tool name="SAM/BAM Alignment Summary Metrics" id="PicardASMetrics" version="0.03.1">
   <command interpreter="python">
     picard_wrapper.py -i "$input_file" -d "$html_file.files_path" -t "$html_file"
-    --assumesorted "$sorted" -b "$bisulphite" --adaptors "$adaptors" --maxinsert "$maxinsert" -n "$out_prefix"
+    --assumesorted "$sorted" -b "$bisulphite" --adaptors "$adaptors" --maxinsert "$maxinsert" -n "$out_prefix" --datatype "$input_file.ext"
     -j ${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/CollectAlignmentSummaryMetrics.jar
 #if $genomeSource.refGenomeSource == "history":
     --ref-file "$genomeSource.ownFile"
diff --git a/tools/picard/rgPicardInsertSize.xml b/tools/picard/rgPicardInsertSize.xml
index 6dd937f0f50..2cbda571a7d 100644
--- a/tools/picard/rgPicardInsertSize.xml
+++ b/tools/picard/rgPicardInsertSize.xml
@@ -1,9 +1,9 @@
-<tool name="Insertion size metrics" id="PicardInsertSize" version="0.3.1">
+<tool name="Insertion size metrics" id="PicardInsertSize" version="0.3.2">
   <description>for PAIRED data</description>
   <requirements><requirement type="package">picard</requirement></requirements>
   <command interpreter="python">
-   picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --taillimit "$tailLimit"
-   --histwidth "$histWidth" --minpct "$minPct"
+   picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --deviations "$deviations"
+   --histwidth "$histWidth" --minpct "$minPct" --malevel "$malevel"
    -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/CollectInsertSizeMetrics.jar" -d "$html_file.files_path" -t "$html_file"
   </command>
   <inputs>
@@ -11,15 +11,22 @@
       help="If empty, upload or import a SAM/BAM dataset."/>
     <param name="out_prefix" value="Insertion size metrics" type="text"
       label="Title for the output file" help="Use this remind you what the job was for" size="120" />
-    <param name="tailLimit" value="10000" type="integer"
-      label="Tail limit" size="5" 
-      help="When calculating mean and stdev stop when the bins in the tail of the distribution contain fewer than mode/TAIL_LIMIT items" />
+    <param name="deviations" value="10.0" type="float"
+      label="Deviations" size="5" 
+      help="See Picard documentation: Generate mean, sd and plots by trimming the data down to MEDIAN + DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION" />
      <param name="histWidth" value="0" type="integer"
       label="Histogram width" size="5" 
-      help="Explicitly sets the histogram width, overriding the TAIL_LIMIT option - leave 0 to ignore" />
-     <param name="minPct" value="0.01" type="float"
+      help="Explicitly sets the histogram width option - leave 0 to ignore" />
+     <param name="minPct" value="0.05" type="float"
       label="Minimum percentage" size="5" 
       help="Discard any data categories (out of FR, TANDEM, RF) that have fewer than this percentage of overall reads" />
+     <param name="malevel" value="0" type="select" multiple="true"  label="Metric Accumulation Level"
+      help="Level(s) at which metrics will be accumulated">
+      <option value="ALL_READS" selected="true">All reads (default)</option>
+      <option value="SAMPLE" default="true">Sample</option>
+      <option value="LIBRARY" default="true">Library</option>
+      <option value="READ_GROUP" default="true">Read group</option>
+     </param>
   </inputs>
   <outputs>
     <data format="html" name="html_file" label="InsertSize_${out_prefix}.html"/>
@@ -28,9 +35,10 @@
     <test>
       <param name="input_file" value="picard_input_tiny.sam" />
       <param name="out_prefix" value="Insertion size metrics" />
-      <param name="tailLimit" value="10000" />
+      <param name="deviations" value="10.0" />
       <param name="histWidth" value="0" />
       <param name="minPct" value="0.01" />
+      <param name="malevel" value="ALL_READS" />
       <output name="html_file" file="picard_output_insertsize_tinysam.html" ftype="html" compare="contains" lines_diff="40" />
     </test>
   </tests>

From 07bc9161719f8d7c5509938679243eeaf36d653f Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Thu, 10 Nov 2011 19:01:31 -0500
Subject: [PATCH 181/362] Trackster: use icon to set track mode.

---
 static/images/fugue/chevron-expand-bw.png | Bin 0 -> 1214 bytes
 static/images/fugue/toggle-bw.png         | Bin 0 -> 1200 bytes
 static/images/fugue/toggle-expand-bw.png  | Bin 0 -> 1269 bytes
 static/june_2007_style/blue/trackster.css |   2 +
 static/june_2007_style/trackster.css.tmpl |   6 ++
 static/scripts/trackster.js               |  75 +++++++++++-----------
 6 files changed, 46 insertions(+), 37 deletions(-)
 create mode 100644 static/images/fugue/chevron-expand-bw.png
 create mode 100644 static/images/fugue/toggle-bw.png
 create mode 100644 static/images/fugue/toggle-expand-bw.png

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new file mode 100644
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diff --git a/static/june_2007_style/blue/trackster.css b/static/june_2007_style/blue/trackster.css
index 2d30f57f93d..9ac99cd5ea7 100644
--- a/static/june_2007_style/blue/trackster.css
+++ b/static/june_2007_style/blue/trackster.css
@@ -57,6 +57,8 @@ input{font:10px verdana;}
 .param-row{margin-top:0.2em;margin-left:1em;}
 .param-label{float:left;font-weight:bold;padding-top:0.2em;}
 .menu-button{margin:0px 4px 0px 4px;}
+.chevron-expand{background:transparent url(../images/fugue/chevron-expand-bw.png) no-repeat;}
+.chevron-expand:hover{background:transparent url(../images/fugue/chevron-expand.png) no-repeat;}
 .settings-icon{background:transparent url(../images/fugue/gear-bw.png) no-repeat;}
 .settings-icon:hover{background:transparent url(../images/fugue/gear.png) no-repeat;}
 .overview-icon{background:transparent url(../images/fugue/application-dock-270-bw.png) no-repeat;}
diff --git a/static/june_2007_style/trackster.css.tmpl b/static/june_2007_style/trackster.css.tmpl
index 4602f49bf01..98d68c0bf02 100644
--- a/static/june_2007_style/trackster.css.tmpl
+++ b/static/june_2007_style/trackster.css.tmpl
@@ -297,6 +297,12 @@ input {
 .menu-button {
     margin: 0px 4px 0px 4px;
 }
+.chevron-expand {
+    background: transparent url(../images/fugue/chevron-expand-bw.png) no-repeat;
+}
+.chevron-expand:hover {
+    background:transparent url(../images/fugue/chevron-expand.png) no-repeat;
+}
 .settings-icon {
     background: transparent url(../images/fugue/gear-bw.png) no-repeat;
 }
diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index a4960ad1cd9..7053975da8a 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -2381,16 +2381,18 @@ var Track = function(name, view, container, show_header, prefs, data_url, data_q
     
     // Create and initialize track header and icons.
     if (show_header) {
-        this.header_div = $("<div class='track-header' />").appendTo(this.container_div);
+        this.header_div = $("<div class='track-header'/>").appendTo(this.container_div);
         if (this.view.editor) { this.drag_div = $("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div); }
         this.name_div = $("<div/>").addClass("track-name").appendTo(this.header_div).text(this.name)
                         .attr( "id", this.name.replace(/\s+/g,'-').replace(/[^a-zA-Z0-9\-]/g,'').toLowerCase() );
         this.icons_div = $("<div/>").css("float", "left").appendTo(this.header_div).hide();
     
         // Track icons.
+        this.mode_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Set display mode")
+                                  .addClass("icon-button chevron-expand").tipsy( {gravity: 's'} ).appendTo(this.icons_div);
         this.toggle_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Hide/show track content")
-                                      .addClass("icon-button toggle-contract").tipsy( {gravity: 's'} )
-                                      .appendTo(this.icons_div);
+                                    .addClass("icon-button toggle-contract").tipsy( {gravity: 's'} )
+                                    .appendTo(this.icons_div);
         this.settings_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Edit settings")
                                       .addClass("icon-button settings-icon").tipsy( {gravity: 's'} )
                                       .appendTo(this.icons_div);
@@ -2407,21 +2409,42 @@ var Track = function(name, view, container, show_header, prefs, data_url, data_q
                                     .addClass("icon-button remove-icon").tipsy( {gravity: 's'} )
                                     .appendTo(this.icons_div);
         var track = this;
-            
+                    
         // Suppress double clicks in header so that they do not impact viz.
         this.header_div.dblclick( function(e) { e.stopPropagation(); } );
+        
+        // Set up behavior for modes popup.
+        if (track.display_modes !== undefined) {
+            var init_mode = (track.config && track.config.values['mode'] ? 
+                             track.config.values['mode'] : track.display_modes[0]);
+            track.mode = init_mode;
+            this.mode_icon.attr("title", "Set display mode (now: " + track.mode + ")");
+            
+            var mode_mapping = {};
+            for (var i = 0, len = track.display_modes.length; i < len; i++) {
+                var mode = track.display_modes[i];
+                mode_mapping[mode] = function(mode) {
+                    return function() { 
+                        track.change_mode(mode);
+                        // HACK: the popup menu messes with the track's hover event, so manually show/hide
+                        // icons div for now.
+                        track.icons_div.show(); 
+                        track.container_div.mouseleave(function() { track.icons_div.hide(); } ); };
+                }(mode);
+            }
+            
+            make_popupmenu(this.mode_icon, mode_mapping);
+        }
 
-        // Toggle icon hides or shows the track content
+        // Toggle icon hides or shows the track content.
         this.toggle_icon.click( function() {
             if ( track.content_visible ) {
                 track.toggle_icon.addClass("toggle-expand").removeClass("toggle-contract");
                 track.hide_contents();
-                track.mode_div.hide();
                 track.content_visible = false;
             } else {
                 track.toggle_icon.addClass("toggle-contract").removeClass("toggle-expand");
                 track.content_visible = true;
-                track.mode_div.show();
                 track.show_contents();
             }
         });
@@ -2481,35 +2504,12 @@ var Track = function(name, view, container, show_header, prefs, data_url, data_q
             $(".tipsy").remove();
             track.remove();
         });
+                
+        // Show icons when users is hovering over track.
+        this.container_div.hover( function() { track.icons_div.show(); }, function() { track.icons_div.hide(); } );
         
-        // Set up behavior for modes popup.
-        if (track.display_modes !== undefined) {
-            if (track.mode_div === undefined) {
-                track.mode_div = $("<div class='right-float menubutton popup' />").appendTo(track.header_div);
-                var init_mode = (track.config && track.config.values['mode'] ? 
-                                 track.config.values['mode'] : track.display_modes[0]);
-                track.mode = init_mode;
-                track.mode_div.text(init_mode);
-
-                var mode_mapping = {};
-                for (var i = 0, len = track.display_modes.length; i < len; i++) {
-                    var mode = track.display_modes[i];
-                    mode_mapping[mode] = function(mode) {
-                        return function() { track.change_mode(mode); };
-                    }(mode);
-                }
-                make_popupmenu(track.mode_div, mode_mapping);
-            } else {
-                track.mode_div.hide();
-            }
-
-            this.header_div.append( $("<div/>").css("clear", "both") );        
-        
-            // Set up config icon.
-        
-            // Show icons when users is hovering over track.
-            this.container_div.hover( function() { track.icons_div.show(); }, function() { track.icons_div.hide(); } );
-        }
+        // Needed for floating elts in header.
+        $("<div style='clear: both'/>").appendTo(this.container_div);
     }
     
     //
@@ -2696,12 +2696,12 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
      */
     change_mode: function(name) {
         var track = this;
-        track.mode_div.text(name);
         // TODO: is it necessary to store the mode in two places (.mode and track_config)?
         track.mode = name;
         track.config.values['mode'] = name;
         track.tile_cache.clear();
         track.request_draw();
+        this.mode_icon.attr("title", "Set display mode (now: " + track.mode + ")");
         return track;
      },
     /**
@@ -3405,13 +3405,14 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
         }
     },
     update_auto_mode: function( mode ) {
+        var mode;
         if ( this.mode == "Auto" ) {
             if ( mode == "no_detail" ) {
                 mode = "feature spans";
             } else if ( mode == "summary_tree" ) {
                 mode = "coverage histogram";
             }
-            this.mode_div.text( "Auto (" + mode + ")" );
+            this.mode_icon.attr("title", "Set display mode (now: Auto/" + mode + ")");
         }
     },
     /**

From 20cdd121fb2e3f25b31109262cc3e0eaf3b35051 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Thu, 10 Nov 2011 19:23:44 -0500
Subject: [PATCH 182/362] Fix grid operations for use in UserListGrid to allow
 for Delete, Undelete, Purge of users if the allow_user_deletion config
 setting is true.

---
 lib/galaxy/web/base/controller.py           | 11 ++++++++++-
 lib/galaxy/web/controllers/admin.py         |  8 +++-----
 lib/galaxy/webapps/community/config.py      |  1 +
 lib/galaxy/webapps/demo_sequencer/config.py |  1 +
 lib/galaxy/webapps/reports/config.py        |  2 ++
 5 files changed, 17 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/web/base/controller.py b/lib/galaxy/web/base/controller.py
index 2cb1db6ce55..a7b6f076f97 100644
--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -19,7 +19,6 @@ from galaxy.exceptions import *
 
 from Cheetah.Template import Template
 
-
 pkg_resources.require( 'elementtree' )
 from elementtree import ElementTree, ElementInclude
 from elementtree.ElementTree import Element
@@ -1298,6 +1297,9 @@ class Admin( object ):
     group_list_grid = None
     quota_list_grid = None
     repository_list_grid = None
+    delete_operation = None
+    undelete_operation = None
+    purge_operation = None
 
     @web.expose
     @web.require_admin
@@ -2217,6 +2219,13 @@ class Admin( object ):
                                                                       **kwd ) )
             elif operation == "manage roles and groups":
                 return self.manage_roles_and_groups_for_user( trans, **kwd )
+        if trans.app.config.allow_user_deletion:
+            if self.delete_operation not in self.user_list_grid.operations:
+                self.user_list_grid.operations.append( self.delete_operation )
+            if self.undelete_operation not in self.user_list_grid.operations:
+                self.user_list_grid.operations.append( self.undelete_operation )
+            if self.purge_operation not in self.user_list_grid.operations:
+                self.user_list_grid.operations.append( self.purge_operation )
         # Render the list view
         return self.user_list_grid( trans, **kwd )
     @web.expose
diff --git a/lib/galaxy/web/controllers/admin.py b/lib/galaxy/web/controllers/admin.py
index bde9352111b..abb58421387 100644
--- a/lib/galaxy/web/controllers/admin.py
+++ b/lib/galaxy/web/controllers/admin.py
@@ -93,11 +93,6 @@ class UserListGrid( grids.Grid ):
                              allow_popup=False,
                              url_args=dict( webapp="galaxy", action="reset_user_password" ) )
     ]
-    #TODO: enhance to account for trans.app.config.allow_user_deletion here so that we can eliminate these operations if 
-    # the setting is False
-    #operations.append( grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), allow_multiple=True ) )
-    #operations.append( grids.GridOperation( "Undelete", condition=( lambda item: item.deleted and not item.purged ), allow_multiple=True ) )
-    #operations.append( grids.GridOperation( "Purge", condition=( lambda item: item.deleted and not item.purged ), allow_multiple=True ) )
     standard_filters = [
         grids.GridColumnFilter( "Active", args=dict( deleted=False ) ),
         grids.GridColumnFilter( "Deleted", args=dict( deleted=True, purged=False ) ),
@@ -443,6 +438,9 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
     group_list_grid = GroupListGrid()
     quota_list_grid = QuotaListGrid()
     repository_list_grid = RepositoryListGrid()
+    delete_operation = grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), allow_multiple=True )
+    undelete_operation = grids.GridOperation( "Undelete", condition=( lambda item: item.deleted and not item.purged ), allow_multiple=True )
+    purge_operation = grids.GridOperation( "Purge", condition=( lambda item: item.deleted and not item.purged ), allow_multiple=True )
 
     @web.expose
     @web.require_admin
diff --git a/lib/galaxy/webapps/community/config.py b/lib/galaxy/webapps/community/config.py
index 574aad0cf2c..2211959d532 100644
--- a/lib/galaxy/webapps/community/config.py
+++ b/lib/galaxy/webapps/community/config.py
@@ -61,6 +61,7 @@ class Configuration( object ):
         self.remote_user_logout_href = kwargs.get( "remote_user_logout_href", None )
         self.require_login = string_as_bool( kwargs.get( "require_login", "False" ) )
         self.allow_user_creation = string_as_bool( kwargs.get( "allow_user_creation", "True" ) )
+        self.allow_user_deletion = string_as_bool( kwargs.get( "allow_user_deletion", "False" ) )
         self.enable_openid = string_as_bool( kwargs.get( 'enable_openid', False ) )
         self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root )
         self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates/community" ), self.root )
diff --git a/lib/galaxy/webapps/demo_sequencer/config.py b/lib/galaxy/webapps/demo_sequencer/config.py
index e5d80248d76..20729c7a1bb 100644
--- a/lib/galaxy/webapps/demo_sequencer/config.py
+++ b/lib/galaxy/webapps/demo_sequencer/config.py
@@ -40,6 +40,7 @@ class Configuration( object ):
         self.remote_user_logout_href = kwargs.get( "remote_user_logout_href", None )
         self.require_login = string_as_bool( kwargs.get( "require_login", "False" ) )
         self.allow_user_creation = string_as_bool( kwargs.get( "allow_user_creation", "True" ) )
+        self.allow_user_deletion = string_as_bool( kwargs.get( "allow_user_deletion", "False" ) )
         self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root )
         self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates/demo_sequencer" ), self.root )
         self.admin_users = kwargs.get( "admin_users", "" )
diff --git a/lib/galaxy/webapps/reports/config.py b/lib/galaxy/webapps/reports/config.py
index 1a7508d2c6d..3e5aad27454 100644
--- a/lib/galaxy/webapps/reports/config.py
+++ b/lib/galaxy/webapps/reports/config.py
@@ -31,6 +31,8 @@ class Configuration( object ):
         self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root )
         self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates/reports" ), self.root )
         self.sendmail_path = kwargs.get('sendmail_path',"/usr/sbin/sendmail")
+        self.allow_user_creation = string_as_bool( kwargs.get( "allow_user_creation", "True" ) )
+        self.allow_user_deletion = string_as_bool( kwargs.get( "allow_user_deletion", "False" ) )
         self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) )
         self.brand = kwargs.get( 'brand', None )
         self.wiki_url = kwargs.get( 'wiki_url', 'http://wiki.g2.bx.psu.edu/FrontPage' )

From a32e99ee9afbe9f5b3bf5e84fafa8c89fd284790 Mon Sep 17 00:00:00 2001
From: Ross Lazarus <ross.lazarus@gmail.com>
Date: Fri, 11 Nov 2011 12:01:07 +1100
Subject: [PATCH 183/362] Some minor additional cleanup to the picard suite

---
 tools/picard/picard_wrapper.py | 35 ++++++++++++++--------------------
 1 file changed, 14 insertions(+), 21 deletions(-)

diff --git a/tools/picard/picard_wrapper.py b/tools/picard/picard_wrapper.py
index 03fbbb90ca3..d6987f581d1 100644
--- a/tools/picard/picard_wrapper.py
+++ b/tools/picard/picard_wrapper.py
@@ -102,7 +102,7 @@ class PicardBase():
                 pass
             tmp.close()
         except Exception, e:
-            stop_err( 'Error : %s' % str( e ) )   
+            stop_err( 'Read Large Exception : %s' % str( e ) )   
         return s
     
     def runCL(self,cl=None,output_dir=None):
@@ -154,15 +154,6 @@ class PicardBase():
         tlog,stdouts,rval = self.runCL(cl,outdir)
         return tlog,tempbam,rval
 
-    #def bamToSam(self,infile=None,outdir=None):
-    #    """
-    #    use samtools view to convert bam to sam
-    #    """
-    #    fd,tempsam = tempfile.mkstemp(dir=outdir,suffix='rgutilsTemp.sam')
-    #    cl = ['samtools view -h -o ',tempsam,infile]
-    #    tlog,stdouts = self.runCL(cl,outdir)
-    #    return tlog,tempsam
-
     def sortSam(self, infile=None,outfile=None,outdir=None):
         """
         """
@@ -243,10 +234,11 @@ class PicardBase():
         pdflist = [x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf']
         if len(pdflist) > 0: # assumes all pdfs come with thumbnail .jpgs
             for p in pdflist:
-                imghref = '%s.jpg' % os.path.splitext(p)[0] # removes .pdf
-                mimghref = '%s-0.jpg' % os.path.splitext(p)[0] # multiple pages pdf -> multiple thumbnails without asking!
+                pbase = os.path.splitext(p)[0] # removes .pdf
+                imghref = '%s.jpg' % pbase
+                mimghref = '%s-0.jpg' % pbase # multiple pages pdf -> multiple thumbnails without asking!
                 if mimghref in flist:
-                    imghref=mimghref
+                    imghref=mimghref # only one for thumbnail...it's a multi page pdf
                 res.append('<table cellpadding="10"><tr><td>\n')
                 res.append('<a href="%s"><img src="%s" title="Click image preview for a print quality PDF version" hspace="10" align="middle"></a>\n' % (p,imghref)) 
                 res.append('</tr></td></table>\n')   
@@ -387,7 +379,7 @@ def __main__():
     op.add_option('', '--taillimit', default="0")
     op.add_option('', '--histwidth', default="0")
     op.add_option('', '--minpct', default="0.01")
-    op.add_option('', '--malevel', default="")
+    op.add_option('', '--malevel', action='append', type="string")
     op.add_option('', '--deviations', default="0.0")
     # CollectAlignmentSummaryMetrics
     op.add_option('', '--maxinsert', default="20")
@@ -529,13 +521,14 @@ def __main__():
         stdouts,rval = pic.runPic(opts.jar, cl)
 
     elif pic.picname == 'CollectAlignmentSummaryMetrics':
-        # Why do we do this fakefasta thing? Because we need NO fai to be available or picard barfs unless it has the same length as the input data.
+        # Why do we do this fakefasta thing? 
+        # Because we need NO fai to be available or picard barfs unless it matches the input data.
         # why? Dunno Seems to work without complaining if the .bai file is AWOL....
         fakefasta = os.path.join(opts.outdir,'%s_fake.fasta' % os.path.basename(ref_file_name))
         try:
             os.symlink(ref_file_name,fakefasta)
         except:
-            s = '## unable to symlink %s to %s - different devices? May need to replace with shutil.copy'
+            s = '## unable to symlink %s to %s - different devices? Will shutil.copy'
             info = s
             shutil.copy(ref_file_name,fakefasta)
         pic.delme.append(fakefasta)
@@ -550,7 +543,7 @@ def __main__():
         if not opts.assumesorted.lower() == 'true': # we need to sort input
             sortedfile = '%s.sorted' % os.path.basename(opts.input)
             if opts.datatype == 'sam': # need to work with a bam 
-                tlog,tempbam,rval = pic.samToBam(opts.input,opts.outdir)
+                tlog,tempbam,trval = pic.samToBam(opts.input,opts.outdir)
                 pic.delme.append(tempbam)
                 try:
                     tlog = pic.sortSam(tempbam,sortedfile,opts.outdir)
@@ -559,8 +552,8 @@ def __main__():
             else: # is already bam
                 try:
                     tlog = pic.sortSam(opts.input,sortedfile,opts.outdir)
-                except: # bug - [bam_sort_core] not being ignored - TODO fixme
-                    print '## exception on sorting bam file %s' % opts.input
+                except : # bug - [bam_sort_core] not being ignored - TODO fixme
+                    print '## exception %s on sorting bam file %s' % (sys.exc_info()[0],opts.input)
             cl.append('INPUT=%s.bam' % os.path.abspath(os.path.join(opts.outdir,sortedfile)))
             pic.delme.append(os.path.join(opts.outdir,sortedfile))
         else:
@@ -625,8 +618,8 @@ def __main__():
             cl.append('MINIMUM_PCT=%s' % opts.minpct)
         if float(opts.deviations) > 0.0:
             cl.append('DEVIATIONS=%s' % opts.deviations)
-        if opts.malevel.strip():
-            malevels = ['METRIC_ACCUMULATION_LEVEL=%s' % x for x in opts.malevel.split(',')]
+        if opts.malevel:
+            malevels = ['METRIC_ACCUMULATION_LEVEL=%s' % x for x in opts.malevel]
             cl.append(' '.join(malevels))
         stdouts,rval = pic.runPic(opts.jar, cl)
         if os.path.exists(pdfpath): # automake thumbnail - will be added to html 

From a6719bff5decddd95e1f8f060d93ba0e08356f21 Mon Sep 17 00:00:00 2001
From: Ross Lazarus <ross.lazarus@gmail.com>
Date: Sat, 12 Nov 2011 04:25:19 +1100
Subject: [PATCH 184/362] Bumped ALL picard tool versions and made them
 uniformly 1.56.0 to reflect the current picard tools version Nate's about to
 unleash.

---
 tools/picard/picard_AddOrReplaceReadGroups.xml | 2 +-
 tools/picard/picard_BamIndexStats.xml          | 2 +-
 tools/picard/picard_FastqToSam.xml             | 2 +-
 tools/picard/picard_MarkDuplicates.xml         | 2 +-
 tools/picard/picard_ReorderSam.xml             | 2 +-
 tools/picard/picard_ReplaceSamHeader.xml       | 2 +-
 tools/picard/picard_SamToFastq.xml             | 2 +-
 tools/picard/rgPicardASMetrics.xml             | 2 +-
 tools/picard/rgPicardFixMate.xml               | 2 +-
 tools/picard/rgPicardGCBiasMetrics.xml         | 2 +-
 tools/picard/rgPicardHsMetrics.xml             | 2 +-
 tools/picard/rgPicardInsertSize.xml            | 2 +-
 tools/picard/rgPicardLibComplexity.xml         | 2 +-
 tools/picard/rgPicardMarkDups.xml              | 2 +-
 14 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/tools/picard/picard_AddOrReplaceReadGroups.xml b/tools/picard/picard_AddOrReplaceReadGroups.xml
index d70b2294846..cc670abb9f0 100644
--- a/tools/picard/picard_AddOrReplaceReadGroups.xml
+++ b/tools/picard/picard_AddOrReplaceReadGroups.xml
@@ -1,4 +1,4 @@
-<tool name="Add or Replace Groups" id="picard_ARRG" version="0.2.1">
+<tool name="Add or Replace Groups" id="picard_ARRG" version="1.56.0">
   <requirements><requirement type="package">picard</requirement></requirements>
   <command interpreter="python">
     picard_wrapper.py
diff --git a/tools/picard/picard_BamIndexStats.xml b/tools/picard/picard_BamIndexStats.xml
index 53258ae83cf..8855a91d6a9 100644
--- a/tools/picard/picard_BamIndexStats.xml
+++ b/tools/picard/picard_BamIndexStats.xml
@@ -1,4 +1,4 @@
-<tool name="BAM Index Statistics" id="picard_BamIndexStats" version="0.2.1">
+<tool name="BAM Index Statistics" id="picard_BamIndexStats" version="1.56.0">
   <requirements><requirement type="package">picard</requirement></requirements>
   <command interpreter="python">
     picard_wrapper.py
diff --git a/tools/picard/picard_FastqToSam.xml b/tools/picard/picard_FastqToSam.xml
index f1674688fb7..2f736b3be96 100644
--- a/tools/picard/picard_FastqToSam.xml
+++ b/tools/picard/picard_FastqToSam.xml
@@ -1,4 +1,4 @@
-<tool id="picard_FastqToSam" name="FASTQ to BAM" version="0.0.1">
+<tool id="picard_FastqToSam" name="FASTQ to BAM" version="1.56.0">
   <description>creates an unaligned BAM file</description>
   <requirements><requirement type="package">picard</requirement></requirements>
   <command>java  -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC
diff --git a/tools/picard/picard_MarkDuplicates.xml b/tools/picard/picard_MarkDuplicates.xml
index 61835e209e9..5c8cb86ad30 100644
--- a/tools/picard/picard_MarkDuplicates.xml
+++ b/tools/picard/picard_MarkDuplicates.xml
@@ -1,4 +1,4 @@
-<tool name="Mark Duplicates" id="picard_MarkDuplicates" version="0.01.1">
+<tool name="Mark Duplicates" id="picard_MarkDuplicates" version="1.56.0">
   <command interpreter="python">
     picard_wrapper.py
       --input="$input_file"
diff --git a/tools/picard/picard_ReorderSam.xml b/tools/picard/picard_ReorderSam.xml
index 7fb41a573b3..09d15d1d63c 100644
--- a/tools/picard/picard_ReorderSam.xml
+++ b/tools/picard/picard_ReorderSam.xml
@@ -1,4 +1,4 @@
-<tool name="Reorder SAM/BAM" id="picard_ReorderSam" version="0.3.1">
+<tool name="Reorder SAM/BAM" id="picard_ReorderSam" version="1.56.0">
   <requirements><requirement type="package">picard</requirement></requirements>
   <command interpreter="python">
     picard_wrapper.py
diff --git a/tools/picard/picard_ReplaceSamHeader.xml b/tools/picard/picard_ReplaceSamHeader.xml
index 95a584068da..6cd30eb9596 100644
--- a/tools/picard/picard_ReplaceSamHeader.xml
+++ b/tools/picard/picard_ReplaceSamHeader.xml
@@ -1,4 +1,4 @@
-<tool name="Replace SAM/BAM Header" id="picard_ReplaceSamHeader" version="0.2.1">
+<tool name="Replace SAM/BAM Header" id="picard_ReplaceSamHeader" version="1.56.0">
   <requirements><requirement type="package">picard</requirement></requirements>
   <command interpreter="python">
     picard_wrapper.py
diff --git a/tools/picard/picard_SamToFastq.xml b/tools/picard/picard_SamToFastq.xml
index 2274ad1caed..278f42934c6 100644
--- a/tools/picard/picard_SamToFastq.xml
+++ b/tools/picard/picard_SamToFastq.xml
@@ -1,4 +1,4 @@
-<tool id="picard_SamToFastq" name="SAM to FASTQ" version="0.0.1">
+<tool id="picard_SamToFastq" name="SAM to FASTQ" version="1.56.0">
   <description>creates a FASTQ file</description>
   <requirements><requirement type="package">picard</requirement></requirements>
   <command>java -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC
diff --git a/tools/picard/rgPicardASMetrics.xml b/tools/picard/rgPicardASMetrics.xml
index 15381bbfcac..dcd1f998588 100644
--- a/tools/picard/rgPicardASMetrics.xml
+++ b/tools/picard/rgPicardASMetrics.xml
@@ -1,4 +1,4 @@
-<tool name="SAM/BAM Alignment Summary Metrics" id="PicardASMetrics" version="0.03.1">
+<tool name="SAM/BAM Alignment Summary Metrics" id="PicardASMetrics" version="1.56.0">
   <command interpreter="python">
     picard_wrapper.py -i "$input_file" -d "$html_file.files_path" -t "$html_file"
     --assumesorted "$sorted" -b "$bisulphite" --adaptors "$adaptors" --maxinsert "$maxinsert" -n "$out_prefix" --datatype "$input_file.ext"
diff --git a/tools/picard/rgPicardFixMate.xml b/tools/picard/rgPicardFixMate.xml
index 5d7ecb6142e..83859e551df 100644
--- a/tools/picard/rgPicardFixMate.xml
+++ b/tools/picard/rgPicardFixMate.xml
@@ -1,4 +1,4 @@
-<tool name="Paired Read Mate Fixer" id="rgPicFixMate" version="0.2.1">
+<tool name="Paired Read Mate Fixer" id="rgPicFixMate" version="1.56.0">
   <description>for paired data</description>
   <command interpreter="python">
    picard_wrapper.py -i "$input_file" -o "$out_file" --tmpdir "${__new_file_path__}" -n "$out_prefix" 
diff --git a/tools/picard/rgPicardGCBiasMetrics.xml b/tools/picard/rgPicardGCBiasMetrics.xml
index f5eab53d0de..7adce089f04 100644
--- a/tools/picard/rgPicardGCBiasMetrics.xml
+++ b/tools/picard/rgPicardGCBiasMetrics.xml
@@ -1,4 +1,4 @@
-<tool name="SAM/BAM GC Bias Metrics" id="PicardGCBiasMetrics" version="0.02.1">
+<tool name="SAM/BAM GC Bias Metrics" id="PicardGCBiasMetrics" version="1.56.0">
   <command interpreter="python">
     picard_wrapper.py -i "$input_file" -d "$html_file.files_path" -t "$html_file"
     --windowsize "$windowsize" --mingenomefrac "$mingenomefrac" -n "$out_prefix" --tmpdir "${__new_file_path__}"
diff --git a/tools/picard/rgPicardHsMetrics.xml b/tools/picard/rgPicardHsMetrics.xml
index d2d3017befe..56c7ef9123d 100644
--- a/tools/picard/rgPicardHsMetrics.xml
+++ b/tools/picard/rgPicardHsMetrics.xml
@@ -1,4 +1,4 @@
-<tool name="SAM/BAM Hybrid Selection Metrics" id="PicardHsMetrics" version="0.02.1">
+<tool name="SAM/BAM Hybrid Selection Metrics" id="PicardHsMetrics" version="1.56.0">
   <description>for targeted resequencing data</description>
   <command interpreter="python">
 
diff --git a/tools/picard/rgPicardInsertSize.xml b/tools/picard/rgPicardInsertSize.xml
index 2cbda571a7d..5d188095582 100644
--- a/tools/picard/rgPicardInsertSize.xml
+++ b/tools/picard/rgPicardInsertSize.xml
@@ -1,4 +1,4 @@
-<tool name="Insertion size metrics" id="PicardInsertSize" version="0.3.2">
+<tool name="Insertion size metrics" id="PicardInsertSize" version="1.56.0">
   <description>for PAIRED data</description>
   <requirements><requirement type="package">picard</requirement></requirements>
   <command interpreter="python">
diff --git a/tools/picard/rgPicardLibComplexity.xml b/tools/picard/rgPicardLibComplexity.xml
index ab252100ec2..3e0fc72775a 100644
--- a/tools/picard/rgPicardLibComplexity.xml
+++ b/tools/picard/rgPicardLibComplexity.xml
@@ -1,4 +1,4 @@
-<tool name="Estimate Library Complexity" id="rgEstLibComp" version="0.01.1">
+<tool name="Estimate Library Complexity" id="rgEstLibComp" version="1.56.0">
   <command interpreter="python">
    picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --minid "$minIDbases"
    --maxdiff "$maxDiff" --minmeanq "$minMeanQ" --readregex "$readRegex" --optdupdist "$optDupeDist"
diff --git a/tools/picard/rgPicardMarkDups.xml b/tools/picard/rgPicardMarkDups.xml
index 5a6947b85a8..07894d90683 100644
--- a/tools/picard/rgPicardMarkDups.xml
+++ b/tools/picard/rgPicardMarkDups.xml
@@ -1,4 +1,4 @@
-<tool name="Mark Duplicate reads" id="rgPicardMarkDups" version="0.01.1">
+<tool name="Mark Duplicate reads" id="rgPicardMarkDups" version="1.56.0">
   <command interpreter="python">
    picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" -o "$out_file"
    --remdups "$remDups" --assumesorted "$assumeSorted" --readregex "$readRegex" --optdupdist "$optDupeDist"

From 73f68f226ac5eec23e714a8e64855d4ba1eff5cb Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Mon, 14 Nov 2011 10:49:51 -0500
Subject: [PATCH 185/362] Fix for renaming a tool shed repository - hopefully
 resolves race condition.

---
 .../community/controllers/repository.py       | 48 ++++++++++---------
 1 file changed, 25 insertions(+), 23 deletions(-)

diff --git a/lib/galaxy/webapps/community/controllers/repository.py b/lib/galaxy/webapps/community/controllers/repository.py
index 140bc636f2d..bcbfe6f1ee9 100644
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -1,4 +1,4 @@
-import os, logging, urllib, ConfigParser, tempfile, shutil
+import os, logging, tempfile, shutil
 from time import strftime
 from datetime import date, datetime
 from galaxy import util
@@ -1001,20 +1001,23 @@ class RepositoryController( BaseUIController, ItemRatings ):
         hgweb_config_copy = '%s/hgweb.config_%s_backup' % ( trans.app.config.root, backup_date )
         shutil.copy( os.path.abspath( hgweb_config ), os.path.abspath( hgweb_config_copy ) )
     def __add_hgweb_config_entry( self, trans, repository, repository_path ):
-        # Add an entry in the hgweb.config file for a new repository.
-        # An entry looks something like:
+        # Add an entry in the hgweb.config file for a new repository.  An entry looks something like:
         # repos/test/mira_assembler = database/community_files/000/repo_123.
         hgweb_config = "%s/hgweb.config" %  trans.app.config.root
-        # Make a backup of the hgweb.config file since we're going to be changing it.
-        self.__make_hgweb_config_copy( trans, hgweb_config )
+        if repository_path.startswith( './' ):
+            repository_path = repository_path.replace( './', '', 1 )
         entry = "repos/%s/%s = %s" % ( repository.user.username, repository.name, repository_path.lstrip( './' ) )
         if os.path.exists( hgweb_config ):
-            output = open( hgweb_config, 'a' )
+            # Make a backup of the hgweb.config file since we're going to be changing it.
+            self.__make_hgweb_config_copy( trans, hgweb_config )
+            tmp_fname = tempfile.NamedTemporaryFile()
+            for i, line in enumerate( open( hgweb_config ) ):
+                tmp_fname.write( line )
         else:
-            output = open( hgweb_config, 'w' )
-            output.write( '[paths]\n' )
-        output.write( "%s\n" % entry )
-        output.close()
+            tmp_fname.write( '[paths]\n' )
+        tmp_fname.write( "%s\n" % entry )
+        tmp_fname.flush()
+        shutil.move( tmp_fname.name, os.path.abspath( hgweb_config ) )
     def __change_hgweb_config_entry( self, trans, repository, old_repository_name, new_repository_name ):
         # Change an entry in the hgweb.config file for a repository.  This only happens when
         # the owner changes the name of the repository.  An entry looks something like:
@@ -1024,16 +1027,15 @@ class RepositoryController( BaseUIController, ItemRatings ):
         self.__make_hgweb_config_copy( trans, hgweb_config )
         repo_dir = repository.repo_path
         old_lhs = "repos/%s/%s" % ( repository.user.username, old_repository_name )
-        old_entry = "%s = %s" % ( old_lhs, repo_dir )
         new_entry = "repos/%s/%s = %s\n" % ( repository.user.username, new_repository_name, repo_dir )
-        tmp_fd, tmp_fname = tempfile.mkstemp()
-        new_hgweb_config = open( tmp_fname, 'wb' )
+        tmp_fname = tempfile.NamedTemporaryFile()
         for i, line in enumerate( open( hgweb_config ) ):
             if line.startswith( old_lhs ):
-                new_hgweb_config.write( new_entry )
+                tmp_fname.write( new_entry )
             else:
-                new_hgweb_config.write( line )
-        shutil.move( tmp_fname, os.path.abspath( hgweb_config ) )
+                tmp_fname.write( line )
+        tmp_fname.flush()
+        shutil.move( tmp_fname.name, os.path.abspath( hgweb_config ) )
     def __create_hgrc_file( self, repository ):
         # At this point, an entry for the repository is required to be in the hgweb.config
         # file so we can call repository.repo_path.
@@ -1306,7 +1308,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
         if params.get( 'edit_repository_button', False ):
             flush_needed = False
             # TODO: add a can_manage in the security agent.
-            if user != repository.user:
+            if user != repository.user or not trans.user_is_admin():
                 message = "You are not the owner of this repository, so you cannot manage it."
                 status = error
                 return trans.response.send_redirect( web.url_for( controller='repository',
@@ -1315,6 +1317,12 @@ class RepositoryController( BaseUIController, ItemRatings ):
                                                                   webapp='community',
                                                                   message=message,
                                                                   status=status ) )
+            if description != repository.description:
+                repository.description = description
+                flush_needed = True
+            if long_description != repository.long_description:
+                repository.long_description = long_description
+                flush_needed = True
             if repo_name != repository.name:
                 message = self.__validate_repository_name( repo_name, user )
                 if message:
@@ -1323,12 +1331,6 @@ class RepositoryController( BaseUIController, ItemRatings ):
                     self.__change_hgweb_config_entry( trans, repository, repository.name, repo_name )
                     repository.name = repo_name
                     flush_needed = True
-            if description != repository.description:
-                repository.description = description
-                flush_needed = True
-            if long_description != repository.long_description:
-                repository.long_description = long_description
-                flush_needed = True
             if flush_needed:
                 trans.sa_session.add( repository )
                 trans.sa_session.flush()

From 03097a32c604423a625e276499a32760b43bee78 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Mon, 14 Nov 2011 11:37:02 -0500
Subject: [PATCH 186/362] Fixes for Data source async controller.

---
 lib/galaxy/jobs/__init__.py         |  2 +-
 lib/galaxy/web/controllers/async.py | 24 ++++++++++++------------
 2 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index b1bb8549eb7..b15103a335f 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -591,7 +591,7 @@ class JobWrapper( object ):
 
                 dataset.blurb = 'done'
                 dataset.peek  = 'no peek'
-                dataset.info  = context['stdout'] + context['stderr']
+                dataset.info = ( dataset.info  or '' ) + context['stdout'] + context['stderr']
                 dataset.tool_version = self.version_string
                 dataset.set_size()
                 if context['stderr']:
diff --git a/lib/galaxy/web/controllers/async.py b/lib/galaxy/web/controllers/async.py
index e17d15ffcf1..dc100ed2b8d 100644
--- a/lib/galaxy/web/controllers/async.py
+++ b/lib/galaxy/web/controllers/async.py
@@ -67,7 +67,7 @@ class ASync( BaseUIController ):
                 trans.log_event( 'Async executing tool %s' % tool.id, tool_id=tool.id )
                 galaxy_url  = trans.request.base + '/async/%s/%s/%s' % ( tool_id, data.id, key )
                 galaxy_url = params.get("GALAXY_URL",galaxy_url)
-                params = dict( url=URL, GALAXY_URL=galaxy_url )
+                params = dict( URL=URL, GALAXY_URL=galaxy_url, name=data.name, info=data.info, dbkey=data.dbkey, data_type=data.ext )
                 # Assume there is exactly one output file possible
                 params[tool.outputs.keys()[0]] = data.id
                 tool.execute( trans, incoming=params )
@@ -80,20 +80,20 @@ class ASync( BaseUIController ):
             trans.sa_session.flush()
             
             return "Data %s with status %s received. OK" % (data_id, STATUS)
-   
-        #            
-        # no data_id must be parameter submission
-        #
-        if not data_id and len(params)>3:
-            
-            if params.galaxyFileFormat == 'wig':
+        else:
+            #            
+            # no data_id must be parameter submission
+            #
+            if params.data_type:
+                GALAXY_TYPE = params.data_type
+            elif params.galaxyFileFormat == 'wig': #this is an undocumented legacy special case
                 GALAXY_TYPE = 'wig'
             else:
-                GALAXY_TYPE = params.GALAXY_TYPE  or 'interval'
+                GALAXY_TYPE = params.GALAXY_TYPE  or  tool.outputs.values()[0].format
                 
-            GALAXY_NAME  = params.GALAXY_NAME  or '%s query' % tool.name
-            GALAXY_INFO  = params.GALAXY_INFO  or params.galaxyDescription or ''
-            GALAXY_BUILD = params.GALAXY_BUILD or params.galaxyFreeze or 'hg17'
+            GALAXY_NAME = params.name or params.GALAXY_NAME or '%s query' % tool.name
+            GALAXY_INFO = params.info or params.GALAXY_INFO or params.galaxyDescription or ''
+            GALAXY_BUILD = params.dbkey or params.GALAXY_BUILD or params.galaxyFreeze or '?'
             
             #data = datatypes.factory(ext=GALAXY_TYPE)()
             #data.ext   = GALAXY_TYPE

From 5b19eed45ef406017504979de9899a62028fedaa Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Mon, 14 Nov 2011 12:12:52 -0500
Subject: [PATCH 187/362] Make history UI icons compatible with changes in
 9dbc82483bd2.

---
 static/scripts/galaxy.base.js | 2 +-
 templates/root/history.mako   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/static/scripts/galaxy.base.js b/static/scripts/galaxy.base.js
index 1c501c8533d..41a9bd66b98 100644
--- a/static/scripts/galaxy.base.js
+++ b/static/scripts/galaxy.base.js
@@ -555,7 +555,7 @@ function init_history_items(historywrapper, noinit, nochanges) {
         });
         
         // Generate 'collapse all' link
-        $("#top-links > a.toggle").click( function() {
+        $("#top-links > a.toggle-contract").click( function() {
             var prefs = $.jStorage.get("history_expand_state");
             if (!prefs) { prefs = {}; }
             $( "div.historyItemBody:visible" ).each( function() {
diff --git a/templates/root/history.mako b/templates/root/history.mako
index 9340cd1921a..63bf2bdc30f 100644
--- a/templates/root/history.mako
+++ b/templates/root/history.mako
@@ -432,7 +432,7 @@ div.form-row {
 <div id="top-links" class="historyLinks">
     
     <a title="${_('refresh')}" class="icon-button arrow-circle tooltip" href="${h.url_for('history', show_deleted=show_deleted)}"></a>
-    <a title='${_('collapse all')}' class='icon-button toggle tooltip' href='#' style="display: none;"></a>
+    <a title='${_('collapse all')}' class='icon-button toggle-contract tooltip' href='#' style="display: none"></a>
     
     %if trans.get_user():
     <div style="width: 40px; float: right; white-space: nowrap;">

From 7c930f1c9222da1b076e28166128df6257a43428 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Mon, 14 Nov 2011 13:26:29 -0500
Subject: [PATCH 188/362] Tool help updates.

---
 tools/filters/secure_hash_message_digest.xml | 6 ++++++
 tools/filters/wc_gnu.xml                     | 6 ++++++
 tools/peak_calling/ccat_wrapper.xml          | 4 +++-
 tools/peak_calling/macs_wrapper.xml          | 2 ++
 4 files changed, 17 insertions(+), 1 deletion(-)

diff --git a/tools/filters/secure_hash_message_digest.xml b/tools/filters/secure_hash_message_digest.xml
index bb74edc1137..e20ce80969a 100644
--- a/tools/filters/secure_hash_message_digest.xml
+++ b/tools/filters/secure_hash_message_digest.xml
@@ -35,5 +35,11 @@
 
 This tool outputs Secure Hashes / Message Digests of a dataset using the user selected algorithms.
 
+------
+
+**Citation**
+
+If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
+
     </help>
 </tool>
diff --git a/tools/filters/wc_gnu.xml b/tools/filters/wc_gnu.xml
index 5d3ad1e3565..9138fef505c 100644
--- a/tools/filters/wc_gnu.xml
+++ b/tools/filters/wc_gnu.xml
@@ -62,5 +62,11 @@ This tool outputs counts of specified attributes (lines, words, characters) of a
   #lines  words  characters
   7499	  41376	 624971
 
+------
+
+**Citation**
+
+If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
+
     </help>
 </tool>
diff --git a/tools/peak_calling/ccat_wrapper.xml b/tools/peak_calling/ccat_wrapper.xml
index 47a107586be..76cc93cbeee 100644
--- a/tools/peak_calling/ccat_wrapper.xml
+++ b/tools/peak_calling/ccat_wrapper.xml
@@ -112,7 +112,7 @@ bootstrapPass	${options_type[ 'bootstrap_pass' ]}
       <output name="output_top_file" file="peakcalling_ccat/3.0/ccat_test_top_out_1.interval.sorted.re_match" compare="re_match" sort="true" />
       <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_1.txt" />
     </test>
-    <!-- Test below gives different results on different architectures, 
+    <!-- Test below gives different answers on different architectures, 
     e.g.: x86_64 GNU/Linux gave an extra line (additional peak called) when compared to the version running on 10.6.0 Darwin i386 
     slidingWinSize was fixed to be 1000, default as per readme.txt
     -->
@@ -140,6 +140,8 @@ View the original CCAT documentation: http://cmb.gis.a-star.edu.sg/ChIPSeq/paper
 
 **Citation**
 
+For the underlying tool, please cite `Xu H, Handoko L, Wei X, Ye C, Sheng J, Wei CL, Lin F, Sung WK. A signal-noise model for significance analysis of ChIP-seq with negative control. Bioinformatics. 2010 May 1;26(9):1199-204. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20371496&gt;`_
+
 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
 
   </help>
diff --git a/tools/peak_calling/macs_wrapper.xml b/tools/peak_calling/macs_wrapper.xml
index a32c801a6bc..6601102b306 100644
--- a/tools/peak_calling/macs_wrapper.xml
+++ b/tools/peak_calling/macs_wrapper.xml
@@ -231,6 +231,8 @@ View the original MACS documentation: http://liulab.dfci.harvard.edu/MACS/00READ
 
 **Citation**
 
+For the underlying tool, please cite `Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137. &lt;http://www.ncbi.nlm.nih.gov/pubmed/18798982&gt;`_
+
 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
 
   </help>

From 3e9865cfb485343ba1e81fd783e3ad79c3bddb17 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Mon, 14 Nov 2011 16:19:56 -0500
Subject: [PATCH 189/362] Add baseline support for handling data types included
 in tool shed repositories, add the ability to upload files to tool shed
 repositories by entering a URL in the upload form, provide much better file
 content checking when uploading either single files or archives to a tool
 shed repository (niether html content nor images are currently allowed),
 enhance error messaging when tool config parameter tags are not functionally
 correct.

---
 lib/galaxy/tools/parameters/basic.py          |   9 +-
 lib/galaxy/web/base/controller.py             |   1 +
 lib/galaxy/web/controllers/admin.py           |  50 +++++-
 .../webapps/community/controllers/common.py   | 160 ++++++++++++------
 .../community/controllers/repository.py       |  25 +--
 .../webapps/community/controllers/upload.py   | 104 ++++++++----
 .../webapps/community/repository/common.mako  |  41 ++++-
 .../repository/manage_repository.mako         |   2 +-
 .../preview_tools_in_changeset.mako           |   2 +-
 .../webapps/community/repository/upload.mako  |  11 +-
 .../community/repository/view_repository.mako |   2 +-
 11 files changed, 300 insertions(+), 107 deletions(-)

diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index 5073a9d20ca..f0c0bbb3448 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -164,9 +164,14 @@ class ToolParameter( object ):
     @classmethod
     def build( cls, tool, param ):
         """Factory method to create parameter of correct type"""
+        param_name = param.get( "name" )
+        if not param_name:
+            raise ValueError( "Tool parameters require a 'name'" )
         param_type = param.get("type")
-        if not param_type or param_type not in parameter_types:
-            raise ValueError( "Unknown tool parameter type '%s'" % param_type )
+        if not param_type:
+            raise ValueError( "Tool parameter '%s' requires a 'type'" % ( param_name ) )
+        elif param_type not in parameter_types:
+            raise ValueError( "Tool parameter '%s' uses an unknown type '%s'" % ( param_name, param_type ) )
         else:
             return parameter_types[param_type]( tool, param )
         
diff --git a/lib/galaxy/web/base/controller.py b/lib/galaxy/web/base/controller.py
index a7b6f076f97..568049e3ff1 100644
--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -6,6 +6,7 @@ from datetime import date, datetime, timedelta
 from time import strftime
 from galaxy import config, tools, web, util
 from galaxy.util.hash_util import *
+from galaxy.util.json import json_fix
 from galaxy.web import error, form, url_for
 from galaxy.model.orm import *
 from galaxy.workflow.modules import *
diff --git a/lib/galaxy/web/controllers/admin.py b/lib/galaxy/web/controllers/admin.py
index abb58421387..315510387a7 100644
--- a/lib/galaxy/web/controllers/admin.py
+++ b/lib/galaxy/web/controllers/admin.py
@@ -4,12 +4,14 @@ from galaxy.model.orm import *
 from galaxy.web.framework.helpers import time_ago, iff, grids
 from galaxy.tools.search import ToolBoxSearch
 from galaxy.tools import ToolSection, json_fix
+from galaxy.util import inflector
 import logging
 log = logging.getLogger( __name__ )
 
 from galaxy.actions.admin import AdminActions
 from galaxy.web.params import QuotaParamParser
 from galaxy.exceptions import *
+import galaxy.datatypes.registry
 
 class UserListGrid( grids.Grid ):
     class EmailColumn( grids.TextColumn ):
@@ -871,6 +873,10 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
                             os.chdir( current_working_dir )
                             tmp_stderr.close()
                             if returncode == 0:
+                                # Load data types required by tools.
+                                # TODO: uncomment the following when we're ready...
+                                #self.__load_datatypes( trans, repo_files_dir )
+                                # Load tools and tool data files required by them.
                                 sample_files, repository_tools_tups = self.__get_repository_tools_and_sample_files( trans, tool_path, repo_files_dir )
                                 if repository_tools_tups:
                                     # Handle missing data table entries for tool parameters that are dynamically generated select lists.
@@ -920,8 +926,9 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
                             status = 'error'
                 if installed_repository_names:
                     installed_repository_names.sort()
-                    message += 'These %d repositories were installed and all tools were loaded into tool panel section <b>%s</b>:<br/>' % \
-                        ( len( installed_repository_names ), tool_section.name )
+                    num_repositories_installed = len( installed_repository_names )
+                    message += 'Installed %d %s and all tools were loaded into tool panel section <b>%s</b>:<br/>Installed repositories: ' % \
+                        ( num_repositories_installed, inflector.cond_plural( num_repositories_installed, 'repository' ), tool_section.name )
                     for i, repo_name in enumerate( installed_repository_names ):
                         if i == len( installed_repository_names ) -1:
                             message += '%s.<br/>' % repo_name
@@ -1171,6 +1178,45 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
                             error = tmp_stderr.read()
                             tmp_stderr.close()
                             log.debug( 'Problem installing dependencies for tool "%s"\n%s' % ( repository_tool.name, error ) )
+    def __load_datatypes( self, trans, repo_files_dir ):
+        # Find datatypes_conf.xml if it exists.
+        datatypes_config = None
+        for root, dirs, files in os.walk( repo_files_dir ):
+            if root.find( '.hg' ) < 0:
+                for name in files:
+                    if name == 'datatypes_conf.xml':
+                        datatypes_config = os.path.abspath( os.path.join( root, name ) )
+                        break
+        if datatypes_config:
+            # Parse datatypes_config.
+            tree = ElementTree.parse( datatypes_config )
+            root = tree.getroot()
+            ElementInclude.include( root )
+            datatype_files = root.find( 'datatype_files' )
+            for elem in datatype_files.findall( 'datatype_file' ):
+                datatype_file_name = elem.get( 'name', None )
+                if datatype_file_name:
+                    # Find the file in the installed repository.
+                    relative_path = None
+                    for root, dirs, files in os.walk( repo_files_dir ):
+                        if root.find( '.hg' ) < 0:
+                            for name in files:
+                                if name == datatype_file_name:
+                                    relative_path = os.path.join( root, name )
+                                    break
+                    relative_head, relative_tail = os.path.split( relative_path )
+                    # TODO: get the import_module by parsing the <registration><datatype> tags
+                    if datatype_file_name.find( '.' ) > 0:
+                        import_module = datatype_file_name.split( '.' )[ 0 ]
+                    else:
+                        import_module = datatype_file_name
+                    try:
+                        sys.path.insert( 0, relative_head )
+                        module = __import__( import_module )
+                        sys.path.pop( 0 )
+                    except Exception, e:
+                        log.debug( "Execption importing datatypes code file included in installed repository: %s" % str( e ) )
+                    trans.app.datatypes_registry = galaxy.datatypes.registry.Registry( trans.app.config.root, datatypes_config )
     def __get_repository_tools_and_sample_files( self, trans, tool_path, repo_files_dir ):
         # The sample_files list contains all files whose name ends in .sample
         sample_files = []
diff --git a/lib/galaxy/webapps/community/controllers/common.py b/lib/galaxy/webapps/community/controllers/common.py
index a493713d4b4..bc57b336cff 100644
--- a/lib/galaxy/webapps/community/controllers/common.py
+++ b/lib/galaxy/webapps/community/controllers/common.py
@@ -124,34 +124,6 @@ def get_latest_repository_metadata( trans, id ):
                            .filter( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ) ) \
                            .order_by( trans.model.RepositoryMetadata.table.c.id.desc() ) \
                            .first()
-def generate_workflow_metadata( trans, id, changeset_revision, exported_workflow_dict, metadata_dict ):
-    """
-    Update the received metadata_dict with changes that have been applied
-    to the received exported_workflow_dict.  Store everything in the database.
-    """
-    if 'workflows' in metadata_dict:
-        metadata_dict[ 'workflows' ].append( exported_workflow_dict )
-    else:
-        metadata_dict[ 'workflows' ] = [ exported_workflow_dict ]
-    return metadata_dict
-def new_workflow_metadata_required( trans, id, metadata_dict ):
-    """
-    Currently everything about an exported workflow except the name is hard-coded, so there's
-    no real way to differentiate versions of exported workflows.  If this changes at some future
-    time, this method should be enhanced accordingly.
-    """
-    if 'workflows' in metadata_dict:
-        repository_metadata = get_latest_repository_metadata( trans, id )
-        if repository_metadata:
-            if repository_metadata.metadata:
-                # The repository has metadata, so update the workflows value - no new record is needed.
-                return False
-        else:
-            # There is no saved repository metadata, so we need to create a new repository_metadata table record.
-            return True
-    # The received metadata_dict includes no metadata for workflows, so a new repository_metadata table
-    # record is not needed.
-    return False
 def generate_clone_url( trans, repository_id ):
     repository = get_repository( trans, repository_id )
     protocol, base = trans.request.base.split( '://' )
@@ -313,6 +285,62 @@ def new_tool_metadata_required( trans, id, metadata_dict ):
     # The received metadata_dict includes no metadata for tools, so a new repository_metadata table
     # record is not needed.
     return False
+def generate_workflow_metadata( trans, id, changeset_revision, exported_workflow_dict, metadata_dict ):
+    """
+    Update the received metadata_dict with changes that have been applied
+    to the received exported_workflow_dict.  Store everything in the database.
+    """
+    if 'workflows' in metadata_dict:
+        metadata_dict[ 'workflows' ].append( exported_workflow_dict )
+    else:
+        metadata_dict[ 'workflows' ] = [ exported_workflow_dict ]
+    return metadata_dict
+def new_workflow_metadata_required( trans, id, metadata_dict ):
+    """
+    Currently everything about an exported workflow except the name is hard-coded, so there's
+    no real way to differentiate versions of exported workflows.  If this changes at some future
+    time, this method should be enhanced accordingly.
+    """
+    if 'workflows' in metadata_dict:
+        repository_metadata = get_latest_repository_metadata( trans, id )
+        if repository_metadata:
+            if repository_metadata.metadata:
+                # The repository has metadata, so update the workflows value - no new record is needed.
+                return False
+        else:
+            # There is no saved repository metadata, so we need to create a new repository_metadata table record.
+            return True
+    # The received metadata_dict includes no metadata for workflows, so a new repository_metadata table
+    # record is not needed.
+    return False
+def generate_datatypes_metadata( trans, id, changeset_revision, datatypes_config, metadata_dict ):
+    """
+    Update the received metadata_dict with changes that have been applied
+    to the received datatypes_config.
+    """
+    # Parse datatypes_config.
+    tree = ElementTree.parse( datatypes_config )
+    root = tree.getroot()
+    ElementInclude.include( root )
+    repository_datatype_code_files = []
+    datatype_files = root.find( 'datatype_files' )
+    if datatype_files:
+        for elem in datatype_files.findall( 'datatype_file' ):
+            name = elem.get( 'name', None )
+            repository_datatype_code_files.append( name )
+        metadata_dict[ 'datatype_files' ] = repository_datatype_code_files
+    datatypes = []
+    registration = root.find( 'registration' )
+    if registration:
+        for elem in registration.findall( 'datatype' ):
+            extension = elem.get( 'extension', None ) 
+            dtype = elem.get( 'type', None )
+            mimetype = elem.get( 'mimetype', None )
+            datatypes.append( dict( extension=extension,
+                                    dtype=dtype,
+                                    mimetype=mimetype ) )
+        metadata_dict[ 'datatypes' ] = datatypes
+    return metadata_dict
 def set_repository_metadata( trans, id, changeset_revision, **kwd ):
     """Set repository metadata"""
     message = ''
@@ -322,28 +350,34 @@ def set_repository_metadata( trans, id, changeset_revision, **kwd ):
     repo = hg.repository( get_configured_ui(), repo_dir )
     invalid_files = []
     sample_files = []
+    datatypes_config = None
     ctx = get_changectx_for_changeset( trans, repo, changeset_revision )
     if ctx is not None:
         metadata_dict = {}
         if changeset_revision == repository.tip:
-            # Find all special .sample files first.
+            # Find datatypes_conf.xml if it exists.
+            for root, dirs, files in os.walk( repo_dir ):
+                if root.find( '.hg' ) < 0:
+                    for name in files:
+                        if name == 'datatypes_conf.xml':
+                            datatypes_config = os.path.abspath( os.path.join( root, name ) )
+                            break
+            if datatypes_config:
+                metadata_dict = generate_datatypes_metadata( trans, id, changeset_revision, datatypes_config, metadata_dict )
+            # Find all special .sample files.
             for root, dirs, files in os.walk( repo_dir ):
                 if root.find( '.hg' ) < 0:
                     for name in files:
                         if name.endswith( '.sample' ):
                             sample_files.append( os.path.abspath( os.path.join( root, name ) ) )
+            # Find all tool configs and exported workflows.
             for root, dirs, files in os.walk( repo_dir ):
                 if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0:
                     if '.hg' in dirs:
-                        # Don't visit .hg directories - should be impossible since we don't
-                        # allow uploaded archives that contain .hg dirs, but just in case...
                         dirs.remove( '.hg' )
-                    if 'hgrc' in files:
-                         # Don't include hgrc files in commit.
-                        files.remove( 'hgrc' )
                     for name in files:
                         # Find all tool configs.
-                        if name.endswith( '.xml' ):
+                        if name != 'datatypes_conf.xml' and name.endswith( '.xml' ):
                             try:
                                 full_path = os.path.abspath( os.path.join( root, name ) )
                                 tool = load_tool( trans, full_path )
@@ -373,11 +407,13 @@ def set_repository_metadata( trans, id, changeset_revision, **kwd ):
             # Find all special .sample files first.
             for filename in ctx:
                 if filename.endswith( '.sample' ):
-                    sample_files.append( os.path.abspath( os.path.join( root, filename ) ) )
+                    sample_files.append( os.path.abspath( filename ) )
             # Get all tool config file names from the hgweb url, something like:
             # /repos/test/convert_chars1/file/e58dcf0026c7/convert_characters.xml
             for filename in ctx:
-                # Find all tool configs - should not have to update metadata for workflows for now.
+                # Find all tool configs - we do not have to update metadata for workflows or datatypes in anything
+                # but repository tips (handled above) since at the time this code was written, no workflows or
+                # dataytpes_conf.xml files exist in tool shed repositories, so they can only be added in future tips.
                 if filename.endswith( '.xml' ):
                     fctx = ctx[ filename ]
                     # Write the contents of the old tool config to a temporary file.
@@ -532,25 +568,41 @@ def update_for_browsing( trans, repository, current_working_dir, commit_message=
     # The following will delete the disk copy of only the files in the repository.
     #os.system( 'hg update -r null > /dev/null 2>&1' )
     repo.ui.pushbuffer()
-    commands.status( repo.ui, repo, all=True )
-    status_and_file_names = repo.ui.popbuffer().strip().split( "\n" )
-    # status_and_file_names looks something like:
-    # ['? README', '? tmap_tool/tmap-0.0.9.tar.gz', '? dna_filtering.py', 'C filtering.py', 'C filtering.xml']
-    # The codes used to show the status of files are:
-    # M = modified
-    # A = added
-    # R = removed
-    # C = clean
-    # ! = deleted, but still tracked
-    # ? = not tracked
-    # I = ignored
     files_to_remove_from_disk = []
     files_to_commit = []
-    for status_and_file_name in status_and_file_names:
-        if status_and_file_name.startswith( '?' ) or status_and_file_name.startswith( 'I' ):
-            files_to_remove_from_disk.append( os.path.abspath( os.path.join( repo_dir, status_and_file_name.split()[1] ) ) )
-        elif status_and_file_name.startswith( 'M' ) or status_and_file_name.startswith( 'A' ) or status_and_file_name.startswith( 'R' ):
-            files_to_commit.append( os.path.abspath( os.path.join( repo_dir, status_and_file_name.split()[1] ) ) )
+    commands.status( repo.ui, repo, all=True )
+    status_and_file_names = repo.ui.popbuffer().strip().split( "\n" )
+    if status_and_file_names and status_and_file_names[ 0 ] not in [ '' ]:
+        # status_and_file_names looks something like:
+        # ['? README', '? tmap_tool/tmap-0.0.9.tar.gz', '? dna_filtering.py', 'C filtering.py', 'C filtering.xml']
+        # The codes used to show the status of files are:
+        # M = modified
+        # A = added
+        # R = removed
+        # C = clean
+        # ! = deleted, but still tracked
+        # ? = not tracked
+        # I = ignored
+        for status_and_file_name in status_and_file_names:
+            if status_and_file_name.startswith( '?' ) or status_and_file_name.startswith( 'I' ):
+                files_to_remove_from_disk.append( os.path.abspath( os.path.join( repo_dir, status_and_file_name.split()[1] ) ) )
+            elif status_and_file_name.startswith( 'M' ) or status_and_file_name.startswith( 'A' ) or status_and_file_name.startswith( 'R' ):
+                files_to_commit.append( os.path.abspath( os.path.join( repo_dir, status_and_file_name.split()[1] ) ) )
+    # We may have files on disk in the repo directory that aren't being tracked, so they must be removed.
+    cmd = 'hg status'
+    tmp_name = tempfile.NamedTemporaryFile().name
+    tmp_stdout = open( tmp_name, 'wb' )
+    os.chdir( repo_dir )
+    proc = subprocess.Popen( args=cmd, shell=True, stdout=tmp_stdout.fileno() )
+    returncode = proc.wait()
+    os.chdir( current_working_dir )
+    tmp_stdout.close()
+    if returncode == 0:
+        for i, line in enumerate( open( tmp_name ) ):
+            if line.startswith( '?' ) or line.startswith( 'I' ):
+                files_to_remove_from_disk.append( os.path.abspath( os.path.join( repo_dir, line.split()[1] ) ) )
+            elif line.startswith( 'M' ) or line.startswith( 'A' ) or line.startswith( 'R' ):
+                files_to_commit.append( os.path.abspath( os.path.join( repo_dir, line.split()[1] ) ) )
     for full_path in files_to_remove_from_disk:
         # We'll remove all files that are not tracked or ignored.
         if os.path.isdir( full_path ):
diff --git a/lib/galaxy/webapps/community/controllers/repository.py b/lib/galaxy/webapps/community/controllers/repository.py
index bcbfe6f1ee9..fabfef3faf7 100644
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -1007,17 +1007,19 @@ class RepositoryController( BaseUIController, ItemRatings ):
         if repository_path.startswith( './' ):
             repository_path = repository_path.replace( './', '', 1 )
         entry = "repos/%s/%s = %s" % ( repository.user.username, repository.name, repository_path.lstrip( './' ) )
+        tmp_fd, tmp_fname = tempfile.mkstemp()
         if os.path.exists( hgweb_config ):
             # Make a backup of the hgweb.config file since we're going to be changing it.
             self.__make_hgweb_config_copy( trans, hgweb_config )
-            tmp_fname = tempfile.NamedTemporaryFile()
+            new_hgweb_config = open( tmp_fname, 'wb' )
             for i, line in enumerate( open( hgweb_config ) ):
-                tmp_fname.write( line )
+                new_hgweb_config.write( line )
         else:
-            tmp_fname.write( '[paths]\n' )
-        tmp_fname.write( "%s\n" % entry )
-        tmp_fname.flush()
-        shutil.move( tmp_fname.name, os.path.abspath( hgweb_config ) )
+            new_hgweb_config = open( tmp_fname, 'wb' )
+            new_hgweb_config.write( '[paths]\n' )
+        new_hgweb_config.write( "%s\n" % entry )
+        new_hgweb_config.flush()
+        shutil.move( tmp_fname, os.path.abspath( hgweb_config ) )
     def __change_hgweb_config_entry( self, trans, repository, old_repository_name, new_repository_name ):
         # Change an entry in the hgweb.config file for a repository.  This only happens when
         # the owner changes the name of the repository.  An entry looks something like:
@@ -1028,14 +1030,15 @@ class RepositoryController( BaseUIController, ItemRatings ):
         repo_dir = repository.repo_path
         old_lhs = "repos/%s/%s" % ( repository.user.username, old_repository_name )
         new_entry = "repos/%s/%s = %s\n" % ( repository.user.username, new_repository_name, repo_dir )
-        tmp_fname = tempfile.NamedTemporaryFile()
+        tmp_fd, tmp_fname = tempfile.mkstemp()
+        new_hgweb_config = open( tmp_fname, 'wb' )
         for i, line in enumerate( open( hgweb_config ) ):
             if line.startswith( old_lhs ):
-                tmp_fname.write( new_entry )
+                new_hgweb_config.write( new_entry )
             else:
-                tmp_fname.write( line )
-        tmp_fname.flush()
-        shutil.move( tmp_fname.name, os.path.abspath( hgweb_config ) )
+                new_hgweb_config.write( line )
+        new_hgweb_config.flush()
+        shutil.move( tmp_fname, os.path.abspath( hgweb_config ) )
     def __create_hgrc_file( self, repository ):
         # At this point, an entry for the repository is required to be in the hgweb.config
         # file so we can call repository.repo_path.
diff --git a/lib/galaxy/webapps/community/controllers/upload.py b/lib/galaxy/webapps/community/controllers/upload.py
index 9a691eb5250..3aa7df3e842 100644
--- a/lib/galaxy/webapps/community/controllers/upload.py
+++ b/lib/galaxy/webapps/community/controllers/upload.py
@@ -1,4 +1,4 @@
-import sys, os, shutil, logging, tarfile, tempfile
+import sys, os, shutil, logging, tarfile, tempfile, urllib
 from galaxy.web.base.controller import *
 from galaxy.model.orm import *
 from galaxy.datatypes.checkers import *
@@ -11,9 +11,6 @@ log = logging.getLogger( __name__ )
 SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error"
 CHUNK_SIZE = 2**20 # 1Mb
 
-class UploadError( Exception ):
-    pass
-
 class UploadController( BaseUIController ):
     @web.expose
     @web.require_login( 'upload', use_panels=True, webapp='community' )
@@ -32,20 +29,40 @@ class UploadController( BaseUIController ):
         remove_repo_files_not_in_tar = util.string_as_bool( params.get( 'remove_repo_files_not_in_tar', 'true' ) )
         uploaded_file = None
         upload_point = self.__get_upload_point( repository, **kwd )
-        # Get the current repository tip.
         tip = repository.tip
+        file_data = params.get( 'file_data', '' )
+        url = params.get( 'url', '' )
         if params.get( 'upload_button', False ):
             current_working_dir = os.getcwd()
-            file_data = params.get( 'file_data', '' )
-            if file_data == '':
+            if file_data == '' and url == '':
                 message = 'No files were entered on the upload form.'
                 status = 'error'
                 uploaded_file = None
+            elif url:
+                valid_url = True
+                try:
+                    stream = urllib.urlopen( url )
+                except Exception, e:
+                    valid_url = False
+                    message = 'Error uploading file via http: %s' % str( e )
+                    status = 'error'
+                    uploaded_file = None
+                if valid_url:
+                    fd, uploaded_file_name = tempfile.mkstemp()
+                    uploaded_file = open( uploaded_file_name, 'wb' )
+                    while 1:
+                        chunk = stream.read( CHUNK_SIZE )
+                        if not chunk:
+                            break
+                        uploaded_file.write( chunk )
+                    uploaded_file.flush()
+                    uploaded_file_filename = url.split( '/' )[ -1 ]
+                    isempty = os.path.getsize( os.path.abspath( uploaded_file_name ) ) == 0
             elif file_data not in ( '', None ):
                 uploaded_file = file_data.file
                 uploaded_file_name = uploaded_file.name
                 uploaded_file_filename = file_data.filename
-            isempty = os.path.getsize( os.path.abspath( uploaded_file_name ) ) == 0
+                isempty = os.path.getsize( os.path.abspath( uploaded_file_name ) ) == 0
             if uploaded_file:
                 isgzip = False
                 isbz2 = False
@@ -84,30 +101,32 @@ class UploadController( BaseUIController ):
                         full_path = os.path.abspath( os.path.join( repo_dir, upload_point, uploaded_file_filename ) )
                     else:
                         full_path = os.path.abspath( os.path.join( repo_dir, uploaded_file_filename ) )
-                    # Move the uploaded file to the load_point within the repository hierarchy.
-                    shutil.move( uploaded_file_name, full_path )
-                    commands.add( repo.ui, repo, full_path )
-                    try:
-                        commands.commit( repo.ui, repo, full_path, user=trans.user.username, message=commit_message )
-                    except Exception, e:
-                        # I never have a problem with commands.commit on a Mac, but in the test/production
-                        # tool shed environment, it occasionally throws a "TypeError: array item must be char"
-                        # exception.  If this happens, we'll try the following.
-                        repo.dirstate.write()
-                        repo.commit( user=trans.user.username, text=commit_message )
-                    if full_path.endswith( 'tool_data_table_conf.xml.sample' ):
-                        # Handle the special case where a tool_data_table_conf.xml.sample
-                        # file is being uploaded by parsing the file and adding new entries
-                        # to the in-memory trans.app.tool_data_tables dictionary as well as
-                        # appending them to the shed's tool_data_table_conf.xml file on disk.
-                        error, error_message = handle_sample_tool_data_table_conf_file( trans, full_path )
-                        if error:
-                            message = '%s<br/>%s' % ( message, error_message )
-                    if full_path.endswith( '.loc.sample' ):
-                        # Handle the special case where a xxx.loc.sample file is
-                        # being uploaded by copying it to ~/tool-data/xxx.loc.
-                        copy_sample_loc_file( trans, full_path )
-                    handle_email_alerts( trans, repository )
+                    ok, message = self.__check_file_content( uploaded_file_name )
+                    if ok:
+                        # Move the uploaded file to the load_point within the repository hierarchy.
+                        shutil.move( uploaded_file_name, full_path )
+                        commands.add( repo.ui, repo, full_path )
+                        try:
+                            commands.commit( repo.ui, repo, full_path, user=trans.user.username, message=commit_message )
+                        except Exception, e:
+                            # I never have a problem with commands.commit on a Mac, but in the test/production
+                            # tool shed environment, it occasionally throws a "TypeError: array item must be char"
+                            # exception.  If this happens, we'll try the following.
+                            repo.dirstate.write()
+                            repo.commit( user=trans.user.username, text=commit_message )
+                        if full_path.endswith( 'tool_data_table_conf.xml.sample' ):
+                            # Handle the special case where a tool_data_table_conf.xml.sample
+                            # file is being uploaded by parsing the file and adding new entries
+                            # to the in-memory trans.app.tool_data_tables dictionary as well as
+                            # appending them to the shed's tool_data_table_conf.xml file on disk.
+                            error, error_message = handle_sample_tool_data_table_conf_file( trans, full_path )
+                            if error:
+                                message = '%s<br/>%s' % ( message, error_message )
+                        if full_path.endswith( '.loc.sample' ):
+                            # Handle the special case where a xxx.loc.sample file is
+                            # being uploaded by copying it to ~/tool-data/xxx.loc.
+                            copy_sample_loc_file( trans, full_path )
+                        handle_email_alerts( trans, repository )
                 if ok:
                     # Update the repository files for browsing.
                     update_for_browsing( trans, repository, current_working_dir, commit_message=commit_message )
@@ -146,6 +165,7 @@ class UploadController( BaseUIController ):
         selected_categories = [ trans.security.decode_id( id ) for id in category_ids ]
         return trans.fill_template( '/webapps/community/repository/upload.mako',
                                     repository=repository,
+                                    url=url,
                                     commit_message=commit_message,
                                     uncompress_file=uncompress_file,
                                     remove_repo_files_not_in_tar=remove_repo_files_not_in_tar,
@@ -172,6 +192,14 @@ class UploadController( BaseUIController ):
             tar.extractall( path=full_path )
             tar.close()
             uploaded_file.close()
+            for filename_in_archive in filenames_in_archive:
+                if os.path.isfile( filename_in_archive ):
+                    ok, message = self.__check_file_content( filename_in_archive )
+                    if not ok:
+                        # Refresh the repository files for browsing.
+                        current_working_dir = os.getcwd()
+                        update_for_browsing( trans, repository, current_working_dir )
+                        return False, message, []
             if remove_repo_files_not_in_tar and not repository.is_new:
                 # We have a repository that is not new (it contains files), so discover
                 # those files that are in the repository, but not in the uploaded archive.
@@ -314,4 +342,14 @@ class UploadController( BaseUIController ):
                 message = "Uploaded archives cannot contain hgrc files."
                 return False, message
         return True, ''
-                            
+    def __check_file_content( self, file_path ):
+        message = ''
+        ok = True
+        if check_html( file_path ):
+            message = 'Files containing HTML content cannot be uploaded to a Galaxy tool shed.'
+            ok = False
+        elif check_image( file_path ):
+            # For now we won't allow images to be uploaded.
+            message = 'Files containing images cannot be uploaded to a Galaxy tool shed.'
+            ok = False
+        return ok, message
diff --git a/templates/webapps/community/repository/common.mako b/templates/webapps/community/repository/common.mako
index 63736bacca3..56d820628f4 100644
--- a/templates/webapps/community/repository/common.mako
+++ b/templates/webapps/community/repository/common.mako
@@ -83,7 +83,7 @@
     hg clone <a href="${clone_str}">${clone_str}</a>
 </%def>
 
-<%def name="render_repository_tools_and_workflows( repository_metadata_id, metadata, can_set_metadata=False, webapp='community' )">
+<%def name="render_repository_items( repository_metadata_id, metadata, can_set_metadata=False, webapp='community' )">
     <% from galaxy.webapps.community.controllers.common import encode, decode %>
     %if metadata or can_set_metadata:
         <p/>
@@ -195,6 +195,45 @@
                         </div>
                         <div style="clear: both"></div>
                     %endif
+                    %if 'datatypes' in metadata:
+                        <div class="form-row">
+                            <table width="100%">
+                                <tr bgcolor="#D8D8D8" width="100%">
+                                    <td><b>Data types</b></td>
+                                </tr>
+                            </table>
+                        </div>
+                        <div style="clear: both"></div>
+                        <div class="form-row">
+                            <% datatypes_dicts = metadata[ 'datatypes' ] %>
+                            <table class="grid">
+                                <tr>
+                                    <td><b>extension</b></td>
+                                    <td><b>dtype</b></td>
+                                    <td><b>mimetype</b></td>
+                                </tr>
+                                %for datatypes_dict in datatypes_dicts:
+                                    <% 
+                                        extension = datatypes_dict[ 'extension' ]
+                                        dtype = datatypes_dict[ 'dtype' ]
+                                        mimetype = datatypes_dict[ 'mimetype' ]
+                                    %>
+                                    <tr>
+                                        <td>${extension}</td>
+                                        <td>${dtype}</td>
+                                        <td>
+                                            %if mimetype:
+                                                ${mimetype}
+                                            %else:
+                                                &nbsp;
+                                            %endif
+                                        </td>
+                                    </tr>
+                                %endfor
+                            </table>
+                        </div>
+                        <div style="clear: both"></div>
+                    %endif
                 %endif
                 %if can_set_metadata:
                     <form name="set_metadata" action="${h.url_for( controller='repository', action='set_metadata', id=trans.security.encode_id( repository.id ), ctx_str=changeset_revision )}" method="post">
diff --git a/templates/webapps/community/repository/manage_repository.mako b/templates/webapps/community/repository/manage_repository.mako
index c056413c34e..1345448414d 100644
--- a/templates/webapps/community/repository/manage_repository.mako
+++ b/templates/webapps/community/repository/manage_repository.mako
@@ -184,7 +184,7 @@
         </form>
     </div>
 </div>
-${render_repository_tools_and_workflows( repository_metadata_id, metadata, can_set_metadata=True )}
+${render_repository_items( repository_metadata_id, metadata, can_set_metadata=True )}
 <p/>
 <div class="toolForm">
     <div class="toolFormTitle">Manage categories</div>
diff --git a/templates/webapps/community/repository/preview_tools_in_changeset.mako b/templates/webapps/community/repository/preview_tools_in_changeset.mako
index 25a0ddd1d92..e7ad6172f06 100644
--- a/templates/webapps/community/repository/preview_tools_in_changeset.mako
+++ b/templates/webapps/community/repository/preview_tools_in_changeset.mako
@@ -104,4 +104,4 @@
     </div>
 </div>
 <p/>
-${render_repository_tools_and_workflows( repository_metadata_id, metadata, webapp=webapp )}
+${render_repository_items( repository_metadata_id, metadata, webapp=webapp )}
diff --git a/templates/webapps/community/repository/upload.mako b/templates/webapps/community/repository/upload.mako
index 20df043cc8d..b225c8f69e1 100644
--- a/templates/webapps/community/repository/upload.mako
+++ b/templates/webapps/community/repository/upload.mako
@@ -73,7 +73,16 @@
                 </div>
                 <div style="clear: both"></div>
             </div>
-        
+            <div class="form-row">
+                <label>Url:</label>
+                <div class="form-row-input">
+                    <input name="url" type="textfield" value="${url}" size="40"/>
+                </div>
+                <div class="toolParamHelp" style="clear: both;">
+                     Enter a URL to upload your files via http.
+                </div>
+                <div style="clear: both"></div>
+            </div>
             <div class="form-row">
                 <%
                     if uncompress_file:
diff --git a/templates/webapps/community/repository/view_repository.mako b/templates/webapps/community/repository/view_repository.mako
index 3cf2ef01fcd..8a243c03381 100644
--- a/templates/webapps/community/repository/view_repository.mako
+++ b/templates/webapps/community/repository/view_repository.mako
@@ -186,7 +186,7 @@
         %endif
     </div>
 </div>
-${render_repository_tools_and_workflows( repository_metadata_id, metadata, webapp=webapp )}
+${render_repository_items( repository_metadata_id, metadata, webapp=webapp )}
 %if repository.categories:
     <p/>
     <div class="toolForm">

From 58aeed8f762560265d6a29db6296b3de39a1f6b4 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Mon, 14 Nov 2011 16:59:26 -0500
Subject: [PATCH 190/362] Revert file content checks when up0loading to a tool
 shed repository as they're currently too restrictive.

---
 .../webapps/community/controllers/upload.py   | 64 +++++++++++--------
 1 file changed, 36 insertions(+), 28 deletions(-)

diff --git a/lib/galaxy/webapps/community/controllers/upload.py b/lib/galaxy/webapps/community/controllers/upload.py
index 3aa7df3e842..cdcf6bc5e75 100644
--- a/lib/galaxy/webapps/community/controllers/upload.py
+++ b/lib/galaxy/webapps/community/controllers/upload.py
@@ -101,32 +101,34 @@ class UploadController( BaseUIController ):
                         full_path = os.path.abspath( os.path.join( repo_dir, upload_point, uploaded_file_filename ) )
                     else:
                         full_path = os.path.abspath( os.path.join( repo_dir, uploaded_file_filename ) )
-                    ok, message = self.__check_file_content( uploaded_file_name )
-                    if ok:
-                        # Move the uploaded file to the load_point within the repository hierarchy.
-                        shutil.move( uploaded_file_name, full_path )
-                        commands.add( repo.ui, repo, full_path )
-                        try:
-                            commands.commit( repo.ui, repo, full_path, user=trans.user.username, message=commit_message )
-                        except Exception, e:
-                            # I never have a problem with commands.commit on a Mac, but in the test/production
-                            # tool shed environment, it occasionally throws a "TypeError: array item must be char"
-                            # exception.  If this happens, we'll try the following.
-                            repo.dirstate.write()
-                            repo.commit( user=trans.user.username, text=commit_message )
-                        if full_path.endswith( 'tool_data_table_conf.xml.sample' ):
-                            # Handle the special case where a tool_data_table_conf.xml.sample
-                            # file is being uploaded by parsing the file and adding new entries
-                            # to the in-memory trans.app.tool_data_tables dictionary as well as
-                            # appending them to the shed's tool_data_table_conf.xml file on disk.
-                            error, error_message = handle_sample_tool_data_table_conf_file( trans, full_path )
-                            if error:
-                                message = '%s<br/>%s' % ( message, error_message )
-                        if full_path.endswith( '.loc.sample' ):
-                            # Handle the special case where a xxx.loc.sample file is
-                            # being uploaded by copying it to ~/tool-data/xxx.loc.
-                            copy_sample_loc_file( trans, full_path )
-                        handle_email_alerts( trans, repository )
+                    # TODO: enhance this method to set a flag and alert an admin to review content since
+                    # the hard checks are too restrictive.
+                    #ok, message = self.__check_file_content( uploaded_file_name )
+                    #if ok:
+                    # Move the uploaded file to the load_point within the repository hierarchy.
+                    shutil.move( uploaded_file_name, full_path )
+                    commands.add( repo.ui, repo, full_path )
+                    try:
+                        commands.commit( repo.ui, repo, full_path, user=trans.user.username, message=commit_message )
+                    except Exception, e:
+                        # I never have a problem with commands.commit on a Mac, but in the test/production
+                        # tool shed environment, it occasionally throws a "TypeError: array item must be char"
+                        # exception.  If this happens, we'll try the following.
+                        repo.dirstate.write()
+                        repo.commit( user=trans.user.username, text=commit_message )
+                    if full_path.endswith( 'tool_data_table_conf.xml.sample' ):
+                        # Handle the special case where a tool_data_table_conf.xml.sample
+                        # file is being uploaded by parsing the file and adding new entries
+                        # to the in-memory trans.app.tool_data_tables dictionary as well as
+                        # appending them to the shed's tool_data_table_conf.xml file on disk.
+                        error, error_message = handle_sample_tool_data_table_conf_file( trans, full_path )
+                        if error:
+                            message = '%s<br/>%s' % ( message, error_message )
+                    if full_path.endswith( '.loc.sample' ):
+                        # Handle the special case where a xxx.loc.sample file is
+                        # being uploaded by copying it to ~/tool-data/xxx.loc.
+                        copy_sample_loc_file( trans, full_path )
+                    handle_email_alerts( trans, repository )
                 if ok:
                     # Update the repository files for browsing.
                     update_for_browsing( trans, repository, current_working_dir, commit_message=commit_message )
@@ -192,6 +194,9 @@ class UploadController( BaseUIController ):
             tar.extractall( path=full_path )
             tar.close()
             uploaded_file.close()
+            """
+            # TODO: enhance this method to set a flag and alert an admin to review content since
+            # the hard checks are too restrictive.
             for filename_in_archive in filenames_in_archive:
                 if os.path.isfile( filename_in_archive ):
                     ok, message = self.__check_file_content( filename_in_archive )
@@ -200,6 +205,7 @@ class UploadController( BaseUIController ):
                         current_working_dir = os.getcwd()
                         update_for_browsing( trans, repository, current_working_dir )
                         return False, message, []
+            """
             if remove_repo_files_not_in_tar and not repository.is_new:
                 # We have a repository that is not new (it contains files), so discover
                 # those files that are in the repository, but not in the uploaded archive.
@@ -343,13 +349,15 @@ class UploadController( BaseUIController ):
                 return False, message
         return True, ''
     def __check_file_content( self, file_path ):
+        return True, ''
         message = ''
         ok = True
+        head, tail = os.path.split( file_path )
         if check_html( file_path ):
-            message = 'Files containing HTML content cannot be uploaded to a Galaxy tool shed.'
+            message = 'The file <b>%s</b> contains HTML content which cannot be uploaded to a Galaxy tool shed.' % str( tail )
             ok = False
         elif check_image( file_path ):
             # For now we won't allow images to be uploaded.
-            message = 'Files containing images cannot be uploaded to a Galaxy tool shed.'
+            message = 'The file <b>%s</b> contains image content that cannot be uploaded to a Galaxy tool shed.' % str( tail )
             ok = False
         return ok, message

From 5e6d1139967f7d45edc173fd891f286c4e072080 Mon Sep 17 00:00:00 2001
From: Ross Lazarus <ross.lazarus@gmail.com>
Date: Tue, 15 Nov 2011 11:09:50 -0500
Subject: [PATCH 191/362] Bump FastQC version in preparation for updating
 executable version

---
 tools/rgenetics/rgFastQC.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/rgenetics/rgFastQC.xml b/tools/rgenetics/rgFastQC.xml
index 4d65aea5c66..cee79d861ae 100644
--- a/tools/rgenetics/rgFastQC.xml
+++ b/tools/rgenetics/rgFastQC.xml
@@ -1,4 +1,4 @@
-<tool name="Fastqc: Fastqc QC" id="fastqc" version="0.1">
+<tool name="Fastqc: Fastqc QC" id="fastqc" version="0.2">
   <description>using FastQC from Babraham</description>
   <command interpreter="python">
     rgFastQC.py -i $input_file -d $html_file.files_path -o $html_file -n "$out_prefix" -f $input_file.ext -e ${GALAXY_DATA_INDEX_DIR}/shared/jars/FastQC/fastqc

From 2e55392f4aeef0b72f2f4d5a42044a018067f53c Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Tue, 15 Nov 2011 11:51:05 -0500
Subject: [PATCH 192/362] Use mercurial's purge extension to remove untracked
 repository files and empty directories, and fix a bug related to deleting
 repository files.

---
 .../webapps/community/controllers/common.py   | 56 +++++++++----------
 .../community/controllers/repository.py       | 12 ++--
 2 files changed, 34 insertions(+), 34 deletions(-)

diff --git a/lib/galaxy/webapps/community/controllers/common.py b/lib/galaxy/webapps/community/controllers/common.py
index bc57b336cff..0f8464f298e 100644
--- a/lib/galaxy/webapps/community/controllers/common.py
+++ b/lib/galaxy/webapps/community/controllers/common.py
@@ -589,36 +589,36 @@ def update_for_browsing( trans, repository, current_working_dir, commit_message=
             elif status_and_file_name.startswith( 'M' ) or status_and_file_name.startswith( 'A' ) or status_and_file_name.startswith( 'R' ):
                 files_to_commit.append( os.path.abspath( os.path.join( repo_dir, status_and_file_name.split()[1] ) ) )
     # We may have files on disk in the repo directory that aren't being tracked, so they must be removed.
-    cmd = 'hg status'
-    tmp_name = tempfile.NamedTemporaryFile().name
-    tmp_stdout = open( tmp_name, 'wb' )
+    # We'll use mercurial's purge extension to do this.  Using this extension requires the following entry 
+    # in the repository's hgrc file which was not required for some time, so we'll add it if it's missing.
+    # [extensions]
+    # hgext.purge=
+    lines = repo.opener( 'hgrc', 'rb' ).readlines()
+    if not '[extensions]\n' in lines:
+        # No extensions have been added at all, so just append to the file.
+        fp = repo.opener( 'hgrc', 'a' )
+        fp.write( '[extensions]\n' )
+        fp.write( 'hgext.purge=\n' )
+        fp.close()
+    elif not 'hgext.purge=\n' in lines:
+        # The file includes and [extensions] section, but we need to add the
+        # purge extension.
+        fp = repo.opener( 'hgrc', 'wb' )
+        for line in lines:
+            if line.startswith( '[extensions]' ):
+                fp.write( line )
+                fp.write( 'hgext.purge=\n' )
+            else:
+                fp.write( line )
+        fp.close()
+    cmd = 'hg purge'
     os.chdir( repo_dir )
-    proc = subprocess.Popen( args=cmd, shell=True, stdout=tmp_stdout.fileno() )
-    returncode = proc.wait()
+    proc = subprocess.Popen( args=cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT )
+    return_code = proc.wait()
     os.chdir( current_working_dir )
-    tmp_stdout.close()
-    if returncode == 0:
-        for i, line in enumerate( open( tmp_name ) ):
-            if line.startswith( '?' ) or line.startswith( 'I' ):
-                files_to_remove_from_disk.append( os.path.abspath( os.path.join( repo_dir, line.split()[1] ) ) )
-            elif line.startswith( 'M' ) or line.startswith( 'A' ) or line.startswith( 'R' ):
-                files_to_commit.append( os.path.abspath( os.path.join( repo_dir, line.split()[1] ) ) )
-    for full_path in files_to_remove_from_disk:
-        # We'll remove all files that are not tracked or ignored.
-        if os.path.isdir( full_path ):
-            try:
-                os.rmdir( full_path )
-            except OSError, e:
-                # The directory is not empty
-                pass
-        elif os.path.isfile( full_path ):
-            os.remove( full_path )
-            dir = os.path.split( full_path )[0]
-            try:
-                os.rmdir( dir )
-            except OSError, e:
-                # The directory is not empty
-                pass
+    if return_code != 0:
+        output = proc.stdout.read( 32768 )
+        log.debug( 'hg purge failed in repository directory %s, reason: %s' % ( repo_dir, output ) )
     if files_to_commit:
         if not commit_message:
             commit_message = 'Committed changes to: %s' % ', '.join( files_to_commit )
diff --git a/lib/galaxy/webapps/community/controllers/repository.py b/lib/galaxy/webapps/community/controllers/repository.py
index fabfef3faf7..6c1878f817a 100644
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -1042,13 +1042,11 @@ class RepositoryController( BaseUIController, ItemRatings ):
     def __create_hgrc_file( self, repository ):
         # At this point, an entry for the repository is required to be in the hgweb.config
         # file so we can call repository.repo_path.
-        # Create a .hg/hgrc file that looks something like this:
-        # [web]
-        # allow_push = test
-        # name = convert_characters1
-        # push_ssl = False
         # Since we support both http and https, we set push_ssl to False to override
         # the default (which is True) in the mercurial api.
+        # The hg purge extension purges all files and directories not being tracked by
+        # mercurial in the current repository.  It'll remove unknown files and empty
+        # directories.  This is used in the update_for_browsing() method.
         repo = hg.repository( get_configured_ui(), path=repository.repo_path )
         fp = repo.opener( 'hgrc', 'wb' )
         fp.write( '[paths]\n' )
@@ -1058,6 +1056,8 @@ class RepositoryController( BaseUIController, ItemRatings ):
         fp.write( 'allow_push = %s\n' % repository.user.username )
         fp.write( 'name = %s\n' % repository.name )
         fp.write( 'push_ssl = false\n' )
+        fp.write( '[extensions]\n' )
+        fp.write( 'hgext.purge=' )
         fp.close()
     @web.expose
     def browse_repository( self, trans, id, **kwd ):
@@ -1150,7 +1150,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
                 tip = repository.tip
                 for selected_file in selected_files_to_delete:
                     try:
-                        commands.remove( repo.ui, repo, repo_file, force=True )
+                        commands.remove( repo.ui, repo, selected_file, force=True )
                     except Exception, e:
                         # I never have a problem with commands.remove on a Mac, but in the test/production
                         # tool shed environment, it throws an exception whenever I delete all files from a

From 3388a0b063d61036026a4146f59831ac54be7a37 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Tue, 15 Nov 2011 12:11:09 -0500
Subject: [PATCH 193/362] External display applications will now return HTTP
 not found for non-existant parameters/datasets when requested.

---
 lib/galaxy/web/controllers/dataset.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/web/controllers/dataset.py b/lib/galaxy/web/controllers/dataset.py
index 214da8948a4..ae32e915d3c 100644
--- a/lib/galaxy/web/controllers/dataset.py
+++ b/lib/galaxy/web/controllers/dataset.py
@@ -806,7 +806,11 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesHistory, UsesHist
                         #in case some display app wants all files to be in the same 'directory', 
                         #data can be forced to param, but not the other way (no filename for other direction)
                         #get param name from url param name
-                        action_param = display_link.get_param_name_by_url( action_param )
+                        try:
+                            action_param = display_link.get_param_name_by_url( action_param )
+                        except ValueError, e:
+                            log.debug( e )
+                            return paste.httpexceptions.HTTPNotFound( str( e ) )
                         value = display_link.get_param_value( action_param )
                         assert value, "An invalid parameter name was provided: %s" % action_param
                         assert value.parameter.viewable, "This parameter is not viewable."

From 3e232e23e543fc26838d43674a349b43933b8bf6 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Tue, 15 Nov 2011 12:34:47 -0500
Subject: [PATCH 194/362] Add the boto egg for S3 Object Store.

---
 eggs.ini                                      | 1 +
 lib/galaxy/objectstore/s3_multipart_upload.py | 3 +++
 2 files changed, 4 insertions(+)

diff --git a/eggs.ini b/eggs.ini
index 7bec53d8b6f..7e3f9f805d7 100644
--- a/eggs.ini
+++ b/eggs.ini
@@ -32,6 +32,7 @@ guppy = 0.1.8
 [eggs:noplatform]
 amqplib = 0.6.1
 Beaker = 1.4
+boto = 1.8d
 decorator = 3.1.2
 docutils = 0.7
 drmaa = 0.4b3
diff --git a/lib/galaxy/objectstore/s3_multipart_upload.py b/lib/galaxy/objectstore/s3_multipart_upload.py
index 85b6b3e34a1..56e52b3efd8 100644
--- a/lib/galaxy/objectstore/s3_multipart_upload.py
+++ b/lib/galaxy/objectstore/s3_multipart_upload.py
@@ -12,6 +12,9 @@ import functools
 import multiprocessing
 from multiprocessing.pool import IMapIterator
 
+from galaxy import eggs
+eggs.require('boto')
+
 import boto
 
 def map_wrap(f):

From 0f98fc6814d7dbd4a71aeb02c09be90b208f7259 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Tue, 15 Nov 2011 14:28:08 -0500
Subject: [PATCH 195/362] Add 'type_extension' attribute to datatypes_conf.xml
 that allows creating a datatype from an earlier declared datatype by
 referencing extension. Make several datatypes that had been direct
 instantiations from Data become subclasses of Binary.

---
 datatypes_conf.xml.sample        | 10 +++++-----
 lib/galaxy/datatypes/binary.py   |  2 +-
 lib/galaxy/datatypes/registry.py | 22 +++++++++++++---------
 3 files changed, 19 insertions(+), 15 deletions(-)

diff --git a/datatypes_conf.xml.sample b/datatypes_conf.xml.sample
index 029903fc08c..eb2dbf5e276 100644
--- a/datatypes_conf.xml.sample
+++ b/datatypes_conf.xml.sample
@@ -88,7 +88,7 @@
     <datatype extension="gif" type="galaxy.datatypes.images:Gif" mimetype="image/gif"/>
     <datatype extension="gmaj.zip" type="galaxy.datatypes.images:Gmaj" mimetype="application/zip"/>
     <datatype extension="gtf" type="galaxy.datatypes.interval:Gtf" display_in_upload="true"/>
-    <datatype extension="h5" type="galaxy.datatypes.data:Data" mimetype="application/octet-stream"/>
+    <datatype extension="h5" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" subclass="True" />
     <datatype extension="html" type="galaxy.datatypes.images:Html" mimetype="text/html"/>
     <datatype extension="interval" type="galaxy.datatypes.interval:Interval" display_in_upload="true">
       <converter file="interval_to_bed_converter.xml" target_datatype="bed"/>
@@ -164,10 +164,10 @@
       <converter file="wiggle_to_simple_converter.xml" target_datatype="interval"/>
       <!-- <display file="gbrowse/gbrowse_wig.xml" /> -->
     </datatype>
-    <datatype extension="summary_tree" type="galaxy.datatypes.data:Data" />
-    <datatype extension="interval_index" type="galaxy.datatypes.data:Data" />
-    <datatype extension="tabix" type="galaxy.datatypes.data:Data" />
-    <datatype extension="bgzip" type="galaxy.datatypes.data:Data" />
+    <datatype extension="summary_tree" type="galaxy.datatypes.binary:Binary" subclass="True" />
+    <datatype extension="interval_index" type="galaxy.datatypes.binary:Binary" subclass="True" />
+    <datatype extension="tabix" type="galaxy.datatypes.binary:Binary" subclass="True" />
+    <datatype extension="bgzip" type="galaxy.datatypes.binary:Binary" subclass="True" />
     <!-- Start EMBOSS tools -->
     <datatype extension="acedb" type="galaxy.datatypes.data:Text"/>
     <datatype extension="asn1" type="galaxy.datatypes.data:Text"/>
diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index 59c4213f46e..938d1e37f22 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -26,7 +26,7 @@ class Binary( data.Data ):
         """Set the peek and blurb text"""
         if not dataset.dataset.purged:
             dataset.peek = 'binary data'
-            dataset.blurb = 'data'
+            dataset.blurb = data.nice_size( dataset.get_size() )
         else:
             dataset.peek = 'file does not exist'
             dataset.blurb = 'file purged from disk'
diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
index 9d3f8d02c6f..1dfec5b6fe2 100644
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -46,18 +46,22 @@ class Registry( object ):
                 try:
                     extension = elem.get( 'extension', None ) 
                     dtype = elem.get( 'type', None )
+                    type_extension = elem.get( 'type_extension', None )
                     mimetype = elem.get( 'mimetype', None )
                     display_in_upload = elem.get( 'display_in_upload', False )
                     make_subclass = galaxy.util.string_as_bool( elem.get( 'subclass', False ) )
-                    if extension and dtype:
-                        fields = dtype.split( ':' )
-                        datatype_module = fields[0]
-                        datatype_class_name = fields[1]
-                        fields = datatype_module.split( '.' )
-                        module = __import__( fields.pop(0) )
-                        for mod in fields:
-                            module = getattr( module, mod )
-                        datatype_class = getattr( module, datatype_class_name )
+                    if extension and ( dtype or type_extension ):
+                        if dtype:
+                            fields = dtype.split( ':' )
+                            datatype_module = fields[0]
+                            datatype_class_name = fields[1]
+                            fields = datatype_module.split( '.' )
+                            module = __import__( fields.pop(0) )
+                            for mod in fields:
+                                module = getattr( module, mod )
+                            datatype_class = getattr( module, datatype_class_name )
+                        elif type_extension:
+                            datatype_class = self.datatypes_by_extension[type_extension].__class__
                         if make_subclass:
                             datatype_class = type( datatype_class_name, (datatype_class,), {} )
                         self.datatypes_by_extension[extension] = datatype_class()

From f12a1c706166ea7bf60e90ef71af4562d5539acf Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Tue, 15 Nov 2011 14:50:08 -0500
Subject: [PATCH 196/362] A tool shed admin will now receive content alerts (as
 part of the alert message) for each file uploaded to a repository that
 contains either image content or html content if the admin has chosen to
 receive email alerts for changes to the repository.

---
 .../webapps/community/controllers/common.py   | 63 +++++++++++--------
 .../webapps/community/controllers/upload.py   | 40 ++++--------
 .../webapps/community/repository/upload.mako  |  8 ++-
 3 files changed, 57 insertions(+), 54 deletions(-)

diff --git a/lib/galaxy/webapps/community/controllers/common.py b/lib/galaxy/webapps/community/controllers/common.py
index 0f8464f298e..51f5131640d 100644
--- a/lib/galaxy/webapps/community/controllers/common.py
+++ b/lib/galaxy/webapps/community/controllers/common.py
@@ -26,6 +26,8 @@ Revision: ${revision}
 Change description:
 ${description}
 
+${content_alert_str}
+
 -----------------------------------------------------------------------------
 This change alert was sent from the Galaxy tool shed hosted on the server
 "${host}"
@@ -520,7 +522,7 @@ def get_configured_ui():
 def get_user( trans, id ):
     """Get a user from the database by id"""
     return trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( id ) )
-def handle_email_alerts( trans, repository ):
+def handle_email_alerts( trans, repository, content_alert_str='' ):
     repo_dir = repository.repo_path
     repo = hg.repository( get_configured_ui(), repo_dir )
     smtp_server = trans.app.config.smtp_server
@@ -541,14 +543,25 @@ def handle_email_alerts( trans, repository ):
             username = ctx.user().split()[0]
         except:
             username = ctx.user()
-        # Build the email message
+        # We'll use 2 template bodies because we only want to send content
+        # alerts to tool shed admin users.
+        admin_body = string.Template( email_alert_template ) \
+            .safe_substitute( host=trans.request.host,
+                              repository_name=repository.name,
+                              revision='%s:%s' %( str( ctx.rev() ), ctx ),
+                              display_date=display_date,
+                              description=ctx.description(),
+                              username=username,
+                              content_alert_str=content_alert_str )
         body = string.Template( email_alert_template ) \
             .safe_substitute( host=trans.request.host,
                               repository_name=repository.name,
                               revision='%s:%s' %( str( ctx.rev() ), ctx ),
                               display_date=display_date,
                               description=ctx.description(),
-                              username=username )
+                              username=username,
+                              content_alert_str='' )
+        admin_users = trans.app.config.get( "admin_users", "" ).split( "," )
         frm = email_from
         subject = "Galaxy tool shed repository update alert"
         email_alerts = from_json_string( repository.email_alerts )
@@ -556,7 +569,10 @@ def handle_email_alerts( trans, repository ):
             to = email.strip()
             # Send it
             try:
-                util.send_mail( frm, to, subject, body, trans.app.config )
+                if to in admin_users:
+                    util.send_mail( frm, to, subject, admin_body, trans.app.config )
+                else:
+                    util.send_mail( frm, to, subject, body, trans.app.config )
             except Exception, e:
                 log.exception( "An error occurred sending a tool shed repository update alert by email." )
 def update_for_browsing( trans, repository, current_working_dir, commit_message='' ):
@@ -567,30 +583,20 @@ def update_for_browsing( trans, repository, current_working_dir, commit_message=
     repo = hg.repository( get_configured_ui(), repo_dir )
     # The following will delete the disk copy of only the files in the repository.
     #os.system( 'hg update -r null > /dev/null 2>&1' )
-    repo.ui.pushbuffer()
     files_to_remove_from_disk = []
     files_to_commit = []
-    commands.status( repo.ui, repo, all=True )
-    status_and_file_names = repo.ui.popbuffer().strip().split( "\n" )
-    if status_and_file_names and status_and_file_names[ 0 ] not in [ '' ]:
-        # status_and_file_names looks something like:
-        # ['? README', '? tmap_tool/tmap-0.0.9.tar.gz', '? dna_filtering.py', 'C filtering.py', 'C filtering.xml']
-        # The codes used to show the status of files are:
-        # M = modified
-        # A = added
-        # R = removed
-        # C = clean
-        # ! = deleted, but still tracked
-        # ? = not tracked
-        # I = ignored
-        for status_and_file_name in status_and_file_names:
-            if status_and_file_name.startswith( '?' ) or status_and_file_name.startswith( 'I' ):
-                files_to_remove_from_disk.append( os.path.abspath( os.path.join( repo_dir, status_and_file_name.split()[1] ) ) )
-            elif status_and_file_name.startswith( 'M' ) or status_and_file_name.startswith( 'A' ) or status_and_file_name.startswith( 'R' ):
-                files_to_commit.append( os.path.abspath( os.path.join( repo_dir, status_and_file_name.split()[1] ) ) )
     # We may have files on disk in the repo directory that aren't being tracked, so they must be removed.
-    # We'll use mercurial's purge extension to do this.  Using this extension requires the following entry 
-    # in the repository's hgrc file which was not required for some time, so we'll add it if it's missing.
+    # The codes used to show the status of files are as follows.
+    # M = modified
+    # A = added
+    # R = removed
+    # C = clean
+    # ! = deleted, but still tracked
+    # ? = not tracked
+    # I = ignored
+    # We'll use mercurial's purge extension to remove untracked file.  Using this extension requires the
+    # following entry in the repository's hgrc file which was not required for some time, so we'll add it
+    # if it's missing.
     # [extensions]
     # hgext.purge=
     lines = repo.opener( 'hgrc', 'rb' ).readlines()
@@ -624,9 +630,14 @@ def update_for_browsing( trans, repository, current_working_dir, commit_message=
             commit_message = 'Committed changes to: %s' % ', '.join( files_to_commit )
         repo.dirstate.write()
         repo.commit( user=trans.user.username, text=commit_message )
+    cmd = 'hg update > /dev/null 2>&1'
     os.chdir( repo_dir )
-    os.system( 'hg update > /dev/null 2>&1' )
+    proc = subprocess.Popen( args=cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT )
+    return_code = proc.wait()
     os.chdir( current_working_dir )
+    if return_code != 0:
+        output = proc.stdout.read( 32768 )
+        log.debug( 'hg update > /dev/null 2>&1 failed in repository directory %s, reason: %s' % ( repo_dir, output ) )
 def load_tool( trans, config_file ):
     """
     Load a single tool from the file named by `config_file` and return 
diff --git a/lib/galaxy/webapps/community/controllers/upload.py b/lib/galaxy/webapps/community/controllers/upload.py
index cdcf6bc5e75..8e313bb25d9 100644
--- a/lib/galaxy/webapps/community/controllers/upload.py
+++ b/lib/galaxy/webapps/community/controllers/upload.py
@@ -101,12 +101,12 @@ class UploadController( BaseUIController ):
                         full_path = os.path.abspath( os.path.join( repo_dir, upload_point, uploaded_file_filename ) )
                     else:
                         full_path = os.path.abspath( os.path.join( repo_dir, uploaded_file_filename ) )
-                    # TODO: enhance this method to set a flag and alert an admin to review content since
-                    # the hard checks are too restrictive.
-                    #ok, message = self.__check_file_content( uploaded_file_name )
-                    #if ok:
                     # Move the uploaded file to the load_point within the repository hierarchy.
                     shutil.move( uploaded_file_name, full_path )
+                    if os.path.isfile( full_path ):
+                        content_alert_str = self.__check_file_content( full_path )
+                    else:
+                        content_alert_str = ''
                     commands.add( repo.ui, repo, full_path )
                     try:
                         commands.commit( repo.ui, repo, full_path, user=trans.user.username, message=commit_message )
@@ -128,7 +128,7 @@ class UploadController( BaseUIController ):
                         # Handle the special case where a xxx.loc.sample file is
                         # being uploaded by copying it to ~/tool-data/xxx.loc.
                         copy_sample_loc_file( trans, full_path )
-                    handle_email_alerts( trans, repository )
+                    handle_email_alerts( trans, repository, content_alert_str=content_alert_str )
                 if ok:
                     # Update the repository files for browsing.
                     update_for_browsing( trans, repository, current_working_dir, commit_message=commit_message )
@@ -194,18 +194,7 @@ class UploadController( BaseUIController ):
             tar.extractall( path=full_path )
             tar.close()
             uploaded_file.close()
-            """
-            # TODO: enhance this method to set a flag and alert an admin to review content since
-            # the hard checks are too restrictive.
-            for filename_in_archive in filenames_in_archive:
-                if os.path.isfile( filename_in_archive ):
-                    ok, message = self.__check_file_content( filename_in_archive )
-                    if not ok:
-                        # Refresh the repository files for browsing.
-                        current_working_dir = os.getcwd()
-                        update_for_browsing( trans, repository, current_working_dir )
-                        return False, message, []
-            """
+            content_alert_str = ''
             if remove_repo_files_not_in_tar and not repository.is_new:
                 # We have a repository that is not new (it contains files), so discover
                 # those files that are in the repository, but not in the uploaded archive.
@@ -250,6 +239,9 @@ class UploadController( BaseUIController ):
                                 # The directory is not empty
                                 pass
             for filename_in_archive in filenames_in_archive:
+                # Check file content to ensure it is appropriate.
+                if os.path.isfile( filename_in_archive ):
+                    content_alert_str += self.__check_file_content( filename_in_archive )
                 commands.add( repo.ui, repo, filename_in_archive )
                 if filename_in_archive.endswith( 'tool_data_table_conf.xml.sample' ):
                     # Handle the special case where a tool_data_table_conf.xml.sample
@@ -271,7 +263,7 @@ class UploadController( BaseUIController ):
                 # exception.  If this happens, we'll try the following.
                 repo.dirstate.write()
                 repo.commit( user=trans.user.username, text=commit_message )
-            handle_email_alerts( trans, repository )
+            handle_email_alerts( trans, repository, content_alert_str )
             return True, '', files_to_remove
     def uncompress( self, repository, uploaded_file_name, uploaded_file_filename, isgzip, isbz2 ):
         if isgzip:
@@ -349,15 +341,9 @@ class UploadController( BaseUIController ):
                 return False, message
         return True, ''
     def __check_file_content( self, file_path ):
-        return True, ''
         message = ''
-        ok = True
-        head, tail = os.path.split( file_path )
         if check_html( file_path ):
-            message = 'The file <b>%s</b> contains HTML content which cannot be uploaded to a Galaxy tool shed.' % str( tail )
-            ok = False
+            message = 'The file "%s" contains HTML content.\n' % str( file_path )
         elif check_image( file_path ):
-            # For now we won't allow images to be uploaded.
-            message = 'The file <b>%s</b> contains image content that cannot be uploaded to a Galaxy tool shed.' % str( tail )
-            ok = False
-        return ok, message
+            message = 'The file "%s" contains image content.\n' % str( file_path )
+        return message
diff --git a/templates/webapps/community/repository/upload.mako b/templates/webapps/community/repository/upload.mako
index b225c8f69e1..2b71e897ab7 100644
--- a/templates/webapps/community/repository/upload.mako
+++ b/templates/webapps/community/repository/upload.mako
@@ -64,7 +64,13 @@
 <div class="toolForm">
     <div class="toolFormTitle">Upload a single file or a tarball</div>
     <div class="toolFormBody">
-        ## TODO: nginx
+        <div class="form-row">
+            <div class="warningmessage">
+                Uploading may take a while, depending upon the size of the file.  Wait until a message is displayed in your 
+                browser after clicking the <b>Upload</b> button below.
+            </div>
+            <div style="clear: both"></div>
+        </div>
         <form id="upload_form" name="upload_form" action="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}" enctype="multipart/form-data" method="post">
             <div class="form-row">
                 <label>File:</label>

From be4b903d28584041d21b828322adea0b382e4633 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Tue, 15 Nov 2011 15:29:25 -0500
Subject: [PATCH 197/362] Rename toggle-contract to toggle in CSS so that CSS
 class name matches icon file name.

---
 static/june_2007_style/base.css.tmpl |  2 +-
 static/june_2007_style/blue/base.css |  4 ++--
 static/scripts/galaxy.base.js        |  2 +-
 static/scripts/trackster.js          |  6 +++---
 templates/embed_base.mako            |  2 +-
 templates/page/display.mako          | 10 +++++-----
 templates/root/history.mako          |  2 +-
 7 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/static/june_2007_style/base.css.tmpl b/static/june_2007_style/base.css.tmpl
index d135799caad..b0ac542efc2 100644
--- a/static/june_2007_style/base.css.tmpl
+++ b/static/june_2007_style/base.css.tmpl
@@ -865,7 +865,7 @@ div.permissionContainer {
     -sprite-group: fugue;
     -sprite-image: fugue/toggle-expand.png;
 }
-.icon-button.toggle-contract {
+.icon-button.toggle {
     -sprite-group: fugue;
     -sprite-image: fugue/toggle.png;
 }
diff --git a/static/june_2007_style/blue/base.css b/static/june_2007_style/blue/base.css
index 16d3898bded..b66e3fd146b 100644
--- a/static/june_2007_style/blue/base.css
+++ b/static/june_2007_style/blue/base.css
@@ -153,8 +153,8 @@ div.permissionContainer{padding-left:20px;}
 .icon-button.tag--plus{background:url(fugue.png) no-repeat 0px -52px;}
 .icon-button.toggle-expand{background:transparent url(../images/fugue/toggle-expand-bw.png) no-repeat;}
 .icon-button.toggle-expand:hover{background:url(fugue.png) no-repeat 0px -78px;}
-.icon-button.toggle-contract{background:transparent url(../images/fugue/toggle-bw.png) no-repeat;}
-.icon-button.toggle-contract:hover{background:url(fugue.png) no-repeat 0px -104px;}
+.icon-button.toggle{background:transparent url(../images/fugue/toggle-bw.png) no-repeat;}
+.icon-button.toggle:hover{background:url(fugue.png) no-repeat 0px -104px;}
 .icon-button.arrow-circle{background:url(fugue.png) no-repeat 0px -130px;}
 .icon-button.chevron{background:url(fugue.png) no-repeat 0px -156px;}
 .icon-button.bug{background:url(fugue.png) no-repeat 0px -182px;}
diff --git a/static/scripts/galaxy.base.js b/static/scripts/galaxy.base.js
index 41a9bd66b98..1c501c8533d 100644
--- a/static/scripts/galaxy.base.js
+++ b/static/scripts/galaxy.base.js
@@ -555,7 +555,7 @@ function init_history_items(historywrapper, noinit, nochanges) {
         });
         
         // Generate 'collapse all' link
-        $("#top-links > a.toggle-contract").click( function() {
+        $("#top-links > a.toggle").click( function() {
             var prefs = $.jStorage.get("history_expand_state");
             if (!prefs) { prefs = {}; }
             $( "div.historyItemBody:visible" ).each( function() {
diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index 7053975da8a..86afe0343be 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -2391,7 +2391,7 @@ var Track = function(name, view, container, show_header, prefs, data_url, data_q
         this.mode_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Set display mode")
                                   .addClass("icon-button chevron-expand").tipsy( {gravity: 's'} ).appendTo(this.icons_div);
         this.toggle_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Hide/show track content")
-                                    .addClass("icon-button toggle-contract").tipsy( {gravity: 's'} )
+                                    .addClass("icon-button toggle").tipsy( {gravity: 's'} )
                                     .appendTo(this.icons_div);
         this.settings_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Edit settings")
                                       .addClass("icon-button settings-icon").tipsy( {gravity: 's'} )
@@ -2439,11 +2439,11 @@ var Track = function(name, view, container, show_header, prefs, data_url, data_q
         // Toggle icon hides or shows the track content.
         this.toggle_icon.click( function() {
             if ( track.content_visible ) {
-                track.toggle_icon.addClass("toggle-expand").removeClass("toggle-contract");
+                track.toggle_icon.addClass("toggle-expand").removeClass("toggle");
                 track.hide_contents();
                 track.content_visible = false;
             } else {
-                track.toggle_icon.addClass("toggle-contract").removeClass("toggle-expand");
+                track.toggle_icon.addClass("toggle").removeClass("toggle-expand");
                 track.content_visible = true;
                 track.show_contents();
             }
diff --git a/templates/embed_base.mako b/templates/embed_base.mako
index b55ebb13b93..f5af1de33b3 100644
--- a/templates/embed_base.mako
+++ b/templates/embed_base.mako
@@ -44,7 +44,7 @@
     <div style="float: left">
         <a class="display_in_embed icon-button toggle-expand tooltip" item_id="${trans.security.encode_id( item.id )}" item_class="$item.__class__.__name__" href="${display_href}"
             title="Show ${item_display_name} content"></a>
-        <a class="toggle-contract icon-button tooltip" href="${display_href}" title="Hide ${item_display_name} content"></a>
+        <a class="toggle icon-button tooltip" href="${display_href}" title="Hide ${item_display_name} content"></a>
     </div>
     <div style="float: right;">
         ${self.render_item_links( item )}
diff --git a/templates/page/display.mako b/templates/page/display.mako
index b0cd25eee5b..93e639a54b1 100644
--- a/templates/page/display.mako
+++ b/templates/page/display.mako
@@ -26,7 +26,7 @@
                                 container.find(".summary-content").hide("fast");
                                 container.find(".item-content").html(item_content).show("fast");
                                 container.find(".toggle-expand").hide();
-                                container.find(".toggle-contract").show();
+                                container.find(".toggle").show();
 
                                 // Init needed for history items.
                                 init_history_items( container.find("div.historyItemWrapper"), "noinit", "nochanges" ); 
@@ -43,7 +43,7 @@
                         container.find(".summary-content").hide("fast");
                         container.find(".item-content").show("fast");
                         container.find(".toggle-expand").hide();
-                        container.find(".toggle-contract").show();
+                        container.find(".toggle").show();
                     }
                 };
             
@@ -51,7 +51,7 @@
                 var hide_embedded_item = function() {
                     container.find(".item-content").hide("fast");
                     container.find(".summary-content").show("fast");
-                    container.find(".toggle-contract").hide();
+                    container.find(".toggle").hide();
                     container.find(".toggle-expand").show();
                 };
             
@@ -63,7 +63,7 @@
                 });
             
                 // Setup toggle contract.
-                var toggle_contract = $(this).find('.toggle-contract');
+                var toggle_contract = $(this).find('.toggle');
                 toggle_contract.click( function() {
                     hide_embedded_item();
                     return false;
@@ -89,7 +89,7 @@
     ${parent.stylesheets()}
     ${h.css( "base", "history", "autocomplete_tagging" )}
     <style type="text/css">
-        .toggle-contract { display: none; }
+        .toggle { display: none; }
         .embedded-item h4 {
             margin: 0px;
         }
diff --git a/templates/root/history.mako b/templates/root/history.mako
index 63bf2bdc30f..fde1d565a58 100644
--- a/templates/root/history.mako
+++ b/templates/root/history.mako
@@ -432,7 +432,7 @@ div.form-row {
 <div id="top-links" class="historyLinks">
     
     <a title="${_('refresh')}" class="icon-button arrow-circle tooltip" href="${h.url_for('history', show_deleted=show_deleted)}"></a>
-    <a title='${_('collapse all')}' class='icon-button toggle-contract tooltip' href='#' style="display: none"></a>
+    <a title='${_('collapse all')}' class='icon-button toggle tooltip' href='#' style="display: none"></a>
     
     %if trans.get_user():
     <div style="width: 40px; float: right; white-space: nowrap;">

From 8da51093f4c567f6312676101bd75b260d20a857 Mon Sep 17 00:00:00 2001
From: Ross Lazarus <ross.lazarus@gmail.com>
Date: Wed, 16 Nov 2011 07:34:51 +1100
Subject: [PATCH 198/362] Fixes for the new horrible FastQC html layout. Now
 wastes a whole lot of space on the left with a fancy TOC - ugh. Test updated
 also.

---
 tools/rgenetics/rgFastQC.py  | 18 +++++++++---------
 tools/rgenetics/rgFastQC.xml |  2 +-
 2 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/tools/rgenetics/rgFastQC.py b/tools/rgenetics/rgFastQC.py
index 811ca375e27..64a35972033 100644
--- a/tools/rgenetics/rgFastQC.py
+++ b/tools/rgenetics/rgFastQC.py
@@ -91,21 +91,20 @@ class FastQC():
     def fix_fastqc(self,rep=[],flist=[],runlog=[]):
         """ add some of our stuff to the html
         """
-        bs = '</body></html>\n' # hope they don't change this
-        try:
-            bodyindex = rep.index(bs) # hope they don't change this
-        except:
-            bodyindex = len(rep) - 1
-        res = []
-        res.append('<table>\n')
+        bodyindex = len(rep) -1  # hope they don't change this
+        footrow = bodyindex - 1 
+        footer = rep[footrow]
+        rep = rep[:footrow] + rep[footrow+1:]
+        res = ['<div class="module"><h2>Files created by FastQC</h2><table cellspacing="2" cellpadding="2">\n']
         flist.sort()
         for i,f in enumerate(flist):
              if not(os.path.isdir(f)):
                  fn = os.path.split(f)[-1]
                  res.append('<tr><td><a href="%s">%s</a></td></tr>\n' % (fn,getFileString(fn, self.opts.outputdir)))
-        res.append('</table><p/>\n') 
+        res.append('</table>\n') 
         res.append('<a href="http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/">FastQC documentation and full attribution is here</a><br/><hr/>\n')
-        res.append('FastQC was run by Galaxy using the rgenetics rgFastQC wrapper - see http://rgenetics.org for details and licensing\n')
+        res.append('FastQC was run by Galaxy using the rgenetics rgFastQC wrapper - see http://rgenetics.org for details and licensing\n</div>')
+        res.append(footer)
         fixed = rep[:bodyindex] + res + rep[bodyindex:]
         return fixed # with our additions
 
@@ -147,3 +146,4 @@ if __name__ == '__main__':
     f.write(''.join(html))
     f.close()
     
+
diff --git a/tools/rgenetics/rgFastQC.xml b/tools/rgenetics/rgFastQC.xml
index cee79d861ae..4cb45cd220b 100644
--- a/tools/rgenetics/rgFastQC.xml
+++ b/tools/rgenetics/rgFastQC.xml
@@ -1,4 +1,4 @@
-<tool name="Fastqc: Fastqc QC" id="fastqc" version="0.2">
+<tool name="Fastqc: Fastqc QC" id="fastqc" version="0.3">
   <description>using FastQC from Babraham</description>
   <command interpreter="python">
     rgFastQC.py -i $input_file -d $html_file.files_path -o $html_file -n "$out_prefix" -f $input_file.ext -e ${GALAXY_DATA_INDEX_DIR}/shared/jars/FastQC/fastqc

From c8042d99521e8fb2773e6d97b0b873b9066d4488 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Tue, 15 Nov 2011 15:50:36 -0500
Subject: [PATCH 199/362] Fix bug in Trackster's 'Add Datasets to
 Visualization' button.

---
 static/scripts/trackster.js | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index 86afe0343be..c57b76bad31 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -909,7 +909,7 @@ extend( View.prototype, DrawableCollection.prototype, {
         this.content_div = this.viewport_container;
         is_container(this.viewport_container, view);
         // Introduction div shown when there are no tracks.
-        this.intro_div = $("<div/>").addClass("intro");
+        this.intro_div = $("<div/>").addClass("intro").appendTo(this.viewport_container).hide();
         var add_tracks_button = $("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function () {
             add_tracks();
         });
@@ -1077,10 +1077,10 @@ extend( View.prototype, DrawableCollection.prototype, {
     /** Add or remove intro div depending on view state. */
     update_intro_div: function() {
         if (this.drawables.length === 0) {
-            this.intro_div.appendTo(this.viewport_container);
+            this.intro_div.show();
         }
         else {
-            this.intro_div.remove();
+            this.intro_div.hide();
         }
     },
     update_location: function(low, high) {

From 09bcf6e95afd6de5a09231ed410d9e1fcedd755f Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Tue, 15 Nov 2011 17:24:38 -0500
Subject: [PATCH 200/362] Add VCF viewer for IGV.  Add necessary datatypes and
 converters to support this view (vcf_bgzip; vcf_bgzip to tabix).

---
 datatypes_conf.xml.sample                     |  8 +-
 display_applications/igv/bam.xml              | 55 ++++++++---
 display_applications/igv/vcf.xml              | 95 +++++++++++++++++++
 .../vcf_bgzip_to_tabix_converter.xml          | 14 +++
 .../converters/vcf_to_vcf_bgzip_converter.xml | 14 +++
 run.sh                                        |  1 +
 .../shared/igv/igv_build_sites.txt.sample     |  4 +
 7 files changed, 175 insertions(+), 16 deletions(-)
 create mode 100644 display_applications/igv/vcf.xml
 create mode 100644 lib/galaxy/datatypes/converters/vcf_bgzip_to_tabix_converter.xml
 create mode 100644 lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml
 create mode 100644 tool-data/shared/igv/igv_build_sites.txt.sample

diff --git a/datatypes_conf.xml.sample b/datatypes_conf.xml.sample
index eb2dbf5e276..cd87e71aae0 100644
--- a/datatypes_conf.xml.sample
+++ b/datatypes_conf.xml.sample
@@ -9,7 +9,7 @@
       <converter file="bam_to_summary_tree_converter.xml" target_datatype="summary_tree" depends_on="bai"/>
       <display file="ucsc/bam.xml" />
       <display file="ensembl/ensembl_bam.xml" />
-      <!-- <display file="igv/bam.xml" /> -->
+      <display file="igv/bam.xml" />
     </datatype>
     <datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true">
       <converter file="bed_to_gff_converter.xml" target_datatype="gff"/>
@@ -154,8 +154,10 @@
     <datatype extension="blastxml" type="galaxy.datatypes.xml:BlastXml" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="vcf" type="galaxy.datatypes.tabular:Vcf" display_in_upload="true">
       <converter file="vcf_to_bgzip_converter.xml" target_datatype="bgzip"/>
+      <converter file="vcf_to_vcf_bgzip_converter.xml" target_datatype="vcf_bgzip"/>
       <converter file="vcf_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
       <converter file="vcf_to_summary_tree_converter.xml" target_datatype="summary_tree"/>
+      <display file="igv/vcf.xml" />
     </datatype>
     <datatype extension="wsf" type="galaxy.datatypes.wsf:SnpFile" display_in_upload="true"/>
     <datatype extension="velvet" type="galaxy.datatypes.assembly:Velvet" display_in_upload="false"/>
@@ -168,6 +170,10 @@
     <datatype extension="interval_index" type="galaxy.datatypes.binary:Binary" subclass="True" />
     <datatype extension="tabix" type="galaxy.datatypes.binary:Binary" subclass="True" />
     <datatype extension="bgzip" type="galaxy.datatypes.binary:Binary" subclass="True" />
+    <datatype extension="vcf_bgzip" type_extension="bgzip" subclass="True" >
+      <display file="igv/vcf.xml" />
+      <converter file="vcf_bgzip_to_tabix_converter.xml" target_datatype="tabix"/>
+    </datatype>
     <!-- Start EMBOSS tools -->
     <datatype extension="acedb" type="galaxy.datatypes.data:Text"/>
     <datatype extension="asn1" type="galaxy.datatypes.data:Text"/>
diff --git a/display_applications/igv/bam.xml b/display_applications/igv/bam.xml
index 03c1bbf3543..cbe652f39e7 100644
--- a/display_applications/igv/bam.xml
+++ b/display_applications/igv/bam.xml
@@ -1,12 +1,32 @@
+<?xml version="1.0"?>
 <display id="igv_bam" version="1.0.0" name="display with IGV">
-    <link id="web" name="web">
-        <url>$jnlp.url</url>
-        <param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" strip_https="True" />
-        <param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" strip_https="True" />
-        <param type="template" name="jnlp" url="galaxy_${DATASET_HASH}.jnlp" viewable="True" strip_https="True" mimetype="application/x-java-jnlp-file">&lt;?xml version=&quot;1.0&quot; encoding=&quot;utf-8&quot;?&gt;
+    
+    <!-- Load links from file: one line to one link -->
+    <dynamic_links from_file="tool-data/shared/igv/igv_build_sites.txt" skip_startswith="#" id="0" name="1">
+        
+        <!-- Define parameters by column from file, allow splitting on builds -->
+        <dynamic_param name="site_id" value="0"/>
+        <dynamic_param name="site_name" value="1"/>
+        <dynamic_param name="site_link" value="2"/>
+        <dynamic_param name="site_dbkeys" value="3" split="True" separator="," />
+        <dynamic_param name="site_organisms" value="4" split="True" separator="," />
+        
+        <!-- Filter out some of the links based upon matching site_dbkeys to dataset dbkey -->
+        <filter>${dataset.dbkey in $site_dbkeys}</filter>
+        
+        <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
+        <url>${redirect_url}</url>
+        
+        <param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" />
+        <param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" />
+        <param type="template" name="site_organism" strip="True" >
+            $site_organisms[ $site_dbkeys.index( $bam_file.dbkey ) ]
+        </param>
+        
+        <param type="template" name="jnlp" url="galaxy_${DATASET_HASH}.jnlp" viewable="True" mimetype="application/x-java-jnlp-file">&lt;?xml version=&quot;1.0&quot; encoding=&quot;utf-8&quot;?&gt;
 &lt;jnlp
   spec=&quot;1.0+&quot;
-  codebase=&quot;http://www.broadinstitute.org/igvdata/jws/prod&quot;&gt;
+  codebase=&quot;${site_link}&quot;&gt;
   &lt;information&gt;
     &lt;title&gt;IGV 1.5&lt;/title&gt;
     &lt;vendor&gt;The Broad Institute&lt;/vendor&gt;
@@ -54,17 +74,22 @@
 
   &lt;application-desc main-class=&quot;org.broad.igv.ui.IGVMainFrame&quot;&gt;
      &lt;argument&gt;-g&lt;/argument&gt;
-     &lt;argument&gt;${bam_file.dbkey}&lt;/argument&gt;
+     &lt;argument&gt;${site_organism}&lt;/argument&gt;
      &lt;argument&gt;${bam_file.url}&lt;/argument&gt;
   &lt;/application-desc&gt;
 &lt;/jnlp&gt;
-
 		</param>
-	</link>
-		
-    <link id="local" name="local">
-        <url>http://localhost:60151/load?file=${qp($bam_file.url)}&amp;genome=${qp($bam_file.dbkey)}&amp;merge=true</url>
-        <param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" strip_https="True" />
-        <param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" strip_https="True" />
-	</link>
+        <param type="template" name="redirect_url" strip="True" >
+            #if $site_id.startswith( 'local_' )
+                ${site_link}?file=${bam_file.qp}&amp;genome=${site_organism}&amp;merge=true
+            #elif $site_id.startswith( 'web_link_' ):
+                ${site_link}?sessionURL=${bam_file.qp}&amp;genome=${site_organism}&amp;merge=true
+            #else:
+                ${jnlp.url}
+            #end if
+        </param>
+    </dynamic_links>
+    
+    
 </display>
+<!-- Dan Blankenberg -->
\ No newline at end of file
diff --git a/display_applications/igv/vcf.xml b/display_applications/igv/vcf.xml
new file mode 100644
index 00000000000..16ae71b749f
--- /dev/null
+++ b/display_applications/igv/vcf.xml
@@ -0,0 +1,95 @@
+<?xml version="1.0"?>
+<display id="igv_vcf" version="1.0.0" name="display with IGV">
+    
+    <!-- Load links from file: one line to one link -->
+    <dynamic_links from_file="tool-data/shared/igv/igv_build_sites.txt" skip_startswith="#" id="0" name="1">
+        
+        <!-- Define parameters by column from file, allow splitting on builds -->
+        <dynamic_param name="site_id" value="0"/>
+        <dynamic_param name="site_name" value="1"/>
+        <dynamic_param name="site_link" value="2"/>
+        <dynamic_param name="site_dbkeys" value="3" split="True" separator="," />
+        <dynamic_param name="site_organisms" value="4" split="True" separator="," />
+        
+        <!-- Filter out some of the links based upon matching site_dbkeys to dataset dbkey -->
+        <filter>${dataset.dbkey in $site_dbkeys}</filter>
+        
+        <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
+        <url>${redirect_url}</url>
+        
+        <param type="data" name="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz" format="vcf_bgzip" />
+        <param type="data" name="tabix_file" dataset="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz.tbi" format="tabix" />
+        <param type="template" name="site_organism" strip="True" >
+            $site_organisms[ $site_dbkeys.index( $bgzip_file.dbkey ) ]
+        </param>
+        
+        <param type="template" name="jnlp" url="galaxy_${DATASET_HASH}.jnlp" viewable="True" mimetype="application/x-java-jnlp-file">&lt;?xml version=&quot;1.0&quot; encoding=&quot;utf-8&quot;?&gt;
+&lt;jnlp
+  spec=&quot;1.0+&quot;
+  codebase=&quot;${site_link}&quot;&gt;
+  &lt;information&gt;
+    &lt;title&gt;IGV 1.5&lt;/title&gt;
+    &lt;vendor&gt;The Broad Institute&lt;/vendor&gt;
+    &lt;homepage href=&quot;http://www.broadinstitute.org/igv&quot;/&gt;
+    &lt;description&gt;IGV Software&lt;/description&gt;
+    &lt;description kind=&quot;short&quot;&gt;IGV&lt;/description&gt;
+  &lt;/information&gt;
+  &lt;security&gt;
+      &lt;all-permissions/&gt;
+  &lt;/security&gt;
+  &lt;resources&gt;
+  
+&lt;j2se version=&quot;1.5+&quot; initial-heap-size=&quot;256m&quot; max-heap-size=&quot;1100m&quot;/&gt;    
+	&lt;jar href=&quot;igv.jar&quot; download=&quot;eager&quot; main=&quot;true&quot;/&gt;
+    &lt;jar href=&quot;batik-codec.jar&quot; download=&quot;eager&quot;/&gt; 
+    &lt;property name=&quot;apple.laf.useScreenMenuBar&quot; value=&quot;true&quot;/&gt;
+    &lt;property name=&quot;com.apple.mrj.application.growbox.intrudes&quot; value=&quot;false&quot;/&gt;
+    &lt;property name=&quot;com.apple.mrj.application.live-resize&quot; value=&quot;true&quot;/&gt;
+    &lt;property name=&quot;com.apple.macos.smallTabs&quot; value=&quot;true&quot;/&gt;
+  &lt;/resources&gt;
+	
+    &lt;resources os=&quot;Mac&quot; arch=&quot;i386&quot;&gt;
+        &lt;property name=&quot;apple.awt.graphics.UseQuartz&quot; value=&quot;false&quot;/&gt;
+        &lt;nativelib href=&quot;hdfnative-macintel.jar&quot;/&gt; 
+    &lt;/resources&gt;
+
+    &lt;resources os=&quot;Mac&quot; arch=&quot;ppc&quot;&gt;
+        &lt;property name=&quot;apple.awt.graphics.UseQuartz&quot; value=&quot;false&quot;/&gt;
+        &lt;nativelib href=&quot;hdfnative-macppc.jar&quot;/&gt; 
+    &lt;/resources&gt;
+    
+    &lt;resources os=&quot;Mac&quot; arch=&quot;PowerPC&quot;&gt;
+        &lt;property name=&quot;apple.awt.graphics.UseQuartz&quot; value=&quot;false&quot;/&gt;
+        &lt;nativelib href=&quot;hdfnative-macppc.jar&quot;/&gt; 
+    &lt;/resources&gt;
+
+    &lt;resources os=&quot;Windows&quot;&gt;
+        &lt;property name=&quot;sun.java2d.noddraw&quot; value=&quot;true&quot;/&gt;
+        &lt;nativelib href=&quot;hdfnative-win.jar&quot;/&gt; 
+    &lt;/resources&gt;
+
+    &lt;resources os=&quot;Linux&quot;&gt;
+        &lt;nativelib href=&quot;hdfnative-linux64.jar&quot;/&gt; 
+    &lt;/resources&gt;
+
+  &lt;application-desc main-class=&quot;org.broad.igv.ui.IGVMainFrame&quot;&gt;
+     &lt;argument&gt;-g&lt;/argument&gt;
+     &lt;argument&gt;${site_organism}&lt;/argument&gt;
+     &lt;argument&gt;${bgzip_file.url}&lt;/argument&gt;
+  &lt;/application-desc&gt;
+&lt;/jnlp&gt;
+		</param>
+        <param type="template" name="redirect_url" strip="True" >
+            #if $site_id.startswith( 'local_' )
+                ${site_link}?file=${bgzip_file.qp}&amp;genome=${site_organism}&amp;merge=true
+            #elif $site_id.startswith( 'web_link_' ):
+                ${site_link}?sessionURL=${bgzip_file.qp}&amp;genome=${site_organism}&amp;merge=true
+            #else:
+                ${jnlp.url}
+            #end if
+        </param>
+    </dynamic_links>
+    
+    
+</display>
+<!-- Dan Blankenberg -->
\ No newline at end of file
diff --git a/lib/galaxy/datatypes/converters/vcf_bgzip_to_tabix_converter.xml b/lib/galaxy/datatypes/converters/vcf_bgzip_to_tabix_converter.xml
new file mode 100644
index 00000000000..c3acea1feac
--- /dev/null
+++ b/lib/galaxy/datatypes/converters/vcf_bgzip_to_tabix_converter.xml
@@ -0,0 +1,14 @@
+<tool id="CONVERTER_vcf_bgzip_to_tabix_0" name="Convert BGZ VCF to tabix" version="1.0.0" hidden="true">
+<!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
+  <command interpreter="python">interval_to_tabix_converter.py 'vcf' '' '$input1' '$output1'</command>
+  <inputs>
+    <page>
+        <param format="vcf_bgzip" name="input1" type="data" label="Choose BGZIP'd VCF file"/>
+    </page>
+   </inputs>
+  <outputs>
+    <data format="tabix" name="output1"/>
+  </outputs>
+  <help>
+  </help>
+</tool>
diff --git a/lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml b/lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml
new file mode 100644
index 00000000000..88e04b891c8
--- /dev/null
+++ b/lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml
@@ -0,0 +1,14 @@
+<tool id="CONVERTER_vcf_to_vcf_bgzip_0" name="Convert VCF to VCF_BGZIP" version="1.0.0" hidden="true">
+<!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
+  <command interpreter="python">bgzip.py vcf $input1 $output1</command>
+  <inputs>
+    <page>
+        <param format="vcf" name="input1" type="data" label="Choose Vcf file"/>
+    </page>
+   </inputs>
+  <outputs>
+    <data format="vcf_bgzip" name="output1"/>
+  </outputs>
+  <help>
+  </help>
+</tool>
diff --git a/run.sh b/run.sh
index b6804830d30..40093083dd5 100755
--- a/run.sh
+++ b/run.sh
@@ -15,6 +15,7 @@ SAMPLES="
     tool_sheds_conf.xml.sample
     universe_wsgi.ini.sample
     tool-data/shared/ucsc/builds.txt.sample
+    tool-data/shared/igv/igv_build_sites.txt.sample
     tool-data/*.sample
     static/welcome.html.sample
 "
diff --git a/tool-data/shared/igv/igv_build_sites.txt.sample b/tool-data/shared/igv/igv_build_sites.txt.sample
new file mode 100644
index 00000000000..ae08070dcbf
--- /dev/null
+++ b/tool-data/shared/igv/igv_build_sites.txt.sample
@@ -0,0 +1,4 @@
+#site_id	site_name	site_url	dbkey	ivg_build_name
+web_link_main	web current	http://www.broadinstitute.org/igv/projects/current/igv.php	hg19,hg_g1k_v37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum	hg19,b37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum
+#web_jnlp_1.5	web 1.5	http://www.broadinstitute.org/igvdata/jws/prod	hg19,hg_g1k_v37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum	hg19,b37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum
+local_default	local	http://localhost:60151/load	hg19,hg_g1k_v37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum	hg19,b37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum
\ No newline at end of file

From 8ed4d08bea018b5f2d47fde0c180c2ad69a79b64 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Tue, 15 Nov 2011 18:04:09 -0500
Subject: [PATCH 201/362] Trackster: significant refactoring to unify
 Drawables' HTML structure and also facilitate customization. Groups now use
 icons and can show/hide content.

---
 static/scripts/trackster.js | 286 +++++++++++++++++++++++-------------
 1 file changed, 181 insertions(+), 105 deletions(-)

diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index c57b76bad31..28633f8eecf 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -650,8 +650,13 @@ extend(ReferenceTrackDataManager.prototype, DataManager.prototype, Cache.prototy
  */
 
 /**
- * Base interface for all drawable objects. Drawable objects have a name and are
- * associated with a view and container. They optionally have a drag handle class. 
+ * Base class for all drawable objects. Drawable objects are associated with a view and live in a 
+ * container. They have the following HTML elements and structure:
+ *  <container_div>
+ *      <header_div>
+ *      <content_div>
+ *
+ * They optionally have a drag handle class. 
  */
 var Drawable = function(name, view, container, prefs, drag_handle_class) {
     if (!Drawable.id_counter) { Drawable.id_counter = 0; }
@@ -672,6 +677,33 @@ var Drawable = function(name, view, container, prefs, drag_handle_class) {
     this.prefs = this.config.values;
     this.drag_handle_class = drag_handle_class;
     this.is_overview = false;
+    
+    // FIXME: this should be a saved setting
+    this.content_visible = true;
+    
+    // Build Drawable HTML and behaviors.
+    this.container_div = this.build_container_div();
+    this.header_div = this.build_header_div();
+    
+    if (this.header_div) { 
+        this.container_div.append(this.header_div);
+        
+        this.icons_div = this.build_icons_div().hide();
+        this.header_div.append(this.icons_div);
+        
+        // Suppress double clicks in header so that they do not impact viz.
+        this.header_div.dblclick( function(e) { e.stopPropagation(); } );
+        
+        // Show icons when users is hovering over track.
+        var drawable = this;
+        this.container_div.hover(
+            function() { drawable.icons_div.show(); }, 
+            function() { drawable.icons_div.hide(); }
+        );
+        
+        // Needed for floating elts in header.
+        $("<div style='clear: both'/>").appendTo(this.container_div);
+    }
 };
 
 extend(Drawable.prototype, {
@@ -707,7 +739,31 @@ extend(Drawable.prototype, {
             view.update_intro_div();
             view.has_changes = true;
         });
-    }
+    },
+    /**
+     * Build drawable's container div; this is the parent div for all drawable's elements.
+     */ 
+    build_container_div: function() {},
+    /**
+     * Build drawable's header div.
+     */
+    build_header_div: function() {},
+    /**
+     * Build drawable's icons div.
+     */
+    build_icons_div: function() {},
+    /**
+     * Update icons.
+     */
+    update_icons: function() {},
+    /**
+     * Hide drawable's contents.
+     */
+    hide_contents: function () {},
+    /**
+     * Show drawable's contents.
+     */
+    show_contents: function() {}
 });
 
 /**
@@ -805,36 +861,54 @@ extend(DrawableCollection.prototype, Drawable.prototype, {
 var DrawableGroup = function(name, view, container, prefs) {
     DrawableCollection.call(this, "DrawableGroup", name, view, container, prefs, "group-handle");
         
-    // HTML elements.
-    this.container_div = $("<div/>").addClass("group").attr("id", "group_" + this.id).appendTo(this.container.content_div);
-    this.header_div = $("<div/>").addClass("track-header").appendTo(this.container_div);
-    this.header_div.append($("<div/>").addClass(this.drag_handle_class));
-    this.name_div = $("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);    
-    this.content_div = $("<div/>").addClass("content-div").attr("id", "group_" + this.id + "_content_div").appendTo(this.container_div);
-    
     // Set up containers/moving for group: register both container_div and content div as container
     // because both are used as containers (container div to recognize container, content_div to 
     // store elements). Group can be moved.
+    this.content_div = $("<div/>").addClass("content-div").attr("id", "group_" + this.id + "_content_div").appendTo(this.container_div);
     is_container(this.container_div, this);
     is_container(this.content_div, this);
     moveable(this.container_div, this.drag_handle_class, ".group", this);
-    
-    this.update_icons();
 };
 
 extend(DrawableGroup.prototype, Drawable.prototype, DrawableCollection.prototype, {
-    /**
-     * Make popup menu for group.
-     */
-    update_icons: function() {
+    build_container_div: function() {
+        return $("<div/>").addClass("group").attr("id", "group_" + this.id).appendTo(this.container.content_div);
+    },
+    build_header_div: function() {
+        var header_div = $("<div/>").addClass("track-header");
+        header_div.append($("<div/>").addClass(this.drag_handle_class));
+        this.name_div = $("<div/>").addClass("track-name").text(this.name).appendTo(header_div);
+        return header_div;
+    },
+    build_icons_div: function() {
+        var icons_div = $("<div/>").css("float", "left");
+
+        this.toggle_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Hide/show group content")
+                                    .addClass("icon-button toggle").tipsy( {gravity: 's'} )
+                                    .appendTo(icons_div);
+        this.settings_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Edit settings")
+                                      .addClass("icon-button settings-icon").tipsy( {gravity: 's'} )
+                                      .appendTo(icons_div);
+        this.remove_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Remove")
+                                    .addClass("icon-button remove-icon").tipsy( {gravity: 's'} )
+                                    .appendTo(icons_div);
         var group = this;
-        
-        var group_dropdown = {};
-                
-        //
-        // Edit config option.
-        //
-        group_dropdown["Edit configuration"] = function() {
+
+        // Toggle icon hides or shows the group content.
+        this.toggle_icon.click( function() {
+            if ( group.content_visible ) {
+                group.toggle_icon.addClass("toggle-expand").removeClass("toggle");
+                group.hide_contents();
+                group.content_visible = false;
+            } else {
+                group.toggle_icon.addClass("toggle").removeClass("toggle-expand");
+                group.content_visible = true;
+                group.show_contents();
+            }
+        });
+
+        // Clicking on settings icon opens group config.
+        this.settings_icon.click( function() {
             var cancel_fn = function() { hide_modal(); $(window).unbind("keypress.check_enter_esc"); },
                 ok_fn = function() { 
                     group.config.update_from_form( $(".dialog-box") );
@@ -854,16 +928,25 @@ extend(DrawableGroup.prototype, Drawable.prototype, DrawableCollection.prototype
                 "Cancel": cancel_fn,
                 "OK": ok_fn
             });
-        };
+        });
         
-        //
-        // Remove option.
-        //
-        group_dropdown.Remove = function() {
+        // Clicking on remove icon removes group.
+        this.remove_icon.click( function() {
+            // Tipsy for remove icon must be deleted when group is deleted.
+            $(".tipsy").remove();
             group.remove();
-        };
+        });
         
-        make_popupmenu(group.name_div, group_dropdown);
+        return icons_div;        
+    },
+    hide_contents : function () {
+        this.content_div.hide();
+    },
+    show_contents : function() {
+        // Show the contents div and labels (if present)
+        this.content_div.show();
+        // Request a redraw of the content
+        this.request_draw();
     }
 });
 
@@ -2356,7 +2439,7 @@ FeatureTrackTile.prototype.predisplay_actions = function() {
  * -------> ReadTrack
  * -------> VcfTrack
  */
-var Track = function(name, view, container, show_header, prefs, data_url, data_query_wait) {
+var Track = function(name, view, container, prefs, data_url, data_query_wait) {
     // For now, track's container is always view.
     Drawable.call(this, name, view, container, {}, "draghandle");
     
@@ -2368,58 +2451,59 @@ var Track = function(name, view, container, show_header, prefs, data_url, data_q
     this.data_query_wait = (data_query_wait ? data_query_wait : DEFAULT_DATA_QUERY_WAIT);
     this.dataset_check_url = converted_datasets_state_url;
 
-    // FIXME: this should be a saved setting
-    this.content_visible = true;
-
     if (!Track.id_counter) { Track.id_counter = 0; }
     this.id = Track.id_counter++;
-    
+        
     //
-    // Create HTML element structure for track.
+    // Create content div, which is where track is displayed.
     //
-    this.container_div = $("<div />").addClass('track').attr("id", "track_" + this.id).css("position", "relative");
-    
-    // Create and initialize track header and icons.
-    if (show_header) {
-        this.header_div = $("<div class='track-header'/>").appendTo(this.container_div);
-        if (this.view.editor) { this.drag_div = $("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div); }
-        this.name_div = $("<div/>").addClass("track-name").appendTo(this.header_div).text(this.name)
+    this.content_div = $("<div class='track-content'>").appendTo(this.container_div);
+    this.container.content_div.append(this.container_div);
+};
+extend(Track.prototype, Drawable.prototype, {
+    build_container_div: function () {
+        return $("<div/>").addClass('track').attr("id", "track_" + this.id).css("position", "relative");
+    },
+    build_header_div: function() {
+        var header_div = $("<div class='track-header'/>");
+        if (this.view.editor) { this.drag_div = $("<div/>").addClass(this.drag_handle_class).appendTo(header_div); }
+        this.name_div = $("<div/>").addClass("track-name").appendTo(header_div).text(this.name)
                         .attr( "id", this.name.replace(/\s+/g,'-').replace(/[^a-zA-Z0-9\-]/g,'').toLowerCase() );
-        this.icons_div = $("<div/>").css("float", "left").appendTo(this.header_div).hide();
-    
+        return header_div;
+    },
+    build_icons_div: function() {
+        var icons_div = $("<div/>").css("float", "left");
+
         // Track icons.
         this.mode_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Set display mode")
-                                  .addClass("icon-button chevron-expand").tipsy( {gravity: 's'} ).appendTo(this.icons_div);
+                                  .addClass("icon-button chevron-expand").tipsy( {gravity: 's'} ).appendTo(icons_div);
         this.toggle_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Hide/show track content")
                                     .addClass("icon-button toggle").tipsy( {gravity: 's'} )
-                                    .appendTo(this.icons_div);
+                                    .appendTo(icons_div);
         this.settings_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Edit settings")
                                       .addClass("icon-button settings-icon").tipsy( {gravity: 's'} )
-                                      .appendTo(this.icons_div);
+                                      .appendTo(icons_div);
         this.overview_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Set as overview")
                                       .addClass("icon-button overview-icon").tipsy( {gravity: 's'} )
-                                      .appendTo(this.icons_div);
+                                      .appendTo(icons_div);
         this.filters_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Filters")
                                      .addClass("icon-button filters-icon").tipsy( {gravity: 's'} )
-                                     .appendTo(this.icons_div).hide();
+                                     .appendTo(icons_div).hide();
         this.tools_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Tools")
                                    .addClass("icon-button tools-icon").tipsy( {gravity: 's'} )
-                                   .appendTo(this.icons_div).hide();
+                                   .appendTo(icons_div).hide();
         this.remove_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Remove")
                                     .addClass("icon-button remove-icon").tipsy( {gravity: 's'} )
-                                    .appendTo(this.icons_div);
+                                    .appendTo(icons_div);
         var track = this;
-                    
-        // Suppress double clicks in header so that they do not impact viz.
-        this.header_div.dblclick( function(e) { e.stopPropagation(); } );
-        
+
         // Set up behavior for modes popup.
         if (track.display_modes !== undefined) {
             var init_mode = (track.config && track.config.values['mode'] ? 
                              track.config.values['mode'] : track.display_modes[0]);
             track.mode = init_mode;
             this.mode_icon.attr("title", "Set display mode (now: " + track.mode + ")");
-            
+
             var mode_mapping = {};
             for (var i = 0, len = track.display_modes.length; i < len; i++) {
                 var mode = track.display_modes[i];
@@ -2432,7 +2516,7 @@ var Track = function(name, view, container, show_header, prefs, data_url, data_q
                         track.container_div.mouseleave(function() { track.icons_div.hide(); } ); };
                 }(mode);
             }
-            
+
             make_popupmenu(this.mode_icon, mode_mapping);
         }
 
@@ -2448,7 +2532,7 @@ var Track = function(name, view, container, show_header, prefs, data_url, data_q
                 track.show_contents();
             }
         });
-        
+
         // Clicking on settings icon opens track config.
         this.settings_icon.click( function() {
             var cancel_fn = function() { hide_modal(); $(window).unbind("keypress.check_enter_esc"); },
@@ -2471,22 +2555,22 @@ var Track = function(name, view, container, show_header, prefs, data_url, data_q
                 "OK": ok_fn
             });
         });
-        
+
         this.overview_icon.click( function() {
             track.view.set_overview(track);
         });
-                
+
         this.filters_icon.click( function() {
             // TODO: update tipsy text.            
             track.filters_div.toggle();
             track.filters_manager.reset_filters();
         });
-        
+
         this.tools_icon.click( function() {
             // TODO: update tipsy text.
-            
+
             track.dynamic_tool_div.toggle();
-            
+
             // Update track name.
             if (track.dynamic_tool_div.is(":visible")) {
                 track.set_name(track.name + track.tool_region_and_parameters_str());
@@ -2497,29 +2581,39 @@ var Track = function(name, view, container, show_header, prefs, data_url, data_q
             // HACK: name change modifies icon placement, which leaves tooltip incorrectly placed.
             $(".tipsy").remove();
         });
-        
+
         // Clicking on remove icon removes track.
         this.remove_icon.click( function() {
             // Tipsy for remove icon must be deleted when track is deleted.
             $(".tipsy").remove();
             track.remove();
         });
-                
-        // Show icons when users is hovering over track.
-        this.container_div.hover( function() { track.icons_div.show(); }, function() { track.icons_div.hide(); } );
         
-        // Needed for floating elts in header.
-        $("<div style='clear: both'/>").appendTo(this.container_div);
-    }
-    
-    //
-    // Create content div, which is where track is displayed.
-    //
-    this.content_div = $("<div class='track-content'>").appendTo(this.container_div);
-    this.container.content_div.append(this.container_div);
-};
-extend(Track.prototype, Drawable.prototype, {
-    /** Returns track type. */
+        return icons_div;  
+    },
+    /**
+     * Hide any elements that are part of the tracks contents area. Should
+     * remove as approprite, the track will be redrawn by show_contents.
+     */
+    hide_contents : function () {
+        // Clear contents by removing any elements that are contained in
+        // the tracks content_div
+        this.content_div.children().remove();
+        // Hide the content div
+        this.content_div.hide();
+        // And any y axis labels (common to several track types)
+        this.container_div.find(".yaxislabel, .track-resize").hide()
+    },
+    show_contents : function() {
+        // Show the contents div and labels (if present)
+        this.content_div.show();
+        this.container_div.find(".yaxislabel, .track-resize").show()
+        // Request a redraw of the content
+        this.request_draw();
+    },
+    /** 
+     * Returns track type. 
+     */
     get_type: function() {
         // Order is important: start with most-specific classes and go up the track hierarchy.
         if (this instanceof LabelTrack) {
@@ -2611,34 +2705,14 @@ extend(Track.prototype, Drawable.prototype, {
         
         this.update_icons();
     },
-    /**
-     * Hide any elements that are part of the tracks contents area. Should
-     * remove as approprite, the track will be redrawn by show_contents.
-     */
-    hide_contents : function () {
-        // Clear contents by removing any elements that are contained in
-        // the tracks content_div
-        this.content_div.children().remove();
-        // Hide the content div
-        this.content_div.hide();
-        // And any y axis labels (common to several track types)
-        this.container_div.find(".yaxislabel, .track-resize").hide()
-    },
-    show_contents : function() {
-        // Show the contents div and labels (if present)
-        this.content_div.show();
-        this.container_div.find(".yaxislabel, .track-resize").show()
-        // Request a redraw of the content
-        this.request_draw();
-    },
     /**
      * Additional initialization required before drawing track for the first time.
      */
     predraw_init: function() {}
 });
 
-var TiledTrack = function(name, view, container, show_header, prefs, filters_list, tool_dict) {
-    Track.call(this, name, view, container, show_header, prefs);
+var TiledTrack = function(name, view, container, prefs, filters_list, tool_dict) {
+    Track.call(this, name, view, container, prefs);
 
     var track = this,
         view = track.view;
@@ -3031,6 +3105,7 @@ var LabelTrack = function (view, container) {
     this.container_div.addClass( "label-track" );
 };
 extend(LabelTrack.prototype, Track.prototype, {
+    build_header_div: function() {},
     init: function() {
         // Enable by default because there should always be data when drawing track.
         this.enabled = true;  
@@ -3057,7 +3132,7 @@ extend(LabelTrack.prototype, Track.prototype, {
 });
 
 var ReferenceTrack = function (view) {
-    TiledTrack.call(this, "reference", view, { content_div: view.top_labeltrack }, false, {});
+    TiledTrack.call(this, "reference", view, { content_div: view.top_labeltrack }, {});
     
     view.reference_track = this;
     this.left_offset = 200;
@@ -3072,6 +3147,7 @@ var ReferenceTrack = function (view) {
     this.tile_cache = new Cache(CACHED_TILES_LINE);
 };
 extend(ReferenceTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
+    build_header_div: function() {},
     init: function() {
         // Enable by default because there should always be data when drawing track.
         this.enabled = true;  
@@ -3109,7 +3185,7 @@ var LineTrack = function (name, view, container, hda_ldda, dataset_id, prefs) {
     var track = this;
     this.display_modes = ["Histogram", "Line", "Filled", "Intensity"];
     this.mode = "Histogram";
-    TiledTrack.call( this, name, view, container, true, prefs );
+    TiledTrack.call( this, name, view, container, prefs );
    
     this.min_height_px = 16; 
     this.max_height_px = 400; 
@@ -3269,7 +3345,7 @@ var FeatureTrack = function(name, view, container, hda_ldda, dataset_id, prefs,
     //
     // Initialization.
     //    
-    TiledTrack.call(this, name, view, container, true, prefs, filters, tool);
+    TiledTrack.call(this, name, view, container, prefs, filters, tool);
 
     // Define and restore track configuration.
     this.config = new DrawableConfig( {

From 384b303686d9e83c2b33603b085b40ef464e2f12 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Wed, 16 Nov 2011 09:50:34 -0500
Subject: [PATCH 202/362] Add EMBOSS citation to EMBOSS tools.

---
 tools/emboss_5/emboss_antigenic.xml      | 6 ++++--
 tools/emboss_5/emboss_backtranseq.xml    | 6 ++++--
 tools/emboss_5/emboss_banana.xml         | 6 ++++--
 tools/emboss_5/emboss_biosed.xml         | 6 ++++--
 tools/emboss_5/emboss_btwisted.xml       | 6 ++++--
 tools/emboss_5/emboss_cai.xml            | 6 ++++--
 tools/emboss_5/emboss_cai_custom.xml     | 6 ++++--
 tools/emboss_5/emboss_chaos.xml          | 6 ++++--
 tools/emboss_5/emboss_charge.xml         | 6 ++++--
 tools/emboss_5/emboss_checktrans.xml     | 6 ++++--
 tools/emboss_5/emboss_chips.xml          | 6 ++++--
 tools/emboss_5/emboss_cirdna.xml         | 6 ++++--
 tools/emboss_5/emboss_codcmp.xml         | 6 ++++--
 tools/emboss_5/emboss_coderet.xml        | 6 ++++--
 tools/emboss_5/emboss_compseq.xml        | 6 ++++--
 tools/emboss_5/emboss_cpgplot.xml        | 6 ++++--
 tools/emboss_5/emboss_cpgreport.xml      | 6 ++++--
 tools/emboss_5/emboss_cusp.xml           | 6 ++++--
 tools/emboss_5/emboss_cutseq.xml         | 6 ++++--
 tools/emboss_5/emboss_dan.xml            | 6 ++++--
 tools/emboss_5/emboss_degapseq.xml       | 6 ++++--
 tools/emboss_5/emboss_descseq.xml        | 6 ++++--
 tools/emboss_5/emboss_diffseq.xml        | 6 ++++--
 tools/emboss_5/emboss_digest.xml         | 6 ++++--
 tools/emboss_5/emboss_dotmatcher.xml     | 6 ++++--
 tools/emboss_5/emboss_dotpath.xml        | 6 ++++--
 tools/emboss_5/emboss_dottup.xml         | 6 ++++--
 tools/emboss_5/emboss_dreg.xml           | 6 ++++--
 tools/emboss_5/emboss_einverted.xml      | 6 ++++--
 tools/emboss_5/emboss_epestfind.xml      | 6 ++++--
 tools/emboss_5/emboss_equicktandem.xml   | 6 ++++--
 tools/emboss_5/emboss_est2genome.xml     | 6 ++++--
 tools/emboss_5/emboss_etandem.xml        | 6 ++++--
 tools/emboss_5/emboss_extractfeat.xml    | 2 ++
 tools/emboss_5/emboss_extractseq.xml     | 6 ++++--
 tools/emboss_5/emboss_freak.xml          | 6 ++++--
 tools/emboss_5/emboss_fuzznuc.xml        | 6 ++++--
 tools/emboss_5/emboss_fuzzpro.xml        | 6 ++++--
 tools/emboss_5/emboss_fuzztran.xml       | 6 ++++--
 tools/emboss_5/emboss_garnier.xml        | 6 ++++--
 tools/emboss_5/emboss_geecee.xml         | 6 ++++--
 tools/emboss_5/emboss_getorf.xml         | 6 ++++--
 tools/emboss_5/emboss_helixturnhelix.xml | 6 ++++--
 tools/emboss_5/emboss_hmoment.xml        | 6 ++++--
 tools/emboss_5/emboss_iep.xml            | 6 ++++--
 tools/emboss_5/emboss_infoseq.xml        | 6 ++++--
 tools/emboss_5/emboss_isochore.xml       | 2 ++
 tools/emboss_5/emboss_lindna.xml         | 6 ++++--
 tools/emboss_5/emboss_marscan.xml        | 6 ++++--
 tools/emboss_5/emboss_maskfeat.xml       | 6 ++++--
 tools/emboss_5/emboss_maskseq.xml        | 6 ++++--
 tools/emboss_5/emboss_matcher.xml        | 6 ++++--
 tools/emboss_5/emboss_megamerger.xml     | 6 ++++--
 tools/emboss_5/emboss_merger.xml         | 6 ++++--
 tools/emboss_5/emboss_msbar.xml          | 6 ++++--
 tools/emboss_5/emboss_needle.xml         | 6 ++++--
 tools/emboss_5/emboss_newcpgreport.xml   | 6 ++++--
 tools/emboss_5/emboss_newcpgseek.xml     | 6 ++++--
 tools/emboss_5/emboss_newseq.xml         | 6 ++++--
 tools/emboss_5/emboss_noreturn.xml       | 6 ++++--
 tools/emboss_5/emboss_notseq.xml         | 6 ++++--
 tools/emboss_5/emboss_nthseq.xml         | 6 ++++--
 tools/emboss_5/emboss_octanol.xml        | 2 ++
 tools/emboss_5/emboss_oddcomp.xml        | 6 ++++--
 tools/emboss_5/emboss_palindrome.xml     | 6 ++++--
 tools/emboss_5/emboss_pasteseq.xml       | 6 ++++--
 tools/emboss_5/emboss_patmatdb.xml       | 6 ++++--
 tools/emboss_5/emboss_pepcoil.xml        | 6 ++++--
 tools/emboss_5/emboss_pepinfo.xml        | 6 ++++--
 tools/emboss_5/emboss_pepnet.xml         | 6 ++++--
 tools/emboss_5/emboss_pepstats.xml       | 6 ++++--
 tools/emboss_5/emboss_pepwheel.xml       | 6 ++++--
 tools/emboss_5/emboss_pepwindow.xml      | 6 ++++--
 tools/emboss_5/emboss_pepwindowall.xml   | 6 ++++--
 tools/emboss_5/emboss_plotcon.xml        | 6 ++++--
 tools/emboss_5/emboss_plotorf.xml        | 6 ++++--
 tools/emboss_5/emboss_polydot.xml        | 6 ++++--
 tools/emboss_5/emboss_preg.xml           | 6 ++++--
 tools/emboss_5/emboss_prettyplot.xml     | 6 ++++--
 tools/emboss_5/emboss_prettyseq.xml      | 6 ++++--
 tools/emboss_5/emboss_primersearch.xml   | 6 ++++--
 tools/emboss_5/emboss_revseq.xml         | 6 ++++--
 tools/emboss_5/emboss_seqmatchall.xml    | 6 ++++--
 tools/emboss_5/emboss_seqret.xml         | 6 ++++--
 tools/emboss_5/emboss_showfeat.xml       | 6 ++++--
 tools/emboss_5/emboss_shuffleseq.xml     | 6 ++++--
 tools/emboss_5/emboss_sigcleave.xml      | 6 ++++--
 tools/emboss_5/emboss_sirna.xml          | 6 ++++--
 tools/emboss_5/emboss_sixpack.xml        | 6 ++++--
 tools/emboss_5/emboss_skipseq.xml        | 6 ++++--
 tools/emboss_5/emboss_splitter.xml       | 6 ++++--
 tools/emboss_5/emboss_supermatcher.xml   | 6 ++++--
 tools/emboss_5/emboss_syco.xml           | 6 ++++--
 tools/emboss_5/emboss_tcode.xml          | 6 ++++--
 tools/emboss_5/emboss_textsearch.xml     | 6 ++++--
 tools/emboss_5/emboss_tmap.xml           | 6 ++++--
 tools/emboss_5/emboss_tranalign.xml      | 6 ++++--
 tools/emboss_5/emboss_transeq.xml        | 6 ++++--
 tools/emboss_5/emboss_trimest.xml        | 6 ++++--
 tools/emboss_5/emboss_trimseq.xml        | 6 ++++--
 tools/emboss_5/emboss_twofeat.xml        | 6 ++++--
 tools/emboss_5/emboss_union.xml          | 6 ++++--
 tools/emboss_5/emboss_vectorstrip.xml    | 6 ++++--
 tools/emboss_5/emboss_water.xml          | 6 ++++--
 tools/emboss_5/emboss_wobble.xml         | 6 ++++--
 tools/emboss_5/emboss_wordcount.xml      | 6 ++++--
 tools/emboss_5/emboss_wordmatch.xml      | 6 ++++--
 107 files changed, 422 insertions(+), 208 deletions(-)

diff --git a/tools/emboss_5/emboss_antigenic.xml b/tools/emboss_5/emboss_antigenic.xml
index 776cd01e128..50dfdb53783 100644
--- a/tools/emboss_5/emboss_antigenic.xml
+++ b/tools/emboss_5/emboss_antigenic.xml
@@ -48,8 +48,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
     
   </help>
diff --git a/tools/emboss_5/emboss_backtranseq.xml b/tools/emboss_5/emboss_backtranseq.xml
index edca79a3f7e..b2ba60beb62 100644
--- a/tools/emboss_5/emboss_backtranseq.xml
+++ b/tools/emboss_5/emboss_backtranseq.xml
@@ -219,8 +219,10 @@ The input dataset needs to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_banana.xml b/tools/emboss_5/emboss_banana.xml
index 5be4616bdff..9948d6f6907 100644
--- a/tools/emboss_5/emboss_banana.xml
+++ b/tools/emboss_5/emboss_banana.xml
@@ -23,8 +23,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_biosed.xml b/tools/emboss_5/emboss_biosed.xml
index 7a41b0cfe28..dd516869ee1 100644
--- a/tools/emboss_5/emboss_biosed.xml
+++ b/tools/emboss_5/emboss_biosed.xml
@@ -72,8 +72,10 @@ The input dataset needs to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_btwisted.xml b/tools/emboss_5/emboss_btwisted.xml
index ae1df7a1de5..d363ec80f77 100644
--- a/tools/emboss_5/emboss_btwisted.xml
+++ b/tools/emboss_5/emboss_btwisted.xml
@@ -23,8 +23,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_cai.xml b/tools/emboss_5/emboss_cai.xml
index ca3914d0903..0d9bb463809 100644
--- a/tools/emboss_5/emboss_cai.xml
+++ b/tools/emboss_5/emboss_cai.xml
@@ -184,8 +184,10 @@ The input dataset needs to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_cai_custom.xml b/tools/emboss_5/emboss_cai_custom.xml
index f498953bd24..3e6572717f0 100644
--- a/tools/emboss_5/emboss_cai_custom.xml
+++ b/tools/emboss_5/emboss_cai_custom.xml
@@ -26,8 +26,10 @@ The input dataset needs to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_chaos.xml b/tools/emboss_5/emboss_chaos.xml
index 45094d3a1d2..2e36f52a10a 100644
--- a/tools/emboss_5/emboss_chaos.xml
+++ b/tools/emboss_5/emboss_chaos.xml
@@ -22,8 +22,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_charge.xml b/tools/emboss_5/emboss_charge.xml
index 7918458d444..158bbb72bb0 100644
--- a/tools/emboss_5/emboss_charge.xml
+++ b/tools/emboss_5/emboss_charge.xml
@@ -34,8 +34,10 @@ The input dataset needs to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_checktrans.xml b/tools/emboss_5/emboss_checktrans.xml
index 49282da99be..dfc6e5d74d3 100644
--- a/tools/emboss_5/emboss_checktrans.xml
+++ b/tools/emboss_5/emboss_checktrans.xml
@@ -86,8 +86,10 @@ The input dataset needs to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_chips.xml b/tools/emboss_5/emboss_chips.xml
index 5e45c496699..2a280c3361c 100644
--- a/tools/emboss_5/emboss_chips.xml
+++ b/tools/emboss_5/emboss_chips.xml
@@ -29,8 +29,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_cirdna.xml b/tools/emboss_5/emboss_cirdna.xml
index 47d2b9ed465..ce92358d017 100644
--- a/tools/emboss_5/emboss_cirdna.xml
+++ b/tools/emboss_5/emboss_cirdna.xml
@@ -22,8 +22,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_codcmp.xml b/tools/emboss_5/emboss_codcmp.xml
index ea43f755b29..9ef6063a358 100644
--- a/tools/emboss_5/emboss_codcmp.xml
+++ b/tools/emboss_5/emboss_codcmp.xml
@@ -329,8 +329,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_coderet.xml b/tools/emboss_5/emboss_coderet.xml
index 251d37b2980..38f3b4dc656 100644
--- a/tools/emboss_5/emboss_coderet.xml
+++ b/tools/emboss_5/emboss_coderet.xml
@@ -72,8 +72,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_compseq.xml b/tools/emboss_5/emboss_compseq.xml
index cf4b6747a1f..4d8f4323d52 100644
--- a/tools/emboss_5/emboss_compseq.xml
+++ b/tools/emboss_5/emboss_compseq.xml
@@ -41,8 +41,10 @@ The input dataset needs to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_cpgplot.xml b/tools/emboss_5/emboss_cpgplot.xml
index d036e9a7774..be4873f5df6 100644
--- a/tools/emboss_5/emboss_cpgplot.xml
+++ b/tools/emboss_5/emboss_cpgplot.xml
@@ -32,8 +32,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_cpgreport.xml b/tools/emboss_5/emboss_cpgreport.xml
index 270858e70ce..148ca65511f 100644
--- a/tools/emboss_5/emboss_cpgreport.xml
+++ b/tools/emboss_5/emboss_cpgreport.xml
@@ -48,8 +48,10 @@ The input dataset needs to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_cusp.xml b/tools/emboss_5/emboss_cusp.xml
index acd3ea421c3..d0f88f7c9b1 100644
--- a/tools/emboss_5/emboss_cusp.xml
+++ b/tools/emboss_5/emboss_cusp.xml
@@ -29,8 +29,10 @@ The input dataset needs to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_cutseq.xml b/tools/emboss_5/emboss_cutseq.xml
index c2895918a2d..c7f91865a5b 100644
--- a/tools/emboss_5/emboss_cutseq.xml
+++ b/tools/emboss_5/emboss_cutseq.xml
@@ -71,8 +71,10 @@ The input dataset needs to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_dan.xml b/tools/emboss_5/emboss_dan.xml
index 4b2f98dfa65..aa968ac0ac0 100644
--- a/tools/emboss_5/emboss_dan.xml
+++ b/tools/emboss_5/emboss_dan.xml
@@ -83,8 +83,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_degapseq.xml b/tools/emboss_5/emboss_degapseq.xml
index be000acbd5b..d2241b7ce54 100644
--- a/tools/emboss_5/emboss_degapseq.xml
+++ b/tools/emboss_5/emboss_degapseq.xml
@@ -57,8 +57,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_descseq.xml b/tools/emboss_5/emboss_descseq.xml
index c87aa049ca7..6b472bf074f 100644
--- a/tools/emboss_5/emboss_descseq.xml
+++ b/tools/emboss_5/emboss_descseq.xml
@@ -71,8 +71,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_diffseq.xml b/tools/emboss_5/emboss_diffseq.xml
index 426653571ee..8b76b5f4bab 100644
--- a/tools/emboss_5/emboss_diffseq.xml
+++ b/tools/emboss_5/emboss_diffseq.xml
@@ -63,8 +63,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_digest.xml b/tools/emboss_5/emboss_digest.xml
index cc2b4ff52a6..bd1b56624a5 100644
--- a/tools/emboss_5/emboss_digest.xml
+++ b/tools/emboss_5/emboss_digest.xml
@@ -64,8 +64,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_dotmatcher.xml b/tools/emboss_5/emboss_dotmatcher.xml
index 144a8420c79..e9233031dce 100644
--- a/tools/emboss_5/emboss_dotmatcher.xml
+++ b/tools/emboss_5/emboss_dotmatcher.xml
@@ -28,8 +28,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_dotpath.xml b/tools/emboss_5/emboss_dotpath.xml
index 9e7fd16f6e5..1baa769c597 100644
--- a/tools/emboss_5/emboss_dotpath.xml
+++ b/tools/emboss_5/emboss_dotpath.xml
@@ -35,8 +35,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_dottup.xml b/tools/emboss_5/emboss_dottup.xml
index ef7ae8f1f4a..4fbe3dd68a1 100644
--- a/tools/emboss_5/emboss_dottup.xml
+++ b/tools/emboss_5/emboss_dottup.xml
@@ -29,8 +29,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_dreg.xml b/tools/emboss_5/emboss_dreg.xml
index f061c5a0a29..b40ca586e9d 100644
--- a/tools/emboss_5/emboss_dreg.xml
+++ b/tools/emboss_5/emboss_dreg.xml
@@ -21,8 +21,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_einverted.xml b/tools/emboss_5/emboss_einverted.xml
index 46ec763baa8..9e74eb570da 100644
--- a/tools/emboss_5/emboss_einverted.xml
+++ b/tools/emboss_5/emboss_einverted.xml
@@ -49,8 +49,10 @@ The input dataset needs to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_epestfind.xml b/tools/emboss_5/emboss_epestfind.xml
index 0a2cbb57bad..fd23ebc6a53 100644
--- a/tools/emboss_5/emboss_epestfind.xml
+++ b/tools/emboss_5/emboss_epestfind.xml
@@ -64,8 +64,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_equicktandem.xml b/tools/emboss_5/emboss_equicktandem.xml
index 1f77114fa43..49ffe86d886 100644
--- a/tools/emboss_5/emboss_equicktandem.xml
+++ b/tools/emboss_5/emboss_equicktandem.xml
@@ -59,8 +59,10 @@ The input dataset needs to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_est2genome.xml b/tools/emboss_5/emboss_est2genome.xml
index 132800c7caa..a2cff4106b1 100644
--- a/tools/emboss_5/emboss_est2genome.xml
+++ b/tools/emboss_5/emboss_est2genome.xml
@@ -102,8 +102,10 @@ The input dataset needs to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_etandem.xml b/tools/emboss_5/emboss_etandem.xml
index bd78594bb84..4b92e125f95 100644
--- a/tools/emboss_5/emboss_etandem.xml
+++ b/tools/emboss_5/emboss_etandem.xml
@@ -75,8 +75,10 @@ The input dataset needs to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_extractfeat.xml b/tools/emboss_5/emboss_extractfeat.xml
index 742738daec1..b8d92c325d4 100644
--- a/tools/emboss_5/emboss_extractfeat.xml
+++ b/tools/emboss_5/emboss_extractfeat.xml
@@ -97,6 +97,8 @@
 
 **Citation**
 
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_extractseq.xml b/tools/emboss_5/emboss_extractseq.xml
index 1f82d662b4d..cd5430c4384 100644
--- a/tools/emboss_5/emboss_extractseq.xml
+++ b/tools/emboss_5/emboss_extractseq.xml
@@ -67,8 +67,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_freak.xml b/tools/emboss_5/emboss_freak.xml
index 098b7ce2196..0c2ba29ee6b 100644
--- a/tools/emboss_5/emboss_freak.xml
+++ b/tools/emboss_5/emboss_freak.xml
@@ -35,8 +35,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_fuzznuc.xml b/tools/emboss_5/emboss_fuzznuc.xml
index b3a784ff49f..d2dbf7f9c29 100644
--- a/tools/emboss_5/emboss_fuzznuc.xml
+++ b/tools/emboss_5/emboss_fuzznuc.xml
@@ -74,8 +74,10 @@ The input dataset needs to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_fuzzpro.xml b/tools/emboss_5/emboss_fuzzpro.xml
index a9e5b1eaed1..a4d73112c3c 100644
--- a/tools/emboss_5/emboss_fuzzpro.xml
+++ b/tools/emboss_5/emboss_fuzzpro.xml
@@ -43,8 +43,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_fuzztran.xml b/tools/emboss_5/emboss_fuzztran.xml
index 3c7908146c0..63f4e596df6 100644
--- a/tools/emboss_5/emboss_fuzztran.xml
+++ b/tools/emboss_5/emboss_fuzztran.xml
@@ -94,8 +94,10 @@ The input dataset needs to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_garnier.xml b/tools/emboss_5/emboss_garnier.xml
index 18accfee3e1..cfd5ecc0093 100644
--- a/tools/emboss_5/emboss_garnier.xml
+++ b/tools/emboss_5/emboss_garnier.xml
@@ -57,8 +57,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_geecee.xml b/tools/emboss_5/emboss_geecee.xml
index 1645d66f102..570e8fc4a1a 100644
--- a/tools/emboss_5/emboss_geecee.xml
+++ b/tools/emboss_5/emboss_geecee.xml
@@ -23,8 +23,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_getorf.xml b/tools/emboss_5/emboss_getorf.xml
index dc7cf618d59..24ea0d8ebab 100644
--- a/tools/emboss_5/emboss_getorf.xml
+++ b/tools/emboss_5/emboss_getorf.xml
@@ -128,8 +128,10 @@ The input dataset needs to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_helixturnhelix.xml b/tools/emboss_5/emboss_helixturnhelix.xml
index 1ce12154d47..519d4ed36e6 100644
--- a/tools/emboss_5/emboss_helixturnhelix.xml
+++ b/tools/emboss_5/emboss_helixturnhelix.xml
@@ -62,8 +62,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_hmoment.xml b/tools/emboss_5/emboss_hmoment.xml
index 3b797d560ae..3d485a7e495 100644
--- a/tools/emboss_5/emboss_hmoment.xml
+++ b/tools/emboss_5/emboss_hmoment.xml
@@ -31,8 +31,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_iep.xml b/tools/emboss_5/emboss_iep.xml
index 38a6872c86d..28e513fce41 100644
--- a/tools/emboss_5/emboss_iep.xml
+++ b/tools/emboss_5/emboss_iep.xml
@@ -37,8 +37,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_infoseq.xml b/tools/emboss_5/emboss_infoseq.xml
index 26780d9418a..14404d24548 100644
--- a/tools/emboss_5/emboss_infoseq.xml
+++ b/tools/emboss_5/emboss_infoseq.xml
@@ -75,8 +75,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_isochore.xml b/tools/emboss_5/emboss_isochore.xml
index f4533c637de..a167740941b 100644
--- a/tools/emboss_5/emboss_isochore.xml
+++ b/tools/emboss_5/emboss_isochore.xml
@@ -82,6 +82,8 @@ This application plots GC content over a sequence. It is intended for large sequ
 
 **Citation**
 
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
 
   </help>
diff --git a/tools/emboss_5/emboss_lindna.xml b/tools/emboss_5/emboss_lindna.xml
index bc5fd5d821a..7ab378709a9 100644
--- a/tools/emboss_5/emboss_lindna.xml
+++ b/tools/emboss_5/emboss_lindna.xml
@@ -98,8 +98,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_marscan.xml b/tools/emboss_5/emboss_marscan.xml
index 925496d480f..bd19131cc98 100644
--- a/tools/emboss_5/emboss_marscan.xml
+++ b/tools/emboss_5/emboss_marscan.xml
@@ -44,8 +44,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_maskfeat.xml b/tools/emboss_5/emboss_maskfeat.xml
index e2dfd87b887..11ac741c30d 100644
--- a/tools/emboss_5/emboss_maskfeat.xml
+++ b/tools/emboss_5/emboss_maskfeat.xml
@@ -71,8 +71,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_maskseq.xml b/tools/emboss_5/emboss_maskseq.xml
index 86a398bd011..96b4cdd9087 100644
--- a/tools/emboss_5/emboss_maskseq.xml
+++ b/tools/emboss_5/emboss_maskseq.xml
@@ -71,8 +71,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_matcher.xml b/tools/emboss_5/emboss_matcher.xml
index e2dea21f00a..7a55b6c802a 100644
--- a/tools/emboss_5/emboss_matcher.xml
+++ b/tools/emboss_5/emboss_matcher.xml
@@ -56,8 +56,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_megamerger.xml b/tools/emboss_5/emboss_megamerger.xml
index a4cec675d06..fad3be07d68 100644
--- a/tools/emboss_5/emboss_megamerger.xml
+++ b/tools/emboss_5/emboss_megamerger.xml
@@ -62,8 +62,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_merger.xml b/tools/emboss_5/emboss_merger.xml
index 4fa7f29266b..9b10641a75c 100644
--- a/tools/emboss_5/emboss_merger.xml
+++ b/tools/emboss_5/emboss_merger.xml
@@ -75,8 +75,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_msbar.xml b/tools/emboss_5/emboss_msbar.xml
index f922f18775b..1980f0f3a7c 100644
--- a/tools/emboss_5/emboss_msbar.xml
+++ b/tools/emboss_5/emboss_msbar.xml
@@ -116,8 +116,10 @@ The input dataset needs to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_needle.xml b/tools/emboss_5/emboss_needle.xml
index 8af3a8095dc..10bfb9461b6 100644
--- a/tools/emboss_5/emboss_needle.xml
+++ b/tools/emboss_5/emboss_needle.xml
@@ -125,8 +125,10 @@ You can view the original documentation here_.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_newcpgreport.xml b/tools/emboss_5/emboss_newcpgreport.xml
index cc29f93b54a..868851b1a1e 100644
--- a/tools/emboss_5/emboss_newcpgreport.xml
+++ b/tools/emboss_5/emboss_newcpgreport.xml
@@ -43,8 +43,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_newcpgseek.xml b/tools/emboss_5/emboss_newcpgseek.xml
index 1b3f72c779e..8bbde6f0b7a 100644
--- a/tools/emboss_5/emboss_newcpgseek.xml
+++ b/tools/emboss_5/emboss_newcpgseek.xml
@@ -34,8 +34,10 @@ The input dataset needs to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_newseq.xml b/tools/emboss_5/emboss_newseq.xml
index 61f674cc4a7..99c510ca6f8 100644
--- a/tools/emboss_5/emboss_newseq.xml
+++ b/tools/emboss_5/emboss_newseq.xml
@@ -71,8 +71,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_noreturn.xml b/tools/emboss_5/emboss_noreturn.xml
index 5a37e0639a7..76f9dde8070 100644
--- a/tools/emboss_5/emboss_noreturn.xml
+++ b/tools/emboss_5/emboss_noreturn.xml
@@ -30,8 +30,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_notseq.xml b/tools/emboss_5/emboss_notseq.xml
index 3554d066d54..783141e2272 100644
--- a/tools/emboss_5/emboss_notseq.xml
+++ b/tools/emboss_5/emboss_notseq.xml
@@ -68,8 +68,10 @@ The input dataset needs to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_nthseq.xml b/tools/emboss_5/emboss_nthseq.xml
index a629ac14661..ae0d178d13a 100644
--- a/tools/emboss_5/emboss_nthseq.xml
+++ b/tools/emboss_5/emboss_nthseq.xml
@@ -68,8 +68,10 @@ The input dataset needs to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_octanol.xml b/tools/emboss_5/emboss_octanol.xml
index 8263c60a091..ad389f77607 100644
--- a/tools/emboss_5/emboss_octanol.xml
+++ b/tools/emboss_5/emboss_octanol.xml
@@ -39,6 +39,8 @@
 
 **Citation**
 
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_oddcomp.xml b/tools/emboss_5/emboss_oddcomp.xml
index ae98e0fbd12..c482b44850c 100644
--- a/tools/emboss_5/emboss_oddcomp.xml
+++ b/tools/emboss_5/emboss_oddcomp.xml
@@ -39,8 +39,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_palindrome.xml b/tools/emboss_5/emboss_palindrome.xml
index b8a9fbaa89f..957b8be3cd2 100644
--- a/tools/emboss_5/emboss_palindrome.xml
+++ b/tools/emboss_5/emboss_palindrome.xml
@@ -52,8 +52,10 @@ The input dataset needs to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_pasteseq.xml b/tools/emboss_5/emboss_pasteseq.xml
index fcc8aa8641a..816c36b420d 100644
--- a/tools/emboss_5/emboss_pasteseq.xml
+++ b/tools/emboss_5/emboss_pasteseq.xml
@@ -72,8 +72,10 @@ The input datasets need to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_patmatdb.xml b/tools/emboss_5/emboss_patmatdb.xml
index c067e22acc9..500e4f0d5ad 100644
--- a/tools/emboss_5/emboss_patmatdb.xml
+++ b/tools/emboss_5/emboss_patmatdb.xml
@@ -48,8 +48,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_pepcoil.xml b/tools/emboss_5/emboss_pepcoil.xml
index 4acaac678a7..a2c43a183ce 100644
--- a/tools/emboss_5/emboss_pepcoil.xml
+++ b/tools/emboss_5/emboss_pepcoil.xml
@@ -45,8 +45,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_pepinfo.xml b/tools/emboss_5/emboss_pepinfo.xml
index 4865f898e03..72555294d36 100644
--- a/tools/emboss_5/emboss_pepinfo.xml
+++ b/tools/emboss_5/emboss_pepinfo.xml
@@ -27,8 +27,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_pepnet.xml b/tools/emboss_5/emboss_pepnet.xml
index 0ff9716d49e..77c4ed171f2 100644
--- a/tools/emboss_5/emboss_pepnet.xml
+++ b/tools/emboss_5/emboss_pepnet.xml
@@ -32,8 +32,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_pepstats.xml b/tools/emboss_5/emboss_pepstats.xml
index 071133ee435..40c32bbe3a9 100644
--- a/tools/emboss_5/emboss_pepstats.xml
+++ b/tools/emboss_5/emboss_pepstats.xml
@@ -29,8 +29,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_pepwheel.xml b/tools/emboss_5/emboss_pepwheel.xml
index 3d4e155bea8..748a761981a 100644
--- a/tools/emboss_5/emboss_pepwheel.xml
+++ b/tools/emboss_5/emboss_pepwheel.xml
@@ -44,8 +44,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_pepwindow.xml b/tools/emboss_5/emboss_pepwindow.xml
index 92e8a00eade..60c0883eac9 100644
--- a/tools/emboss_5/emboss_pepwindow.xml
+++ b/tools/emboss_5/emboss_pepwindow.xml
@@ -21,8 +21,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_pepwindowall.xml b/tools/emboss_5/emboss_pepwindowall.xml
index f8fb5f7fcd7..a6f4d26398c 100644
--- a/tools/emboss_5/emboss_pepwindowall.xml
+++ b/tools/emboss_5/emboss_pepwindowall.xml
@@ -21,8 +21,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_plotcon.xml b/tools/emboss_5/emboss_plotcon.xml
index 10d3b149638..5a44b6bf9d8 100644
--- a/tools/emboss_5/emboss_plotcon.xml
+++ b/tools/emboss_5/emboss_plotcon.xml
@@ -21,8 +21,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_plotorf.xml b/tools/emboss_5/emboss_plotorf.xml
index 170de4ddb87..050c95fb688 100644
--- a/tools/emboss_5/emboss_plotorf.xml
+++ b/tools/emboss_5/emboss_plotorf.xml
@@ -39,8 +39,10 @@ The input dataset needs to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_polydot.xml b/tools/emboss_5/emboss_polydot.xml
index 3eda259eaf8..268fa80bb9d 100644
--- a/tools/emboss_5/emboss_polydot.xml
+++ b/tools/emboss_5/emboss_polydot.xml
@@ -47,8 +47,10 @@ The input dataset needs to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_preg.xml b/tools/emboss_5/emboss_preg.xml
index efc38852601..3e8b479d8da 100644
--- a/tools/emboss_5/emboss_preg.xml
+++ b/tools/emboss_5/emboss_preg.xml
@@ -20,8 +20,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_prettyplot.xml b/tools/emboss_5/emboss_prettyplot.xml
index 53d436b5918..3b5a8507653 100644
--- a/tools/emboss_5/emboss_prettyplot.xml
+++ b/tools/emboss_5/emboss_prettyplot.xml
@@ -112,8 +112,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_prettyseq.xml b/tools/emboss_5/emboss_prettyseq.xml
index c8c25942ade..e1d59c9147c 100644
--- a/tools/emboss_5/emboss_prettyseq.xml
+++ b/tools/emboss_5/emboss_prettyseq.xml
@@ -52,8 +52,10 @@ The input dataset needs to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_primersearch.xml b/tools/emboss_5/emboss_primersearch.xml
index 0693e076540..7687eb3dc53 100644
--- a/tools/emboss_5/emboss_primersearch.xml
+++ b/tools/emboss_5/emboss_primersearch.xml
@@ -32,8 +32,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_revseq.xml b/tools/emboss_5/emboss_revseq.xml
index 7d65f8e2a7c..eaad8ae383c 100644
--- a/tools/emboss_5/emboss_revseq.xml
+++ b/tools/emboss_5/emboss_revseq.xml
@@ -76,8 +76,10 @@ The input dataset needs to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_seqmatchall.xml b/tools/emboss_5/emboss_seqmatchall.xml
index cdc85944b66..a697dcb6162 100644
--- a/tools/emboss_5/emboss_seqmatchall.xml
+++ b/tools/emboss_5/emboss_seqmatchall.xml
@@ -53,8 +53,10 @@ The input dataset needs to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_seqret.xml b/tools/emboss_5/emboss_seqret.xml
index 3471b8dd2de..654603e6b97 100644
--- a/tools/emboss_5/emboss_seqret.xml
+++ b/tools/emboss_5/emboss_seqret.xml
@@ -69,8 +69,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_showfeat.xml b/tools/emboss_5/emboss_showfeat.xml
index 82a958ed656..7c9394eefe0 100644
--- a/tools/emboss_5/emboss_showfeat.xml
+++ b/tools/emboss_5/emboss_showfeat.xml
@@ -122,8 +122,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_shuffleseq.xml b/tools/emboss_5/emboss_shuffleseq.xml
index 23be68f742c..fb269fb98fa 100644
--- a/tools/emboss_5/emboss_shuffleseq.xml
+++ b/tools/emboss_5/emboss_shuffleseq.xml
@@ -61,8 +61,10 @@ The input dataset needs to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_sigcleave.xml b/tools/emboss_5/emboss_sigcleave.xml
index e5b3e24de24..5c41976acde 100644
--- a/tools/emboss_5/emboss_sigcleave.xml
+++ b/tools/emboss_5/emboss_sigcleave.xml
@@ -54,8 +54,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_sirna.xml b/tools/emboss_5/emboss_sirna.xml
index 9b84066dfb1..3e0deab97c4 100644
--- a/tools/emboss_5/emboss_sirna.xml
+++ b/tools/emboss_5/emboss_sirna.xml
@@ -117,8 +117,10 @@ The input dataset needs to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_sixpack.xml b/tools/emboss_5/emboss_sixpack.xml
index 2aaea50d2b7..49d3f29c6b6 100644
--- a/tools/emboss_5/emboss_sixpack.xml
+++ b/tools/emboss_5/emboss_sixpack.xml
@@ -161,8 +161,10 @@ The input dataset needs to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_skipseq.xml b/tools/emboss_5/emboss_skipseq.xml
index 9dc0577d615..dddc257e20a 100644
--- a/tools/emboss_5/emboss_skipseq.xml
+++ b/tools/emboss_5/emboss_skipseq.xml
@@ -58,8 +58,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_splitter.xml b/tools/emboss_5/emboss_splitter.xml
index 87a968487c5..c46102fe816 100644
--- a/tools/emboss_5/emboss_splitter.xml
+++ b/tools/emboss_5/emboss_splitter.xml
@@ -78,8 +78,10 @@ The input dataset needs to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_supermatcher.xml b/tools/emboss_5/emboss_supermatcher.xml
index 41360ecbd6b..5d1ccccd6a7 100644
--- a/tools/emboss_5/emboss_supermatcher.xml
+++ b/tools/emboss_5/emboss_supermatcher.xml
@@ -63,8 +63,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_syco.xml b/tools/emboss_5/emboss_syco.xml
index 970d79ee242..e5baaec51a0 100644
--- a/tools/emboss_5/emboss_syco.xml
+++ b/tools/emboss_5/emboss_syco.xml
@@ -196,8 +196,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_tcode.xml b/tools/emboss_5/emboss_tcode.xml
index 958aa37774e..beda491636d 100644
--- a/tools/emboss_5/emboss_tcode.xml
+++ b/tools/emboss_5/emboss_tcode.xml
@@ -43,8 +43,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_textsearch.xml b/tools/emboss_5/emboss_textsearch.xml
index b7a8c12a93f..8d7839f50f1 100644
--- a/tools/emboss_5/emboss_textsearch.xml
+++ b/tools/emboss_5/emboss_textsearch.xml
@@ -57,8 +57,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_tmap.xml b/tools/emboss_5/emboss_tmap.xml
index f1213ed525c..cc775ac1bd5 100644
--- a/tools/emboss_5/emboss_tmap.xml
+++ b/tools/emboss_5/emboss_tmap.xml
@@ -38,8 +38,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_tranalign.xml b/tools/emboss_5/emboss_tranalign.xml
index 2aaa2adda26..5e7411567ce 100644
--- a/tools/emboss_5/emboss_tranalign.xml
+++ b/tools/emboss_5/emboss_tranalign.xml
@@ -83,8 +83,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_transeq.xml b/tools/emboss_5/emboss_transeq.xml
index 2b72127c602..eeffcadc320 100644
--- a/tools/emboss_5/emboss_transeq.xml
+++ b/tools/emboss_5/emboss_transeq.xml
@@ -121,8 +121,10 @@ The input dataset needs to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_trimest.xml b/tools/emboss_5/emboss_trimest.xml
index 6bf52d0cade..e6349807813 100644
--- a/tools/emboss_5/emboss_trimest.xml
+++ b/tools/emboss_5/emboss_trimest.xml
@@ -91,8 +91,10 @@ The input dataset needs to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_trimseq.xml b/tools/emboss_5/emboss_trimseq.xml
index 6693d60cb0f..f9abe94f102 100644
--- a/tools/emboss_5/emboss_trimseq.xml
+++ b/tools/emboss_5/emboss_trimseq.xml
@@ -96,8 +96,10 @@ The input dataset needs to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_twofeat.xml b/tools/emboss_5/emboss_twofeat.xml
index 4c90ebae96b..6ddf2057761 100644
--- a/tools/emboss_5/emboss_twofeat.xml
+++ b/tools/emboss_5/emboss_twofeat.xml
@@ -129,8 +129,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
\ No newline at end of file
diff --git a/tools/emboss_5/emboss_union.xml b/tools/emboss_5/emboss_union.xml
index 2836f42df9c..ffac0550066 100644
--- a/tools/emboss_5/emboss_union.xml
+++ b/tools/emboss_5/emboss_union.xml
@@ -64,8 +64,10 @@ The input dataset needs to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_vectorstrip.xml b/tools/emboss_5/emboss_vectorstrip.xml
index f028e9e7953..37be239ea82 100644
--- a/tools/emboss_5/emboss_vectorstrip.xml
+++ b/tools/emboss_5/emboss_vectorstrip.xml
@@ -81,8 +81,10 @@
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_water.xml b/tools/emboss_5/emboss_water.xml
index d3d44add3ab..eeea0953ffe 100644
--- a/tools/emboss_5/emboss_water.xml
+++ b/tools/emboss_5/emboss_water.xml
@@ -65,8 +65,10 @@ The input datasets need to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_wobble.xml b/tools/emboss_5/emboss_wobble.xml
index 2f41c6b9414..e7050ade0e3 100644
--- a/tools/emboss_5/emboss_wobble.xml
+++ b/tools/emboss_5/emboss_wobble.xml
@@ -39,8 +39,10 @@ The input dataset needs to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_wordcount.xml b/tools/emboss_5/emboss_wordcount.xml
index 4998e29656a..7ad5af4dfe8 100644
--- a/tools/emboss_5/emboss_wordcount.xml
+++ b/tools/emboss_5/emboss_wordcount.xml
@@ -34,8 +34,10 @@ The input dataset needs to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>
diff --git a/tools/emboss_5/emboss_wordmatch.xml b/tools/emboss_5/emboss_wordmatch.xml
index 2f82a53c15e..e6cc78c8ba6 100644
--- a/tools/emboss_5/emboss_wordmatch.xml
+++ b/tools/emboss_5/emboss_wordmatch.xml
@@ -73,8 +73,10 @@ The input datasets need to be sequences.
 
 ------
 
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
   </help>
 </tool>

From f3549704e308b7c39c7a2ae4005a3b565142bded Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Wed, 16 Nov 2011 10:40:55 -0500
Subject: [PATCH 203/362] Add information for UCSC data to annotation profiler.

---
 tools/annotation_profiler/annotation_profiler.xml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tools/annotation_profiler/annotation_profiler.xml b/tools/annotation_profiler/annotation_profiler.xml
index abfdc53d043..ba0c0536098 100644
--- a/tools/annotation_profiler/annotation_profiler.xml
+++ b/tools/annotation_profiler/annotation_profiler.xml
@@ -136,6 +136,8 @@ Where::
 
 **Citation**
 
+For the underlying data, please see http://genome.ucsc.edu/cite.html for the proper citation.
+
 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
 
   </help>

From 0973a79935cf834771c212f7f5873156302d2c0a Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Wed, 16 Nov 2011 11:03:14 -0500
Subject: [PATCH 204/362] Improve exception handling when loading and
 displaying tools in the tool shed, check content of files uploaded to a tool
 shed repository only when necessary, and clarify that borwsing repository
 files is only available for the repository tip.

---
 .../webapps/community/controllers/common.py   | 49 +++++++----
 .../community/controllers/repository.py       | 82 +++++++++++--------
 .../webapps/community/controllers/upload.py   | 10 ++-
 .../repository/browse_repository.mako         |  2 +-
 .../community/repository/contact_owner.mako   |  4 +-
 .../repository/manage_repository.mako         |  4 +-
 .../preview_tools_in_changeset.mako           |  4 +-
 .../community/repository/rate_repository.mako |  4 +-
 .../community/repository/tool_form.mako       |  4 +-
 .../community/repository/view_changelog.mako  |  4 +-
 .../community/repository/view_changeset.mako  |  4 +-
 .../community/repository/view_repository.mako |  4 +-
 .../repository/view_tool_metadata.mako        |  4 +-
 .../community/repository/view_workflow.mako   |  4 +-
 14 files changed, 107 insertions(+), 76 deletions(-)

diff --git a/lib/galaxy/webapps/community/controllers/common.py b/lib/galaxy/webapps/community/controllers/common.py
index 51f5131640d..38b58f18524 100644
--- a/lib/galaxy/webapps/community/controllers/common.py
+++ b/lib/galaxy/webapps/community/controllers/common.py
@@ -380,17 +380,19 @@ def set_repository_metadata( trans, id, changeset_revision, **kwd ):
                     for name in files:
                         # Find all tool configs.
                         if name != 'datatypes_conf.xml' and name.endswith( '.xml' ):
+                            full_path = os.path.abspath( os.path.join( root, name ) )
                             try:
-                                full_path = os.path.abspath( os.path.join( root, name ) )
                                 tool = load_tool( trans, full_path )
-                                if tool is not None:
-                                    can_set_metadata, invalid_files = check_tool_input_params( trans, name, tool, sample_files, invalid_files )
-                                    if can_set_metadata:
-                                        # Update the list of metadata dictionaries for tools in metadata_dict.
-                                        tool_config = os.path.join( root, name )
-                                        metadata_dict = generate_tool_metadata( trans, id, changeset_revision, tool_config, tool, metadata_dict )
+                                valid = True
                             except Exception, e:
+                                valid = False
                                 invalid_files.append( ( name, str( e ) ) )
+                            if valid and tool is not None:
+                                can_set_metadata, invalid_files = check_tool_input_params( trans, name, tool, sample_files, invalid_files )
+                                if can_set_metadata:
+                                    # Update the list of metadata dictionaries for tools in metadata_dict.
+                                    tool_config = os.path.join( root, name )
+                                    metadata_dict = generate_tool_metadata( trans, id, changeset_revision, tool_config, tool, metadata_dict )
                         # Find all exported workflows
                         elif name.endswith( '.ga' ):
                             try:
@@ -427,17 +429,19 @@ def set_repository_metadata( trans, id, changeset_revision, **kwd ):
                     fh.close()
                     try:
                         tool = load_tool( trans, tmp_filename )
-                        if tool is not None:
-                            can_set_metadata, invalid_files = check_tool_input_params( trans, filename, tool, sample_files, invalid_files )
-                            if can_set_metadata:
-                                # Update the list of metadata dictionaries for tools in metadata_dict.  Note that filename
-                                # here is the relative path to the config file within the change set context, something
-                                # like filtering.xml, but when the change set was the repository tip, the value was
-                                # something like database/community_files/000/repo_1/filtering.xml.  This shouldn't break
-                                # anything, but may result in a bit of confusion when maintaining the code / data over time.
-                                metadata_dict = generate_tool_metadata( trans, id, changeset_revision, filename, tool, metadata_dict )
+                        valid = True
                     except Exception, e:
-                        invalid_files.append( ( name, str( e ) ) )
+                        invalid_files.append( ( filename, str( e ) ) )
+                        valid = False
+                    if valid and tool is not None:
+                        can_set_metadata, invalid_files = check_tool_input_params( trans, filename, tool, sample_files, invalid_files )
+                        if can_set_metadata:
+                            # Update the list of metadata dictionaries for tools in metadata_dict.  Note that filename
+                            # here is the relative path to the config file within the change set context, something
+                            # like filtering.xml, but when the change set was the repository tip, the value was
+                            # something like database/community_files/000/repo_1/filtering.xml.  This shouldn't break
+                            # anything, but may result in a bit of confusion when maintaining the code / data over time.
+                            metadata_dict = generate_tool_metadata( trans, id, changeset_revision, filename, tool, metadata_dict )
                     try:
                         os.unlink( tmp_filename )
                     except:
@@ -575,6 +579,17 @@ def handle_email_alerts( trans, repository, content_alert_str='' ):
                     util.send_mail( frm, to, subject, body, trans.app.config )
             except Exception, e:
                 log.exception( "An error occurred sending a tool shed repository update alert by email." )
+def check_file_contents( trans ):
+    # See if any admin users have chosen to receive email alerts when a repository is updated.
+    # If so, the file contents of the update must be checked for inappropriate content.
+    admin_users = trans.app.config.get( "admin_users", "" ).split( "," )
+    for repository in trans.sa_session.query( trans.model.Repository ) \
+                                      .filter( trans.model.Repository.table.c.email_alerts != None ):
+        email_alerts = from_json_string( repository.email_alerts )
+        for user_email in email_alerts:
+            if user_email in admin_users:
+                return True
+    return False
 def update_for_browsing( trans, repository, current_working_dir, commit_message='' ):
     # Make a copy of a repository's files for browsing, remove from disk all files that
     # are not tracked, and commit all added, modified or removed files that have not yet
diff --git a/lib/galaxy/webapps/community/controllers/repository.py b/lib/galaxy/webapps/community/controllers/repository.py
index 6c1878f817a..b1bddd8fddc 100644
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -773,7 +773,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
                     tool_guids = []
                     for filename in ctx:
                         # Find all tool configs in this repository changeset_revision.
-                        if filename.endswith( '.xml' ):
+                        if filename != 'datatypes_conf.xml' and filename.endswith( '.xml' ):
                             fctx = ctx[ filename ]
                             # Write the contents of the old tool config to a temporary file.
                             fh = tempfile.NamedTemporaryFile( 'w' )
@@ -784,11 +784,11 @@ class RepositoryController( BaseUIController, ItemRatings ):
                             fh.close()
                             try:
                                 tool = load_tool( trans, tmp_filename )
-                                if tool is not None:
-                                    tool_guids.append( generate_tool_guid( trans, repository, tool ) )
+                                valid = True
                             except:
-                                # File must not be a valid tool config even though it has a .xml extension.
-                                pass
+                                valid = False
+                            if valid and tool is not None:
+                                tool_guids.append( generate_tool_guid( trans, repository, tool ) )
                             try:
                                 os.unlink( tmp_filename )
                             except:
@@ -1614,39 +1614,49 @@ class RepositoryController( BaseUIController, ItemRatings ):
         status = params.get( 'status', 'done' )
         webapp = params.get( 'webapp', 'community' )
         repository = get_repository( trans, repository_id )
-        repo = hg.repository( get_configured_ui(), repository.repo_path )          
-        try:
-            if changeset_revision == repository.tip:
-                # Get the tool config from the file system we use for browsing.
+        repo = hg.repository( get_configured_ui(), repository.repo_path )
+        valid = True
+        if changeset_revision == repository.tip:
+            try:
                 tool = load_tool( trans, os.path.abspath( tool_config ) )
-            else:
-                # Get the tool config file name from the hgweb url, something like:
-                # /repos/test/convert_chars1/file/e58dcf0026c7/convert_characters.xml
-                old_tool_config_file_name = tool_config.split( '/' )[ -1 ]
-                ctx = get_changectx_for_changeset( trans, repo, changeset_revision )
-                fctx = None
-                for filename in ctx:
-                    filename_head, filename_tail = os.path.split( filename )
-                    if filename_tail == old_tool_config_file_name:
-                        fctx = ctx[ filename ]
-                        break
-                if fctx:
-                    # Write the contents of the old tool config to a temporary file.
-                    fh = tempfile.NamedTemporaryFile( 'w' )
-                    tmp_filename = fh.name
-                    fh.close()
-                    fh = open( tmp_filename, 'w' )
-                    fh.write( fctx.data() )
-                    fh.close()
+            except Exception, e:
+                tool = None
+                valid = False
+                message = "Error loading tool: %s.  Clicking <b>Reset metadata</b> may correct this error." % str( e )
+        else:
+            # Get the tool config file name from the hgweb url, something like:
+            # /repos/test/convert_chars1/file/e58dcf0026c7/convert_characters.xml
+            old_tool_config_file_name = tool_config.split( '/' )[ -1 ]
+            ctx = get_changectx_for_changeset( trans, repo, changeset_revision )
+            fctx = None
+            for filename in ctx:
+                filename_head, filename_tail = os.path.split( filename )
+                if filename_tail == old_tool_config_file_name:
+                    fctx = ctx[ filename ]
+                    break
+            if fctx:
+                # Write the contents of the old tool config to a temporary file.
+                fh = tempfile.NamedTemporaryFile( 'w' )
+                tmp_filename = fh.name
+                fh.close()
+                fh = open( tmp_filename, 'w' )
+                fh.write( fctx.data() )
+                fh.close()
+                try:
                     tool = load_tool( trans, tmp_filename )
-                    try:
-                        os.unlink( tmp_filename )
-                    except:
-                        pass
-                else:
+                except Exception, e:
                     tool = None
-            tool_state = self.__new_state( trans )
-            is_malicious = change_set_is_malicious( trans, repository_id, repository.tip )
+                    valid = False
+                    message = "Error loading tool: %s.  Clicking <b>Reset metadata</b> may correct this error." % str( e )
+                try:
+                    os.unlink( tmp_filename )
+                except:
+                    pass
+            else:
+                tool = None
+        tool_state = self.__new_state( trans )
+        is_malicious = change_set_is_malicious( trans, repository_id, repository.tip )
+        try:
             return trans.fill_template( "/webapps/community/repository/tool_form.mako",
                                         repository=repository,
                                         changeset_revision=changeset_revision,
@@ -1657,7 +1667,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
                                         message=message,
                                         status=status )
         except Exception, e:
-            message = "Error loading tool: %s.  Click <b>Reset metadata</b> to correct this error." % str( e )
+            message = "Error displaying tool, probably due to a problem in the tool config.  The exception is: %s." % str( e )
         if webapp == 'galaxy':
             return trans.response.send_redirect( web.url_for( controller='repository',
                                                               action='preview_tools_in_changeset',
diff --git a/lib/galaxy/webapps/community/controllers/upload.py b/lib/galaxy/webapps/community/controllers/upload.py
index 8e313bb25d9..1a0e981d67a 100644
--- a/lib/galaxy/webapps/community/controllers/upload.py
+++ b/lib/galaxy/webapps/community/controllers/upload.py
@@ -103,7 +103,10 @@ class UploadController( BaseUIController ):
                         full_path = os.path.abspath( os.path.join( repo_dir, uploaded_file_filename ) )
                     # Move the uploaded file to the load_point within the repository hierarchy.
                     shutil.move( uploaded_file_name, full_path )
-                    if os.path.isfile( full_path ):
+                    # See if any admin users have chosen to receive email alerts when a repository is
+                    # updated.  If so, check every uploaded file to ensure content is appropriate.
+                    check_contents = check_file_contents( trans )
+                    if check_contents and os.path.isfile( full_path ):
                         content_alert_str = self.__check_file_content( full_path )
                     else:
                         content_alert_str = ''
@@ -238,9 +241,12 @@ class UploadController( BaseUIController ):
                             except OSError, e:
                                 # The directory is not empty
                                 pass
+            # See if any admin users have chosen to receive email alerts when a repository is
+            # updated.  If so, check every uploaded file to ensure content is appropriate.
+            check_contents = check_file_contents( trans )
             for filename_in_archive in filenames_in_archive:
                 # Check file content to ensure it is appropriate.
-                if os.path.isfile( filename_in_archive ):
+                if check_contents and os.path.isfile( filename_in_archive ):
                     content_alert_str += self.__check_file_content( filename_in_archive )
                 commands.add( repo.ui, repo, filename_in_archive )
                 if filename_in_archive.endswith( 'tool_data_table_conf.xml.sample' ):
diff --git a/templates/webapps/community/repository/browse_repository.mako b/templates/webapps/community/repository/browse_repository.mako
index 054e682fc48..1d3c5ab2761 100644
--- a/templates/webapps/community/repository/browse_repository.mako
+++ b/templates/webapps/community/repository/browse_repository.mako
@@ -97,7 +97,7 @@
 
 %if can_browse_contents:
     <div class="toolForm">
-        <div class="toolFormTitle">Browse ${repository.name}</div>
+        <div class="toolFormTitle">Browse ${repository.name} revision ${repository.tip} (repository tip)</div>
         %if can_download:
             <div class="form-row">
                 <label>Clone this repository:</label>
diff --git a/templates/webapps/community/repository/contact_owner.mako b/templates/webapps/community/repository/contact_owner.mako
index d8a27beaf55..a9cf8211eba 100644
--- a/templates/webapps/community/repository/contact_owner.mako
+++ b/templates/webapps/community/repository/contact_owner.mako
@@ -13,9 +13,9 @@
     can_manage = is_admin or repository.user == trans.user
     can_view_change_log = not is_new
     if can_push:
-        browse_label = 'Browse or delete repository files'
+        browse_label = 'Browse or delete repository tip files'
     else:
-        browse_label = 'Browse repository files'
+        browse_label = 'Browse repository tip files'
 %>
 
 <%!
diff --git a/templates/webapps/community/repository/manage_repository.mako b/templates/webapps/community/repository/manage_repository.mako
index 1345448414d..e60f8d7b539 100644
--- a/templates/webapps/community/repository/manage_repository.mako
+++ b/templates/webapps/community/repository/manage_repository.mako
@@ -16,9 +16,9 @@
     can_rate = not is_new and trans.user and repository.user != trans.user
     can_view_change_log = not is_new
     if can_push:
-        browse_label = 'Browse or delete repository files'
+        browse_label = 'Browse or delete repository tip files'
     else:
-        browse_label = 'Browse repository files'
+        browse_label = 'Browse repository tip files'
     can_set_malicious = metadata and can_set_metadata and is_admin and changeset_revision == repository.tip
 %>
 
diff --git a/templates/webapps/community/repository/preview_tools_in_changeset.mako b/templates/webapps/community/repository/preview_tools_in_changeset.mako
index e7ad6172f06..1c2dfb0c9f6 100644
--- a/templates/webapps/community/repository/preview_tools_in_changeset.mako
+++ b/templates/webapps/community/repository/preview_tools_in_changeset.mako
@@ -13,9 +13,9 @@
     can_browse_contents = not is_new
     can_view_change_log = not is_new
     if can_push:
-        browse_label = 'Browse or delete repository files'
+        browse_label = 'Browse or delete repository tip files'
     else:
-        browse_label = 'Browse repository files'
+        browse_label = 'Browse repository tip files'
 %>
 
 <%!
diff --git a/templates/webapps/community/repository/rate_repository.mako b/templates/webapps/community/repository/rate_repository.mako
index 23baa8fc031..37b13346e32 100644
--- a/templates/webapps/community/repository/rate_repository.mako
+++ b/templates/webapps/community/repository/rate_repository.mako
@@ -16,9 +16,9 @@
     can_manage = is_admin or repository.user == trans.user
     can_view_change_log = not is_new
     if can_push:
-        browse_label = 'Browse or delete repository files'
+        browse_label = 'Browse or delete repository tip files'
     else:
-        browse_label = 'Browse repository files'
+        browse_label = 'Browse repository tip files'
 %>
 
 <%!
diff --git a/templates/webapps/community/repository/tool_form.mako b/templates/webapps/community/repository/tool_form.mako
index 2ecf77cd4f8..57bbc90a11b 100644
--- a/templates/webapps/community/repository/tool_form.mako
+++ b/templates/webapps/community/repository/tool_form.mako
@@ -18,9 +18,9 @@
     can_manage = is_admin or repository.user == trans.user
     can_view_change_log = not is_new
     if can_push:
-        browse_label = 'Browse or delete repository files'
+        browse_label = 'Browse or delete repository tip files'
     else:
-        browse_label = 'Browse repository files'
+        browse_label = 'Browse repository tip files'
 %>
 
 <html>
diff --git a/templates/webapps/community/repository/view_changelog.mako b/templates/webapps/community/repository/view_changelog.mako
index 38ba45a8bb5..5e8fd1f889b 100644
--- a/templates/webapps/community/repository/view_changelog.mako
+++ b/templates/webapps/community/repository/view_changelog.mako
@@ -15,9 +15,9 @@
     can_upload = can_push
     can_download = not is_new and ( not is_malicious or can_push )
     if can_push:
-        browse_label = 'Browse or delete repository files'
+        browse_label = 'Browse or delete repository tip files'
     else:
-        browse_label = 'Browse repository files'
+        browse_label = 'Browse repository tip files'
 %>
 
 <%!
diff --git a/templates/webapps/community/repository/view_changeset.mako b/templates/webapps/community/repository/view_changeset.mako
index 4c2aa5a0551..00a65ec1dd0 100644
--- a/templates/webapps/community/repository/view_changeset.mako
+++ b/templates/webapps/community/repository/view_changeset.mako
@@ -16,9 +16,9 @@
     can_upload = can_push
     can_download = not is_new and ( not is_malicious or can_push )
     if can_push:
-        browse_label = 'Browse or delete repository files'
+        browse_label = 'Browse or delete repository tip files'
     else:
-        browse_label = 'Browse repository files'
+        browse_label = 'Browse repository tip files'
 %>
 
 <%!
diff --git a/templates/webapps/community/repository/view_repository.mako b/templates/webapps/community/repository/view_repository.mako
index 8a243c03381..cdf34fdcb09 100644
--- a/templates/webapps/community/repository/view_repository.mako
+++ b/templates/webapps/community/repository/view_repository.mako
@@ -14,9 +14,9 @@
     can_browse_contents = webapp == 'community' and not is_new
     can_view_change_log = webapp == 'community' and not is_new
     if can_push:
-        browse_label = 'Browse or delete repository files'
+        browse_label = 'Browse or delete repository tip files'
     else:
-        browse_label = 'Browse repository files'
+        browse_label = 'Browse repository tip files'
 %>
 
 <%!
diff --git a/templates/webapps/community/repository/view_tool_metadata.mako b/templates/webapps/community/repository/view_tool_metadata.mako
index d444f5871b6..32ea68d25cd 100644
--- a/templates/webapps/community/repository/view_tool_metadata.mako
+++ b/templates/webapps/community/repository/view_tool_metadata.mako
@@ -17,9 +17,9 @@
     can_manage = is_admin or repository.user == trans.user
     can_view_change_log = webapp == 'community' and not is_new
     if can_push:
-        browse_label = 'Browse or delete repository files'
+        browse_label = 'Browse or delete repository tip files'
     else:
-        browse_label = 'Browse repository files'
+        browse_label = 'Browse repository tip files'
 %>
 
 <%!
diff --git a/templates/webapps/community/repository/view_workflow.mako b/templates/webapps/community/repository/view_workflow.mako
index fc79bf889f2..eac597375aa 100644
--- a/templates/webapps/community/repository/view_workflow.mako
+++ b/templates/webapps/community/repository/view_workflow.mako
@@ -20,9 +20,9 @@
     can_rate = in_tool_shed and not is_new and trans.user and repository.user != trans.user
     can_view_change_log = in_tool_shed and not is_new
     if can_push:
-        browse_label = 'Browse or delete repository files'
+        browse_label = 'Browse or delete repository tip files'
     else:
-        browse_label = 'Browse repository files'
+        browse_label = 'Browse repository tip files'
 %>
 
 <%!

From 437822b5ab430a9d7d0061db5a995872787286f0 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Wed, 16 Nov 2011 13:38:24 -0500
Subject: [PATCH 205/362] Make linking data in a library upload a job parameter
 so it can be checked during job finish to ensure the linked files are not
 overwritten when using outputs_to_working_directory.  This special-case fix
 is a temporary solution that should be removed as soon as we have a smarter
 way to handle "immutable outputs."

---
 lib/galaxy/jobs/__init__.py                  | 11 ++++++++++-
 lib/galaxy/tools/actions/upload.py           |  2 +-
 lib/galaxy/tools/actions/upload_common.py    |  7 ++-----
 lib/galaxy/web/controllers/library_common.py |  7 ++++++-
 4 files changed, 19 insertions(+), 8 deletions(-)

diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index b15103a335f..a76f32a08d7 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -541,7 +541,7 @@ class JobWrapper( object ):
                 self.version_string = open(version_filename).read()
                 os.unlink(version_filename)
 
-        if self.app.config.outputs_to_working_directory:
+        if self.app.config.outputs_to_working_directory and not self.__link_file_check():
             for dataset_path in self.get_output_fnames():
                 try:
                     shutil.move( dataset_path.false_path, dataset_path.real_path )
@@ -879,6 +879,15 @@ class JobWrapper( object ):
         else:
             return 'anonymous@unknown'
 
+    def __link_file_check( self ):
+        """ outputs_to_working_directory breaks library uploads where data is
+        linked.  This method is a hack that solves that problem, but is
+        specific to the upload tool and relies on an injected job param.  This
+        method should be removed ASAP and replaced with some properly generic
+        and stateful way of determining link-only datasets. -nate
+        """
+        return self.tool.id == 'upload1' and self.param_dict.get( 'link_data_only', None ) == 'link_to_files'
+
 class TaskWrapper(JobWrapper):
     """
     Extension of JobWrapper intended for running tasks.
diff --git a/lib/galaxy/tools/actions/upload.py b/lib/galaxy/tools/actions/upload.py
index 757f7fba866..ea99339aa5c 100644
--- a/lib/galaxy/tools/actions/upload.py
+++ b/lib/galaxy/tools/actions/upload.py
@@ -25,4 +25,4 @@ class UploadToolAction( ToolAction ):
         
         json_file_path = upload_common.create_paramfile( trans, uploaded_datasets )
         data_list = [ ud.data for ud in uploaded_datasets ]
-        return upload_common.create_job( trans, incoming, tool, json_file_path, data_list, return_job=True )
+        return upload_common.create_job( trans, incoming, tool, json_file_path, data_list )
diff --git a/lib/galaxy/tools/actions/upload_common.py b/lib/galaxy/tools/actions/upload_common.py
index c6b7bb3f53e..bc20cb2d588 100644
--- a/lib/galaxy/tools/actions/upload_common.py
+++ b/lib/galaxy/tools/actions/upload_common.py
@@ -294,7 +294,7 @@ def create_paramfile( trans, uploaded_datasets ):
         json_file.write( to_json_string( json ) + '\n' )
     json_file.close()
     return json_file_path
-def create_job( trans, params, tool, json_file_path, data_list, folder=None, return_job=False ):
+def create_job( trans, params, tool, json_file_path, data_list, folder=None ):
     """
     Create the upload job.
     """
@@ -341,10 +341,7 @@ def create_job( trans, params, tool, json_file_path, data_list, folder=None, ret
     output = odict()
     for i, v in enumerate( data_list ):
         output[ 'output%i' % i ] = v
-    if return_job:
-        return job, output
-    else:
-        return output
+    return job, output
 def active_folders( trans, folder ):
     # Stolen from galaxy.web.controllers.library_common (importing from which causes a circular issues).
     # Much faster way of retrieving all active sub-folders within a given folder than the
diff --git a/lib/galaxy/web/controllers/library_common.py b/lib/galaxy/web/controllers/library_common.py
index 1c2b2e61e15..d464c063688 100644
--- a/lib/galaxy/web/controllers/library_common.py
+++ b/lib/galaxy/web/controllers/library_common.py
@@ -1045,7 +1045,12 @@ class LibraryCommon( BaseUIController, UsesFormDefinitions ):
                                                        status='error' ) )
         json_file_path = upload_common.create_paramfile( trans, uploaded_datasets )
         data_list = [ ud.data for ud in uploaded_datasets ]
-        return upload_common.create_job( trans, tool_params, tool, json_file_path, data_list, folder=library_bunch.folder )
+        job, output = upload_common.create_job( trans, tool_params, tool, json_file_path, data_list, folder=library_bunch.folder )
+        # HACK: Prevent outputs_to_working_directory from overwriting inputs when "linking"
+        job.add_parameter( 'link_data_only', to_json_string( kwd.get( 'link_data_only', 'copy_files' ) ) )
+        trans.sa_session.add( job )
+        trans.sa_session.flush()
+        return output
     def make_library_uploaded_dataset( self, trans, cntrller, params, name, path, type, library_bunch, in_folder=None ):
         library_bunch.replace_dataset = None # not valid for these types of upload
         uploaded_dataset = util.bunch.Bunch()

From 55bf9f0589a23443092923e7195842b1760621a8 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Wed, 16 Nov 2011 13:53:05 -0500
Subject: [PATCH 206/362] Bugfix for the last commit, since
 JobWrapper.param_dict doesn't exist after a server restart.

---
 lib/galaxy/jobs/__init__.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index a76f32a08d7..98987a719be 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -886,7 +886,9 @@ class JobWrapper( object ):
         method should be removed ASAP and replaced with some properly generic
         and stateful way of determining link-only datasets. -nate
         """
-        return self.tool.id == 'upload1' and self.param_dict.get( 'link_data_only', None ) == 'link_to_files'
+        job = self.get_job()
+        param_dict = job.get_param_values( self.app )
+        return self.tool.id == 'upload1' and param_dict.get( 'link_data_only', None ) == 'link_to_files'
 
 class TaskWrapper(JobWrapper):
     """

From ce6a989dd7f1b65858c5a3df1f56c56413c16eb9 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Wed, 16 Nov 2011 16:10:29 -0500
Subject: [PATCH 207/362] Update Tophat functional tests for tool version 1.3.3


From 1ba3bae29cadbf8e59f74bd26b806592658c44fb Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Wed, 16 Nov 2011 16:55:44 -0500
Subject: [PATCH 208/362] Hierarchical object store with weighting.

---
 lib/galaxy/config.py               |   1 +
 lib/galaxy/datatypes/metadata.py   |   4 +-
 lib/galaxy/jobs/runners/local.py   |   2 +-
 lib/galaxy/objectstore/__init__.py | 117 ++++++++++++++++++++++++++---
 4 files changed, 110 insertions(+), 14 deletions(-)

diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py
index 6edd6885a54..c94a58caad6 100644
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -152,6 +152,7 @@ class Configuration( object ):
         self.s3_bucket = kwargs.get( 's3_bucket', None)
         self.use_reduced_redundancy = kwargs.get( 'use_reduced_redundancy', False )
         self.object_store_cache_size = float(kwargs.get( 'object_store_cache_size', -1 ))
+        self.hierarchical_object_store_config_file = kwargs.get( 'hierarchical_object_store_config_file', None )
         # Parse global_conf and save the parser
         global_conf = kwargs.get( 'global_conf', None )
         global_conf_parser = ConfigParser.ConfigParser()
diff --git a/lib/galaxy/datatypes/metadata.py b/lib/galaxy/datatypes/metadata.py
index f4713d8f1de..fc87870511a 100644
--- a/lib/galaxy/datatypes/metadata.py
+++ b/lib/galaxy/datatypes/metadata.py
@@ -438,9 +438,9 @@ class FileParameter( MetadataParameter ):
             mf = parent.metadata.get( self.spec.name, None)
             if mf is None:
                 mf = self.new_file( dataset = parent, **value.kwds )
-            shutil.move( value.file_name, mf.file_name )
             # Ensure the metadata file gets updated with content
-            parent.dataset.object_store.update_from_file( parent.dataset.id, file_name=mf.file_name, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name=os.path.basename(mf.file_name) )
+            parent.dataset.object_store.update_from_file( parent.dataset.id, file_name=value.file_name, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name=os.path.basename(mf.file_name) )
+            os.unlink( value.file_name )
             value = mf.id
         return value
     
diff --git a/lib/galaxy/jobs/runners/local.py b/lib/galaxy/jobs/runners/local.py
index ff509dab5fe..ec13423c319 100644
--- a/lib/galaxy/jobs/runners/local.py
+++ b/lib/galaxy/jobs/runners/local.py
@@ -58,8 +58,8 @@ class LocalJobRunner( BaseJobRunner ):
             job_wrapper.prepare()
             command_line = self.build_command_line( job_wrapper )
         except:
-            job_wrapper.fail( "failure preparing job", exception=True )
             log.exception("failure running job %d" % job_wrapper.job_id)
+            job_wrapper.fail( "failure preparing job", exception=True )
             return
         # If we were able to get a command line, run the job
         if command_line:
diff --git a/lib/galaxy/objectstore/__init__.py b/lib/galaxy/objectstore/__init__.py
index d318a1f4b5b..d540451a987 100644
--- a/lib/galaxy/objectstore/__init__.py
+++ b/lib/galaxy/objectstore/__init__.py
@@ -6,6 +6,7 @@ tools
 
 import os
 import time
+import random
 import shutil
 import logging
 import threading
@@ -138,16 +139,16 @@ class ObjectStore(object):
         """
         raise NotImplementedError()
     
-    def update_from_file(self, dataset_id, extra_dir=None, extra_dir_at_root=False, alt_name=None, filename=None, create=False):
+    def update_from_file(self, dataset_id, extra_dir=None, extra_dir_at_root=False, alt_name=None, file_name=None, create=False):
         """
         Inform the store that the file associated with the object has been
-        updated. If `filename` is provided, update from that file instead
+        updated. If `file_name` is provided, update from that file instead
         of the default.
         If the object does not exist raises `ObjectNotFound`.
         See `exists` method for the description of other fields.
         
-        :type filename: string
-        :param filename: Use file pointed to by `filename` as the source for 
+        :type file_name: string
+        :param file_name: Use file pointed to by `file_name` as the source for 
                          updating the dataset identified by `dataset_id`
         
         :type create: bool
@@ -179,9 +180,9 @@ class DiskObjectStore(ObjectStore):
     Standard Galaxy object store, stores objects in files under a specific
     directory on disk.
     """
-    def __init__(self, config):
+    def __init__(self, config, file_path=None):
         super(DiskObjectStore, self).__init__()
-        self.file_path = config.file_path
+        self.file_path = file_path or config.file_path
     
     def _get_filename(self, dataset_id, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None):
         """Class method that returns the absolute path for the file corresponding
@@ -819,13 +820,107 @@ class S3ObjectStore(ObjectStore):
 class HierarchicalObjectStore(ObjectStore):
     """
     ObjectStore that defers to a list of backends, for getting objects the
-    first store where the object exists is used, objects are always created
-    in the first store.
+    first store where the object exists is used, objects are created in a
+    store selected randomly, but with weighting.
     """
     
-    def __init__(self, backends=[]):
+    def __init__(self, config):
         super(HierarchicalObjectStore, self).__init__()
-    
+        assert config is not None, "hierarchical object store ('object_store = hierarchical') " \
+                                   "requires a config file, please set one in " \
+                                   "'hierarchical_object_store_config_file')"
+        self.hierarchical_config = config
+        self.backends = {}
+        self.weighted_backend_names = []
+
+        random.seed()
+
+        self.__parse_hierarchical_config(config)
+
+    def __parse_hierarchical_config(self, config):
+        tree = util.parse_xml(self.hierarchical_config)
+        root = tree.getroot()
+        log.debug('Loading backends for hierarchical object store from %s' % self.hierarchical_config)
+        for elem in [ e for e in root if e.tag == 'backend' ]:
+            name = elem.get('name')
+            weight = int(elem.get('weight', 1))
+            if elem.get('type', 'disk'):
+                path = None
+                for sub in elem:
+                    if sub.tag == 'path':
+                        path = sub.get('value')
+                self.backends[name] = DiskObjectStore(config, file_path=path)
+                log.debug("Loaded disk backend '%s' with weight %s and disk path '%s'" % (name, weight, path))
+            for i in range(0, weight):
+                # The simplest way to do weighting: add backend names to a
+                # sequence the number of times equalling weight, then randomly
+                # choose a backend from that sequence at creation
+                self.weighted_backend_names.append(name)
+
+    def exists(self, dataset_id, **kwargs):
+        store = self.__get_store_for(dataset_id, **kwargs)
+        return store is not None
+
+    def file_ready(self, dataset_id, **kwargs):
+        store = self.__get_store_for(dataset_id, **kwargs)
+        if store is not None:
+            return store.file_ready(dataset_id, **kwargs)
+        return False
+
+    def create(self, dataset_id, **kwargs):
+        if not self.exists(dataset_id, **kwargs):
+            store_name = random.choice(self.weighted_backend_names)
+            log.debug("Selected backend '%s' for creation of dataset %s" % (store_name, dataset_id))
+            return self.backends[store_name].create(dataset_id, **kwargs)
+
+    def empty(self, dataset_id, **kwargs):
+        store = self.__get_store_for(dataset_id, **kwargs):
+        if store is not None:
+            return store.empty(dataset_id, **kwargs)
+        return True
+
+    def size(self, dataset_id, **kwargs):
+        store = self.__get_store_for(dataset_id, **kwargs):
+        if store is not None:
+            return store.size(dataset_id, **kwargs)
+        return 0
+
+    def delete(self, dataset_id, entire_dir=False, **kwargs):
+        store = self.__get_store_for(dataset_id, **kwargs):
+        if store is not None:
+            return store.delete(dataset_id, entire_dir=entire_dir, **kwargs)
+        return False
+
+    def get_data(self, dataset_id, start=0, count=-1, **kwargs):
+        store = self.__get_store_for(dataset_id, **kwargs):
+        if store is not None:
+            return store.get_data(dataset_id, start=0, count=-1, **kwargs)
+        raise ObjectNotFound()
+
+    def get_filename(self, dataset_id, **kwargs):
+        store = self.__get_store_for(dataset_id, **kwargs):
+        if store is not None:
+            return store.get_filename(dataset_id, **kwargs)
+        raise ObjectNotFound()
+
+    def update_from_file(self, dataset_id, file_name=None, create=False, **kwargs):
+        store = self.__get_store_for(dataset_id, **kwargs):
+        if store is not None:
+            return store.update_from_file(dataset_id, file_name=file_name, create=create, **kwargs)
+        raise ObjectNotFound()
+
+    def get_object_url(self, dataset_id, **kwargs):
+        # FIXME: dir_only
+        store = self.__get_store_for(dataset_id, **kwargs):
+        if store is not None:
+            return store.get_object_url(dataset_id, **kwargs)
+        return None
+
+    def __get_store_for(self, dataset_id, **kwargs):
+        for store in self.backends.values():
+            if store.exists(dataset_id, **kwargs):
+                return store
+        return None
 
 def build_object_store_from_config(config):
     """ Depending on the configuration setting, invoke the appropriate object store
@@ -838,7 +933,7 @@ def build_object_store_from_config(config):
         os.environ['AWS_SECRET_ACCESS_KEY'] = config.aws_secret_key
         return S3ObjectStore(config=config)
     elif store == 'hierarchical':
-        return HierarchicalObjectStore()
+        return HierarchicalObjectStore(config.hierarchical_object_store_config_file)
 
 def convert_bytes(bytes):
     """ A helper function used for pretty printing disk usage """

From 210e0fa11509173fecb0cbb6074d5e6fada0c490 Mon Sep 17 00:00:00 2001
From: Eric Paniagua <paniagua.cshl@gmail.com>
Date: Wed, 16 Nov 2011 17:25:26 -0500
Subject: [PATCH 209/362] fix tool_form.mako js typo affecting "drill_down"
 input

---
 templates/tool_form.mako | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/templates/tool_form.mako b/templates/tool_form.mako
index 2bc185be038..383ac266b1a 100644
--- a/templates/tool_form.mako
+++ b/templates/tool_form.mako
@@ -38,7 +38,7 @@
 
             parent_li.find( 'span' ).wrapInner( '<a/>' ).find( 'a' ).click( function() {
                 sub_ul.toggle();
-                (this).html( sub_ul.is(":hidden") ? '[+]' : '[-]' );
+                $(this).html( sub_ul.is(":hidden") ? '[+]' : '[-]' );
             });
             parent_li.append( sub_ul );
         });

From 65719d734824cded9862bce2b6e5f9116e5b221f Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Wed, 16 Nov 2011 17:53:27 -0500
Subject: [PATCH 210/362] Refactor data providers to use the
 get_iterator/process_data framework whenever providing individual data
 points.

---
 .../visualization/tracks/data_providers.py    | 130 ++++++++++--------
 1 file changed, 74 insertions(+), 56 deletions(-)

diff --git a/lib/galaxy/visualization/tracks/data_providers.py b/lib/galaxy/visualization/tracks/data_providers.py
index a909699ab69..377160dca61 100644
--- a/lib/galaxy/visualization/tracks/data_providers.py
+++ b/lib/galaxy/visualization/tracks/data_providers.py
@@ -84,6 +84,21 @@ class TracksDataProvider( object ):
         # Override.
         pass
         
+    def get_iterator( self, chrom, start, end ):
+        """
+        Returns an iterator that provides data in the region chrom:start-end
+        """
+        # Override.
+        pass
+        
+    def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ):
+        """
+        Process data from an iterator to a format that can be provided to client.
+        """
+        # Override.
+        pass
+        
+        
     def get_data( self, chrom, start, end, start_val=0, max_vals=None, **kwargs ):
         """ 
         Returns data in region defined by chrom, start, and end. start_val and
@@ -93,8 +108,8 @@ class TracksDataProvider( object ):
         Return value must be a dictionary with the following attributes:
             dataset_type, data
         """
-        # Override.
-        pass
+        iterator = self.get_iterator( chrom, start, end )
+        return self.process_data( iterator, start_val, max_vals, **kwargs )
         
     def get_filters( self ):
         """ 
@@ -236,8 +251,6 @@ class TabixDataProvider( FilterableMixin, TracksDataProvider ):
                     
         bgzip_fname = self.dependencies['bgzip'].file_name
         
-        # if os.path.getsize(self.converted_dataset.file_name) == 0:
-            # return { 'kind': messages.ERROR, 'message': "Tabix converted size was 0, meaning the input file had invalid values." }
         tabix = ctabix.Tabixfile(bgzip_fname, index_filename=self.converted_dataset.file_name)
         
         # If chrom is not found in indexes, try removing the first three 
@@ -248,11 +261,7 @@ class TabixDataProvider( FilterableMixin, TracksDataProvider ):
             chrom = chrom[3:]
         
         return tabix.fetch(reference=chrom, start=start, end=end)
-        
-    def get_data( self, chrom, start, end, start_val=0, max_vals=None, **kwargs ):
-        iterator = self.get_iterator( chrom, start, end )
-        return self.process_data( iterator, start_val, max_vals, **kwargs )
-        
+                
     def write_data_to_file( self, chrom, start, end, filename ):
         iterator = self.get_iterator( chrom, start, end )
         out = open( filename, "w" )
@@ -273,11 +282,7 @@ class BedDataProvider( TracksDataProvider ):
     
     def get_iterator( self, chrom, start, end ):
         raise "Unimplemented Method"
-        
-    def get_data( self, chrom, start, end, start_val=0, max_vals=None, **kwargs ):
-        iterator = self.get_iterator( chrom, start, end )
-        return self.process_data( iterator, start_val, max_vals, **kwargs )
-    
+            
     def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ):
         """
         Provides
@@ -392,14 +397,6 @@ class VcfDataProvider( TracksDataProvider ):
     
     col_name_data_attr_mapping = { 'Qual' : { 'index': 6 , 'name' : 'Qual' } }
     
-
-    def get_iterator( self, chrom, start, end ):
-        raise "Unimplemented Method"
-
-    def get_data( self, chrom, start, end, start_val=0, max_vals=None, **kwargs ):
-        iterator = self.get_iterator( chrom, start, end )
-        return self.process_data( iterator, start_val, max_vals, **kwargs )
-
     def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ):
         """
         Returns a dict with the following attributes:
@@ -607,11 +604,32 @@ class BamDataProvider( TracksDataProvider ):
         
         # Cleanup.
         bamfile.close()
-    
-    def get_data( self, chrom, start, end, start_val=0, max_vals=sys.maxint, **kwargs ):
-        """
-        Fetch reads in the region and additional metadata.
         
+    def get_iterator( self, chrom, start, end ):
+        """
+        Returns an iterator that provides data in the region chrom:start-end
+        """
+        start, end = int(start), int(end)
+        orig_data_filename = self.original_dataset.file_name
+        index_filename = self.converted_dataset.file_name
+        
+        # Attempt to open the BAM file with index
+        bamfile = csamtools.Samfile( filename=orig_data_filename, mode='rb', index_filename=index_filename )
+        try:
+            data = bamfile.fetch(start=start, end=end, reference=chrom)
+        except ValueError, e:
+            # Some BAM files do not prefix chromosome names with chr, try without
+            if chrom.startswith( 'chr' ):
+                try:
+                    data = bamfile.fetch( start=start, end=end, reference=chrom[3:] )
+                except ValueError:
+                    return None
+            else:
+                return None
+        return data
+                
+    def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ):
+        """
         Returns a dict with the following attributes:
             data - a list of reads with the format 
                     [<guid>, <start>, <end>, <name>, <read_1>, <read_2>] 
@@ -628,26 +646,6 @@ class BamDataProvider( TracksDataProvider ):
             max_high - highest coordinate for the returned reads
             message - error/informative message
         """
-        start, end = int(start), int(end)
-        orig_data_filename = self.original_dataset.file_name
-        index_filename = self.converted_dataset.file_name
-        no_detail = "no_detail" in kwargs
-        
-        # Attempt to open the BAM file with index
-        bamfile = csamtools.Samfile( filename=orig_data_filename, mode='rb', index_filename=index_filename )
-        message = None
-        try:
-            data = bamfile.fetch(start=start, end=end, reference=chrom)
-        except ValueError, e:
-            # Some BAM files do not prefix chromosome names with chr, try without
-            if chrom.startswith( 'chr' ):
-                try:
-                    data = bamfile.fetch( start=start, end=end, reference=chrom[3:] )
-                except ValueError:
-                    return None
-            else:
-                return None
-                
         # Decode strand from read flag.
         def decode_strand( read_flag, mask ):
             strand_flag = ( read_flag & mask == 0 )
@@ -660,7 +658,8 @@ class BamDataProvider( TracksDataProvider ):
         results = []
         paired_pending = {}
         unmapped = 0
-        for count, read in enumerate( data ):
+        message = None
+        for count, read in enumerate( iterator ):
             if count < start_val:
                 continue
             if ( count - start_val - unmapped ) >= max_vals:
@@ -720,8 +719,8 @@ class BamDataProvider( TracksDataProvider ):
 
             results.append( [ "%i_%s" % ( read_start, qname ), read_start, read_end, qname, r1, r2 ] )
             
-        # Clean up.
-        bamfile.close()
+        # Clean up. TODO: is this needed? If so, we'll need a cleanup function after processing the data.
+        # bamfile.close()
         
         max_low, max_high = get_bounds( results, 1, 2 )
                 
@@ -848,13 +847,15 @@ class IntervalIndexDataProvider( FilterableMixin, TracksDataProvider ):
             for interval in feature.intervals:
                 out.write(interval.raw_line + '\n')
         out.close()
-    
-    def get_data( self, chrom, start, end, start_val=0, max_vals=sys.maxint, **kwargs ):
+        
+    def get_iterator( self, chrom, start, end ):
+        """
+        Returns an array with values: (a) source file and (b) an iterator that
+        provides data in the region chrom:start-end
+        """
         start, end = int(start), int(end)
         source = open( self.original_dataset.file_name )
         index = Indexes( self.converted_dataset.file_name )
-        results = []
-        message = None
 
         # If chrom is not found in indexes, try removing the first three 
         # characters (e.g. 'chr') and see if that works. This enables the
@@ -862,6 +863,13 @@ class IntervalIndexDataProvider( FilterableMixin, TracksDataProvider ):
         chrom = str(chrom)
         if chrom not in index.indexes and chrom[3:] in index.indexes:
             chrom = chrom[3:]
+            
+        return index.find(chrom, start, end)
+
+    def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ):
+        results = []
+        message = None
+        source = open( self.original_dataset.file_name )
 
         #
         # Build data to return. Payload format is:
@@ -872,7 +880,7 @@ class IntervalIndexDataProvider( FilterableMixin, TracksDataProvider ):
         #
         filter_cols = from_json_string( kwargs.get( "filter_cols", "[]" ) )
         no_detail = ( "no_detail" in kwargs )
-        for count, val in enumerate( index.find(chrom, start, end) ):
+        for count, val in enumerate( iterator ):
             start, end, offset = val[0], val[1], val[2]
             if count < start_val:
                 continue
@@ -899,14 +907,24 @@ class GFFDataProvider( TracksDataProvider ):
     NOTE: this data provider does not use indices, and hence will be very slow
     for large datasets.
     """
-    def get_data( self, chrom, start, end, start_val=0, max_vals=sys.maxint, **kwargs ):
+    
+    def get_iterator( self, chrom, start, end ):
+        """
+        Returns an iterator that provides data in the region chrom:start-end
+        """
         start, end = int( start ), int( end )
         source = open( self.original_dataset.file_name )
+        return GFFReaderWrapper( source, fix_strand=True )
+        
+    def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ):
+        """
+        Process data from an iterator to a format that can be provided to client.
+        """
         results = []
         message = None
         offset = 0
         
-        for count, feature in enumerate( GFFReaderWrapper( source, fix_strand=True ) ):
+        for count, feature in enumerate( iterator ):
             if count < start_val:
                 continue
             if count-start_val >= max_vals:

From a59e4d3d417ff8771292796725b548c06d875f3e Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Thu, 17 Nov 2011 09:12:19 -0500
Subject: [PATCH 211/362] When fetching BAM data for Trackster, use BAI from
 metadata when possible rather than waiting for converted dataset with
 duplicate BAI.

---
 lib/galaxy/web/controllers/tracks.py | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/web/controllers/tracks.py b/lib/galaxy/web/controllers/tracks.py
index 8dd0d3fa22f..06eed0039b5 100644
--- a/lib/galaxy/web/controllers/tracks.py
+++ b/lib/galaxy/web/controllers/tracks.py
@@ -607,8 +607,16 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
         else:
             tracks_dataset_type = data_sources['data']['name']
             data_provider_class = get_data_provider( name=tracks_dataset_type, original_dataset=dataset )
-            converted_dataset = dataset.get_converted_dataset( trans, tracks_dataset_type )
-            deps = dataset.get_converted_dataset_deps( trans, tracks_dataset_type )
+            # HACK: Use bai from bam HDA's metadata if available. This saves 
+            # the client from waiting a long time to generate a duplicate
+            # bam via a converted dataset.
+            if dataset.ext == "bam" and dataset.metadata.get( "bam_index", None ) is not None:
+                converted_dataset = dataset.metadata.bam_index
+                deps = None
+            else:
+                # Default behavior.    
+                converted_dataset = dataset.get_converted_dataset( trans, tracks_dataset_type )
+                deps = dataset.get_converted_dataset_deps( trans, tracks_dataset_type )
             data_provider = data_provider_class( converted_dataset=converted_dataset, original_dataset=dataset, dependencies=deps )
         
         # Get and return data from data_provider.

From 4c844ee5abc7a15e779e1d3cfe2f63c37a806346 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Thu, 17 Nov 2011 11:13:53 -0500
Subject: [PATCH 212/362] Update GATK to version 1.3.

---
 tools/gatk/analyze_covariates.xml          | 7 +++----
 tools/gatk/count_covariates.xml            | 4 ++--
 tools/gatk/indel_realigner.xml             | 4 ++--
 tools/gatk/realigner_target_creator.xml    | 4 ++--
 tools/gatk/table_recalibration.xml         | 4 ++--
 tools/gatk/unified_genotyper.xml           | 8 ++------
 tools/gatk/variant_annotator.xml           | 4 ++--
 tools/gatk/variant_apply_recalibration.xml | 4 ++--
 tools/gatk/variant_combine.xml             | 4 ++--
 tools/gatk/variant_eval.xml                | 4 ++--
 tools/gatk/variant_filtration.xml          | 4 ++--
 tools/gatk/variant_recalibrator.xml        | 4 ++--
 tools/gatk/variants_validate.xml           | 4 ++--
 13 files changed, 27 insertions(+), 32 deletions(-)

diff --git a/tools/gatk/analyze_covariates.xml b/tools/gatk/analyze_covariates.xml
index d6efcb5436b..cfa5110b4f1 100644
--- a/tools/gatk/analyze_covariates.xml
+++ b/tools/gatk/analyze_covariates.xml
@@ -1,7 +1,7 @@
-<tool id="gatk_analyze_covariates" name="Analyze Covariates" version="0.0.3">
+<tool id="gatk_analyze_covariates" name="Analyze Covariates" version="0.0.4">
   <description>- draw plots</description>
   <requirements>
-      <requirement type="package" version="1.2">gatk</requirement>
+      <requirement type="package" version="1.3">gatk</requirement>
   </requirements>
   <command interpreter="python">gatk_wrapper.py
    --max_jvm_heap_fraction "1"
@@ -13,8 +13,7 @@
     -outputDir "${output_html.files_path}"
     ##--num_threads 4 ##hard coded, for now
     ##-log "${output_log}"
-    ##-Rscript,--path_to_Rscript path_to_Rscript; on path is good enough
-    -resources "${GALAXY_DATA_INDEX_DIR}/gatk/R"         
+    ##-Rscript,--path_to_Rscript path_to_Rscript; on path is good enough         
     #if $analysis_param_type.analysis_param_type_selector == "advanced":
         --ignoreQ "${analysis_param_type.ignore_q}"
         --numRG "${analysis_param_type.num_read_groups}"
diff --git a/tools/gatk/count_covariates.xml b/tools/gatk/count_covariates.xml
index 5a9da7a6e82..46730396a3f 100644
--- a/tools/gatk/count_covariates.xml
+++ b/tools/gatk/count_covariates.xml
@@ -1,7 +1,7 @@
-<tool id="gatk_count_covariates" name="Count Covariates" version="0.0.3">
+<tool id="gatk_count_covariates" name="Count Covariates" version="0.0.4">
   <description>on BAM files</description>
   <requirements>
-      <requirement type="package" version="1.2">gatk</requirement>
+      <requirement type="package" version="1.3">gatk</requirement>
   </requirements>
   <command interpreter="python">gatk_wrapper.py
    --max_jvm_heap_fraction "1"
diff --git a/tools/gatk/indel_realigner.xml b/tools/gatk/indel_realigner.xml
index 0e8c4635f93..5b4d0113ab0 100644
--- a/tools/gatk/indel_realigner.xml
+++ b/tools/gatk/indel_realigner.xml
@@ -1,7 +1,7 @@
-<tool id="gatk_indel_realigner" name="Indel Realigner" version="0.0.4">
+<tool id="gatk_indel_realigner" name="Indel Realigner" version="0.0.5">
   <description>- perform local realignment</description>
   <requirements>
-      <requirement type="package" version="1.2">gatk</requirement>
+      <requirement type="package" version="1.3">gatk</requirement>
   </requirements>
   <command interpreter="python">gatk_wrapper.py
    --max_jvm_heap_fraction "1"
diff --git a/tools/gatk/realigner_target_creator.xml b/tools/gatk/realigner_target_creator.xml
index c9c3172bdcb..dad4ace9320 100644
--- a/tools/gatk/realigner_target_creator.xml
+++ b/tools/gatk/realigner_target_creator.xml
@@ -1,7 +1,7 @@
-<tool id="gatk_realigner_target_creator" name="Realigner Target Creator" version="0.0.3">
+<tool id="gatk_realigner_target_creator" name="Realigner Target Creator" version="0.0.4">
   <description>for use in local realignment</description>
   <requirements>
-      <requirement type="package" version="1.2">gatk</requirement>
+      <requirement type="package" version="1.3">gatk</requirement>
   </requirements>
   <command interpreter="python">gatk_wrapper.py
    --max_jvm_heap_fraction "1"
diff --git a/tools/gatk/table_recalibration.xml b/tools/gatk/table_recalibration.xml
index 3c40af6def1..d10c9291b63 100644
--- a/tools/gatk/table_recalibration.xml
+++ b/tools/gatk/table_recalibration.xml
@@ -1,7 +1,7 @@
-<tool id="gatk_table_recalibration" name="Table Recalibration" version="0.0.3">
+<tool id="gatk_table_recalibration" name="Table Recalibration" version="0.0.4">
   <description>on BAM files</description>
   <requirements>
-      <requirement type="package" version="1.2">gatk</requirement>
+      <requirement type="package" version="1.3">gatk</requirement>
   </requirements>
   <command interpreter="python">gatk_wrapper.py
    --max_jvm_heap_fraction "1"
diff --git a/tools/gatk/unified_genotyper.xml b/tools/gatk/unified_genotyper.xml
index 08490b17cff..5e1d8d53d44 100644
--- a/tools/gatk/unified_genotyper.xml
+++ b/tools/gatk/unified_genotyper.xml
@@ -1,7 +1,7 @@
-<tool id="gatk_unified_genotyper" name="Unified Genotyper" version="0.0.3">
+<tool id="gatk_unified_genotyper" name="Unified Genotyper" version="0.0.4">
   <description>SNP and indel caller</description>
   <requirements>
-      <requirement type="package" version="1.2">gatk</requirement>
+      <requirement type="package" version="1.3">gatk</requirement>
   </requirements>
   <command interpreter="python">gatk_wrapper.py
    --max_jvm_heap_fraction "1"
@@ -104,7 +104,6 @@
         --output_mode "${analysis_param_type.output_mode}"
         ${analysis_param_type.compute_SLOD}
         --min_base_quality_score "${analysis_param_type.min_base_quality_score}"
-        --min_mapping_quality_score "${analysis_param_type.min_mapping_quality_score}"
         --max_deletion_fraction "${analysis_param_type.max_deletion_fraction}"
         --min_indel_count_for_genotyping "${analysis_param_type.min_indel_count_for_genotyping}"
         --indel_heterozygosity "${analysis_param_type.indel_heterozygosity}"
@@ -343,7 +342,6 @@
         </param>
         <param name="compute_SLOD" type="boolean" truevalue="--computeSLOD" falsevalue="" label="Compute the SLOD" />
         <param name="min_base_quality_score" type="integer" value="17" label="Minimum base quality required to consider a base for calling" />
-        <param name="min_mapping_quality_score" type="integer" value="20" label="Minimum read mapping quality required to consider a read for calling" />
         <param name="max_deletion_fraction" type="float" value="0.05" label="Maximum fraction of reads with deletions spanning this locus for it to be callable" help="to disable, set to &lt; 0 or &gt; 1" />
         <param name="min_indel_count_for_genotyping" type="integer" value="5" label="Minimum number of consensus indels required to trigger genotyping run" />
         <param name="indel_heterozygosity" type="float" value="0.000125" label="Heterozygosity for indel calling" help="1.0/8000==0.000125"/>
@@ -417,7 +415,6 @@
           <param name="output_mode" value="EMIT_ALL_CONFIDENT_SITES" />
           <param name="compute_SLOD" />
           <param name="min_base_quality_score" value="17" />
-          <param name="min_mapping_quality_score" value="20" />
           <param name="max_deletion_fraction" value="-1" />
           <param name="min_indel_count_for_genotyping" value="2" />
           <param name="indel_heterozygosity" value="0.000125" />
@@ -471,7 +468,6 @@ Go `here &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_th
  standard_min_confidence_threshold_for_emitting    The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be emitted (and filtered if less than the calling threshold)
  noSLOD                                            If provided, we will not calculate the SLOD
  min_base_quality_score                            Minimum base quality required to consider a base for calling
- min_mapping_quality_score                         Minimum read mapping quality required to consider a read for calling
  max_deletion_fraction                             Maximum fraction of reads with deletions spanning this locus for it to be callable [to disable, set to &lt; 0 or &gt; 1; default:0.05]
  min_indel_count_for_genotyping                    Minimum number of consensus indels required to trigger genotyping run
  indel_heterozygosity                              Heterozygosity for indel calling
diff --git a/tools/gatk/variant_annotator.xml b/tools/gatk/variant_annotator.xml
index 3dc654c151b..01ca23a1e36 100644
--- a/tools/gatk/variant_annotator.xml
+++ b/tools/gatk/variant_annotator.xml
@@ -1,7 +1,7 @@
-<tool id="gatk_variant_annotator" name="Variant Annotator" version="0.0.2">
+<tool id="gatk_variant_annotator" name="Variant Annotator" version="0.0.3">
   <description></description>
   <requirements>
-      <requirement type="package" version="1.2">gatk</requirement>
+      <requirement type="package" version="1.3">gatk</requirement>
   </requirements>
   <command interpreter="python">gatk_wrapper.py
    --max_jvm_heap_fraction "1"
diff --git a/tools/gatk/variant_apply_recalibration.xml b/tools/gatk/variant_apply_recalibration.xml
index 308eec009b3..639f5979dc7 100644
--- a/tools/gatk/variant_apply_recalibration.xml
+++ b/tools/gatk/variant_apply_recalibration.xml
@@ -1,7 +1,7 @@
-<tool id="gatk_variant_apply_recalibration" name="Apply Variant Recalibration" version="0.0.2">
+<tool id="gatk_variant_apply_recalibration" name="Apply Variant Recalibration" version="0.0.3">
   <description></description>
   <requirements>
-      <requirement type="package" version="1.2">gatk</requirement>
+      <requirement type="package" version="1.3">gatk</requirement>
   </requirements>
   <command interpreter="python">gatk_wrapper.py
    --max_jvm_heap_fraction "1"
diff --git a/tools/gatk/variant_combine.xml b/tools/gatk/variant_combine.xml
index 69b4f7d76e9..23c3d18a6c9 100644
--- a/tools/gatk/variant_combine.xml
+++ b/tools/gatk/variant_combine.xml
@@ -1,7 +1,7 @@
-<tool id="gatk_variant_combine" name="Combine Variants" version="0.0.2">
+<tool id="gatk_variant_combine" name="Combine Variants" version="0.0.3">
   <description></description>
   <requirements>
-      <requirement type="package" version="1.2">gatk</requirement>
+      <requirement type="package" version="1.3">gatk</requirement>
   </requirements>
   <command interpreter="python">gatk_wrapper.py
    --max_jvm_heap_fraction "1"
diff --git a/tools/gatk/variant_eval.xml b/tools/gatk/variant_eval.xml
index 9ade980aa94..95fa3a26610 100644
--- a/tools/gatk/variant_eval.xml
+++ b/tools/gatk/variant_eval.xml
@@ -1,7 +1,7 @@
-<tool id="gatk_variant_eval" name="Eval Variants" version="0.0.2">
+<tool id="gatk_variant_eval" name="Eval Variants" version="0.0.3">
   <description></description>
   <requirements>
-      <requirement type="package" version="1.2">gatk</requirement>
+      <requirement type="package" version="1.3">gatk</requirement>
   </requirements>
   <command interpreter="python">gatk_wrapper.py
    --max_jvm_heap_fraction "1"
diff --git a/tools/gatk/variant_filtration.xml b/tools/gatk/variant_filtration.xml
index 679c3210211..040a0cb56d5 100644
--- a/tools/gatk/variant_filtration.xml
+++ b/tools/gatk/variant_filtration.xml
@@ -1,7 +1,7 @@
-<tool id="gatk_variant_filtration" name="Variant Filtration" version="0.0.2">
+<tool id="gatk_variant_filtration" name="Variant Filtration" version="0.0.3">
   <description>on VCF files</description>
   <requirements>
-      <requirement type="package" version="1.2">gatk</requirement>
+      <requirement type="package" version="1.3">gatk</requirement>
   </requirements>
   <command interpreter="python">gatk_wrapper.py
    --max_jvm_heap_fraction "1"
diff --git a/tools/gatk/variant_recalibrator.xml b/tools/gatk/variant_recalibrator.xml
index 65a26f47ada..80310f0c2d6 100644
--- a/tools/gatk/variant_recalibrator.xml
+++ b/tools/gatk/variant_recalibrator.xml
@@ -1,7 +1,7 @@
-<tool id="gatk_variant_recalibrator" name="Variant Recalibrator" version="0.0.2">
+<tool id="gatk_variant_recalibrator" name="Variant Recalibrator" version="0.0.3">
   <description></description>
   <requirements>
-      <requirement type="package" version="1.2">gatk</requirement>
+      <requirement type="package" version="1.3">gatk</requirement>
   </requirements>
   <command interpreter="python">gatk_wrapper.py
    --max_jvm_heap_fraction "1"
diff --git a/tools/gatk/variants_validate.xml b/tools/gatk/variants_validate.xml
index 957d9f4f0fc..752fcd60914 100644
--- a/tools/gatk/variants_validate.xml
+++ b/tools/gatk/variants_validate.xml
@@ -1,7 +1,7 @@
-<tool id="gatk_validate_variants" name="Validate Variants" version="0.0.2">
+<tool id="gatk_validate_variants" name="Validate Variants" version="0.0.3">
   <description></description>
   <requirements>
-      <requirement type="package" version="1.2">gatk</requirement>
+      <requirement type="package" version="1.3">gatk</requirement>
   </requirements>
   <command interpreter="python">gatk_wrapper.py
    --max_jvm_heap_fraction "1"

From 1cdcbb6851f9c72a5f550594b295e633184d3e20 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Thu, 17 Nov 2011 14:17:42 -0500
Subject: [PATCH 213/362] Add DepthOfCoverage GATK tool.

---
 tools/gatk/depth_of_coverage.xml | 923 +++++++++++++++++++++++++++++++
 1 file changed, 923 insertions(+)
 create mode 100644 tools/gatk/depth_of_coverage.xml

diff --git a/tools/gatk/depth_of_coverage.xml b/tools/gatk/depth_of_coverage.xml
new file mode 100644
index 00000000000..f735a6d7619
--- /dev/null
+++ b/tools/gatk/depth_of_coverage.xml
@@ -0,0 +1,923 @@
+<tool id="gatk_depth_of_coverage" name="Depth of Coverage" version="0.0.1">
+  <description>on BAM files</description>
+  <requirements>
+      <requirement type="package" version="1.3">gatk</requirement>
+  </requirements>
+  <command interpreter="python">gatk_wrapper.py
+   --max_jvm_heap_fraction "1"
+   --stdout "${output_log}"
+   #for $i, $input_bam in enumerate( $reference_source.input_bams ):
+       -d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "gatk_input_${i}"
+       -d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index
+   #end for
+   -p 'java 
+    -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar"
+    -T "DepthOfCoverage"
+    ##--num_threads 4 ##hard coded, for now
+    
+    -et "NO_ET" ##ET no phone home
+    #if $reference_source.reference_source_selector != "history":
+        -R "${reference_source.ref_file.fields.path}"
+    #end if
+    #if str( $input_calculate_coverage_over_genes ) != "None":
+        --calculateCoverageOverGenes "${input_calculate_coverage_over_genes}"
+    #end if
+    #if str( $partition_type ) != "None":
+        #for $pt in str( $partition_type ).split( ',' ):
+            --partitionType "${pt}"
+        #end for
+    #end if
+    --out "${output_per_locus_coverage}"
+    
+    #for $ct_group in $summary_coverage_threshold_group:
+        --summaryCoverageThreshold "${ct_group.summary_coverage_threshold}"
+    #end for
+    --outputFormat "${output_format}"
+   '
+   
+    ##start standard gatk options
+    #if $gatk_param_type.gatk_param_type_selector == "advanced":
+        #for $sample_metadata in $gatk_param_type.sample_metadata:
+            -p '--sample_metadata "${sample_metadata.sample_metadata_file}"'
+        #end for
+        #for $read_filter in $gatk_param_type.read_filter:
+            -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
+            ###raise Exception( str( dir( $read_filter ) ) )
+            #for $name, $param in $read_filter.read_filter_type.iteritems():
+                #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
+                    --${name} "${param}"
+                #end if
+            #end for
+            '
+        #end for
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
+            -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
+        #end for
+        
+        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
+            -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
+        #end for
+
+        -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        
+        -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
+        #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
+            -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
+        #end if
+        -p '
+        --baq "${gatk_param_type.baq}"
+        --baqGapOpenPenalty "${gatk_param_type.baq_gap_open_penalty}"
+        ${gatk_param_type.use_original_qualities}
+        --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
+        --validation_strictness "${gatk_param_type.validation_strictness}"
+        --interval_merging "${gatk_param_type.interval_merging}"
+        ${gatk_param_type.disable_experimental_low_memory_sharding}
+        ${gatk_param_type.non_deterministic_random_seed}
+        '
+        #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
+            #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
+                -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
+            #else
+                -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
+            #end if
+        #end for
+    #end if
+    
+    #if $reference_source.reference_source_selector == "history":
+        -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
+    #end if
+    ##end standard gatk options
+    ##start analysis specific options
+    #if $analysis_param_type.analysis_param_type_selector == "advanced":
+        -p '
+        ${analysis_param_type.ignore_deletion_sites}
+        ${analysis_param_type.include_deletions}
+        --maxBaseQuality "${analysis_param_type.max_base_quality}"
+        --maxMappingQuality "${analysis_param_type.max_mapping_quality}"
+        --minBaseQuality "${analysis_param_type.min_base_quality}"
+        --minMappingQuality "${analysis_param_type.min_mapping_quality}"
+        --nBins "${analysis_param_type.n_bins}"
+        ${analysis_param_type.omit_depth_output_at_each_base}
+        ${analysis_param_type.omit_interval_statistics}
+        ${analysis_param_type.omit_locus_table}
+        ${analysis_param_type.omit_per_sample_stats}
+        ${analysis_param_type.print_base_counts}
+        ${analysis_param_type.print_bin_endpoints_and_exit}
+        --start "${analysis_param_type.start}"
+        --stop "${analysis_param_type.stop}"
+        '
+    #end if
+    ##Move additional files to final location
+    #if str( $partition_type ) != "None":
+       #set $partition_types = str( $partition_type ).split( ',' )
+    #else:
+        #set $partition_types = [ 'sample' ]
+    #end if
+    #if 'sample' in $partition_types and ( str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.print_bin_endpoints_and_exit ) == "" ):
+        #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "":
+            &amp;&amp; mv ${output_per_locus_coverage}.sample_summary ${output_summary_sample}
+            &amp;&amp; mv ${output_per_locus_coverage}.sample_statistics ${output_statistics_sample}
+        #end if
+        #if $gatk_param_type.gatk_param_type_selector == "advanced" and len( $gatk_param_type.input_interval_repeat ) and str( $gatk_param_type.omit_interval_statistics ) == "":
+            &amp;&amp; mv ${output_per_locus_coverage}.sample_interval_summary ${output_interval_summary_sample}
+            &amp;&amp; mv ${output_per_locus_coverage}.sample_interval_statistics ${output_interval_statistics_sample}
+        #end if
+        #if str( $input_calculate_coverage_over_genes ) != "None":
+            &amp;&amp; mv ${output_per_locus_coverage}.sample_gene_summary ${output_gene_summary_sample}
+            &amp;&amp; mv ${output_per_locus_coverage}.sample_gene_statistics ${output_gene_statistics_sample}
+        #end if
+        #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_depth_output_at_each_base ) == "":
+            &amp;&amp; mv ${output_per_locus_coverage}.sample_cumulative_coverage_counts ${output_cumulative_coverage_counts_sample}
+            &amp;&amp; mv ${output_per_locus_coverage}.sample_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_sample}
+        #end if
+    #end if
+    
+    #if 'readgroup' in $partition_types and ( str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.print_bin_endpoints_and_exit ) == "" ):
+        #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "":
+            &amp;&amp; mv ${output_per_locus_coverage}.read_group_summary ${output_summary_readgroup}
+            &amp;&amp; mv ${output_per_locus_coverage}.read_group_statistics ${output_statistics_readgroup}
+        #end if
+        #if $gatk_param_type.gatk_param_type_selector == "advanced" and len( $gatk_param_type.input_interval_repeat ) and str( $gatk_param_type.omit_interval_statistics ) == "":
+            &amp;&amp; mv ${output_per_locus_coverage}.read_group_interval_summary ${output_interval_summary_readgroup}
+            &amp;&amp; mv ${output_per_locus_coverage}.read_group_interval_statistics ${output_interval_statistics_readgroup}
+        #end if
+        #if str( $input_calculate_coverage_over_genes ) != "None":
+            &amp;&amp; mv ${output_per_locus_coverage}.read_group_gene_summary ${output_gene_summary_readgroup}
+            &amp;&amp; mv ${output_per_locus_coverage}.read_group_gene_statistics ${output_gene_statistics_readgroup}
+        #end if
+        #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_depth_output_at_each_base ) == "":
+            &amp;&amp; mv ${output_per_locus_coverage}.read_group_cumulative_coverage_counts ${output_cumulative_coverage_counts_readgroup}
+            &amp;&amp; mv ${output_per_locus_coverage}.read_group_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_readgroup}
+        #end if
+    #end if
+    
+    #if 'library' in $partition_types and ( str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.print_bin_endpoints_and_exit ) == "" ):
+        #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "":
+            &amp;&amp; mv ${output_per_locus_coverage}.library_summary ${output_summary_library}
+            &amp;&amp; mv ${output_per_locus_coverage}.library_statistics ${output_statistics_library}
+        #end if
+        #if $gatk_param_type.gatk_param_type_selector == "advanced" and len( $gatk_param_type.input_interval_repeat ) and str( $gatk_param_type.omit_interval_statistics ) == "":
+            &amp;&amp; mv ${output_per_locus_coverage}.library_interval_summary ${output_interval_summary_library}
+            &amp;&amp; mv ${output_per_locus_coverage}.library_interval_statistics ${output_interval_statistics_library}
+        #end if
+        #if str( $input_calculate_coverage_over_genes ) != "None":
+            &amp;&amp; mv ${output_per_locus_coverage}.library_gene_summary ${output_gene_summary_library}
+            &amp;&amp; mv ${output_per_locus_coverage}.library_gene_statistics ${output_gene_statistics_library}
+        #end if
+        #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_depth_output_at_each_base ) == "":
+            &amp;&amp; mv ${output_per_locus_coverage}.library_cumulative_coverage_counts ${output_cumulative_coverage_counts_library}
+            &amp;&amp; mv ${output_per_locus_coverage}.library_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_library}
+        #end if
+    #end if
+    
+
+  </command>
+  <inputs>
+    <conditional name="reference_source">
+      <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
+        <option value="cached">Locally cached</option>
+        <option value="history">History</option>
+      </param>
+      <when value="cached">
+        <repeat name="input_bams" title="BAM file" min="1">
+            <param name="input_bam" type="data" format="bam" label="BAM file">
+              <validator type="unspecified_build" />
+              <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
+              <validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
+            </param>
+        </repeat>
+        <param name="ref_file" type="select" label="Using reference genome">
+          <options from_data_table="gatk_picard_indexes">
+            <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...--> 
+          </options>
+        </param>
+      </when>
+      <when value="history"> <!-- FIX ME!!!! -->
+        <repeat name="input_bams" title="BAM file" min="1">
+            <param name="input_bam" type="data" format="bam" label="BAM file" >
+              <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
+            </param>
+        </repeat>
+        <param name="ref_file" type="data" format="fasta" label="Using reference file" />
+      </when>
+    </conditional>
+    
+    <param name="input_calculate_coverage_over_genes" type="data" format="data" label="RefSeq Rod" optional="True" />
+    
+    <param name="partition_type" type="select" label="Partition type for depth of coverage" multiple="True" display="checkboxes">
+      <option value="sample" selected="True">sample</option>
+      <option value="readgroup">readgroup</option>
+      <option value="library">library</option>
+    </param>
+    
+    <repeat name="summary_coverage_threshold_group" title="Summary coverage threshold">
+        <param name="summary_coverage_threshold" type="integer" value="15" label="for summary file outputs, report the % of bases covered to &gt;= this number" />
+    </repeat>
+    
+    <param name="output_format" type="select" label="Output format" >
+      <option value="csv">csv</option>
+      <option value="table">table</option>
+      <option value="rtable" selected="True">rtable</option>
+    </param>
+    
+    <conditional name="gatk_param_type">
+      <param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options">
+        <option value="basic" selected="True">Basic</option>
+        <option value="advanced">Advanced</option>
+      </param>
+      <when value="basic">
+        <!-- Do nothing here -->
+      </when>
+      <when value="advanced">
+        <repeat name="sample_metadata" title="Sample Metadata">
+            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" />
+        </repeat>
+        <repeat name="read_filter" title="Read Filter">
+            <conditional name="read_filter_type">
+		      <param name="read_filter_type_selector" type="select" label="Read Filter Type">
+		        <option value="MaxReadLength" selected="True">MaxReadLength</option>
+		        <option value="ZeroMappingQualityRead">ZeroMappingQualityRead</option>
+		      </param>
+	          <when value="ZeroMappingQualityRead">
+	              <!-- no extra options -->
+	          </when>
+	          <when value="MaxReadLength">
+	              <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
+	          </when>
+            </conditional>
+        </repeat>
+        <repeat name="input_interval_repeat" title="Operate on Genomic intervals">
+          <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
+        </repeat>
+        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals">
+          <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
+        </repeat>
+        
+        <param name="BTI_merge_rule" type="select" label="BTI merge rule">
+          <option value="UNION" selected="True">UNION</option>
+          <option value="INTERSECTION">INTERSECTION</option>
+        </param>
+        
+        <conditional name="downsampling_type">
+          <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
+            <option value="NONE" selected="True">NONE</option>
+            <option value="ALL_READS">ALL_READS</option>
+            <option value="BY_SAMPLE">BY_SAMPLE</option>
+          </param>
+          <when value="NONE">
+	          <!-- no more options here -->
+	      </when>
+          <when value="ALL_READS">
+	          <conditional name="downsample_to_type">
+	              <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
+	                  <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
+	                  <option value="downsample_to_coverage">Downsample by Coverage</option>
+	              </param>
+	              <when value="downsample_to_fraction">
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
+	              </when>
+	              <when value="downsample_to_coverage">
+	                  <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
+	              </when>
+	          </conditional>
+	      </when>
+          <when value="BY_SAMPLE">
+	          <conditional name="downsample_to_type">
+	              <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
+	                  <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
+	                  <option value="downsample_to_coverage">Downsample by Coverage</option>
+	              </param>
+	              <when value="downsample_to_fraction">
+	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/>
+	              </when>
+	              <when value="downsample_to_coverage">
+	                  <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
+	              </when>
+	          </conditional>
+	      </when>
+        </conditional>
+        <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine">
+          <option value="OFF" selected="True">OFF</option>
+          <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
+          <option value="RECALCULATE">RECALCULATE</option>
+        </param>
+        <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
+        <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" />
+        <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/>
+        <param name="validation_strictness" type="select" label="How strict should we be with validation">
+          <option value="STRICT" selected="True">STRICT</option>
+          <option value="LENIENT">LENIENT</option>
+          <option value="SILENT">SILENT</option>
+          <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
+        </param>
+        <param name="interval_merging" type="select" label="Interval merging rule">
+          <option value="ALL" selected="True">ALL</option>
+          <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
+        </param>
+        
+        <repeat name="read_group_black_list_repeat" title="Read group black list">
+          <conditional name="read_group_black_list_type">
+            <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
+              <option value="file" selected="True">Filters in file</option>
+              <option value="text">Specify filters as a string</option>
+            </param>
+            <when value="file">
+	          <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
+	        </when>
+            <when value="text">
+	          <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
+	        </when>
+          </conditional>
+        </repeat>
+        
+        <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/>
+        <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" />
+        
+      </when>
+    </conditional>
+    
+    <conditional name="analysis_param_type">
+      <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
+        <option value="basic" selected="True">Basic</option>
+        <option value="advanced">Advanced</option>
+      </param>
+      <when value="basic">
+        <!-- Do nothing here -->
+      </when>
+      <when value="advanced">
+        <param name="ignore_deletion_sites" type="boolean" truevalue="--ignoreDeletionSites" falsevalue="" checked="False" label="Ignore sites consisting only of deletions" />
+        <param name="include_deletions" type="boolean" truevalue="--includeDeletions" falsevalue="" checked="False" label="Include information on deletions" />
+        <param name="max_base_quality" type="integer" value="127" label="Maximum quality of bases to count towards depth" />
+        <param name="min_base_quality" type="integer" value="-1" label="Minimum quality of bases to count towards depth" />
+        <param name="max_mapping_quality" type="integer" value="2147483647" label="Maximum mapping quality of reads to count towards depth." />
+        <param name="min_mapping_quality" type="integer" value="127" label="Minimum mapping quality of reads to count towards depth" />
+        <param name="n_bins" type="integer" value="499" label="Number of bins to use for granular binning" />
+        <param name="omit_depth_output_at_each_base" type="boolean" truevalue="--omitDepthOutputAtEachBase" falsevalue="" checked="False" label="Omit the output of the depth of coverage at each base" />
+        <param name="omit_interval_statistics" type="boolean" truevalue="--omitIntervalStatistics" falsevalue="" checked="False" label="Omit the per-interval statistics section" />
+        <param name="omit_locus_table" type="boolean" truevalue="--omitLocusTable" falsevalue="" checked="False" label="Do not calculate the per-sample per-depth counts of loci" />
+        <param name="omit_per_sample_stats" type="boolean" truevalue="--omitPerSampleStats" falsevalue="" checked="False" label="Omit the summary files per-sample." />
+        <param name="print_base_counts" type="boolean" truevalue="--printBaseCounts" falsevalue="" checked="False" label="Add base counts to per-locus output" />
+        <param name="print_bin_endpoints_and_exit" type="boolean" truevalue="--printBinEndpointsAndExit" falsevalue="" checked="False" label="Print the bin values and exits immediately" />
+        <param name="start" type="integer" value="1" label="Starting (left endpoint) for granular binning" />
+        <param name="stop" type="integer" value="500" label="Ending (right endpoint) for granular binning" />
+      </when>
+    </conditional>
+  </inputs>
+  <outputs>
+    <data format="tabular" name="output_per_locus_coverage" label="${tool.name} on ${on_string} (per locus coverage)" >
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
+        <actions>
+            <conditional name="output_format">
+                <when value="rtable">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+                <when value="csv">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+            </conditional>
+        </actions>
+    </data>
+    <data format="tabular" name="output_summary_sample" label="${tool.name} on ${on_string} (output summary sample)" >
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
+        <filter>'sample' in partition_type or not partition_type</filter>
+        <actions>
+            <conditional name="output_format">
+                <when value="rtable">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+                <when value="csv">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+            </conditional>
+        </actions>
+    </data>
+    <data format="tabular" name="output_statistics_sample" label="${tool.name} on ${on_string} (output statistics sample)" >
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
+        <filter>'sample' in partition_type or not partition_type</filter>
+        <actions>
+            <conditional name="output_format">
+                <when value="rtable">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+                <when value="csv">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+            </conditional>
+        </actions>
+    </data>
+    <data format="tabular" name="output_interval_summary_sample" label="${tool.name} on ${on_string} (output interval summary sample)" >
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
+        <filter>'sample' in partition_type or not partition_type</filter>
+        <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
+        <actions>
+            <conditional name="output_format">
+                <when value="rtable">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+                <when value="csv">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+            </conditional>
+        </actions>
+    </data>
+    <data format="tabular" name="output_interval_statistics_sample" label="${tool.name} on ${on_string} (output interval statistics sample)" >
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
+        <filter>'sample' in partition_type or not partition_type</filter>
+        <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
+        <actions>
+            <conditional name="output_format">
+                <when value="rtable">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+                <when value="csv">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+            </conditional>
+        </actions>
+    </data>
+    <data format="tabular" name="output_gene_summary_sample" label="${tool.name} on ${on_string} (output gene summary sample)" >
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
+        <filter>input_calculate_coverage_over_genes is not None and 'sample' in partition_type or not partition_type</filter>
+        <actions>
+            <conditional name="output_format">
+                <when value="rtable">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+                <when value="csv">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+            </conditional>
+        </actions>
+    </data>
+    <data format="tabular" name="output_gene_statistics_sample" label="${tool.name} on ${on_string} (output gene statistics sample)" >
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
+        <filter>input_calculate_coverage_over_genes is not None and 'sample' in partition_type or not partition_type</filter>
+        <actions>
+            <conditional name="output_format">
+                <when value="rtable">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+                <when value="csv">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+            </conditional>
+        </actions>
+    </data>
+    <data format="tabular" name="output_cumulative_coverage_counts_sample" label="${tool.name} on ${on_string} (output cumulative coverage counts sample)" >
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
+        <filter>'sample' in partition_type or not partition_type</filter>
+        <actions>
+            <conditional name="output_format">
+                <when value="rtable">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+                <when value="csv">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+            </conditional>
+        </actions>
+    </data>
+    <data format="tabular" name="output_cumulative_coverage_proportions_sample" label="${tool.name} on ${on_string} (output cumulative coverage proportions sample)" >
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
+        <filter>'sample' in partition_type or not partition_type</filter>
+        <actions>
+            <conditional name="output_format">
+                <when value="rtable">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+                <when value="csv">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+            </conditional>
+        </actions>
+    </data>
+    
+    <data format="tabular" name="output_summary_readgroup" label="${tool.name} on ${on_string} (output summary readgroup)" >
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
+        <filter>'readgroup' in partition_type</filter>
+        <actions>
+            <conditional name="output_format">
+                <when value="rtable">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+                <when value="csv">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+            </conditional>
+        </actions>
+    </data>
+    <data format="tabular" name="output_statistics_readgroup" label="${tool.name} on ${on_string} (output statistics readgroup)" >
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
+        <filter>'readgroup' in partition_type</filter>
+        <actions>
+            <conditional name="output_format">
+                <when value="rtable">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+                <when value="csv">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+            </conditional>
+        </actions>
+    </data>
+    <data format="tabular" name="output_interval_summary_readgroup" label="${tool.name} on ${on_string} (output interval summary readgroup)" >
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
+        <filter>'readgroup' in partition_type</filter>
+        <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
+        <actions>
+            <conditional name="output_format">
+                <when value="rtable">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+                <when value="csv">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+            </conditional>
+        </actions>
+    </data>
+    <data format="tabular" name="output_interval_statistics_readgroup" label="${tool.name} on ${on_string} (output interval statistics readgroup)" >
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
+        <filter>'readgroup' in partition_type</filter>
+        <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
+        <actions>
+            <conditional name="output_format">
+                <when value="rtable">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+                <when value="csv">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+            </conditional>
+        </actions>
+    </data>
+    <data format="tabular" name="output_gene_summary_readgroup" label="${tool.name} on ${on_string} (output gene summary readgroup)" >
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
+        <filter>input_calculate_coverage_over_genes is not None and 'readgroup' in partition_type or not partition_type</filter>
+        <actions>
+            <conditional name="output_format">
+                <when value="rtable">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+                <when value="csv">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+            </conditional>
+        </actions>
+    </data>
+    <data format="tabular" name="output_gene_statistics_readgroup" label="${tool.name} on ${on_string} (output gene statistics readgroup)" >
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
+        <filter>input_calculate_coverage_over_genes is not None and 'readgroup' in partition_type or not partition_type</filter>
+        <actions>
+            <conditional name="output_format">
+                <when value="rtable">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+                <when value="csv">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+            </conditional>
+        </actions>
+    </data>
+    <data format="tabular" name="output_cumulative_coverage_counts_readgroup" label="${tool.name} on ${on_string} (output cumulative coverage counts readgroup)" >
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
+        <filter>'readgroup' in partition_type</filter>
+        <actions>
+            <conditional name="output_format">
+                <when value="rtable">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+                <when value="csv">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+            </conditional>
+        </actions>
+    </data>
+    <data format="tabular" name="output_cumulative_coverage_proportions_readgroup" label="${tool.name} on ${on_string} (output cumulative coverage proportions readgroup)" >
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
+        <filter>'readgroup' in partition_type</filter>
+        <actions>
+            <conditional name="output_format">
+                <when value="rtable">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+                <when value="csv">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+            </conditional>
+        </actions>
+    </data>
+    
+    <data format="tabular" name="output_summary_library" label="${tool.name} on ${on_string} (output summary library)" >
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
+        <filter>'library' in partition_type</filter>
+        <actions>
+            <conditional name="output_format">
+                <when value="rtable">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+                <when value="csv">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+            </conditional>
+        </actions>
+    </data>
+    <data format="tabular" name="output_statistics_library" label="${tool.name} on ${on_string} (output statistics library)" >
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
+        <filter>'library' in partition_type</filter>
+        <actions>
+            <conditional name="output_format">
+                <when value="rtable">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+                <when value="csv">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+            </conditional>
+        </actions>
+    </data>
+    <data format="tabular" name="output_interval_summary_library" label="${tool.name} on ${on_string} (output interval summary library)" >
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
+        <filter>'library' in partition_type</filter>
+        <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
+        <actions>
+            <conditional name="output_format">
+                <when value="rtable">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+                <when value="csv">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+            </conditional>
+        </actions>
+    </data>
+    <data format="tabular" name="output_interval_statistics_library" label="${tool.name} on ${on_string} (output interval statistics library)" >
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
+        <filter>'library' in partition_type</filter>
+        <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
+        <actions>
+            <conditional name="output_format">
+                <when value="rtable">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+                <when value="csv">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+            </conditional>
+        </actions>
+    </data>
+    <data format="tabular" name="output_gene_summary_library" label="${tool.name} on ${on_string} (output gene summary library)" >
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
+        <filter>input_calculate_coverage_over_genes is not None and 'library' in partition_type or not partition_type</filter>
+        <actions>
+            <conditional name="output_format">
+                <when value="rtable">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+                <when value="csv">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+            </conditional>
+        </actions>
+    </data>
+    <data format="tabular" name="output_gene_statistics_library" label="${tool.name} on ${on_string} (output gene statistics library)" >
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
+        <filter>input_calculate_coverage_over_genes is not None and 'library' in partition_type or not partition_type</filter>
+        <actions>
+            <conditional name="output_format">
+                <when value="rtable">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+                <when value="csv">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+            </conditional>
+        </actions>
+    </data>
+    <data format="tabular" name="output_cumulative_coverage_counts_library" label="${tool.name} on ${on_string} (output cumulative coverage counts library)" >
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
+        <filter>'library' in partition_type</filter>
+        <actions>
+            <conditional name="output_format">
+                <when value="rtable">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+                <when value="csv">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+            </conditional>
+        </actions>
+    </data>
+    <data format="tabular" name="output_cumulative_coverage_proportions_library" label="${tool.name} on ${on_string} (output cumulative coverage proportions library)" >
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
+        <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
+        <filter>'library' in partition_type</filter>
+        <actions>
+            <conditional name="output_format">
+                <when value="rtable">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+                <when value="csv">
+                    <action type="format">
+                        <option type="from_param" name="output_format" />
+                    </action>
+                </when>
+            </conditional>
+        </actions>
+    </data>
+    
+    <data format="tabular" name="output_log" label="${tool.name} on ${on_string} (log)" />
+  </outputs>
+  <trackster_conf/>
+  <tests>
+      <test>
+          <param name="reference_source_selector" value="history" />
+          <param name="ref_file" value="phiX.fasta" ftype="fasta" />
+          <param name="input_bam" value="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" />
+          <param name="input_calculate_coverage_over_genes" />
+          <param name="partition_type" value="sample" />
+          <param name="summary_coverage_threshold_group" value="0" />
+          <param name="output_format" value="rtable" />
+          <param name="gatk_param_type_selector" value="basic" />
+          <param name="analysis_param_type_selector" value="basic" />
+          <output name="output_per_locus_coverage" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_per_locus_coverage.tabular" />
+          <output name="output_summary_sample" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_summary_sample.tabular" />
+          <output name="output_statistics_sample" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_statistics_sample.tabular" />
+          <output name="output_cumulative_coverage_counts_sample" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_cumulative_coverage_counts_sample.tabular" />
+          <output name="output_cumulative_coverage_proportions_sample" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_output_cumulative_coverage_proportions_sample.tabular" />
+          <output name="output_log" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1.log.contains" compare="contains" />
+      </test>
+  </tests>
+  <help>
+**What it does**
+
+DepthOfCoverage processes a set of bam files to determine coverage at different levels of partitioning and aggregation. Coverage can be analyzed per locus, per interval, per gene, or in total; can be partitioned by sample, by read group, by technology, by center, or by library; and can be summarized by mean, median, quartiles, and/or percentage of bases covered to or beyond a threshold. Additionally, reads and bases can be filtered by mapping or base quality score. 
+
+For more information on the GATK Depth of Coverage, see this `tool specific page &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Depth_of_Coverage&gt;`_.
+
+To learn about best practices for variant detection using GATK, see this `overview &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v3&gt;`_.
+
+If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Frequently_Asked_Questions&gt;`_.
+
+------
+
+**Inputs**
+
+GenomeAnalysisTK: DepthOfCoverage accepts aligned BAM input files.
+
+
+**Outputs**
+
+The output is in various table formats.
+
+
+Go `here &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_the_GATK&gt;`_ for details on GATK file formats.
+
+-------
+
+**Settings**::
+
+ calculateCoverageOverGenes 	File 	NA 	Calculate the coverage statistics over this list of genes. Currently accepts RefSeq.
+ ignoreDeletionSites 	boolean 	false 	Ignore sites consisting only of deletions
+ includeDeletions 	boolean 	false 	Include information on deletions
+ maxBaseQuality 	byte 	127 	Maximum quality of bases to count towards depth. Defaults to 127 (Byte.MAX_VALUE).
+ maxMappingQuality 	int 	2147483647 	Maximum mapping quality of reads to count towards depth. Defaults to 2^31-1 (Integer.MAX_VALUE).
+ minBaseQuality 	byte 	-1 	Minimum quality of bases to count towards depth. Defaults to -1.
+ minMappingQuality 	int 	-1 	Minimum mapping quality of reads to count towards depth. Defaults to -1.
+ nBins 	int 	499 	Number of bins to use for granular binning
+ omitDepthOutputAtEachBase 	boolean 	false 	Will omit the output of the depth of coverage at each base, which should result in speedup
+ omitIntervalStatistics 	boolean 	false 	Will omit the per-interval statistics section, which should result in speedup
+ omitLocusTable 	boolean 	false 	Will not calculate the per-sample per-depth counts of loci, which should result in speedup
+ omitPerSampleStats 	boolean 	false 	Omits the summary files per-sample. These statistics are still calculated, so this argument will not improve runtime.
+ outputFormat 	String 	rtable 	the format of the output file (e.g. csv, table, rtable); defaults to r-readable table
+ partitionType 	Set[Partition] 	[sample] 	Partition type for depth of coverage. Defaults to sample. Can be any combination of sample, readgroup, library.
+ printBaseCounts 	boolean 	false 	Will add base counts to per-locus output.
+ printBinEndpointsAndExit 	boolean 	false 	Prints the bin values and exits immediately. Use to calibrate what bins you want before running on data.
+ start 	int 	1 	Starting (left endpoint) for granular binning
+ stop 	int 	500 	Ending (right endpoint) for granular binning
+ summaryCoverageThreshold 	int[] 	[15] 	for summary file outputs, report the % of bases coverd to >= this number. Defaults to 15; can take multiple arguments.
+
+------
+
+**Citation**
+
+For the underlying tool, please cite `DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011 May;43(5):491-8. &lt;http://www.ncbi.nlm.nih.gov/pubmed/21478889&gt;`_
+
+If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
+
+  </help>
+</tool>

From d4f1f1e497a565f219a66b4f0686fb4cdabb376d Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Thu, 17 Nov 2011 14:18:55 -0500
Subject: [PATCH 214/362] Update tool_conf.xml.sample.

---
 tool_conf.xml.sample | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index 93f171d1a28..ce4347e756f 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -378,6 +378,8 @@
     <tool file="samtools/samtools_rmdup.xml" />
   </section>
   <section name="NGS: GATK Tools (beta)" id="gatk">
+    <label text="Alignment Utilities" id="gatk_bam_utilities"/>
+    <tool file="gatk/depth_of_coverage.xml" />
     
     <label text="Realignment" id="gatk_realignment" />
     <tool file="gatk/realigner_target_creator.xml" />

From 65e47b189d6fa0ef3554126eb01815b0c9f44757 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Thu, 17 Nov 2011 15:08:49 -0500
Subject: [PATCH 215/362] Pack js scripts.

---
 static/scripts/packed/trackster.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/static/scripts/packed/trackster.js b/static/scripts/packed/trackster.js
index c8edfa0975b..c87a6529b4d 100644
--- a/static/scripts/packed/trackster.js
+++ b/static/scripts/packed/trackster.js
@@ -1 +1 @@
-var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var m=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(u,t,v,r,i,s){return(Math.max(u,r)-Math.min(u,r))+(Math.max(t,i)-Math.min(t,i))+(Math.max(v,s)-Math.min(v,s))};var g,n,f,k,p,h,q,c,d,b,o,l=false;do{g=Math.random()*16777215;n=g|16711680;f=g|65280;k=g|255;d=m(n,f,k);l=true;for(var j=0;j<a.length;j++){p=a[j];h=p|16711680;q=p|65280;c=p|255;b=m(h,q,c);o=e(n,f,k,h,q,c);if((Math.abs(d-b)<125)||(o<500)){l=false;break}}}while(!l);return"#"+(16777216+g).toString(16).substr(1,6)};var trackster_module=function(f,X){var p=f("class").extend,s=f("slotting"),M=f("painters");var ae=function(af,ag){this.document=af;this.default_font=ag!==undefined?ag:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};p(ae.prototype,{load_pattern:function(af,aj){var ag=this.patterns,ah=this.dummy_context,ai=new Image();ai.src=image_path+aj;ai.onload=function(){ag[af]=ah.createPattern(ai,"repeat")}},get_pattern:function(af){return this.patterns[af]},new_canvas:function(){var af=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(af)}af.manager=this;return af}});var n={};var l=function(af,ag){n[af.attr("id")]=ag};var m=function(af,ah,aj,ai){aj=".group";var ag={};n[af.attr("id")]=ai;af.bind("drag",{handle:"."+ah,relative:true},function(ar,at){var aq=$(this);var aw=$(this).parent(),an=aw.children(),ap=n[$(this).attr("id")],am,al,au,ak,ao;al=$(this).parents(aj);if(al.length!==0){au=al.position().top;ak=au+al.outerHeight();if(at.offsetY<au){$(this).insertBefore(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable_before(ap,av);return}else{if(at.offsetY>ak){$(this).insertAfter(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable(ap);return}}}al=null;for(ao=0;ao<an.length;ao++){am=$(an.get(ao));au=am.position().top;ak=au+am.outerHeight();if(am.is(aj)&&this!==am.get(0)&&at.offsetY>=au&&at.offsetY<=ak){if(at.offsetY-au<ak-at.offsetY){am.find(".content-div").prepend(this)}else{am.find(".content-div").append(this)}if(ap.container){ap.container.remove_drawable(ap)}n[am.attr("id")].add_drawable(ap);return}}for(ao=0;ao<an.length;ao++){if(at.offsetY<$(an.get(ao)).position().top){break}}if(ao===an.length){if(this!==an.get(ao-1)){aw.append(this);n[aw.attr("id")].move_drawable(ap,ao)}}else{if(this!==an.get(ao)){$(this).insertBefore(an.get(ao));n[aw.attr("id")].move_drawable(ap,(at.deltaY>0?ao-1:ao))}}}).bind("dragstart",function(){ag["border-top"]=af.css("border-top");ag["border-bottom"]=af.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ag)})};X.moveable=m;var ad=16,H=9,E=20,T=H+2,z=100,J=12000,R=200,C=5,v=10,L=5000,w=100,o="There was an error in indexing this dataset. 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Please check your datatypes_conf.xml file.",F="No data for this chrom/contig.",t="Currently indexing... please wait",x="Tool cannot be rerun: ",a="Loading data...",Y="Ready for display",d=10,u=5,B=5;function Z(ag,af){if(!af){af=0}var ah=Math.pow(10,af);return Math.round(ag*ah)/ah}var c=function(af){this.num_elements=af;this.clear()};p(c.prototype,{get:function(ag){var af=this.key_ary.indexOf(ag);if(af!==-1){if(this.obj_cache[ag].stale){this.key_ary.splice(af,1);delete this.obj_cache[ag]}else{this.move_key_to_end(ag,af)}}return this.obj_cache[ag]},set:function(ag,ah){if(!this.obj_cache[ag]){if(this.key_ary.length>=this.num_elements){var af=this.key_ary.shift();delete this.obj_cache[af]}this.key_ary.push(ag)}this.obj_cache[ag]=ah;return ah},move_key_to_end:function(ag,af){this.key_ary.splice(af,1);this.key_ary.push(ag)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var S=function(ag,af,ah){c.call(this,ag);this.track=af;this.subset=(ah!==undefined?ah:true)};p(S.prototype,c.prototype,{load_data:function(ao,aj,am,ag,al){var an=this.track.view.chrom,ai={chrom:an,low:ao,high:aj,mode:am,resolution:ag,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ai,al);if(this.track.filters_manager){var ap=[];var af=this.track.filters_manager.filters;for(var ak=0;ak<af.length;ak++){ap[ap.length]=af[ak].name}ai.filter_cols=JSON.stringify(ap)}var ah=this;return $.getJSON(this.track.data_url,ai,function(aq){ah.set_data(ao,aj,am,aq)})},get_data:function(af,aj,ak,ag,ai){var ah=this.get_data_from_cache(af,aj,ak);if(ah){return ah}ah=this.load_data(af,aj,ak,ag,ai);this.set_data(af,aj,ak,ah);return ah},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(an,ai,am,ah,al,aj){var ao=this.get_data_from_cache(an,ai,am);if(!ao){console.log("ERROR: no current data for: ",this.track,an,ai,am,ah,al);return}ao.stale=true;var 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S.prototype.load_data.call(this,af,ai,aj,ag,ah)}});var q=function(ai,ag,af,ah,aj){if(!q.id_counter){q.id_counter=0}this.id=q.id_counter++;this.name=ai;this.view=ag;this.container=af;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ai}],saved_values:ah,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=aj;this.is_overview=false};p(q.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},update_icons:function(){},set_name:function(af){this.old_name=this.name;this.name=af;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.hide(0,function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var y=function(aj,ai,ag,af,ah,ak){q.call(this,ai,ag,af,ah,ak);this.obj_type=aj;this.drawables=[]};p(y.prototype,q.prototype,{init:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af].init()}},_draw:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af]._draw()}},to_json:function(){var ag=[];for(var af=0;af<this.drawables.length;af++){ag.push(this.drawables[af].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ag}},add_drawable:function(af){this.drawables.push(af);af.container=this},add_drawable_before:function(ah,af){var ag=this.drawables.indexOf(af);if(ag!=-1){this.drawables.splice(ag,0,ah);return true}return false},remove_drawable:function(ag){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);ag.container=null;return true}return false},move_drawable:function(ag,ah){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);this.drawables.splice(ah,0,ag);return true}return 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ah=this.container,af=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ah);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ah);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ah);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,af);this.intro_div=$("<div/>").addClass("intro");var ai=$("<div/>").text("Add Datasets to 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ab(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){af.resize_window()});$(document).bind("redraw",function(){af.redraw()});this.reset();$(window).trigger("resize")},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(af,ag){this.location_span.text(commatize(af)+" - "+commatize(ag));this.nav_input.val(this.chrom+":"+commatize(af)+"-"+commatize(ag))},load_chroms:function(ah){ah.num=w;$.extend(ah,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var af=this,ag=$.Deferred();$.ajax({url:chrom_url,data:ah,dataType:"json",success:function(aj){if(aj.chrom_info.length===0){alert("Invalid chromosome: "+ah.chrom);return}if(aj.reference){af.add_label_track(new A(af))}af.chrom_data=aj.chrom_info;var am='<option value="">Select Chrom/Contig</option>';for(var al=0,ai=af.chrom_data.length;al<ai;al++){var ak=af.chrom_data[al].chrom;am+='<option value="'+ak+'">'+ak+"</option>"}if(aj.prev_chroms){am+='<option value="previous">Previous '+w+"</option>"}if(aj.next_chroms){am+='<option value="next">Next '+w+"</option>"}af.chrom_select.html(am);af.chrom_start_index=aj.start_index;ag.resolve(aj)},error:function(){alert("Could not load chroms for this dbkey:",af.dbkey)}});return ag},change_chrom:function(ak,ag,am){if(!ak||ak==="None"){return}var ah=this;if(ak==="previous"){ah.load_chroms({low:this.chrom_start_index-w});return}if(ak==="next"){ah.load_chroms({low:this.chrom_start_index+w});return}var al=$.grep(ah.chrom_data,function(an,ao){return an.chrom===ak})[0];if(al===undefined){ah.load_chroms({chrom:ak},function(){ah.change_chrom(ak,ag,am)});return}else{if(ak!==ah.chrom){ah.chrom=ak;ah.chrom_select.val(ah.chrom);ah.max_high=al.len-1;ah.reset();ah.request_redraw(true);for(var aj=0,af=ah.drawables.length;aj<af;aj++){var ai=ah.drawables[aj];if(ai.init){ai.init()}}}if(ag!==undefined&&am!==undefined){ah.low=Math.max(ag,0);ah.high=Math.min(am,ah.max_high)}ah.reset_overview();ah.request_redraw()}},go_to:function(aj){aj=aj.replace(/ |,/g,"");var an=this,af,ai,ag=aj.split(":"),al=ag[0],am=ag[1];if(am!==undefined){try{var ak=am.split("-");af=parseInt(ak[0],10);ai=parseInt(ak[1],10)}catch(ah){return false}}an.change_chrom(al,af,ai)},move_fraction:function(ah){var af=this;var ag=af.high-af.low;this.move_delta(ah*ag)},move_delta:function(ah){var af=this;var ag=af.high-af.low;if(af.low-ah<af.max_low){af.low=af.max_low;af.high=af.max_low+ag}else{if(af.high-ah>af.max_high){af.high=af.max_high;af.low=af.max_high-ag}else{af.high-=ah;af.low-=ah}}af.request_redraw()},add_drawable:function(af){y.prototype.add_drawable.call(this,af);af.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(af){af.view=this;af.init();this.label_tracks.push(af)},remove_drawable:function(ah,ag){y.prototype.remove_drawable.call(this,ah);if(ag){var af=this;ah.container_div.hide(0,function(){$(this).remove();af.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(an,af,am,ag){var al=this,aj=(ag?[ag]:al.drawables),ah;var ag;for(var ak=0;ak<aj.length;ak++){ag=aj[ak];ah=-1;for(var ai=0;ai<al.tracks_to_be_redrawn.length;ai++){if(al.tracks_to_be_redrawn[ai][0]===ag){ah=ai;break}}if(ah<0){al.tracks_to_be_redrawn.push([ag,af,am])}else{al.tracks_to_be_redrawn[ak][1]=af;al.tracks_to_be_redrawn[ak][2]=am}}requestAnimationFrame(function(){al._redraw(an)})},_redraw:function(ap){var am=this.low,ai=this.high;if(am<this.max_low){am=this.max_low}if(ai>this.max_high){ai=this.max_high}var ao=this.high-this.low;if(this.high!==0&&ao<this.min_separation){ai=am+this.min_separation}this.low=Math.floor(am);this.high=Math.ceil(ai);this.resolution=Math.pow(C,Math.ceil(Math.log((this.high-this.low)/R)/Math.log(C)));this.zoom_res=Math.pow(v,Math.max(0,Math.ceil(Math.log(this.resolution,v)/Math.log(v))));var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var al=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var aq=13;this.overview_box.css({left:af,width:Math.max(aq,al)}).show();if(al<aq){this.overview_box.css("left",af-(aq-al)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:al})}this.update_location(this.low,this.high);if(!ap){var ah,ag,an;for(var aj=0,ak=this.tracks_to_be_redrawn.length;aj<ak;aj++){ah=this.tracks_to_be_redrawn[aj][0];ag=this.tracks_to_be_redrawn[aj][1];an=this.tracks_to_be_redrawn[aj][2];if(ah){ah._draw(ag,an)}}this.tracks_to_be_redrawn=[];for(aj=0,ak=this.label_tracks.length;aj<ak;aj++){this.label_tracks[aj]._draw()}}},zoom_in:function(ag,ah){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ai=this.high-this.low,aj=ai/2+this.low,af=(ai/this.zoom_factor)/2;if(ag){aj=ag/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(aj-af);this.high=Math.round(aj+af);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ag=this.high-this.low,ah=ag/2+this.low,af=(ag*this.zoom_factor)/2;this.low=Math.round(ah-af);this.high=Math.round(ah+af);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ah.dataset_id){return}this.overview_viewport.find(".track").remove()}var ag=ah.copy({content_div:this.overview_viewport}),af=this;ag.header_div.hide();ag.is_overview=true;af.overview_drawable=ag;this.overview_drawable.postdraw_actions=function(){af.overview_highlight.show().height(af.overview_drawable.content_div.height());af.overview_viewport.height(af.overview_drawable.content_div.height()+af.overview_box.outerHeight());af.overview_close.show();af.resize_window()};this.overview_drawable.init();af.has_changes=true},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var r=function(ah,al){this.track=ah;this.name=al.name;this.params=[];var at=al.params;for(var ai=0;ai<at.length;ai++){var an=at[ai],ag=an.name,ar=an.label,aj=unescape(an.html),au=an.value,ap=an.type;if(ap==="number"){this.params[this.params.length]=new g(ag,ar,aj,au,an.min,an.max)}else{if(ap=="select"){this.params[this.params.length]=new O(ag,ar,aj,au)}else{console.log("WARNING: unrecognized tool parameter type:",ag,ap)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aw){aw.stopPropagation()}).click(function(aw){aw.stopPropagation()}).bind("dblclick",function(aw){aw.stopPropagation()});var aq=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ao=this.params;var am=this;$.each(this.params,function(ax,aA){var az=$("<div>").addClass("param-row").appendTo(am.parent_div);var aw=$("<div>").addClass("param-label").text(aA.label).appendTo(az);var ay=$("<div/>").addClass("slider").html(aA.html).appendTo(az);ay.find(":input").val(aA.value);$("<div style='clear: both;'/>").appendTo(az)});this.parent_div.find("input").click(function(){$(this).select()});var av=$("<div>").addClass("param-row").appendTo(this.parent_div);var ak=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(av);var af=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(av);var am=this;af.click(function(){am.run_on_region()});ak.click(function(){am.run_on_dataset()})};p(r.prototype,{get_param_values_dict:function(){var af={};this.parent_div.find(":input").each(function(){var ag=$(this).attr("name"),ah=$(this).val();af[ag]=JSON.stringify(ah)});return af},get_param_values:function(){var ag=[];var af={};this.parent_div.find(":input").each(function(){var ah=$(this).attr("name"),ai=$(this).val();if(ah){ag[ag.length]=ai}});return ag},run_on_dataset:function(){var af=this;af.run({dataset_id:this.track.original_dataset_id,tool_id:af.name},null,function(ag){show_modal(af.name+" is Running",af.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ag={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},aj=this.track,ah=ag.tool_id+aj.tool_region_and_parameters_str(ag.chrom,ag.low,ag.high),af;if(aj.container===view){var ai=new Q(this.name,this.track.view,this.track.container);aj.container.add_drawable(ai);aj.container.remove_drawable(aj);ai.add_drawable(aj);aj.container_div.appendTo(ai.content_div);af=ai}else{af=aj.container}var ak=new aj.constructor(ah,view,af,"hda");ak.init_for_tool_data();ak.change_mode(aj.mode);af.add_drawable(ak);ak.content_div.text("Starting job.");this.run(ag,ak,function(al){ak.dataset_id=al.dataset_id;ak.content_div.text("Running job.");ak.init()})},run:function(ag,ah,ai){$.extend(ag,this.get_param_values_dict());var af=function(){$.getJSON(rerun_tool_url,ag,function(aj){if(aj==="no converter"){ah.container_div.addClass("error");ah.content_div.text(K)}else{if(aj.error){ah.container_div.addClass("error");ah.content_div.text(x+aj.message)}else{if(aj==="pending"){ah.container_div.addClass("pending");ah.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(af,2000)}else{ai(aj)}}}})};af()}});var O=function(ag,af,ah,ai){this.name=ag;this.label=af;this.html=ah;this.value=ai};var g=function(ah,ag,aj,ak,ai,af){O.call(this,ah,ag,aj,ak);this.min=ai;this.max=af};var h=function(ag,af,ah,ai){this.name=ag;this.index=af;this.tool_id=ah;this.tool_exp_name=ai};var V=function(ag,af,ah,ai){h.call(this,ag,af,ah,ai);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};p(V.prototype,{applies_to:function(af){if(af.length>this.index){return true}return false},keep:function(af){if(!this.applies_to(af)){return true}var ag=af[this.index];return(isNaN(ag)||(ag>=this.low&&ag<=this.high))},update_attrs:function(ag){var af=false;if(!this.applies_to(ag)){return af}if(ag[this.index]<this.min){this.min=Math.floor(ag[this.index]);af=true}if(ag[this.index]>this.max){this.max=Math.ceil(ag[this.index]);af=true}return af},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var ah=function(ak,ai){var aj=ai-ak;return(aj<=2?0.01:1)};var ag=this.slider.slider("option","min"),af=this.slider.slider("option","max");if(this.min<ag||this.max>af){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ah(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var aa=function(aq,ay){this.track=aq;this.filters=[];for(var at=0;at<ay.length;at++){var au=ay[at],az=au.name,af=au.type,ah=au.index,ax=au.tool_id,aw=au.tool_exp_name;if(af==="int"||af==="float"){this.filters[at]=new V(az,ah,ax,aw)}else{console.log("ERROR: unsupported filter: ",az,af)}}var ai=function(aA,aB,aC){aA.click(function(){var aD=aB.text();max=parseFloat(aC.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aC.slider("option","values")){input_size=2*input_size+1;multi_value=true}aB.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aD).appendTo(aB).focus().select().click(function(aE){aE.stopPropagation()}).blur(function(){$(this).remove();aB.text(aD)}).keyup(function(aI){if(aI.keyCode===27){$(this).trigger("blur")}else{if(aI.keyCode===13){var aG=aC.slider("option","min"),aE=aC.slider("option","max"),aH=function(aJ){return(isNaN(aJ)||aJ>aE||aJ<aG)},aF=$(this).val();if(!multi_value){aF=parseFloat(aF);if(aH(aF)){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}else{aF=aF.split("-");aF=[parseFloat(aF[0]),parseFloat(aF[1])];if(aH(aF[0])||aH(aF[1])){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}aC.slider((multi_value?"values":"value"),aF)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aA){aA.stopPropagation()}).click(function(aA){aA.stopPropagation()}).bind("dblclick",function(aA){aA.stopPropagation()}).bind("keydown",function(aA){aA.stopPropagation()});var av=$("<div/>").addClass("sliders").appendTo(this.parent_div);var an=this;$.each(this.filters,function(aD,aF){aF.container=$("<div/>").addClass("filter-row slider-row").appendTo(av);var aE=$("<div/>").addClass("elt-label").appendTo(aF.container);var aC=$("<span/>").addClass("slider-name").text(aF.name+"  ").appendTo(aE);var aB=$("<span/>");var aH=$("<span/>").addClass("slider-value").appendTo(aE).append("[").append(aB).append("]");var aA=$("<div/>").addClass("slider").appendTo(aF.container);aF.control_element=$("<div/>").attr("id",aF.name+"-filter-control").appendTo(aA);var aG=[0,0];aF.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aJ,aK){var aI=aK.values;aB.text(aI[0]+"-"+aI[1]);aF.low=aI[0];aF.high=aI[1];an.track.request_draw(true,true)},change:function(aI,aJ){aF.control_element.slider("option","slide").call(aF.control_element,aI,aJ)}});aF.slider=aF.control_element;aF.slider_label=aB;ai(aH,aB,aF.control_element);$("<div style='clear: both;'/>").appendTo(aF.container)});if(this.filters.length!==0){var ak=$("<div/>").addClass("param-row").appendTo(av);var am=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ak);var ag=this;am.click(function(){ag.run_on_dataset()})}var ap=$("<div/>").addClass("display-controls").appendTo(this.parent_div),ar,al,ao,aj={Transparency:function(aA){an.alpha_filter=aA},Height:function(aA){an.height_filter=aA}};$.each(aj,function(aC,aB){ar=$("<div/>").addClass("filter-row").appendTo(ap),al=$("<span/>").addClass("elt-label").text(aC+":").appendTo(ar),ao=$("<select/>").attr("name",aC+"_dropdown").css("float","right").appendTo(ar);$("<option/>").attr("value",-1).text("== None ==").appendTo(ao);for(var aA=0;aA<an.filters.length;aA++){$("<option/>").attr("value",aA).text(an.filters[aA].name).appendTo(ao)}ao.change(function(){$(this).children("option:selected").each(function(){var aD=parseInt($(this).val());aj[aC]((aD>=0?an.filters[aD]:null));an.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(ar)});$("<div style='clear: both;'/>").appendTo(this.parent_div)};p(aa.prototype,{reset_filters:function(){for(var af=0;af<this.filters.length;af++){filter=this.filters[af];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var an=function(ar,ap,aq){if(!(ap in ar)){ar[ap]=aq}return ar[ap]};var ah={},af,ag,ai;for(var aj=0;aj<this.filters.length;aj++){af=this.filters[aj];if(af.tool_id){if(af.min!=af.low){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" >= "+af.low}if(af.max!=af.high){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" <= "+af.high}}}var al=[];for(var ao in ah){al[al.length]=[ao,ah[ao]]}var am=al.length;(function ak(aw,at){var aq=at[0],ar=aq[0],av=aq[1],au="("+av.join(") and (")+")",ap={cond:au,input:aw,target_dataset_id:aw,tool_id:ar},at=at.slice(1);$.getJSON(run_tool_url,ap,function(ax){if(ax.error){show_modal("Filter Dataset","Error running tool "+ar,{Close:hide_modal})}else{if(at.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ak(ax.dataset_id,at)}}})})(this.track.dataset_id,al)}});var D=function(af,ag){M.Scaler.call(this,ag);this.filter=af};D.prototype.gen_val=function(af){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(af[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var G=function(af){this.track=af.track;this.params=af.params;this.values={};this.restore_values((af.saved_values?af.saved_values:{}));this.onchange=af.onchange};p(G.prototype,{restore_values:function(af){var ag=this;$.each(this.params,function(ah,ai){if(af[ai.key]!==undefined){ag.values[ai.key]=af[ai.key]}else{ag.values[ai.key]=ai.default_value}})},build_form:function(){var ai=this;var af=$("<div />");var ah;function ag(am,aj){for(var ao=0;ao<am.length;ao++){ah=am[ao];if(ah.hidden){continue}var ak="param_"+ao;var at=ai.values[ah.key];var av=$("<div class='form-row' />").appendTo(aj);av.append($("<label />").attr("for",ak).text(ah.label+":"));if(ah.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ak).attr("name",ak).attr("checked",at))}else{if(ah.type==="text"){av.append($('<input type="text"/>').attr("id",ak).val(at).click(function(){$(this).select()}))}else{if(ah.type=="select"){var aq=$("<select />").attr("id",ak);for(var an=0;an<ah.options.length;an++){$("<option/>").text(ah.options[an].label).attr("value",ah.options[an].value).appendTo(aq)}aq.val(at);av.append(aq)}else{if(ah.type==="color"){var ap=$("<input />").attr("id",ak).attr("name",ak).val(at);var ar=$("<div class='tipsy tipsy-west' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ar);var au=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:ap,color:at});$("<div />").append(ap).append(ar).appendTo(av).bind("click",function(aw){ar.css({left:$(this).position().left+$(ap).width()+5,top:$(this).position().top-($(ar).height()/2)+($(ap).height()/2)}).show();$(document).bind("click.color-picker",function(){ar.hide();$(document).unbind("click.color-picker")});aw.stopPropagation()})}else{av.append($("<input />").attr("id",ak).attr("name",ak).val(at))}}}}if(ah.help){av.append($("<div class='help'/>").text(ah.help))}}}ag(this.params,af);return af},update_from_form:function(af){var ah=this;var ag=false;$.each(this.params,function(ai,ak){if(!ak.hidden){var al="param_"+ai;var aj=af.find("#"+al).val();if(ak.type==="float"){aj=parseFloat(aj)}else{if(ak.type==="int"){aj=parseInt(aj)}else{if(ak.type==="bool"){aj=af.find("#"+al).is(":checked")}}}if(aj!==ah.values[ak.key]){ah.values[ak.key]=aj;ag=true}}});if(ag){this.onchange()}}});var b=function(af,ai,ah,ag,aj){this.track=af;this.index=ai;this.low=ai*R*ah;this.high=(ai+1)*R*ah;this.resolution=ah;this.canvas=$("<div class='track-tile'/>").append(ag);this.data=aj;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(af,ai,ah,ag,aj,ak){b.call(this,af,ai,ah,ag,aj);this.max_val=ak};p(k.prototype,b.prototype);var P=function(af,aj,ai,ah,al,am,ak,ag){b.call(this,af,aj,ai,ah,al);this.mode=am;this.message=ak;this.feature_mapper=ag};p(P.prototype,b.prototype);P.prototype.predisplay_actions=function(){var ag=this,af={};if(ag.mode!=="Pack"){return}$(this.canvas).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).siblings(".feature-popup").remove()}).mousemove(function(ar){if(!this.hovered){return}var am=$(this).offset(),aq=ar.pageX-am.left,ap=ar.pageY-am.top,aw=ag.feature_mapper.get_feature_data(aq,ap),an=(aw?aw[0]:null);$(this).siblings(".feature-popup").each(function(){if(!an||$(this).attr("id")!==an.toString()){$(this).remove()}});if(aw){var ai=af[an];if(!ai){var an=aw[0],at={name:aw[3],start:aw[1],end:aw[2],strand:aw[4]},al=ag.track.filters_manager.filters,ak;for(var ao=0;ao<al.length;ao++){ak=al[ao];at[ak.name]=aw[ak.index]}var ai=$("<div/>").attr("id",an).addClass("feature-popup"),ax=$("<table/>"),av,au,ay;for(av in at){au=at[av];ay=$("<tr/>").appendTo(ax);$("<th/>").appendTo(ay).text(av);$("<td/>").attr("align","left").appendTo(ay).text(typeof(au)=="number"?Z(au,2):au)}ai.append($("<div class='feature-popup-inner'>").append(ax));af[an]=ai}ai.appendTo($(ag.canvas).parent());var aj=aq+parseInt(ag.canvas.css("left"))-ai.width()/2,ah=ap+parseInt(ag.canvas.css("top"))+7;ai.css("left",aj+"px").css("top",ah+"px")}else{if(!ar.isPropagationStopped()){ar.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ar)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var i=function(ai,aq,aj,am,ar,ah,ag){q.call(this,ai,aq,aj,{},"draghandle");this.data_url=(ah?ah:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ag?ag:L);this.dataset_check_url=converted_datasets_state_url;this.content_visible=true;if(!i.id_counter){i.id_counter=0}this.id=i.id_counter++;this.container_div=$("<div />").addClass("track").attr("id","track_"+this.id).css("position","relative");if(am){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div/>").addClass("track-name").appendTo(this.header_div).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());this.icons_div=$("<div/>").css("float","left").appendTo(this.header_div).hide();this.toggle_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Hide/show track content").addClass("icon-button toggle").tipsy({gravity:"s"}).appendTo(this.icons_div);this.settings_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Edit settings").addClass("icon-button settings-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.overview_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Set as overview").addClass("icon-button overview-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.filters_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Filters").addClass("icon-button filters-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.tools_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Tools").addClass("icon-button tools-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.remove_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Remove").addClass("icon-button remove-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);var ak=this;this.header_div.dblclick(function(at){at.stopPropagation()});this.toggle_icon.click(function(){if(ak.content_visible){ak.toggle_icon.addClass("toggle-expand").removeClass("toggle");ak.hide_contents();ak.mode_div.hide();ak.content_visible=false}else{ak.toggle_icon.addClass("toggle").removeClass("toggle-expand");ak.content_visible=true;ak.mode_div.show();ak.show_contents()}});this.settings_icon.click(function(){var av=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},at=function(){ak.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},au=function(aw){if((aw.keyCode||aw.which)===27){av()}else{if((aw.keyCode||aw.which)===13){at()}}};$(window).bind("keypress.check_enter_esc",au);show_modal("Configure Track",ak.config.build_form(),{Cancel:av,OK:at})});this.overview_icon.click(function(){ak.view.set_overview(ak)});this.filters_icon.click(function(){ak.filters_div.toggle();ak.filters_manager.reset_filters()});this.tools_icon.click(function(){ak.dynamic_tool_div.toggle();if(ak.dynamic_tool_div.is(":visible")){ak.set_name(ak.name+ak.tool_region_and_parameters_str())}else{ak.revert_name()}$(".tipsy").remove()});this.remove_icon.click(function(){$(".tipsy").remove();ak.remove()});if(ak.display_modes!==undefined){if(ak.mode_div===undefined){ak.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ak.header_div);var al=(ak.config&&ak.config.values.mode?ak.config.values.mode:ak.display_modes[0]);ak.mode=al;ak.mode_div.text(al);var af={};for(var an=0,ap=ak.display_modes.length;an<ap;an++){var ao=ak.display_modes[an];af[ao]=function(at){return function(){ak.change_mode(at)}}(ao)}make_popupmenu(ak.mode_div,af)}else{ak.mode_div.hide()}this.header_div.append($("<div/>").css("clear","both"));this.container_div.hover(function(){ak.icons_div.show()},function(){ak.icons_div.hide()})}}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};p(i.prototype,q.prototype,{get_type:function(){if(this instanceof ab){return"LabelTrack"}else{if(this instanceof A){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof W){return"ReadTrack"}else{if(this instanceof U){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}return""},init:function(){var af=this;af.enabled=false;af.tile_cache.clear();af.data_manager.clear();af.initial_canvas=undefined;af.content_div.css("height","auto");af.container_div.removeClass("nodata error pending");if(!af.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:af.hda_ldda,dataset_id:af.dataset_id,chrom:af.view.chrom},function(ag){if(!ag||ag==="error"||ag.kind==="error"){af.container_div.addClass("error");af.content_div.text(o);if(ag.message){var ah=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})});af.content_div.append(ah)}}else{if(ag==="no converter"){af.container_div.addClass("error");af.content_div.text(K)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){af.container_div.addClass("nodata");af.content_div.text(F)}else{if(ag==="pending"){af.container_div.addClass("pending");af.content_div.text(t);setTimeout(function(){af.init()},af.data_query_wait)}else{if(ag.status==="data"){if(ag.valid_chroms){af.valid_chroms=ag.valid_chroms;af.update_icons()}af.content_div.text(Y);if(af.view.chrom){af.content_div.text("");af.content_div.css("height",af.height_px+"px");af.enabled=true;$.when(af.predraw_init()).done(function(){af.container_div.removeClass("nodata error pending");af.request_draw()})}}}}}}});this.update_icons()},hide_contents:function(){this.content_div.children().remove();this.content_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.content_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},predraw_init:function(){}});var N=function(aj,ah,ag,am,ai,al,ak){i.call(this,aj,ah,ag,am,ai);var af=this,ah=af.view;m(af.container_div,af.drag_handle_class,".group",af);this.filters_manager=new aa(this,(al!==undefined?al:{}));this.filters_available=false;this.filters_visible=false;this.tool=(ak!==undefined&&obj_length(ak)>0?new r(this,ak):undefined);if(this.header_div){if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}};p(N.prototype,q.prototype,i.prototype,{copy:function(af){return new this.constructor(this.name,this.view,af,this.hda_ldda,this.dataset_id,this.prefs,this.filters,this.tool)},to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ag){var af=this;af.mode_div.text(ag);af.mode=ag;af.config.values.mode=ag;af.tile_cache.clear();af.request_draw();return af},update_icons:function(){var af=this;if(af.filters_available>0){af.filters_icon.show()}else{af.filters_icon.hide()}if(af.tool){af.tools_icon.show()}else{af.tools_icon.hide()}},_gen_tile_cache_key:function(ag,ah,af){return ag+"_"+ah+"_"+af},request_draw:function(ag,af){this.view.request_redraw(false,ag,af,this)},_draw:function(ah,ap){if(!this.enabled){return}if(!this.content_visible){return}if(!(this instanceof A)&&(!this.dataset_id)){return}var ao=this.view.low,al=this.view.high,am=al-ao,ai=this.view.container.width(),at=ai/am,ak=this.view.resolution,ar=$("<div style='position: relative;'></div>");if(this.is_overview){ao=this.view.max_low;al=this.view.max_high;ak=Math.pow(C,Math.ceil(Math.log((view.max_high-view.max_low)/R)/Math.log(C)));at=ai/(view.max_high-view.max_low)}if(!ap){this.content_div.children().remove()}this.content_div.append(ar);this.max_height=0;var ag=Math.floor(ao/ak/R);var an=true;var aq=[];var af=0;while((ag*R*ak)<al){tile=this.draw_helper(ah,ai,ag,ak,ar,at);if(tile){aq.push(tile)}else{an=false}ag+=1;af++}var aj=this;if(an){aj.postdraw_actions(aq,ai,at,ap)}},postdraw_actions:function(aj,ak,al,af){var ah=this;var ai=false;for(var ag=0;ag<aj.length;ag++){if(aj[ag].message){ai=true;break}}if(ai){for(var ag=0;ag<aj.length;ag++){tile=aj[ag];if(!tile.message){tile.canvas.css("padding-top",E)}}}},draw_helper:function(ag,ah,ai,al,ar,aw,at,am){var aj=this,aq=this._gen_tile_cache_key(ah,aw,ai),an=ai*R*al,av=an+R*al;var ao=(ag?undefined:aj.tile_cache.get(aq));if(ao){aj.show_tile(ao,ar,aw);return ao}var ap=function(ax){return("isResolved" in ax)};var ak=true;var af=aj.data_manager.get_data(an,av,aj.mode,al,aj.data_url_extra_params);if(ap(af)){ak=false}var au;if(view.reference_track&&aw>view.canvas_manager.char_width_px){au=view.reference_track.data_manager.get_data(an,av,aj.mode,al,view.reference_track.data_url_extra_params);if(ap(au)){ak=false}}if(ak){p(af,am);var ao=aj.draw_tile(af,aj.mode,al,ai,aw,au);if(ao!==undefined){aj.tile_cache.set(aq,ao);aj.show_tile(ao,ar,aw)}return ao}$.when(af,au).then(function(){view.request_redraw(false,false,false,aj)});return null},show_tile:function(al,an,ao){var ah=this,ag=al.canvas,ak=ag;if(al.message){var ap=$("<div/>"),am=$("<div/>").addClass("tile-message").text(al.message).css({height:E-1,width:al.canvas.width}).appendTo(ap),aj=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(am),af=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(am);ap.append(ag);ak=ap;aj.click(function(){al.stale=true;ah.data_manager.get_more_data(al.low,al.high,ah.mode,al.resolution,{},ah.data_manager.DEEP_DATA_REQ);ah.request_draw()}).dblclick(function(aq){aq.stopPropagation()});af.click(function(){al.stale=true;ah.data_manager.get_more_data(al.low,al.high,ah.mode,al.resolution,{},ah.data_manager.BROAD_DATA_REQ);ah.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}al.predisplay_actions();var ai=(al.low-(this.is_overview?this.view.max_low:this.view.low))*ao;if(this.left_offset){ai-=this.left_offset}ak.css({position:"absolute",top:0,left:ai,height:""});an.append(ak);ah.max_height=Math.max(ah.max_height,ak.height());ah.content_div.css("height",ah.max_height+"px");an.children().css("height",ah.max_height+"px")},_get_tile_bounds:function(af,ag){var ai=af*R*ag,aj=R*ag,ah=(ai+aj<=this.view.max_high?ai+aj:this.view.max_high);return[ai,ah]},tool_region_and_parameters_str:function(ah,af,ai){var ag=this,aj=(ah!==undefined&&af!==undefined&&ai!==undefined?ah+":"+af+"-"+ai:"all");return" - region=["+aj+"], parameters=["+ag.tool.get_param_values().join(", ")+"]"},init_for_tool_data:function(){this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.predraw_init=function(){var ag=this;var af=function(){if(ag.data_manager.size()===0){setTimeout(af,300)}else{ag.data_url=default_data_url;ag.data_query_wait=L;ag.dataset_state_url=converted_datasets_state_url;$.getJSON(ag.dataset_state_url,{dataset_id:ag.dataset_id,hda_ldda:ag.hda_ldda},function(ah){})}};af()}}});var ab=function(ag,af){i.call(this,"label",ag,af,false,{});this.container_div.addClass("label-track")};p(ab.prototype,i.prototype,{init:function(){this.enabled=true},_draw:function(){var ah=this.view,ai=ah.high-ah.low,al=Math.floor(Math.pow(10,Math.floor(Math.log(ai)/Math.log(10)))),af=Math.floor(ah.low/al)*al,aj=this.view.container.width(),ag=$("<div style='position: relative; height: 1.3em;'></div>");while(af<ah.high){var ak=(af-ah.low)/ai*aj;ag.append($("<div class='label'>"+commatize(af)+"</div>").css({position:"absolute",left:ak-1}));af+=al}this.content_div.children(":first").remove();this.content_div.append(ag)}});var A=function(af){N.call(this,"reference",af,{content_div:af.top_labeltrack},false,{});af.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:af.dbkey};this.data_manager=new I(B,this,false);this.tile_cache=new c(u)};p(A.prototype,q.prototype,N.prototype,{init:function(){this.enabled=true},draw_tile:function(ap,al,ak,ag,aq){var aj=this,ah=R*ak;if(aq>this.view.canvas_manager.char_width_px){if(ap.data===null){aj.content_div.css("height","0px");return}var ai=this.view.canvas_manager.new_canvas();var ao=ai.getContext("2d");ai.width=Math.ceil(ah*aq+aj.left_offset);ai.height=aj.height_px;ao.font=ao.canvas.manager.default_font;ao.textAlign="center";ap=ap.data;for(var am=0,an=ap.length;am<an;am++){var af=Math.round(am*aq);ao.fillText(ap[am],af+aj.left_offset,10)}return new b(aj,ag,ak,ai,ap)}this.content_div.css("height","0px")}});var j=function(ak,ai,ah,al,af,aj){var ag=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";N.call(this,ak,ai,ah,true,aj);this.min_height_px=16;this.max_height_px=400;this.height_px=32;this.hda_ldda=al;this.dataset_id=af;this.original_dataset_id=af;this.data_manager=new S(B,this);this.tile_cache=new c(u);this.left_offset=0;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:aj,onchange:function(){ag.set_name(ag.prefs.name);ag.vertical_range=ag.prefs.max_value-ag.prefs.min_value;$("#linetrack_"+ag.dataset_id+"_minval").text(ag.prefs.min_value);$("#linetrack_"+ag.dataset_id+"_maxval").text(ag.prefs.max_value);ag.tile_cache.clear();ag.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};p(j.prototype,q.prototype,N.prototype,{add_resize_handle:function(){var af=this;var ai=false;var ah=false;var ag=$("<div class='track-resize'>");$(af.container_div).hover(function(){if(af.content_visible){ai=true;ag.show()}},function(){ai=false;if(!ah){ag.hide()}});ag.hide().bind("dragstart",function(aj,ak){ah=true;ak.original_height=$(af.content_div).height()}).bind("drag",function(ak,al){var aj=Math.min(Math.max(al.original_height+al.deltaY,af.min_height_px),af.max_height_px);$(af.content_div).css("height",aj);af.height_px=aj;af.request_draw(true)}).bind("dragend",function(aj,ak){af.tile_cache.clear();ah=false;if(!ai){ag.hide()}af.config.values.height=af.height_px}).appendTo(af.container_div)},predraw_init:function(){var af=this;af.vertical_range=undefined;return $.getJSON(af.data_url,{stats:true,chrom:af.view.chrom,low:null,high:null,hda_ldda:af.hda_ldda,dataset_id:af.dataset_id},function(ag){af.container_div.addClass("line-track");var aj=ag.data;if(isNaN(parseFloat(af.prefs.min_value))||isNaN(parseFloat(af.prefs.max_value))){var ah=aj.min;var al=aj.max;ah=Math.floor(Math.min(0,Math.max(ah,aj.mean-2*aj.sd)));al=Math.ceil(Math.max(0,Math.min(al,aj.mean+2*aj.sd)));af.prefs.min_value=ah;af.prefs.max_value=al;$("#track_"+af.dataset_id+"_minval").val(af.prefs.min_value);$("#track_"+af.dataset_id+"_maxval").val(af.prefs.max_value)}af.vertical_range=af.prefs.max_value-af.prefs.min_value;af.total_frequency=aj.total_frequency;af.container_div.find(".yaxislabel").remove();var ak=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_minval").text(Z(af.prefs.min_value,3));var ai=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_maxval").text(Z(af.prefs.max_value,3));ai.css({position:"absolute",top:"24px",left:"10px"});ai.prependTo(af.container_div);ak.css({position:"absolute",bottom:"2px",left:"10px"});ak.prependTo(af.container_div)})},draw_tile:function(ar,ak,aj,ah,aq){if(this.vertical_range===undefined){return}var af=this._get_tile_bounds(ah,aj),al=af[0],ap=af[1],ag=Math.ceil((ap-al)*aq),an=this.height_px;var ai=this.view.canvas_manager.new_canvas();ai.width=ag,ai.height=an;var ao=ai.getContext("2d");var am=new M.LinePainter(ar.data,al,ap,this.prefs,ak);am.draw(ao,ag,an);return new b(this.track,ah,aj,ai,ar.data)}});var e=function(af,al,ag,ak,an,am,ai,aj){var ah=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];N.call(this,af,al,ag,true,am,ai,aj);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:am,onchange:function(){ah.set_name(ah.prefs.name);ah.tile_cache.clear();ah.set_painter_from_config();ah.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=ak;this.dataset_id=an;this.original_dataset_id=an;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new S(20,this);this.left_offset=200;this.set_painter_from_config()};p(e.prototype,q.prototype,N.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style=="arcs"){this.painter=M.ArcLinkedFeaturePainter}else{this.painter=M.LinkedFeaturePainter}},postdraw_actions:function(av,af,aw,au){N.prototype.postdraw_actions.call(this,av,au);var ai=this;if(au){var ak=ai.content_div.children();var al=false;for(var aj=ak.length-1,ap=0;aj>=ap;aj--){var ah=$(ak[aj]);if(al){ah.remove()}else{if(ah.children().length!==0){al=true}}}}if(ai.mode=="Histogram"){var ao=-1;for(var aj=0;aj<av.length;aj++){var at=av[aj].max_val;if(at>ao){ao=at}}for(var aj=0;aj<av.length;aj++){var ar=av[aj];if(ar.max_val!==ao){ar.canvas.remove();ai.draw_helper(true,af,ar.index,ar.resolution,ar.canvas.parent(),aw,[],{max:ao})}}}if(ai.filters_manager){var ag=ai.filters_manager.filters;for(var an=0;an<ag.length;an++){ag[an].update_ui_elt()}var am=false,aq;for(var aj=0;aj<av.length;aj++){if(av[aj].data.length){aq=av[aj].data[0];for(var an=0;an<ag.length;an++){if(ag[an].applies_to(aq)){am=true;break}}}}if(ai.filters_available!==am){ai.filters_available=am;if(!ai.filters_available){ai.filters_div.hide()}ai.update_icons()}}},update_auto_mode:function(af){if(this.mode=="Auto"){if(af=="no_detail"){af="feature spans"}else{if(af=="summary_tree"){af="coverage histogram"}}this.mode_div.text("Auto ("+af+")")}},incremental_slots:function(aj,ag,ai){var ah=this.view.canvas_manager.dummy_context,af=this.inc_slots[aj];if(!af||(af.mode!==ai)){af=new (s.FeatureSlotter)(aj,ai==="Pack",z,function(ak){return ah.measureText(ak)});af.mode=ai;this.inc_slots[aj]=af}return af.slot_features(ag)},get_summary_tree_data:function(aj,am,ah,av){if(av>ah-am){av=ah-am}var aq=Math.floor((ah-am)/av),au=[],ai=0;var ak=0,al=0,ap,at=0,an=[],ar,ao;var ag=function(ay,ax,az,aw){ay[0]=ax+az*aw;ay[1]=ax+(az+1)*aw};while(at<av&&ak!==aj.length){var af=false;for(;at<av&&!af;at++){ag(an,am,at,aq);for(al=ak;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){af=true;break}}if(af){break}}data_start_index=al;au[au.length]=ar=[an[0],0];for(;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){ar[1]++}else{break}}if(ar[1]>ai){ai=ar[1]}at++}return{max:ai,delta:aq,data:au}},draw_tile:function(au,ax,aB,aF,ap,ai){var ay=this,ak=ay._get_tile_bounds(aF,aB),aI=ak[0],ag=ak[1],aw=ag-aI,az=Math.ceil(aw*ap),aO=25,aj=this.left_offset,av,al;if(ax==="Auto"){if(au.dataset_type==="summary_tree"){ax=au.dataset_type}else{if(au.extra_info==="no_detail"||ay.is_overview){ax="no_detail"}else{var aN=au.data;if(this.view.high-this.view.low>J){ax="Squish"}else{ax="Pack"}}}this.update_auto_mode(ax)}if(ax==="summary_tree"||ax==="Histogram"){al=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var af=$("<div />").addClass("yaxislabel");af.text(au.max);af.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});af.prependTo(this.container_div);var ah=this.view.canvas_manager.new_canvas();ah.width=az+aj;ah.height=al+T;if(au.dataset_type!="summary_tree"){var aq=this.get_summary_tree_data(au.data,aI,ag,200);if(au.max){aq.max=au.max}au=aq}var aK=new M.SummaryTreePainter(au,aI,ag,this.prefs);var aA=ah.getContext("2d");aA.translate(aj,T);aK.draw(aA,az,al);return new k(ay,aF,aB,ah,au.data,au.max)}var av,an=1;if(ax==="no_detail"||ax==="Squish"||ax==="Pack"){an=this.incremental_slots(ap,au.data,ax);av=this.inc_slots[ap].slots}var ao=[];if(au.data){var ar=this.filters_manager.filters;for(var aC=0,aE=au.data.length;aC<aE;aC++){var am=au.data[aC];var aD=false;var at;for(var aH=0,aM=ar.length;aH<aM;aH++){at=ar[aH];at.update_attrs(am);if(!at.keep(am)){aD=true;break}}if(!aD){ao.push(am)}}}var aL=(this.filters_manager.alpha_filter?new D(this.filters_manager.alpha_filter):null);var aJ=(this.filters_manager.height_filter?new D(this.filters_manager.height_filter):null);var aK=new (this.painter)(ao,aI,ag,this.prefs,ax,aL,aJ,ai);var al=Math.max(ad,aK.get_required_height(an,az));var ah=this.view.canvas_manager.new_canvas();var aG=null;ah.width=az+aj;ah.height=al;var aA=ah.getContext("2d");aA.fillStyle=this.prefs.block_color;aA.font=aA.canvas.manager.default_font;aA.textAlign="right";this.container_div.find(".yaxislabel").remove();if(au.data){aA.translate(aj,0);aG=aK.draw(aA,az,al,av);aG.translation=-aj}return new P(ay,aF,aB,ah,au.data,ax,au.message,aG)}});var U=function(ak,ah,ag,am,af,aj,al,ai){e.call(this,ak,ah,ag,am,af,aj,al,ai);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:aj,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter};p(U.prototype,q.prototype,N.prototype,e.prototype);var W=function(af,ak,ag,aj,an,am,ah){e.call(this,af,ak,ag,aj,an,am,ah);var ai=get_random_color(),al=get_random_color([ai,"#ffffff"]);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ai},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:al},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:am,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter;this.update_icons()};p(W.prototype,q.prototype,N.prototype,e.prototype);X.View=ac;X.DrawableGroup=Q;X.LineTrack=j;X.FeatureTrack=e;X.ReadTrack=W;X.VcfTrack=U};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(F,G){for(var E=0;E<=z;E++){var C=false,H=h[E];if(H!==undefined){for(var B=0,D=H.length;B<D;B++){var i=H[B];if(G>i[0]&&F<i[1]){C=true;break}}}if(!C){return E}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(i,x){var u=i("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y<E;y++,A+=J,G+=H){if(y%2!==0){continue}I.fillRect(A,G,D,1)}};var q=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var d=function(y){this.default_val=(y?y:1)};d.prototype.gen_val=function(y){return this.default_val};var l=function(A,C,y,z,B){this.data=A;this.view_start=C;this.view_end=y;this.prefs=u({},this.default_prefs,z);this.mode=B};l.prototype.default_prefs={};var v=function(A,C,y,z,B){l.call(this,A,C,y,z,B)};v.prototype.default_prefs={show_counts:false};v.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var b=function(y,C,E,F,A){l.call(this,y,C,E,F,A);if(this.prefs.min_value===undefined){var G=Infinity;for(var z=0,B=this.data.length;z<B;z++){G=Math.min(G,this.data[z][1])}this.prefs.min_value=G}if(this.prefs.max_value===undefined){var D=-Infinity;for(var z=0,B=this.data.length;z<B;z++){D=Math.max(D,this.data[z][1])}this.prefs.max_value=D}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var m=function(y){this.feature_positions={};this.slot_height=y;this.translation=0;this.y_translation=0};m.prototype.map_feature_data=function(z,B,y,A){if(!this.feature_positions[B]){this.feature_positions[B]=[]}this.feature_positions[B].push({data:z,x_start:y,x_end:A})};m.prototype.get_feature_data=function(z,D){var C=Math.floor((D-this.y_translation)/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var o=function(A,D,y,z,C,E,B){l.call(this,A,D,y,z,C);this.alpha_scaler=(E?E:new d());this.height_scaler=(B?B:new d())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(A,z){var y=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){y=A*y_scale}return y+this.get_top_padding(z)+this.get_bottom_padding(z)},get_top_padding:function(y){return 0},get_bottom_padding:function(y){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(K,I,G,F){var Q=this.data,D=this.view_start,M=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var H=this.view_end-this.view_start,E=I/H,L=this.get_row_height(),P=new m(L),B;for(var N=0,O=Q.length;N<O;N++){var A=Q[N],C=A[0],J=A[1],y=A[2],z=(F&&F[C]!==undefined?F[C]:null);if((J<M&&y>D)&&(this.mode=="Dense"||z!==null)){B=this.draw_element(K,this.mode,A,z,D,M,E,L,I);P.map_feature_data(A,z,B[0],B[1])}}K.restore();P.y_translation=this.get_top_padding(I);return P},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.");return[0,0]}});var c=10,h=3,k=5,w=10,f=1,s=9,e=3,a=9,j=2,g="#ccc";var r=function(A,D,y,z,C,E,B){o.call(this,A,D,y,z,C,E,B);this.draw_background_connector=true;this.draw_individual_connectors=false};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=c}else{if(z==="no_detail"){y=h}else{if(z==="Squish"){y=k}else{y=w}}}return y},draw_element:function(M,D,X,H,O,aj,an,ap,y){var T=X[0],al=X[1],ad=X[2],Q=X[3],ae=Math.floor(Math.max(0,(al-O)*an)),N=Math.ceil(Math.min(y,Math.max(0,(ad-O)*an))),ac=ae,ao=N,aa=(D==="Dense"?0:(0+H))*ap+this.get_top_padding(y),L,ah,R=null,ar=null,B=this.prefs.block_color,ag=this.prefs.label_color;M.globalAlpha=this.alpha_scaler.gen_val(X);if(D==="Dense"){H=1}if(D==="no_detail"){M.fillStyle=B;M.fillRect(ae,aa+5,N-ae,f)}else{var K=X[4],Z=X[5],af=X[6],C=X[7],V=true;if(Z&&af){R=Math.floor(Math.max(0,(Z-O)*an));ar=Math.ceil(Math.min(y,Math.max(0,(af-O)*an)))}var am,U;if(D==="Squish"){am=1;U=e;V=false}else{if(D==="Dense"){am=5;U=s}else{am=5;U=a}}if(!C){M.fillStyle=B;M.fillRect(ae,aa+1,N-ae,U);if(K&&V){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}M.fillRect(ae,aa+1,N-ae,U)}}else{var J,W;if(D==="Squish"||D==="Dense"){J=aa+Math.floor(e/2)+1;W=1}else{if(K){J=aa;W=U}else{J+=(e/2)+1;W=1}}if(this.draw_background_connector){if(D==="Squish"||D==="Dense"){M.fillStyle=g}else{if(K){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand")}}}else{M.fillStyle=g}}M.fillRect(ae,J,N-ae,W)}var E;for(var ak=0,A=C.length;ak<A;ak++){var F=C[ak],z=Math.floor(Math.max(0,(F[0]-O)*an)),Y=Math.ceil(Math.min(y,Math.max((F[1]-O)*an))),S,ab;if(z>Y){continue}M.fillStyle=B;M.fillRect(z,aa+(U-am)/2+1,Y-z,am);if(R!==undefined&&af>Z&&!(z>ar||Y<R)){var ai=Math.max(z,R),I=Math.min(Y,ar);M.fillRect(ai,aa+1,I-ai,U);if(C.length==1&&D=="Pack"){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}if(ai+14<I){ai+=2;I-=2}M.fillRect(ai,aa+1,I-ai,U)}}if(this.draw_individual_connectors&&S){this.draw_connector(M,S,ab,z,Y,aa)}S=z;ab=Y}if(D==="Pack"){M.globalAlpha=1;M.fillStyle="white";var G=this.height_scaler.gen_val(X),P=Math.ceil(U*G),aq=Math.round((U-P)/2);if(G!==1){M.fillRect(ae,J+1,N-ae,aq);M.fillRect(ae,J+U-aq+1,N-ae,aq)}}}M.globalAlpha=1;if(D==="Pack"&&al>O){M.fillStyle=ag;if(O===0&&ae-M.measureText(Q).width<0){M.textAlign="left";M.fillText(Q,N+j,aa+8);ao+=M.measureText(Q).width+j}else{M.textAlign="right";M.fillText(Q,ae-j,aa+8);ac-=M.measureText(Q).width+j}}}M.globalAlpha=1;return[ac,ao]}});var t=function(B,E,y,A,D,F,C,z){o.call(this,B,E,y,A,D,F,C);this.ref_seq=(z?z.data:null)};u(t.prototype,o.prototype,{get_row_height:function(){var y,z=this.mode;if(z==="Dense"){y=c}else{if(z==="Squish"){y=k}else{y=w;if(this.prefs.show_insertions){y*=2}}}return y},draw_read:function(K,A,ag,V,L,aa,ad,C,B,M){K.textAlign="center";var J=this,R=[L,aa],Z=0,W=0,D=0,F=K.canvas.manager.char_width_px,y=(B==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var O=[];if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){D=Math.round(ag/2)}if(!C){C=[[0,M.length]]}for(var G=0,I=C.length;G<I;G++){var z=C[G],E="MIDNSHP=X"[z[0]],S=z[1];if(E==="H"||E==="S"){Z-=S}var U=ad+Z,Y=Math.floor(Math.max(0,(U-L)*ag)),ab=Math.floor(Math.max(0,(U+S-L)*ag));if(Y===ab){ab+=1}switch(E){case"H":break;case"S":case"M":case"=":if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(D>0){K.fillStyle=y;K.fillRect(Y-D,V+1,ab-Y,9);K.fillStyle=g;for(var af=0,H=N.length;af<H;af++){if(this.prefs.show_differences&&this.ref_seq){var P=this.ref_seq[U-L+af];if(!P||P.toLowerCase()===N[af].toLowerCase()){continue}}if(U+af>=L&&U+af<=aa){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X,V+9)}}}else{K.fillStyle=y;K.fillRect(Y,V+4,ab-Y,e)}}W+=S;Z+=S;break;case"N":K.fillStyle=g;K.fillRect(Y-D,V+5,ab-Y,1);Z+=S;break;case"D":K.fillStyle="red";K.fillRect(Y-D,V+4,ab-Y,3);Z+=S;break;case"P":break;case"I":var ah=Y-D;if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(this.prefs.show_insertions){var T=Y-(ab-Y)/2;if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){K.fillStyle="yellow";K.fillRect(T-D,V-9,ab-Y,9);O[O.length]={type:"triangle",data:[ah,V+4,5]};K.fillStyle=g;switch(compute_overlap([U,U+S],R)){case (OVERLAP_START):N=N.slice(L-U);break;case (OVERLAP_END):N=N.slice(0,U-aa);break;case (CONTAINED_BY):break;case (CONTAINS):N=N.slice(L-U,U-aa);break}for(var af=0,H=N.length;af<H;af++){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X-(ab-Y)/2,V)}}else{K.fillStyle="yellow";K.fillRect(T,V+(this.mode!=="Dense"?2:5),ab-Y,(A!=="Dense"?e:s))}}else{if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){O.push({type:"text",data:[N.length,ah,V+9]})}else{}}}W+=S;break;case"X":W+=S;break}}K.fillStyle="yellow";var Q,ai,ae;for(var ac=0;ac<O.length;ac++){Q=O[ac];ai=Q.type;ae=Q.data;if(ai==="text"){K.save();K.font="bold "+K.font;K.fillText(ae[0],ae[1],ae[2]);K.restore()}else{if(ai=="triangle"){q(K,ae[0],ae[1],ae[2])}}}},draw_element:function(R,M,E,B,U,z,I,S,P){var H=E[0],Q=E[1],A=E[2],J=E[3],D=Math.floor(Math.max(0,(Q-U)*I)),F=Math.ceil(Math.min(P,Math.max(0,(A-U)*I))),C=(M==="Dense"?0:(0+B))*S,G=this.prefs.label_color,O=0;if((M==="Pack"||this.mode==="Auto")&&I>R.canvas.manager.char_width_px){var O=Math.round(I/2)}if(E[5] instanceof Array){var N=Math.floor(Math.max(0,(E[4][0]-U)*I)),L=Math.ceil(Math.min(P,Math.max(0,(E[4][1]-U)*I))),K=Math.floor(Math.max(0,(E[5][0]-U)*I)),y=Math.ceil(Math.min(P,Math.max(0,(E[5][1]-U)*I)));if(E[4][1]>=U&&E[4][0]<=z&&E[4][2]){this.draw_read(R,M,I,C,U,z,E[4][0],E[4][2],E[4][3],E[4][4])}if(E[5][1]>=U&&E[5][0]<=z&&E[5][2]){this.draw_read(R,M,I,C,U,z,E[5][0],E[5][2],E[5][3],E[5][4])}if(K>L){R.fillStyle=g;p(R,L-O,C+5,K-O,C+5)}}else{this.draw_read(R,M,I,C,U,z,Q,E[4],E[5],E[6])}if(M==="Pack"&&Q>U&&J!=="."){R.fillStyle=this.prefs.label_color;var T=1;if(T===0&&D-R.measureText(J).width<0){R.textAlign="left";R.fillText(J,F+j-O,C+8)}else{R.textAlign="right";R.fillText(J,D-j-O,C+8)}}return[0,0]}});var n=function(A,D,y,z,C,E,B){r.call(this,A,D,y,z,C,E,B);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};u(n.prototype,o.prototype,r.prototype,{calculate_longest_feature_length:function(){var z=0;for(var C=0,y=this.data.length;C<y;C++){var B=this.data[C],A=B[1],D=B[2];z=Math.max(z,D-A)}return z},get_top_padding:function(z){var y=this.view_end-this.view_start,A=z/y;return Math.min(128,Math.ceil((this.longest_feature_length/2)*A))},draw_connector:function(G,B,F,H,E,D){var y=(F+H)/2,C=H-y;var A=Math.PI,z=0;if(C>0){G.beginPath();G.arc(y,D,H-y,Math.PI,0);G.stroke()}}});x.Scaler=d;x.SummaryTreePainter=v;x.LinePainter=b;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.ArcLinkedFeaturePainter=n};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window);
\ No newline at end of file
+var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var m=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(u,t,v,r,i,s){return(Math.max(u,r)-Math.min(u,r))+(Math.max(t,i)-Math.min(t,i))+(Math.max(v,s)-Math.min(v,s))};var g,n,f,k,p,h,q,c,d,b,o,l=false;do{g=Math.random()*16777215;n=g|16711680;f=g|65280;k=g|255;d=m(n,f,k);l=true;for(var j=0;j<a.length;j++){p=a[j];h=p|16711680;q=p|65280;c=p|255;b=m(h,q,c);o=e(n,f,k,h,q,c);if((Math.abs(d-b)<125)||(o<500)){l=false;break}}}while(!l);return"#"+(16777216+g).toString(16).substr(1,6)};var trackster_module=function(f,X){var p=f("class").extend,s=f("slotting"),M=f("painters");var ae=function(af,ag){this.document=af;this.default_font=ag!==undefined?ag:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};p(ae.prototype,{load_pattern:function(af,aj){var ag=this.patterns,ah=this.dummy_context,ai=new Image();ai.src=image_path+aj;ai.onload=function(){ag[af]=ah.createPattern(ai,"repeat")}},get_pattern:function(af){return this.patterns[af]},new_canvas:function(){var af=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(af)}af.manager=this;return af}});var n={};var l=function(af,ag){n[af.attr("id")]=ag};var m=function(af,ah,aj,ai){aj=".group";var ag={};n[af.attr("id")]=ai;af.bind("drag",{handle:"."+ah,relative:true},function(ar,at){var aq=$(this);var aw=$(this).parent(),an=aw.children(),ap=n[$(this).attr("id")],am,al,au,ak,ao;al=$(this).parents(aj);if(al.length!==0){au=al.position().top;ak=au+al.outerHeight();if(at.offsetY<au){$(this).insertBefore(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable_before(ap,av);return}else{if(at.offsetY>ak){$(this).insertAfter(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable(ap);return}}}al=null;for(ao=0;ao<an.length;ao++){am=$(an.get(ao));au=am.position().top;ak=au+am.outerHeight();if(am.is(aj)&&this!==am.get(0)&&at.offsetY>=au&&at.offsetY<=ak){if(at.offsetY-au<ak-at.offsetY){am.find(".content-div").prepend(this)}else{am.find(".content-div").append(this)}if(ap.container){ap.container.remove_drawable(ap)}n[am.attr("id")].add_drawable(ap);return}}for(ao=0;ao<an.length;ao++){if(at.offsetY<$(an.get(ao)).position().top){break}}if(ao===an.length){if(this!==an.get(ao-1)){aw.append(this);n[aw.attr("id")].move_drawable(ap,ao)}}else{if(this!==an.get(ao)){$(this).insertBefore(an.get(ao));n[aw.attr("id")].move_drawable(ap,(at.deltaY>0?ao-1:ao))}}}).bind("dragstart",function(){ag["border-top"]=af.css("border-top");ag["border-bottom"]=af.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ag)})};X.moveable=m;var ad=16,H=9,E=20,T=H+2,z=100,J=12000,R=200,C=5,v=10,L=5000,w=100,o="There was an error in indexing this dataset. ",K="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",F="No data for this chrom/contig.",t="Currently indexing... please wait",x="Tool cannot be rerun: ",a="Loading data...",Y="Ready for display",d=10,u=5,B=5;function Z(ag,af){if(!af){af=0}var ah=Math.pow(10,af);return Math.round(ag*ah)/ah}var c=function(af){this.num_elements=af;this.clear()};p(c.prototype,{get:function(ag){var af=this.key_ary.indexOf(ag);if(af!==-1){if(this.obj_cache[ag].stale){this.key_ary.splice(af,1);delete this.obj_cache[ag]}else{this.move_key_to_end(ag,af)}}return this.obj_cache[ag]},set:function(ag,ah){if(!this.obj_cache[ag]){if(this.key_ary.length>=this.num_elements){var af=this.key_ary.shift();delete this.obj_cache[af]}this.key_ary.push(ag)}this.obj_cache[ag]=ah;return ah},move_key_to_end:function(ag,af){this.key_ary.splice(af,1);this.key_ary.push(ag)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var S=function(ag,af,ah){c.call(this,ag);this.track=af;this.subset=(ah!==undefined?ah:true)};p(S.prototype,c.prototype,{load_data:function(ao,aj,am,ag,al){var an=this.track.view.chrom,ai={chrom:an,low:ao,high:aj,mode:am,resolution:ag,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ai,al);if(this.track.filters_manager){var ap=[];var af=this.track.filters_manager.filters;for(var ak=0;ak<af.length;ak++){ap[ap.length]=af[ak].name}ai.filter_cols=JSON.stringify(ap)}var ah=this;return $.getJSON(this.track.data_url,ai,function(aq){ah.set_data(ao,aj,am,aq)})},get_data:function(af,aj,ak,ag,ai){var ah=this.get_data_from_cache(af,aj,ak);if(ah){return ah}ah=this.load_data(af,aj,ak,ag,ai);this.set_data(af,aj,ak,ah);return ah},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(an,ai,am,ah,al,aj){var ao=this.get_data_from_cache(an,ai,am);if(!ao){console.log("ERROR: no current data for: ",this.track,an,ai,am,ah,al);return}ao.stale=true;var ag=an;if(aj===this.DEEP_DATA_REQ){$.extend(al,{start_val:ao.data.length+1})}else{if(aj===this.BROAD_DATA_REQ){ag=(ao.max_high?ao.max_high:ao.data[ao.data.length-1][2])+1}}var af=this,ak=this.load_data(ag,ai,am,ah,al);new_data_available=$.Deferred();this.set_data(an,ai,am,new_data_available);$.when(ak).then(function(ap){if(ap.data){ap.data=ao.data.concat(ap.data);if(ap.max_low){ap.max_low=ao.max_low}if(ap.message){ap.message=ap.message.replace(/[0-9]+/,ap.data.length)}}af.set_data(an,ai,am,ap);new_data_available.resolve(ap)});return new_data_available},get_data_from_cache:function(af,ag,ah){return this.get(this.gen_key(af,ag,ah))},set_data:function(ag,ah,ai,af){return this.set(this.gen_key(ag,ah,ai),af)},gen_key:function(af,ah,ai){var ag=af+"_"+ah+"_"+ai;return ag},split_key:function(af){return af.split("_")}});var I=function(ag,af,ah){S.call(this,ag,af,ah)};p(I.prototype,S.prototype,c.prototype,{load_data:function(af,ai,aj,ag,ah){if(ag>1){return{data:null}}return S.prototype.load_data.call(this,af,ai,aj,ag,ah)}});var q=function(ai,ag,af,ah,ak){if(!q.id_counter){q.id_counter=0}this.id=q.id_counter++;this.name=ai;this.view=ag;this.container=af;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ai}],saved_values:ah,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ak;this.is_overview=false;this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=this.build_icons_div().hide();this.header_div.append(this.icons_div);this.header_div.dblclick(function(al){al.stopPropagation()});var aj=this;this.container_div.hover(function(){aj.icons_div.show()},function(){aj.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p(q.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},update_icons:function(){},set_name:function(af){this.old_name=this.name;this.name=af;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.hide(0,function(){$(this).remove();view.update_intro_div();view.has_changes=true})},build_container_div:function(){},build_header_div:function(){},build_icons_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){}});var y=function(aj,ai,ag,af,ah,ak){q.call(this,ai,ag,af,ah,ak);this.obj_type=aj;this.drawables=[]};p(y.prototype,q.prototype,{init:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af].init()}},_draw:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af]._draw()}},to_json:function(){var ag=[];for(var af=0;af<this.drawables.length;af++){ag.push(this.drawables[af].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ag}},add_drawable:function(af){this.drawables.push(af);af.container=this},add_drawable_before:function(ah,af){var ag=this.drawables.indexOf(af);if(ag!=-1){this.drawables.splice(ag,0,ah);return true}return false},remove_drawable:function(ag){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);ag.container=null;return true}return false},move_drawable:function(ag,ah){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);this.drawables.splice(ah,0,ag);return true}return false}});var Q=function(ai,ag,af,ah){y.call(this,"DrawableGroup",ai,ag,af,ah,"group-handle");this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this)};p(Q.prototype,q.prototype,y.prototype,{build_container_div:function(){return $("<div/>").addClass("group").attr("id","group_"+this.id).appendTo(this.container.content_div)},build_header_div:function(){var af=$("<div/>").addClass("track-header");af.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(af);return af},build_icons_div:function(){var af=$("<div/>").css("float","left");this.toggle_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Hide/show group content").addClass("icon-button toggle").tipsy({gravity:"s"}).appendTo(af);this.settings_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Edit settings").addClass("icon-button settings-icon").tipsy({gravity:"s"}).appendTo(af);this.remove_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Remove").addClass("icon-button remove-icon").tipsy({gravity:"s"}).appendTo(af);var ag=this;this.toggle_icon.click(function(){if(ag.content_visible){ag.toggle_icon.addClass("toggle-expand").removeClass("toggle");ag.hide_contents();ag.content_visible=false}else{ag.toggle_icon.addClass("toggle").removeClass("toggle-expand");ag.content_visible=true;ag.show_contents()}});this.settings_icon.click(function(){var aj=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ah=function(){ag.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ai=function(ak){if((ak.keyCode||ak.which)===27){aj()}else{if((ak.keyCode||ak.which)===13){ah()}}};$(window).bind("keypress.check_enter_esc",ai);show_modal("Configure Group",ag.config.build_form(),{Cancel:aj,OK:ah})});this.remove_icon.click(function(){$(".tipsy").remove();ag.remove()});return af},hide_contents:function(){this.content_div.hide()},show_contents:function(){this.content_div.show();this.request_draw()}});var ac=function(af,ai,ah,ag){y.call(this,"View");this.container=af;this.chrom=null;this.vis_id=ah;this.dbkey=ag;this.title=ai;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ae(af.get(0).ownerDocument);this.reset()};p(ac.prototype,y.prototype,{init:function(){var ah=this.container,af=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ah);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ah);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ah);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,af);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ai=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ag=function(aj){if(aj.type==="focusout"||(aj.keyCode||aj.which)===13||(aj.keyCode||aj.which)===27){if((aj.keyCode||aj.which)!==27){af.go_to($(this).val())}$(this).hide();$(this).val("");af.location_span.show();af.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ag).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tipsy({gravity:"n"}).appendTo(this.nav_controls);this.location_span.click(function(){af.location_span.hide();af.chrom_select.hide();af.nav_input.val(af.chrom+":"+af.low+"-"+af.high);af.nav_input.css("display","inline-block");af.nav_input.select();af.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tipsy({gravity:"n"}).click(function(){af.zoom_out();af.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tipsy({gravity:"n"}).click(function(){af.zoom_in();af.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){af.change_chrom(af.chrom_select.val())});this.browser_content_div.click(function(aj){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(aj){af.zoom_in(aj.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(aj,ak){this.current_x=ak.offsetX}).bind("drag",function(aj,al){var am=al.offsetX-this.current_x;this.current_x=al.offsetX;var ak=Math.round(am/af.viewport_container.width()*(af.max_high-af.max_low));af.move_delta(-ak)});this.overview_close.click(function(){af.reset_overview()});this.viewport_container.bind("draginit",function(aj,ak){if(aj.clientX>af.viewport_container.width()-16){return false}}).bind("dragstart",function(aj,ak){ak.original_low=af.low;ak.current_height=aj.clientY;ak.current_x=ak.offsetX}).bind("drag",function(al,an){var aj=$(this);var ao=an.offsetX-an.current_x;var ak=aj.scrollTop()-(al.clientY-an.current_height);aj.scrollTop(ak);an.current_height=al.clientY;an.current_x=an.offsetX;var am=Math.round(ao/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}).bind("mousewheel",function(al,an,ak,aj){if(ak){ak*=50;var am=Math.round(-ak/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}});this.top_labeltrack.bind("dragstart",function(aj,ak){return $("<div />").css({height:af.browser_content_div.height()+af.top_labeltrack.height()+af.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(an,ao){$(ao.proxy).css({left:Math.min(an.pageX,ao.startX),width:Math.abs(an.pageX-ao.startX)});var ak=Math.min(an.pageX,ao.startX)-af.container.offset().left,aj=Math.max(an.pageX,ao.startX)-af.container.offset().left,am=(af.high-af.low),al=af.viewport_container.width();af.update_location(Math.round(ak/al*am)+af.low,Math.round(aj/al*am)+af.low)}).bind("dragend",function(ao,ap){var ak=Math.min(ao.pageX,ap.startX),aj=Math.max(ao.pageX,ap.startX),am=(af.high-af.low),al=af.viewport_container.width(),an=af.low;af.low=Math.round(ak/al*am)+an;af.high=Math.round(aj/al*am)+an;$(ap.proxy).remove();af.request_redraw()});this.add_label_track(new ab(this,{content_div:this.top_labeltrack}));this.add_label_track(new ab(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){af.resize_window()});$(document).bind("redraw",function(){af.redraw()});this.reset();$(window).trigger("resize")},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},update_location:function(af,ag){this.location_span.text(commatize(af)+" - "+commatize(ag));this.nav_input.val(this.chrom+":"+commatize(af)+"-"+commatize(ag))},load_chroms:function(ah){ah.num=w;$.extend(ah,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var af=this,ag=$.Deferred();$.ajax({url:chrom_url,data:ah,dataType:"json",success:function(aj){if(aj.chrom_info.length===0){alert("Invalid chromosome: "+ah.chrom);return}if(aj.reference){af.add_label_track(new A(af))}af.chrom_data=aj.chrom_info;var am='<option value="">Select Chrom/Contig</option>';for(var al=0,ai=af.chrom_data.length;al<ai;al++){var ak=af.chrom_data[al].chrom;am+='<option value="'+ak+'">'+ak+"</option>"}if(aj.prev_chroms){am+='<option value="previous">Previous '+w+"</option>"}if(aj.next_chroms){am+='<option value="next">Next '+w+"</option>"}af.chrom_select.html(am);af.chrom_start_index=aj.start_index;ag.resolve(aj)},error:function(){alert("Could not load chroms for this dbkey:",af.dbkey)}});return ag},change_chrom:function(ak,ag,am){if(!ak||ak==="None"){return}var ah=this;if(ak==="previous"){ah.load_chroms({low:this.chrom_start_index-w});return}if(ak==="next"){ah.load_chroms({low:this.chrom_start_index+w});return}var al=$.grep(ah.chrom_data,function(an,ao){return an.chrom===ak})[0];if(al===undefined){ah.load_chroms({chrom:ak},function(){ah.change_chrom(ak,ag,am)});return}else{if(ak!==ah.chrom){ah.chrom=ak;ah.chrom_select.val(ah.chrom);ah.max_high=al.len-1;ah.reset();ah.request_redraw(true);for(var aj=0,af=ah.drawables.length;aj<af;aj++){var ai=ah.drawables[aj];if(ai.init){ai.init()}}}if(ag!==undefined&&am!==undefined){ah.low=Math.max(ag,0);ah.high=Math.min(am,ah.max_high)}ah.reset_overview();ah.request_redraw()}},go_to:function(aj){aj=aj.replace(/ |,/g,"");var an=this,af,ai,ag=aj.split(":"),al=ag[0],am=ag[1];if(am!==undefined){try{var ak=am.split("-");af=parseInt(ak[0],10);ai=parseInt(ak[1],10)}catch(ah){return false}}an.change_chrom(al,af,ai)},move_fraction:function(ah){var af=this;var ag=af.high-af.low;this.move_delta(ah*ag)},move_delta:function(ah){var af=this;var ag=af.high-af.low;if(af.low-ah<af.max_low){af.low=af.max_low;af.high=af.max_low+ag}else{if(af.high-ah>af.max_high){af.high=af.max_high;af.low=af.max_high-ag}else{af.high-=ah;af.low-=ah}}af.request_redraw()},add_drawable:function(af){y.prototype.add_drawable.call(this,af);af.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(af){af.view=this;af.init();this.label_tracks.push(af)},remove_drawable:function(ah,ag){y.prototype.remove_drawable.call(this,ah);if(ag){var af=this;ah.container_div.hide(0,function(){$(this).remove();af.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(an,af,am,ag){var al=this,aj=(ag?[ag]:al.drawables),ah;var ag;for(var ak=0;ak<aj.length;ak++){ag=aj[ak];ah=-1;for(var ai=0;ai<al.tracks_to_be_redrawn.length;ai++){if(al.tracks_to_be_redrawn[ai][0]===ag){ah=ai;break}}if(ah<0){al.tracks_to_be_redrawn.push([ag,af,am])}else{al.tracks_to_be_redrawn[ak][1]=af;al.tracks_to_be_redrawn[ak][2]=am}}requestAnimationFrame(function(){al._redraw(an)})},_redraw:function(ap){var am=this.low,ai=this.high;if(am<this.max_low){am=this.max_low}if(ai>this.max_high){ai=this.max_high}var ao=this.high-this.low;if(this.high!==0&&ao<this.min_separation){ai=am+this.min_separation}this.low=Math.floor(am);this.high=Math.ceil(ai);this.resolution=Math.pow(C,Math.ceil(Math.log((this.high-this.low)/R)/Math.log(C)));this.zoom_res=Math.pow(v,Math.max(0,Math.ceil(Math.log(this.resolution,v)/Math.log(v))));var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var al=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var aq=13;this.overview_box.css({left:af,width:Math.max(aq,al)}).show();if(al<aq){this.overview_box.css("left",af-(aq-al)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:al})}this.update_location(this.low,this.high);if(!ap){var ah,ag,an;for(var aj=0,ak=this.tracks_to_be_redrawn.length;aj<ak;aj++){ah=this.tracks_to_be_redrawn[aj][0];ag=this.tracks_to_be_redrawn[aj][1];an=this.tracks_to_be_redrawn[aj][2];if(ah){ah._draw(ag,an)}}this.tracks_to_be_redrawn=[];for(aj=0,ak=this.label_tracks.length;aj<ak;aj++){this.label_tracks[aj]._draw()}}},zoom_in:function(ag,ah){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ai=this.high-this.low,aj=ai/2+this.low,af=(ai/this.zoom_factor)/2;if(ag){aj=ag/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(aj-af);this.high=Math.round(aj+af);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ag=this.high-this.low,ah=ag/2+this.low,af=(ag*this.zoom_factor)/2;this.low=Math.round(ah-af);this.high=Math.round(ah+af);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ah.dataset_id){return}this.overview_viewport.find(".track").remove()}var ag=ah.copy({content_div:this.overview_viewport}),af=this;ag.header_div.hide();ag.is_overview=true;af.overview_drawable=ag;this.overview_drawable.postdraw_actions=function(){af.overview_highlight.show().height(af.overview_drawable.content_div.height());af.overview_viewport.height(af.overview_drawable.content_div.height()+af.overview_box.outerHeight());af.overview_close.show();af.resize_window()};this.overview_drawable.init();af.has_changes=true},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var r=function(ah,al){this.track=ah;this.name=al.name;this.params=[];var at=al.params;for(var ai=0;ai<at.length;ai++){var an=at[ai],ag=an.name,ar=an.label,aj=unescape(an.html),au=an.value,ap=an.type;if(ap==="number"){this.params[this.params.length]=new g(ag,ar,aj,au,an.min,an.max)}else{if(ap=="select"){this.params[this.params.length]=new O(ag,ar,aj,au)}else{console.log("WARNING: unrecognized tool parameter type:",ag,ap)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aw){aw.stopPropagation()}).click(function(aw){aw.stopPropagation()}).bind("dblclick",function(aw){aw.stopPropagation()});var aq=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ao=this.params;var am=this;$.each(this.params,function(ax,aA){var az=$("<div>").addClass("param-row").appendTo(am.parent_div);var aw=$("<div>").addClass("param-label").text(aA.label).appendTo(az);var ay=$("<div/>").addClass("slider").html(aA.html).appendTo(az);ay.find(":input").val(aA.value);$("<div style='clear: both;'/>").appendTo(az)});this.parent_div.find("input").click(function(){$(this).select()});var av=$("<div>").addClass("param-row").appendTo(this.parent_div);var ak=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(av);var af=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(av);var am=this;af.click(function(){am.run_on_region()});ak.click(function(){am.run_on_dataset()})};p(r.prototype,{get_param_values_dict:function(){var af={};this.parent_div.find(":input").each(function(){var ag=$(this).attr("name"),ah=$(this).val();af[ag]=JSON.stringify(ah)});return af},get_param_values:function(){var ag=[];var af={};this.parent_div.find(":input").each(function(){var ah=$(this).attr("name"),ai=$(this).val();if(ah){ag[ag.length]=ai}});return ag},run_on_dataset:function(){var af=this;af.run({dataset_id:this.track.original_dataset_id,tool_id:af.name},null,function(ag){show_modal(af.name+" is Running",af.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ag={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},aj=this.track,ah=ag.tool_id+aj.tool_region_and_parameters_str(ag.chrom,ag.low,ag.high),af;if(aj.container===view){var ai=new Q(this.name,this.track.view,this.track.container);aj.container.add_drawable(ai);aj.container.remove_drawable(aj);ai.add_drawable(aj);aj.container_div.appendTo(ai.content_div);af=ai}else{af=aj.container}var ak=new aj.constructor(ah,view,af,"hda");ak.init_for_tool_data();ak.change_mode(aj.mode);af.add_drawable(ak);ak.content_div.text("Starting job.");this.run(ag,ak,function(al){ak.dataset_id=al.dataset_id;ak.content_div.text("Running job.");ak.init()})},run:function(ag,ah,ai){$.extend(ag,this.get_param_values_dict());var af=function(){$.getJSON(rerun_tool_url,ag,function(aj){if(aj==="no converter"){ah.container_div.addClass("error");ah.content_div.text(K)}else{if(aj.error){ah.container_div.addClass("error");ah.content_div.text(x+aj.message)}else{if(aj==="pending"){ah.container_div.addClass("pending");ah.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(af,2000)}else{ai(aj)}}}})};af()}});var O=function(ag,af,ah,ai){this.name=ag;this.label=af;this.html=ah;this.value=ai};var g=function(ah,ag,aj,ak,ai,af){O.call(this,ah,ag,aj,ak);this.min=ai;this.max=af};var h=function(ag,af,ah,ai){this.name=ag;this.index=af;this.tool_id=ah;this.tool_exp_name=ai};var V=function(ag,af,ah,ai){h.call(this,ag,af,ah,ai);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};p(V.prototype,{applies_to:function(af){if(af.length>this.index){return true}return false},keep:function(af){if(!this.applies_to(af)){return true}var ag=af[this.index];return(isNaN(ag)||(ag>=this.low&&ag<=this.high))},update_attrs:function(ag){var af=false;if(!this.applies_to(ag)){return af}if(ag[this.index]<this.min){this.min=Math.floor(ag[this.index]);af=true}if(ag[this.index]>this.max){this.max=Math.ceil(ag[this.index]);af=true}return af},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var ah=function(ak,ai){var aj=ai-ak;return(aj<=2?0.01:1)};var ag=this.slider.slider("option","min"),af=this.slider.slider("option","max");if(this.min<ag||this.max>af){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ah(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var aa=function(aq,ay){this.track=aq;this.filters=[];for(var at=0;at<ay.length;at++){var au=ay[at],az=au.name,af=au.type,ah=au.index,ax=au.tool_id,aw=au.tool_exp_name;if(af==="int"||af==="float"){this.filters[at]=new V(az,ah,ax,aw)}else{console.log("ERROR: unsupported filter: ",az,af)}}var ai=function(aA,aB,aC){aA.click(function(){var aD=aB.text();max=parseFloat(aC.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aC.slider("option","values")){input_size=2*input_size+1;multi_value=true}aB.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aD).appendTo(aB).focus().select().click(function(aE){aE.stopPropagation()}).blur(function(){$(this).remove();aB.text(aD)}).keyup(function(aI){if(aI.keyCode===27){$(this).trigger("blur")}else{if(aI.keyCode===13){var aG=aC.slider("option","min"),aE=aC.slider("option","max"),aH=function(aJ){return(isNaN(aJ)||aJ>aE||aJ<aG)},aF=$(this).val();if(!multi_value){aF=parseFloat(aF);if(aH(aF)){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}else{aF=aF.split("-");aF=[parseFloat(aF[0]),parseFloat(aF[1])];if(aH(aF[0])||aH(aF[1])){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}aC.slider((multi_value?"values":"value"),aF)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aA){aA.stopPropagation()}).click(function(aA){aA.stopPropagation()}).bind("dblclick",function(aA){aA.stopPropagation()}).bind("keydown",function(aA){aA.stopPropagation()});var av=$("<div/>").addClass("sliders").appendTo(this.parent_div);var an=this;$.each(this.filters,function(aD,aF){aF.container=$("<div/>").addClass("filter-row slider-row").appendTo(av);var aE=$("<div/>").addClass("elt-label").appendTo(aF.container);var aC=$("<span/>").addClass("slider-name").text(aF.name+"  ").appendTo(aE);var aB=$("<span/>");var aH=$("<span/>").addClass("slider-value").appendTo(aE).append("[").append(aB).append("]");var aA=$("<div/>").addClass("slider").appendTo(aF.container);aF.control_element=$("<div/>").attr("id",aF.name+"-filter-control").appendTo(aA);var aG=[0,0];aF.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aJ,aK){var aI=aK.values;aB.text(aI[0]+"-"+aI[1]);aF.low=aI[0];aF.high=aI[1];an.track.request_draw(true,true)},change:function(aI,aJ){aF.control_element.slider("option","slide").call(aF.control_element,aI,aJ)}});aF.slider=aF.control_element;aF.slider_label=aB;ai(aH,aB,aF.control_element);$("<div style='clear: both;'/>").appendTo(aF.container)});if(this.filters.length!==0){var ak=$("<div/>").addClass("param-row").appendTo(av);var am=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ak);var ag=this;am.click(function(){ag.run_on_dataset()})}var ap=$("<div/>").addClass("display-controls").appendTo(this.parent_div),ar,al,ao,aj={Transparency:function(aA){an.alpha_filter=aA},Height:function(aA){an.height_filter=aA}};$.each(aj,function(aC,aB){ar=$("<div/>").addClass("filter-row").appendTo(ap),al=$("<span/>").addClass("elt-label").text(aC+":").appendTo(ar),ao=$("<select/>").attr("name",aC+"_dropdown").css("float","right").appendTo(ar);$("<option/>").attr("value",-1).text("== None ==").appendTo(ao);for(var aA=0;aA<an.filters.length;aA++){$("<option/>").attr("value",aA).text(an.filters[aA].name).appendTo(ao)}ao.change(function(){$(this).children("option:selected").each(function(){var aD=parseInt($(this).val());aj[aC]((aD>=0?an.filters[aD]:null));an.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(ar)});$("<div style='clear: both;'/>").appendTo(this.parent_div)};p(aa.prototype,{reset_filters:function(){for(var af=0;af<this.filters.length;af++){filter=this.filters[af];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var an=function(ar,ap,aq){if(!(ap in ar)){ar[ap]=aq}return ar[ap]};var ah={},af,ag,ai;for(var aj=0;aj<this.filters.length;aj++){af=this.filters[aj];if(af.tool_id){if(af.min!=af.low){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" >= "+af.low}if(af.max!=af.high){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" <= "+af.high}}}var al=[];for(var ao in ah){al[al.length]=[ao,ah[ao]]}var am=al.length;(function ak(aw,at){var aq=at[0],ar=aq[0],av=aq[1],au="("+av.join(") and (")+")",ap={cond:au,input:aw,target_dataset_id:aw,tool_id:ar},at=at.slice(1);$.getJSON(run_tool_url,ap,function(ax){if(ax.error){show_modal("Filter Dataset","Error running tool "+ar,{Close:hide_modal})}else{if(at.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ak(ax.dataset_id,at)}}})})(this.track.dataset_id,al)}});var D=function(af,ag){M.Scaler.call(this,ag);this.filter=af};D.prototype.gen_val=function(af){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(af[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var G=function(af){this.track=af.track;this.params=af.params;this.values={};this.restore_values((af.saved_values?af.saved_values:{}));this.onchange=af.onchange};p(G.prototype,{restore_values:function(af){var ag=this;$.each(this.params,function(ah,ai){if(af[ai.key]!==undefined){ag.values[ai.key]=af[ai.key]}else{ag.values[ai.key]=ai.default_value}})},build_form:function(){var ai=this;var af=$("<div />");var ah;function ag(am,aj){for(var ao=0;ao<am.length;ao++){ah=am[ao];if(ah.hidden){continue}var ak="param_"+ao;var at=ai.values[ah.key];var av=$("<div class='form-row' />").appendTo(aj);av.append($("<label />").attr("for",ak).text(ah.label+":"));if(ah.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ak).attr("name",ak).attr("checked",at))}else{if(ah.type==="text"){av.append($('<input type="text"/>').attr("id",ak).val(at).click(function(){$(this).select()}))}else{if(ah.type=="select"){var aq=$("<select />").attr("id",ak);for(var an=0;an<ah.options.length;an++){$("<option/>").text(ah.options[an].label).attr("value",ah.options[an].value).appendTo(aq)}aq.val(at);av.append(aq)}else{if(ah.type==="color"){var ap=$("<input />").attr("id",ak).attr("name",ak).val(at);var ar=$("<div class='tipsy tipsy-west' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ar);var au=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:ap,color:at});$("<div />").append(ap).append(ar).appendTo(av).bind("click",function(aw){ar.css({left:$(this).position().left+$(ap).width()+5,top:$(this).position().top-($(ar).height()/2)+($(ap).height()/2)}).show();$(document).bind("click.color-picker",function(){ar.hide();$(document).unbind("click.color-picker")});aw.stopPropagation()})}else{av.append($("<input />").attr("id",ak).attr("name",ak).val(at))}}}}if(ah.help){av.append($("<div class='help'/>").text(ah.help))}}}ag(this.params,af);return af},update_from_form:function(af){var ah=this;var ag=false;$.each(this.params,function(ai,ak){if(!ak.hidden){var al="param_"+ai;var aj=af.find("#"+al).val();if(ak.type==="float"){aj=parseFloat(aj)}else{if(ak.type==="int"){aj=parseInt(aj)}else{if(ak.type==="bool"){aj=af.find("#"+al).is(":checked")}}}if(aj!==ah.values[ak.key]){ah.values[ak.key]=aj;ag=true}}});if(ag){this.onchange()}}});var b=function(af,ai,ah,ag,aj){this.track=af;this.index=ai;this.low=ai*R*ah;this.high=(ai+1)*R*ah;this.resolution=ah;this.canvas=$("<div class='track-tile'/>").append(ag);this.data=aj;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(af,ai,ah,ag,aj,ak){b.call(this,af,ai,ah,ag,aj);this.max_val=ak};p(k.prototype,b.prototype);var P=function(af,aj,ai,ah,al,am,ak,ag){b.call(this,af,aj,ai,ah,al);this.mode=am;this.message=ak;this.feature_mapper=ag};p(P.prototype,b.prototype);P.prototype.predisplay_actions=function(){var ag=this,af={};if(ag.mode!=="Pack"){return}$(this.canvas).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).siblings(".feature-popup").remove()}).mousemove(function(ar){if(!this.hovered){return}var am=$(this).offset(),aq=ar.pageX-am.left,ap=ar.pageY-am.top,aw=ag.feature_mapper.get_feature_data(aq,ap),an=(aw?aw[0]:null);$(this).siblings(".feature-popup").each(function(){if(!an||$(this).attr("id")!==an.toString()){$(this).remove()}});if(aw){var ai=af[an];if(!ai){var an=aw[0],at={name:aw[3],start:aw[1],end:aw[2],strand:aw[4]},al=ag.track.filters_manager.filters,ak;for(var ao=0;ao<al.length;ao++){ak=al[ao];at[ak.name]=aw[ak.index]}var ai=$("<div/>").attr("id",an).addClass("feature-popup"),ax=$("<table/>"),av,au,ay;for(av in at){au=at[av];ay=$("<tr/>").appendTo(ax);$("<th/>").appendTo(ay).text(av);$("<td/>").attr("align","left").appendTo(ay).text(typeof(au)=="number"?Z(au,2):au)}ai.append($("<div class='feature-popup-inner'>").append(ax));af[an]=ai}ai.appendTo($(ag.canvas).parent());var aj=aq+parseInt(ag.canvas.css("left"))-ai.width()/2,ah=ap+parseInt(ag.canvas.css("top"))+7;ai.css("left",aj+"px").css("top",ah+"px")}else{if(!ar.isPropagationStopped()){ar.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ar)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var i=function(ai,ag,af,ah,aj,ak){q.call(this,ai,ag,af,{},"draghandle");this.data_url=(aj?aj:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ak?ak:L);this.dataset_check_url=converted_datasets_state_url;if(!i.id_counter){i.id_counter=0}this.id=i.id_counter++;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};p(i.prototype,q.prototype,{build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var af=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(af)}this.name_div=$("<div/>").addClass("track-name").appendTo(af).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return af},build_icons_div:function(){var aj=$("<div/>").css("float","left");this.mode_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Set display mode").addClass("icon-button chevron-expand").tipsy({gravity:"s"}).appendTo(aj);this.toggle_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Hide/show track content").addClass("icon-button toggle").tipsy({gravity:"s"}).appendTo(aj);this.settings_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Edit settings").addClass("icon-button settings-icon").tipsy({gravity:"s"}).appendTo(aj);this.overview_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Set as overview").addClass("icon-button overview-icon").tipsy({gravity:"s"}).appendTo(aj);this.filters_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Filters").addClass("icon-button filters-icon").tipsy({gravity:"s"}).appendTo(aj).hide();this.tools_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Tools").addClass("icon-button tools-icon").tipsy({gravity:"s"}).appendTo(aj).hide();this.remove_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Remove").addClass("icon-button remove-icon").tipsy({gravity:"s"}).appendTo(aj);var ag=this;if(ag.display_modes!==undefined){var al=(ag.config&&ag.config.values.mode?ag.config.values.mode:ag.display_modes[0]);ag.mode=al;this.mode_icon.attr("title","Set display mode (now: "+ag.mode+")");var ai={};for(var ah=0,af=ag.display_modes.length;ah<af;ah++){var ak=ag.display_modes[ah];ai[ak]=function(am){return function(){ag.change_mode(am);ag.icons_div.show();ag.container_div.mouseleave(function(){ag.icons_div.hide()})}}(ak)}make_popupmenu(this.mode_icon,ai)}this.toggle_icon.click(function(){if(ag.content_visible){ag.toggle_icon.addClass("toggle-expand").removeClass("toggle");ag.hide_contents();ag.content_visible=false}else{ag.toggle_icon.addClass("toggle").removeClass("toggle-expand");ag.content_visible=true;ag.show_contents()}});this.settings_icon.click(function(){var ao=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},am=function(){ag.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},an=function(ap){if((ap.keyCode||ap.which)===27){ao()}else{if((ap.keyCode||ap.which)===13){am()}}};$(window).bind("keypress.check_enter_esc",an);show_modal("Configure Track",ag.config.build_form(),{Cancel:ao,OK:am})});this.overview_icon.click(function(){ag.view.set_overview(ag)});this.filters_icon.click(function(){ag.filters_div.toggle();ag.filters_manager.reset_filters()});this.tools_icon.click(function(){ag.dynamic_tool_div.toggle();if(ag.dynamic_tool_div.is(":visible")){ag.set_name(ag.name+ag.tool_region_and_parameters_str())}else{ag.revert_name()}$(".tipsy").remove()});this.remove_icon.click(function(){$(".tipsy").remove();ag.remove()});return aj},hide_contents:function(){this.content_div.children().remove();this.content_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.content_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof ab){return"LabelTrack"}else{if(this instanceof A){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof W){return"ReadTrack"}else{if(this instanceof U){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}return""},init:function(){var af=this;af.enabled=false;af.tile_cache.clear();af.data_manager.clear();af.initial_canvas=undefined;af.content_div.css("height","auto");af.container_div.removeClass("nodata error pending");if(!af.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:af.hda_ldda,dataset_id:af.dataset_id,chrom:af.view.chrom},function(ag){if(!ag||ag==="error"||ag.kind==="error"){af.container_div.addClass("error");af.content_div.text(o);if(ag.message){var ah=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})});af.content_div.append(ah)}}else{if(ag==="no converter"){af.container_div.addClass("error");af.content_div.text(K)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){af.container_div.addClass("nodata");af.content_div.text(F)}else{if(ag==="pending"){af.container_div.addClass("pending");af.content_div.text(t);setTimeout(function(){af.init()},af.data_query_wait)}else{if(ag.status==="data"){if(ag.valid_chroms){af.valid_chroms=ag.valid_chroms;af.update_icons()}af.content_div.text(Y);if(af.view.chrom){af.content_div.text("");af.content_div.css("height",af.height_px+"px");af.enabled=true;$.when(af.predraw_init()).done(function(){af.container_div.removeClass("nodata error pending");af.request_draw()})}}}}}}});this.update_icons()},predraw_init:function(){}});var N=function(aj,ah,ag,ai,al,ak){i.call(this,aj,ah,ag,ai);var af=this,ah=af.view;m(af.container_div,af.drag_handle_class,".group",af);this.filters_manager=new aa(this,(al!==undefined?al:{}));this.filters_available=false;this.filters_visible=false;this.tool=(ak!==undefined&&obj_length(ak)>0?new r(this,ak):undefined);if(this.header_div){if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}};p(N.prototype,q.prototype,i.prototype,{copy:function(af){return new this.constructor(this.name,this.view,af,this.hda_ldda,this.dataset_id,this.prefs,this.filters,this.tool)},to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ag){var af=this;af.mode=ag;af.config.values.mode=ag;af.tile_cache.clear();af.request_draw();this.mode_icon.attr("title","Set display mode (now: "+af.mode+")");return af},update_icons:function(){var af=this;if(af.filters_available>0){af.filters_icon.show()}else{af.filters_icon.hide()}if(af.tool){af.tools_icon.show()}else{af.tools_icon.hide()}},_gen_tile_cache_key:function(ag,ah,af){return ag+"_"+ah+"_"+af},request_draw:function(ag,af){this.view.request_redraw(false,ag,af,this)},_draw:function(ah,ap){if(!this.enabled){return}if(!this.content_visible){return}if(!(this instanceof A)&&(!this.dataset_id)){return}var ao=this.view.low,al=this.view.high,am=al-ao,ai=this.view.container.width(),at=ai/am,ak=this.view.resolution,ar=$("<div style='position: relative;'></div>");if(this.is_overview){ao=this.view.max_low;al=this.view.max_high;ak=Math.pow(C,Math.ceil(Math.log((view.max_high-view.max_low)/R)/Math.log(C)));at=ai/(view.max_high-view.max_low)}if(!ap){this.content_div.children().remove()}this.content_div.append(ar);this.max_height=0;var ag=Math.floor(ao/ak/R);var an=true;var aq=[];var af=0;while((ag*R*ak)<al){tile=this.draw_helper(ah,ai,ag,ak,ar,at);if(tile){aq.push(tile)}else{an=false}ag+=1;af++}var aj=this;if(an){aj.postdraw_actions(aq,ai,at,ap)}},postdraw_actions:function(aj,ak,al,af){var ah=this;var ai=false;for(var ag=0;ag<aj.length;ag++){if(aj[ag].message){ai=true;break}}if(ai){for(var ag=0;ag<aj.length;ag++){tile=aj[ag];if(!tile.message){tile.canvas.css("padding-top",E)}}}},draw_helper:function(ag,ah,ai,al,ar,aw,at,am){var aj=this,aq=this._gen_tile_cache_key(ah,aw,ai),an=ai*R*al,av=an+R*al;var ao=(ag?undefined:aj.tile_cache.get(aq));if(ao){aj.show_tile(ao,ar,aw);return ao}var ap=function(ax){return("isResolved" in ax)};var ak=true;var af=aj.data_manager.get_data(an,av,aj.mode,al,aj.data_url_extra_params);if(ap(af)){ak=false}var au;if(view.reference_track&&aw>view.canvas_manager.char_width_px){au=view.reference_track.data_manager.get_data(an,av,aj.mode,al,view.reference_track.data_url_extra_params);if(ap(au)){ak=false}}if(ak){p(af,am);var ao=aj.draw_tile(af,aj.mode,al,ai,aw,au);if(ao!==undefined){aj.tile_cache.set(aq,ao);aj.show_tile(ao,ar,aw)}return ao}$.when(af,au).then(function(){view.request_redraw(false,false,false,aj)});return null},show_tile:function(al,an,ao){var ah=this,ag=al.canvas,ak=ag;if(al.message){var ap=$("<div/>"),am=$("<div/>").addClass("tile-message").text(al.message).css({height:E-1,width:al.canvas.width}).appendTo(ap),aj=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(am),af=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(am);ap.append(ag);ak=ap;aj.click(function(){al.stale=true;ah.data_manager.get_more_data(al.low,al.high,ah.mode,al.resolution,{},ah.data_manager.DEEP_DATA_REQ);ah.request_draw()}).dblclick(function(aq){aq.stopPropagation()});af.click(function(){al.stale=true;ah.data_manager.get_more_data(al.low,al.high,ah.mode,al.resolution,{},ah.data_manager.BROAD_DATA_REQ);ah.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}al.predisplay_actions();var ai=(al.low-(this.is_overview?this.view.max_low:this.view.low))*ao;if(this.left_offset){ai-=this.left_offset}ak.css({position:"absolute",top:0,left:ai,height:""});an.append(ak);ah.max_height=Math.max(ah.max_height,ak.height());ah.content_div.css("height",ah.max_height+"px");an.children().css("height",ah.max_height+"px")},_get_tile_bounds:function(af,ag){var ai=af*R*ag,aj=R*ag,ah=(ai+aj<=this.view.max_high?ai+aj:this.view.max_high);return[ai,ah]},tool_region_and_parameters_str:function(ah,af,ai){var ag=this,aj=(ah!==undefined&&af!==undefined&&ai!==undefined?ah+":"+af+"-"+ai:"all");return" - region=["+aj+"], parameters=["+ag.tool.get_param_values().join(", ")+"]"},init_for_tool_data:function(){this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.predraw_init=function(){var ag=this;var af=function(){if(ag.data_manager.size()===0){setTimeout(af,300)}else{ag.data_url=default_data_url;ag.data_query_wait=L;ag.dataset_state_url=converted_datasets_state_url;$.getJSON(ag.dataset_state_url,{dataset_id:ag.dataset_id,hda_ldda:ag.hda_ldda},function(ah){})}};af()}}});var ab=function(ag,af){i.call(this,"label",ag,af,false,{});this.container_div.addClass("label-track")};p(ab.prototype,i.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ah=this.view,ai=ah.high-ah.low,al=Math.floor(Math.pow(10,Math.floor(Math.log(ai)/Math.log(10)))),af=Math.floor(ah.low/al)*al,aj=this.view.container.width(),ag=$("<div style='position: relative; height: 1.3em;'></div>");while(af<ah.high){var ak=(af-ah.low)/ai*aj;ag.append($("<div class='label'>"+commatize(af)+"</div>").css({position:"absolute",left:ak-1}));af+=al}this.content_div.children(":first").remove();this.content_div.append(ag)}});var A=function(af){N.call(this,"reference",af,{content_div:af.top_labeltrack},{});af.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:af.dbkey};this.data_manager=new I(B,this,false);this.tile_cache=new c(u)};p(A.prototype,q.prototype,N.prototype,{build_header_div:function(){},init:function(){this.enabled=true},draw_tile:function(ap,al,ak,ag,aq){var aj=this,ah=R*ak;if(aq>this.view.canvas_manager.char_width_px){if(ap.data===null){aj.content_div.css("height","0px");return}var ai=this.view.canvas_manager.new_canvas();var ao=ai.getContext("2d");ai.width=Math.ceil(ah*aq+aj.left_offset);ai.height=aj.height_px;ao.font=ao.canvas.manager.default_font;ao.textAlign="center";ap=ap.data;for(var am=0,an=ap.length;am<an;am++){var af=Math.round(am*aq);ao.fillText(ap[am],af+aj.left_offset,10)}return new b(aj,ag,ak,ai,ap)}this.content_div.css("height","0px")}});var j=function(ak,ai,ah,al,af,aj){var ag=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";N.call(this,ak,ai,ah,aj);this.min_height_px=16;this.max_height_px=400;this.height_px=32;this.hda_ldda=al;this.dataset_id=af;this.original_dataset_id=af;this.data_manager=new S(B,this);this.tile_cache=new c(u);this.left_offset=0;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:aj,onchange:function(){ag.set_name(ag.prefs.name);ag.vertical_range=ag.prefs.max_value-ag.prefs.min_value;$("#linetrack_"+ag.dataset_id+"_minval").text(ag.prefs.min_value);$("#linetrack_"+ag.dataset_id+"_maxval").text(ag.prefs.max_value);ag.tile_cache.clear();ag.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};p(j.prototype,q.prototype,N.prototype,{add_resize_handle:function(){var af=this;var ai=false;var ah=false;var ag=$("<div class='track-resize'>");$(af.container_div).hover(function(){if(af.content_visible){ai=true;ag.show()}},function(){ai=false;if(!ah){ag.hide()}});ag.hide().bind("dragstart",function(aj,ak){ah=true;ak.original_height=$(af.content_div).height()}).bind("drag",function(ak,al){var aj=Math.min(Math.max(al.original_height+al.deltaY,af.min_height_px),af.max_height_px);$(af.content_div).css("height",aj);af.height_px=aj;af.request_draw(true)}).bind("dragend",function(aj,ak){af.tile_cache.clear();ah=false;if(!ai){ag.hide()}af.config.values.height=af.height_px}).appendTo(af.container_div)},predraw_init:function(){var af=this;af.vertical_range=undefined;return $.getJSON(af.data_url,{stats:true,chrom:af.view.chrom,low:null,high:null,hda_ldda:af.hda_ldda,dataset_id:af.dataset_id},function(ag){af.container_div.addClass("line-track");var aj=ag.data;if(isNaN(parseFloat(af.prefs.min_value))||isNaN(parseFloat(af.prefs.max_value))){var ah=aj.min;var al=aj.max;ah=Math.floor(Math.min(0,Math.max(ah,aj.mean-2*aj.sd)));al=Math.ceil(Math.max(0,Math.min(al,aj.mean+2*aj.sd)));af.prefs.min_value=ah;af.prefs.max_value=al;$("#track_"+af.dataset_id+"_minval").val(af.prefs.min_value);$("#track_"+af.dataset_id+"_maxval").val(af.prefs.max_value)}af.vertical_range=af.prefs.max_value-af.prefs.min_value;af.total_frequency=aj.total_frequency;af.container_div.find(".yaxislabel").remove();var ak=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_minval").text(Z(af.prefs.min_value,3));var ai=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_maxval").text(Z(af.prefs.max_value,3));ai.css({position:"absolute",top:"24px",left:"10px"});ai.prependTo(af.container_div);ak.css({position:"absolute",bottom:"2px",left:"10px"});ak.prependTo(af.container_div)})},draw_tile:function(ar,ak,aj,ah,aq){if(this.vertical_range===undefined){return}var af=this._get_tile_bounds(ah,aj),al=af[0],ap=af[1],ag=Math.ceil((ap-al)*aq),an=this.height_px;var ai=this.view.canvas_manager.new_canvas();ai.width=ag,ai.height=an;var ao=ai.getContext("2d");var am=new M.LinePainter(ar.data,al,ap,this.prefs,ak);am.draw(ao,ag,an);return new b(this.track,ah,aj,ai,ar.data)}});var e=function(af,al,ag,ak,an,am,ai,aj){var ah=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];N.call(this,af,al,ag,am,ai,aj);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:am,onchange:function(){ah.set_name(ah.prefs.name);ah.tile_cache.clear();ah.set_painter_from_config();ah.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=ak;this.dataset_id=an;this.original_dataset_id=an;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new S(20,this);this.left_offset=200;this.set_painter_from_config()};p(e.prototype,q.prototype,N.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style=="arcs"){this.painter=M.ArcLinkedFeaturePainter}else{this.painter=M.LinkedFeaturePainter}},postdraw_actions:function(av,af,aw,au){N.prototype.postdraw_actions.call(this,av,au);var ai=this;if(au){var ak=ai.content_div.children();var al=false;for(var aj=ak.length-1,ap=0;aj>=ap;aj--){var ah=$(ak[aj]);if(al){ah.remove()}else{if(ah.children().length!==0){al=true}}}}if(ai.mode=="Histogram"){var ao=-1;for(var aj=0;aj<av.length;aj++){var at=av[aj].max_val;if(at>ao){ao=at}}for(var aj=0;aj<av.length;aj++){var ar=av[aj];if(ar.max_val!==ao){ar.canvas.remove();ai.draw_helper(true,af,ar.index,ar.resolution,ar.canvas.parent(),aw,[],{max:ao})}}}if(ai.filters_manager){var ag=ai.filters_manager.filters;for(var an=0;an<ag.length;an++){ag[an].update_ui_elt()}var am=false,aq;for(var aj=0;aj<av.length;aj++){if(av[aj].data.length){aq=av[aj].data[0];for(var an=0;an<ag.length;an++){if(ag[an].applies_to(aq)){am=true;break}}}}if(ai.filters_available!==am){ai.filters_available=am;if(!ai.filters_available){ai.filters_div.hide()}ai.update_icons()}}},update_auto_mode:function(af){var af;if(this.mode=="Auto"){if(af=="no_detail"){af="feature spans"}else{if(af=="summary_tree"){af="coverage histogram"}}this.mode_icon.attr("title","Set display mode (now: Auto/"+af+")")}},incremental_slots:function(aj,ag,ai){var ah=this.view.canvas_manager.dummy_context,af=this.inc_slots[aj];if(!af||(af.mode!==ai)){af=new (s.FeatureSlotter)(aj,ai==="Pack",z,function(ak){return ah.measureText(ak)});af.mode=ai;this.inc_slots[aj]=af}return af.slot_features(ag)},get_summary_tree_data:function(aj,am,ah,av){if(av>ah-am){av=ah-am}var aq=Math.floor((ah-am)/av),au=[],ai=0;var ak=0,al=0,ap,at=0,an=[],ar,ao;var ag=function(ay,ax,az,aw){ay[0]=ax+az*aw;ay[1]=ax+(az+1)*aw};while(at<av&&ak!==aj.length){var af=false;for(;at<av&&!af;at++){ag(an,am,at,aq);for(al=ak;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){af=true;break}}if(af){break}}data_start_index=al;au[au.length]=ar=[an[0],0];for(;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){ar[1]++}else{break}}if(ar[1]>ai){ai=ar[1]}at++}return{max:ai,delta:aq,data:au}},draw_tile:function(au,ax,aB,aF,ap,ai){var ay=this,ak=ay._get_tile_bounds(aF,aB),aI=ak[0],ag=ak[1],aw=ag-aI,az=Math.ceil(aw*ap),aO=25,aj=this.left_offset,av,al;if(ax==="Auto"){if(au.dataset_type==="summary_tree"){ax=au.dataset_type}else{if(au.extra_info==="no_detail"||ay.is_overview){ax="no_detail"}else{var aN=au.data;if(this.view.high-this.view.low>J){ax="Squish"}else{ax="Pack"}}}this.update_auto_mode(ax)}if(ax==="summary_tree"||ax==="Histogram"){al=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var af=$("<div />").addClass("yaxislabel");af.text(au.max);af.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});af.prependTo(this.container_div);var ah=this.view.canvas_manager.new_canvas();ah.width=az+aj;ah.height=al+T;if(au.dataset_type!="summary_tree"){var aq=this.get_summary_tree_data(au.data,aI,ag,200);if(au.max){aq.max=au.max}au=aq}var aK=new M.SummaryTreePainter(au,aI,ag,this.prefs);var aA=ah.getContext("2d");aA.translate(aj,T);aK.draw(aA,az,al);return new k(ay,aF,aB,ah,au.data,au.max)}var av,an=1;if(ax==="no_detail"||ax==="Squish"||ax==="Pack"){an=this.incremental_slots(ap,au.data,ax);av=this.inc_slots[ap].slots}var ao=[];if(au.data){var ar=this.filters_manager.filters;for(var aC=0,aE=au.data.length;aC<aE;aC++){var am=au.data[aC];var aD=false;var at;for(var aH=0,aM=ar.length;aH<aM;aH++){at=ar[aH];at.update_attrs(am);if(!at.keep(am)){aD=true;break}}if(!aD){ao.push(am)}}}var aL=(this.filters_manager.alpha_filter?new D(this.filters_manager.alpha_filter):null);var aJ=(this.filters_manager.height_filter?new D(this.filters_manager.height_filter):null);var aK=new (this.painter)(ao,aI,ag,this.prefs,ax,aL,aJ,ai);var al=Math.max(ad,aK.get_required_height(an,az));var ah=this.view.canvas_manager.new_canvas();var aG=null;ah.width=az+aj;ah.height=al;var aA=ah.getContext("2d");aA.fillStyle=this.prefs.block_color;aA.font=aA.canvas.manager.default_font;aA.textAlign="right";this.container_div.find(".yaxislabel").remove();if(au.data){aA.translate(aj,0);aG=aK.draw(aA,az,al,av);aG.translation=-aj}return new P(ay,aF,aB,ah,au.data,ax,au.message,aG)}});var U=function(ak,ah,ag,am,af,aj,al,ai){e.call(this,ak,ah,ag,am,af,aj,al,ai);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:aj,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter};p(U.prototype,q.prototype,N.prototype,e.prototype);var W=function(af,ak,ag,aj,an,am,ah){e.call(this,af,ak,ag,aj,an,am,ah);var ai=get_random_color(),al=get_random_color([ai,"#ffffff"]);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ai},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:al},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:am,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter;this.update_icons()};p(W.prototype,q.prototype,N.prototype,e.prototype);X.View=ac;X.DrawableGroup=Q;X.LineTrack=j;X.FeatureTrack=e;X.ReadTrack=W;X.VcfTrack=U};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(F,G){for(var E=0;E<=z;E++){var C=false,H=h[E];if(H!==undefined){for(var B=0,D=H.length;B<D;B++){var i=H[B];if(G>i[0]&&F<i[1]){C=true;break}}}if(!C){return E}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(i,x){var u=i("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y<E;y++,A+=J,G+=H){if(y%2!==0){continue}I.fillRect(A,G,D,1)}};var q=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var d=function(y){this.default_val=(y?y:1)};d.prototype.gen_val=function(y){return this.default_val};var l=function(A,C,y,z,B){this.data=A;this.view_start=C;this.view_end=y;this.prefs=u({},this.default_prefs,z);this.mode=B};l.prototype.default_prefs={};var v=function(A,C,y,z,B){l.call(this,A,C,y,z,B)};v.prototype.default_prefs={show_counts:false};v.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var b=function(y,C,E,F,A){l.call(this,y,C,E,F,A);if(this.prefs.min_value===undefined){var G=Infinity;for(var z=0,B=this.data.length;z<B;z++){G=Math.min(G,this.data[z][1])}this.prefs.min_value=G}if(this.prefs.max_value===undefined){var D=-Infinity;for(var z=0,B=this.data.length;z<B;z++){D=Math.max(D,this.data[z][1])}this.prefs.max_value=D}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var m=function(y){this.feature_positions={};this.slot_height=y;this.translation=0;this.y_translation=0};m.prototype.map_feature_data=function(z,B,y,A){if(!this.feature_positions[B]){this.feature_positions[B]=[]}this.feature_positions[B].push({data:z,x_start:y,x_end:A})};m.prototype.get_feature_data=function(z,D){var C=Math.floor((D-this.y_translation)/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var o=function(A,D,y,z,C,E,B){l.call(this,A,D,y,z,C);this.alpha_scaler=(E?E:new d());this.height_scaler=(B?B:new d())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(A,z){var y=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){y=A*y_scale}return y+this.get_top_padding(z)+this.get_bottom_padding(z)},get_top_padding:function(y){return 0},get_bottom_padding:function(y){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(K,I,G,F){var Q=this.data,D=this.view_start,M=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var H=this.view_end-this.view_start,E=I/H,L=this.get_row_height(),P=new m(L),B;for(var N=0,O=Q.length;N<O;N++){var A=Q[N],C=A[0],J=A[1],y=A[2],z=(F&&F[C]!==undefined?F[C]:null);if((J<M&&y>D)&&(this.mode=="Dense"||z!==null)){B=this.draw_element(K,this.mode,A,z,D,M,E,L,I);P.map_feature_data(A,z,B[0],B[1])}}K.restore();P.y_translation=this.get_top_padding(I);return P},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.");return[0,0]}});var c=10,h=3,k=5,w=10,f=1,s=9,e=3,a=9,j=2,g="#ccc";var r=function(A,D,y,z,C,E,B){o.call(this,A,D,y,z,C,E,B);this.draw_background_connector=true;this.draw_individual_connectors=false};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=c}else{if(z==="no_detail"){y=h}else{if(z==="Squish"){y=k}else{y=w}}}return y},draw_element:function(M,D,X,H,O,aj,an,ap,y){var T=X[0],al=X[1],ad=X[2],Q=X[3],ae=Math.floor(Math.max(0,(al-O)*an)),N=Math.ceil(Math.min(y,Math.max(0,(ad-O)*an))),ac=ae,ao=N,aa=(D==="Dense"?0:(0+H))*ap+this.get_top_padding(y),L,ah,R=null,ar=null,B=this.prefs.block_color,ag=this.prefs.label_color;M.globalAlpha=this.alpha_scaler.gen_val(X);if(D==="Dense"){H=1}if(D==="no_detail"){M.fillStyle=B;M.fillRect(ae,aa+5,N-ae,f)}else{var K=X[4],Z=X[5],af=X[6],C=X[7],V=true;if(Z&&af){R=Math.floor(Math.max(0,(Z-O)*an));ar=Math.ceil(Math.min(y,Math.max(0,(af-O)*an)))}var am,U;if(D==="Squish"){am=1;U=e;V=false}else{if(D==="Dense"){am=5;U=s}else{am=5;U=a}}if(!C){M.fillStyle=B;M.fillRect(ae,aa+1,N-ae,U);if(K&&V){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}M.fillRect(ae,aa+1,N-ae,U)}}else{var J,W;if(D==="Squish"||D==="Dense"){J=aa+Math.floor(e/2)+1;W=1}else{if(K){J=aa;W=U}else{J+=(e/2)+1;W=1}}if(this.draw_background_connector){if(D==="Squish"||D==="Dense"){M.fillStyle=g}else{if(K){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand")}}}else{M.fillStyle=g}}M.fillRect(ae,J,N-ae,W)}var E;for(var ak=0,A=C.length;ak<A;ak++){var F=C[ak],z=Math.floor(Math.max(0,(F[0]-O)*an)),Y=Math.ceil(Math.min(y,Math.max((F[1]-O)*an))),S,ab;if(z>Y){continue}M.fillStyle=B;M.fillRect(z,aa+(U-am)/2+1,Y-z,am);if(R!==undefined&&af>Z&&!(z>ar||Y<R)){var ai=Math.max(z,R),I=Math.min(Y,ar);M.fillRect(ai,aa+1,I-ai,U);if(C.length==1&&D=="Pack"){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}if(ai+14<I){ai+=2;I-=2}M.fillRect(ai,aa+1,I-ai,U)}}if(this.draw_individual_connectors&&S){this.draw_connector(M,S,ab,z,Y,aa)}S=z;ab=Y}if(D==="Pack"){M.globalAlpha=1;M.fillStyle="white";var G=this.height_scaler.gen_val(X),P=Math.ceil(U*G),aq=Math.round((U-P)/2);if(G!==1){M.fillRect(ae,J+1,N-ae,aq);M.fillRect(ae,J+U-aq+1,N-ae,aq)}}}M.globalAlpha=1;if(D==="Pack"&&al>O){M.fillStyle=ag;if(O===0&&ae-M.measureText(Q).width<0){M.textAlign="left";M.fillText(Q,N+j,aa+8);ao+=M.measureText(Q).width+j}else{M.textAlign="right";M.fillText(Q,ae-j,aa+8);ac-=M.measureText(Q).width+j}}}M.globalAlpha=1;return[ac,ao]}});var t=function(B,E,y,A,D,F,C,z){o.call(this,B,E,y,A,D,F,C);this.ref_seq=(z?z.data:null)};u(t.prototype,o.prototype,{get_row_height:function(){var y,z=this.mode;if(z==="Dense"){y=c}else{if(z==="Squish"){y=k}else{y=w;if(this.prefs.show_insertions){y*=2}}}return y},draw_read:function(K,A,ag,V,L,aa,ad,C,B,M){K.textAlign="center";var J=this,R=[L,aa],Z=0,W=0,D=0,F=K.canvas.manager.char_width_px,y=(B==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var O=[];if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){D=Math.round(ag/2)}if(!C){C=[[0,M.length]]}for(var G=0,I=C.length;G<I;G++){var z=C[G],E="MIDNSHP=X"[z[0]],S=z[1];if(E==="H"||E==="S"){Z-=S}var U=ad+Z,Y=Math.floor(Math.max(0,(U-L)*ag)),ab=Math.floor(Math.max(0,(U+S-L)*ag));if(Y===ab){ab+=1}switch(E){case"H":break;case"S":case"M":case"=":if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(D>0){K.fillStyle=y;K.fillRect(Y-D,V+1,ab-Y,9);K.fillStyle=g;for(var af=0,H=N.length;af<H;af++){if(this.prefs.show_differences&&this.ref_seq){var P=this.ref_seq[U-L+af];if(!P||P.toLowerCase()===N[af].toLowerCase()){continue}}if(U+af>=L&&U+af<=aa){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X,V+9)}}}else{K.fillStyle=y;K.fillRect(Y,V+4,ab-Y,e)}}W+=S;Z+=S;break;case"N":K.fillStyle=g;K.fillRect(Y-D,V+5,ab-Y,1);Z+=S;break;case"D":K.fillStyle="red";K.fillRect(Y-D,V+4,ab-Y,3);Z+=S;break;case"P":break;case"I":var ah=Y-D;if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(this.prefs.show_insertions){var T=Y-(ab-Y)/2;if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){K.fillStyle="yellow";K.fillRect(T-D,V-9,ab-Y,9);O[O.length]={type:"triangle",data:[ah,V+4,5]};K.fillStyle=g;switch(compute_overlap([U,U+S],R)){case (OVERLAP_START):N=N.slice(L-U);break;case (OVERLAP_END):N=N.slice(0,U-aa);break;case (CONTAINED_BY):break;case (CONTAINS):N=N.slice(L-U,U-aa);break}for(var af=0,H=N.length;af<H;af++){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X-(ab-Y)/2,V)}}else{K.fillStyle="yellow";K.fillRect(T,V+(this.mode!=="Dense"?2:5),ab-Y,(A!=="Dense"?e:s))}}else{if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){O.push({type:"text",data:[N.length,ah,V+9]})}else{}}}W+=S;break;case"X":W+=S;break}}K.fillStyle="yellow";var Q,ai,ae;for(var ac=0;ac<O.length;ac++){Q=O[ac];ai=Q.type;ae=Q.data;if(ai==="text"){K.save();K.font="bold "+K.font;K.fillText(ae[0],ae[1],ae[2]);K.restore()}else{if(ai=="triangle"){q(K,ae[0],ae[1],ae[2])}}}},draw_element:function(R,M,E,B,U,z,I,S,P){var H=E[0],Q=E[1],A=E[2],J=E[3],D=Math.floor(Math.max(0,(Q-U)*I)),F=Math.ceil(Math.min(P,Math.max(0,(A-U)*I))),C=(M==="Dense"?0:(0+B))*S,G=this.prefs.label_color,O=0;if((M==="Pack"||this.mode==="Auto")&&I>R.canvas.manager.char_width_px){var O=Math.round(I/2)}if(E[5] instanceof Array){var N=Math.floor(Math.max(0,(E[4][0]-U)*I)),L=Math.ceil(Math.min(P,Math.max(0,(E[4][1]-U)*I))),K=Math.floor(Math.max(0,(E[5][0]-U)*I)),y=Math.ceil(Math.min(P,Math.max(0,(E[5][1]-U)*I)));if(E[4][1]>=U&&E[4][0]<=z&&E[4][2]){this.draw_read(R,M,I,C,U,z,E[4][0],E[4][2],E[4][3],E[4][4])}if(E[5][1]>=U&&E[5][0]<=z&&E[5][2]){this.draw_read(R,M,I,C,U,z,E[5][0],E[5][2],E[5][3],E[5][4])}if(K>L){R.fillStyle=g;p(R,L-O,C+5,K-O,C+5)}}else{this.draw_read(R,M,I,C,U,z,Q,E[4],E[5],E[6])}if(M==="Pack"&&Q>U&&J!=="."){R.fillStyle=this.prefs.label_color;var T=1;if(T===0&&D-R.measureText(J).width<0){R.textAlign="left";R.fillText(J,F+j-O,C+8)}else{R.textAlign="right";R.fillText(J,D-j-O,C+8)}}return[0,0]}});var n=function(A,D,y,z,C,E,B){r.call(this,A,D,y,z,C,E,B);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};u(n.prototype,o.prototype,r.prototype,{calculate_longest_feature_length:function(){var z=0;for(var C=0,y=this.data.length;C<y;C++){var B=this.data[C],A=B[1],D=B[2];z=Math.max(z,D-A)}return z},get_top_padding:function(z){var y=this.view_end-this.view_start,A=z/y;return Math.min(128,Math.ceil((this.longest_feature_length/2)*A))},draw_connector:function(G,B,F,H,E,D){var y=(F+H)/2,C=H-y;var A=Math.PI,z=0;if(C>0){G.beginPath();G.arc(y,D,H-y,Math.PI,0);G.stroke()}}});x.Scaler=d;x.SummaryTreePainter=v;x.LinePainter=b;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.ArcLinkedFeaturePainter=n};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window);
\ No newline at end of file

From df5d169ebdaf1e0ce987511924a5b568e669acdb Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Fri, 18 Nov 2011 10:10:18 -0500
Subject: [PATCH 216/362] Commit missing template for user impersonation
 (Thanks Dan).

---
 templates/admin/impersonate.mako | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)
 create mode 100644 templates/admin/impersonate.mako

diff --git a/templates/admin/impersonate.mako b/templates/admin/impersonate.mako
new file mode 100644
index 00000000000..a53e2034ab7
--- /dev/null
+++ b/templates/admin/impersonate.mako
@@ -0,0 +1,29 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+%if message:
+    ${render_msg( message, status )}
+%endif
+
+%if emails:
+    <div class="toolForm">
+        <div class="toolFormTitle">Impersonate another user</div>
+        <div class="toolFormBody">
+        <form name="impersonate" id="impersonate" action="${h.url_for( controller='admin', action='impersonate' )}" method="post" >
+            <div class="form-row">
+                <label>
+                    User to impersonate:
+                </label>
+                <select name="email" class='text-and-autocomplete-select'>
+                    %for email in emails:
+                        <option>${email}</option>
+                    %endfor
+                </select>
+            </div>
+            <div class="form-row">
+                <input type="submit" name="impersonate_button" value="Impersonate"/>
+            </div>
+        </form>
+        </div>
+    </div>
+%endif

From b7699f7cf01246a8acfb23759f4752cdd3ee100c Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Fri, 18 Nov 2011 11:52:24 -0500
Subject: [PATCH 217/362] Trackster performance improvements: (a) build tile
 messages only once during tile creation and (b) move tiles rather than
 show/hide tiles when scrolling.

---
 static/june_2007_style/blue/trackster.css |   2 +-
 static/june_2007_style/trackster.css.tmpl |   1 +
 static/scripts/packed/trackster.js        |   2 +-
 static/scripts/trackster.js               | 112 +++++++++++++---------
 4 files changed, 68 insertions(+), 49 deletions(-)

diff --git a/static/june_2007_style/blue/trackster.css b/static/june_2007_style/blue/trackster.css
index 9ac99cd5ea7..dab20f2faed 100644
--- a/static/june_2007_style/blue/trackster.css
+++ b/static/june_2007_style/blue/trackster.css
@@ -24,7 +24,7 @@
 .track{background:white;}
 .track-header{text-align:left;padding:4px 0px;color:#666;}
 .track-header .menubutton{margin-left:0px;}
-.track-content{text-align:center;border-top:1px solid #eee;border-bottom:2px solid #eee;background:#eee url('../images/tracks/diag_bg.gif');min-height:16px;}
+.track-content{text-align:center;border-top:1px solid #eee;border-bottom:2px solid #eee;background:#eee url('../images/tracks/diag_bg.gif');min-height:16px;position:relative;}
 .track-name{float:left;margin-top:2px;height:16px;}
 .label-track .track-content{background:white;}
 .track-tile{background:white;}
diff --git a/static/june_2007_style/trackster.css.tmpl b/static/june_2007_style/trackster.css.tmpl
index 98d68c0bf02..bccf5540313 100644
--- a/static/june_2007_style/trackster.css.tmpl
+++ b/static/june_2007_style/trackster.css.tmpl
@@ -161,6 +161,7 @@
     border-bottom: 2px solid #eee;
     background: #eee url('../images/tracks/diag_bg.gif');
     min-height: 16px;
+    position: relative;
 }
 
 .track-name {
diff --git a/static/scripts/packed/trackster.js b/static/scripts/packed/trackster.js
index c87a6529b4d..a314d9b6318 100644
--- a/static/scripts/packed/trackster.js
+++ b/static/scripts/packed/trackster.js
@@ -1 +1 @@
-var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var m=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(u,t,v,r,i,s){return(Math.max(u,r)-Math.min(u,r))+(Math.max(t,i)-Math.min(t,i))+(Math.max(v,s)-Math.min(v,s))};var g,n,f,k,p,h,q,c,d,b,o,l=false;do{g=Math.random()*16777215;n=g|16711680;f=g|65280;k=g|255;d=m(n,f,k);l=true;for(var j=0;j<a.length;j++){p=a[j];h=p|16711680;q=p|65280;c=p|255;b=m(h,q,c);o=e(n,f,k,h,q,c);if((Math.abs(d-b)<125)||(o<500)){l=false;break}}}while(!l);return"#"+(16777216+g).toString(16).substr(1,6)};var trackster_module=function(f,X){var p=f("class").extend,s=f("slotting"),M=f("painters");var ae=function(af,ag){this.document=af;this.default_font=ag!==undefined?ag:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};p(ae.prototype,{load_pattern:function(af,aj){var ag=this.patterns,ah=this.dummy_context,ai=new Image();ai.src=image_path+aj;ai.onload=function(){ag[af]=ah.createPattern(ai,"repeat")}},get_pattern:function(af){return this.patterns[af]},new_canvas:function(){var af=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(af)}af.manager=this;return af}});var n={};var l=function(af,ag){n[af.attr("id")]=ag};var m=function(af,ah,aj,ai){aj=".group";var ag={};n[af.attr("id")]=ai;af.bind("drag",{handle:"."+ah,relative:true},function(ar,at){var aq=$(this);var aw=$(this).parent(),an=aw.children(),ap=n[$(this).attr("id")],am,al,au,ak,ao;al=$(this).parents(aj);if(al.length!==0){au=al.position().top;ak=au+al.outerHeight();if(at.offsetY<au){$(this).insertBefore(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable_before(ap,av);return}else{if(at.offsetY>ak){$(this).insertAfter(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable(ap);return}}}al=null;for(ao=0;ao<an.length;ao++){am=$(an.get(ao));au=am.position().top;ak=au+am.outerHeight();if(am.is(aj)&&this!==am.get(0)&&at.offsetY>=au&&at.offsetY<=ak){if(at.offsetY-au<ak-at.offsetY){am.find(".content-div").prepend(this)}else{am.find(".content-div").append(this)}if(ap.container){ap.container.remove_drawable(ap)}n[am.attr("id")].add_drawable(ap);return}}for(ao=0;ao<an.length;ao++){if(at.offsetY<$(an.get(ao)).position().top){break}}if(ao===an.length){if(this!==an.get(ao-1)){aw.append(this);n[aw.attr("id")].move_drawable(ap,ao)}}else{if(this!==an.get(ao)){$(this).insertBefore(an.get(ao));n[aw.attr("id")].move_drawable(ap,(at.deltaY>0?ao-1:ao))}}}).bind("dragstart",function(){ag["border-top"]=af.css("border-top");ag["border-bottom"]=af.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ag)})};X.moveable=m;var ad=16,H=9,E=20,T=H+2,z=100,J=12000,R=200,C=5,v=10,L=5000,w=100,o="There was an error in indexing this dataset. ",K="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",F="No data for this chrom/contig.",t="Currently indexing... please wait",x="Tool cannot be rerun: ",a="Loading data...",Y="Ready for display",d=10,u=5,B=5;function Z(ag,af){if(!af){af=0}var ah=Math.pow(10,af);return Math.round(ag*ah)/ah}var c=function(af){this.num_elements=af;this.clear()};p(c.prototype,{get:function(ag){var af=this.key_ary.indexOf(ag);if(af!==-1){if(this.obj_cache[ag].stale){this.key_ary.splice(af,1);delete this.obj_cache[ag]}else{this.move_key_to_end(ag,af)}}return this.obj_cache[ag]},set:function(ag,ah){if(!this.obj_cache[ag]){if(this.key_ary.length>=this.num_elements){var af=this.key_ary.shift();delete this.obj_cache[af]}this.key_ary.push(ag)}this.obj_cache[ag]=ah;return ah},move_key_to_end:function(ag,af){this.key_ary.splice(af,1);this.key_ary.push(ag)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var S=function(ag,af,ah){c.call(this,ag);this.track=af;this.subset=(ah!==undefined?ah:true)};p(S.prototype,c.prototype,{load_data:function(ao,aj,am,ag,al){var an=this.track.view.chrom,ai={chrom:an,low:ao,high:aj,mode:am,resolution:ag,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ai,al);if(this.track.filters_manager){var ap=[];var af=this.track.filters_manager.filters;for(var ak=0;ak<af.length;ak++){ap[ap.length]=af[ak].name}ai.filter_cols=JSON.stringify(ap)}var ah=this;return $.getJSON(this.track.data_url,ai,function(aq){ah.set_data(ao,aj,am,aq)})},get_data:function(af,aj,ak,ag,ai){var ah=this.get_data_from_cache(af,aj,ak);if(ah){return ah}ah=this.load_data(af,aj,ak,ag,ai);this.set_data(af,aj,ak,ah);return ah},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(an,ai,am,ah,al,aj){var ao=this.get_data_from_cache(an,ai,am);if(!ao){console.log("ERROR: no current data for: ",this.track,an,ai,am,ah,al);return}ao.stale=true;var ag=an;if(aj===this.DEEP_DATA_REQ){$.extend(al,{start_val:ao.data.length+1})}else{if(aj===this.BROAD_DATA_REQ){ag=(ao.max_high?ao.max_high:ao.data[ao.data.length-1][2])+1}}var af=this,ak=this.load_data(ag,ai,am,ah,al);new_data_available=$.Deferred();this.set_data(an,ai,am,new_data_available);$.when(ak).then(function(ap){if(ap.data){ap.data=ao.data.concat(ap.data);if(ap.max_low){ap.max_low=ao.max_low}if(ap.message){ap.message=ap.message.replace(/[0-9]+/,ap.data.length)}}af.set_data(an,ai,am,ap);new_data_available.resolve(ap)});return new_data_available},get_data_from_cache:function(af,ag,ah){return this.get(this.gen_key(af,ag,ah))},set_data:function(ag,ah,ai,af){return this.set(this.gen_key(ag,ah,ai),af)},gen_key:function(af,ah,ai){var ag=af+"_"+ah+"_"+ai;return ag},split_key:function(af){return af.split("_")}});var I=function(ag,af,ah){S.call(this,ag,af,ah)};p(I.prototype,S.prototype,c.prototype,{load_data:function(af,ai,aj,ag,ah){if(ag>1){return{data:null}}return S.prototype.load_data.call(this,af,ai,aj,ag,ah)}});var q=function(ai,ag,af,ah,ak){if(!q.id_counter){q.id_counter=0}this.id=q.id_counter++;this.name=ai;this.view=ag;this.container=af;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ai}],saved_values:ah,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ak;this.is_overview=false;this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=this.build_icons_div().hide();this.header_div.append(this.icons_div);this.header_div.dblclick(function(al){al.stopPropagation()});var aj=this;this.container_div.hover(function(){aj.icons_div.show()},function(){aj.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p(q.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},update_icons:function(){},set_name:function(af){this.old_name=this.name;this.name=af;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.hide(0,function(){$(this).remove();view.update_intro_div();view.has_changes=true})},build_container_div:function(){},build_header_div:function(){},build_icons_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){}});var y=function(aj,ai,ag,af,ah,ak){q.call(this,ai,ag,af,ah,ak);this.obj_type=aj;this.drawables=[]};p(y.prototype,q.prototype,{init:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af].init()}},_draw:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af]._draw()}},to_json:function(){var ag=[];for(var af=0;af<this.drawables.length;af++){ag.push(this.drawables[af].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ag}},add_drawable:function(af){this.drawables.push(af);af.container=this},add_drawable_before:function(ah,af){var ag=this.drawables.indexOf(af);if(ag!=-1){this.drawables.splice(ag,0,ah);return true}return false},remove_drawable:function(ag){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);ag.container=null;return true}return false},move_drawable:function(ag,ah){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);this.drawables.splice(ah,0,ag);return true}return false}});var Q=function(ai,ag,af,ah){y.call(this,"DrawableGroup",ai,ag,af,ah,"group-handle");this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this)};p(Q.prototype,q.prototype,y.prototype,{build_container_div:function(){return $("<div/>").addClass("group").attr("id","group_"+this.id).appendTo(this.container.content_div)},build_header_div:function(){var af=$("<div/>").addClass("track-header");af.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(af);return af},build_icons_div:function(){var af=$("<div/>").css("float","left");this.toggle_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Hide/show group content").addClass("icon-button toggle").tipsy({gravity:"s"}).appendTo(af);this.settings_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Edit settings").addClass("icon-button settings-icon").tipsy({gravity:"s"}).appendTo(af);this.remove_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Remove").addClass("icon-button remove-icon").tipsy({gravity:"s"}).appendTo(af);var ag=this;this.toggle_icon.click(function(){if(ag.content_visible){ag.toggle_icon.addClass("toggle-expand").removeClass("toggle");ag.hide_contents();ag.content_visible=false}else{ag.toggle_icon.addClass("toggle").removeClass("toggle-expand");ag.content_visible=true;ag.show_contents()}});this.settings_icon.click(function(){var aj=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ah=function(){ag.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ai=function(ak){if((ak.keyCode||ak.which)===27){aj()}else{if((ak.keyCode||ak.which)===13){ah()}}};$(window).bind("keypress.check_enter_esc",ai);show_modal("Configure Group",ag.config.build_form(),{Cancel:aj,OK:ah})});this.remove_icon.click(function(){$(".tipsy").remove();ag.remove()});return af},hide_contents:function(){this.content_div.hide()},show_contents:function(){this.content_div.show();this.request_draw()}});var ac=function(af,ai,ah,ag){y.call(this,"View");this.container=af;this.chrom=null;this.vis_id=ah;this.dbkey=ag;this.title=ai;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ae(af.get(0).ownerDocument);this.reset()};p(ac.prototype,y.prototype,{init:function(){var ah=this.container,af=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ah);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ah);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ah);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,af);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ai=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ag=function(aj){if(aj.type==="focusout"||(aj.keyCode||aj.which)===13||(aj.keyCode||aj.which)===27){if((aj.keyCode||aj.which)!==27){af.go_to($(this).val())}$(this).hide();$(this).val("");af.location_span.show();af.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ag).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tipsy({gravity:"n"}).appendTo(this.nav_controls);this.location_span.click(function(){af.location_span.hide();af.chrom_select.hide();af.nav_input.val(af.chrom+":"+af.low+"-"+af.high);af.nav_input.css("display","inline-block");af.nav_input.select();af.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tipsy({gravity:"n"}).click(function(){af.zoom_out();af.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tipsy({gravity:"n"}).click(function(){af.zoom_in();af.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){af.change_chrom(af.chrom_select.val())});this.browser_content_div.click(function(aj){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(aj){af.zoom_in(aj.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(aj,ak){this.current_x=ak.offsetX}).bind("drag",function(aj,al){var am=al.offsetX-this.current_x;this.current_x=al.offsetX;var ak=Math.round(am/af.viewport_container.width()*(af.max_high-af.max_low));af.move_delta(-ak)});this.overview_close.click(function(){af.reset_overview()});this.viewport_container.bind("draginit",function(aj,ak){if(aj.clientX>af.viewport_container.width()-16){return false}}).bind("dragstart",function(aj,ak){ak.original_low=af.low;ak.current_height=aj.clientY;ak.current_x=ak.offsetX}).bind("drag",function(al,an){var aj=$(this);var ao=an.offsetX-an.current_x;var ak=aj.scrollTop()-(al.clientY-an.current_height);aj.scrollTop(ak);an.current_height=al.clientY;an.current_x=an.offsetX;var am=Math.round(ao/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}).bind("mousewheel",function(al,an,ak,aj){if(ak){ak*=50;var am=Math.round(-ak/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}});this.top_labeltrack.bind("dragstart",function(aj,ak){return $("<div />").css({height:af.browser_content_div.height()+af.top_labeltrack.height()+af.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(an,ao){$(ao.proxy).css({left:Math.min(an.pageX,ao.startX),width:Math.abs(an.pageX-ao.startX)});var ak=Math.min(an.pageX,ao.startX)-af.container.offset().left,aj=Math.max(an.pageX,ao.startX)-af.container.offset().left,am=(af.high-af.low),al=af.viewport_container.width();af.update_location(Math.round(ak/al*am)+af.low,Math.round(aj/al*am)+af.low)}).bind("dragend",function(ao,ap){var ak=Math.min(ao.pageX,ap.startX),aj=Math.max(ao.pageX,ap.startX),am=(af.high-af.low),al=af.viewport_container.width(),an=af.low;af.low=Math.round(ak/al*am)+an;af.high=Math.round(aj/al*am)+an;$(ap.proxy).remove();af.request_redraw()});this.add_label_track(new ab(this,{content_div:this.top_labeltrack}));this.add_label_track(new ab(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){af.resize_window()});$(document).bind("redraw",function(){af.redraw()});this.reset();$(window).trigger("resize")},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},update_location:function(af,ag){this.location_span.text(commatize(af)+" - "+commatize(ag));this.nav_input.val(this.chrom+":"+commatize(af)+"-"+commatize(ag))},load_chroms:function(ah){ah.num=w;$.extend(ah,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var af=this,ag=$.Deferred();$.ajax({url:chrom_url,data:ah,dataType:"json",success:function(aj){if(aj.chrom_info.length===0){alert("Invalid chromosome: "+ah.chrom);return}if(aj.reference){af.add_label_track(new A(af))}af.chrom_data=aj.chrom_info;var am='<option value="">Select Chrom/Contig</option>';for(var al=0,ai=af.chrom_data.length;al<ai;al++){var ak=af.chrom_data[al].chrom;am+='<option value="'+ak+'">'+ak+"</option>"}if(aj.prev_chroms){am+='<option value="previous">Previous '+w+"</option>"}if(aj.next_chroms){am+='<option value="next">Next '+w+"</option>"}af.chrom_select.html(am);af.chrom_start_index=aj.start_index;ag.resolve(aj)},error:function(){alert("Could not load chroms for this dbkey:",af.dbkey)}});return ag},change_chrom:function(ak,ag,am){if(!ak||ak==="None"){return}var ah=this;if(ak==="previous"){ah.load_chroms({low:this.chrom_start_index-w});return}if(ak==="next"){ah.load_chroms({low:this.chrom_start_index+w});return}var al=$.grep(ah.chrom_data,function(an,ao){return an.chrom===ak})[0];if(al===undefined){ah.load_chroms({chrom:ak},function(){ah.change_chrom(ak,ag,am)});return}else{if(ak!==ah.chrom){ah.chrom=ak;ah.chrom_select.val(ah.chrom);ah.max_high=al.len-1;ah.reset();ah.request_redraw(true);for(var aj=0,af=ah.drawables.length;aj<af;aj++){var ai=ah.drawables[aj];if(ai.init){ai.init()}}}if(ag!==undefined&&am!==undefined){ah.low=Math.max(ag,0);ah.high=Math.min(am,ah.max_high)}ah.reset_overview();ah.request_redraw()}},go_to:function(aj){aj=aj.replace(/ |,/g,"");var an=this,af,ai,ag=aj.split(":"),al=ag[0],am=ag[1];if(am!==undefined){try{var ak=am.split("-");af=parseInt(ak[0],10);ai=parseInt(ak[1],10)}catch(ah){return false}}an.change_chrom(al,af,ai)},move_fraction:function(ah){var af=this;var ag=af.high-af.low;this.move_delta(ah*ag)},move_delta:function(ah){var af=this;var ag=af.high-af.low;if(af.low-ah<af.max_low){af.low=af.max_low;af.high=af.max_low+ag}else{if(af.high-ah>af.max_high){af.high=af.max_high;af.low=af.max_high-ag}else{af.high-=ah;af.low-=ah}}af.request_redraw()},add_drawable:function(af){y.prototype.add_drawable.call(this,af);af.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(af){af.view=this;af.init();this.label_tracks.push(af)},remove_drawable:function(ah,ag){y.prototype.remove_drawable.call(this,ah);if(ag){var af=this;ah.container_div.hide(0,function(){$(this).remove();af.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(an,af,am,ag){var al=this,aj=(ag?[ag]:al.drawables),ah;var ag;for(var ak=0;ak<aj.length;ak++){ag=aj[ak];ah=-1;for(var ai=0;ai<al.tracks_to_be_redrawn.length;ai++){if(al.tracks_to_be_redrawn[ai][0]===ag){ah=ai;break}}if(ah<0){al.tracks_to_be_redrawn.push([ag,af,am])}else{al.tracks_to_be_redrawn[ak][1]=af;al.tracks_to_be_redrawn[ak][2]=am}}requestAnimationFrame(function(){al._redraw(an)})},_redraw:function(ap){var am=this.low,ai=this.high;if(am<this.max_low){am=this.max_low}if(ai>this.max_high){ai=this.max_high}var ao=this.high-this.low;if(this.high!==0&&ao<this.min_separation){ai=am+this.min_separation}this.low=Math.floor(am);this.high=Math.ceil(ai);this.resolution=Math.pow(C,Math.ceil(Math.log((this.high-this.low)/R)/Math.log(C)));this.zoom_res=Math.pow(v,Math.max(0,Math.ceil(Math.log(this.resolution,v)/Math.log(v))));var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var al=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var aq=13;this.overview_box.css({left:af,width:Math.max(aq,al)}).show();if(al<aq){this.overview_box.css("left",af-(aq-al)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:al})}this.update_location(this.low,this.high);if(!ap){var ah,ag,an;for(var aj=0,ak=this.tracks_to_be_redrawn.length;aj<ak;aj++){ah=this.tracks_to_be_redrawn[aj][0];ag=this.tracks_to_be_redrawn[aj][1];an=this.tracks_to_be_redrawn[aj][2];if(ah){ah._draw(ag,an)}}this.tracks_to_be_redrawn=[];for(aj=0,ak=this.label_tracks.length;aj<ak;aj++){this.label_tracks[aj]._draw()}}},zoom_in:function(ag,ah){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ai=this.high-this.low,aj=ai/2+this.low,af=(ai/this.zoom_factor)/2;if(ag){aj=ag/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(aj-af);this.high=Math.round(aj+af);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ag=this.high-this.low,ah=ag/2+this.low,af=(ag*this.zoom_factor)/2;this.low=Math.round(ah-af);this.high=Math.round(ah+af);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ah.dataset_id){return}this.overview_viewport.find(".track").remove()}var ag=ah.copy({content_div:this.overview_viewport}),af=this;ag.header_div.hide();ag.is_overview=true;af.overview_drawable=ag;this.overview_drawable.postdraw_actions=function(){af.overview_highlight.show().height(af.overview_drawable.content_div.height());af.overview_viewport.height(af.overview_drawable.content_div.height()+af.overview_box.outerHeight());af.overview_close.show();af.resize_window()};this.overview_drawable.init();af.has_changes=true},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var r=function(ah,al){this.track=ah;this.name=al.name;this.params=[];var at=al.params;for(var ai=0;ai<at.length;ai++){var an=at[ai],ag=an.name,ar=an.label,aj=unescape(an.html),au=an.value,ap=an.type;if(ap==="number"){this.params[this.params.length]=new g(ag,ar,aj,au,an.min,an.max)}else{if(ap=="select"){this.params[this.params.length]=new O(ag,ar,aj,au)}else{console.log("WARNING: unrecognized tool parameter type:",ag,ap)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aw){aw.stopPropagation()}).click(function(aw){aw.stopPropagation()}).bind("dblclick",function(aw){aw.stopPropagation()});var aq=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ao=this.params;var am=this;$.each(this.params,function(ax,aA){var az=$("<div>").addClass("param-row").appendTo(am.parent_div);var aw=$("<div>").addClass("param-label").text(aA.label).appendTo(az);var ay=$("<div/>").addClass("slider").html(aA.html).appendTo(az);ay.find(":input").val(aA.value);$("<div style='clear: both;'/>").appendTo(az)});this.parent_div.find("input").click(function(){$(this).select()});var av=$("<div>").addClass("param-row").appendTo(this.parent_div);var ak=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(av);var af=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(av);var am=this;af.click(function(){am.run_on_region()});ak.click(function(){am.run_on_dataset()})};p(r.prototype,{get_param_values_dict:function(){var af={};this.parent_div.find(":input").each(function(){var ag=$(this).attr("name"),ah=$(this).val();af[ag]=JSON.stringify(ah)});return af},get_param_values:function(){var ag=[];var af={};this.parent_div.find(":input").each(function(){var ah=$(this).attr("name"),ai=$(this).val();if(ah){ag[ag.length]=ai}});return ag},run_on_dataset:function(){var af=this;af.run({dataset_id:this.track.original_dataset_id,tool_id:af.name},null,function(ag){show_modal(af.name+" is Running",af.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ag={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},aj=this.track,ah=ag.tool_id+aj.tool_region_and_parameters_str(ag.chrom,ag.low,ag.high),af;if(aj.container===view){var ai=new Q(this.name,this.track.view,this.track.container);aj.container.add_drawable(ai);aj.container.remove_drawable(aj);ai.add_drawable(aj);aj.container_div.appendTo(ai.content_div);af=ai}else{af=aj.container}var ak=new aj.constructor(ah,view,af,"hda");ak.init_for_tool_data();ak.change_mode(aj.mode);af.add_drawable(ak);ak.content_div.text("Starting job.");this.run(ag,ak,function(al){ak.dataset_id=al.dataset_id;ak.content_div.text("Running job.");ak.init()})},run:function(ag,ah,ai){$.extend(ag,this.get_param_values_dict());var af=function(){$.getJSON(rerun_tool_url,ag,function(aj){if(aj==="no converter"){ah.container_div.addClass("error");ah.content_div.text(K)}else{if(aj.error){ah.container_div.addClass("error");ah.content_div.text(x+aj.message)}else{if(aj==="pending"){ah.container_div.addClass("pending");ah.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(af,2000)}else{ai(aj)}}}})};af()}});var O=function(ag,af,ah,ai){this.name=ag;this.label=af;this.html=ah;this.value=ai};var g=function(ah,ag,aj,ak,ai,af){O.call(this,ah,ag,aj,ak);this.min=ai;this.max=af};var h=function(ag,af,ah,ai){this.name=ag;this.index=af;this.tool_id=ah;this.tool_exp_name=ai};var V=function(ag,af,ah,ai){h.call(this,ag,af,ah,ai);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};p(V.prototype,{applies_to:function(af){if(af.length>this.index){return true}return false},keep:function(af){if(!this.applies_to(af)){return true}var ag=af[this.index];return(isNaN(ag)||(ag>=this.low&&ag<=this.high))},update_attrs:function(ag){var af=false;if(!this.applies_to(ag)){return af}if(ag[this.index]<this.min){this.min=Math.floor(ag[this.index]);af=true}if(ag[this.index]>this.max){this.max=Math.ceil(ag[this.index]);af=true}return af},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var ah=function(ak,ai){var aj=ai-ak;return(aj<=2?0.01:1)};var ag=this.slider.slider("option","min"),af=this.slider.slider("option","max");if(this.min<ag||this.max>af){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ah(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var aa=function(aq,ay){this.track=aq;this.filters=[];for(var at=0;at<ay.length;at++){var au=ay[at],az=au.name,af=au.type,ah=au.index,ax=au.tool_id,aw=au.tool_exp_name;if(af==="int"||af==="float"){this.filters[at]=new V(az,ah,ax,aw)}else{console.log("ERROR: unsupported filter: ",az,af)}}var ai=function(aA,aB,aC){aA.click(function(){var aD=aB.text();max=parseFloat(aC.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aC.slider("option","values")){input_size=2*input_size+1;multi_value=true}aB.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aD).appendTo(aB).focus().select().click(function(aE){aE.stopPropagation()}).blur(function(){$(this).remove();aB.text(aD)}).keyup(function(aI){if(aI.keyCode===27){$(this).trigger("blur")}else{if(aI.keyCode===13){var aG=aC.slider("option","min"),aE=aC.slider("option","max"),aH=function(aJ){return(isNaN(aJ)||aJ>aE||aJ<aG)},aF=$(this).val();if(!multi_value){aF=parseFloat(aF);if(aH(aF)){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}else{aF=aF.split("-");aF=[parseFloat(aF[0]),parseFloat(aF[1])];if(aH(aF[0])||aH(aF[1])){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}aC.slider((multi_value?"values":"value"),aF)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aA){aA.stopPropagation()}).click(function(aA){aA.stopPropagation()}).bind("dblclick",function(aA){aA.stopPropagation()}).bind("keydown",function(aA){aA.stopPropagation()});var av=$("<div/>").addClass("sliders").appendTo(this.parent_div);var an=this;$.each(this.filters,function(aD,aF){aF.container=$("<div/>").addClass("filter-row slider-row").appendTo(av);var aE=$("<div/>").addClass("elt-label").appendTo(aF.container);var aC=$("<span/>").addClass("slider-name").text(aF.name+"  ").appendTo(aE);var aB=$("<span/>");var aH=$("<span/>").addClass("slider-value").appendTo(aE).append("[").append(aB).append("]");var aA=$("<div/>").addClass("slider").appendTo(aF.container);aF.control_element=$("<div/>").attr("id",aF.name+"-filter-control").appendTo(aA);var aG=[0,0];aF.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aJ,aK){var aI=aK.values;aB.text(aI[0]+"-"+aI[1]);aF.low=aI[0];aF.high=aI[1];an.track.request_draw(true,true)},change:function(aI,aJ){aF.control_element.slider("option","slide").call(aF.control_element,aI,aJ)}});aF.slider=aF.control_element;aF.slider_label=aB;ai(aH,aB,aF.control_element);$("<div style='clear: both;'/>").appendTo(aF.container)});if(this.filters.length!==0){var ak=$("<div/>").addClass("param-row").appendTo(av);var am=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ak);var ag=this;am.click(function(){ag.run_on_dataset()})}var ap=$("<div/>").addClass("display-controls").appendTo(this.parent_div),ar,al,ao,aj={Transparency:function(aA){an.alpha_filter=aA},Height:function(aA){an.height_filter=aA}};$.each(aj,function(aC,aB){ar=$("<div/>").addClass("filter-row").appendTo(ap),al=$("<span/>").addClass("elt-label").text(aC+":").appendTo(ar),ao=$("<select/>").attr("name",aC+"_dropdown").css("float","right").appendTo(ar);$("<option/>").attr("value",-1).text("== None ==").appendTo(ao);for(var aA=0;aA<an.filters.length;aA++){$("<option/>").attr("value",aA).text(an.filters[aA].name).appendTo(ao)}ao.change(function(){$(this).children("option:selected").each(function(){var aD=parseInt($(this).val());aj[aC]((aD>=0?an.filters[aD]:null));an.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(ar)});$("<div style='clear: both;'/>").appendTo(this.parent_div)};p(aa.prototype,{reset_filters:function(){for(var af=0;af<this.filters.length;af++){filter=this.filters[af];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var an=function(ar,ap,aq){if(!(ap in ar)){ar[ap]=aq}return ar[ap]};var ah={},af,ag,ai;for(var aj=0;aj<this.filters.length;aj++){af=this.filters[aj];if(af.tool_id){if(af.min!=af.low){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" >= "+af.low}if(af.max!=af.high){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" <= "+af.high}}}var al=[];for(var ao in ah){al[al.length]=[ao,ah[ao]]}var am=al.length;(function ak(aw,at){var aq=at[0],ar=aq[0],av=aq[1],au="("+av.join(") and (")+")",ap={cond:au,input:aw,target_dataset_id:aw,tool_id:ar},at=at.slice(1);$.getJSON(run_tool_url,ap,function(ax){if(ax.error){show_modal("Filter Dataset","Error running tool "+ar,{Close:hide_modal})}else{if(at.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ak(ax.dataset_id,at)}}})})(this.track.dataset_id,al)}});var D=function(af,ag){M.Scaler.call(this,ag);this.filter=af};D.prototype.gen_val=function(af){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(af[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var G=function(af){this.track=af.track;this.params=af.params;this.values={};this.restore_values((af.saved_values?af.saved_values:{}));this.onchange=af.onchange};p(G.prototype,{restore_values:function(af){var ag=this;$.each(this.params,function(ah,ai){if(af[ai.key]!==undefined){ag.values[ai.key]=af[ai.key]}else{ag.values[ai.key]=ai.default_value}})},build_form:function(){var ai=this;var af=$("<div />");var ah;function ag(am,aj){for(var ao=0;ao<am.length;ao++){ah=am[ao];if(ah.hidden){continue}var ak="param_"+ao;var at=ai.values[ah.key];var av=$("<div class='form-row' />").appendTo(aj);av.append($("<label />").attr("for",ak).text(ah.label+":"));if(ah.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ak).attr("name",ak).attr("checked",at))}else{if(ah.type==="text"){av.append($('<input type="text"/>').attr("id",ak).val(at).click(function(){$(this).select()}))}else{if(ah.type=="select"){var aq=$("<select />").attr("id",ak);for(var an=0;an<ah.options.length;an++){$("<option/>").text(ah.options[an].label).attr("value",ah.options[an].value).appendTo(aq)}aq.val(at);av.append(aq)}else{if(ah.type==="color"){var ap=$("<input />").attr("id",ak).attr("name",ak).val(at);var ar=$("<div class='tipsy tipsy-west' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ar);var au=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:ap,color:at});$("<div />").append(ap).append(ar).appendTo(av).bind("click",function(aw){ar.css({left:$(this).position().left+$(ap).width()+5,top:$(this).position().top-($(ar).height()/2)+($(ap).height()/2)}).show();$(document).bind("click.color-picker",function(){ar.hide();$(document).unbind("click.color-picker")});aw.stopPropagation()})}else{av.append($("<input />").attr("id",ak).attr("name",ak).val(at))}}}}if(ah.help){av.append($("<div class='help'/>").text(ah.help))}}}ag(this.params,af);return af},update_from_form:function(af){var ah=this;var ag=false;$.each(this.params,function(ai,ak){if(!ak.hidden){var al="param_"+ai;var aj=af.find("#"+al).val();if(ak.type==="float"){aj=parseFloat(aj)}else{if(ak.type==="int"){aj=parseInt(aj)}else{if(ak.type==="bool"){aj=af.find("#"+al).is(":checked")}}}if(aj!==ah.values[ak.key]){ah.values[ak.key]=aj;ag=true}}});if(ag){this.onchange()}}});var b=function(af,ai,ah,ag,aj){this.track=af;this.index=ai;this.low=ai*R*ah;this.high=(ai+1)*R*ah;this.resolution=ah;this.canvas=$("<div class='track-tile'/>").append(ag);this.data=aj;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(af,ai,ah,ag,aj,ak){b.call(this,af,ai,ah,ag,aj);this.max_val=ak};p(k.prototype,b.prototype);var P=function(af,aj,ai,ah,al,am,ak,ag){b.call(this,af,aj,ai,ah,al);this.mode=am;this.message=ak;this.feature_mapper=ag};p(P.prototype,b.prototype);P.prototype.predisplay_actions=function(){var ag=this,af={};if(ag.mode!=="Pack"){return}$(this.canvas).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).siblings(".feature-popup").remove()}).mousemove(function(ar){if(!this.hovered){return}var am=$(this).offset(),aq=ar.pageX-am.left,ap=ar.pageY-am.top,aw=ag.feature_mapper.get_feature_data(aq,ap),an=(aw?aw[0]:null);$(this).siblings(".feature-popup").each(function(){if(!an||$(this).attr("id")!==an.toString()){$(this).remove()}});if(aw){var ai=af[an];if(!ai){var an=aw[0],at={name:aw[3],start:aw[1],end:aw[2],strand:aw[4]},al=ag.track.filters_manager.filters,ak;for(var ao=0;ao<al.length;ao++){ak=al[ao];at[ak.name]=aw[ak.index]}var ai=$("<div/>").attr("id",an).addClass("feature-popup"),ax=$("<table/>"),av,au,ay;for(av in at){au=at[av];ay=$("<tr/>").appendTo(ax);$("<th/>").appendTo(ay).text(av);$("<td/>").attr("align","left").appendTo(ay).text(typeof(au)=="number"?Z(au,2):au)}ai.append($("<div class='feature-popup-inner'>").append(ax));af[an]=ai}ai.appendTo($(ag.canvas).parent());var aj=aq+parseInt(ag.canvas.css("left"))-ai.width()/2,ah=ap+parseInt(ag.canvas.css("top"))+7;ai.css("left",aj+"px").css("top",ah+"px")}else{if(!ar.isPropagationStopped()){ar.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ar)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var i=function(ai,ag,af,ah,aj,ak){q.call(this,ai,ag,af,{},"draghandle");this.data_url=(aj?aj:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ak?ak:L);this.dataset_check_url=converted_datasets_state_url;if(!i.id_counter){i.id_counter=0}this.id=i.id_counter++;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};p(i.prototype,q.prototype,{build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var af=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(af)}this.name_div=$("<div/>").addClass("track-name").appendTo(af).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return af},build_icons_div:function(){var aj=$("<div/>").css("float","left");this.mode_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Set display mode").addClass("icon-button chevron-expand").tipsy({gravity:"s"}).appendTo(aj);this.toggle_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Hide/show track content").addClass("icon-button toggle").tipsy({gravity:"s"}).appendTo(aj);this.settings_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Edit settings").addClass("icon-button settings-icon").tipsy({gravity:"s"}).appendTo(aj);this.overview_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Set as overview").addClass("icon-button overview-icon").tipsy({gravity:"s"}).appendTo(aj);this.filters_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Filters").addClass("icon-button filters-icon").tipsy({gravity:"s"}).appendTo(aj).hide();this.tools_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Tools").addClass("icon-button tools-icon").tipsy({gravity:"s"}).appendTo(aj).hide();this.remove_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Remove").addClass("icon-button remove-icon").tipsy({gravity:"s"}).appendTo(aj);var ag=this;if(ag.display_modes!==undefined){var al=(ag.config&&ag.config.values.mode?ag.config.values.mode:ag.display_modes[0]);ag.mode=al;this.mode_icon.attr("title","Set display mode (now: "+ag.mode+")");var ai={};for(var ah=0,af=ag.display_modes.length;ah<af;ah++){var ak=ag.display_modes[ah];ai[ak]=function(am){return function(){ag.change_mode(am);ag.icons_div.show();ag.container_div.mouseleave(function(){ag.icons_div.hide()})}}(ak)}make_popupmenu(this.mode_icon,ai)}this.toggle_icon.click(function(){if(ag.content_visible){ag.toggle_icon.addClass("toggle-expand").removeClass("toggle");ag.hide_contents();ag.content_visible=false}else{ag.toggle_icon.addClass("toggle").removeClass("toggle-expand");ag.content_visible=true;ag.show_contents()}});this.settings_icon.click(function(){var ao=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},am=function(){ag.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},an=function(ap){if((ap.keyCode||ap.which)===27){ao()}else{if((ap.keyCode||ap.which)===13){am()}}};$(window).bind("keypress.check_enter_esc",an);show_modal("Configure Track",ag.config.build_form(),{Cancel:ao,OK:am})});this.overview_icon.click(function(){ag.view.set_overview(ag)});this.filters_icon.click(function(){ag.filters_div.toggle();ag.filters_manager.reset_filters()});this.tools_icon.click(function(){ag.dynamic_tool_div.toggle();if(ag.dynamic_tool_div.is(":visible")){ag.set_name(ag.name+ag.tool_region_and_parameters_str())}else{ag.revert_name()}$(".tipsy").remove()});this.remove_icon.click(function(){$(".tipsy").remove();ag.remove()});return aj},hide_contents:function(){this.content_div.children().remove();this.content_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.content_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof ab){return"LabelTrack"}else{if(this instanceof A){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof W){return"ReadTrack"}else{if(this instanceof U){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}return""},init:function(){var af=this;af.enabled=false;af.tile_cache.clear();af.data_manager.clear();af.initial_canvas=undefined;af.content_div.css("height","auto");af.container_div.removeClass("nodata error pending");if(!af.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:af.hda_ldda,dataset_id:af.dataset_id,chrom:af.view.chrom},function(ag){if(!ag||ag==="error"||ag.kind==="error"){af.container_div.addClass("error");af.content_div.text(o);if(ag.message){var ah=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})});af.content_div.append(ah)}}else{if(ag==="no converter"){af.container_div.addClass("error");af.content_div.text(K)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){af.container_div.addClass("nodata");af.content_div.text(F)}else{if(ag==="pending"){af.container_div.addClass("pending");af.content_div.text(t);setTimeout(function(){af.init()},af.data_query_wait)}else{if(ag.status==="data"){if(ag.valid_chroms){af.valid_chroms=ag.valid_chroms;af.update_icons()}af.content_div.text(Y);if(af.view.chrom){af.content_div.text("");af.content_div.css("height",af.height_px+"px");af.enabled=true;$.when(af.predraw_init()).done(function(){af.container_div.removeClass("nodata error pending");af.request_draw()})}}}}}}});this.update_icons()},predraw_init:function(){}});var N=function(aj,ah,ag,ai,al,ak){i.call(this,aj,ah,ag,ai);var af=this,ah=af.view;m(af.container_div,af.drag_handle_class,".group",af);this.filters_manager=new aa(this,(al!==undefined?al:{}));this.filters_available=false;this.filters_visible=false;this.tool=(ak!==undefined&&obj_length(ak)>0?new r(this,ak):undefined);if(this.header_div){if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}};p(N.prototype,q.prototype,i.prototype,{copy:function(af){return new this.constructor(this.name,this.view,af,this.hda_ldda,this.dataset_id,this.prefs,this.filters,this.tool)},to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ag){var af=this;af.mode=ag;af.config.values.mode=ag;af.tile_cache.clear();af.request_draw();this.mode_icon.attr("title","Set display mode (now: "+af.mode+")");return af},update_icons:function(){var af=this;if(af.filters_available>0){af.filters_icon.show()}else{af.filters_icon.hide()}if(af.tool){af.tools_icon.show()}else{af.tools_icon.hide()}},_gen_tile_cache_key:function(ag,ah,af){return ag+"_"+ah+"_"+af},request_draw:function(ag,af){this.view.request_redraw(false,ag,af,this)},_draw:function(ah,ap){if(!this.enabled){return}if(!this.content_visible){return}if(!(this instanceof A)&&(!this.dataset_id)){return}var ao=this.view.low,al=this.view.high,am=al-ao,ai=this.view.container.width(),at=ai/am,ak=this.view.resolution,ar=$("<div style='position: relative;'></div>");if(this.is_overview){ao=this.view.max_low;al=this.view.max_high;ak=Math.pow(C,Math.ceil(Math.log((view.max_high-view.max_low)/R)/Math.log(C)));at=ai/(view.max_high-view.max_low)}if(!ap){this.content_div.children().remove()}this.content_div.append(ar);this.max_height=0;var ag=Math.floor(ao/ak/R);var an=true;var aq=[];var af=0;while((ag*R*ak)<al){tile=this.draw_helper(ah,ai,ag,ak,ar,at);if(tile){aq.push(tile)}else{an=false}ag+=1;af++}var aj=this;if(an){aj.postdraw_actions(aq,ai,at,ap)}},postdraw_actions:function(aj,ak,al,af){var ah=this;var ai=false;for(var ag=0;ag<aj.length;ag++){if(aj[ag].message){ai=true;break}}if(ai){for(var ag=0;ag<aj.length;ag++){tile=aj[ag];if(!tile.message){tile.canvas.css("padding-top",E)}}}},draw_helper:function(ag,ah,ai,al,ar,aw,at,am){var aj=this,aq=this._gen_tile_cache_key(ah,aw,ai),an=ai*R*al,av=an+R*al;var ao=(ag?undefined:aj.tile_cache.get(aq));if(ao){aj.show_tile(ao,ar,aw);return ao}var ap=function(ax){return("isResolved" in ax)};var ak=true;var af=aj.data_manager.get_data(an,av,aj.mode,al,aj.data_url_extra_params);if(ap(af)){ak=false}var au;if(view.reference_track&&aw>view.canvas_manager.char_width_px){au=view.reference_track.data_manager.get_data(an,av,aj.mode,al,view.reference_track.data_url_extra_params);if(ap(au)){ak=false}}if(ak){p(af,am);var ao=aj.draw_tile(af,aj.mode,al,ai,aw,au);if(ao!==undefined){aj.tile_cache.set(aq,ao);aj.show_tile(ao,ar,aw)}return ao}$.when(af,au).then(function(){view.request_redraw(false,false,false,aj)});return null},show_tile:function(al,an,ao){var ah=this,ag=al.canvas,ak=ag;if(al.message){var ap=$("<div/>"),am=$("<div/>").addClass("tile-message").text(al.message).css({height:E-1,width:al.canvas.width}).appendTo(ap),aj=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(am),af=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(am);ap.append(ag);ak=ap;aj.click(function(){al.stale=true;ah.data_manager.get_more_data(al.low,al.high,ah.mode,al.resolution,{},ah.data_manager.DEEP_DATA_REQ);ah.request_draw()}).dblclick(function(aq){aq.stopPropagation()});af.click(function(){al.stale=true;ah.data_manager.get_more_data(al.low,al.high,ah.mode,al.resolution,{},ah.data_manager.BROAD_DATA_REQ);ah.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}al.predisplay_actions();var ai=(al.low-(this.is_overview?this.view.max_low:this.view.low))*ao;if(this.left_offset){ai-=this.left_offset}ak.css({position:"absolute",top:0,left:ai,height:""});an.append(ak);ah.max_height=Math.max(ah.max_height,ak.height());ah.content_div.css("height",ah.max_height+"px");an.children().css("height",ah.max_height+"px")},_get_tile_bounds:function(af,ag){var ai=af*R*ag,aj=R*ag,ah=(ai+aj<=this.view.max_high?ai+aj:this.view.max_high);return[ai,ah]},tool_region_and_parameters_str:function(ah,af,ai){var ag=this,aj=(ah!==undefined&&af!==undefined&&ai!==undefined?ah+":"+af+"-"+ai:"all");return" - region=["+aj+"], parameters=["+ag.tool.get_param_values().join(", ")+"]"},init_for_tool_data:function(){this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.predraw_init=function(){var ag=this;var af=function(){if(ag.data_manager.size()===0){setTimeout(af,300)}else{ag.data_url=default_data_url;ag.data_query_wait=L;ag.dataset_state_url=converted_datasets_state_url;$.getJSON(ag.dataset_state_url,{dataset_id:ag.dataset_id,hda_ldda:ag.hda_ldda},function(ah){})}};af()}}});var ab=function(ag,af){i.call(this,"label",ag,af,false,{});this.container_div.addClass("label-track")};p(ab.prototype,i.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ah=this.view,ai=ah.high-ah.low,al=Math.floor(Math.pow(10,Math.floor(Math.log(ai)/Math.log(10)))),af=Math.floor(ah.low/al)*al,aj=this.view.container.width(),ag=$("<div style='position: relative; height: 1.3em;'></div>");while(af<ah.high){var ak=(af-ah.low)/ai*aj;ag.append($("<div class='label'>"+commatize(af)+"</div>").css({position:"absolute",left:ak-1}));af+=al}this.content_div.children(":first").remove();this.content_div.append(ag)}});var A=function(af){N.call(this,"reference",af,{content_div:af.top_labeltrack},{});af.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:af.dbkey};this.data_manager=new I(B,this,false);this.tile_cache=new c(u)};p(A.prototype,q.prototype,N.prototype,{build_header_div:function(){},init:function(){this.enabled=true},draw_tile:function(ap,al,ak,ag,aq){var aj=this,ah=R*ak;if(aq>this.view.canvas_manager.char_width_px){if(ap.data===null){aj.content_div.css("height","0px");return}var ai=this.view.canvas_manager.new_canvas();var ao=ai.getContext("2d");ai.width=Math.ceil(ah*aq+aj.left_offset);ai.height=aj.height_px;ao.font=ao.canvas.manager.default_font;ao.textAlign="center";ap=ap.data;for(var am=0,an=ap.length;am<an;am++){var af=Math.round(am*aq);ao.fillText(ap[am],af+aj.left_offset,10)}return new b(aj,ag,ak,ai,ap)}this.content_div.css("height","0px")}});var j=function(ak,ai,ah,al,af,aj){var ag=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";N.call(this,ak,ai,ah,aj);this.min_height_px=16;this.max_height_px=400;this.height_px=32;this.hda_ldda=al;this.dataset_id=af;this.original_dataset_id=af;this.data_manager=new S(B,this);this.tile_cache=new c(u);this.left_offset=0;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:aj,onchange:function(){ag.set_name(ag.prefs.name);ag.vertical_range=ag.prefs.max_value-ag.prefs.min_value;$("#linetrack_"+ag.dataset_id+"_minval").text(ag.prefs.min_value);$("#linetrack_"+ag.dataset_id+"_maxval").text(ag.prefs.max_value);ag.tile_cache.clear();ag.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};p(j.prototype,q.prototype,N.prototype,{add_resize_handle:function(){var af=this;var ai=false;var ah=false;var ag=$("<div class='track-resize'>");$(af.container_div).hover(function(){if(af.content_visible){ai=true;ag.show()}},function(){ai=false;if(!ah){ag.hide()}});ag.hide().bind("dragstart",function(aj,ak){ah=true;ak.original_height=$(af.content_div).height()}).bind("drag",function(ak,al){var aj=Math.min(Math.max(al.original_height+al.deltaY,af.min_height_px),af.max_height_px);$(af.content_div).css("height",aj);af.height_px=aj;af.request_draw(true)}).bind("dragend",function(aj,ak){af.tile_cache.clear();ah=false;if(!ai){ag.hide()}af.config.values.height=af.height_px}).appendTo(af.container_div)},predraw_init:function(){var af=this;af.vertical_range=undefined;return $.getJSON(af.data_url,{stats:true,chrom:af.view.chrom,low:null,high:null,hda_ldda:af.hda_ldda,dataset_id:af.dataset_id},function(ag){af.container_div.addClass("line-track");var aj=ag.data;if(isNaN(parseFloat(af.prefs.min_value))||isNaN(parseFloat(af.prefs.max_value))){var ah=aj.min;var al=aj.max;ah=Math.floor(Math.min(0,Math.max(ah,aj.mean-2*aj.sd)));al=Math.ceil(Math.max(0,Math.min(al,aj.mean+2*aj.sd)));af.prefs.min_value=ah;af.prefs.max_value=al;$("#track_"+af.dataset_id+"_minval").val(af.prefs.min_value);$("#track_"+af.dataset_id+"_maxval").val(af.prefs.max_value)}af.vertical_range=af.prefs.max_value-af.prefs.min_value;af.total_frequency=aj.total_frequency;af.container_div.find(".yaxislabel").remove();var ak=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_minval").text(Z(af.prefs.min_value,3));var ai=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_maxval").text(Z(af.prefs.max_value,3));ai.css({position:"absolute",top:"24px",left:"10px"});ai.prependTo(af.container_div);ak.css({position:"absolute",bottom:"2px",left:"10px"});ak.prependTo(af.container_div)})},draw_tile:function(ar,ak,aj,ah,aq){if(this.vertical_range===undefined){return}var af=this._get_tile_bounds(ah,aj),al=af[0],ap=af[1],ag=Math.ceil((ap-al)*aq),an=this.height_px;var ai=this.view.canvas_manager.new_canvas();ai.width=ag,ai.height=an;var ao=ai.getContext("2d");var am=new M.LinePainter(ar.data,al,ap,this.prefs,ak);am.draw(ao,ag,an);return new b(this.track,ah,aj,ai,ar.data)}});var e=function(af,al,ag,ak,an,am,ai,aj){var ah=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];N.call(this,af,al,ag,am,ai,aj);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:am,onchange:function(){ah.set_name(ah.prefs.name);ah.tile_cache.clear();ah.set_painter_from_config();ah.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=ak;this.dataset_id=an;this.original_dataset_id=an;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new S(20,this);this.left_offset=200;this.set_painter_from_config()};p(e.prototype,q.prototype,N.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style=="arcs"){this.painter=M.ArcLinkedFeaturePainter}else{this.painter=M.LinkedFeaturePainter}},postdraw_actions:function(av,af,aw,au){N.prototype.postdraw_actions.call(this,av,au);var ai=this;if(au){var ak=ai.content_div.children();var al=false;for(var aj=ak.length-1,ap=0;aj>=ap;aj--){var ah=$(ak[aj]);if(al){ah.remove()}else{if(ah.children().length!==0){al=true}}}}if(ai.mode=="Histogram"){var ao=-1;for(var aj=0;aj<av.length;aj++){var at=av[aj].max_val;if(at>ao){ao=at}}for(var aj=0;aj<av.length;aj++){var ar=av[aj];if(ar.max_val!==ao){ar.canvas.remove();ai.draw_helper(true,af,ar.index,ar.resolution,ar.canvas.parent(),aw,[],{max:ao})}}}if(ai.filters_manager){var ag=ai.filters_manager.filters;for(var an=0;an<ag.length;an++){ag[an].update_ui_elt()}var am=false,aq;for(var aj=0;aj<av.length;aj++){if(av[aj].data.length){aq=av[aj].data[0];for(var an=0;an<ag.length;an++){if(ag[an].applies_to(aq)){am=true;break}}}}if(ai.filters_available!==am){ai.filters_available=am;if(!ai.filters_available){ai.filters_div.hide()}ai.update_icons()}}},update_auto_mode:function(af){var af;if(this.mode=="Auto"){if(af=="no_detail"){af="feature spans"}else{if(af=="summary_tree"){af="coverage histogram"}}this.mode_icon.attr("title","Set display mode (now: Auto/"+af+")")}},incremental_slots:function(aj,ag,ai){var ah=this.view.canvas_manager.dummy_context,af=this.inc_slots[aj];if(!af||(af.mode!==ai)){af=new (s.FeatureSlotter)(aj,ai==="Pack",z,function(ak){return ah.measureText(ak)});af.mode=ai;this.inc_slots[aj]=af}return af.slot_features(ag)},get_summary_tree_data:function(aj,am,ah,av){if(av>ah-am){av=ah-am}var aq=Math.floor((ah-am)/av),au=[],ai=0;var ak=0,al=0,ap,at=0,an=[],ar,ao;var ag=function(ay,ax,az,aw){ay[0]=ax+az*aw;ay[1]=ax+(az+1)*aw};while(at<av&&ak!==aj.length){var af=false;for(;at<av&&!af;at++){ag(an,am,at,aq);for(al=ak;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){af=true;break}}if(af){break}}data_start_index=al;au[au.length]=ar=[an[0],0];for(;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){ar[1]++}else{break}}if(ar[1]>ai){ai=ar[1]}at++}return{max:ai,delta:aq,data:au}},draw_tile:function(au,ax,aB,aF,ap,ai){var ay=this,ak=ay._get_tile_bounds(aF,aB),aI=ak[0],ag=ak[1],aw=ag-aI,az=Math.ceil(aw*ap),aO=25,aj=this.left_offset,av,al;if(ax==="Auto"){if(au.dataset_type==="summary_tree"){ax=au.dataset_type}else{if(au.extra_info==="no_detail"||ay.is_overview){ax="no_detail"}else{var aN=au.data;if(this.view.high-this.view.low>J){ax="Squish"}else{ax="Pack"}}}this.update_auto_mode(ax)}if(ax==="summary_tree"||ax==="Histogram"){al=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var af=$("<div />").addClass("yaxislabel");af.text(au.max);af.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});af.prependTo(this.container_div);var ah=this.view.canvas_manager.new_canvas();ah.width=az+aj;ah.height=al+T;if(au.dataset_type!="summary_tree"){var aq=this.get_summary_tree_data(au.data,aI,ag,200);if(au.max){aq.max=au.max}au=aq}var aK=new M.SummaryTreePainter(au,aI,ag,this.prefs);var aA=ah.getContext("2d");aA.translate(aj,T);aK.draw(aA,az,al);return new k(ay,aF,aB,ah,au.data,au.max)}var av,an=1;if(ax==="no_detail"||ax==="Squish"||ax==="Pack"){an=this.incremental_slots(ap,au.data,ax);av=this.inc_slots[ap].slots}var ao=[];if(au.data){var ar=this.filters_manager.filters;for(var aC=0,aE=au.data.length;aC<aE;aC++){var am=au.data[aC];var aD=false;var at;for(var aH=0,aM=ar.length;aH<aM;aH++){at=ar[aH];at.update_attrs(am);if(!at.keep(am)){aD=true;break}}if(!aD){ao.push(am)}}}var aL=(this.filters_manager.alpha_filter?new D(this.filters_manager.alpha_filter):null);var aJ=(this.filters_manager.height_filter?new D(this.filters_manager.height_filter):null);var aK=new (this.painter)(ao,aI,ag,this.prefs,ax,aL,aJ,ai);var al=Math.max(ad,aK.get_required_height(an,az));var ah=this.view.canvas_manager.new_canvas();var aG=null;ah.width=az+aj;ah.height=al;var aA=ah.getContext("2d");aA.fillStyle=this.prefs.block_color;aA.font=aA.canvas.manager.default_font;aA.textAlign="right";this.container_div.find(".yaxislabel").remove();if(au.data){aA.translate(aj,0);aG=aK.draw(aA,az,al,av);aG.translation=-aj}return new P(ay,aF,aB,ah,au.data,ax,au.message,aG)}});var U=function(ak,ah,ag,am,af,aj,al,ai){e.call(this,ak,ah,ag,am,af,aj,al,ai);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:aj,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter};p(U.prototype,q.prototype,N.prototype,e.prototype);var W=function(af,ak,ag,aj,an,am,ah){e.call(this,af,ak,ag,aj,an,am,ah);var ai=get_random_color(),al=get_random_color([ai,"#ffffff"]);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ai},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:al},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:am,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter;this.update_icons()};p(W.prototype,q.prototype,N.prototype,e.prototype);X.View=ac;X.DrawableGroup=Q;X.LineTrack=j;X.FeatureTrack=e;X.ReadTrack=W;X.VcfTrack=U};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(F,G){for(var E=0;E<=z;E++){var C=false,H=h[E];if(H!==undefined){for(var B=0,D=H.length;B<D;B++){var i=H[B];if(G>i[0]&&F<i[1]){C=true;break}}}if(!C){return E}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(i,x){var u=i("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y<E;y++,A+=J,G+=H){if(y%2!==0){continue}I.fillRect(A,G,D,1)}};var q=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var d=function(y){this.default_val=(y?y:1)};d.prototype.gen_val=function(y){return this.default_val};var l=function(A,C,y,z,B){this.data=A;this.view_start=C;this.view_end=y;this.prefs=u({},this.default_prefs,z);this.mode=B};l.prototype.default_prefs={};var v=function(A,C,y,z,B){l.call(this,A,C,y,z,B)};v.prototype.default_prefs={show_counts:false};v.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var 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r=function(A,D,y,z,C,E,B){o.call(this,A,D,y,z,C,E,B);this.draw_background_connector=true;this.draw_individual_connectors=false};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=c}else{if(z==="no_detail"){y=h}else{if(z==="Squish"){y=k}else{y=w}}}return y},draw_element:function(M,D,X,H,O,aj,an,ap,y){var T=X[0],al=X[1],ad=X[2],Q=X[3],ae=Math.floor(Math.max(0,(al-O)*an)),N=Math.ceil(Math.min(y,Math.max(0,(ad-O)*an))),ac=ae,ao=N,aa=(D==="Dense"?0:(0+H))*ap+this.get_top_padding(y),L,ah,R=null,ar=null,B=this.prefs.block_color,ag=this.prefs.label_color;M.globalAlpha=this.alpha_scaler.gen_val(X);if(D==="Dense"){H=1}if(D==="no_detail"){M.fillStyle=B;M.fillRect(ae,aa+5,N-ae,f)}else{var K=X[4],Z=X[5],af=X[6],C=X[7],V=true;if(Z&&af){R=Math.floor(Math.max(0,(Z-O)*an));ar=Math.ceil(Math.min(y,Math.max(0,(af-O)*an)))}var 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y,z=this.mode;if(z==="Dense"){y=c}else{if(z==="Squish"){y=k}else{y=w;if(this.prefs.show_insertions){y*=2}}}return y},draw_read:function(K,A,ag,V,L,aa,ad,C,B,M){K.textAlign="center";var J=this,R=[L,aa],Z=0,W=0,D=0,F=K.canvas.manager.char_width_px,y=(B==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var O=[];if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){D=Math.round(ag/2)}if(!C){C=[[0,M.length]]}for(var G=0,I=C.length;G<I;G++){var z=C[G],E="MIDNSHP=X"[z[0]],S=z[1];if(E==="H"||E==="S"){Z-=S}var U=ad+Z,Y=Math.floor(Math.max(0,(U-L)*ag)),ab=Math.floor(Math.max(0,(U+S-L)*ag));if(Y===ab){ab+=1}switch(E){case"H":break;case"S":case"M":case"=":if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(D>0){K.fillStyle=y;K.fillRect(Y-D,V+1,ab-Y,9);K.fillStyle=g;for(var af=0,H=N.length;af<H;af++){if(this.prefs.show_differences&&this.ref_seq){var P=this.ref_seq[U-L+af];if(!P||P.toLowerCase()===N[af].toLowerCase()){continue}}if(U+af>=L&&U+af<=aa){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X,V+9)}}}else{K.fillStyle=y;K.fillRect(Y,V+4,ab-Y,e)}}W+=S;Z+=S;break;case"N":K.fillStyle=g;K.fillRect(Y-D,V+5,ab-Y,1);Z+=S;break;case"D":K.fillStyle="red";K.fillRect(Y-D,V+4,ab-Y,3);Z+=S;break;case"P":break;case"I":var ah=Y-D;if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(this.prefs.show_insertions){var T=Y-(ab-Y)/2;if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){K.fillStyle="yellow";K.fillRect(T-D,V-9,ab-Y,9);O[O.length]={type:"triangle",data:[ah,V+4,5]};K.fillStyle=g;switch(compute_overlap([U,U+S],R)){case (OVERLAP_START):N=N.slice(L-U);break;case (OVERLAP_END):N=N.slice(0,U-aa);break;case (CONTAINED_BY):break;case (CONTAINS):N=N.slice(L-U,U-aa);break}for(var af=0,H=N.length;af<H;af++){var 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+var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var m=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(u,t,v,r,i,s){return(Math.max(u,r)-Math.min(u,r))+(Math.max(t,i)-Math.min(t,i))+(Math.max(v,s)-Math.min(v,s))};var g,n,f,k,p,h,q,c,d,b,o,l=false;do{g=Math.random()*16777215;n=g|16711680;f=g|65280;k=g|255;d=m(n,f,k);l=true;for(var j=0;j<a.length;j++){p=a[j];h=p|16711680;q=p|65280;c=p|255;b=m(h,q,c);o=e(n,f,k,h,q,c);if((Math.abs(d-b)<125)||(o<500)){l=false;break}}}while(!l);return"#"+(16777216+g).toString(16).substr(1,6)};var trackster_module=function(f,X){var p=f("class").extend,s=f("slotting"),M=f("painters");var ae=function(af,ag){this.document=af;this.default_font=ag!==undefined?ag:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};p(ae.prototype,{load_pattern:function(af,aj){var ag=this.patterns,ah=this.dummy_context,ai=new Image();ai.src=image_path+aj;ai.onload=function(){ag[af]=ah.createPattern(ai,"repeat")}},get_pattern:function(af){return this.patterns[af]},new_canvas:function(){var af=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(af)}af.manager=this;return af}});var n={};var l=function(af,ag){n[af.attr("id")]=ag};var m=function(af,ah,aj,ai){aj=".group";var ag={};n[af.attr("id")]=ai;af.bind("drag",{handle:"."+ah,relative:true},function(ar,at){var aq=$(this);var aw=$(this).parent(),an=aw.children(),ap=n[$(this).attr("id")],am,al,au,ak,ao;al=$(this).parents(aj);if(al.length!==0){au=al.position().top;ak=au+al.outerHeight();if(at.offsetY<au){$(this).insertBefore(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable_before(ap,av);return}else{if(at.offsetY>ak){$(this).insertAfter(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable(ap);return}}}al=null;for(ao=0;ao<an.length;ao++){am=$(an.get(ao));au=am.position().top;ak=au+am.outerHeight();if(am.is(aj)&&this!==am.get(0)&&at.offsetY>=au&&at.offsetY<=ak){if(at.offsetY-au<ak-at.offsetY){am.find(".content-div").prepend(this)}else{am.find(".content-div").append(this)}if(ap.container){ap.container.remove_drawable(ap)}n[am.attr("id")].add_drawable(ap);return}}for(ao=0;ao<an.length;ao++){if(at.offsetY<$(an.get(ao)).position().top){break}}if(ao===an.length){if(this!==an.get(ao-1)){aw.append(this);n[aw.attr("id")].move_drawable(ap,ao)}}else{if(this!==an.get(ao)){$(this).insertBefore(an.get(ao));n[aw.attr("id")].move_drawable(ap,(at.deltaY>0?ao-1:ao))}}}).bind("dragstart",function(){ag["border-top"]=af.css("border-top");ag["border-bottom"]=af.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ag)})};X.moveable=m;var ad=16,H=9,E=20,T=H+2,z=100,J=12000,R=200,C=5,v=10,L=5000,w=100,o="There was an error in indexing this dataset. ",K="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",F="No data for this chrom/contig.",t="Currently indexing... please wait",x="Tool cannot be rerun: ",a="Loading data...",Y="Ready for display",d=10,u=5,B=5;function Z(ag,af){if(!af){af=0}var ah=Math.pow(10,af);return Math.round(ag*ah)/ah}var c=function(af){this.num_elements=af;this.clear()};p(c.prototype,{get:function(ag){var af=this.key_ary.indexOf(ag);if(af!==-1){if(this.obj_cache[ag].stale){this.key_ary.splice(af,1);delete this.obj_cache[ag]}else{this.move_key_to_end(ag,af)}}return this.obj_cache[ag]},set:function(ag,ah){if(!this.obj_cache[ag]){if(this.key_ary.length>=this.num_elements){var af=this.key_ary.shift();delete this.obj_cache[af]}this.key_ary.push(ag)}this.obj_cache[ag]=ah;return ah},move_key_to_end:function(ag,af){this.key_ary.splice(af,1);this.key_ary.push(ag)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var S=function(ag,af,ah){c.call(this,ag);this.track=af;this.subset=(ah!==undefined?ah:true)};p(S.prototype,c.prototype,{load_data:function(ao,aj,am,ag,al){var an=this.track.view.chrom,ai={chrom:an,low:ao,high:aj,mode:am,resolution:ag,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ai,al);if(this.track.filters_manager){var ap=[];var af=this.track.filters_manager.filters;for(var ak=0;ak<af.length;ak++){ap[ap.length]=af[ak].name}ai.filter_cols=JSON.stringify(ap)}var ah=this;return $.getJSON(this.track.data_url,ai,function(aq){ah.set_data(ao,aj,am,aq)})},get_data:function(af,aj,ak,ag,ai){var ah=this.get_data_from_cache(af,aj,ak);if(ah){return ah}ah=this.load_data(af,aj,ak,ag,ai);this.set_data(af,aj,ak,ah);return ah},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(an,ai,am,ah,al,aj){var ao=this.get_data_from_cache(an,ai,am);if(!ao){console.log("ERROR: no current data for: ",this.track,an,ai,am,ah,al);return}ao.stale=true;var ag=an;if(aj===this.DEEP_DATA_REQ){$.extend(al,{start_val:ao.data.length+1})}else{if(aj===this.BROAD_DATA_REQ){ag=(ao.max_high?ao.max_high:ao.data[ao.data.length-1][2])+1}}var af=this,ak=this.load_data(ag,ai,am,ah,al);new_data_available=$.Deferred();this.set_data(an,ai,am,new_data_available);$.when(ak).then(function(ap){if(ap.data){ap.data=ao.data.concat(ap.data);if(ap.max_low){ap.max_low=ao.max_low}if(ap.message){ap.message=ap.message.replace(/[0-9]+/,ap.data.length)}}af.set_data(an,ai,am,ap);new_data_available.resolve(ap)});return new_data_available},get_data_from_cache:function(af,ag,ah){return this.get(this.gen_key(af,ag,ah))},set_data:function(ag,ah,ai,af){return this.set(this.gen_key(ag,ah,ai),af)},gen_key:function(af,ah,ai){var ag=af+"_"+ah+"_"+ai;return ag},split_key:function(af){return af.split("_")}});var I=function(ag,af,ah){S.call(this,ag,af,ah)};p(I.prototype,S.prototype,c.prototype,{load_data:function(af,ai,aj,ag,ah){if(ag>1){return{data:null}}return S.prototype.load_data.call(this,af,ai,aj,ag,ah)}});var q=function(ai,ag,af,ah,ak){if(!q.id_counter){q.id_counter=0}this.id=q.id_counter++;this.name=ai;this.view=ag;this.container=af;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ai}],saved_values:ah,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ak;this.is_overview=false;this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=this.build_icons_div().hide();this.header_div.append(this.icons_div);this.header_div.dblclick(function(al){al.stopPropagation()});var aj=this;this.container_div.hover(function(){aj.icons_div.show()},function(){aj.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p(q.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},update_icons:function(){},set_name:function(af){this.old_name=this.name;this.name=af;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.hide(0,function(){$(this).remove();view.update_intro_div();view.has_changes=true})},build_container_div:function(){},build_header_div:function(){},build_icons_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){}});var y=function(aj,ai,ag,af,ah,ak){q.call(this,ai,ag,af,ah,ak);this.obj_type=aj;this.drawables=[]};p(y.prototype,q.prototype,{init:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af].init()}},_draw:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af]._draw()}},to_json:function(){var ag=[];for(var af=0;af<this.drawables.length;af++){ag.push(this.drawables[af].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ag}},add_drawable:function(af){this.drawables.push(af);af.container=this},add_drawable_before:function(ah,af){var ag=this.drawables.indexOf(af);if(ag!=-1){this.drawables.splice(ag,0,ah);return true}return false},remove_drawable:function(ag){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);ag.container=null;return true}return false},move_drawable:function(ag,ah){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);this.drawables.splice(ah,0,ag);return true}return false}});var Q=function(ai,ag,af,ah){y.call(this,"DrawableGroup",ai,ag,af,ah,"group-handle");this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this)};p(Q.prototype,q.prototype,y.prototype,{build_container_div:function(){return $("<div/>").addClass("group").attr("id","group_"+this.id).appendTo(this.container.content_div)},build_header_div:function(){var af=$("<div/>").addClass("track-header");af.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(af);return af},build_icons_div:function(){var af=$("<div/>").css("float","left");this.toggle_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Hide/show group content").addClass("icon-button toggle").tipsy({gravity:"s"}).appendTo(af);this.settings_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Edit settings").addClass("icon-button settings-icon").tipsy({gravity:"s"}).appendTo(af);this.remove_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Remove").addClass("icon-button remove-icon").tipsy({gravity:"s"}).appendTo(af);var ag=this;this.toggle_icon.click(function(){if(ag.content_visible){ag.toggle_icon.addClass("toggle-expand").removeClass("toggle");ag.hide_contents();ag.content_visible=false}else{ag.toggle_icon.addClass("toggle").removeClass("toggle-expand");ag.content_visible=true;ag.show_contents()}});this.settings_icon.click(function(){var aj=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ah=function(){ag.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ai=function(ak){if((ak.keyCode||ak.which)===27){aj()}else{if((ak.keyCode||ak.which)===13){ah()}}};$(window).bind("keypress.check_enter_esc",ai);show_modal("Configure Group",ag.config.build_form(),{Cancel:aj,OK:ah})});this.remove_icon.click(function(){$(".tipsy").remove();ag.remove()});return af},hide_contents:function(){this.content_div.hide()},show_contents:function(){this.content_div.show();this.request_draw()}});var ac=function(af,ai,ah,ag){y.call(this,"View");this.container=af;this.chrom=null;this.vis_id=ah;this.dbkey=ag;this.title=ai;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ae(af.get(0).ownerDocument);this.reset()};p(ac.prototype,y.prototype,{init:function(){var ah=this.container,af=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ah);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ah);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ah);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,af);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ai=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ag=function(aj){if(aj.type==="focusout"||(aj.keyCode||aj.which)===13||(aj.keyCode||aj.which)===27){if((aj.keyCode||aj.which)!==27){af.go_to($(this).val())}$(this).hide();$(this).val("");af.location_span.show();af.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ag).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tipsy({gravity:"n"}).appendTo(this.nav_controls);this.location_span.click(function(){af.location_span.hide();af.chrom_select.hide();af.nav_input.val(af.chrom+":"+af.low+"-"+af.high);af.nav_input.css("display","inline-block");af.nav_input.select();af.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tipsy({gravity:"n"}).click(function(){af.zoom_out();af.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tipsy({gravity:"n"}).click(function(){af.zoom_in();af.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){af.change_chrom(af.chrom_select.val())});this.browser_content_div.click(function(aj){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(aj){af.zoom_in(aj.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(aj,ak){this.current_x=ak.offsetX}).bind("drag",function(aj,al){var am=al.offsetX-this.current_x;this.current_x=al.offsetX;var ak=Math.round(am/af.viewport_container.width()*(af.max_high-af.max_low));af.move_delta(-ak)});this.overview_close.click(function(){af.reset_overview()});this.viewport_container.bind("draginit",function(aj,ak){if(aj.clientX>af.viewport_container.width()-16){return false}}).bind("dragstart",function(aj,ak){ak.original_low=af.low;ak.current_height=aj.clientY;ak.current_x=ak.offsetX}).bind("drag",function(al,an){var aj=$(this);var ao=an.offsetX-an.current_x;var ak=aj.scrollTop()-(al.clientY-an.current_height);aj.scrollTop(ak);an.current_height=al.clientY;an.current_x=an.offsetX;var am=Math.round(ao/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}).bind("mousewheel",function(al,an,ak,aj){if(ak){ak*=50;var am=Math.round(-ak/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}});this.top_labeltrack.bind("dragstart",function(aj,ak){return $("<div />").css({height:af.browser_content_div.height()+af.top_labeltrack.height()+af.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(an,ao){$(ao.proxy).css({left:Math.min(an.pageX,ao.startX),width:Math.abs(an.pageX-ao.startX)});var ak=Math.min(an.pageX,ao.startX)-af.container.offset().left,aj=Math.max(an.pageX,ao.startX)-af.container.offset().left,am=(af.high-af.low),al=af.viewport_container.width();af.update_location(Math.round(ak/al*am)+af.low,Math.round(aj/al*am)+af.low)}).bind("dragend",function(ao,ap){var ak=Math.min(ao.pageX,ap.startX),aj=Math.max(ao.pageX,ap.startX),am=(af.high-af.low),al=af.viewport_container.width(),an=af.low;af.low=Math.round(ak/al*am)+an;af.high=Math.round(aj/al*am)+an;$(ap.proxy).remove();af.request_redraw()});this.add_label_track(new ab(this,{content_div:this.top_labeltrack}));this.add_label_track(new ab(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){af.resize_window()});$(document).bind("redraw",function(){af.redraw()});this.reset();$(window).trigger("resize")},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},update_location:function(af,ag){this.location_span.text(commatize(af)+" - "+commatize(ag));this.nav_input.val(this.chrom+":"+commatize(af)+"-"+commatize(ag))},load_chroms:function(ah){ah.num=w;$.extend(ah,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var af=this,ag=$.Deferred();$.ajax({url:chrom_url,data:ah,dataType:"json",success:function(aj){if(aj.chrom_info.length===0){alert("Invalid chromosome: "+ah.chrom);return}if(aj.reference){af.add_label_track(new A(af))}af.chrom_data=aj.chrom_info;var am='<option value="">Select Chrom/Contig</option>';for(var al=0,ai=af.chrom_data.length;al<ai;al++){var ak=af.chrom_data[al].chrom;am+='<option value="'+ak+'">'+ak+"</option>"}if(aj.prev_chroms){am+='<option value="previous">Previous '+w+"</option>"}if(aj.next_chroms){am+='<option value="next">Next '+w+"</option>"}af.chrom_select.html(am);af.chrom_start_index=aj.start_index;ag.resolve(aj)},error:function(){alert("Could not load chroms for this dbkey:",af.dbkey)}});return ag},change_chrom:function(ak,ag,am){if(!ak||ak==="None"){return}var ah=this;if(ak==="previous"){ah.load_chroms({low:this.chrom_start_index-w});return}if(ak==="next"){ah.load_chroms({low:this.chrom_start_index+w});return}var al=$.grep(ah.chrom_data,function(an,ao){return an.chrom===ak})[0];if(al===undefined){ah.load_chroms({chrom:ak},function(){ah.change_chrom(ak,ag,am)});return}else{if(ak!==ah.chrom){ah.chrom=ak;ah.chrom_select.val(ah.chrom);ah.max_high=al.len-1;ah.reset();ah.request_redraw(true);for(var aj=0,af=ah.drawables.length;aj<af;aj++){var ai=ah.drawables[aj];if(ai.init){ai.init()}}}if(ag!==undefined&&am!==undefined){ah.low=Math.max(ag,0);ah.high=Math.min(am,ah.max_high)}ah.reset_overview();ah.request_redraw()}},go_to:function(aj){aj=aj.replace(/ |,/g,"");var an=this,af,ai,ag=aj.split(":"),al=ag[0],am=ag[1];if(am!==undefined){try{var ak=am.split("-");af=parseInt(ak[0],10);ai=parseInt(ak[1],10)}catch(ah){return false}}an.change_chrom(al,af,ai)},move_fraction:function(ah){var af=this;var ag=af.high-af.low;this.move_delta(ah*ag)},move_delta:function(ah){var af=this;var ag=af.high-af.low;if(af.low-ah<af.max_low){af.low=af.max_low;af.high=af.max_low+ag}else{if(af.high-ah>af.max_high){af.high=af.max_high;af.low=af.max_high-ag}else{af.high-=ah;af.low-=ah}}af.request_redraw()},add_drawable:function(af){y.prototype.add_drawable.call(this,af);af.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(af){af.view=this;af.init();this.label_tracks.push(af)},remove_drawable:function(ah,ag){y.prototype.remove_drawable.call(this,ah);if(ag){var af=this;ah.container_div.hide(0,function(){$(this).remove();af.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(an,af,am,ag){var al=this,aj=(ag?[ag]:al.drawables),ah;var ag;for(var ak=0;ak<aj.length;ak++){ag=aj[ak];ah=-1;for(var ai=0;ai<al.tracks_to_be_redrawn.length;ai++){if(al.tracks_to_be_redrawn[ai][0]===ag){ah=ai;break}}if(ah<0){al.tracks_to_be_redrawn.push([ag,af,am])}else{al.tracks_to_be_redrawn[ak][1]=af;al.tracks_to_be_redrawn[ak][2]=am}}requestAnimationFrame(function(){al._redraw(an)})},_redraw:function(ap){var am=this.low,ai=this.high;if(am<this.max_low){am=this.max_low}if(ai>this.max_high){ai=this.max_high}var ao=this.high-this.low;if(this.high!==0&&ao<this.min_separation){ai=am+this.min_separation}this.low=Math.floor(am);this.high=Math.ceil(ai);this.resolution=Math.pow(C,Math.ceil(Math.log((this.high-this.low)/R)/Math.log(C)));this.zoom_res=Math.pow(v,Math.max(0,Math.ceil(Math.log(this.resolution,v)/Math.log(v))));var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var al=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var aq=13;this.overview_box.css({left:af,width:Math.max(aq,al)}).show();if(al<aq){this.overview_box.css("left",af-(aq-al)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:al})}this.update_location(this.low,this.high);if(!ap){var ah,ag,an;for(var aj=0,ak=this.tracks_to_be_redrawn.length;aj<ak;aj++){ah=this.tracks_to_be_redrawn[aj][0];ag=this.tracks_to_be_redrawn[aj][1];an=this.tracks_to_be_redrawn[aj][2];if(ah){ah._draw(ag,an)}}this.tracks_to_be_redrawn=[];for(aj=0,ak=this.label_tracks.length;aj<ak;aj++){this.label_tracks[aj]._draw()}}},zoom_in:function(ag,ah){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ai=this.high-this.low,aj=ai/2+this.low,af=(ai/this.zoom_factor)/2;if(ag){aj=ag/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(aj-af);this.high=Math.round(aj+af);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ag=this.high-this.low,ah=ag/2+this.low,af=(ag*this.zoom_factor)/2;this.low=Math.round(ah-af);this.high=Math.round(ah+af);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ah.dataset_id){return}this.overview_viewport.find(".track").remove()}var ag=ah.copy({content_div:this.overview_viewport}),af=this;ag.header_div.hide();ag.is_overview=true;af.overview_drawable=ag;this.overview_drawable.postdraw_actions=function(){af.overview_highlight.show().height(af.overview_drawable.content_div.height());af.overview_viewport.height(af.overview_drawable.content_div.height()+af.overview_box.outerHeight());af.overview_close.show();af.resize_window()};this.overview_drawable.init();af.has_changes=true},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var r=function(ah,al){this.track=ah;this.name=al.name;this.params=[];var at=al.params;for(var ai=0;ai<at.length;ai++){var an=at[ai],ag=an.name,ar=an.label,aj=unescape(an.html),au=an.value,ap=an.type;if(ap==="number"){this.params[this.params.length]=new g(ag,ar,aj,au,an.min,an.max)}else{if(ap=="select"){this.params[this.params.length]=new O(ag,ar,aj,au)}else{console.log("WARNING: unrecognized tool parameter type:",ag,ap)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aw){aw.stopPropagation()}).click(function(aw){aw.stopPropagation()}).bind("dblclick",function(aw){aw.stopPropagation()});var aq=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ao=this.params;var am=this;$.each(this.params,function(ax,aA){var az=$("<div>").addClass("param-row").appendTo(am.parent_div);var aw=$("<div>").addClass("param-label").text(aA.label).appendTo(az);var ay=$("<div/>").addClass("slider").html(aA.html).appendTo(az);ay.find(":input").val(aA.value);$("<div style='clear: both;'/>").appendTo(az)});this.parent_div.find("input").click(function(){$(this).select()});var av=$("<div>").addClass("param-row").appendTo(this.parent_div);var ak=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(av);var af=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(av);var am=this;af.click(function(){am.run_on_region()});ak.click(function(){am.run_on_dataset()})};p(r.prototype,{get_param_values_dict:function(){var af={};this.parent_div.find(":input").each(function(){var ag=$(this).attr("name"),ah=$(this).val();af[ag]=JSON.stringify(ah)});return af},get_param_values:function(){var ag=[];var af={};this.parent_div.find(":input").each(function(){var ah=$(this).attr("name"),ai=$(this).val();if(ah){ag[ag.length]=ai}});return ag},run_on_dataset:function(){var af=this;af.run({dataset_id:this.track.original_dataset_id,tool_id:af.name},null,function(ag){show_modal(af.name+" is Running",af.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ag={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},aj=this.track,ah=ag.tool_id+aj.tool_region_and_parameters_str(ag.chrom,ag.low,ag.high),af;if(aj.container===view){var ai=new Q(this.name,this.track.view,this.track.container);aj.container.add_drawable(ai);aj.container.remove_drawable(aj);ai.add_drawable(aj);aj.container_div.appendTo(ai.content_div);af=ai}else{af=aj.container}var ak=new aj.constructor(ah,view,af,"hda");ak.init_for_tool_data();ak.change_mode(aj.mode);af.add_drawable(ak);ak.content_div.text("Starting job.");this.run(ag,ak,function(al){ak.dataset_id=al.dataset_id;ak.content_div.text("Running job.");ak.init()})},run:function(ag,ah,ai){$.extend(ag,this.get_param_values_dict());var af=function(){$.getJSON(rerun_tool_url,ag,function(aj){if(aj==="no converter"){ah.container_div.addClass("error");ah.content_div.text(K)}else{if(aj.error){ah.container_div.addClass("error");ah.content_div.text(x+aj.message)}else{if(aj==="pending"){ah.container_div.addClass("pending");ah.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(af,2000)}else{ai(aj)}}}})};af()}});var O=function(ag,af,ah,ai){this.name=ag;this.label=af;this.html=ah;this.value=ai};var g=function(ah,ag,aj,ak,ai,af){O.call(this,ah,ag,aj,ak);this.min=ai;this.max=af};var h=function(ag,af,ah,ai){this.name=ag;this.index=af;this.tool_id=ah;this.tool_exp_name=ai};var V=function(ag,af,ah,ai){h.call(this,ag,af,ah,ai);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};p(V.prototype,{applies_to:function(af){if(af.length>this.index){return true}return false},keep:function(af){if(!this.applies_to(af)){return true}var ag=af[this.index];return(isNaN(ag)||(ag>=this.low&&ag<=this.high))},update_attrs:function(ag){var af=false;if(!this.applies_to(ag)){return af}if(ag[this.index]<this.min){this.min=Math.floor(ag[this.index]);af=true}if(ag[this.index]>this.max){this.max=Math.ceil(ag[this.index]);af=true}return af},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var ah=function(ak,ai){var aj=ai-ak;return(aj<=2?0.01:1)};var ag=this.slider.slider("option","min"),af=this.slider.slider("option","max");if(this.min<ag||this.max>af){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ah(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var aa=function(aq,ay){this.track=aq;this.filters=[];for(var at=0;at<ay.length;at++){var au=ay[at],az=au.name,af=au.type,ah=au.index,ax=au.tool_id,aw=au.tool_exp_name;if(af==="int"||af==="float"){this.filters[at]=new V(az,ah,ax,aw)}else{console.log("ERROR: unsupported filter: ",az,af)}}var ai=function(aA,aB,aC){aA.click(function(){var aD=aB.text();max=parseFloat(aC.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aC.slider("option","values")){input_size=2*input_size+1;multi_value=true}aB.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aD).appendTo(aB).focus().select().click(function(aE){aE.stopPropagation()}).blur(function(){$(this).remove();aB.text(aD)}).keyup(function(aI){if(aI.keyCode===27){$(this).trigger("blur")}else{if(aI.keyCode===13){var aG=aC.slider("option","min"),aE=aC.slider("option","max"),aH=function(aJ){return(isNaN(aJ)||aJ>aE||aJ<aG)},aF=$(this).val();if(!multi_value){aF=parseFloat(aF);if(aH(aF)){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}else{aF=aF.split("-");aF=[parseFloat(aF[0]),parseFloat(aF[1])];if(aH(aF[0])||aH(aF[1])){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}aC.slider((multi_value?"values":"value"),aF)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aA){aA.stopPropagation()}).click(function(aA){aA.stopPropagation()}).bind("dblclick",function(aA){aA.stopPropagation()}).bind("keydown",function(aA){aA.stopPropagation()});var av=$("<div/>").addClass("sliders").appendTo(this.parent_div);var an=this;$.each(this.filters,function(aD,aF){aF.container=$("<div/>").addClass("filter-row slider-row").appendTo(av);var aE=$("<div/>").addClass("elt-label").appendTo(aF.container);var aC=$("<span/>").addClass("slider-name").text(aF.name+"  ").appendTo(aE);var aB=$("<span/>");var aH=$("<span/>").addClass("slider-value").appendTo(aE).append("[").append(aB).append("]");var aA=$("<div/>").addClass("slider").appendTo(aF.container);aF.control_element=$("<div/>").attr("id",aF.name+"-filter-control").appendTo(aA);var aG=[0,0];aF.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aJ,aK){var aI=aK.values;aB.text(aI[0]+"-"+aI[1]);aF.low=aI[0];aF.high=aI[1];an.track.request_draw(true,true)},change:function(aI,aJ){aF.control_element.slider("option","slide").call(aF.control_element,aI,aJ)}});aF.slider=aF.control_element;aF.slider_label=aB;ai(aH,aB,aF.control_element);$("<div style='clear: both;'/>").appendTo(aF.container)});if(this.filters.length!==0){var ak=$("<div/>").addClass("param-row").appendTo(av);var am=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ak);var ag=this;am.click(function(){ag.run_on_dataset()})}var ap=$("<div/>").addClass("display-controls").appendTo(this.parent_div),ar,al,ao,aj={Transparency:function(aA){an.alpha_filter=aA},Height:function(aA){an.height_filter=aA}};$.each(aj,function(aC,aB){ar=$("<div/>").addClass("filter-row").appendTo(ap),al=$("<span/>").addClass("elt-label").text(aC+":").appendTo(ar),ao=$("<select/>").attr("name",aC+"_dropdown").css("float","right").appendTo(ar);$("<option/>").attr("value",-1).text("== None ==").appendTo(ao);for(var aA=0;aA<an.filters.length;aA++){$("<option/>").attr("value",aA).text(an.filters[aA].name).appendTo(ao)}ao.change(function(){$(this).children("option:selected").each(function(){var aD=parseInt($(this).val());aj[aC]((aD>=0?an.filters[aD]:null));an.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(ar)});$("<div style='clear: both;'/>").appendTo(this.parent_div)};p(aa.prototype,{reset_filters:function(){for(var af=0;af<this.filters.length;af++){filter=this.filters[af];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var an=function(ar,ap,aq){if(!(ap in ar)){ar[ap]=aq}return ar[ap]};var ah={},af,ag,ai;for(var aj=0;aj<this.filters.length;aj++){af=this.filters[aj];if(af.tool_id){if(af.min!=af.low){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" >= "+af.low}if(af.max!=af.high){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" <= "+af.high}}}var al=[];for(var ao in ah){al[al.length]=[ao,ah[ao]]}var am=al.length;(function ak(aw,at){var aq=at[0],ar=aq[0],av=aq[1],au="("+av.join(") and (")+")",ap={cond:au,input:aw,target_dataset_id:aw,tool_id:ar},at=at.slice(1);$.getJSON(run_tool_url,ap,function(ax){if(ax.error){show_modal("Filter Dataset","Error running tool "+ar,{Close:hide_modal})}else{if(at.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ak(ax.dataset_id,at)}}})})(this.track.dataset_id,al)}});var D=function(af,ag){M.Scaler.call(this,ag);this.filter=af};D.prototype.gen_val=function(af){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(af[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var G=function(af){this.track=af.track;this.params=af.params;this.values={};this.restore_values((af.saved_values?af.saved_values:{}));this.onchange=af.onchange};p(G.prototype,{restore_values:function(af){var ag=this;$.each(this.params,function(ah,ai){if(af[ai.key]!==undefined){ag.values[ai.key]=af[ai.key]}else{ag.values[ai.key]=ai.default_value}})},build_form:function(){var ai=this;var af=$("<div />");var ah;function ag(am,aj){for(var ao=0;ao<am.length;ao++){ah=am[ao];if(ah.hidden){continue}var ak="param_"+ao;var at=ai.values[ah.key];var av=$("<div class='form-row' />").appendTo(aj);av.append($("<label />").attr("for",ak).text(ah.label+":"));if(ah.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ak).attr("name",ak).attr("checked",at))}else{if(ah.type==="text"){av.append($('<input type="text"/>').attr("id",ak).val(at).click(function(){$(this).select()}))}else{if(ah.type=="select"){var aq=$("<select />").attr("id",ak);for(var an=0;an<ah.options.length;an++){$("<option/>").text(ah.options[an].label).attr("value",ah.options[an].value).appendTo(aq)}aq.val(at);av.append(aq)}else{if(ah.type==="color"){var ap=$("<input />").attr("id",ak).attr("name",ak).val(at);var ar=$("<div class='tipsy tipsy-west' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ar);var au=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:ap,color:at});$("<div />").append(ap).append(ar).appendTo(av).bind("click",function(aw){ar.css({left:$(this).position().left+$(ap).width()+5,top:$(this).position().top-($(ar).height()/2)+($(ap).height()/2)}).show();$(document).bind("click.color-picker",function(){ar.hide();$(document).unbind("click.color-picker")});aw.stopPropagation()})}else{av.append($("<input />").attr("id",ak).attr("name",ak).val(at))}}}}if(ah.help){av.append($("<div class='help'/>").text(ah.help))}}}ag(this.params,af);return af},update_from_form:function(af){var ah=this;var ag=false;$.each(this.params,function(ai,ak){if(!ak.hidden){var al="param_"+ai;var aj=af.find("#"+al).val();if(ak.type==="float"){aj=parseFloat(aj)}else{if(ak.type==="int"){aj=parseInt(aj)}else{if(ak.type==="bool"){aj=af.find("#"+al).is(":checked")}}}if(aj!==ah.values[ak.key]){ah.values[ak.key]=aj;ag=true}}});if(ag){this.onchange()}}});var b=function(af,ai,ah,ag,aj){this.track=af;this.index=ai;this.low=ai*R*ah;this.high=(ai+1)*R*ah;this.resolution=ah;this.canvas=$("<div class='track-tile'/>").append(ag);this.data=aj;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(af,ai,ah,ag,aj,ak){b.call(this,af,ai,ah,ag,aj);this.max_val=ak};p(k.prototype,b.prototype);var P=function(ah,am,ai,ag,ak,al,ap,an){b.call(this,ah,am,ai,ag,ak);this.mode=al;this.message=ap;this.feature_mapper=an;if(this.message){var ag=this.canvas.children()[0],ao=$("<div/>").addClass("tile-message").text(this.message).css({height:E-1,width:ag.width}).prependTo(this.canvas),aj=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ao),af=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ao);aj.click(function(){tile.stale=true;ah.data_manager.get_more_data(tile.low,tile.high,ah.mode,tile.resolution,{},ah.data_manager.DEEP_DATA_REQ);ah.request_draw()}).dblclick(function(aq){aq.stopPropagation()});af.click(function(){tile.stale=true;ah.data_manager.get_more_data(tile.low,tile.high,ah.mode,tile.resolution,{},ah.data_manager.BROAD_DATA_REQ);ah.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}};p(P.prototype,b.prototype);P.prototype.predisplay_actions=function(){var ag=this,af={};if(ag.mode!=="Pack"){return}$(this.canvas).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).siblings(".feature-popup").remove()}).mousemove(function(ar){if(!this.hovered){return}var am=$(this).offset(),aq=ar.pageX-am.left,ap=ar.pageY-am.top,aw=ag.feature_mapper.get_feature_data(aq,ap),an=(aw?aw[0]:null);$(this).siblings(".feature-popup").each(function(){if(!an||$(this).attr("id")!==an.toString()){$(this).remove()}});if(aw){var ai=af[an];if(!ai){var an=aw[0],at={name:aw[3],start:aw[1],end:aw[2],strand:aw[4]},al=ag.track.filters_manager.filters,ak;for(var ao=0;ao<al.length;ao++){ak=al[ao];at[ak.name]=aw[ak.index]}var ai=$("<div/>").attr("id",an).addClass("feature-popup"),ax=$("<table/>"),av,au,ay;for(av in at){au=at[av];ay=$("<tr/>").appendTo(ax);$("<th/>").appendTo(ay).text(av);$("<td/>").attr("align","left").appendTo(ay).text(typeof(au)=="number"?Z(au,2):au)}ai.append($("<div class='feature-popup-inner'>").append(ax));af[an]=ai}ai.appendTo($(ag.canvas).parent());var aj=aq+parseInt(ag.canvas.css("left"))-ai.width()/2,ah=ap+parseInt(ag.canvas.css("top"))+7;ai.css("left",aj+"px").css("top",ah+"px")}else{if(!ar.isPropagationStopped()){ar.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ar)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var i=function(ai,ag,af,ah,aj,ak){q.call(this,ai,ag,af,{},"draghandle");this.data_url=(aj?aj:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ak?ak:L);this.dataset_check_url=converted_datasets_state_url;if(!i.id_counter){i.id_counter=0}this.id=i.id_counter++;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};p(i.prototype,q.prototype,{build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var af=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(af)}this.name_div=$("<div/>").addClass("track-name").appendTo(af).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return af},build_icons_div:function(){var aj=$("<div/>").css("float","left");this.mode_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Set display mode").addClass("icon-button chevron-expand").tipsy({gravity:"s"}).appendTo(aj);this.toggle_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Hide/show track content").addClass("icon-button toggle").tipsy({gravity:"s"}).appendTo(aj);this.settings_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Edit settings").addClass("icon-button settings-icon").tipsy({gravity:"s"}).appendTo(aj);this.overview_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Set as overview").addClass("icon-button overview-icon").tipsy({gravity:"s"}).appendTo(aj);this.filters_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Filters").addClass("icon-button filters-icon").tipsy({gravity:"s"}).appendTo(aj).hide();this.tools_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Tools").addClass("icon-button tools-icon").tipsy({gravity:"s"}).appendTo(aj).hide();this.remove_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Remove").addClass("icon-button remove-icon").tipsy({gravity:"s"}).appendTo(aj);var ag=this;if(ag.display_modes!==undefined){var al=(ag.config&&ag.config.values.mode?ag.config.values.mode:ag.display_modes[0]);ag.mode=al;this.mode_icon.attr("title","Set display mode (now: "+ag.mode+")");var ai={};for(var ah=0,af=ag.display_modes.length;ah<af;ah++){var ak=ag.display_modes[ah];ai[ak]=function(am){return function(){ag.change_mode(am);ag.icons_div.show();ag.container_div.mouseleave(function(){ag.icons_div.hide()})}}(ak)}make_popupmenu(this.mode_icon,ai)}this.toggle_icon.click(function(){if(ag.content_visible){ag.toggle_icon.addClass("toggle-expand").removeClass("toggle");ag.hide_contents();ag.content_visible=false}else{ag.toggle_icon.addClass("toggle").removeClass("toggle-expand");ag.content_visible=true;ag.show_contents()}});this.settings_icon.click(function(){var ao=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},am=function(){ag.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},an=function(ap){if((ap.keyCode||ap.which)===27){ao()}else{if((ap.keyCode||ap.which)===13){am()}}};$(window).bind("keypress.check_enter_esc",an);show_modal("Configure Track",ag.config.build_form(),{Cancel:ao,OK:am})});this.overview_icon.click(function(){ag.view.set_overview(ag)});this.filters_icon.click(function(){ag.filters_div.toggle();ag.filters_manager.reset_filters()});this.tools_icon.click(function(){ag.dynamic_tool_div.toggle();if(ag.dynamic_tool_div.is(":visible")){ag.set_name(ag.name+ag.tool_region_and_parameters_str())}else{ag.revert_name()}$(".tipsy").remove()});this.remove_icon.click(function(){$(".tipsy").remove();ag.remove()});return aj},hide_contents:function(){this.content_div.children().remove();this.content_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.content_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof ab){return"LabelTrack"}else{if(this instanceof A){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof W){return"ReadTrack"}else{if(this instanceof U){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}return""},init:function(){var af=this;af.enabled=false;af.tile_cache.clear();af.data_manager.clear();af.initial_canvas=undefined;af.content_div.css("height","auto");af.container_div.removeClass("nodata error pending");if(!af.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:af.hda_ldda,dataset_id:af.dataset_id,chrom:af.view.chrom},function(ag){if(!ag||ag==="error"||ag.kind==="error"){af.container_div.addClass("error");af.content_div.text(o);if(ag.message){var ah=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})});af.content_div.append(ah)}}else{if(ag==="no converter"){af.container_div.addClass("error");af.content_div.text(K)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){af.container_div.addClass("nodata");af.content_div.text(F)}else{if(ag==="pending"){af.container_div.addClass("pending");af.content_div.text(t);setTimeout(function(){af.init()},af.data_query_wait)}else{if(ag.status==="data"){if(ag.valid_chroms){af.valid_chroms=ag.valid_chroms;af.update_icons()}af.content_div.text(Y);if(af.view.chrom){af.content_div.text("");af.content_div.css("height",af.height_px+"px");af.enabled=true;$.when(af.predraw_init()).done(function(){af.container_div.removeClass("nodata error pending");af.request_draw()})}}}}}}});this.update_icons()},predraw_init:function(){}});var N=function(aj,ah,ag,ai,al,ak){i.call(this,aj,ah,ag,ai);var af=this,ah=af.view;m(af.container_div,af.drag_handle_class,".group",af);this.filters_manager=new aa(this,(al!==undefined?al:{}));this.filters_available=false;this.filters_visible=false;this.tool=(ak!==undefined&&obj_length(ak)>0?new r(this,ak):undefined);if(this.header_div){if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}};p(N.prototype,q.prototype,i.prototype,{copy:function(af){return new this.constructor(this.name,this.view,af,this.hda_ldda,this.dataset_id,this.prefs,this.filters,this.tool)},to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ag){var af=this;af.mode=ag;af.config.values.mode=ag;af.tile_cache.clear();af.request_draw();this.mode_icon.attr("title","Set display mode (now: "+af.mode+")");return af},update_icons:function(){var af=this;if(af.filters_available>0){af.filters_icon.show()}else{af.filters_icon.hide()}if(af.tool){af.tools_icon.show()}else{af.tools_icon.hide()}},_gen_tile_cache_key:function(ag,ah,af){return ag+"_"+ah+"_"+af},request_draw:function(ag,af){this.view.request_redraw(false,ag,af,this)},_draw:function(ah,ap){if(!this.enabled){return}if(!this.content_visible){return}if(!(this instanceof A)&&(!this.dataset_id)){return}var ao=this.view.low,al=this.view.high,am=al-ao,ai=this.view.container.width(),at=ai/am,ak=this.view.resolution,ar=this.content_div;if(this.is_overview){ao=this.view.max_low;al=this.view.max_high;ak=Math.pow(C,Math.ceil(Math.log((view.max_high-view.max_low)/R)/Math.log(C)));at=ai/(view.max_high-view.max_low)}if(!ap){this.content_div.children().addClass("remove")}this.max_height=0;var ag=Math.floor(ao/ak/R);var an=true;var aq=[];var af=0;while((ag*R*ak)<al){tile=this.draw_helper(ah,ai,ag,ak,ar,at);if(tile){aq.push(tile)}else{an=false}ag+=1;af++}if(!ap){this.content_div.children(".remove").remove()}var aj=this;if(an){aj.postdraw_actions(aq,ai,at,ap)}},postdraw_actions:function(aj,ak,al,af){var ah=this;var ai=false;for(var ag=0;ag<aj.length;ag++){if(aj[ag].message){ai=true;break}}if(ai){for(var ag=0;ag<aj.length;ag++){tile=aj[ag];if(!tile.message){tile.canvas.css("padding-top",E)}}}},draw_helper:function(ag,ah,ai,al,ar,aw,at,am){var aj=this,aq=this._gen_tile_cache_key(ah,aw,ai),an=ai*R*al,av=an+R*al;var ao=(ag?undefined:aj.tile_cache.get(aq));if(ao){aj.show_tile(ao,ar,aw);return ao}var ap=function(ax){return("isResolved" in ax)};var ak=true;var af=aj.data_manager.get_data(an,av,aj.mode,al,aj.data_url_extra_params);if(ap(af)){ak=false}var au;if(view.reference_track&&aw>view.canvas_manager.char_width_px){au=view.reference_track.data_manager.get_data(an,av,aj.mode,al,view.reference_track.data_url_extra_params);if(ap(au)){ak=false}}if(ak){p(af,am);var ao=aj.draw_tile(af,aj.mode,al,ai,aw,au);if(ao!==undefined){aj.tile_cache.set(aq,ao);aj.show_tile(ao,ar,aw)}return ao}$.when(af,au).then(function(){view.request_redraw(false,false,false,aj)});return null},show_tile:function(ah,aj,ak){var ag=this,af=ah.canvas;ah.predisplay_actions();var ai=(ah.low-(this.is_overview?this.view.max_low:this.view.low))*ak;if(this.left_offset){ai-=this.left_offset}af.css({position:"absolute",top:0,left:ai,height:""});if(af.hasClass("remove")){af.removeClass("remove")}else{aj.append(af)}ag.max_height=Math.max(ag.max_height,af.height());ag.content_div.css("height",ag.max_height+"px");aj.children().css("height",ag.max_height+"px")},_get_tile_bounds:function(af,ag){var ai=af*R*ag,aj=R*ag,ah=(ai+aj<=this.view.max_high?ai+aj:this.view.max_high);return[ai,ah]},tool_region_and_parameters_str:function(ah,af,ai){var ag=this,aj=(ah!==undefined&&af!==undefined&&ai!==undefined?ah+":"+af+"-"+ai:"all");return" - region=["+aj+"], parameters=["+ag.tool.get_param_values().join(", ")+"]"},init_for_tool_data:function(){this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.predraw_init=function(){var ag=this;var af=function(){if(ag.data_manager.size()===0){setTimeout(af,300)}else{ag.data_url=default_data_url;ag.data_query_wait=L;ag.dataset_state_url=converted_datasets_state_url;$.getJSON(ag.dataset_state_url,{dataset_id:ag.dataset_id,hda_ldda:ag.hda_ldda},function(ah){})}};af()}}});var ab=function(ag,af){i.call(this,"label",ag,af,false,{});this.container_div.addClass("label-track")};p(ab.prototype,i.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ah=this.view,ai=ah.high-ah.low,al=Math.floor(Math.pow(10,Math.floor(Math.log(ai)/Math.log(10)))),af=Math.floor(ah.low/al)*al,aj=this.view.container.width(),ag=$("<div style='position: relative; height: 1.3em;'></div>");while(af<ah.high){var ak=(af-ah.low)/ai*aj;ag.append($("<div class='label'>"+commatize(af)+"</div>").css({position:"absolute",left:ak-1}));af+=al}this.content_div.children(":first").remove();this.content_div.append(ag)}});var A=function(af){N.call(this,"reference",af,{content_div:af.top_labeltrack},{});af.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:af.dbkey};this.data_manager=new I(B,this,false);this.tile_cache=new c(u)};p(A.prototype,q.prototype,N.prototype,{build_header_div:function(){},init:function(){this.enabled=true},draw_tile:function(ap,al,ak,ag,aq){var aj=this,ah=R*ak;if(aq>this.view.canvas_manager.char_width_px){if(ap.data===null){aj.content_div.css("height","0px");return}var ai=this.view.canvas_manager.new_canvas();var ao=ai.getContext("2d");ai.width=Math.ceil(ah*aq+aj.left_offset);ai.height=aj.height_px;ao.font=ao.canvas.manager.default_font;ao.textAlign="center";ap=ap.data;for(var am=0,an=ap.length;am<an;am++){var af=Math.round(am*aq);ao.fillText(ap[am],af+aj.left_offset,10)}return new b(aj,ag,ak,ai,ap)}this.content_div.css("height","0px")}});var j=function(ak,ai,ah,al,af,aj){var ag=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";N.call(this,ak,ai,ah,aj);this.min_height_px=16;this.max_height_px=400;this.height_px=32;this.hda_ldda=al;this.dataset_id=af;this.original_dataset_id=af;this.data_manager=new S(B,this);this.tile_cache=new c(u);this.left_offset=0;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:aj,onchange:function(){ag.set_name(ag.prefs.name);ag.vertical_range=ag.prefs.max_value-ag.prefs.min_value;$("#linetrack_"+ag.dataset_id+"_minval").text(ag.prefs.min_value);$("#linetrack_"+ag.dataset_id+"_maxval").text(ag.prefs.max_value);ag.tile_cache.clear();ag.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};p(j.prototype,q.prototype,N.prototype,{add_resize_handle:function(){var af=this;var ai=false;var ah=false;var ag=$("<div class='track-resize'>");$(af.container_div).hover(function(){if(af.content_visible){ai=true;ag.show()}},function(){ai=false;if(!ah){ag.hide()}});ag.hide().bind("dragstart",function(aj,ak){ah=true;ak.original_height=$(af.content_div).height()}).bind("drag",function(ak,al){var aj=Math.min(Math.max(al.original_height+al.deltaY,af.min_height_px),af.max_height_px);$(af.content_div).css("height",aj);af.height_px=aj;af.request_draw(true)}).bind("dragend",function(aj,ak){af.tile_cache.clear();ah=false;if(!ai){ag.hide()}af.config.values.height=af.height_px}).appendTo(af.container_div)},predraw_init:function(){var af=this;af.vertical_range=undefined;return $.getJSON(af.data_url,{stats:true,chrom:af.view.chrom,low:null,high:null,hda_ldda:af.hda_ldda,dataset_id:af.dataset_id},function(ag){af.container_div.addClass("line-track");var aj=ag.data;if(isNaN(parseFloat(af.prefs.min_value))||isNaN(parseFloat(af.prefs.max_value))){var ah=aj.min;var al=aj.max;ah=Math.floor(Math.min(0,Math.max(ah,aj.mean-2*aj.sd)));al=Math.ceil(Math.max(0,Math.min(al,aj.mean+2*aj.sd)));af.prefs.min_value=ah;af.prefs.max_value=al;$("#track_"+af.dataset_id+"_minval").val(af.prefs.min_value);$("#track_"+af.dataset_id+"_maxval").val(af.prefs.max_value)}af.vertical_range=af.prefs.max_value-af.prefs.min_value;af.total_frequency=aj.total_frequency;af.container_div.find(".yaxislabel").remove();var ak=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_minval").text(Z(af.prefs.min_value,3));var ai=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_maxval").text(Z(af.prefs.max_value,3));ai.css({position:"absolute",top:"24px",left:"10px"});ai.prependTo(af.container_div);ak.css({position:"absolute",bottom:"2px",left:"10px"});ak.prependTo(af.container_div)})},draw_tile:function(ar,ak,aj,ah,aq){if(this.vertical_range===undefined){return}var af=this._get_tile_bounds(ah,aj),al=af[0],ap=af[1],ag=Math.ceil((ap-al)*aq),an=this.height_px;var ai=this.view.canvas_manager.new_canvas();ai.width=ag,ai.height=an;var ao=ai.getContext("2d");var am=new M.LinePainter(ar.data,al,ap,this.prefs,ak);am.draw(ao,ag,an);return new b(this.track,ah,aj,ai,ar.data)}});var e=function(af,al,ag,ak,an,am,ai,aj){var ah=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];N.call(this,af,al,ag,am,ai,aj);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:am,onchange:function(){ah.set_name(ah.prefs.name);ah.tile_cache.clear();ah.set_painter_from_config();ah.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=ak;this.dataset_id=an;this.original_dataset_id=an;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new S(20,this);this.left_offset=200;this.set_painter_from_config()};p(e.prototype,q.prototype,N.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style=="arcs"){this.painter=M.ArcLinkedFeaturePainter}else{this.painter=M.LinkedFeaturePainter}},postdraw_actions:function(av,af,aw,au){N.prototype.postdraw_actions.call(this,av,au);var ai=this;if(au){var ak=ai.content_div.children();var al=false;for(var aj=ak.length-1,ap=0;aj>=ap;aj--){var ah=$(ak[aj]);if(al){ah.remove()}else{if(ah.children().length!==0){al=true}}}}if(ai.mode=="Histogram"){var ao=-1;for(var aj=0;aj<av.length;aj++){var at=av[aj].max_val;if(at>ao){ao=at}}for(var aj=0;aj<av.length;aj++){var ar=av[aj];if(ar.max_val!==ao){ar.canvas.remove();ai.draw_helper(true,af,ar.index,ar.resolution,ar.canvas.parent(),aw,[],{max:ao})}}}if(ai.filters_manager){var ag=ai.filters_manager.filters;for(var an=0;an<ag.length;an++){ag[an].update_ui_elt()}var am=false,aq;for(var aj=0;aj<av.length;aj++){if(av[aj].data.length){aq=av[aj].data[0];for(var an=0;an<ag.length;an++){if(ag[an].applies_to(aq)){am=true;break}}}}if(ai.filters_available!==am){ai.filters_available=am;if(!ai.filters_available){ai.filters_div.hide()}ai.update_icons()}}},update_auto_mode:function(af){var af;if(this.mode=="Auto"){if(af=="no_detail"){af="feature spans"}else{if(af=="summary_tree"){af="coverage histogram"}}this.mode_icon.attr("title","Set display mode (now: Auto/"+af+")")}},incremental_slots:function(aj,ag,ai){var ah=this.view.canvas_manager.dummy_context,af=this.inc_slots[aj];if(!af||(af.mode!==ai)){af=new (s.FeatureSlotter)(aj,ai==="Pack",z,function(ak){return ah.measureText(ak)});af.mode=ai;this.inc_slots[aj]=af}return af.slot_features(ag)},get_summary_tree_data:function(aj,am,ah,av){if(av>ah-am){av=ah-am}var aq=Math.floor((ah-am)/av),au=[],ai=0;var ak=0,al=0,ap,at=0,an=[],ar,ao;var ag=function(ay,ax,az,aw){ay[0]=ax+az*aw;ay[1]=ax+(az+1)*aw};while(at<av&&ak!==aj.length){var af=false;for(;at<av&&!af;at++){ag(an,am,at,aq);for(al=ak;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){af=true;break}}if(af){break}}data_start_index=al;au[au.length]=ar=[an[0],0];for(;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){ar[1]++}else{break}}if(ar[1]>ai){ai=ar[1]}at++}return{max:ai,delta:aq,data:au}},draw_tile:function(au,ax,aB,aF,ap,ai){var ay=this,ak=ay._get_tile_bounds(aF,aB),aI=ak[0],ag=ak[1],aw=ag-aI,az=Math.ceil(aw*ap),aO=25,aj=this.left_offset,av,al;if(ax==="Auto"){if(au.dataset_type==="summary_tree"){ax=au.dataset_type}else{if(au.extra_info==="no_detail"||ay.is_overview){ax="no_detail"}else{var aN=au.data;if(this.view.high-this.view.low>J){ax="Squish"}else{ax="Pack"}}}this.update_auto_mode(ax)}if(ax==="summary_tree"||ax==="Histogram"){al=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var af=$("<div />").addClass("yaxislabel");af.text(au.max);af.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});af.prependTo(this.container_div);var ah=this.view.canvas_manager.new_canvas();ah.width=az+aj;ah.height=al+T;if(au.dataset_type!="summary_tree"){var aq=this.get_summary_tree_data(au.data,aI,ag,200);if(au.max){aq.max=au.max}au=aq}var aK=new M.SummaryTreePainter(au,aI,ag,this.prefs);var aA=ah.getContext("2d");aA.translate(aj,T);aK.draw(aA,az,al);return new k(ay,aF,aB,ah,au.data,au.max)}var av,an=1;if(ax==="no_detail"||ax==="Squish"||ax==="Pack"){an=this.incremental_slots(ap,au.data,ax);av=this.inc_slots[ap].slots}var ao=[];if(au.data){var ar=this.filters_manager.filters;for(var aC=0,aE=au.data.length;aC<aE;aC++){var am=au.data[aC];var aD=false;var at;for(var aH=0,aM=ar.length;aH<aM;aH++){at=ar[aH];at.update_attrs(am);if(!at.keep(am)){aD=true;break}}if(!aD){ao.push(am)}}}var aL=(this.filters_manager.alpha_filter?new D(this.filters_manager.alpha_filter):null);var aJ=(this.filters_manager.height_filter?new D(this.filters_manager.height_filter):null);var aK=new (this.painter)(ao,aI,ag,this.prefs,ax,aL,aJ,ai);var al=Math.max(ad,aK.get_required_height(an,az));var ah=this.view.canvas_manager.new_canvas();var aG=null;ah.width=az+aj;ah.height=al;var aA=ah.getContext("2d");aA.fillStyle=this.prefs.block_color;aA.font=aA.canvas.manager.default_font;aA.textAlign="right";this.container_div.find(".yaxislabel").remove();if(au.data){aA.translate(aj,0);aG=aK.draw(aA,az,al,av);aG.translation=-aj}return new P(ay,aF,aB,ah,au.data,ax,au.message,aG)}});var U=function(ak,ah,ag,am,af,aj,al,ai){e.call(this,ak,ah,ag,am,af,aj,al,ai);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:aj,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter};p(U.prototype,q.prototype,N.prototype,e.prototype);var W=function(af,ak,ag,aj,an,am,ah){e.call(this,af,ak,ag,aj,an,am,ah);var ai=get_random_color(),al=get_random_color([ai,"#ffffff"]);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ai},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:al},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:am,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter;this.update_icons()};p(W.prototype,q.prototype,N.prototype,e.prototype);X.View=ac;X.DrawableGroup=Q;X.LineTrack=j;X.FeatureTrack=e;X.ReadTrack=W;X.VcfTrack=U};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(F,G){for(var E=0;E<=z;E++){var C=false,H=h[E];if(H!==undefined){for(var B=0,D=H.length;B<D;B++){var i=H[B];if(G>i[0]&&F<i[1]){C=true;break}}}if(!C){return E}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(i,x){var u=i("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y<E;y++,A+=J,G+=H){if(y%2!==0){continue}I.fillRect(A,G,D,1)}};var q=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var d=function(y){this.default_val=(y?y:1)};d.prototype.gen_val=function(y){return this.default_val};var l=function(A,C,y,z,B){this.data=A;this.view_start=C;this.view_end=y;this.prefs=u({},this.default_prefs,z);this.mode=B};l.prototype.default_prefs={};var v=function(A,C,y,z,B){l.call(this,A,C,y,z,B)};v.prototype.default_prefs={show_counts:false};v.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var b=function(y,C,E,F,A){l.call(this,y,C,E,F,A);if(this.prefs.min_value===undefined){var G=Infinity;for(var z=0,B=this.data.length;z<B;z++){G=Math.min(G,this.data[z][1])}this.prefs.min_value=G}if(this.prefs.max_value===undefined){var D=-Infinity;for(var z=0,B=this.data.length;z<B;z++){D=Math.max(D,this.data[z][1])}this.prefs.max_value=D}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var m=function(y){this.feature_positions={};this.slot_height=y;this.translation=0;this.y_translation=0};m.prototype.map_feature_data=function(z,B,y,A){if(!this.feature_positions[B]){this.feature_positions[B]=[]}this.feature_positions[B].push({data:z,x_start:y,x_end:A})};m.prototype.get_feature_data=function(z,D){var C=Math.floor((D-this.y_translation)/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var o=function(A,D,y,z,C,E,B){l.call(this,A,D,y,z,C);this.alpha_scaler=(E?E:new d());this.height_scaler=(B?B:new d())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(A,z){var y=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){y=A*y_scale}return y+this.get_top_padding(z)+this.get_bottom_padding(z)},get_top_padding:function(y){return 0},get_bottom_padding:function(y){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(K,I,G,F){var Q=this.data,D=this.view_start,M=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var H=this.view_end-this.view_start,E=I/H,L=this.get_row_height(),P=new m(L),B;for(var N=0,O=Q.length;N<O;N++){var A=Q[N],C=A[0],J=A[1],y=A[2],z=(F&&F[C]!==undefined?F[C]:null);if((J<M&&y>D)&&(this.mode=="Dense"||z!==null)){B=this.draw_element(K,this.mode,A,z,D,M,E,L,I);P.map_feature_data(A,z,B[0],B[1])}}K.restore();P.y_translation=this.get_top_padding(I);return P},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.");return[0,0]}});var c=10,h=3,k=5,w=10,f=1,s=9,e=3,a=9,j=2,g="#ccc";var r=function(A,D,y,z,C,E,B){o.call(this,A,D,y,z,C,E,B);this.draw_background_connector=true;this.draw_individual_connectors=false};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=c}else{if(z==="no_detail"){y=h}else{if(z==="Squish"){y=k}else{y=w}}}return y},draw_element:function(M,D,X,H,O,aj,an,ap,y){var T=X[0],al=X[1],ad=X[2],Q=X[3],ae=Math.floor(Math.max(0,(al-O)*an)),N=Math.ceil(Math.min(y,Math.max(0,(ad-O)*an))),ac=ae,ao=N,aa=(D==="Dense"?0:(0+H))*ap+this.get_top_padding(y),L,ah,R=null,ar=null,B=this.prefs.block_color,ag=this.prefs.label_color;M.globalAlpha=this.alpha_scaler.gen_val(X);if(D==="Dense"){H=1}if(D==="no_detail"){M.fillStyle=B;M.fillRect(ae,aa+5,N-ae,f)}else{var K=X[4],Z=X[5],af=X[6],C=X[7],V=true;if(Z&&af){R=Math.floor(Math.max(0,(Z-O)*an));ar=Math.ceil(Math.min(y,Math.max(0,(af-O)*an)))}var am,U;if(D==="Squish"){am=1;U=e;V=false}else{if(D==="Dense"){am=5;U=s}else{am=5;U=a}}if(!C){M.fillStyle=B;M.fillRect(ae,aa+1,N-ae,U);if(K&&V){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}M.fillRect(ae,aa+1,N-ae,U)}}else{var J,W;if(D==="Squish"||D==="Dense"){J=aa+Math.floor(e/2)+1;W=1}else{if(K){J=aa;W=U}else{J+=(e/2)+1;W=1}}if(this.draw_background_connector){if(D==="Squish"||D==="Dense"){M.fillStyle=g}else{if(K){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand")}}}else{M.fillStyle=g}}M.fillRect(ae,J,N-ae,W)}var E;for(var ak=0,A=C.length;ak<A;ak++){var F=C[ak],z=Math.floor(Math.max(0,(F[0]-O)*an)),Y=Math.ceil(Math.min(y,Math.max((F[1]-O)*an))),S,ab;if(z>Y){continue}M.fillStyle=B;M.fillRect(z,aa+(U-am)/2+1,Y-z,am);if(R!==undefined&&af>Z&&!(z>ar||Y<R)){var ai=Math.max(z,R),I=Math.min(Y,ar);M.fillRect(ai,aa+1,I-ai,U);if(C.length==1&&D=="Pack"){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}if(ai+14<I){ai+=2;I-=2}M.fillRect(ai,aa+1,I-ai,U)}}if(this.draw_individual_connectors&&S){this.draw_connector(M,S,ab,z,Y,aa)}S=z;ab=Y}if(D==="Pack"){M.globalAlpha=1;M.fillStyle="white";var G=this.height_scaler.gen_val(X),P=Math.ceil(U*G),aq=Math.round((U-P)/2);if(G!==1){M.fillRect(ae,J+1,N-ae,aq);M.fillRect(ae,J+U-aq+1,N-ae,aq)}}}M.globalAlpha=1;if(D==="Pack"&&al>O){M.fillStyle=ag;if(O===0&&ae-M.measureText(Q).width<0){M.textAlign="left";M.fillText(Q,N+j,aa+8);ao+=M.measureText(Q).width+j}else{M.textAlign="right";M.fillText(Q,ae-j,aa+8);ac-=M.measureText(Q).width+j}}}M.globalAlpha=1;return[ac,ao]}});var t=function(B,E,y,A,D,F,C,z){o.call(this,B,E,y,A,D,F,C);this.ref_seq=(z?z.data:null)};u(t.prototype,o.prototype,{get_row_height:function(){var y,z=this.mode;if(z==="Dense"){y=c}else{if(z==="Squish"){y=k}else{y=w;if(this.prefs.show_insertions){y*=2}}}return y},draw_read:function(K,A,ag,V,L,aa,ad,C,B,M){K.textAlign="center";var J=this,R=[L,aa],Z=0,W=0,D=0,F=K.canvas.manager.char_width_px,y=(B==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var O=[];if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){D=Math.round(ag/2)}if(!C){C=[[0,M.length]]}for(var G=0,I=C.length;G<I;G++){var z=C[G],E="MIDNSHP=X"[z[0]],S=z[1];if(E==="H"||E==="S"){Z-=S}var U=ad+Z,Y=Math.floor(Math.max(0,(U-L)*ag)),ab=Math.floor(Math.max(0,(U+S-L)*ag));if(Y===ab){ab+=1}switch(E){case"H":break;case"S":case"M":case"=":if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(D>0){K.fillStyle=y;K.fillRect(Y-D,V+1,ab-Y,9);K.fillStyle=g;for(var af=0,H=N.length;af<H;af++){if(this.prefs.show_differences&&this.ref_seq){var P=this.ref_seq[U-L+af];if(!P||P.toLowerCase()===N[af].toLowerCase()){continue}}if(U+af>=L&&U+af<=aa){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X,V+9)}}}else{K.fillStyle=y;K.fillRect(Y,V+4,ab-Y,e)}}W+=S;Z+=S;break;case"N":K.fillStyle=g;K.fillRect(Y-D,V+5,ab-Y,1);Z+=S;break;case"D":K.fillStyle="red";K.fillRect(Y-D,V+4,ab-Y,3);Z+=S;break;case"P":break;case"I":var ah=Y-D;if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(this.prefs.show_insertions){var T=Y-(ab-Y)/2;if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){K.fillStyle="yellow";K.fillRect(T-D,V-9,ab-Y,9);O[O.length]={type:"triangle",data:[ah,V+4,5]};K.fillStyle=g;switch(compute_overlap([U,U+S],R)){case (OVERLAP_START):N=N.slice(L-U);break;case (OVERLAP_END):N=N.slice(0,U-aa);break;case (CONTAINED_BY):break;case (CONTAINS):N=N.slice(L-U,U-aa);break}for(var af=0,H=N.length;af<H;af++){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X-(ab-Y)/2,V)}}else{K.fillStyle="yellow";K.fillRect(T,V+(this.mode!=="Dense"?2:5),ab-Y,(A!=="Dense"?e:s))}}else{if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){O.push({type:"text",data:[N.length,ah,V+9]})}else{}}}W+=S;break;case"X":W+=S;break}}K.fillStyle="yellow";var Q,ai,ae;for(var ac=0;ac<O.length;ac++){Q=O[ac];ai=Q.type;ae=Q.data;if(ai==="text"){K.save();K.font="bold "+K.font;K.fillText(ae[0],ae[1],ae[2]);K.restore()}else{if(ai=="triangle"){q(K,ae[0],ae[1],ae[2])}}}},draw_element:function(R,M,E,B,U,z,I,S,P){var H=E[0],Q=E[1],A=E[2],J=E[3],D=Math.floor(Math.max(0,(Q-U)*I)),F=Math.ceil(Math.min(P,Math.max(0,(A-U)*I))),C=(M==="Dense"?0:(0+B))*S,G=this.prefs.label_color,O=0;if((M==="Pack"||this.mode==="Auto")&&I>R.canvas.manager.char_width_px){var O=Math.round(I/2)}if(E[5] instanceof Array){var N=Math.floor(Math.max(0,(E[4][0]-U)*I)),L=Math.ceil(Math.min(P,Math.max(0,(E[4][1]-U)*I))),K=Math.floor(Math.max(0,(E[5][0]-U)*I)),y=Math.ceil(Math.min(P,Math.max(0,(E[5][1]-U)*I)));if(E[4][1]>=U&&E[4][0]<=z&&E[4][2]){this.draw_read(R,M,I,C,U,z,E[4][0],E[4][2],E[4][3],E[4][4])}if(E[5][1]>=U&&E[5][0]<=z&&E[5][2]){this.draw_read(R,M,I,C,U,z,E[5][0],E[5][2],E[5][3],E[5][4])}if(K>L){R.fillStyle=g;p(R,L-O,C+5,K-O,C+5)}}else{this.draw_read(R,M,I,C,U,z,Q,E[4],E[5],E[6])}if(M==="Pack"&&Q>U&&J!=="."){R.fillStyle=this.prefs.label_color;var T=1;if(T===0&&D-R.measureText(J).width<0){R.textAlign="left";R.fillText(J,F+j-O,C+8)}else{R.textAlign="right";R.fillText(J,D-j-O,C+8)}}return[0,0]}});var n=function(A,D,y,z,C,E,B){r.call(this,A,D,y,z,C,E,B);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};u(n.prototype,o.prototype,r.prototype,{calculate_longest_feature_length:function(){var z=0;for(var C=0,y=this.data.length;C<y;C++){var B=this.data[C],A=B[1],D=B[2];z=Math.max(z,D-A)}return z},get_top_padding:function(z){var y=this.view_end-this.view_start,A=z/y;return Math.min(128,Math.ceil((this.longest_feature_length/2)*A))},draw_connector:function(G,B,F,H,E,D){var y=(F+H)/2,C=H-y;var A=Math.PI,z=0;if(C>0){G.beginPath();G.arc(y,D,H-y,Math.PI,0);G.stroke()}}});x.Scaler=d;x.SummaryTreePainter=v;x.LinePainter=b;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.ArcLinkedFeaturePainter=n};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window);
\ No newline at end of file
diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index 28633f8eecf..2740f334bf5 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -2318,10 +2318,43 @@ var SummaryTreeTile = function(track, index, resolution, canvas, data, max_val)
 extend(SummaryTreeTile.prototype, Tile.prototype);
 
 var FeatureTrackTile = function(track, index, resolution, canvas, data, mode, message, feature_mapper) {
+    // Attribute init.
     Tile.call(this, track, index, resolution, canvas, data);
     this.mode = mode;
     this.message = message;
     this.feature_mapper = feature_mapper;
+    
+    // Add message + action icons to tile's "canvas" TODO: rename canvas to element/html or something similar.
+    if (this.message) {
+        var 
+            canvas = this.canvas.children()[0],
+            message_div = $("<div/>").addClass("tile-message").text(this.message).
+                            // -1 to account for border.
+                            css({'height': ERROR_PADDING-1, 'width': canvas.width}).prependTo(this.canvas),
+            more_down_icon = $("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(message_div),
+            more_across_icon = $("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(message_div);
+
+        // Set up actions for icons.
+        more_down_icon.click(function() {
+            // Mark tile as stale, request more data, and redraw track.
+            tile.stale = true;
+            track.data_manager.get_more_data(tile.low, tile.high, track.mode, tile.resolution, {}, track.data_manager.DEEP_DATA_REQ);
+            track.request_draw();
+        }).dblclick(function(e) {
+            // Do not propogate as this would normally zoom in.
+            e.stopPropagation();
+        });
+
+        more_across_icon.click(function() {
+            // Mark tile as stale, request more data, and redraw track.
+            tile.stale = true;
+            track.data_manager.get_more_data(tile.low, tile.high, track.mode, tile.resolution, {}, track.data_manager.BROAD_DATA_REQ);
+            track.request_draw();
+        }).dblclick(function(e) {
+            // Do not propogate as this would normally zoom in.
+            e.stopPropagation();
+        });
+    }
 };
 extend(FeatureTrackTile.prototype, Tile.prototype);
 
@@ -2852,7 +2885,8 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
             // w_scale units are pixels per base.
             w_scale = width / range,
             resolution = this.view.resolution,
-            parent_element = $("<div style='position: relative;'></div>");
+            // FIXME: parent element is not currently needed, but it may be useful for multitrack drawing.
+            parent_element = this.content_div;
 
         // For overview, adjust high, low, resolution, and w_scale.
         if (this.is_overview) {
@@ -2861,9 +2895,19 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
             resolution = Math.pow(RESOLUTION, Math.ceil( Math.log( (view.max_high - view.max_low) / DENSITY ) / Math.log(RESOLUTION) ));
             w_scale = width / (view.max_high - view.max_low);
         }
+
+        //
+        // Method for moving and/or removing tiles:
+        // (a) mark all elements for removal using class 'remove'
+        // (b) during tile drawing/placement, remove class for elements that are moved; 
+        //     this occurs in show_tile()
+        // (c) after drawing all tiles, remove elements still marked for removal 
+        //     (i.e. that still have class 'remove').
+        //
         
-        if (!clear_after) { this.content_div.children().remove(); }
-        this.content_div.append( parent_element );
+        // Step (a) for (re)moving tiles.
+        if (!clear_after) { this.content_div.children().addClass("remove"); }
+
         this.max_height = 0;
         // Index of first tile that overlaps visible region
         var tile_index = Math.floor( low / resolution / DENSITY );
@@ -2882,6 +2926,9 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
             tile_index += 1;
             tile_count++;
         }
+        
+        // Step (c) for (re)moving tiles.
+        if (!clear_after) { this.content_div.children(".remove").remove(); }
                 
         // Use interval to check if tiles have been drawn. When all tiles are drawn, call post-draw actions.
         var track = this;
@@ -2978,65 +3025,36 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
         return null;
     }, 
     /**
-     * Show track tile and perform associated actions.
+     * Show track tile and perform associated actions. Showing tile may actually move
+     * an existing tile rather than reshowing it.
      */
     show_tile: function(tile, parent_element, w_scale) {
-        // Readability.
         var 
             track = this,
-            canvas = tile.canvas,
-            tile_element = canvas;
+            tile_element = tile.canvas;
         
         //
-        // If tile has message, display message and button to show more data.
-        // TODO: need to handle other messages, not assume message === show more data.
-        //
-        if (tile.message) {
-            var 
-                container_div = $("<div/>"),
-                message_div = $("<div/>").addClass("tile-message").text(tile.message).
-                                // -1 to account for border.
-                                css({'height': ERROR_PADDING-1, 'width': tile.canvas.width}).appendTo(container_div),
-                more_down_icon = $("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(message_div),
-                more_across_icon = $("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(message_div);
-            container_div.append(canvas);
-            tile_element = container_div;
-            
-            // Set up actions for icons.
-            more_down_icon.click(function() {
-                // Mark tile as stale, request more data, and redraw track.
-                tile.stale = true;
-                track.data_manager.get_more_data(tile.low, tile.high, track.mode, tile.resolution, {}, track.data_manager.DEEP_DATA_REQ);
-                track.request_draw();
-            }).dblclick(function(e) {
-                // Do not propogate as this would normally zoom in.
-                e.stopPropagation();
-            });
-            
-            more_across_icon.click(function() {
-                // Mark tile as stale, request more data, and redraw track.
-                tile.stale = true;
-                track.data_manager.get_more_data(tile.low, tile.high, track.mode, tile.resolution, {}, track.data_manager.BROAD_DATA_REQ);
-                track.request_draw();
-            }).dblclick(function(e) {
-                // Do not propogate as this would normally zoom in.
-                e.stopPropagation();
-            });
-        }
-        
-        //
-        // Show tile element.
+        // Show/move tile element.
         //
         
         tile.predisplay_actions();
       
-        // Position tile element, recalculate left position at display time
+        // Position tile element based on current viewport.
         var left = ( tile.low - (this.is_overview? this.view.max_low : this.view.low) ) * w_scale;
         if (this.left_offset) {
             left -= this.left_offset;
         }
         tile_element.css({ position: 'absolute', top: 0, left: left, height: '' });
-        parent_element.append(tile_element);
+        
+        if ( tile_element.hasClass("remove") ) {
+            // Step (b) for (re)moving tiles. See _draw() function for description of algorithm
+            // for removing tiles.
+            tile_element.removeClass("remove");
+        }
+        else {
+            // Showing new tile.
+            parent_element.append(tile_element);
+        }
         
         // Set track height.
         track.max_height = Math.max(track.max_height, tile_element.height());

From e7c4d8557b28286ffe11f87a07974ba2a5d1f160 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Fri, 18 Nov 2011 13:48:06 -0500
Subject: [PATCH 218/362] Update GenomeSpace import from file browser tool to
 use new versioned API.

---
 tools/data_source/genomespace_file_browser.py | 76 +++++++++----------
 .../genomespace_file_browser_dev.xml          |  4 +-
 2 files changed, 37 insertions(+), 43 deletions(-)

diff --git a/tools/data_source/genomespace_file_browser.py b/tools/data_source/genomespace_file_browser.py
index ba46af26117..73687c43990 100644
--- a/tools/data_source/genomespace_file_browser.py
+++ b/tools/data_source/genomespace_file_browser.py
@@ -8,32 +8,16 @@ import pkg_resources
 pkg_resources.require( "simplejson" )
 import simplejson
 
+GENOMESPACE_API_VERSION_STRING = "v1.0"
+GENOMESPACE_SERVER_URL_PROPERTIES = "http://www.genomespace.org/sites/genomespacefiles/config/serverurl.properties"
+
 CHUNK_SIZE = 2**20 #1mb
 
 DEFAULT_GALAXY_EXT = "data"
 
 #genomespace format identifier is the URL
-GENOMESPACE_FORMAT_IDENTIFIER_TO_GENOMESPACE_EXT = { 'http://www.genomespace.org/datamanager/dataformat/res/0.0.0': 'res', 
-                                               'http://www.genomespace.org/datamanager/dataformat/cbs/0.0.0': 'CBS', 
-                                               'http://www.genomespace.org/datamanager/dataformat/lowercasetxt/0.0.0': 'lowercasetxt', 
-                                               'http://www.genomespace.org/datamanager/dataformat/gff/0.0.0': 'GFF', 
-                                               'http://www.genomespace.org/datamanager/dataformat/reversedtxt/0.0.0': 'reversedtxt', 
-                                               'http://www.genomespace.org/datamanager/dataformat/gxp/0.0.0': 'gxp', 
-                                               'http://www.genomespace.org/datamanager/dataformat/unknown/0.0.0': 'unknown', 
-                                               'http://www.genomespace.org/datamanager/dataformat/gtf/0.0.0': 'GTF', 
-                                               'http://www.genomespace.org/datamanager/dataformat/cn/0.0.0': 'cn', 
-                                               'http://www.genomespace.org/datamanager/dataformat/gct/0.0.0': 'gct', 
-                                               'http://www.genomespace.org/datamanager/dataformat/nowhitespace/0.0.0': 'nowhitespace', 
-                                               'http://www.genomespace.org/datamanager/dataformat/gistic/0.0.0': 'GISTIC', 
-                                               'http://www.genomespace.org/datamanager/dataformat/rifles/0.0.0': 'rifles', 
-                                               'http://www.genomespace.org/datamanager/dataformat/bed/0.0.0': 'bed', 
-                                               'http://www.genomespace.org/datamanager/dataformat/txt/0.0.0': 'txt', 
-                                               'http://www.genomespace.org/datamanager/dataformat/uppercasetxt/0.0.0': 'uppercasetxt', 
-                                               'http://www.genomespace.org/datamanager/dataformat/xcn/0.0.0': 'xcn', 
-                                               'http://www.genomespace.org/datamanager/dataformat/gmt/0.0.0': 'gmt', 
-                                               'http://www.genomespace.org/datamanager/dataformat/genomicatab/0.0.0': 'genomicatab', 
-                                               'http://www.genomespace.org/datamanager/dataformat/lifes/0.0.0': 'lifes' }
-
+GENOMESPACE_FORMAT_IDENTIFIER_TO_GENOMESPACE_EXT = {} #TODO: fix this so it is not a global variable
+#TODO: we should use a better way to set up this mapping
 GENOMESPACE_EXT_TO_GALAXY_EXT = {'rifles': 'rifles', 
                                  'lifes': 'lifes', 
                                  'cn': 'cn', 
@@ -48,29 +32,13 @@ GENOMESPACE_EXT_TO_GALAXY_EXT = {'rifles': 'rifles',
                                  'reversedtxt': 'reversedtxt', 
                                  'nowhitespace': 'nowhitespace', 
                                  'unknown': 'unknown', 
-                                 'txt': 'txt', 'uppercasetxt': 
-                                 'uppercasetxt', 
+                                 'txt': 'txt', 
+                                 'uppercasetxt': 'uppercasetxt', 
                                  'GISTIC': 'gistic', 
                                  'GFF': 'gff', 
                                  'gmt': 'gmt', 
                                  'gct': 'gct'}
 
-'''
-https://dmdev.genomespace.org:8444/datamanager/dataformat/list
-from galaxy import eggs
-import pkg_resources
-pkg_resources.require( "simplejson" )
-import simplejson
-formats = simplejson.loads( '[{"name":"GISTIC","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/gistic\/0.0.0","fileExtension":"gistic"},{"name":"GFF","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/gff\/0.0.0","fileExtension":"seg"},{"name":"gct","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/gct\/0.0.0","fileExtension":"gct"},{"name":"lifes","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/lifes\/0.0.0","fileExtension":"lifes"},{"name":"GTF","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/gtf\/0.0.0","fileExtension":"gtf"},{"name":"rifles","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/rifles\/0.0.0","fileExtension":"rifles"},{"name":"CBS","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/cbs\/0.0.0","fileExtension":"cbs"},{"name":"unknown","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/unknown\/0.0.0"},{"name":"reversedtxt","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/reversedtxt\/0.0.0","fileExtension":"reversedtxt"},{"name":"res","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/res\/0.0.0","fileExtension":"res"},{"name":"cn","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/cn\/0.0.0","fileExtension":"cn"},{"name":"gmt","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/gmt\/0.0.0","fileExtension":"gmt"},{"name":"bed","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/bed\/0.0.0","fileExtension":"bed"},{"name":"gxp","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/gxp\/0.0.0","fileExtension":"gxp"},{"name":"uppercasetxt","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/uppercasetxt\/0.0.0","fileExtension":"uppertxt"},{"name":"lowercasetxt","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/lowercasetxt\/0.0.0","fileExtension":"lowertxt"},{"name":"genomicatab","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/genomicatab\/0.0.0","fileExtension":"tab"},{"name":"nowhitespace","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/nowhitespace\/0.0.0","fileExtension":"nowhitespace"},{"name":"xcn","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/xcn\/0.0.0","fileExtension":"xcn"},{"name":"txt","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/txt\/0.0.0","fileExtension":"txt"}]' )
-formats = [{"name":"GISTIC","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/gistic\/0.0.0","fileExtension":"gistic"},{"name":"GFF","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/gff\/0.0.0","fileExtension":"seg"},{"name":"gct","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/gct\/0.0.0","fileExtension":"gct"},{"name":"lifes","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/lifes\/0.0.0","fileExtension":"lifes"},{"name":"GTF","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/gtf\/0.0.0","fileExtension":"gtf"},{"name":"rifles","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/rifles\/0.0.0","fileExtension":"rifles"},{"name":"CBS","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/cbs\/0.0.0","fileExtension":"cbs"},{"name":"unknown","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/unknown\/0.0.0"},{"name":"reversedtxt","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/reversedtxt\/0.0.0","fileExtension":"reversedtxt"},{"name":"res","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/res\/0.0.0","fileExtension":"res"},{"name":"cn","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/cn\/0.0.0","fileExtension":"cn"},{"name":"gmt","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/gmt\/0.0.0","fileExtension":"gmt"},{"name":"bed","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/bed\/0.0.0","fileExtension":"bed"},{"name":"gxp","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/gxp\/0.0.0","fileExtension":"gxp"},{"name":"uppercasetxt","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/uppercasetxt\/0.0.0","fileExtension":"uppertxt"},{"name":"lowercasetxt","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/lowercasetxt\/0.0.0","fileExtension":"lowertxt"},{"name":"genomicatab","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/genomicatab\/0.0.0","fileExtension":"tab"},{"name":"nowhitespace","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/nowhitespace\/0.0.0","fileExtension":"nowhitespace"},{"name":"xcn","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/xcn\/0.0.0","fileExtension":"xcn"},{"name":"txt","version":"0.0.0","url":"http:\/\/www.genomespace.org\/datamanager\/dataformat\/txt\/0.0.0","fileExtension":"txt"}]
-GENOMESPACE_FORMAT_IDENTIFIER_TO_GALAXY_EXT = {}
-for format in formats:
-    GENOMESPACE_FORMAT_IDENTIFIER_TO_GALAXY_EXT[ format[ 'url' ] ] = format['name']
-
-print GENOMESPACE_FORMAT_IDENTIFIER_TO_GALAXY_EXT
-#do manual change to galaxy exts
-'''
-
 
 def chunk_write( source_stream, target_stream, source_method = "read", target_method="write" ):
     source_method = getattr( source_stream, source_method )
@@ -101,7 +69,28 @@ def get_galaxy_ext_from_genomespace_format_url( url_opener, file_format_url ):
         ext = DEFAULT_GALAXY_EXT
     return ext
 
-def download_from_genomespace_file_browser( json_parameter_file ):
+def get_genomespace_site_urls():
+    genomespace_sites = {}
+    for line in urllib2.urlopen( GENOMESPACE_SERVER_URL_PROPERTIES ).read().split( '\n' ):
+        line = line.rstrip()
+        if not line or line.startswith( "#" ):
+            continue
+        server, line = line.split( '.', 1 )
+        if server not in genomespace_sites:
+            genomespace_sites[server] = {}
+        line = line.split( "=", 1 )
+        genomespace_sites[server][line[0]] = line[1]
+    return genomespace_sites
+
+def set_genomespace_format_identifiers( url_opener, dm_site ):
+    gs_request = urllib2.Request( "%s/%s/dataformat/list" % ( dm_site, GENOMESPACE_API_VERSION_STRING ) )
+    gs_request.get_method = lambda: 'GET'
+    opened_gs_request = url_opener.open( gs_request )
+    genomespace_formats = simplejson.loads( opened_gs_request.read() )
+    for format in genomespace_formats:
+        GENOMESPACE_FORMAT_IDENTIFIER_TO_GENOMESPACE_EXT[ format['url'] ] = format['name']
+
+def download_from_genomespace_file_browser( json_parameter_file, genomespace_site ):
     json_params = simplejson.loads( open( json_parameter_file, 'r' ).read() )
     datasource_params = json_params.get( 'param_dict' )
     username = datasource_params.get( "gs-username", None )
@@ -111,6 +100,10 @@ def download_from_genomespace_file_browser( json_parameter_file ):
     dataset_id = json_params['output_data'][0]['dataset_id']
     hda_id = json_params['output_data'][0]['hda_id']
     url_opener = get_cookie_opener( username, token )
+    #load and set genomespace format ids to galaxy exts
+    genomespace_site_dict = get_genomespace_site_urls()[ genomespace_site ]
+    set_genomespace_format_identifiers( url_opener, genomespace_site_dict['dmServer'] )
+    
     file_url_prefix = "fileUrl"
     file_type_prefix = "fileFormat"
     metadata_parameter_file = open( json_params['job_config']['TOOL_PROVIDED_JOB_METADATA_FILE'], 'wb' )
@@ -149,6 +142,7 @@ if __name__ == '__main__':
     #Parse Command Line
     parser = optparse.OptionParser()
     parser.add_option( '-p', '--json_parameter_file', dest='json_parameter_file', action='store', type="string", default=None, help='json_parameter_file' )
+    parser.add_option( '-s', '--genomespace_site', dest='genomespace_site', action='store', type="string", default=None, help='genomespace_site' )
     (options, args) = parser.parse_args()
     
-    download_from_genomespace_file_browser( options.json_parameter_file )
+    download_from_genomespace_file_browser( options.json_parameter_file, options.genomespace_site )
diff --git a/tools/data_source/genomespace_file_browser_dev.xml b/tools/data_source/genomespace_file_browser_dev.xml
index 584f1603c66..d97bf96eb5c 100644
--- a/tools/data_source/genomespace_file_browser_dev.xml
+++ b/tools/data_source/genomespace_file_browser_dev.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool name="GenomeSpace import" id="genomespace_file_browser_dev" tool_type="data_source" add_galaxy_url="False" force_history_refresh="True" version="0.0.1">
-    <description>from file browser</description>
-    <command interpreter="python">genomespace_file_browser.py --json_parameter_file "${output}"</command>
+    <description>from file browser (development)</description>
+    <command interpreter="python">genomespace_file_browser.py --json_parameter_file "${output}" --genomespace_site "dev"</command>
     <inputs action="https://dmdev.genomespace.org:8444/datamanager/defaultdirectory" check_values="False" method="post"> 
         <display>go to GenomeSpace Data Manager </display>
         <param name="appCallbackUrl" type="baseurl" value="/tool_runner?tool_id=genomespace_file_browser_dev&amp;runtool_btn=Execute" />

From 62cf5b90c66d81613853614057a2f8f8802e2005 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Fri, 18 Nov 2011 13:56:19 -0500
Subject: [PATCH 219/362] Do not use route memory when creating URLs to
 metadata files.

---
 templates/root/history_common.mako | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/templates/root/history_common.mako b/templates/root/history_common.mako
index ebe46f6317b..e0585d871e3 100644
--- a/templates/root/history_common.mako
+++ b/templates/root/history_common.mako
@@ -13,7 +13,7 @@
                     to_ext=data.ext )}">Download Dataset</a>
                 <a>Additional Files</a>
             %for file_type in meta_files:
-                <a class="action-button" href="${h.url_for( controller='dataset', action='get_metadata_file', \
+                <a class="action-button" href="${h.url_for( controller='/dataset', action='get_metadata_file', \
                     hda_id=dataset_id, metadata_name=file_type )}">Download ${file_type}</a>
             %endfor
             </div>

From 30aaa2ce2d89642654d04547fb2dc94989e5a1e7 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Fri, 18 Nov 2011 14:04:29 -0500
Subject: [PATCH 220/362] Add disk_usage methods to tool shed's User model
 object - fixes server error when viewing User Preferences.

---
 lib/galaxy/webapps/community/config.py         | 1 +
 lib/galaxy/webapps/community/model/__init__.py | 8 ++++++++
 2 files changed, 9 insertions(+)

diff --git a/lib/galaxy/webapps/community/config.py b/lib/galaxy/webapps/community/config.py
index 2211959d532..5a820a18502 100644
--- a/lib/galaxy/webapps/community/config.py
+++ b/lib/galaxy/webapps/community/config.py
@@ -41,6 +41,7 @@ class Configuration( object ):
         self.cookie_path = kwargs.get( "cookie_path", "/" )
         # web API
         self.enable_api = string_as_bool( kwargs.get( 'enable_api', False ) )
+        self.enable_quotas = string_as_bool( kwargs.get( 'enable_quotas', False ) )
         self.datatypes_config = kwargs.get( 'datatypes_config_file', 'datatypes_conf.xml' )
         self.test_conf = resolve_path( kwargs.get( "test_conf", "" ), self.root )
         self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" )
diff --git a/lib/galaxy/webapps/community/model/__init__.py b/lib/galaxy/webapps/community/model/__init__.py
index f32862cdb04..1373ffe3ccb 100644
--- a/lib/galaxy/webapps/community/model/__init__.py
+++ b/lib/galaxy/webapps/community/model/__init__.py
@@ -26,6 +26,14 @@ class User( object ):
     def check_password( self, cleartext ):
         """Check if 'cleartext' matches 'self.password' when hashed."""
         return self.password == new_secure_hash( text_type=cleartext )
+    def get_disk_usage( self, nice_size=False ):
+        return 0
+    def set_disk_usage( self, bytes ):
+        pass
+    total_disk_usage = property( get_disk_usage, set_disk_usage )
+    @property
+    def nice_total_disk_usage( self ):
+        return 0
 
 class Group( object ):
     def __init__( self, name = None ):

From 5b603fcb02d0cc0d646c91c7269dd33c0a082470 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Fri, 18 Nov 2011 14:16:47 -0500
Subject: [PATCH 221/362] Closed branch updates-for-tophat-1.3.1+


From 1d6a2ebd5a0d9f9db32e65f9c063c23f44b8c2d5 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Fri, 18 Nov 2011 14:37:43 -0500
Subject: [PATCH 222/362] Update test data for cufflinks v1.1.0


From 77518b1cf14aed8f680982797a2f0d514093c652 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Fri, 18 Nov 2011 14:58:25 -0500
Subject: [PATCH 223/362] Update Cuffcompare test data to be compatible with
 v1.1.0


From 47403a20456143a1ccf79dc39c67cfcf7497feb3 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Fri, 18 Nov 2011 15:14:39 -0500
Subject: [PATCH 224/362] Update Cuffdiff test data to be compatible with
 v1.1.0

---
 tools/ngs_rna/cuffdiff_wrapper.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/ngs_rna/cuffdiff_wrapper.xml b/tools/ngs_rna/cuffdiff_wrapper.xml
index fd2701caa82..9f4f7e72171 100644
--- a/tools/ngs_rna/cuffdiff_wrapper.xml
+++ b/tools/ngs_rna/cuffdiff_wrapper.xml
@@ -164,7 +164,7 @@
                 <output name="cds_diff" file="cuffdiff_out11.txt"/>
                 <output name="cds_exp_fpkm_tracking" file="cuffdiff_out4.txt"/>
                 <output name="cds_fpkm_tracking" file="cuffdiff_out8.txt"/>
-                <output name="tss_groups_exp" file="cuffdiff_out3.txt"/>
+                <output name="tss_groups_exp" file="cuffdiff_out3.txt" lines_diff="200"/>
                 <output name="tss_groups_fpkm_tracking" file="cuffdiff_out7.txt"/>
                 <output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="200"/>
                 <output name="genes_fpkm_tracking" file="cuffdiff_out6.txt" lines_diff="200"/>

From 5e643a673c9a3d1c3a3734285505bad500e86026 Mon Sep 17 00:00:00 2001
From: Richard Burhans <burhans@bx.psu.edu>
Date: Fri, 18 Nov 2011 16:15:11 -0500
Subject: [PATCH 225/362] Bug fixes for the ctd tool

---
 tools/human_genome_variation/ctd.pl  |  4 ++--
 tools/human_genome_variation/ctd.xml | 11 ++++-------
 2 files changed, 6 insertions(+), 9 deletions(-)

diff --git a/tools/human_genome_variation/ctd.pl b/tools/human_genome_variation/ctd.pl
index a2a823f9111..644e0789870 100755
--- a/tools/human_genome_variation/ctd.pl
+++ b/tools/human_genome_variation/ctd.pl
@@ -38,8 +38,8 @@ while (<FH>) {
 }
 close FH or die "Couldn't close $in, $!\n";
 
-my $url = 'http://ctd.mdibl.org/tools/batchQuery.go';
-#my $url = 'http://globin.bx.psu.edu/cgi-bin/print-query';
+my $url = 'http://ctdbase.org/tools/batchQuery.go';
+#my $url = 'http://ctd.mdibl.org/tools/batchQuery.go';
 my $d = join("\n", @data);
 #list maintains order, where hash doesn't
 #order matters at ctd
diff --git a/tools/human_genome_variation/ctd.xml b/tools/human_genome_variation/ctd.xml
index 4c0ab896975..345adabdff5 100644
--- a/tools/human_genome_variation/ctd.xml
+++ b/tools/human_genome_variation/ctd.xml
@@ -29,15 +29,12 @@
        <when value="genes">
           <!-- do nothing -->
        </when>
-       <when value="pathways">
-          <!-- do nothing -->
-       </when>
-       <when value="pathways_curated">
-          <!-- do nothing -->
-       </when>
        <when value="pathways_inferred">
           <!-- do nothing -->
        </when>
+       <when value="pathways_enriched">
+          <!-- do nothing -->
+       </when>
        <when value="diseases">
           <!-- do nothing -->
        </when>
@@ -247,7 +244,7 @@ interaction type from the search-and-select box.  The choices that
 start with '-' are a subset of a choice above them; you can chose
 either the general interaction type or a more specific one.
 
-Home page: http://ctd.mdibl.org/
+Home page: http://ctdbase.org
 
 .. _tabular: ./static/formatHelp.html#tab
 

From c159b1cf8b97e4ab1fcf1b3c3b0d4bcb67d4f5c8 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Fri, 18 Nov 2011 16:44:10 -0500
Subject: [PATCH 226/362] Add the ability to reset all metadata (for every
 change set) in a tool shed repository (currently restricted to an admin), and
 add a fix for checking security when making changes to tool shed repository
 information on the Manage repsoitory page.

---
 .../webapps/community/controllers/common.py   | 219 ++++++++++--------
 .../community/controllers/repository.py       | 196 +++++++++++++++-
 .../repository/manage_repository.mako         |   4 +
 .../community/repository/view_changelog.mako  |   9 +
 4 files changed, 330 insertions(+), 98 deletions(-)

diff --git a/lib/galaxy/webapps/community/controllers/common.py b/lib/galaxy/webapps/community/controllers/common.py
index 38b58f18524..498716a9af5 100644
--- a/lib/galaxy/webapps/community/controllers/common.py
+++ b/lib/galaxy/webapps/community/controllers/common.py
@@ -343,6 +343,127 @@ def generate_datatypes_metadata( trans, id, changeset_revision, datatypes_config
                                     mimetype=mimetype ) )
         metadata_dict[ 'datatypes' ] = datatypes
     return metadata_dict
+def generate_metadata_for_repository_tip( trans, id, ctx, changeset_revision, repo_dir ):
+    # Browse the repository tip files on disk to generate metadata.  This is faster than
+    # the generate_metadata_for_changeset_revision() method below because fctx.data() does
+    # not have to be written to disk to load tools.  also, since changeset_revision is the
+    # repository tip, we handle things like .loc.sample files here.
+    metadata_dict = {}
+    invalid_files = []
+    sample_files = []
+    datatypes_config = None
+    # Find datatypes_conf.xml if it exists.
+    for root, dirs, files in os.walk( repo_dir ):
+        if root.find( '.hg' ) < 0:
+            for name in files:
+                if name == 'datatypes_conf.xml':
+                    datatypes_config = os.path.abspath( os.path.join( root, name ) )
+                    break
+    if datatypes_config:
+        metadata_dict = generate_datatypes_metadata( trans, id, changeset_revision, datatypes_config, metadata_dict )
+    # Find all special .sample files.
+    for root, dirs, files in os.walk( repo_dir ):
+        if root.find( '.hg' ) < 0:
+            for name in files:
+                if name.endswith( '.sample' ):
+                    sample_files.append( os.path.abspath( os.path.join( root, name ) ) )
+    # Find all tool configs and exported workflows.
+    for root, dirs, files in os.walk( repo_dir ):
+        if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0:
+            if '.hg' in dirs:
+                dirs.remove( '.hg' )
+            for name in files:
+                # Find all tool configs.
+                if name != 'datatypes_conf.xml' and name.endswith( '.xml' ):
+                    full_path = os.path.abspath( os.path.join( root, name ) )
+                    try:
+                        tool = load_tool( trans, full_path )
+                        valid = True
+                    except Exception, e:
+                        valid = False
+                        invalid_files.append( ( name, str( e ) ) )
+                    if valid and tool is not None:
+                        can_set_metadata, invalid_files = check_tool_input_params( trans, name, tool, sample_files, invalid_files )
+                        if can_set_metadata:
+                            # Update the list of metadata dictionaries for tools in metadata_dict.
+                            tool_config = os.path.join( root, name )
+                            metadata_dict = generate_tool_metadata( trans, id, changeset_revision, tool_config, tool, metadata_dict )
+                # Find all exported workflows
+                elif name.endswith( '.ga' ):
+                    try:
+                        full_path = os.path.abspath( os.path.join( root, name ) )
+                        # Convert workflow data from json
+                        fp = open( full_path, 'rb' )
+                        workflow_text = fp.read()
+                        fp.close()
+                        exported_workflow_dict = from_json_string( workflow_text )
+                        if 'a_galaxy_workflow' in exported_workflow_dict and exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true':
+                            # Update the list of metadata dictionaries for workflows in metadata_dict.
+                            metadata_dict = generate_workflow_metadata( trans, id, changeset_revision, exported_workflow_dict, metadata_dict )
+                    except Exception, e:
+                        invalid_files.append( ( name, str( e ) ) )
+    return metadata_dict, invalid_files
+def generate_metadata_for_changeset_revision( trans, id, ctx, changeset_revision, repo_dir ):
+    # Browse repository files within a change set to generate metadata.
+    metadata_dict = {}
+    invalid_files = []
+    sample_files = []
+    datatypes_config = None
+    # Find datatypes_conf.xml if it exists.
+    for filename in ctx:
+        if filename == 'datatypes_conf.xml':
+            fctx = ctx[ filename ]
+            datatypes_config = fctx.data()
+            break
+    if datatypes_config:
+        metadata_dict = generate_datatypes_metadata( trans, id, changeset_revision, datatypes_config, metadata_dict )
+    # Get all tool config file names from the hgweb url, something like:
+    # /repos/test/convert_chars1/file/e58dcf0026c7/convert_characters.xml
+    for filename in ctx:
+        # Find all tool configs.
+        if filename != 'datatypes_conf.xml' and filename.endswith( '.xml' ):
+            fctx = ctx[ filename ]
+            # Write the contents of the old tool config to a temporary file.
+            # TODO: figure out how to enhance the load_tool method so that a
+            # temporary disk file is not necessary in order to pass the tool
+            # config.
+            fh = tempfile.NamedTemporaryFile( 'w' )
+            tmp_filename = fh.name
+            fh.close()
+            fh = open( tmp_filename, 'w' )
+            fh.write( fctx.data() )
+            fh.close()
+            try:
+                tool = load_tool( trans, tmp_filename )
+                valid = True
+            except Exception, e:
+                invalid_files.append( ( filename, str( e ) ) )
+                valid = False
+            if valid and tool is not None:
+                # Update the list of metadata dictionaries for tools in metadata_dict.  Note that filename
+                # here is the relative path to the config file within the change set context, something
+                # like filtering.xml, but when the change set was the repository tip, the value was
+                # something like database/community_files/000/repo_1/filtering.xml.  This shouldn't break
+                # anything, but may result in a bit of confusion when maintaining the code / data over time.
+                # IMPORTANT NOTE:  Here we are assuming that since the current change set is not the repository
+                # tip, we do not have to handle any .loc.sample files since they would have been handled previously.
+                metadata_dict = generate_tool_metadata( trans, id, changeset_revision, filename, tool, metadata_dict )
+            try:
+                os.unlink( tmp_filename )
+            except:
+                pass
+        # Find all exported workflows.
+        elif filename.endswith( '.ga' ):
+            try:
+                fctx = ctx[ filename ]
+                workflow_text = fctx.data()
+                exported_workflow_dict = from_json_string( workflow_text )
+                if 'a_galaxy_workflow' in exported_workflow_dict and exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true':
+                    # Update the list of metadata dictionaries for workflows in metadata_dict.
+                    metadata_dict = generate_workflow_metadata( trans, id, changeset_revision, exported_workflow_dict, metadata_dict )
+            except Exception, e:
+                invalid_files.append( ( name, str( e ) ) )
+    return metadata_dict, invalid_files
 def set_repository_metadata( trans, id, changeset_revision, **kwd ):
     """Set repository metadata"""
     message = ''
@@ -350,102 +471,12 @@ def set_repository_metadata( trans, id, changeset_revision, **kwd ):
     repository = get_repository( trans, id )
     repo_dir = repository.repo_path
     repo = hg.repository( get_configured_ui(), repo_dir )
-    invalid_files = []
-    sample_files = []
-    datatypes_config = None
     ctx = get_changectx_for_changeset( trans, repo, changeset_revision )
     if ctx is not None:
-        metadata_dict = {}
         if changeset_revision == repository.tip:
-            # Find datatypes_conf.xml if it exists.
-            for root, dirs, files in os.walk( repo_dir ):
-                if root.find( '.hg' ) < 0:
-                    for name in files:
-                        if name == 'datatypes_conf.xml':
-                            datatypes_config = os.path.abspath( os.path.join( root, name ) )
-                            break
-            if datatypes_config:
-                metadata_dict = generate_datatypes_metadata( trans, id, changeset_revision, datatypes_config, metadata_dict )
-            # Find all special .sample files.
-            for root, dirs, files in os.walk( repo_dir ):
-                if root.find( '.hg' ) < 0:
-                    for name in files:
-                        if name.endswith( '.sample' ):
-                            sample_files.append( os.path.abspath( os.path.join( root, name ) ) )
-            # Find all tool configs and exported workflows.
-            for root, dirs, files in os.walk( repo_dir ):
-                if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0:
-                    if '.hg' in dirs:
-                        dirs.remove( '.hg' )
-                    for name in files:
-                        # Find all tool configs.
-                        if name != 'datatypes_conf.xml' and name.endswith( '.xml' ):
-                            full_path = os.path.abspath( os.path.join( root, name ) )
-                            try:
-                                tool = load_tool( trans, full_path )
-                                valid = True
-                            except Exception, e:
-                                valid = False
-                                invalid_files.append( ( name, str( e ) ) )
-                            if valid and tool is not None:
-                                can_set_metadata, invalid_files = check_tool_input_params( trans, name, tool, sample_files, invalid_files )
-                                if can_set_metadata:
-                                    # Update the list of metadata dictionaries for tools in metadata_dict.
-                                    tool_config = os.path.join( root, name )
-                                    metadata_dict = generate_tool_metadata( trans, id, changeset_revision, tool_config, tool, metadata_dict )
-                        # Find all exported workflows
-                        elif name.endswith( '.ga' ):
-                            try:
-                                full_path = os.path.abspath( os.path.join( root, name ) )
-                                # Convert workflow data from json
-                                fp = open( full_path, 'rb' )
-                                workflow_text = fp.read()
-                                fp.close()
-                                exported_workflow_dict = from_json_string( workflow_text )
-                                if exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true':
-                                    # Update the list of metadata dictionaries for workflows in metadata_dict.
-                                    metadata_dict = generate_workflow_metadata( trans, id, changeset_revision, exported_workflow_dict, metadata_dict )
-                            except Exception, e:
-                                invalid_files.append( ( name, str( e ) ) )
+            metadata_dict, invalid_files = generate_metadata_for_repository_tip( trans, id, ctx, changeset_revision, repo_dir )
         else:
-            # Find all special .sample files first.
-            for filename in ctx:
-                if filename.endswith( '.sample' ):
-                    sample_files.append( os.path.abspath( filename ) )
-            # Get all tool config file names from the hgweb url, something like:
-            # /repos/test/convert_chars1/file/e58dcf0026c7/convert_characters.xml
-            for filename in ctx:
-                # Find all tool configs - we do not have to update metadata for workflows or datatypes in anything
-                # but repository tips (handled above) since at the time this code was written, no workflows or
-                # dataytpes_conf.xml files exist in tool shed repositories, so they can only be added in future tips.
-                if filename.endswith( '.xml' ):
-                    fctx = ctx[ filename ]
-                    # Write the contents of the old tool config to a temporary file.
-                    fh = tempfile.NamedTemporaryFile( 'w' )
-                    tmp_filename = fh.name
-                    fh.close()
-                    fh = open( tmp_filename, 'w' )
-                    fh.write( fctx.data() )
-                    fh.close()
-                    try:
-                        tool = load_tool( trans, tmp_filename )
-                        valid = True
-                    except Exception, e:
-                        invalid_files.append( ( filename, str( e ) ) )
-                        valid = False
-                    if valid and tool is not None:
-                        can_set_metadata, invalid_files = check_tool_input_params( trans, filename, tool, sample_files, invalid_files )
-                        if can_set_metadata:
-                            # Update the list of metadata dictionaries for tools in metadata_dict.  Note that filename
-                            # here is the relative path to the config file within the change set context, something
-                            # like filtering.xml, but when the change set was the repository tip, the value was
-                            # something like database/community_files/000/repo_1/filtering.xml.  This shouldn't break
-                            # anything, but may result in a bit of confusion when maintaining the code / data over time.
-                            metadata_dict = generate_tool_metadata( trans, id, changeset_revision, filename, tool, metadata_dict )
-                    try:
-                        os.unlink( tmp_filename )
-                    except:
-                        pass
+            metadata_dict, invalid_files = generate_metadata_for_changeset_revision( trans, id, ctx, changeset_revision, repo_dir )
         if metadata_dict:
             if changeset_revision == repository.tip:
                 if new_tool_metadata_required( trans, id, metadata_dict ) or new_workflow_metadata_required( trans, id, metadata_dict ):
@@ -467,8 +498,8 @@ def set_repository_metadata( trans, id, changeset_revision, **kwd ):
                 trans.sa_session.add( repository_metadata )
                 trans.sa_session.flush()
         else:
-            message = "Revision '%s' includes no tools or exported workflows for which metadata can be defined " % str( changeset_revision )
-            message += "so this revision cannot be automatically installed into a local Galaxy instance."
+            message = "Revision '%s' includes no tools, datatypes or exported workflows for which metadata can " % str( changeset_revision )
+            message += "be defined so this revision cannot be automatically installed into a local Galaxy instance."
             status = "error"
     else:
         # change_set is None
diff --git a/lib/galaxy/webapps/community/controllers/repository.py b/lib/galaxy/webapps/community/controllers/repository.py
index b1bddd8fddc..a82bc3f14a0 100644
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -1311,15 +1311,14 @@ class RepositoryController( BaseUIController, ItemRatings ):
         if params.get( 'edit_repository_button', False ):
             flush_needed = False
             # TODO: add a can_manage in the security agent.
-            if user != repository.user or not trans.user_is_admin():
+            if not ( user.email == repository.user.email or trans.user_is_admin() ):
                 message = "You are not the owner of this repository, so you cannot manage it."
-                status = error
                 return trans.response.send_redirect( web.url_for( controller='repository',
                                                                   action='view_repository',
                                                                   id=id,
                                                                   webapp='community',
                                                                   message=message,
-                                                                  status=status ) )
+                                                                  status='error' ) )
             if description != repository.description:
                 repository.description = description
                 flush_needed = True
@@ -1447,6 +1446,10 @@ class RepositoryController( BaseUIController, ItemRatings ):
         changesets = []
         for changeset in repo.changelog:
             ctx = repo.changectx( changeset )
+            if get_repository_metadata_by_changeset_revision( trans, id, str( ctx ) ):
+                has_metadata = True
+            else:
+                has_metadata = False
             t, tz = ctx.date()
             date = datetime( *time.gmtime( float( t ) - tz )[:6] )
             display_date = date.strftime( "%Y-%m-%d" )
@@ -1457,7 +1460,8 @@ class RepositoryController( BaseUIController, ItemRatings ):
                             'description' : ctx.description(),
                             'files' : ctx.files(),
                             'user' : ctx.user(),
-                            'parent' : ctx.parents()[0] }
+                            'parent' : ctx.parents()[0],
+                            'has_metadata' : has_metadata }
             # Make sure we'll view latest changeset first.
             changesets.insert( 0, change_dict )
         is_malicious = change_set_is_malicious( trans, id, repository.tip )
@@ -1608,6 +1612,190 @@ class RepositoryController( BaseUIController, ItemRatings ):
                                                           message=message,
                                                           status=status ) )
     @web.expose
+    def reset_all_metadata( self, trans, id, **kwd ):
+        params = util.Params( kwd )
+        message = util.restore_text( params.get( 'message', ''  ) )
+        status = params.get( 'status', 'done' )
+        repository = get_repository( trans, id )
+        repo_dir = repository.repo_path
+        repo = hg.repository( get_configured_ui(), repo_dir )
+        if len( repo ) == 1:
+            message, status = set_repository_metadata( trans, id, repository.tip, **kwd )
+        else:
+            # The following will be a list of changeset_revisions that have been created or updated.
+            # When the following loop completes, we'll delete all repository_metadata records for
+            # this repository that do not have a changeset_revision value in this list.
+            changeset_revisions = []
+            repository_metadata_tup_for_comparison = ()
+            for changeset in repo.changelog:
+                ctx = repo.changectx( changeset )
+                current_changeset_revision = str( ctx )
+                ctx = get_changectx_for_changeset( trans, repo, current_changeset_revision )
+                current_metadata_dict, invalid_files = generate_metadata_for_changeset_revision( trans, id, ctx, current_changeset_revision, repo_dir )
+                if current_metadata_dict:
+                    if repository_metadata_tup_for_comparison:
+                        ancestor_changeset_revision, ancestor_metadata_dict = repository_metadata_tup_for_comparison
+                        comparison = self.__compare_changeset_revisions( ancestor_changeset_revision,
+                                                                         ancestor_metadata_dict,
+                                                                         current_changeset_revision,
+                                                                         current_metadata_dict )
+                        # The value of comparsion will be one of:
+                        # 'no metadata' - no metadata for either ancestor or current, so continue from current
+                        # 'equal' - ancestor metadata is equivalent to current metadata, so continue from current
+                        # 'subset' - ancestor metadata is a subset of current metadata, so continue from current
+                        # 'not equal and not subset' - ancestor metadata is neither equal to nor a subset of current
+                        #                              metadata, so persist ancestor metadata.
+                        if comparison in [ 'no metadata', 'equal', 'subset' ]:
+                            repository_metadata_tup_for_comparison = ( current_changeset_revision, current_metadata_dict )
+                        elif comparison == 'not equal and not subset':
+                            self.__create_or_update_repository_metadata( trans, id, repository, ancestor_changeset_revision, ancestor_metadata_dict )
+                            # keep track of the changeset_revisions that we've persisted.
+                            changeset_revisions.append( ancestor_changeset_revision )
+                            repository_metadata_tup_for_comparison = ()
+                    else:
+                        # We're at the first change set in the change log.
+                        repository_metadata_tup_for_comparison = ( current_changeset_revision, current_metadata_dict )
+                    if not ctx.children():
+                        # We're at the end of the change log.
+                        self.__create_or_update_repository_metadata( trans, id, repository, current_changeset_revision, current_metadata_dict )
+                        changeset_revisions.append( current_changeset_revision )
+                elif ancestor_metadata_dict:
+                    # Our current change set has no metadata, but our ancestor change set has metadata, so save it.
+                    self.__create_or_update_repository_metadata( trans, id, repository, ancestor_changeset_revision, ancestor_metadata_dict )
+                    # keep track of the changeset_revisions that we've persisted.
+                    changeset_revisions.append( ancestor_changeset_revision )
+                    repository_metadata_tup_for_comparison = ()
+                    ancestor_changeset_revision = current_changeset_revision
+                    ancestor_metadata_dict = current_metadata_dict
+            self.__clean_repository_metadata( trans, id, changeset_revisions )
+        if not message:                     
+            message = "Repository metadata has been reset."
+            status = 'done'
+        return trans.response.send_redirect( web.url_for( controller='repository',
+                                                          action='manage_repository',
+                                                          id=id,
+                                                          message=message,
+                                                          status=status ) )
+    def __clean_repository_metadata( self, trans, id, changeset_revisions ):
+        # Delete all repository_metadata reecords associated with the repository
+        # that have a changeset_revision that is not in changeset_revisions.
+        for repository_metadata in trans.sa_session.query( trans.model.RepositoryMetadata ) \
+                                                   .filter( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ) ):
+            if repository_metadata.changeset_revision not in changeset_revisions:
+                trans.sa_session.delete( repository_metadata )
+                trans.sa_session.flush()
+    def __create_or_update_repository_metadata( self, trans, id, repository, changeset_revision, metadata_dict ):
+        repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision )
+        if repository_metadata:
+            # Update RepositoryMetadata.metadata.
+            repository_metadata.metadata = metadata_dict
+            trans.sa_session.add( repository_metadata )
+            trans.sa_session.flush()
+        else:
+            # Create a new repository_metadata table row.
+            repository_metadata = trans.model.RepositoryMetadata( repository.id, changeset_revision, metadata_dict )
+            trans.sa_session.add( repository_metadata )
+            trans.sa_session.flush()
+    def __compare_changeset_revisions( self, ancestor_changeset_revision, ancestor_metadata_dict, current_changeset_revision, current_metadata_dict ):
+        # The metadata associated with ancestor_changeset_revision is ancestor_metadata_dict.  This changeset_revision
+        # is an ancestor of current_changeset_revision which is associated with current_metadata_dict.
+        # Get information about tools.
+        if 'tools' in ancestor_metadata_dict:
+            ancestor_tools = ancestor_metadata_dict[ 'tools' ]
+        else:
+            ancestor_tools = []
+        if 'tools' in current_metadata_dict:
+            current_tools = current_metadata_dict[ 'tools' ]
+        else:
+            current_tools = []
+        ancestor_guids = []
+        for tool_dict in ancestor_tools:
+            ancestor_guids.append( tool_dict[ 'guid' ] )
+        ancestor_guids.sort()
+        current_guids = []
+        for tool_dict in current_tools:
+            current_guids.append( tool_dict[ 'guid' ] )
+        current_guids.sort()
+        # Get information about workflows.
+        if 'workflows' in ancestor_metadata_dict:
+            ancestor_workflows = ancestor_metadata_dict[ 'workflows' ]
+        else:
+            ancestor_workflows = []
+        if 'workflows' in current_metadata_dict:
+            current_workflows = current_metadata_dict[ 'workflows' ]
+        else:
+            current_workflows = []
+        # Get information about datatypes.
+        if 'datatypes' in ancestor_metadata_dict:
+            ancestor_datatypes = ancestor_metadata_dict[ 'datatypes' ]
+        else:
+            ancestor_datatypes = []
+        if 'datatypes' in current_metadata_dict:
+            current_datatypes = current_metadata_dict[ 'datatypes' ]
+        else:
+            current_datatypes = []
+        # Handle case where no metadata exists for either changeset.
+        if not ( ancestor_guids or current_guids or ancestor_workflows or current_workflows or ancestor_datatypes or current_datatypes ):
+            return 'no metadata'
+        workflow_comparison = self.__compare_workflows( ancestor_workflows, current_workflows )
+        datatype_comparison = self.__compare_datatypes( ancestor_datatypes, current_datatypes )
+        # Handle case where all metadata is the same.
+        if ancestor_guids == current_guids and workflow_comparison == 'equal' and datatype_comparison == 'equal':
+            return 'equal'
+        if workflow_comparison == 'subset' and datatype_comparison == 'subset':
+            is_subset = True
+            for guid in ancestor_guids:
+                if guid not in current_guids:
+                    is_subset = False
+                    break
+            if is_subset:
+                return 'subset'
+        return 'not equal and not subset'
+    def __compare_workflows( self, ancestor_workflows, current_workflows ):
+        # Determine if ancestor_workflows is the same as current_workflows
+        # or if ancestor_workflows is a subset of current_workflows.
+        if len( ancestor_workflows ) <= len( current_workflows ):
+            for ancestor_workflow in ancestor_workflows:
+                # Currently the only way to differentiate workflows is by name.
+                ancestor_workflow_name = ancestor_workflow[ 'name' ]
+                found_in_current = False
+                for current_workflow in current_workflows:
+                    if current_workflow[ 'name' ] == ancestor_workflow_name:
+                        found_in_current = True
+                        break
+                if not found_in_current:
+                    return 'not equal and not subset'
+            if len( ancestor_workflows ) == len( current_workflows ):
+                return 'equal'
+            else:
+                return 'subset'
+        return 'not equal and not subset'
+    def __compare_datatypes( self, ancestor_datatypes, current_datatypes ):
+        # Determine if ancestor_datatypes is the same as current_datatypes
+        # or if ancestor_datatypes is a subset of current_datatypes.  Each
+        # datatype dict looks something like:
+        # {"dtype": "galaxy.datatypes.images:Image", "extension": "pdf", "mimetype": "application/pdf"}
+        if len( ancestor_datatypes ) <= len( current_datatypes ):
+            for ancestor_datatype in ancestor_datatypes:
+                # Currently the only way to differentiate datatypes is by name.
+                ancestor_datatype_dtype = ancestor_datatype[ 'dtype' ]
+                ancestor_datatype_extension = ancestor_datatype[ 'extension' ]
+                ancestor_datatype_mimetype = ancestor_datatype[ 'mimetype' ]
+                found_in_current = False
+                for current_datatype in current_datatypes:
+                    if current_datatype[ 'dtype' ] == ancestor_datatype_dtype and \
+                        current_datatype[ 'extension' ] == ancestor_datatype_extension and \
+                        current_datatype[ 'mimetype' ] == ancestor_datatype_mimetype:
+                        found_in_current = True
+                        break
+                if not found_in_current:
+                    return 'not equal and not subset'
+            if len( ancestor_datatypes ) == len( current_datatypes ):
+                return 'equal'
+            else:
+                return 'subset'
+        return 'not equal and not subset'
+    @web.expose
     def display_tool( self, trans, repository_id, tool_config, changeset_revision, **kwd ):
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', ''  ) )
diff --git a/templates/webapps/community/repository/manage_repository.mako b/templates/webapps/community/repository/manage_repository.mako
index e60f8d7b539..5adea847aaa 100644
--- a/templates/webapps/community/repository/manage_repository.mako
+++ b/templates/webapps/community/repository/manage_repository.mako
@@ -20,6 +20,7 @@
     else:
         browse_label = 'Browse repository tip files'
     can_set_malicious = metadata and can_set_metadata and is_admin and changeset_revision == repository.tip
+    can_reset_all_metadata = is_admin and len( repo ) > 0
 %>
 
 <%!
@@ -88,6 +89,9 @@
             %if can_contact_owner:
                 <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp='community' )}">Contact repository owner</a>
             %endif
+            %if can_reset_all_metadata:
+                <a class="action-button" href="${h.url_for( controller='repository', action='reset_all_metadata', id=trans.security.encode_id( repository.id ), webapp='community' )}">Reset all repository metadata</a>
+            %endif
             %if can_download:
                 <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a>
                 <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='bz2' )}">Download as a .tar.bz2 file</a>
diff --git a/templates/webapps/community/repository/view_changelog.mako b/templates/webapps/community/repository/view_changelog.mako
index 5e8fd1f889b..ded2d19fc66 100644
--- a/templates/webapps/community/repository/view_changelog.mako
+++ b/templates/webapps/community/repository/view_changelog.mako
@@ -106,6 +106,10 @@
                         ctx_parent_str = 'None'
                     else:
                         ctx_parent_str = "%s:%s" % ( ctx_parent_rev, ctx_parent )
+                    if changeset[ 'has_metadata' ]:
+                        has_metadata_str = 'Repository metadata is associated with this change set.'
+                    else:
+                        has_metadata_str = ''
                 %>
                 <% display_date = changeset[ 'display_date' ] %>
                 %if test_date != display_date:
@@ -113,6 +117,11 @@
                 %endif
                 <tr>
                     <td>
+                        %if is_admin and has_metadata_str:
+                            <div class="form-row">
+                                ${has_metadata_str}
+                            </div>
+                        %endif
                         <div class="form-row">
                             <label>Description:</label>
                             <a href="${h.url_for( controller='repository', action='view_changeset', id=trans.security.encode_id( repository.id ), ctx_str=ctx_str )}">${changeset[ 'description' ]}</a>

From 1dbc2261ed7abf36ed7f09df864c8a5ac8706f3c Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Sat, 19 Nov 2011 15:28:16 -0500
Subject: [PATCH 227/362] Fix GFFDataProvider bugs introduced in 9b7d5c1c0be6.

---
 lib/galaxy/visualization/tracks/data_providers.py | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/visualization/tracks/data_providers.py b/lib/galaxy/visualization/tracks/data_providers.py
index 377160dca61..66b09652ece 100644
--- a/lib/galaxy/visualization/tracks/data_providers.py
+++ b/lib/galaxy/visualization/tracks/data_providers.py
@@ -99,7 +99,7 @@ class TracksDataProvider( object ):
         pass
         
         
-    def get_data( self, chrom, start, end, start_val=0, max_vals=None, **kwargs ):
+    def get_data( self, chrom, start, end, start_val=0, max_vals=sys.maxint, **kwargs ):
         """ 
         Returns data in region defined by chrom, start, and end. start_val and
         max_vals are used to denote the data to return: start_val is the first element to 
@@ -914,7 +914,15 @@ class GFFDataProvider( TracksDataProvider ):
         """
         start, end = int( start ), int( end )
         source = open( self.original_dataset.file_name )
-        return GFFReaderWrapper( source, fix_strand=True )
+        
+        def features_in_region_iter():
+            for feature in GFFReaderWrapper( source, fix_strand=True ):
+                # Only provide features that are in region.
+                feature_start, feature_end = convert_gff_coords_to_bed( [ feature.start, feature.end ] )
+                if feature.chrom != chrom or feature_start < start or feature_end > end:
+                    continue                
+                yield feature
+        return features_in_region_iter()
         
     def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ):
         """
@@ -931,9 +939,6 @@ class GFFDataProvider( TracksDataProvider ):
                 message = ERROR_MAX_VALS % ( max_vals, "reads" )
                 break
                 
-            feature_start, feature_end = convert_gff_coords_to_bed( [ feature.start, feature.end ] )
-            if feature.chrom != chrom or feature_start < start or feature_end > end:
-                continue
             payload = package_gff_feature( feature )
             payload.insert( 0, offset )
             results.append( payload )

From 85e4fe35477d42ea3e3c118956cbb568f5b09055 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Sat, 19 Nov 2011 18:15:24 -0500
Subject: [PATCH 228/362] Fix Tile variable name so that it connotes what it
 actually stores.

---
 static/scripts/trackster.js | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index 2740f334bf5..336a068b92c 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -2301,7 +2301,7 @@ var Tile = function(track, index, resolution, canvas, data) {
     this.high = (index + 1) * DENSITY * resolution;
     this.resolution = resolution;
     // Wrap element in div for background.
-    this.canvas = $("<div class='track-tile'/>").append(canvas);
+    this.html_elt = $("<div class='track-tile'/>").append(canvas);
     this.data = data;
     this.stale = false;
 };
@@ -2324,13 +2324,13 @@ var FeatureTrackTile = function(track, index, resolution, canvas, data, mode, me
     this.message = message;
     this.feature_mapper = feature_mapper;
     
-    // Add message + action icons to tile's "canvas" TODO: rename canvas to element/html or something similar.
+    // Add message + action icons to tile's html.
     if (this.message) {
         var 
-            canvas = this.canvas.children()[0],
+            canvas = this.html_elt.children()[0],
             message_div = $("<div/>").addClass("tile-message").text(this.message).
                             // -1 to account for border.
-                            css({'height': ERROR_PADDING-1, 'width': canvas.width}).prependTo(this.canvas),
+                            css({'height': ERROR_PADDING-1, 'width': canvas.width}).prependTo(this.html_elt),
             more_down_icon = $("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(message_div),
             more_across_icon = $("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(message_div);
 
@@ -2371,7 +2371,7 @@ FeatureTrackTile.prototype.predisplay_actions = function() {
     // Only show popups in Pack mode.
     if (tile.mode !== "Pack") { return; }
     
-    $(this.canvas).hover( function() { 
+    $(this.html_elt).hover( function() { 
         this.hovered = true; 
         $(this).mousemove();
     }, function() { 
@@ -2435,14 +2435,14 @@ FeatureTrackTile.prototype.predisplay_actions = function() {
             }
             
             // Attach popup to canvas's parent.
-            popup.appendTo($(tile.canvas).parent());
+            popup.appendTo($(tile.html_elt).parent());
             
             // Offsets are within canvas, but popup must be positioned relative to parent element.
             // parseInt strips "px" from left, top measurements. +7 so that mouse pointer does not
             // overlap popup.
             var 
-                popupX = offsetX + parseInt( tile.canvas.css("left") ) - popup.width() / 2,
-                popupY = offsetY + parseInt( tile.canvas.css("top") ) + 7;
+                popupX = offsetX + parseInt( tile.html_elt.css("left") ) - popup.width() / 2,
+                popupY = offsetY + parseInt( tile.html_elt.css("top") ) + 7;
             popup.css("left", popupX + "px").css("top", popupY + "px")
         }
         else if (!e.isPropagationStopped()) {
@@ -2959,7 +2959,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
                 tile = tiles[tile_index];
                 if (!tile.message) {
                     // Need to align with other tile(s) that have message(s).
-                    tile.canvas.css("padding-top", ERROR_PADDING);
+                    tile.html_elt.css("padding-top", ERROR_PADDING);
                 }
             }
         }        
@@ -3031,7 +3031,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
     show_tile: function(tile, parent_element, w_scale) {
         var 
             track = this,
-            tile_element = tile.canvas;
+            tile_element = tile.html_elt;
         
         //
         // Show/move tile element.
@@ -3456,8 +3456,8 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
             for (var i = 0; i < tiles.length; i++) {
                 var tile = tiles[i];
                 if (tile.max_val !== global_max) {
-                    tile.canvas.remove();
-                    track.draw_helper(true, width, tile.index, tile.resolution, tile.canvas.parent(), w_scale, [], { max: global_max });
+                    tile.html_elt.remove();
+                    track.draw_helper(true, width, tile.index, tile.resolution, tile.html_elt.parent(), w_scale, [], { max: global_max });
                 }
             }
         }                

From 54b4dd64b5754b05256b7cf082b8ea8d3a298045 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Mon, 21 Nov 2011 08:52:13 -0500
Subject: [PATCH 229/362] Add picard_FastqToSam.xml and picard_SamToFastq.xml
 to tool_conf.xml.main.

---
 tool_conf.xml.main                 | 3 +++
 tools/picard/picard_FastqToSam.xml | 3 ++-
 tools/picard/picard_SamToFastq.xml | 3 ++-
 3 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/tool_conf.xml.main b/tool_conf.xml.main
index 34f94f96206..2d4ec0dfec6 100644
--- a/tool_conf.xml.main
+++ b/tool_conf.xml.main
@@ -406,6 +406,9 @@
       <tool file="ngs_rna/filter_transcripts_via_tracking.xml" />
   </section>
   <section name="NGS: Picard (beta)" id="picard_beta">
+    <label text="Conversion" id="picard_conversion"/>
+    <tool file="picard/picard_FastqToSam.xml" />
+    <tool file="picard/picard_SamToFastq.xml" />
     <label text="QC/Metrics for sam/bam" id="qcsambam"/>
     <tool file="picard/picard_BamIndexStats.xml" />
     <tool file="picard/rgPicardASMetrics.xml" />
diff --git a/tools/picard/picard_FastqToSam.xml b/tools/picard/picard_FastqToSam.xml
index 2f736b3be96..9dec7c65edc 100644
--- a/tools/picard/picard_FastqToSam.xml
+++ b/tools/picard/picard_FastqToSam.xml
@@ -1,6 +1,7 @@
 <tool id="picard_FastqToSam" name="FASTQ to BAM" version="1.56.0">
   <description>creates an unaligned BAM file</description>
-  <requirements><requirement type="package">picard</requirement></requirements>
+  <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
+  <!-- Dan Blankenberg -->
   <command>java  -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC
     -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/FastqToSam.jar"
     FASTQ="${input_fastq1}"
diff --git a/tools/picard/picard_SamToFastq.xml b/tools/picard/picard_SamToFastq.xml
index 278f42934c6..e0e71a9b7c7 100644
--- a/tools/picard/picard_SamToFastq.xml
+++ b/tools/picard/picard_SamToFastq.xml
@@ -1,6 +1,7 @@
 <tool id="picard_SamToFastq" name="SAM to FASTQ" version="1.56.0">
   <description>creates a FASTQ file</description>
-  <requirements><requirement type="package">picard</requirement></requirements>
+  <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
+  <!-- Dan Blankenberg -->
   <command>java -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC
     -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/SamToFastq.jar"
     INPUT="${input_sam}"

From 9b7518c9a3a3cde1bf4c10e98bc42e5c65539c2e Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Mon, 21 Nov 2011 09:50:37 -0500
Subject: [PATCH 230/362] Update modified generic GATK 1.3 arguments.

---
 tools/gatk/count_covariates.xml            | 23 ++++++++++++++++------
 tools/gatk/depth_of_coverage.xml           | 23 ++++++++++++++++------
 tools/gatk/indel_realigner.xml             | 23 ++++++++++++++++------
 tools/gatk/realigner_target_creator.xml    | 23 ++++++++++++++++------
 tools/gatk/table_recalibration.xml         | 23 ++++++++++++++++------
 tools/gatk/unified_genotyper.xml           | 23 ++++++++++++++++------
 tools/gatk/variant_annotator.xml           | 23 ++++++++++++++++------
 tools/gatk/variant_apply_recalibration.xml | 23 ++++++++++++++++------
 tools/gatk/variant_combine.xml             | 23 ++++++++++++++++------
 tools/gatk/variant_eval.xml                | 23 ++++++++++++++++------
 tools/gatk/variant_filtration.xml          | 23 ++++++++++++++++------
 tools/gatk/variant_recalibrator.xml        | 23 ++++++++++++++++------
 tools/gatk/variants_validate.xml           | 23 ++++++++++++++++------
 13 files changed, 221 insertions(+), 78 deletions(-)

diff --git a/tools/gatk/count_covariates.xml b/tools/gatk/count_covariates.xml
index 46730396a3f..b6bd4efb707 100644
--- a/tools/gatk/count_covariates.xml
+++ b/tools/gatk/count_covariates.xml
@@ -46,9 +46,13 @@
     
     ##start standard gatk options
     #if $gatk_param_type.gatk_param_type_selector == "advanced":
-        #for $sample_metadata in $gatk_param_type.sample_metadata:
-            -p '--sample_metadata "${sample_metadata.sample_metadata_file}"'
+        #for $pedigree in $gatk_param_type.pedigree:
+            -p '--pedigree "${pedigree.pedigree_file}"'
         #end for
+        #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
+            -p '--pedigreeString "${pedigree_string.pedigree_string}"'
+        #end for
+        -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
         #for $read_filter in $gatk_param_type.read_filter:
             -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
             ###raise Exception( str( dir( $read_filter ) ) )
@@ -67,7 +71,7 @@
             -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
         #end for
 
-        -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
         
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
@@ -213,9 +217,16 @@
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" />
+        <repeat name="pedigree" title="Pedigree file">
+            <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
         </repeat>
+        <repeat name="pedigree_string_repeat" title="Pedigree string">
+            <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
+        </repeat>
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
+          <option value="STRICT" selected="True">STRICT</option>
+          <option value="SILENT">SILENT</option>
+        </param>
         <repeat name="read_filter" title="Read Filter">
             <conditional name="read_filter_type">
 		      <param name="read_filter_type_selector" type="select" label="Read Filter Type">
@@ -237,7 +248,7 @@
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
         </repeat>
         
-        <param name="BTI_merge_rule" type="select" label="BTI merge rule">
+        <param name="interval_set_rule" type="select" label="Interval set rule">
           <option value="UNION" selected="True">UNION</option>
           <option value="INTERSECTION">INTERSECTION</option>
         </param>
diff --git a/tools/gatk/depth_of_coverage.xml b/tools/gatk/depth_of_coverage.xml
index f735a6d7619..7157a0a274b 100644
--- a/tools/gatk/depth_of_coverage.xml
+++ b/tools/gatk/depth_of_coverage.xml
@@ -37,9 +37,13 @@
    
     ##start standard gatk options
     #if $gatk_param_type.gatk_param_type_selector == "advanced":
-        #for $sample_metadata in $gatk_param_type.sample_metadata:
-            -p '--sample_metadata "${sample_metadata.sample_metadata_file}"'
+        #for $pedigree in $gatk_param_type.pedigree:
+            -p '--pedigree "${pedigree.pedigree_file}"'
         #end for
+        #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
+            -p '--pedigreeString "${pedigree_string.pedigree_string}"'
+        #end for
+        -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
         #for $read_filter in $gatk_param_type.read_filter:
             -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
             ###raise Exception( str( dir( $read_filter ) ) )
@@ -58,7 +62,7 @@
             -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
         #end for
 
-        -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
         
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
@@ -229,9 +233,16 @@
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" />
+        <repeat name="pedigree" title="Pedigree file">
+            <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
         </repeat>
+        <repeat name="pedigree_string_repeat" title="Pedigree string">
+            <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
+        </repeat>
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
+          <option value="STRICT" selected="True">STRICT</option>
+          <option value="SILENT">SILENT</option>
+        </param>
         <repeat name="read_filter" title="Read Filter">
             <conditional name="read_filter_type">
 		      <param name="read_filter_type_selector" type="select" label="Read Filter Type">
@@ -253,7 +264,7 @@
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
         </repeat>
         
-        <param name="BTI_merge_rule" type="select" label="BTI merge rule">
+        <param name="interval_set_rule" type="select" label="Interval set rule">
           <option value="UNION" selected="True">UNION</option>
           <option value="INTERSECTION">INTERSECTION</option>
         </param>
diff --git a/tools/gatk/indel_realigner.xml b/tools/gatk/indel_realigner.xml
index 5b4d0113ab0..0a94b4eb69f 100644
--- a/tools/gatk/indel_realigner.xml
+++ b/tools/gatk/indel_realigner.xml
@@ -38,9 +38,13 @@
    
     ##start standard gatk options
     #if $gatk_param_type.gatk_param_type_selector == "advanced":
-        #for $sample_metadata in $gatk_param_type.sample_metadata:
-            -p '--sample_metadata "${sample_metadata.sample_metadata_file}"'
+        #for $pedigree in $gatk_param_type.pedigree:
+            -p '--pedigree "${pedigree.pedigree_file}"'
         #end for
+        #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
+            -p '--pedigreeString "${pedigree_string.pedigree_string}"'
+        #end for
+        -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
         #for $read_filter in $gatk_param_type.read_filter:
             -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
             ###raise Exception( str( dir( $read_filter ) ) )
@@ -59,7 +63,7 @@
             -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
         #end for
 
-        -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
         
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
@@ -176,9 +180,16 @@
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" />
+        <repeat name="pedigree" title="Pedigree file">
+            <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
         </repeat>
+        <repeat name="pedigree_string_repeat" title="Pedigree string">
+            <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
+        </repeat>
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
+          <option value="STRICT" selected="True">STRICT</option>
+          <option value="SILENT">SILENT</option>
+        </param>
         <repeat name="read_filter" title="Read Filter">
             <conditional name="read_filter_type">
 		      <param name="read_filter_type_selector" type="select" label="Read Filter Type">
@@ -200,7 +211,7 @@
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
         </repeat>
         
-        <param name="BTI_merge_rule" type="select" label="BTI merge rule">
+        <param name="interval_set_rule" type="select" label="Interval set rule">
           <option value="UNION" selected="True">UNION</option>
           <option value="INTERSECTION">INTERSECTION</option>
         </param>
diff --git a/tools/gatk/realigner_target_creator.xml b/tools/gatk/realigner_target_creator.xml
index dad4ace9320..5d8e4777fb2 100644
--- a/tools/gatk/realigner_target_creator.xml
+++ b/tools/gatk/realigner_target_creator.xml
@@ -35,9 +35,13 @@
    
     ##start standard gatk options
     #if $gatk_param_type.gatk_param_type_selector == "advanced":
-        #for $sample_metadata in $gatk_param_type.sample_metadata:
-            -p '--sample_metadata "${sample_metadata.sample_metadata_file}"'
+        #for $pedigree in $gatk_param_type.pedigree:
+            -p '--pedigree "${pedigree.pedigree_file}"'
         #end for
+        #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
+            -p '--pedigreeString "${pedigree_string.pedigree_string}"'
+        #end for
+        -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
         #for $read_filter in $gatk_param_type.read_filter:
             -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
             ###raise Exception( str( dir( $read_filter ) ) )
@@ -56,7 +60,7 @@
             -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
         #end for
 
-        -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
         
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
@@ -162,9 +166,16 @@
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" />
+        <repeat name="pedigree" title="Pedigree file">
+            <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
         </repeat>
+        <repeat name="pedigree_string_repeat" title="Pedigree string">
+            <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
+        </repeat>
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
+          <option value="STRICT" selected="True">STRICT</option>
+          <option value="SILENT">SILENT</option>
+        </param>
         <repeat name="read_filter" title="Read Filter">
             <conditional name="read_filter_type">
 		      <param name="read_filter_type_selector" type="select" label="Read Filter Type">
@@ -186,7 +197,7 @@
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
         </repeat>
         
-        <param name="BTI_merge_rule" type="select" label="BTI merge rule">
+        <param name="interval_set_rule" type="select" label="Interval set rule">
           <option value="UNION" selected="True">UNION</option>
           <option value="INTERSECTION">INTERSECTION</option>
         </param>
diff --git a/tools/gatk/table_recalibration.xml b/tools/gatk/table_recalibration.xml
index d10c9291b63..2ab733cb74f 100644
--- a/tools/gatk/table_recalibration.xml
+++ b/tools/gatk/table_recalibration.xml
@@ -23,9 +23,13 @@
    '
     ##start standard gatk options
     #if $gatk_param_type.gatk_param_type_selector == "advanced":
-        #for $sample_metadata in $gatk_param_type.sample_metadata:
-            -p '--sample_metadata "${sample_metadata.sample_metadata_file}"'
+        #for $pedigree in $gatk_param_type.pedigree:
+            -p '--pedigree "${pedigree.pedigree_file}"'
         #end for
+        #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
+            -p '--pedigreeString "${pedigree_string.pedigree_string}"'
+        #end for
+        -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
         #for $read_filter in $gatk_param_type.read_filter:
             -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
             ###raise Exception( str( dir( $read_filter ) ) )
@@ -44,7 +48,7 @@
             -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
         #end for
 
-        -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
         
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
@@ -144,9 +148,16 @@
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" />
+        <repeat name="pedigree" title="Pedigree file">
+            <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
         </repeat>
+        <repeat name="pedigree_string_repeat" title="Pedigree string">
+            <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
+        </repeat>
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
+          <option value="STRICT" selected="True">STRICT</option>
+          <option value="SILENT">SILENT</option>
+        </param>
         <repeat name="read_filter" title="Read Filter">
             <conditional name="read_filter_type">
 		      <param name="read_filter_type_selector" type="select" label="Read Filter Type">
@@ -168,7 +179,7 @@
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
         </repeat>
         
-        <param name="BTI_merge_rule" type="select" label="BTI merge rule">
+        <param name="interval_set_rule" type="select" label="Interval set rule">
           <option value="UNION" selected="True">UNION</option>
           <option value="INTERSECTION">INTERSECTION</option>
         </param>
diff --git a/tools/gatk/unified_genotyper.xml b/tools/gatk/unified_genotyper.xml
index 5e1d8d53d44..afeeeff2f17 100644
--- a/tools/gatk/unified_genotyper.xml
+++ b/tools/gatk/unified_genotyper.xml
@@ -41,9 +41,13 @@
    
     ##start standard gatk options
     #if $gatk_param_type.gatk_param_type_selector == "advanced":
-        #for $sample_metadata in $gatk_param_type.sample_metadata:
-            -p '--sample_metadata "${sample_metadata.sample_metadata_file}"'
+        #for $pedigree in $gatk_param_type.pedigree:
+            -p '--pedigree "${pedigree.pedigree_file}"'
         #end for
+        #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
+            -p '--pedigreeString "${pedigree_string.pedigree_string}"'
+        #end for
+        -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
         #for $read_filter in $gatk_param_type.read_filter:
             -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
             ###raise Exception( str( dir( $read_filter ) ) )
@@ -62,7 +66,7 @@
             -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
         #end for
 
-        -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
         
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
@@ -201,9 +205,16 @@
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" />
+        <repeat name="pedigree" title="Pedigree file">
+            <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
         </repeat>
+        <repeat name="pedigree_string_repeat" title="Pedigree string">
+            <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
+        </repeat>
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
+          <option value="STRICT" selected="True">STRICT</option>
+          <option value="SILENT">SILENT</option>
+        </param>
         <repeat name="read_filter" title="Read Filter">
             <conditional name="read_filter_type">
 		      <param name="read_filter_type_selector" type="select" label="Read Filter Type">
@@ -225,7 +236,7 @@
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
         </repeat>
         
-        <param name="BTI_merge_rule" type="select" label="BTI merge rule">
+        <param name="interval_set_rule" type="select" label="Interval set rule">
           <option value="UNION" selected="True">UNION</option>
           <option value="INTERSECTION">INTERSECTION</option>
         </param>
diff --git a/tools/gatk/variant_annotator.xml b/tools/gatk/variant_annotator.xml
index 01ca23a1e36..093aa6049c0 100644
--- a/tools/gatk/variant_annotator.xml
+++ b/tools/gatk/variant_annotator.xml
@@ -76,9 +76,13 @@
     
     ##start standard gatk options
     #if $gatk_param_type.gatk_param_type_selector == "advanced":
-        #for $sample_metadata in $gatk_param_type.sample_metadata:
-            -p '--sample_metadata "${sample_metadata.sample_metadata_file}"'
+        #for $pedigree in $gatk_param_type.pedigree:
+            -p '--pedigree "${pedigree.pedigree_file}"'
         #end for
+        #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
+            -p '--pedigreeString "${pedigree_string.pedigree_string}"'
+        #end for
+        -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
         #for $read_filter in $gatk_param_type.read_filter:
             -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
             ###raise Exception( str( dir( $read_filter ) ) )
@@ -97,7 +101,7 @@
             -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
         #end for
 
-        -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
         
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
@@ -262,9 +266,16 @@
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" />
+        <repeat name="pedigree" title="Pedigree file">
+            <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
         </repeat>
+        <repeat name="pedigree_string_repeat" title="Pedigree string">
+            <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
+        </repeat>
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
+          <option value="STRICT" selected="True">STRICT</option>
+          <option value="SILENT">SILENT</option>
+        </param>
         <repeat name="read_filter" title="Read Filter">
             <conditional name="read_filter_type">
 		      <param name="read_filter_type_selector" type="select" label="Read Filter Type">
@@ -286,7 +297,7 @@
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
         </repeat>
         
-        <param name="BTI_merge_rule" type="select" label="BTI merge rule">
+        <param name="interval_set_rule" type="select" label="Interval set rule">
           <option value="UNION" selected="True">UNION</option>
           <option value="INTERSECTION">INTERSECTION</option>
         </param>
diff --git a/tools/gatk/variant_apply_recalibration.xml b/tools/gatk/variant_apply_recalibration.xml
index 639f5979dc7..6176b03244f 100644
--- a/tools/gatk/variant_apply_recalibration.xml
+++ b/tools/gatk/variant_apply_recalibration.xml
@@ -24,9 +24,13 @@
     
     ##start standard gatk options
     #if $gatk_param_type.gatk_param_type_selector == "advanced":
-        #for $sample_metadata in $gatk_param_type.sample_metadata:
-            -p '--sample_metadata "${sample_metadata.sample_metadata_file}"'
+        #for $pedigree in $gatk_param_type.pedigree:
+            -p '--pedigree "${pedigree.pedigree_file}"'
         #end for
+        #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
+            -p '--pedigreeString "${pedigree_string.pedigree_string}"'
+        #end for
+        -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
         #for $read_filter in $gatk_param_type.read_filter:
             -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
             ###raise Exception( str( dir( $read_filter ) ) )
@@ -45,7 +49,7 @@
             -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
         #end for
 
-        -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
         
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
@@ -126,9 +130,16 @@
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" />
+        <repeat name="pedigree" title="Pedigree file">
+            <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
         </repeat>
+        <repeat name="pedigree_string_repeat" title="Pedigree string">
+            <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
+        </repeat>
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
+          <option value="STRICT" selected="True">STRICT</option>
+          <option value="SILENT">SILENT</option>
+        </param>
         <repeat name="read_filter" title="Read Filter">
             <conditional name="read_filter_type">
 		      <param name="read_filter_type_selector" type="select" label="Read Filter Type">
@@ -150,7 +161,7 @@
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
         </repeat>
         
-        <param name="BTI_merge_rule" type="select" label="BTI merge rule">
+        <param name="interval_set_rule" type="select" label="Interval set rule">
           <option value="UNION" selected="True">UNION</option>
           <option value="INTERSECTION">INTERSECTION</option>
         </param>
diff --git a/tools/gatk/variant_combine.xml b/tools/gatk/variant_combine.xml
index 23c3d18a6c9..fd1aa9db0b1 100644
--- a/tools/gatk/variant_combine.xml
+++ b/tools/gatk/variant_combine.xml
@@ -30,9 +30,13 @@
    
     ##start standard gatk options
     #if $gatk_param_type.gatk_param_type_selector == "advanced":
-        #for $sample_metadata in $gatk_param_type.sample_metadata:
-            -p '--sample_metadata "${sample_metadata.sample_metadata_file}"'
+        #for $pedigree in $gatk_param_type.pedigree:
+            -p '--pedigree "${pedigree.pedigree_file}"'
         #end for
+        #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
+            -p '--pedigreeString "${pedigree_string.pedigree_string}"'
+        #end for
+        -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
         #for $read_filter in $gatk_param_type.read_filter:
             -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
             ###raise Exception( str( dir( $read_filter ) ) )
@@ -51,7 +55,7 @@
             -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
         #end for
 
-        -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
         
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
@@ -146,9 +150,16 @@
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" />
+        <repeat name="pedigree" title="Pedigree file">
+            <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
         </repeat>
+        <repeat name="pedigree_string_repeat" title="Pedigree string">
+            <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
+        </repeat>
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
+          <option value="STRICT" selected="True">STRICT</option>
+          <option value="SILENT">SILENT</option>
+        </param>
         <repeat name="read_filter" title="Read Filter">
             <conditional name="read_filter_type">
 		      <param name="read_filter_type_selector" type="select" label="Read Filter Type">
@@ -170,7 +181,7 @@
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
         </repeat>
         
-        <param name="BTI_merge_rule" type="select" label="BTI merge rule">
+        <param name="interval_set_rule" type="select" label="Interval set rule">
           <option value="UNION" selected="True">UNION</option>
           <option value="INTERSECTION">INTERSECTION</option>
         </param>
diff --git a/tools/gatk/variant_eval.xml b/tools/gatk/variant_eval.xml
index 95fa3a26610..120dd83a331 100644
--- a/tools/gatk/variant_eval.xml
+++ b/tools/gatk/variant_eval.xml
@@ -43,9 +43,13 @@
    
     ##start standard gatk options
     #if $gatk_param_type.gatk_param_type_selector == "advanced":
-        #for $sample_metadata in $gatk_param_type.sample_metadata:
-            -p '--sample_metadata "${sample_metadata.sample_metadata_file}"'
+        #for $pedigree in $gatk_param_type.pedigree:
+            -p '--pedigree "${pedigree.pedigree_file}"'
         #end for
+        #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
+            -p '--pedigreeString "${pedigree_string.pedigree_string}"'
+        #end for
+        -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
         #for $read_filter in $gatk_param_type.read_filter:
             -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
             ###raise Exception( str( dir( $read_filter ) ) )
@@ -64,7 +68,7 @@
             -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
         #end for
 
-        -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
         
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
@@ -204,9 +208,16 @@
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" />
+        <repeat name="pedigree" title="Pedigree file">
+            <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
         </repeat>
+        <repeat name="pedigree_string_repeat" title="Pedigree string">
+            <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
+        </repeat>
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
+          <option value="STRICT" selected="True">STRICT</option>
+          <option value="SILENT">SILENT</option>
+        </param>
         <repeat name="read_filter" title="Read Filter">
             <conditional name="read_filter_type">
 		      <param name="read_filter_type_selector" type="select" label="Read Filter Type">
@@ -228,7 +239,7 @@
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
         </repeat>
         
-        <param name="BTI_merge_rule" type="select" label="BTI merge rule">
+        <param name="interval_set_rule" type="select" label="Interval set rule">
           <option value="UNION" selected="True">UNION</option>
           <option value="INTERSECTION">INTERSECTION</option>
         </param>
diff --git a/tools/gatk/variant_filtration.xml b/tools/gatk/variant_filtration.xml
index 040a0cb56d5..2d52c67aa7b 100644
--- a/tools/gatk/variant_filtration.xml
+++ b/tools/gatk/variant_filtration.xml
@@ -37,9 +37,13 @@
     
     ##start standard gatk options
     #if $gatk_param_type.gatk_param_type_selector == "advanced":
-        #for $sample_metadata in $gatk_param_type.sample_metadata:
-            -p '--sample_metadata "${sample_metadata.sample_metadata_file}"'
+        #for $pedigree in $gatk_param_type.pedigree:
+            -p '--pedigree "${pedigree.pedigree_file}"'
         #end for
+        #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
+            -p '--pedigreeString "${pedigree_string.pedigree_string}"'
+        #end for
+        -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
         #for $read_filter in $gatk_param_type.read_filter:
             -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
             ###raise Exception( str( dir( $read_filter ) ) )
@@ -58,7 +62,7 @@
             -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
         #end for
 
-        -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
         
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
@@ -160,9 +164,16 @@
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" />
+        <repeat name="pedigree" title="Pedigree file">
+            <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
         </repeat>
+        <repeat name="pedigree_string_repeat" title="Pedigree string">
+            <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
+        </repeat>
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
+          <option value="STRICT" selected="True">STRICT</option>
+          <option value="SILENT">SILENT</option>
+        </param>
         <repeat name="read_filter" title="Read Filter">
             <conditional name="read_filter_type">
 		      <param name="read_filter_type_selector" type="select" label="Read Filter Type">
@@ -184,7 +195,7 @@
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
         </repeat>
         
-        <param name="BTI_merge_rule" type="select" label="BTI merge rule">
+        <param name="interval_set_rule" type="select" label="Interval set rule">
           <option value="UNION" selected="True">UNION</option>
           <option value="INTERSECTION">INTERSECTION</option>
         </param>
diff --git a/tools/gatk/variant_recalibrator.xml b/tools/gatk/variant_recalibrator.xml
index 80310f0c2d6..b63ba752527 100644
--- a/tools/gatk/variant_recalibrator.xml
+++ b/tools/gatk/variant_recalibrator.xml
@@ -45,9 +45,13 @@
     
     ##start standard gatk options
     #if $gatk_param_type.gatk_param_type_selector == "advanced":
-        #for $sample_metadata in $gatk_param_type.sample_metadata:
-            -p '--sample_metadata "${sample_metadata.sample_metadata_file}"'
+        #for $pedigree in $gatk_param_type.pedigree:
+            -p '--pedigree "${pedigree.pedigree_file}"'
         #end for
+        #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
+            -p '--pedigreeString "${pedigree_string.pedigree_string}"'
+        #end for
+        -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
         #for $read_filter in $gatk_param_type.read_filter:
             -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
             ###raise Exception( str( dir( $read_filter ) ) )
@@ -66,7 +70,7 @@
             -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
         #end for
 
-        -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
         
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
@@ -390,9 +394,16 @@
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" />
+        <repeat name="pedigree" title="Pedigree file">
+            <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
         </repeat>
+        <repeat name="pedigree_string_repeat" title="Pedigree string">
+            <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
+        </repeat>
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
+          <option value="STRICT" selected="True">STRICT</option>
+          <option value="SILENT">SILENT</option>
+        </param>
         <repeat name="read_filter" title="Read Filter">
             <conditional name="read_filter_type">
 		      <param name="read_filter_type_selector" type="select" label="Read Filter Type">
@@ -414,7 +425,7 @@
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
         </repeat>
         
-        <param name="BTI_merge_rule" type="select" label="BTI merge rule">
+        <param name="interval_set_rule" type="select" label="Interval set rule">
           <option value="UNION" selected="True">UNION</option>
           <option value="INTERSECTION">INTERSECTION</option>
         </param>
diff --git a/tools/gatk/variants_validate.xml b/tools/gatk/variants_validate.xml
index 752fcd60914..e905c2ff38f 100644
--- a/tools/gatk/variants_validate.xml
+++ b/tools/gatk/variants_validate.xml
@@ -30,9 +30,13 @@
    
     ##start standard gatk options
     #if $gatk_param_type.gatk_param_type_selector == "advanced":
-        #for $sample_metadata in $gatk_param_type.sample_metadata:
-            -p '--sample_metadata "${sample_metadata.sample_metadata_file}"'
+        #for $pedigree in $gatk_param_type.pedigree:
+            -p '--pedigree "${pedigree.pedigree_file}"'
         #end for
+        #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
+            -p '--pedigreeString "${pedigree_string.pedigree_string}"'
+        #end for
+        -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
         #for $read_filter in $gatk_param_type.read_filter:
             -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
             ###raise Exception( str( dir( $read_filter ) ) )
@@ -51,7 +55,7 @@
             -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
         #end for
 
-        -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
+        -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
         
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
@@ -130,9 +134,16 @@
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="sample_metadata" title="Sample Metadata">
-            <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" />
+        <repeat name="pedigree" title="Pedigree file">
+            <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" />
         </repeat>
+        <repeat name="pedigree_string_repeat" title="Pedigree string">
+            <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" />
+        </repeat>
+        <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information">
+          <option value="STRICT" selected="True">STRICT</option>
+          <option value="SILENT">SILENT</option>
+        </param>
         <repeat name="read_filter" title="Read Filter">
             <conditional name="read_filter_type">
 		      <param name="read_filter_type_selector" type="select" label="Read Filter Type">
@@ -154,7 +165,7 @@
           <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" />
         </repeat>
         
-        <param name="BTI_merge_rule" type="select" label="BTI merge rule">
+        <param name="interval_set_rule" type="select" label="Interval set rule">
           <option value="UNION" selected="True">UNION</option>
           <option value="INTERSECTION">INTERSECTION</option>
         </param>

From 35ce9317073685989bcca4fabb5c9dca8c22e06b Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Mon, 21 Nov 2011 11:21:23 -0500
Subject: [PATCH 231/362] Subtle but critical fixes in resetting all metadata
 for tool shed repositories ( and some code clean up ).

---
 .../community/controllers/repository.py       | 63 ++++++++++++-------
 lib/galaxy/webapps/community/model/mapping.py |  2 +-
 .../webapps/community/repository/common.mako  |  2 +-
 .../community/repository/view_changelog.mako  |  2 +-
 4 files changed, 42 insertions(+), 27 deletions(-)

diff --git a/lib/galaxy/webapps/community/controllers/repository.py b/lib/galaxy/webapps/community/controllers/repository.py
index a82bc3f14a0..d521e50bdeb 100644
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -1622,51 +1622,56 @@ class RepositoryController( BaseUIController, ItemRatings ):
         if len( repo ) == 1:
             message, status = set_repository_metadata( trans, id, repository.tip, **kwd )
         else:
-            # The following will be a list of changeset_revisions that have been created or updated.
-            # When the following loop completes, we'll delete all repository_metadata records for
-            # this repository that do not have a changeset_revision value in this list.
+            # The list of changeset_revisions refers to repository_metadata records that have been
+            # created or updated.  When the following loop completes, we'll delete all repository_metadata
+            # records for this repository that do not have a changeset_revision value in this list.
             changeset_revisions = []
-            repository_metadata_tup_for_comparison = ()
+            ancestor_changeset_revision = None
+            ancestor_metadata_dict = None
             for changeset in repo.changelog:
-                ctx = repo.changectx( changeset )
-                current_changeset_revision = str( ctx )
+                current_changeset_revision = str( repo.changectx( changeset ) )
                 ctx = get_changectx_for_changeset( trans, repo, current_changeset_revision )
                 current_metadata_dict, invalid_files = generate_metadata_for_changeset_revision( trans, id, ctx, current_changeset_revision, repo_dir )
                 if current_metadata_dict:
-                    if repository_metadata_tup_for_comparison:
-                        ancestor_changeset_revision, ancestor_metadata_dict = repository_metadata_tup_for_comparison
-                        comparison = self.__compare_changeset_revisions( ancestor_changeset_revision,
-                                                                         ancestor_metadata_dict,
-                                                                         current_changeset_revision,
-                                                                         current_metadata_dict )
-                        # The value of comparsion will be one of:
+                    if ancestor_changeset_revision:
+                        # Compare metadata from ancestor and current.  The value of comparsion will be one of:
                         # 'no metadata' - no metadata for either ancestor or current, so continue from current
                         # 'equal' - ancestor metadata is equivalent to current metadata, so continue from current
                         # 'subset' - ancestor metadata is a subset of current metadata, so continue from current
                         # 'not equal and not subset' - ancestor metadata is neither equal to nor a subset of current
                         #                              metadata, so persist ancestor metadata.
+                        comparison = self.__compare_changeset_revisions( ancestor_changeset_revision,
+                                                                         ancestor_metadata_dict,
+                                                                         current_changeset_revision,
+                                                                         current_metadata_dict )
                         if comparison in [ 'no metadata', 'equal', 'subset' ]:
-                            repository_metadata_tup_for_comparison = ( current_changeset_revision, current_metadata_dict )
+                            ancestor_changeset_revision = current_changeset_revision
+                            ancestor_metadata_dict = current_metadata_dict
                         elif comparison == 'not equal and not subset':
                             self.__create_or_update_repository_metadata( trans, id, repository, ancestor_changeset_revision, ancestor_metadata_dict )
-                            # keep track of the changeset_revisions that we've persisted.
+                            # Keep track of the changeset_revisions that we've persisted.
                             changeset_revisions.append( ancestor_changeset_revision )
-                            repository_metadata_tup_for_comparison = ()
+                            ancestor_changeset_revision = None
+                            ancestor_metadata_dict = None
                     else:
-                        # We're at the first change set in the change log.
-                        repository_metadata_tup_for_comparison = ( current_changeset_revision, current_metadata_dict )
+                        # We're either at the first change set in the change log or we have just created or updated
+                        # a repository_metadata record.  At this point we set the ancestor changeset to the current
+                        # changeset for comparison in the next iteration.
+                        ancestor_changeset_revision = current_changeset_revision
+                        ancestor_metadata_dict = current_metadata_dict
                     if not ctx.children():
                         # We're at the end of the change log.
                         self.__create_or_update_repository_metadata( trans, id, repository, current_changeset_revision, current_metadata_dict )
                         changeset_revisions.append( current_changeset_revision )
+                        ancestor_changeset_revision = None
+                        ancestor_metadata_dict = None
                 elif ancestor_metadata_dict:
                     # Our current change set has no metadata, but our ancestor change set has metadata, so save it.
                     self.__create_or_update_repository_metadata( trans, id, repository, ancestor_changeset_revision, ancestor_metadata_dict )
-                    # keep track of the changeset_revisions that we've persisted.
+                    # Keep track of the changeset_revisions that we've persisted.
                     changeset_revisions.append( ancestor_changeset_revision )
-                    repository_metadata_tup_for_comparison = ()
-                    ancestor_changeset_revision = current_changeset_revision
-                    ancestor_metadata_dict = current_metadata_dict
+                    ancestor_changeset_revision = None
+                    ancestor_metadata_dict = None
             self.__clean_repository_metadata( trans, id, changeset_revisions )
         if not message:                     
             message = "Repository metadata has been reset."
@@ -1699,6 +1704,12 @@ class RepositoryController( BaseUIController, ItemRatings ):
     def __compare_changeset_revisions( self, ancestor_changeset_revision, ancestor_metadata_dict, current_changeset_revision, current_metadata_dict ):
         # The metadata associated with ancestor_changeset_revision is ancestor_metadata_dict.  This changeset_revision
         # is an ancestor of current_changeset_revision which is associated with current_metadata_dict.
+        #
+        # TODO: a new repository_metadata record will be created only when this method returns the string
+        # 'not equal and not subset'.  However, we're currently also returning the strings 'no metadata',
+        # 'equal' and 'subset', depending upon how the 2 change sets compare.  We'll leave things this way
+        # for the current time in case we discover a use for these additional result strings.
+        #
         # Get information about tools.
         if 'tools' in ancestor_metadata_dict:
             ancestor_tools = ancestor_metadata_dict[ 'tools' ]
@@ -1735,7 +1746,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
         else:
             current_datatypes = []
         # Handle case where no metadata exists for either changeset.
-        if not ( ancestor_guids or current_guids or ancestor_workflows or current_workflows or ancestor_datatypes or current_datatypes ):
+        if not ancestor_guids and not current_guids and not ancestor_workflows and not current_workflows and not ancestor_datatypes and not current_datatypes:
             return 'no metadata'
         workflow_comparison = self.__compare_workflows( ancestor_workflows, current_workflows )
         datatype_comparison = self.__compare_datatypes( ancestor_datatypes, current_datatypes )
@@ -1758,9 +1769,13 @@ class RepositoryController( BaseUIController, ItemRatings ):
             for ancestor_workflow in ancestor_workflows:
                 # Currently the only way to differentiate workflows is by name.
                 ancestor_workflow_name = ancestor_workflow[ 'name' ]
+                num_ancestor_workflow_steps = len( ancestor_workflow[ 'steps' ] )
                 found_in_current = False
                 for current_workflow in current_workflows:
-                    if current_workflow[ 'name' ] == ancestor_workflow_name:
+                    # Assume that if the name and number of steps are euqal,
+                    # then the workflows are the same.  Of course, this may
+                    # not be true...
+                    if current_workflow[ 'name' ] == ancestor_workflow_name and len( current_workflow[ 'steps' ] ) == num_ancestor_workflow_steps:
                         found_in_current = True
                         break
                 if not found_in_current:
diff --git a/lib/galaxy/webapps/community/model/mapping.py b/lib/galaxy/webapps/community/model/mapping.py
index 8f2e6c36e9e..ea6659d8ddb 100644
--- a/lib/galaxy/webapps/community/model/mapping.py
+++ b/lib/galaxy/webapps/community/model/mapping.py
@@ -194,7 +194,7 @@ assign_mapper( context, Repository, Repository.table,
         categories=relation( RepositoryCategoryAssociation ),
         ratings=relation( RepositoryRatingAssociation, order_by=desc( RepositoryRatingAssociation.table.c.update_time ), backref="repositories" ),
         user=relation( User.mapper ),
-        downloadable_revisions=relation( RepositoryMetadata, order_by=desc( RepositoryMetadata.table.c.id ) ) ) )
+        downloadable_revisions=relation( RepositoryMetadata, order_by=desc( RepositoryMetadata.table.c.update_time ) ) ) )
 
 assign_mapper( context, RepositoryMetadata, RepositoryMetadata.table,
     properties=dict( repository=relation( Repository ) ) )
diff --git a/templates/webapps/community/repository/common.mako b/templates/webapps/community/repository/common.mako
index 56d820628f4..efd69ebaa80 100644
--- a/templates/webapps/community/repository/common.mako
+++ b/templates/webapps/community/repository/common.mako
@@ -181,7 +181,7 @@
                                             <a href="${h.url_for( controller='workflow', action='view_workflow', repository_metadata_id=repository_metadata_id, workflow_name=encode( workflow_name ), webapp=webapp )}">${workflow_name}</a>
                                         </td>
                                         <td>
-                                            %if 'steps' in workflow_dict:
+                                            %if steps:
                                                 ${len( steps )}
                                             %else:
                                                 unknown
diff --git a/templates/webapps/community/repository/view_changelog.mako b/templates/webapps/community/repository/view_changelog.mako
index ded2d19fc66..9d4be4d7e5e 100644
--- a/templates/webapps/community/repository/view_changelog.mako
+++ b/templates/webapps/community/repository/view_changelog.mako
@@ -107,7 +107,7 @@
                     else:
                         ctx_parent_str = "%s:%s" % ( ctx_parent_rev, ctx_parent )
                     if changeset[ 'has_metadata' ]:
-                        has_metadata_str = 'Repository metadata is associated with this change set.'
+                        has_metadata_str = '<table border="0" bgcolor="#D8D8D8"><tr><td>Repository metadata is associated with this change set.</td></tr></table>'
                     else:
                         has_metadata_str = ''
                 %>

From 06cbfc78b79215091f69299a797007543cd7cab5 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Mon, 21 Nov 2011 12:09:25 -0500
Subject: [PATCH 232/362] Fix for generating metadata on the repository tip.

---
 lib/galaxy/webapps/community/controllers/repository.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/webapps/community/controllers/repository.py b/lib/galaxy/webapps/community/controllers/repository.py
index d521e50bdeb..c31c079023d 100644
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -1631,7 +1631,10 @@ class RepositoryController( BaseUIController, ItemRatings ):
             for changeset in repo.changelog:
                 current_changeset_revision = str( repo.changectx( changeset ) )
                 ctx = get_changectx_for_changeset( trans, repo, current_changeset_revision )
-                current_metadata_dict, invalid_files = generate_metadata_for_changeset_revision( trans, id, ctx, current_changeset_revision, repo_dir )
+                if current_changeset_revision == repository.tip:
+                    current_metadata_dict, invalid_files = generate_metadata_for_repository_tip( trans, id, ctx, current_changeset_revision, repo_dir )
+                else:
+                    current_metadata_dict, invalid_files = generate_metadata_for_changeset_revision( trans, id, ctx, current_changeset_revision, repo_dir )
                 if current_metadata_dict:
                     if ancestor_changeset_revision:
                         # Compare metadata from ancestor and current.  The value of comparsion will be one of:

From f84f48265955ad67632df585f02e433f9d0d55f0 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Mon, 21 Nov 2011 12:38:38 -0500
Subject: [PATCH 233/362] Remove --rodToIntervalTrackName from GATK tools; not
 present in version 1.3.

---
 tools/gatk/count_covariates.xml         |  9 ---------
 tools/gatk/indel_realigner.xml          |  8 --------
 tools/gatk/realigner_target_creator.xml |  8 --------
 tools/gatk/unified_genotyper.xml        |  8 --------
 tools/gatk/variant_annotator.xml        | 17 -----------------
 tools/gatk/variant_eval.xml             | 13 ++-----------
 tools/gatk/variant_filtration.xml       |  5 -----
 tools/gatk/variant_recalibrator.xml     | 11 -----------
 tools/gatk/variants_validate.xml        |  5 -----
 9 files changed, 2 insertions(+), 82 deletions(-)

diff --git a/tools/gatk/count_covariates.xml b/tools/gatk/count_covariates.xml
index b6bd4efb707..6b39c225fcb 100644
--- a/tools/gatk/count_covariates.xml
+++ b/tools/gatk/count_covariates.xml
@@ -39,9 +39,6 @@
         #end if
         #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
         -d "--knownSites:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
-        #if str( $rod_binding.rod_bind_type.rodToIntervalTrackName ):
-            -p '--rodToIntervalTrackName "${rod_bind_name}"'
-        #end if
     #end for
     
     ##start standard gatk options
@@ -186,24 +183,19 @@
 	      </param>
           <when value="dbsnp">
               <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
           </when>
           <when value="snps">
               <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
           </when>
           <when value="indels">
               <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
           </when>
           <when value="mask">
               <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
           </when>
           <when value="custom">
               <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/>
               <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
           </when>
         </conditional>
     </repeat>
@@ -416,7 +408,6 @@
           <param name="ref_file" value="phiX.fasta" ftype="fasta" />
           <param name="input_bam" value="gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam" ftype="bam" />
           <param name="rod_bind_type_selector" value="dbsnp" />
-          <param name="rodToIntervalTrackName" />
           <param name="input_rod" value="gatk/fake_phiX_variant_locations.bed" ftype="bed" />
           <param name="standard_covs" value="True" />
           <param name="covariates" value="ReadGroupCovariate,HomopolymerCovariate,MinimumNQSCovariate,PositionCovariate" />
diff --git a/tools/gatk/indel_realigner.xml b/tools/gatk/indel_realigner.xml
index 0a94b4eb69f..37504afcc76 100644
--- a/tools/gatk/indel_realigner.xml
+++ b/tools/gatk/indel_realigner.xml
@@ -31,9 +31,6 @@
         #end if
         #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
         -d "-known:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
-        #if str( $rod_binding.rod_bind_type.rodToIntervalTrackName ):
-            -p '--rodToIntervalTrackName "${rod_bind_name}"'
-        #end if
     #end for
    
     ##start standard gatk options
@@ -151,20 +148,16 @@
 	      </param>
           <when value="dbsnp">
               <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
           </when>
           <when value="snps">
               <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
           </when>
           <when value="indels">
               <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
           </when>
           <when value="custom">
               <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/>
               <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
           </when>
         </conditional>
     </repeat>
@@ -331,7 +324,6 @@
           <param name="target_intervals" value="gatk/gatk_realigner_target_creator/gatk_realigner_target_creator_out_1.gatk_interval" ftype="gatk_interval" />
           <param name="input_bam" value="gatk/fake_phiX_reads_1.bam" ftype="bam" />
           <param name="rod_bind_type_selector" value="snps" />
-          <param name="rodToIntervalTrackName" />
           <param name="input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" />
           <param name="lod_threshold" value="5.0" />
           <param name="knowns_only" />
diff --git a/tools/gatk/realigner_target_creator.xml b/tools/gatk/realigner_target_creator.xml
index 5d8e4777fb2..5524e906ecb 100644
--- a/tools/gatk/realigner_target_creator.xml
+++ b/tools/gatk/realigner_target_creator.xml
@@ -28,9 +28,6 @@
         #end if
         #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
         -d "-known:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
-        #if str( $rod_binding.rod_bind_type.rodToIntervalTrackName ):
-            -p '--rodToIntervalTrackName "${rod_bind_name}"'
-        #end if
     #end for
    
     ##start standard gatk options
@@ -139,20 +136,16 @@
 	      </param>
           <when value="dbsnp">
               <param name="input_rod" type="data" format="vcf" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
           </when>
           <when value="snps">
               <param name="input_rod" type="data" format="vcf" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
           </when>
           <when value="indels">
               <param name="input_rod" type="data" format="vcf" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
           </when>
           <when value="custom">
               <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/>
               <param name="input_rod" type="data" format="vcf" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
           </when>
         </conditional>
     </repeat>
@@ -306,7 +299,6 @@
           <param name="ref_file" value="phiX.fasta" ftype="fasta" />
           <param name="input_bam" value="gatk/fake_phiX_reads_1.bam" ftype="bam" />
           <param name="rod_bind_type_selector" value="dbsnp" />
-          <param name="rodToIntervalTrackName" />
           <param name="input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" />
           <param name="gatk_param_type_selector" value="basic" />
           <param name="analysis_param_type_selector" value="advanced" />
diff --git a/tools/gatk/unified_genotyper.xml b/tools/gatk/unified_genotyper.xml
index afeeeff2f17..d9b4d45c009 100644
--- a/tools/gatk/unified_genotyper.xml
+++ b/tools/gatk/unified_genotyper.xml
@@ -34,9 +34,6 @@
         #end if
         #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
         -d "--dbsnp:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
-        #if str( $rod_binding.rod_bind_type.rodToIntervalTrackName ):
-            -p '--rodToIntervalTrackName "${rod_bind_name}"'
-        #end if
     #end for
    
     ##start standard gatk options
@@ -168,20 +165,16 @@
 	      </param>
           <when value="dbsnp">
               <param name="input_rod" type="data" format="vcf" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
           </when>
           <when value="snps">
               <param name="input_rod" type="data" format="vcf" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
           </when>
           <when value="indels">
               <param name="input_rod" type="data" format="vcf" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
           </when>
           <when value="custom">
               <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/>
               <param name="input_rod" type="data" format="vcf" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
           </when>
         </conditional>
     </repeat>
@@ -413,7 +406,6 @@
           <param name="input_bam" value="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" />
           <param name="rod_bind_type_selector" value="dbsnp" />
           <param name="input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" />
-          <param name="rodToIntervalTrackName" />
           <param name="standard_min_confidence_threshold_for_calling" value="0" />
           <param name="standard_min_confidence_threshold_for_emitting" value="4" />
           <param name="gatk_param_type_selector" value="basic" />
diff --git a/tools/gatk/variant_annotator.xml b/tools/gatk/variant_annotator.xml
index 093aa6049c0..9de7288c69e 100644
--- a/tools/gatk/variant_annotator.xml
+++ b/tools/gatk/variant_annotator.xml
@@ -43,31 +43,19 @@
     
     #for $rod_binding in $comp_rod_bind:
         -d "--comp:${rod_binding.comp_rod_name},%(file_type)s" "${rod_binding.comp_input_rod}" "${rod_binding.comp_input_rod.ext}" "input_comp_${rod_binding.comp_rod_name}"
-        #if str( $rod_binding.comp_rodToIntervalTrackName ):
-            -p '--rodToIntervalTrackName "${rod_binding.comp_rod_name}"'
-        #end if
     #end for
     
     #if str( $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector ) == 'set_dbsnp':
         -d "--dbsnp:${dbsnp_rod_bind_type.dbsnp_rod_name},%(file_type)s" "${dbsnp_rod_bind_type.dbsnp_input_rod}" "${dbsnp_rod_bind_type.dbsnp_input_rod.ext}" "input_dbsnp_${dbsnp_rod_bind_type.dbsnp_rod_name}"
-        #if str( $dbsnp_rod_bind_type.dbsnp_rodToIntervalTrackName ):
-            -p '--rodToIntervalTrackName "${dbsnp_rod_bind_type.dbsnp_rod_name}"'
-        #end if
     #end if
     
     
     #for $rod_binding in $resource_rod_bind:
         -d "--resource:${rod_binding.resource_rod_name},%(file_type)s" "${rod_binding.resource_input_rod}" "${rod_binding.resource_input_rod.ext}" "input_resource_${rod_binding.resource_rod_name}"
-        #if str( $rod_binding.resource_rodToIntervalTrackName ):
-            -p '--rodToIntervalTrackName "${rod_binding.resource_rod_name}"'
-        #end if
     #end for
     
     #if str( $snpEff_rod_bind_type.snpEff_rod_bind_type_selector ) == 'set_snpEff':
         -d "--snpEff:${snpEff_rod_bind_type.snpEff_rod_name},%(file_type)s" "${snpEff_rod_bind_type.snpEff_input_rod}" "${snpEff_rod_bind_type.snpEff_input_rod.ext}" "input_snpEff_${snpEff_rod_bind_type.snpEff_rod_name}"
-        #if str( $snpEff_rod_bind_type.snpEff_rodToIntervalTrackName ):
-            -p '--rodToIntervalTrackName "${snpEff_rod_bind_type.snpEff_rod_name}"'
-        #end if
     #end if
     
     #for $expression in $expressions:
@@ -214,7 +202,6 @@
     <repeat name="comp_rod_bind" title="Binding for reference-ordered comparison data">
       <param name="comp_input_rod" type="data" format="vcf" label="ROD file" />
       <param name="comp_rod_name" type="text" value="Unnamed" label="ROD Name"/>
-      <param name="comp_rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
     </repeat>
     
     <conditional name="dbsnp_rod_bind_type">
@@ -227,7 +214,6 @@
       </when>
       <when value="set_dbsnp">
         <param name="dbsnp_input_rod" type="data" format="vcf" label="ROD file" />
-        <param name="dbsnp_rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
         <param name="dbsnp_rod_name" type="hidden" value="dbsnp" label="ROD Name"/>
       </when>
     </conditional>
@@ -235,7 +221,6 @@
     <repeat name="resource_rod_bind" title="Binding for reference-ordered resource data">
       <param name="resource_input_rod" type="data" format="vcf" label="ROD file" />
       <param name="resource_rod_name" type="text" value="Unnamed" label="ROD Name"/>
-      <param name="resource_rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
     </repeat>
     
     <conditional name="snpEff_rod_bind_type">
@@ -248,7 +233,6 @@
       </when>
       <when value="set_snpEff">
         <param name="snpEff_input_rod" type="data" format="vcf" label="ROD file" />
-        <param name="snpEff_rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
         <param name="snpEff_rod_name" type="hidden" value="snpEff" label="ROD Name"/>
       </when>
     </conditional>
@@ -403,7 +387,6 @@
           <param name="annotations_type_selector" value="choose" />
           <param name="annotations" value="AlleleBalance,BaseQualityRankSumTest,DepthOfCoverage,HomopolymerRun,MappingQualityRankSumTest,MappingQualityZero,QualByDepth,RMSMappingQuality,SpanningDeletions,HaplotypeScore" />
           <param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" />
-          <param name="dbsnp_rodToIntervalTrackName" />
           <param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" />
           <param name="snpEff_rod_bind_type_selector" value="exclude_snpEff" />
           <param name="gatk_param_type_selector" value="basic" />
diff --git a/tools/gatk/variant_eval.xml b/tools/gatk/variant_eval.xml
index 120dd83a331..773b5ee51d7 100644
--- a/tools/gatk/variant_eval.xml
+++ b/tools/gatk/variant_eval.xml
@@ -23,9 +23,6 @@
    
     #for $rod_binding in $comp_rod_bind:
         -d "--comp:${rod_binding.comp_rod_name},%(file_type)s" "${rod_binding.comp_input_rod}" "${rod_binding.comp_input_rod.ext}" "input_comp_${rod_binding.comp_rod_name}"
-        #if str( $rod_binding.comp_rodToIntervalTrackName ):
-            -p '--rodToIntervalTrackName "${rod_binding.comp_rod_name}"'
-        #end if
         #if str( $rod_binding.comp_known_names ):
             -p '--known_names "${rod_binding.comp_rod_name}"'
         #end if
@@ -33,11 +30,8 @@
     
     #if str( $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector ) == 'set_dbsnp':
         -d "--dbsnp:${dbsnp_rod_bind_type.dbsnp_rod_name},%(file_type)s" "${dbsnp_rod_bind_type.dbsnp_input_rod}" "${dbsnp_rod_bind_type.dbsnp_input_rod.ext}" "input_dbsnp_${dbsnp_rod_bind_type.dbsnp_rod_name}"
-        #if str( $dbsnp_rod_bind_type.dbsnp_rodToIntervalTrackName ):
-            -p '--rodToIntervalTrackName "${dbsnp_rod_bind_type.dbsnp_rod_name}"'
-            #if str( $dbsnp_rod_bind_type.dbsnp_known_names ):
-                -p '--known_names "${dbsnp_rod_bind_type.dbsnp_rod_name}"'
-            #end if
+        #if str( $dbsnp_rod_bind_type.dbsnp_known_names ):
+            -p '--known_names "${dbsnp_rod_bind_type.dbsnp_rod_name}"'
         #end if
     #end if
    
@@ -179,7 +173,6 @@
     <repeat name="comp_rod_bind" title="Binding for reference-ordered comparison data">
       <param name="comp_input_rod" type="data" format="vcf" label="Comparison ROD file" />
       <param name="comp_rod_name" type="text" value="Unnamed" label="Comparison ROD Name"/>
-      <param name="comp_rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use Comparison ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
       <param name="comp_known_names" type="boolean" truevalue="--known_names" falsevalue="" label="Use Comparison ROD as known_names" />
     </repeat>
     
@@ -193,7 +186,6 @@
       </when>
       <when value="set_dbsnp">
         <param name="dbsnp_input_rod" type="data" format="vcf" label="dbSNP ROD file" />
-        <param name="dbsnp_rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use dbSNP ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
         <param name="dbsnp_rod_name" type="hidden" value="dbsnp" label="dbSNP ROD Name"/>
         <param name="dbsnp_known_names" type="boolean" truevalue="--known_names" falsevalue="" label="Use dbSNP ROD as known_names" />
       </when>
@@ -405,7 +397,6 @@
           <param name="ref_file" value="phiX.fasta" ftype="fasta" />
           <param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" />
           <param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" />
-          <param name="dbsnp_rodToIntervalTrackName" />
           <param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" />
           <param name="dbsnp_known_names" value="True"/>
           <param name="comp_rod_bind" value="0" />
diff --git a/tools/gatk/variant_filtration.xml b/tools/gatk/variant_filtration.xml
index 2d52c67aa7b..186470ee66c 100644
--- a/tools/gatk/variant_filtration.xml
+++ b/tools/gatk/variant_filtration.xml
@@ -30,9 +30,6 @@
         --maskExtension "${mask_rod_bind_type.mask_extension}"
         --maskName "${mask_rod_bind_type.mask_rod_name}"
         '
-        #if str( $mask_rod_bind_type.mask_rodToIntervalTrackName ):
-            -p '--rodToIntervalTrackName "${mask_rod_bind_type.mask_rod_name}"'
-        #end if
     #end if
     
     ##start standard gatk options
@@ -150,7 +147,6 @@
         <param name="input_mask_rod" type="data" format="bed,gatk_dbsnp,vcf" label="Mask ROD file" />
         <param name="mask_rod_name" type="text" value="Mask" label="Mask Name"/>
         <param name="mask_extension" type="integer" value="0" label="Mask Extension"/>
-        <param name="mask_rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use Mask ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
       </when>
     </conditional>    
     
@@ -308,7 +304,6 @@
           <param name="filter_name" value="Galaxy_filter" />
           <param name="is_genotype_filter" />
           <param name="mask_rod_bind_type_selector" value="set_mask" />
-          <param name="mask_rodToIntervalTrackName" />
           <param name="input_mask_rod" value="gatk/fake_phiX_variant_locations.bed" ftype="bed" />
           <param name="mask_rod_name" value="." />
           <param name="mask_extension" value="0" />
diff --git a/tools/gatk/variant_recalibrator.xml b/tools/gatk/variant_recalibrator.xml
index b63ba752527..0f6a4237fb0 100644
--- a/tools/gatk/variant_recalibrator.xml
+++ b/tools/gatk/variant_recalibrator.xml
@@ -38,9 +38,6 @@
         #else:
         -d "--resource:${rod_bind_name},%(file_type)s,known=${rod_binding.rod_bind_type.rod_training_type.known},training=${rod_binding.rod_bind_type.rod_training_type.training},truth=${rod_binding.rod_bind_type.rod_training_type.truth},bad=${rod_binding.rod_bind_type.rod_training_type.bad},prior=${rod_binding.rod_bind_type.rod_training_type.prior}" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
         #end if
-        #if str( $rod_binding.rod_bind_type.rodToIntervalTrackName ):
-            -p '--rodToIntervalTrackName "${rod_bind_name}"'
-        #end if
     #end for
     
     ##start standard gatk options
@@ -183,7 +180,6 @@
           </param>
           <when value="variant">
               <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="Variant ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
               <conditional name="rod_training_type">
                   <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
                       <option value="is_training_truth_known">Set training/truth/known sites</option>
@@ -204,7 +200,6 @@
           <when value="comp">
               <param name="input_rod" type="data" format="vcf,gatk_dbsnp" label="ROD file" />
               <param name="custom_rod_name" type="text" value="Unnamed" label="ROD Name"/>
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
               <conditional name="rod_training_type">
                   <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
                       <option value="is_training_truth_known">Set training/truth/known sites</option>
@@ -224,7 +219,6 @@
           </when>
           <when value="dbsnp">
               <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
               <conditional name="rod_training_type">
                   <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
                       <option value="is_training_truth_known">Set training/truth/known sites</option>
@@ -244,7 +238,6 @@
           </when>
           <when value="snps">
               <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
               <conditional name="rod_training_type">
                   <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
                       <option value="is_training_truth_known">Set training/truth/known sites</option>
@@ -264,7 +257,6 @@
           </when>
           <when value="hapmap">
               <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
               <conditional name="rod_training_type">
                   <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
                       <option value="is_training_truth_known">Set training/truth/known sites</option>
@@ -284,7 +276,6 @@
           </when>
           <when value="omni">
               <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
               <conditional name="rod_training_type">
                   <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
                       <option value="is_training_truth_known">Set training/truth/known sites</option>
@@ -304,7 +295,6 @@
           </when>
           <when value="indels">
               <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
               <conditional name="rod_training_type">
                   <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
                       <option value="is_training_truth_known">Set training/truth/known sites</option>
@@ -325,7 +315,6 @@
           <when value="custom">
               <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/>
               <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
-              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
               <conditional name="rod_training_type">
                   <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
                       <option value="is_training_truth_known">Set training/truth/known sites</option>
diff --git a/tools/gatk/variants_validate.xml b/tools/gatk/variants_validate.xml
index e905c2ff38f..911d2533189 100644
--- a/tools/gatk/variants_validate.xml
+++ b/tools/gatk/variants_validate.xml
@@ -23,9 +23,6 @@
    
     #if str( $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector ) == 'set_dbsnp':
         -d "--dbsnp:${dbsnp_rod_bind_type.dbsnp_rod_name},%(file_type)s" "${dbsnp_rod_bind_type.dbsnp_input_rod}" "${dbsnp_rod_bind_type.dbsnp_input_rod.ext}" "input_dbsnp_${dbsnp_rod_bind_type.dbsnp_rod_name}"
-        #if str( $dbsnp_rod_bind_type.dbsnp_rodToIntervalTrackName ):
-            -p '--rodToIntervalTrackName "${dbsnp_rod_bind_type.dbsnp_rod_name}"'
-        #end if
     #end if
    
     ##start standard gatk options
@@ -117,7 +114,6 @@
       </when>
       <when value="set_dbsnp">
         <param name="dbsnp_input_rod" type="data" format="vcf" label="ROD file" />
-        <param name="dbsnp_rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
         <param name="dbsnp_rod_name" type="hidden" value="dbsnp" label="ROD Name"/>
       </when>
     </conditional>
@@ -258,7 +254,6 @@
           <param name="ref_file" value="phiX.fasta" ftype="fasta" />
           <param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" />
           <param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" />
-          <param name="dbsnp_rodToIntervalTrackName" />
           <param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" />
           <param name="warn_on_errors" value="True"/>
           <param name="do_not_validate_filtered_records" />

From 8986dc2c812a22489c930f55366a9bbcb08ebab1 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Mon, 21 Nov 2011 16:30:34 -0500
Subject: [PATCH 234/362] Add SAMTools mpileup.

---
 datatypes_conf.xml.sample           |   1 +
 tool_conf.xml.sample                |   1 +
 tool_data_table_conf.xml.sample     |   5 +
 tools/samtools/samtools_mpileup.xml | 213 ++++++++++++++++++++++++++++
 tools/samtools/samtools_wrapper.py  | 110 ++++++++++++++
 5 files changed, 330 insertions(+)
 create mode 100644 tools/samtools/samtools_mpileup.xml
 create mode 100644 tools/samtools/samtools_wrapper.py

diff --git a/datatypes_conf.xml.sample b/datatypes_conf.xml.sample
index cd87e71aae0..5f756eec957 100644
--- a/datatypes_conf.xml.sample
+++ b/datatypes_conf.xml.sample
@@ -159,6 +159,7 @@
       <converter file="vcf_to_summary_tree_converter.xml" target_datatype="summary_tree"/>
       <display file="igv/vcf.xml" />
     </datatype>
+    <datatype extension="bcf" type="galaxy.datatypes.binary:Binary" subclass="True"/>
     <datatype extension="wsf" type="galaxy.datatypes.wsf:SnpFile" display_in_upload="true"/>
     <datatype extension="velvet" type="galaxy.datatypes.assembly:Velvet" display_in_upload="false"/>
     <datatype extension="wig" type="galaxy.datatypes.interval:Wiggle" display_in_upload="true">
diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index ce4347e756f..ee3ba7e8ba1 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -371,6 +371,7 @@
     <tool file="samtools/sam_to_bam.xml" />
     <tool file="samtools/bam_to_sam.xml" />
     <tool file="samtools/sam_merge.xml" />
+    <tool file="samtools/samtools_mpileup.xml" />
     <tool file="samtools/sam_pileup.xml" />
     <tool file="samtools/pileup_parser.xml" />
     <tool file="samtools/pileup_interval.xml" />
diff --git a/tool_data_table_conf.xml.sample b/tool_data_table_conf.xml.sample
index a217776b72a..5a899e0990b 100644
--- a/tool_data_table_conf.xml.sample
+++ b/tool_data_table_conf.xml.sample
@@ -65,6 +65,11 @@
         <columns>value, name, path</columns>
         <file path="tool-data/perm_color_index.loc" />
     </table>
+    <!-- Location of SAMTools indexes and other files -->
+    <table name="sam_fa_indexes" comment_char="#">
+        <columns>line_type, value, path</columns>
+        <file path="tool-data/sam_fa_indices.loc" />
+    </table>
     <!-- Location of Picard dict file and other files -->
     <table name="picard_indexes" comment_char="#">
         <columns>value, dbkey, name, path</columns>
diff --git a/tools/samtools/samtools_mpileup.xml b/tools/samtools/samtools_mpileup.xml
new file mode 100644
index 00000000000..6068e1efaea
--- /dev/null
+++ b/tools/samtools/samtools_mpileup.xml
@@ -0,0 +1,213 @@
+<tool id="samtools_mpileup" name="MPileup" version="0.0.1">
+  <description>SNP and indel caller</description>
+  <requirements>
+      <requirement type="package">samtools</requirement>
+  </requirements>
+  <command interpreter="python">samtools_wrapper.py
+    -p 'samtools mpileup'
+    --stdout "${output_log}"
+    #if $reference_source.reference_source_selector != "history":
+        -p '-f "${reference_source.ref_file.fields.path}"'
+    #else:
+        -d "-f" "${reference_source.ref_file}" "fa" "reference_input"
+    #end if
+    #for $i, $input_bam in enumerate( $reference_source.input_bams ):
+        -d " " "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "bam_input_${i}"
+        -d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "bam_input_${i}" ##hardcode galaxy ext type as bam_index
+    #end for
+    -p '
+    #if str( $advanced_options.advanced_options_selector ) == "advanced":
+        ${advanced_options.skip_anomalous_read_pairs}
+        ${advanced_options.disable_probabilistic_realignment}
+        -C "${advanced_options.coefficient_for_downgrading}"
+        -d "${advanced_options.max_reads_per_bam}"
+        ${advanced_options.extended_BAQ_computation}
+        #if str( $advanced_options.position_list ) != 'None':
+          -l "${advanced_options.position_list}"
+        #end if
+        -q "${advanced_options.minimum_mapping_quality}"
+        -Q "${advanced_options.minimum_base_quality}"
+        #if str( $advanced_options.region_string ):
+            -r "${advanced_options.region_string}"
+        #end if
+        ${advanced_options.output_per_sample_read_depth}
+        ${advanced_options.output_per_sample_strand_bias_p_value}
+    #end if
+    #if str( $genotype_likelihood_computation_type.genotype_likelihood_computation_type_selector ) == 'perform_genotype_likelihood_computation':
+        ##-g or -u
+        -g
+        -e "${genotype_likelihood_computation_type.gap_extension_sequencing_error_probability}"
+        -h "${genotype_likelihood_computation_type.coefficient_for_modeling_homopolymer_errors}"
+        #if str( $genotype_likelihood_computation_type.perform_indel_calling.perform_indel_calling_selector ) == 'perform_indel_calling':
+            -L "${genotype_likelihood_computation_type.perform_indel_calling.skip_indel_calling_above_sample_depth}"
+        #else:
+            -I
+        #end if
+        -o "${genotype_likelihood_computation_type.gap_open_sequencing_error_probability}"
+        #if len( $genotype_likelihood_computation_type.platform_list_repeat ):
+            -P "${ ",".join( [ str( platform.platform_entry ) for platform in $genotype_likelihood_computation_type.platform_list_repeat ] ) }"
+        #end if
+    #end if
+    &gt; "${output_mpileup}"
+    '
+  </command>
+  <inputs>
+    <conditional name="reference_source">
+      <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
+        <option value="cached">Locally cached</option>
+        <option value="history">History</option>
+      </param>
+      <when value="cached">
+        <repeat name="input_bams" title="BAM file" min="1">
+            <param name="input_bam" type="data" format="bam" label="BAM file">
+              <validator type="unspecified_build" />
+              <validator type="dataset_metadata_in_data_table" table_name="sam_fa_indexes" metadata_name="dbkey" metadata_column="value" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
+            </param>
+        </repeat>
+        <param name="ref_file" type="select" label="Using reference genome">
+          <options from_data_table="sam_fa_indexes">
+            <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="value"/> does not yet work in a repeat...--> 
+          </options>
+        </param>
+      </when>
+      <when value="history"> <!-- FIX ME!!!! -->
+        <repeat name="input_bams" title="BAM file" min="1">
+            <param name="input_bam" type="data" format="bam" label="BAM file" >
+              <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
+            </param>
+        </repeat>
+        <param name="ref_file" type="data" format="fasta" label="Using reference file" />
+      </when>
+    </conditional>
+
+    
+    <conditional name="genotype_likelihood_computation_type">
+      <param name="genotype_likelihood_computation_type_selector" type="select" label="Genotype Likelihood Computation">
+        <option value="perform_genotype_likelihood_computation">Perform genotype likelihood computation</option>
+        <option value="do_not_perform_genotype_likelihood_computation" selected="True">Do not perform genotype likelihood computation</option>
+      </param>
+      <when value="perform_genotype_likelihood_computation">
+          <param name="gap_extension_sequencing_error_probability" type="integer" value="20" label="Phred-scaled gap extension sequencing error probability" />
+          <param name="coefficient_for_modeling_homopolymer_errors" type="integer" value="100" label="Coefficient for modeling homopolymer errors." />
+          <conditional name="perform_indel_calling">
+            <param name="perform_indel_calling_selector" type="select" label="Perform INDEL calling">
+              <option value="perform_indel_calling" selected="True">Perform INDEL calling</option>
+              <option value="do_not_perform_indel_calling">Do not perform INDEL calling</option>
+            </param>
+            <when value="perform_indel_calling">
+              <param name="skip_indel_calling_above_sample_depth" type="integer" value="250" label="Skip INDEL calling if the average per-sample depth is above" />
+            </when>
+            <when value="do_no_perform_indel_calling" />
+          </conditional>
+          <param name="gap_open_sequencing_error_probability" type="integer" value="40" label="Phred-scaled gap open sequencing error probability" />
+          <repeat name="platform_list_repeat" title="Platform for INDEL candidates">
+            <param name="platform_entry" type="text" value="" label="Platform to use for INDEL candidates" />
+          </repeat>
+      </when>
+      <when value="do_not_perform_genotype_likelihood_computation">
+          <!-- Do nothing here -->
+      </when>
+    </conditional>
+    <conditional name="advanced_options">
+      <param name="advanced_options_selector" type="select" label="Set advanced options">
+        <option value="basic" selected="True">Basic</option>
+        <option value="advanced">Advanced</option>
+      </param>
+      <when value="advanced">
+        <param name="skip_anomalous_read_pairs" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Do not skip anomalous read pairs in variant calling" />
+        <param name="disable_probabilistic_realignment" type="boolean" truevalue="-B" falsevalue="" checked="False" label="	Disable probabilistic realignment for the computation of base alignment quality (BAQ)" />
+        <param name="coefficient_for_downgrading" type="integer" value="0" label="Coefficient for downgrading mapping quality for reads containing excessive mismatches" />
+        <param name="max_reads_per_bam" type="integer" value="250" label="Max reads per BAM" />
+        <param name="extended_BAQ_computation" type="boolean" truevalue="-E" falsevalue="" checked="False" label="Extended BAQ computation" />
+        <param name="position_list" type="data" format="bed" label="List of regions or sites on which to operate" optional="True" />
+        <param name="minimum_mapping_quality" type="integer" value="0" label="Minimum mapping quality for an alignment to be used" />
+        <param name="minimum_base_quality" type="integer" value="13" label="Minimum base quality for a base to be considered" />
+        <param name="region_string" type="text" value="" label="Only generate pileup in region" />
+        <param name="output_per_sample_read_depth" type="boolean" truevalue="-D" falsevalue="" checked="False" label="Output per-sample read depth" />
+        <param name="output_per_sample_strand_bias_p_value" type="boolean" truevalue="-S" falsevalue="" checked="False" label="Output per-sample Phred-scaled strand bias P-value" />
+      </when>
+      <when value="basic" />
+    </conditional>
+  </inputs>
+  <outputs>
+    <data format="pileup" name="output_mpileup" label="${tool.name} on ${on_string}">
+      <change_format>
+        <when input="genotype_likelihood_computation_type.genotype_likelihood_computation_type_selector" value="perform_genotype_likelihood_computation" format="bcf" />
+      </change_format>
+    </data>
+    <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
+  </outputs>
+  <tests>
+      <test>
+          <param name="reference_source_selector" value="history" />
+          <param name="ref_file" value="phiX.fasta" ftype="fasta" />
+          <param name="input_bam" value="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" />
+          <param name="genotype_likelihood_computation_type_selector" value="do_not_perform_genotype_likelihood_computation" />
+          <param name="advanced_options_selector" value="basic" />
+          <output name="output_mpileup" file="samtools/mpileup/samtools_mpileup_out_1.pileup" /> 
+          <output name="output_log" file="samtools/mpileup/samtools_mpileup_out_1.log" />
+      </test>
+      <test>
+          <param name="reference_source_selector" value="history" />
+          <param name="ref_file" value="phiX.fasta" ftype="fasta" />
+          <param name="input_bam" value="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" />
+          <param name="genotype_likelihood_computation_type_selector" value="perform_genotype_likelihood_computation" />
+          <param name="gap_extension_sequencing_error_probability" value="20" />
+          <param name="coefficient_for_modeling_homopolymer_errors" value="100" />
+          <param name="perform_indel_calling_selector" value="perform_indel_calling" />
+          <param name="skip_indel_calling_above_sample_depth" value="250" />
+          <param name="gap_open_sequencing_error_probability" value="40" />
+          <param name="platform_list_repeat" value="0" />
+          <param name="advanced_options_selector" value="basic" />
+          <output name="output_mpileup" file="samtools/mpileup/samtools_mpileup_out_2.bcf" /> 
+          <output name="output_log" file="samtools/mpileup/samtools_mpileup_out_1.log" />
+      </test>
+  </tests>
+  <help>
+**What it does**
+
+ Generate BCF or pileup for one or multiple BAM files. Alignment records are grouped by sample identifiers in @RG header lines. If sample identifiers are absent, each input file is regarded as one sample. 
+
+------
+
+**Settings**::
+
+ Input Options:
+ -6 	Assume the quality is in the Illumina 1.3+ encoding.
+ -A Do not skip anomalous read pairs in variant calling.
+ -B 	Disable probabilistic realignment for the computation of base alignment quality (BAQ). BAQ is the Phred-scaled probability of a read base being misaligned. Applying this option greatly helps to reduce false SNPs caused by misalignments.
+ -b FILE 	List of input BAM files, one file per line [null]
+ -C INT 	Coefficient for downgrading mapping quality for reads containing excessive mismatches. Given a read with a phred-scaled probability q of being generated from the mapped position, the new mapping quality is about sqrt((INT-q)/INT)*INT. A zero value disables this functionality; if enabled, the recommended value for BWA is 50. [0]
+ -d INT 	At a position, read maximally INT reads per input BAM. [250]
+ -E 	Extended BAQ computation. This option helps sensitivity especially for MNPs, but may hurt specificity a little bit.
+ -f FILE 	The faidx-indexed reference file in the FASTA format. The file can be optionally compressed by razip. [null]
+ -l FILE 	BED or position list file containing a list of regions or sites where pileup or BCF should be generated [null]
+ -q INT 	Minimum mapping quality for an alignment to be used [0]
+ -Q INT 	Minimum base quality for a base to be considered [13]
+ -r STR 	Only generate pileup in region STR [all sites]
+ Output Options:
+ 	
+ -D 	Output per-sample read depth
+ -g 	Compute genotype likelihoods and output them in the binary call format (BCF).
+ -S 	Output per-sample Phred-scaled strand bias P-value
+ -u 	Similar to -g except that the output is uncompressed BCF, which is preferred for piping.
+ 
+ Options for Genotype Likelihood Computation (for -g or -u):
+  	
+ -e INT 	Phred-scaled gap extension sequencing error probability. Reducing INT leads to longer indels. [20]
+ -h INT 	Coefficient for modeling homopolymer errors. Given an l-long homopolymer run, the sequencing error of an indel of size s is modeled as INT*s/l. [100]
+ -I 	Do not perform INDEL calling
+ -L INT 	Skip INDEL calling if the average per-sample depth is above INT. [250]
+ -o INT 	Phred-scaled gap open sequencing error probability. Reducing INT leads to more indel calls. [40]
+ -P STR 	Comma dilimited list of platforms (determined by @RG-PL) from which indel candidates are obtained. It is recommended to collect indel candidates from sequencing technologies that have low indel error rate such as ILLUMINA. [all]
+
+------
+
+**Citation**
+
+For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_
+
+If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
+
+  </help>
+</tool>
diff --git a/tools/samtools/samtools_wrapper.py b/tools/samtools/samtools_wrapper.py
new file mode 100644
index 00000000000..ade066b0b7b
--- /dev/null
+++ b/tools/samtools/samtools_wrapper.py
@@ -0,0 +1,110 @@
+#!/usr/bin/env python
+#Dan Blankenberg
+
+"""
+A wrapper script for running SAMTools commands.
+"""
+
+import sys, optparse, os, tempfile, subprocess, shutil
+from string import Template
+
+GALAXY_EXT_TO_SAMTOOLS_EXT = { 'bam_index':'bam.bai', } #items not listed here will use the galaxy extension as-is
+GALAXY_EXT_TO_SAMTOOLS_FILE_TYPE = GALAXY_EXT_TO_SAMTOOLS_EXT #for now, these are the same, but could be different if needed
+DEFAULT_SAMTOOLS_PREFIX = "SAMTools_file"
+CHUNK_SIZE = 2**20 #1mb
+
+
+def cleanup_before_exit( tmp_dir ):
+    if tmp_dir and os.path.exists( tmp_dir ):
+        shutil.rmtree( tmp_dir )
+
+def SAMTOOLS_filename_from_galaxy( galaxy_filename, galaxy_ext, target_dir = None, prefix = None ):
+    suffix = GALAXY_EXT_TO_SAMTOOLS_EXT.get( galaxy_ext, galaxy_ext )
+    if prefix is None:
+        prefix = DEFAULT_SAMTOOLS_PREFIX
+    if target_dir is None:
+        target_dir = os.getcwd()
+    SAMTools_filename = os.path.join( target_dir, "%s.%s" % ( prefix, suffix ) )
+    os.symlink( galaxy_filename, SAMTools_filename )
+    return SAMTools_filename
+
+def SAMTOOLS_filetype_argument_substitution( argument, galaxy_ext ):
+    return argument % dict( file_type = GALAXY_EXT_TO_SAMTOOLS_FILE_TYPE.get( galaxy_ext, galaxy_ext ) )
+
+def open_file_from_option( filename, mode = 'rb' ):
+    if filename:
+        return open( filename, mode = mode )
+    return None
+
+def html_report_from_directory( html_out, dir ):
+    html_out.write( '<html>\n<head>\n<title>Galaxy - SAMTOOLS Output</title>\n</head>\n<body>\n<p/>\n<ul>\n' )
+    for fname in sorted( os.listdir( dir ) ):
+        html_out.write(  '<li><a href="%s">%s</a></li>\n' % ( fname, fname ) )
+    html_out.write( '</ul>\n</body>\n</html>\n' )
+
+def __main__():
+    #Parse Command Line
+    parser = optparse.OptionParser()
+    parser.add_option( '-p', '--pass_through', dest='pass_through_options', action='append', type="string", help='These options are passed through directly to SAMTOOLS, without any modification.' )
+    parser.add_option( '-d', '--dataset', dest='datasets', action='append', type="string", nargs=4, help='"-argument" "original_filename" "galaxy_filetype" "name_prefix"' )
+    parser.add_option( '', '--stdout', dest='stdout', action='store', type="string", default=None, help='If specified, the output of stdout will be written to this file.' )
+    parser.add_option( '', '--stderr', dest='stderr', action='store', type="string", default=None, help='If specified, the output of stderr will be written to this file.' )
+    parser.add_option( '', '--html_report_from_directory', dest='html_report_from_directory', action='append', type="string", nargs=2, help='"Target HTML File" "Directory"')
+    (options, args) = parser.parse_args()
+    
+    tmp_dir = tempfile.mkdtemp( prefix='tmp-SAMTOOLS-' )
+    
+    #set up stdout and stderr output options
+    stdout = open_file_from_option( options.stdout, mode = 'wb' )
+    stderr = open_file_from_option( options.stderr, mode = 'wb' )
+    #if no stderr file is specified, we'll use our own
+    if stderr is None:
+        stderr = tempfile.NamedTemporaryFile( prefix="SAMTOOLS-stderr-", dir=tmp_dir )
+    
+    if options.pass_through_options:
+        cmd = ' '.join( options.pass_through_options )
+    else:
+        cmd = ''
+    return_code = None
+    if options.datasets:
+        for ( dataset_arg, filename, galaxy_ext, prefix ) in options.datasets:
+            SAMTools_filename = SAMTOOLS_filename_from_galaxy( filename, galaxy_ext, target_dir = tmp_dir, prefix = prefix )
+            if dataset_arg:
+                if '>' in cmd:
+                    cmd = cmd.replace( '>', '  %s "%s" >' % ( SAMTOOLS_filetype_argument_substitution( dataset_arg, galaxy_ext ), SAMTools_filename ), 1 )
+                else:
+                    cmd = '%s %s "%s"' % ( cmd, SAMTOOLS_filetype_argument_substitution( dataset_arg, galaxy_ext ), SAMTools_filename )
+            #auto index fasta files:
+            if galaxy_ext == 'fa':
+                index_cmd = 'samtools faidx %s' % ( SAMTools_filename )
+                proc = subprocess.Popen( args=index_cmd, stdout=stdout, stderr=stderr, shell=True, cwd=tmp_dir )
+                return_code = proc.wait()
+                if return_code:
+                    break
+    if return_code is None or not return_code:
+        proc = subprocess.Popen( args=cmd, stdout=stdout, stderr=stderr, shell=True, cwd=tmp_dir )
+        return_code = proc.wait()
+    if return_code:
+        stderr_target = sys.stderr
+    else:
+        if stdout:
+            stderr_target = stdout
+        else:
+            stderr_target = sys.stdout
+    stderr.flush()
+    stderr.seek(0)
+    while True:
+        chunk = stderr.read( CHUNK_SIZE )
+        if chunk:
+            stderr_target.write( chunk )
+        else:
+            break
+    stderr.close()
+    #generate html reports
+    if options.html_report_from_directory:
+        for ( html_filename, html_dir ) in options.html_report_from_directory:
+            html_report_from_directory( open( html_filename, 'wb' ), html_dir )
+    
+    cleanup_before_exit( tmp_dir )
+
+if __name__=="__main__": __main__()

From d5f735faacedc1beb76d56a3cf3df1c6f29d0fa5 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Mon, 21 Nov 2011 16:41:19 -0500
Subject: [PATCH 235/362] Remove no longer supported ROD datatypes from GATK
 tools (version 1.3).

---
 tools/gatk/indel_realigner.xml      |  8 ++++----
 tools/gatk/variant_recalibrator.xml | 16 ++++++++--------
 2 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/tools/gatk/indel_realigner.xml b/tools/gatk/indel_realigner.xml
index 37504afcc76..fb97635d5fe 100644
--- a/tools/gatk/indel_realigner.xml
+++ b/tools/gatk/indel_realigner.xml
@@ -147,17 +147,17 @@
 	        <option value="custom">Custom</option>
 	      </param>
           <when value="dbsnp">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
           </when>
           <when value="snps">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
           </when>
           <when value="indels">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
           </when>
           <when value="custom">
               <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/>
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
           </when>
         </conditional>
     </repeat>
diff --git a/tools/gatk/variant_recalibrator.xml b/tools/gatk/variant_recalibrator.xml
index 0f6a4237fb0..3e44b0944cd 100644
--- a/tools/gatk/variant_recalibrator.xml
+++ b/tools/gatk/variant_recalibrator.xml
@@ -179,7 +179,7 @@
             <option value="custom">Custom</option>
           </param>
           <when value="variant">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="Variant ROD file" />
+              <param name="input_rod" type="data" format="vcf" label="Variant ROD file" />
               <conditional name="rod_training_type">
                   <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
                       <option value="is_training_truth_known">Set training/truth/known sites</option>
@@ -198,7 +198,7 @@
               </conditional>
           </when>
           <when value="comp">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp" label="ROD file" />
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
               <param name="custom_rod_name" type="text" value="Unnamed" label="ROD Name"/>
               <conditional name="rod_training_type">
                   <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
@@ -218,7 +218,7 @@
               </conditional>
           </when>
           <when value="dbsnp">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
               <conditional name="rod_training_type">
                   <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
                       <option value="is_training_truth_known">Set training/truth/known sites</option>
@@ -237,7 +237,7 @@
               </conditional>
           </when>
           <when value="snps">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
               <conditional name="rod_training_type">
                   <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
                       <option value="is_training_truth_known">Set training/truth/known sites</option>
@@ -256,7 +256,7 @@
               </conditional>
           </when>
           <when value="hapmap">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
               <conditional name="rod_training_type">
                   <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
                       <option value="is_training_truth_known">Set training/truth/known sites</option>
@@ -275,7 +275,7 @@
               </conditional>
           </when>
           <when value="omni">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
               <conditional name="rod_training_type">
                   <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
                       <option value="is_training_truth_known">Set training/truth/known sites</option>
@@ -294,7 +294,7 @@
               </conditional>
           </when>
           <when value="indels">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
               <conditional name="rod_training_type">
                   <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
                       <option value="is_training_truth_known">Set training/truth/known sites</option>
@@ -314,7 +314,7 @@
           </when>
           <when value="custom">
               <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/>
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
               <conditional name="rod_training_type">
                   <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
                       <option value="is_training_truth_known">Set training/truth/known sites</option>

From c1dd3d3eaa0549c3ab8f4ee9822ca49aa82c578e Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Mon, 21 Nov 2011 16:55:16 -0500
Subject: [PATCH 236/362] Update help for some SAMTools.

---
 tools/samtools/bam_to_sam.xml        | 6 ++++++
 tools/samtools/sam_pileup.xml        | 6 ++++++
 tools/samtools/sam_to_bam.xml        | 6 ++++++
 tools/samtools/samtools_flagstat.xml | 8 ++++++++
 tools/samtools/samtools_rmdup.xml    | 8 ++++++++
 5 files changed, 34 insertions(+)

diff --git a/tools/samtools/bam_to_sam.xml b/tools/samtools/bam_to_sam.xml
index 2a72324e481..e9ea217c3f7 100644
--- a/tools/samtools/bam_to_sam.xml
+++ b/tools/samtools/bam_to_sam.xml
@@ -56,5 +56,11 @@ This tool uses the SAMTools_ toolkit to produce a SAM file from a BAM file.
 
 .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
 
+------
+
+**Citation**
+
+For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_
+
   </help>
 </tool>
diff --git a/tools/samtools/sam_pileup.xml b/tools/samtools/sam_pileup.xml
index 430582962bf..bdb3fe92822 100644
--- a/tools/samtools/sam_pileup.xml
+++ b/tools/samtools/sam_pileup.xml
@@ -177,6 +177,12 @@ where::
 
 .. _consensus: http://samtools.sourceforge.net/cns0.shtml
 
+------
+
+**Citation**
+
+For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_
+
 
   </help>
 </tool>
diff --git a/tools/samtools/sam_to_bam.xml b/tools/samtools/sam_to_bam.xml
index 9b295cfb2e0..7364bb4fdac 100644
--- a/tools/samtools/sam_to_bam.xml
+++ b/tools/samtools/sam_to_bam.xml
@@ -87,5 +87,11 @@ This tool uses the SAMTools_ toolkit to produce an indexed BAM file based on a s
 
 .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
 
+------
+
+**Citation**
+
+For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_
+
   </help>
 </tool>
diff --git a/tools/samtools/samtools_flagstat.xml b/tools/samtools/samtools_flagstat.xml
index 5ccc412d47c..eae54b768ec 100644
--- a/tools/samtools/samtools_flagstat.xml
+++ b/tools/samtools/samtools_flagstat.xml
@@ -25,5 +25,13 @@ This tool uses the SAMTools_ toolkit to produce simple stats on a BAM file.
 
 .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
 
+------
+
+**Citation**
+
+For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_
+
+If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
+
   </help>
 </tool>
diff --git a/tools/samtools/samtools_rmdup.xml b/tools/samtools/samtools_rmdup.xml
index b9b7424bdec..835310c8422 100644
--- a/tools/samtools/samtools_rmdup.xml
+++ b/tools/samtools/samtools_rmdup.xml
@@ -57,5 +57,13 @@ This tool uses the SAMTools_ toolkit to remove potential PCR duplicates: if mult
 
 .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
 
+------
+
+**Citation**
+
+For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_
+
+If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
+
   </help>
 </tool>

From 7cf9b6daea26cbde9dcadbd94a0ef039beb3e7af Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Mon, 21 Nov 2011 17:12:07 -0500
Subject: [PATCH 237/362] Updates for GenomeSpace file browser importer.

---
 tool_conf.xml.sample                              |  4 +++-
 .../data_source/genomespace_file_browser_prod.xml | 15 +++++++++++++++
 .../data_source/genomespace_file_browser_test.xml | 15 +++++++++++++++
 3 files changed, 33 insertions(+), 1 deletion(-)
 create mode 100644 tools/data_source/genomespace_file_browser_prod.xml
 create mode 100644 tools/data_source/genomespace_file_browser_test.xml

diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index ee3ba7e8ba1..1f12de1a36f 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -26,7 +26,9 @@
     <tool file="data_source/epigraph_import.xml" />
     <tool file="data_source/epigraph_import_test.xml" />
     <tool file="data_source/hbvar.xml" />
-    <tool file="data_source/genomespace_file_browser_dev.xml" />
+    <tool file="data_source/genomespace_file_browser_prod.xml" />
+    <!-- <tool file="data_source/genomespace_file_browser_test.xml" />
+    <tool file="data_source/genomespace_file_browser_dev.xml" /> -->
     <tool file="validation/fix_errors.xml" />
   </section>
   <section name="Send Data" id="send">
diff --git a/tools/data_source/genomespace_file_browser_prod.xml b/tools/data_source/genomespace_file_browser_prod.xml
new file mode 100644
index 00000000000..0dbb0cb765a
--- /dev/null
+++ b/tools/data_source/genomespace_file_browser_prod.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0"?>
+<tool name="GenomeSpace import" id="genomespace_file_browser_prod" tool_type="data_source" add_galaxy_url="False" force_history_refresh="True" version="0.0.1">
+    <description>from file browser</description>
+    <command interpreter="python">genomespace_file_browser.py --json_parameter_file "${output}" --genomespace_site "prod"</command>
+    <inputs action="https://dm.genomespace.org/datamanager/defaultdirectory" check_values="False" method="post"> 
+        <display>go to GenomeSpace Data Manager </display>
+        <param name="appCallbackUrl" type="baseurl" value="/tool_runner?tool_id=genomespace_file_browser_dev&amp;runtool_btn=Execute" />
+        <param name="appName" type="hidden" value="Galaxy" />
+    </inputs>
+    <uihints minwidth="800"/>
+    <outputs>
+        <data name="output" format="auto" />
+    </outputs>
+    <options sanitize="False" refresh="True"/>
+</tool>
diff --git a/tools/data_source/genomespace_file_browser_test.xml b/tools/data_source/genomespace_file_browser_test.xml
new file mode 100644
index 00000000000..a308f5f3480
--- /dev/null
+++ b/tools/data_source/genomespace_file_browser_test.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0"?>
+<tool name="GenomeSpace import" id="genomespace_file_browser_test" tool_type="data_source" add_galaxy_url="False" force_history_refresh="True" version="0.0.1">
+    <description>from file browser (test)</description>
+    <command interpreter="python">genomespace_file_browser.py --json_parameter_file "${output}" --genomespace_site "test"</command>
+    <inputs action="https://dmtest.genomespace.org:8444/datamanager/defaultdirectory" check_values="False" method="post"> 
+        <display>go to GenomeSpace Data Manager </display>
+        <param name="appCallbackUrl" type="baseurl" value="/tool_runner?tool_id=genomespace_file_browser_dev&amp;runtool_btn=Execute" />
+        <param name="appName" type="hidden" value="Galaxy" />
+    </inputs>
+    <uihints minwidth="800"/>
+    <outputs>
+        <data name="output" format="auto" />
+    </outputs>
+    <options sanitize="False" refresh="True"/>
+</tool>

From 8e154e55e9825b2f47f879797f10b0d59a381f4a Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Tue, 22 Nov 2011 11:05:38 -0500
Subject: [PATCH 238/362] Enhance User preferences within a Galaxy tool shed to
 enable users to elect to receive email when content is first uploaded to a
 new repository.  Also add a new grid interface to enable users to easily
 manage registering with any tool shed respositories to receive email when
 changes are made to the selected repositories.

---
 lib/galaxy/tools/parameters/basic.py          |   2 +-
 .../webapps/community/controllers/admin.py    |   1 +
 .../webapps/community/controllers/common.py   | 101 ++++++++++++++----
 .../community/controllers/repository.py       |  93 +++++++++++++++-
 .../webapps/community/controllers/upload.py   |  39 ++++---
 .../webapps/community/model/__init__.py       |   1 +
 lib/galaxy/webapps/community/model/mapping.py |   1 +
 .../0010_add_new_repo_alert_column.py         |  50 +++++++++
 templates/user/index.mako                     |  18 ++--
 templates/webapps/community/index.mako        |   3 -
 .../community/user/manage_email_alerts.mako   |  54 ++++++++++
 11 files changed, 314 insertions(+), 49 deletions(-)
 create mode 100644 lib/galaxy/webapps/community/model/migrate/versions/0010_add_new_repo_alert_column.py
 create mode 100644 templates/webapps/community/user/manage_email_alerts.mako

diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index f0c0bbb3448..e9aab7a3067 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -166,7 +166,7 @@ class ToolParameter( object ):
         """Factory method to create parameter of correct type"""
         param_name = param.get( "name" )
         if not param_name:
-            raise ValueError( "Tool parameters require a 'name'" )
+            raise ValueError( "Tool parameter '%s' requires a 'name'" % (param_name ) )
         param_type = param.get("type")
         if not param_type:
             raise ValueError( "Tool parameter '%s' requires a 'type'" % ( param_name ) )
diff --git a/lib/galaxy/webapps/community/controllers/admin.py b/lib/galaxy/webapps/community/controllers/admin.py
index 47bd4b84584..0a7cc687ebb 100644
--- a/lib/galaxy/webapps/community/controllers/admin.py
+++ b/lib/galaxy/webapps/community/controllers/admin.py
@@ -475,6 +475,7 @@ class AdminController( BaseUIController, Admin ):
                 kwd[ 'f-Category.name' ] = category.name
             elif operation == "receive email alerts":
                 if kwd[ 'id' ]:
+                    kwd[ 'caller' ] = 'browse_repositories'
                     return trans.response.send_redirect( web.url_for( controller='repository',
                                                                       action='set_email_alerts',
                                                                       **kwd ) )
diff --git a/lib/galaxy/webapps/community/controllers/common.py b/lib/galaxy/webapps/community/controllers/common.py
index 498716a9af5..71b74ae9f2d 100644
--- a/lib/galaxy/webapps/community/controllers/common.py
+++ b/lib/galaxy/webapps/community/controllers/common.py
@@ -12,6 +12,28 @@ from mercurial import hg, ui, commands
 
 log = logging.getLogger( __name__ )
 
+new_repo_email_alert_template = """
+GALAXY TOOL SHED NEW REPOSITORY ALERT
+-----------------------------------------------------------------------------
+You received this alert because you registered to receive email when
+new repositories were created in the Galaxy tool shed named "${host}".
+-----------------------------------------------------------------------------
+
+Repository name:       ${repository_name}
+Date content uploaded: ${display_date}
+Uploaded by:           ${username}
+
+Revision: ${revision}
+Change description:
+${description}
+
+${content_alert_str}
+
+-----------------------------------------------------------------------------
+This change alert was sent from the Galaxy tool shed hosted on the server
+"${host}"
+"""
+
 email_alert_template = """
 GALAXY TOOL SHED REPOSITORY UPDATE ALERT
 -----------------------------------------------------------------------------
@@ -464,7 +486,7 @@ def generate_metadata_for_changeset_revision( trans, id, ctx, changeset_revision
             except Exception, e:
                 invalid_files.append( ( name, str( e ) ) )
     return metadata_dict, invalid_files
-def set_repository_metadata( trans, id, changeset_revision, **kwd ):
+def set_repository_metadata( trans, id, changeset_revision, content_alert_str='', **kwd ):
     """Set repository metadata"""
     message = ''
     status = 'done'
@@ -484,6 +506,9 @@ def set_repository_metadata( trans, id, changeset_revision, **kwd ):
                     repository_metadata = trans.model.RepositoryMetadata( repository.id, changeset_revision, metadata_dict )
                     trans.sa_session.add( repository_metadata )
                     trans.sa_session.flush()
+                    # If this is the first record stored for this repository, see if we need to send any email alerts.
+                    if len( repository.downloadable_revisions ) == 1:
+                        handle_email_alerts( trans, repository, content_alert_str='', new_repo_alert=True, admin_only=False )
                 else:
                     # Update the last saved repository_metadata table row.
                     repository_metadata = get_latest_repository_metadata( trans, id )
@@ -557,11 +582,31 @@ def get_configured_ui():
 def get_user( trans, id ):
     """Get a user from the database by id"""
     return trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( id ) )
-def handle_email_alerts( trans, repository, content_alert_str='' ):
+def handle_email_alerts( trans, repository, content_alert_str='', new_repo_alert=False, admin_only=False ):
+    # There are 2 complementary features that enable a tool shed user to receive email notification:
+    # 1. Within User Preferences, they can elect to receive email when the first (or first valid)
+    #    change set is produced for a new repository.
+    # 2. When viewing or managing a repository, they can check the box labeled "Receive email alerts"
+    #    which caused them to receive email alerts when updates to the repository occur.  This same feature
+    #    is available on a per-repository basis on the repository grid within the tool shed.
+    #
+    # There are currently 4 scenarios for sending email notification when a change is made to a repository:
+    # 1. An admin user elects to receive email when the first change set is produced for a new repository
+    #    from User Preferences.  The change set does not have to include any valid content.  This allows for
+    #    the capture of inappropriate content being uploaded to new repositories.
+    # 2. A regular user elects to receive email when the first valid change set is produced for a new repository
+    #    from User Preferences.  This differs from 1 above in that the user will not receive email until a
+    #    change set tha tincludes valid content is produced.
+    # 3. An admin user checks the "Receive email alerts" check box on the manage repository page.  Since the
+    #    user is an admin user, the email will include information about both HTML and image content that was
+    #    included in the change set.
+    # 4. A regular user checks the "Receive email alerts" check box on the manage repository page.  Since the
+    #    user is not an admin user, the email will not include any information about both HTML and image content
+    #    that was included in the change set.
     repo_dir = repository.repo_path
     repo = hg.repository( get_configured_ui(), repo_dir )
     smtp_server = trans.app.config.smtp_server
-    if smtp_server and repository.email_alerts:
+    if smtp_server and ( new_repo_alert or repository.email_alerts ):
         # Send email alert to users that want them.
         if trans.app.config.email_from is not None:
             email_from = trans.app.config.email_from
@@ -580,26 +625,40 @@ def handle_email_alerts( trans, repository, content_alert_str='' ):
             username = ctx.user()
         # We'll use 2 template bodies because we only want to send content
         # alerts to tool shed admin users.
-        admin_body = string.Template( email_alert_template ) \
-            .safe_substitute( host=trans.request.host,
-                              repository_name=repository.name,
-                              revision='%s:%s' %( str( ctx.rev() ), ctx ),
-                              display_date=display_date,
-                              description=ctx.description(),
-                              username=username,
-                              content_alert_str=content_alert_str )
-        body = string.Template( email_alert_template ) \
-            .safe_substitute( host=trans.request.host,
-                              repository_name=repository.name,
-                              revision='%s:%s' %( str( ctx.rev() ), ctx ),
-                              display_date=display_date,
-                              description=ctx.description(),
-                              username=username,
-                              content_alert_str='' )
+        if new_repo_alert:
+            template = new_repo_email_alert_template
+        else:
+            template = email_alert_template
+        admin_body = string.Template( template ).safe_substitute( host=trans.request.host,
+                                                                  repository_name=repository.name,
+                                                                  revision='%s:%s' %( str( ctx.rev() ), ctx ),
+                                                                  display_date=display_date,
+                                                                  description=ctx.description(),
+                                                                  username=username,
+                                                                  content_alert_str=content_alert_str )
+        body = string.Template( template ).safe_substitute( host=trans.request.host,
+                                                            repository_name=repository.name,
+                                                            revision='%s:%s' %( str( ctx.rev() ), ctx ),
+                                                            display_date=display_date,
+                                                            description=ctx.description(),
+                                                            username=username,
+                                                            content_alert_str='' )
         admin_users = trans.app.config.get( "admin_users", "" ).split( "," )
         frm = email_from
-        subject = "Galaxy tool shed repository update alert"
-        email_alerts = from_json_string( repository.email_alerts )
+        if new_repo_alert:
+            subject = "New Galaxy tool shed repository alert"
+            email_alerts = []
+            for user in trans.sa_session.query( trans.model.User ) \
+                                        .filter( and_( trans.model.User.table.c.deleted == False,
+                                                       trans.model.User.table.c.new_repo_alert == True ) ):
+                if admin_only:
+                    if user.email in admin_users:
+                        email_alerts.append( user.email )
+                else:
+                    email_alerts.append( user.email )
+        else:
+            subject = "Galaxy tool shed repository update alert"
+            email_alerts = from_json_string( repository.email_alerts )
         for email in email_alerts:
             to = email.strip()
             # Send it
diff --git a/lib/galaxy/webapps/community/controllers/repository.py b/lib/galaxy/webapps/community/controllers/repository.py
index c31c079023d..c0e53e9f029 100644
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -182,6 +182,37 @@ class RepositoryListGrid( grids.Grid ):
                                .outerjoin( model.RepositoryCategoryAssociation.table ) \
                                .outerjoin( model.Category.table )
 
+class EmailAlertsRepositoryListGrid( RepositoryListGrid ):
+    columns = [
+        RepositoryListGrid.NameColumn( "Name",
+                                       key="name",
+                                       link=( lambda item: dict( operation="view_or_manage_repository",
+                                                                 id=item.id,
+                                                                 webapp="community" ) ),
+                                       attach_popup=False ),
+        RepositoryListGrid.DescriptionColumn( "Synopsis",
+                                              key="description",
+                                              attach_popup=False ),
+        RepositoryListGrid.UserColumn( "Owner",
+                                       model_class=model.User,
+                                       link=( lambda item: dict( operation="repositories_by_user", id=item.id, webapp="community" ) ),
+                                       attach_popup=False,
+                                       key="User.username" ),
+        RepositoryListGrid.EmailAlertsColumn( "Alert", attach_popup=False ),
+        # Columns that are valid for filtering but are not visible.
+        grids.DeletedColumn( "Deleted",
+                             key="deleted",
+                             visible=False,
+                             filterable="advanced" )
+    ]
+    operations = [ grids.GridOperation( "Receive email alerts",
+                                        allow_multiple=True,
+                                        condition=( lambda item: not item.deleted ),
+                                        async_compatible=False ) ]
+    global_actions = [
+            grids.GridAction( "User preferences", dict( controller='user', action='index', cntrller='repository', webapp='community' ) )
+        ]
+
 class ValidRepositoryListGrid( RepositoryListGrid ):
     class RevisionColumn( grids.GridColumn ):
         def __init__( self, col_name ):
@@ -290,6 +321,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
     matched_repository_list_grid = MatchedRepositoryListGrid()
     valid_repository_list_grid = ValidRepositoryListGrid()
     repository_list_grid = RepositoryListGrid()
+    email_alerts_repository_list_grid = EmailAlertsRepositoryListGrid()
     category_list_grid = CategoryListGrid()
 
     @web.expose
@@ -876,6 +908,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
             elif operation == "receive email alerts":
                 if trans.user:
                     if kwd[ 'id' ]:
+                        kwd[ 'caller' ] = 'browse_repositories'
                         return trans.response.send_redirect( web.url_for( controller='repository',
                                                                           action='set_email_alerts',
                                                                           **kwd ) )
@@ -1550,7 +1583,9 @@ class RepositoryController( BaseUIController, ItemRatings ):
     @web.require_login( "set email alerts" )
     def set_email_alerts( self, trans, **kwd ):
         # Set email alerts for selected repositories
-        params = util.Params( kwd )
+        # This method is called from multiple grids, so
+        # the caller must be passed.
+        caller = kwd[ 'caller' ]
         user = trans.user
         if user:
             repository_ids = util.listify( kwd.get( 'id', '' ) )
@@ -1582,9 +1617,63 @@ class RepositoryController( BaseUIController, ItemRatings ):
             kwd[ 'status' ] = 'done'
         del kwd[ 'operation' ]
         return trans.response.send_redirect( web.url_for( controller='repository',
-                                                          action='browse_repositories',
+                                                          action=caller,
                                                           **kwd ) )
     @web.expose
+    @web.require_login( "manage email alerts" )
+    def manage_email_alerts( self, trans, **kwd ):
+        params = util.Params( kwd )
+        message = util.restore_text( params.get( 'message', ''  ) )
+        status = params.get( 'status', 'done' )
+        new_repo_alert = params.get( 'new_repo_alert', '' )
+        new_repo_alert_checked = CheckboxField.is_checked( new_repo_alert )
+        user = trans.user
+        if params.get( 'new_repo_alert_button', False ):
+            user.new_repo_alert = new_repo_alert_checked
+            trans.sa_session.add( user )
+            trans.sa_session.flush()
+            if new_repo_alert_checked:
+                message = 'You will receive email alerts for all new valid tool shed repositories.'
+            else:
+                message = 'You will not receive any email alerts for new valid tool shed repositories.'
+        checked = new_repo_alert_checked or ( user and user.new_repo_alert )
+        new_repo_alert_check_box = CheckboxField( 'new_repo_alert', checked=checked )
+        email_alert_repositories = []
+        for repository in trans.sa_session.query( trans.model.Repository ) \
+                                          .filter( and_( trans.model.Repository.table.c.deleted == False,
+                                                         trans.model.Repository.table.c.email_alerts != None ) ) \
+                                          .order_by( trans.model.Repository.table.c.name ):
+            if user.email in repository.email_alerts:
+                email_alert_repositories.append( repository )
+        return trans.fill_template( "/webapps/community/user/manage_email_alerts.mako",
+                                    webapp='community',
+                                    new_repo_alert_check_box=new_repo_alert_check_box,
+                                    email_alert_repositories=email_alert_repositories,
+                                    message=message,
+                                    status=status )
+    @web.expose
+    @web.require_login( "manage email alerts" )
+    def multi_select_email_alerts( self, trans, **kwd ):
+        params = util.Params( kwd )
+        message = util.restore_text( params.get( 'message', ''  ) )
+        status = params.get( 'status', 'done' )
+        if 'webapp' not in kwd:
+            kwd[ 'webapp' ] = 'community'
+        if 'operation' in kwd:
+            operation = kwd['operation'].lower()
+            if operation == "receive email alerts":
+                if trans.user:
+                    if kwd[ 'id' ]:
+                        kwd[ 'caller' ] = 'multi_select_email_alerts'
+                        return trans.response.send_redirect( web.url_for( controller='repository',
+                                                                          action='set_email_alerts',
+                                                                          **kwd ) )
+                else:
+                    kwd[ 'message' ] = 'You must be logged in to set email alerts.'
+                    kwd[ 'status' ] = 'error'
+                    del kwd[ 'operation' ]
+        return self.email_alerts_repository_list_grid( trans, **kwd )
+    @web.expose
     @web.require_login( "set repository metadata" )
     def set_metadata( self, trans, id, ctx_str, **kwd ):
         malicious = kwd.get( 'malicious', '' )
diff --git a/lib/galaxy/webapps/community/controllers/upload.py b/lib/galaxy/webapps/community/controllers/upload.py
index 1a0e981d67a..bb848a766a7 100644
--- a/lib/galaxy/webapps/community/controllers/upload.py
+++ b/lib/galaxy/webapps/community/controllers/upload.py
@@ -32,6 +32,10 @@ class UploadController( BaseUIController ):
         tip = repository.tip
         file_data = params.get( 'file_data', '' )
         url = params.get( 'url', '' )
+        # Part of the upload process is sending email notification to those that have registered to
+        # receive them.  One scenario occurs when the first change set is produced for the repository.
+        # See the handle_email_alerts() method for the definition of the scenarios.
+        new_repo_alert = repository.is_new
         if params.get( 'upload_button', False ):
             current_working_dir = os.getcwd()
             if file_data == '' and url == '':
@@ -87,13 +91,14 @@ class UploadController( BaseUIController ):
                         tar = None
                         istar = False
                 if istar:
-                    ok, message, files_to_remove = self.upload_tar( trans,
-                                                                    repository,
-                                                                    tar,
-                                                                    uploaded_file,
-                                                                    upload_point,
-                                                                    remove_repo_files_not_in_tar,
-                                                                    commit_message )
+                    ok, message, files_to_remove, content_alert_str = self.upload_tar( trans,
+                                                                                       repository,
+                                                                                       tar,
+                                                                                       uploaded_file,
+                                                                                       upload_point,
+                                                                                       remove_repo_files_not_in_tar,
+                                                                                       commit_message,
+                                                                                       new_repo_alert )
                 else:
                     if ( isgzip or isbz2 ) and uncompress_file:
                         uploaded_file_filename = self.uncompress( repository, uploaded_file_name, uploaded_file_filename, isgzip, isbz2 )
@@ -131,7 +136,9 @@ class UploadController( BaseUIController ):
                         # Handle the special case where a xxx.loc.sample file is
                         # being uploaded by copying it to ~/tool-data/xxx.loc.
                         copy_sample_loc_file( trans, full_path )
-                    handle_email_alerts( trans, repository, content_alert_str=content_alert_str )
+                    # See if the content of the change set was valid.
+                    admin_only = len( repository.downloadable_revisions ) != 1
+                    handle_email_alerts( trans, repository, content_alert_str=content_alert_str, new_repo_alert=new_repo_alert, admin_only=admin_only )
                 if ok:
                     # Update the repository files for browsing.
                     update_for_browsing( trans, repository, current_working_dir, commit_message=commit_message )
@@ -150,7 +157,7 @@ class UploadController( BaseUIController ):
                     else:
                         message = 'No changes to repository.'      
                     # Set metadata on the repository tip
-                    error_message, status = set_repository_metadata( trans, repository_id, repository.tip, **kwd )
+                    error_message, status = set_repository_metadata( trans, repository_id, repository.tip, content_alert_str=content_alert_str, **kwd )
                     if error_message:
                         message = '%s<br/>%s' % ( message, error_message )
                         return trans.response.send_redirect( web.url_for( controller='repository',
@@ -176,16 +183,17 @@ class UploadController( BaseUIController ):
                                     remove_repo_files_not_in_tar=remove_repo_files_not_in_tar,
                                     message=message,
                                     status=status )
-    def upload_tar( self, trans, repository, tar, uploaded_file, upload_point, remove_repo_files_not_in_tar, commit_message ):
+    def upload_tar( self, trans, repository, tar, uploaded_file, upload_point, remove_repo_files_not_in_tar, commit_message, new_repo_alert ):
         # Upload a tar archive of files.
         repo_dir = repository.repo_path
         repo = hg.repository( get_configured_ui(), repo_dir )
         files_to_remove = []
+        content_alert_str = ''
         ok, message = self.__check_archive( tar )
         if not ok:
             tar.close()
             uploaded_file.close()
-            return ok, message, files_to_remove
+            return ok, message, files_to_remove, content_alert_str
         else:
             if upload_point is not None:
                 full_path = os.path.abspath( os.path.join( repo_dir, upload_point ) )
@@ -197,7 +205,6 @@ class UploadController( BaseUIController ):
             tar.extractall( path=full_path )
             tar.close()
             uploaded_file.close()
-            content_alert_str = ''
             if remove_repo_files_not_in_tar and not repository.is_new:
                 # We have a repository that is not new (it contains files), so discover
                 # those files that are in the repository, but not in the uploaded archive.
@@ -256,7 +263,7 @@ class UploadController( BaseUIController ):
                     # appending them to the shed's tool_data_table_conf.xml file on disk.
                     error, message = handle_sample_tool_data_table_conf_file( trans, filename_in_archive )
                     if error:
-                        return False, message, files_to_remove
+                        return False, message, files_to_remove, content_alert_str
                 if filename_in_archive.endswith( '.loc.sample' ):
                     # Handle the special case where a xxx.loc.sample file is
                     # being uploaded by copying it to ~/tool-data/xxx.loc.
@@ -269,8 +276,10 @@ class UploadController( BaseUIController ):
                 # exception.  If this happens, we'll try the following.
                 repo.dirstate.write()
                 repo.commit( user=trans.user.username, text=commit_message )
-            handle_email_alerts( trans, repository, content_alert_str )
-            return True, '', files_to_remove
+            # See if the content of the change set was valid.
+            admin_only = len( repository.downloadable_revisions ) != 1
+            handle_email_alerts( trans, repository, content_alert_str=content_alert_str, new_repo_alert=new_repo_alert, admin_only=admin_only )
+            return True, '', files_to_remove, content_alert_str
     def uncompress( self, repository, uploaded_file_name, uploaded_file_filename, isgzip, isbz2 ):
         if isgzip:
             self.__handle_gzip( repository, uploaded_file_name )
diff --git a/lib/galaxy/webapps/community/model/__init__.py b/lib/galaxy/webapps/community/model/__init__.py
index 1373ffe3ccb..0f6b7d37206 100644
--- a/lib/galaxy/webapps/community/model/__init__.py
+++ b/lib/galaxy/webapps/community/model/__init__.py
@@ -20,6 +20,7 @@ class User( object ):
         self.deleted = False
         self.purged = False
         self.username = None
+        self.new_repo_alert = False
     def set_password_cleartext( self, cleartext ):
         """Set 'self.password' to the digest of 'cleartext'."""
         self.password = new_secure_hash( text_type=cleartext )
diff --git a/lib/galaxy/webapps/community/model/mapping.py b/lib/galaxy/webapps/community/model/mapping.py
index ea6659d8ddb..51073c83815 100644
--- a/lib/galaxy/webapps/community/model/mapping.py
+++ b/lib/galaxy/webapps/community/model/mapping.py
@@ -45,6 +45,7 @@ User.table = Table( "galaxy_user", metadata,
     Column( "username", String( 255 ), index=True ),
     Column( "password", TrimmedString( 40 ), nullable=False ),
     Column( "external", Boolean, default=False ),
+    Column( "new_repo_alert", Boolean, default=False ),
     Column( "deleted", Boolean, index=True, default=False ),
     Column( "purged", Boolean, index=True, default=False ) )
 
diff --git a/lib/galaxy/webapps/community/model/migrate/versions/0010_add_new_repo_alert_column.py b/lib/galaxy/webapps/community/model/migrate/versions/0010_add_new_repo_alert_column.py
new file mode 100644
index 00000000000..2238e267821
--- /dev/null
+++ b/lib/galaxy/webapps/community/model/migrate/versions/0010_add_new_repo_alert_column.py
@@ -0,0 +1,50 @@
+"""
+Migration script to add the new_repo_alert column to the galaxy_user table.
+"""
+
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+from migrate.changeset import *
+
+import sys, logging
+log = logging.getLogger( __name__ )
+log.setLevel(logging.DEBUG)
+handler = logging.StreamHandler( sys.stdout )
+format = "%(name)s %(levelname)s %(asctime)s %(message)s"
+formatter = logging.Formatter( format )
+handler.setFormatter( formatter )
+log.addHandler( handler )
+
+metadata = MetaData( migrate_engine )
+db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) )
+
+def upgrade():
+    print __doc__
+    metadata.reflect()
+    # Create and initialize imported column in job table.
+    User_table = Table( "galaxy_user", metadata, autoload=True )
+    c = Column( "new_repo_alert", Boolean, default=False, index=True )
+    try:
+        # Create
+        c.create( User_table )
+        assert c is User_table.c.new_repo_alert
+        # Initialize.
+        if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite': 
+            default_false = "0"
+        elif migrate_engine.name == 'postgres':
+            default_false = "false"
+        db_session.execute( "UPDATE galaxy_user SET new_repo_alert=%s" % default_false )
+    except Exception, e:
+        print "Adding new_repo_alert column to the galaxy_user table failed: %s" % str( e )
+        log.debug( "Adding new_repo_alert column to the galaxy_user table failed: %s" % str( e ) )
+    
+def downgrade():
+    metadata.reflect()
+    # Drop new_repo_alert column from galaxy_user table.
+    User_table = Table( "galaxy_user", metadata, autoload=True )
+    try:
+        User_table.c.new_repo_alert.drop()
+    except Exception, e:
+        print "Dropping column new_repo_alert from the galaxy_user table failed: %s" % str( e )
+        log.debug( "Dropping column new_repo_alert from the galaxy_user table failed: %s" % str( e ) )
diff --git a/templates/user/index.mako b/templates/user/index.mako
index 0d5a787294e..42dec0fadab 100644
--- a/templates/user/index.mako
+++ b/templates/user/index.mako
@@ -16,7 +16,7 @@
                 <li><a href="${h.url_for( controller='user', action='api_keys', cntrller=cntrller )}">${_('Manage your API keys')}</a></li>
             %endif
             %if trans.app.config.enable_openid:
-                <li><a href="${h.url_for( controller='user', action='openid_manage', cntrller=cntrller )}">${ ('Manage OpenIDs')}</a> linked to your account</li>
+                <li><a href="${h.url_for( controller='user', action='openid_manage', cntrller=cntrller )}">${_('Manage OpenIDs')}</a> linked to your account</li>
             %endif
             %if trans.app.config.use_remote_user:
                 %if trans.app.config.remote_user_logout_href:
@@ -27,14 +27,18 @@
             %endif
         %else:
             <li><a href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller,  webapp='community' )}">${_('Manage your information')}</a></li>
+            <li><a href="${h.url_for( controller='repository', action='manage_email_alerts', cntrller=cntrller,  webapp='community' )}">${_('Manage your email alerts')}</a></li>
+            <li><a href="${h.url_for( controller='user', action='logout', logout_all=True )}" target="_top">${_('Logout')}</a> ${_('of all user sessions')}</li>
         %endif
     </ul>
-    <p>
-        You are using <strong>${trans.user.get_disk_usage( nice_size=True )}</strong> of disk space in this Galaxy instance.
-        %if trans.app.config.enable_quotas:
-            Your disk quota is: <strong>${trans.app.quota_agent.get_quota( trans.user, nice_size=True )}</strong>.
-        %endif
-    </p>
+    %if webapp == 'galaxy':
+        <p>
+            You are using <strong>${trans.user.get_disk_usage( nice_size=True )}</strong> of disk space in this Galaxy instance.
+            %if trans.app.config.enable_quotas:
+                Your disk quota is: <strong>${trans.app.quota_agent.get_quota( trans.user, nice_size=True )}</strong>.
+            %endif
+        </p>
+    %endif
 %else:
     %if not message:
         <p>${n_('You are currently not logged in.')}</p>
diff --git a/templates/webapps/community/index.mako b/templates/webapps/community/index.mako
index bea7743d006..37a1bf4084f 100644
--- a/templates/webapps/community/index.mako
+++ b/templates/webapps/community/index.mako
@@ -67,9 +67,6 @@
                         <div class="toolTitle">
                             <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_categories', webapp='community' )}">Browse by category</a>
                         </div>
-                        <div class="toolTitle">
-                            <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', webapp='community' )}">Browse all repositories</a>
-                        </div>
                         %if trans.user:
                             <div class="toolTitle">
                                 <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='my_repositories', webapp='community' )}">Browse my repositories</a>
diff --git a/templates/webapps/community/user/manage_email_alerts.mako b/templates/webapps/community/user/manage_email_alerts.mako
new file mode 100644
index 00000000000..e1e6046d996
--- /dev/null
+++ b/templates/webapps/community/user/manage_email_alerts.mako
@@ -0,0 +1,54 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+<br/><br/>
+<ul class="manage-table-actions">
+    <li>
+        <a class="action-button"  href="${h.url_for( controller='repository', action='multi_select_email_alerts', cntrller='repository', webapp=webapp )}">Manage repository alerts</a>
+    </li>
+    <li>
+        <a class="action-button"  href="${h.url_for( controller='user', action='index', cntrller='repository', webapp=webapp )}">User preferences</a>
+    </li>
+</ul>
+
+%if message:
+    ${render_msg( message, status )}
+%endif
+
+<div class="toolForm">
+    <div class="toolFormTitle">Email alerts for new repositories</div>
+    <form name="new_repo_alert" id="new_repo_alert" action="${h.url_for( controller='repository', action='manage_email_alerts', webapp=webapp )}" method="post" >
+        <div class="form-row">
+            <label>New repository alert:</label>
+            ${new_repo_alert_check_box.get_html()}
+            <div class="toolParamHelp" style="clear: both;">
+                Check the box and click <b>Save</b> to receive email when the first change set is created for a new repository.
+            </div>
+        </div>
+        <div class="form-row">
+            <input type="submit" name="new_repo_alert_button" value="Save"/>
+        </div>
+    </form>
+</div>
+<p/>
+%if email_alert_repositories:
+    <div class="toolForm">
+        <div class="toolFormTitle">You are registered to receive email alerts for changes to the following repositories</div>
+        <div class="form-row">
+            <table class="grid">
+                <tr>
+                    <th>Name</th>
+                    <th>Description</th>
+                </tr>
+                %for repository in email_alert_repositories:
+                    <tr>
+                        <td>${repository.name}</td>
+                        <td>${repository.description}</td>
+                    </tr>
+                %endfor
+            </table>
+        </div>
+    </div>
+    <p/>
+%endif
+

From e905e441e37e60f014b73c72e079daecb51a18ce Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Tue, 22 Nov 2011 11:56:53 -0500
Subject: [PATCH 239/362] Have rgPicardGCBiasMetrics.xml use fields.path
 approach instead of directly filtering on data table.

---
 tools/picard/rgPicardGCBiasMetrics.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/picard/rgPicardGCBiasMetrics.xml b/tools/picard/rgPicardGCBiasMetrics.xml
index 7adce089f04..af3a8b4d420 100644
--- a/tools/picard/rgPicardGCBiasMetrics.xml
+++ b/tools/picard/rgPicardGCBiasMetrics.xml
@@ -4,9 +4,9 @@
     --windowsize "$windowsize" --mingenomefrac "$mingenomefrac" -n "$out_prefix" --tmpdir "${__new_file_path__}"
     -j ${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/CollectGcBiasMetrics.jar
 #if $genomeSource.refGenomeSource == "history":
- --ref-file "$genomeSource.ownFile"
+ --ref-file "${genomeSource.ownFile}"
 #else:
- --ref "${ filter( lambda x: str( x[0] ) == str( $genomeSource.index ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1] }"
+ --ref "${genomeSource.index.fields.path}"
 #end if
   </command>
   <requirements><requirement type="package">picard</requirement></requirements>

From cf4dbf7f6a825a502ba6c91d74bec668940e0189 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Tue, 22 Nov 2011 12:21:05 -0500
Subject: [PATCH 240/362] Have fimo.xml use fields.path approach instead of
 directly filtering on data table.

---
 tools/meme/fimo.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/meme/fimo.xml b/tools/meme/fimo.xml
index 6c8fb6e2f7e..f99c5b53e0f 100644
--- a/tools/meme/fimo.xml
+++ b/tools/meme/fimo.xml
@@ -32,7 +32,7 @@
   #if str( $fasta_type.fasta_type_selector ) == 'history':
     "${fasta_type.input_database}"
   #else:
-    "${ filter( lambda x: str( x[0] ) == str( $fasta_type.input_database ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][3] }"
+    "${fasta_type.input_database.fields.path}"
   #end if
 
   '

From c5ea1aaa4382ba6261ae9a5e6d8604073adb38a9 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Tue, 22 Nov 2011 17:09:14 -0500
Subject: [PATCH 241/362] Fixes for Galaxy / tool shed communication.

---
 lib/galaxy/web/controllers/admin.py            | 16 ++++++++--------
 .../community/controllers/repository.py        | 18 +++++++-----------
 2 files changed, 15 insertions(+), 19 deletions(-)

diff --git a/lib/galaxy/web/controllers/admin.py b/lib/galaxy/web/controllers/admin.py
index 315510387a7..133ca8d2f02 100644
--- a/lib/galaxy/web/controllers/admin.py
+++ b/lib/galaxy/web/controllers/admin.py
@@ -774,21 +774,21 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
     @web.require_admin
     def find_tools_in_tool_shed( self, trans, **kwd ):
         tool_shed_url = kwd[ 'tool_shed_url' ]
-        galaxy_url = trans.request.host
+        galaxy_url = url_for( '', qualified=True )
         url = '%s/repository/find_tools?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, galaxy_url )
         return trans.response.send_redirect( url )
     @web.expose
     @web.require_admin
     def find_workflows_in_tool_shed( self, trans, **kwd ):
         tool_shed_url = kwd[ 'tool_shed_url' ]
-        galaxy_url = trans.request.host
+        galaxy_url = url_for( '', qualified=True )
         url = '%s/repository/find_workflows?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, galaxy_url )
         return trans.response.send_redirect( url )
     @web.expose
     @web.require_admin
     def browse_tool_shed( self, trans, **kwd ):
         tool_shed_url = kwd[ 'tool_shed_url' ]
-        galaxy_url = trans.request.host
+        galaxy_url = url_for( '', qualified=True )
         url = '%s/repository/browse_valid_repositories?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, galaxy_url )
         return trans.response.send_redirect( url )
     @web.expose
@@ -986,11 +986,10 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
     @web.expose
     @web.require_admin
     def check_for_updates( self, trans, **kwd ):
-        params = util.Params( kwd )
         repository = get_repository( trans, kwd[ 'id' ] )
-        galaxy_url = trans.request.host
+        galaxy_url = url_for( '', qualified=True )
         # Send a request to the relevant tool shed to see if there are any updates.
-        # TODO: support https in the following url.
+        # TODO: Fix this to use url_for to support locally hosted tool sheds.
         url = 'http://%s/repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \
             ( repository.tool_shed, galaxy_url, repository.name, repository.owner, repository.changeset_revision )
         return trans.response.send_redirect( url )
@@ -1215,7 +1214,7 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
                         module = __import__( import_module )
                         sys.path.pop( 0 )
                     except Exception, e:
-                        log.debug( "Execption importing datatypes code file included in installed repository: %s" % str( e ) )
+                        log.debug( "Exception importing datatypes code file included in installed repository: %s" % str( e ) )
                     trans.app.datatypes_registry = galaxy.datatypes.registry.Registry( trans.app.config.root, datatypes_config )
     def __get_repository_tools_and_sample_files( self, trans, tool_path, repo_files_dir ):
         # The sample_files list contains all files whose name ends in .sample
@@ -1398,10 +1397,11 @@ def get_repository_by_name_owner_changeset_revision( trans, name, owner, changes
                                             trans.model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \
                              .first()
 def get_repository_by_shed_name_owner_changeset_revision( trans, tool_shed, name, owner, changeset_revision ):
+    if tool_shed.find( '//' ) > 0:
+        tool_shed = tool_shed.split( '//' )[1]
     return trans.sa_session.query( trans.model.ToolShedRepository ) \
                            .filter( and_( trans.model.ToolShedRepository.table.c.tool_shed == tool_shed,
                                           trans.model.ToolShedRepository.table.c.name == name,
                                           trans.model.ToolShedRepository.table.c.owner == owner,
                                           trans.model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \
                            .first()
-
diff --git a/lib/galaxy/webapps/community/controllers/repository.py b/lib/galaxy/webapps/community/controllers/repository.py
index c0e53e9f029..13375d9312d 100644
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -437,9 +437,8 @@ class RepositoryController( BaseUIController, ItemRatings ):
                 if operation == "install":
                     galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' )
                     encoded_repo_info_dict = self.__encode_repo_info_dict( trans, webapp, util.listify( item_id ) )
-                    # TODO: support https in the following url.
-                    url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s&webapp=%s&repo_info_dict=%s' % \
-                        ( galaxy_url, trans.request.host, webapp, encoded_repo_info_dict )
+                    url = '%s/admin/install_tool_shed_repository?tool_shed_url=%s&webapp=%s&repo_info_dict=%s' % \
+                        ( galaxy_url, url_for( '', qualified=True ), webapp, encoded_repo_info_dict )
                     return trans.response.send_redirect( url )
             else:
                 # This can only occur when there is a multi-select grid with check boxes and an operation,
@@ -514,9 +513,8 @@ class RepositoryController( BaseUIController, ItemRatings ):
                 if operation == "install":
                     galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' )
                     encoded_repo_info_dict = self.__encode_repo_info_dict( trans, webapp, util.listify( item_id ) )
-                    # TODO: support https in the following url.
-                    url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s&webapp=%s&repo_info_dict=%s' % \
-                        ( galaxy_url, trans.request.host, webapp, encoded_repo_info_dict )
+                    url = '%s/admin/install_tool_shed_repository?tool_shed_url=%s&webapp=%s&repo_info_dict=%s' % \
+                        ( galaxy_url, url_for( '', qualified=True ), webapp, encoded_repo_info_dict )
                     return trans.response.send_redirect( url )
             else:
                 # This can only occur when there is a multi-select grid with check boxes and an operation,
@@ -761,9 +759,8 @@ class RepositoryController( BaseUIController, ItemRatings ):
         repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, changeset_revision )
         encoded_repo_info_dict = encode( repo_info_dict )
         # Redirect back to local Galaxy to perform install.
-        # TODO: support https in the following url.
-        url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s&repo_info_dict=%s' % \
-            ( galaxy_url, trans.request.host, encoded_repo_info_dict )
+        url = '%s/admin/install_tool_shed_repository?tool_shed_url=%s&repo_info_dict=%s' % \
+            ( galaxy_url, url_for( '', qualified=True ), encoded_repo_info_dict )
         return trans.response.send_redirect( url )
     @web.expose
     def check_for_updates( self, trans, **kwd ):
@@ -776,8 +773,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
         changeset_revision = params.get( 'changeset_revision', None )
         webapp = params.get( 'webapp', 'community' )
         # Start building up the url to redirect back to the calling Galaxy instance.
-        # TODO: support https in the following url.
-        url = 'http://%s/admin/update_to_changeset_revision?tool_shed_url=%s' % ( galaxy_url, trans.request.host )
+        url = '%s/admin/update_to_changeset_revision?tool_shed_url=%s' % ( galaxy_url, url_for( '', qualified=True ) )
         repository = get_repository_by_name_and_owner( trans, name, owner )
         url += '&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % \
             ( repository.name, repository.user.username, changeset_revision )

From 874b33c2b8709012494f57fe846f37a46d377d5d Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Wed, 23 Nov 2011 11:24:53 -0500
Subject: [PATCH 242/362] More fixes for Galaxy <-> tool shed communication.

---
 lib/galaxy/web/controllers/admin.py           | 23 +++++++++++++++----
 lib/galaxy/web/controllers/workflow.py        |  7 +++---
 .../webapps/community/controllers/workflow.py |  5 ++--
 3 files changed, 23 insertions(+), 12 deletions(-)

diff --git a/lib/galaxy/web/controllers/admin.py b/lib/galaxy/web/controllers/admin.py
index 133ca8d2f02..6d628b77942 100644
--- a/lib/galaxy/web/controllers/admin.py
+++ b/lib/galaxy/web/controllers/admin.py
@@ -986,12 +986,11 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
     @web.expose
     @web.require_admin
     def check_for_updates( self, trans, **kwd ):
-        repository = get_repository( trans, kwd[ 'id' ] )
-        galaxy_url = url_for( '', qualified=True )
         # Send a request to the relevant tool shed to see if there are any updates.
-        # TODO: Fix this to use url_for to support locally hosted tool sheds.
-        url = 'http://%s/repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \
-            ( repository.tool_shed, galaxy_url, repository.name, repository.owner, repository.changeset_revision )
+        repository = get_repository( trans, kwd[ 'id' ] )
+        tool_shed_url = get_url_from_repository_tool_shed( trans, repository )
+        url = '%s/repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \
+            ( tool_shed_url, url_for( '', qualified=True ), repository.name, repository.owner, repository.changeset_revision )
         return trans.response.send_redirect( url )
     @web.expose
     @web.require_admin
@@ -1405,3 +1404,17 @@ def get_repository_by_shed_name_owner_changeset_revision( trans, tool_shed, name
                                           trans.model.ToolShedRepository.table.c.owner == owner,
                                           trans.model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \
                            .first()
+def get_url_from_repository_tool_shed( trans, repository ):
+    # The stored value of repository.tool_shed is something like:
+    # toolshed.g2.bx.psu.edu
+    # We need the URL to this tool shed, which is something like:
+    # http://toolshed.g2.bx.psu.edu/
+    for shed_name, shed_url in trans.app.tool_shed_registry.tool_sheds.items():
+        if shed_url.find( repository.tool_shed ) >= 0:
+            if shed_url.endswith( '/' ):
+                shed_url = shed_url.rstrip( '/' )
+            return shed_url
+    # The tool shed from which the repository was originally
+    # installed must no longer be configured in tool_sheds_conf.xml.
+    return None
+                                    
\ No newline at end of file
diff --git a/lib/galaxy/web/controllers/workflow.py b/lib/galaxy/web/controllers/workflow.py
index 8f67fc5b28e..2623f279ed0 100644
--- a/lib/galaxy/web/controllers/workflow.py
+++ b/lib/galaxy/web/controllers/workflow.py
@@ -1125,7 +1125,7 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
             import_button = True
         if tool_shed_url and not import_button:
             # Use urllib (send another request to the tool shed) to retrieve the workflow.
-            workflow_url = 'http://%s/workflow/import_workflow?repository_metadata_id=%s&workflow_name=%s&webapp=%s&open_for_url=true' % \
+            workflow_url = '%s/workflow/import_workflow?repository_metadata_id=%s&workflow_name=%s&webapp=%s&open_for_url=true' % \
                 ( tool_shed_url, repository_metadata_id, tool_shed_encode( workflow_name ), webapp )
             response = urllib2.urlopen( workflow_url )
             workflow_text = response.read()
@@ -1197,7 +1197,7 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
                             for shed_name, shed_url in trans.app.tool_shed_registry.tool_sheds.items():
                                 if shed_url.endswith( '/' ):
                                     shed_url = shed_url.rstrip( '/' )
-                                    url = '%s/repository/find_tools?galaxy_url=%s&webapp=%s' % ( shed_url, trans.request.host, webapp )
+                                    url = '%s/repository/find_tools?galaxy_url=%s&webapp=%s' % ( shed_url, url_for( '', qualified=True ), webapp )
                                     if missing_tool_tups:
                                         url += '&tool_id='
                                     for missing_tool_tup in missing_tool_tups:
@@ -1224,8 +1224,7 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
                     if tool_shed_url:
                         # We've received the textual representation of a workflow from a Galaxy tool shed.
                         message = "Workflow <b>%s</b> imported successfully." % workflow.name
-                        # TODO: support https in the following url.
-                        url = 'http://%s/workflow/view_workflow?repository_metadata_id=%s&workflow_name=%s&webapp=%s&message=%s' % \
+                        url = '%s/workflow/view_workflow?repository_metadata_id=%s&workflow_name=%s&webapp=%s&message=%s' % \
                             ( tool_shed_url, repository_metadata_id, tool_shed_encode( workflow_name ), webapp, message )
                         return trans.response.send_redirect( url )
                     elif installed_repository_file:
diff --git a/lib/galaxy/webapps/community/controllers/workflow.py b/lib/galaxy/webapps/community/controllers/workflow.py
index fa5d2a41c2d..ccd7355946a 100644
--- a/lib/galaxy/webapps/community/controllers/workflow.py
+++ b/lib/galaxy/webapps/community/controllers/workflow.py
@@ -379,9 +379,8 @@ class WorkflowController( BaseUIController ):
                 to_file.write( to_json_string( workflow_data ) )
                 return open( tmp_fname )
             galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' )
-            # TODO: support https in the following url.
-            url = 'http://%s/workflow/import_workflow?tool_shed_url=%s&repository_metadata_id=%s&workflow_name=%s&webapp=%s' % \
-                ( galaxy_url, trans.request.host, repository_metadata_id, encode( workflow_name ), webapp )
+            url = '%s/workflow/import_workflow?tool_shed_url=%s&repository_metadata_id=%s&workflow_name=%s&webapp=%s' % \
+                ( galaxy_url, url_for( '', qualified=True ), repository_metadata_id, encode( workflow_name ), webapp )
             return trans.response.send_redirect( url )
         return trans.response.send_redirect( web.url_for( controller='workflow',
                                                           action='view_workflow',

From 1fb135cc15e21e0aed136ac447091cbe59472aee Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Wed, 23 Nov 2011 16:11:39 -0500
Subject: [PATCH 243/362] Trackster: refactor action icon creation and
 initialization.

---
 static/scripts/trackster.js | 321 +++++++++++++++++-------------------
 1 file changed, 153 insertions(+), 168 deletions(-)

diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index 336a068b92c..80addfdfc1b 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -677,6 +677,7 @@ var Drawable = function(name, view, container, prefs, drag_handle_class) {
     this.prefs = this.config.values;
     this.drag_handle_class = drag_handle_class;
     this.is_overview = false;
+    this.action_icons = {};
     
     // FIXME: this should be a saved setting
     this.content_visible = true;
@@ -688,8 +689,10 @@ var Drawable = function(name, view, container, prefs, drag_handle_class) {
     if (this.header_div) { 
         this.container_div.append(this.header_div);
         
-        this.icons_div = this.build_icons_div().hide();
-        this.header_div.append(this.icons_div);
+        this.icons_div = $("<div/>").css("float", "left").hide().appendTo(this.header_div);
+        this.build_action_icons(this.action_icons_def);
+        this.header_div.append( $("<div style='clear: both'/>") );
+        
         
         // Suppress double clicks in header so that they do not impact viz.
         this.header_div.dblclick( function(e) { e.stopPropagation(); } );
@@ -706,6 +709,64 @@ var Drawable = function(name, view, container, prefs, drag_handle_class) {
     }
 };
 
+Drawable.prototype.action_icons_def = [
+    // Hide/show drawable content.
+    {
+        name: "toggle_icon",
+        title: "Hide/show content",
+        css_class: "toggle",
+        on_click_fn: function(drawable) {
+            if ( drawable.content_visible ) {
+                drawable.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");
+                drawable.hide_contents();
+                drawable.content_visible = false;
+            } else {
+                drawable.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");
+                drawable.content_visible = true;
+                drawable.show_contents();
+            }
+        }
+    },
+    // Edit settings.
+    {
+        name: "settings_icon",
+        title: "Edit settings",
+        css_class: "settings-icon",
+        on_click_fn: function(drawable) {
+            var cancel_fn = function() { hide_modal(); $(window).unbind("keypress.check_enter_esc"); },
+                ok_fn = function() { 
+                    drawable.config.update_from_form( $(".dialog-box") );
+                    hide_modal(); 
+                    $(window).unbind("keypress.check_enter_esc"); 
+                },
+                check_enter_esc = function(e) {
+                    if ((e.keyCode || e.which) === 27) { // Escape key
+                        cancel_fn();
+                    } else if ((e.keyCode || e.which) === 13) { // Enter key
+                        ok_fn();
+                    }
+                };
+
+            $(window).bind("keypress.check_enter_esc", check_enter_esc);        
+            show_modal("Configure", drawable.config.build_form(), {
+                "Cancel": cancel_fn,
+                "OK": ok_fn
+            });
+        }
+    },
+    // Remove.
+    {
+        name: "remove_icon",
+        title: "Remove",
+        css_class: "remove-icon",
+        on_click_fn: function(drawable) {
+            // Tipsy for remove icon must be deleted when drawable is deleted.
+            $(".tipsy").remove();
+            drawable.remove();
+        }
+    }
+];
+
 extend(Drawable.prototype, {
     init: function() {},
     request_draw: function() {},
@@ -749,9 +810,27 @@ extend(Drawable.prototype, {
      */
     build_header_div: function() {},
     /**
-     * Build drawable's icons div.
+     * Add an action icon to this object. Appends icon unless prepend flag is specified.
      */
-    build_icons_div: function() {},
+    add_action_icon: function(name, title, css_class, on_click_fn, prepend) {
+        var drawable = this;
+        this.action_icons[name] = $("<a/>").attr("href", "javascript:void(0);").attr("title", title)
+                                           .addClass("icon-button").addClass(css_class).tipsy( {gravity: 's'} )
+                                           .click( function() { on_click_fn(drawable); } )
+                                           .appendTo(this.icons_div);
+    },
+    /**
+     * Build drawable's icons div from object's icons_dict.
+     */
+    build_action_icons: function(action_icons_def) {        
+        // Create icons.
+        var icon_dict;
+        for (var i = 0; i < action_icons_def.length; i++) {
+            icon_dict = action_icons_def[i];
+            this.add_action_icon(icon_dict.name, icon_dict.title, icon_dict.css_class, 
+                                 icon_dict.on_click_fn, icon_dict.prepend);
+        }
+    },
     /**
      * Update icons.
      */
@@ -880,65 +959,6 @@ extend(DrawableGroup.prototype, Drawable.prototype, DrawableCollection.prototype
         this.name_div = $("<div/>").addClass("track-name").text(this.name).appendTo(header_div);
         return header_div;
     },
-    build_icons_div: function() {
-        var icons_div = $("<div/>").css("float", "left");
-
-        this.toggle_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Hide/show group content")
-                                    .addClass("icon-button toggle").tipsy( {gravity: 's'} )
-                                    .appendTo(icons_div);
-        this.settings_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Edit settings")
-                                      .addClass("icon-button settings-icon").tipsy( {gravity: 's'} )
-                                      .appendTo(icons_div);
-        this.remove_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Remove")
-                                    .addClass("icon-button remove-icon").tipsy( {gravity: 's'} )
-                                    .appendTo(icons_div);
-        var group = this;
-
-        // Toggle icon hides or shows the group content.
-        this.toggle_icon.click( function() {
-            if ( group.content_visible ) {
-                group.toggle_icon.addClass("toggle-expand").removeClass("toggle");
-                group.hide_contents();
-                group.content_visible = false;
-            } else {
-                group.toggle_icon.addClass("toggle").removeClass("toggle-expand");
-                group.content_visible = true;
-                group.show_contents();
-            }
-        });
-
-        // Clicking on settings icon opens group config.
-        this.settings_icon.click( function() {
-            var cancel_fn = function() { hide_modal(); $(window).unbind("keypress.check_enter_esc"); },
-                ok_fn = function() { 
-                    group.config.update_from_form( $(".dialog-box") );
-                    hide_modal(); 
-                    $(window).unbind("keypress.check_enter_esc"); 
-                },
-                check_enter_esc = function(e) {
-                    if ((e.keyCode || e.which) === 27) { // Escape key
-                        cancel_fn();
-                    } else if ((e.keyCode || e.which) === 13) { // Enter key
-                        ok_fn();
-                    }
-                };
-
-            $(window).bind("keypress.check_enter_esc", check_enter_esc);        
-            show_modal("Configure Group", group.config.build_form(), {
-                "Cancel": cancel_fn,
-                "OK": ok_fn
-            });
-        });
-        
-        // Clicking on remove icon removes group.
-        this.remove_icon.click( function() {
-            // Tipsy for remove icon must be deleted when group is deleted.
-            $(".tipsy").remove();
-            group.remove();
-        });
-        
-        return icons_div;        
-    },
     hide_contents : function () {
         this.content_div.hide();
     },
@@ -2493,7 +2513,64 @@ var Track = function(name, view, container, prefs, data_url, data_query_wait) {
     this.content_div = $("<div class='track-content'>").appendTo(this.container_div);
     this.container.content_div.append(this.container_div);
 };
+
 extend(Track.prototype, Drawable.prototype, {
+    action_icons_def: [
+        // Change track mode.
+        {
+            name: "mode_icon",
+            title: "Set display mode",
+            css_class: "chevron-expand",
+            on_click_fn: function() {}
+        },
+        // Hide/show content.
+        Drawable.prototype.action_icons_def[0],
+        // Set track as overview.
+        {
+            name: "overview_icon",
+            title: "Set as overview",
+            css_class: "overview-icon",
+            on_click_fn: function() {
+                track.view.set_overview(track);
+            }
+        },
+        // Edit config.
+        Drawable.prototype.action_icons_def[1],
+        // Toggle track filters.
+        {
+            name: "filters_icon",
+            title: "Filters",
+            css_class: "filters-icon",
+            on_click_fn: function(track) {
+                // TODO: update tipsy text.            
+                track.filters_div.toggle();
+                track.filters_manager.reset_filters();
+            }
+        },
+        // Toggle track tool.
+        {
+            name: "tools_icon",
+            title: "Tools",
+            css_class: "tools-icon",
+            on_click_fn: function(track) {
+                // TODO: update tipsy text.
+
+                track.dynamic_tool_div.toggle();
+
+                // Update track name.
+                if (track.dynamic_tool_div.is(":visible")) {
+                    track.set_name(track.name + track.tool_region_and_parameters_str());
+                }
+                else {
+                    track.revert_name();
+                }
+                // HACK: name change modifies icon placement, which leaves tooltip incorrectly placed.
+                $(".tipsy").remove();
+            }
+        },
+        // Remove track.
+        Drawable.prototype.action_icons_def[2]
+    ],
     build_container_div: function () {
         return $("<div/>").addClass('track').attr("id", "track_" + this.id).css("position", "relative");
     },
@@ -2504,38 +2581,17 @@ extend(Track.prototype, Drawable.prototype, {
                         .attr( "id", this.name.replace(/\s+/g,'-').replace(/[^a-zA-Z0-9\-]/g,'').toLowerCase() );
         return header_div;
     },
-    build_icons_div: function() {
-        var icons_div = $("<div/>").css("float", "left");
-
-        // Track icons.
-        this.mode_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Set display mode")
-                                  .addClass("icon-button chevron-expand").tipsy( {gravity: 's'} ).appendTo(icons_div);
-        this.toggle_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Hide/show track content")
-                                    .addClass("icon-button toggle").tipsy( {gravity: 's'} )
-                                    .appendTo(icons_div);
-        this.settings_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Edit settings")
-                                      .addClass("icon-button settings-icon").tipsy( {gravity: 's'} )
-                                      .appendTo(icons_div);
-        this.overview_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Set as overview")
-                                      .addClass("icon-button overview-icon").tipsy( {gravity: 's'} )
-                                      .appendTo(icons_div);
-        this.filters_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Filters")
-                                     .addClass("icon-button filters-icon").tipsy( {gravity: 's'} )
-                                     .appendTo(icons_div).hide();
-        this.tools_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Tools")
-                                   .addClass("icon-button tools-icon").tipsy( {gravity: 's'} )
-                                   .appendTo(icons_div).hide();
-        this.remove_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Remove")
-                                    .addClass("icon-button remove-icon").tipsy( {gravity: 's'} )
-                                    .appendTo(icons_div);
-        var track = this;
-
+    build_action_icons: function() {
+        Drawable.prototype.build_action_icons.call(this, this.action_icons_def);
+        
         // Set up behavior for modes popup.
+        var track = this;
         if (track.display_modes !== undefined) {
             var init_mode = (track.config && track.config.values['mode'] ? 
                              track.config.values['mode'] : track.display_modes[0]);
             track.mode = init_mode;
-            this.mode_icon.attr("title", "Set display mode (now: " + track.mode + ")");
+            
+            this.action_icons.mode_icon.attr("title", "Set display mode (now: " + track.mode + ")");
 
             var mode_mapping = {};
             for (var i = 0, len = track.display_modes.length; i < len; i++) {
@@ -2550,79 +2606,8 @@ extend(Track.prototype, Drawable.prototype, {
                 }(mode);
             }
 
-            make_popupmenu(this.mode_icon, mode_mapping);
+            make_popupmenu(this.action_icons.mode_icon, mode_mapping);
         }
-
-        // Toggle icon hides or shows the track content.
-        this.toggle_icon.click( function() {
-            if ( track.content_visible ) {
-                track.toggle_icon.addClass("toggle-expand").removeClass("toggle");
-                track.hide_contents();
-                track.content_visible = false;
-            } else {
-                track.toggle_icon.addClass("toggle").removeClass("toggle-expand");
-                track.content_visible = true;
-                track.show_contents();
-            }
-        });
-
-        // Clicking on settings icon opens track config.
-        this.settings_icon.click( function() {
-            var cancel_fn = function() { hide_modal(); $(window).unbind("keypress.check_enter_esc"); },
-                ok_fn = function() { 
-                    track.config.update_from_form( $(".dialog-box") );
-                    hide_modal(); 
-                    $(window).unbind("keypress.check_enter_esc"); 
-                },
-                check_enter_esc = function(e) {
-                    if ((e.keyCode || e.which) === 27) { // Escape key
-                        cancel_fn();
-                    } else if ((e.keyCode || e.which) === 13) { // Enter key
-                        ok_fn();
-                    }
-                };
-
-            $(window).bind("keypress.check_enter_esc", check_enter_esc);        
-            show_modal("Configure Track", track.config.build_form(), {
-                "Cancel": cancel_fn,
-                "OK": ok_fn
-            });
-        });
-
-        this.overview_icon.click( function() {
-            track.view.set_overview(track);
-        });
-
-        this.filters_icon.click( function() {
-            // TODO: update tipsy text.            
-            track.filters_div.toggle();
-            track.filters_manager.reset_filters();
-        });
-
-        this.tools_icon.click( function() {
-            // TODO: update tipsy text.
-
-            track.dynamic_tool_div.toggle();
-
-            // Update track name.
-            if (track.dynamic_tool_div.is(":visible")) {
-                track.set_name(track.name + track.tool_region_and_parameters_str());
-            }
-            else {
-                track.revert_name();
-            }
-            // HACK: name change modifies icon placement, which leaves tooltip incorrectly placed.
-            $(".tipsy").remove();
-        });
-
-        // Clicking on remove icon removes track.
-        this.remove_icon.click( function() {
-            // Tipsy for remove icon must be deleted when track is deleted.
-            $(".tipsy").remove();
-            track.remove();
-        });
-        
-        return icons_div;  
     },
     /**
      * Hide any elements that are part of the tracks contents area. Should
@@ -2808,7 +2793,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
         track.config.values['mode'] = name;
         track.tile_cache.clear();
         track.request_draw();
-        this.mode_icon.attr("title", "Set display mode (now: " + track.mode + ")");
+        this.action_icons.mode_icon.attr("title", "Set display mode (now: " + track.mode + ")");
         return track;
      },
     /**
@@ -2821,20 +2806,20 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
         // Show/hide filter icon.
         //
         if (track.filters_available > 0) {
-            track.filters_icon.show();
+            track.action_icons.filters_icon.show();
         }
         else {
-            track.filters_icon.hide();
+            track.action_icons.filters_icon.hide();
         }
         
         //
         // Show/hide tool icon.
         //
         if (track.tool) {
-            track.tools_icon.show();
+            track.action_icons.tools_icon.show();
         }
         else {
-            track.tools_icon.hide();
+            track.action_icons.tools_icon.hide();
         }
                         
         //
@@ -3506,7 +3491,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
             } else if ( mode == "summary_tree" ) {
                 mode = "coverage histogram";
             }
-            this.mode_icon.attr("title", "Set display mode (now: Auto/" + mode + ")");
+            this.action_icons.mode_icon.attr("title", "Set display mode (now: Auto/" + mode + ")");
         }
     },
     /**

From 17c5b27cdc0f727c71cfb6beac98bed2a5f49a12 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Wed, 23 Nov 2011 16:16:15 -0500
Subject: [PATCH 244/362] Re-engineer the datatypes registry so that it is
 initialized once when the Galaxy server is started, but data types can
 continue to be loaded throughout the Galaxy server's session (hopefully this
 doesn't break anything).

Add support for a single "import_module" to be passed to the new load_datatypes() method in the datatypes registry.  This provides the ability to load a single class module from an installed tool shed repository along with a datatypes_conf.xml file included in the installed repository and pass them to the new load_datatypes() method.  In the future, multiple imported modules may be allowed.  The datatypes_conf.xml file included in the repository must conform to a slightly different definition than the same named file that comes with the distribution.  This new definition will be documented in the Galaxy tool shed wiki.

We now have the ability to load new data types into the Galaxy server from an installed tool shed repository without restarting the Galaxy server.
---
 lib/galaxy/app.py                    |  3 +-
 lib/galaxy/datatypes/registry.py     | 58 +++++++++++++--------------
 lib/galaxy/datatypes/sniff.py        |  1 +
 lib/galaxy/model/__init__.py         |  4 +-
 lib/galaxy/tools/parameters/basic.py |  4 +-
 lib/galaxy/util/none_like.py         |  4 +-
 lib/galaxy/web/controllers/admin.py  | 60 +++++++++++++++++-----------
 lib/galaxy/webapps/community/app.py  |  3 +-
 scripts/functional_tests.py          |  4 +-
 scripts/set_metadata.py              |  4 +-
 tools/data_source/data_source.py     |  3 +-
 tools/data_source/upload.py          |  3 +-
 12 files changed, 89 insertions(+), 62 deletions(-)

diff --git a/lib/galaxy/app.py b/lib/galaxy/app.py
index be16f355b1f..e58102d99d5 100644
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -22,7 +22,8 @@ class UniverseApplication( object ):
         self.config.check()
         config.configure_logging( self.config )
         # Set up datatypes registry
-        self.datatypes_registry = galaxy.datatypes.registry.Registry( self.config.root, self.config.datatypes_config )
+        self.datatypes_registry = galaxy.datatypes.registry.Registry()
+        self.datatypes_registry.load_datatypes( self.config.root, self.config.datatypes_config )
         galaxy.model.set_datatypes_registry( self.datatypes_registry )
         # Set up the tool sheds registry
         if os.path.isfile( self.config.tool_sheds_config ):
diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
index 1dfec5b6fe2..e341d649702 100644
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -12,7 +12,7 @@ class ConfigurationError( Exception ):
     pass
 
 class Registry( object ):
-    def __init__( self, root_dir=None, config=None ):
+    def __init__( self ):
         self.log = logging.getLogger(__name__)
         self.log.addHandler( logging.NullHandler() )
         self.datatypes_by_extension = {}
@@ -27,21 +27,33 @@ class Registry( object ):
         self.sniff_order = []
         self.upload_file_formats = []
         self.display_applications = odict() #map a display application id to a display application
-        inherit_display_application_by_class = []
+        self.datatype_converters_path = None
+        self.datatype_indexers_path = None
+        self.display_applications_path = None
+    def load_datatypes( self, root_dir=None, config=None, imported_module=None ):
         if root_dir and config:
+            inherit_display_application_by_class = []
             # Parse datatypes_conf.xml
             tree = galaxy.util.parse_xml( config )
             root = tree.getroot()
             # Load datatypes and converters from config
             self.log.debug( 'Loading datatypes from %s' % config )
             registration = root.find( 'registration' )
-            self.datatype_converters_path = os.path.join( root_dir, registration.get( 'converters_path', 'lib/galaxy/datatypes/converters' ) )
-            self.datatype_indexers_path = os.path.join( root_dir, registration.get( 'indexers_path', 'lib/galaxy/datatypes/indexers' ) )
-            self.display_applications_path = os.path.join( root_dir, registration.get( 'display_path', 'display_applications' ) )
-            if not os.path.isdir( self.datatype_converters_path ):
-                raise ConfigurationError( "Directory does not exist: %s" % self.datatype_converters_path )
-            if not os.path.isdir( self.datatype_indexers_path ):
-                raise ConfigurationError( "Directory does not exist: %s" % self.datatype_indexers_path )                
+            # The following implementation implies that only the first datatypes_conf.xml parsed will
+            # define the various paths.  This is probably ok, since we can justifiably require that the
+            # local datatypes_conf.xml file sets the standard, and all additional datatypes_conf.xml
+            # files installed with repositories from tool sheds must use the same paths.  However, we
+            # may discover at some future time that allowing for multiple paths is more optimal.
+            if not self.datatype_converters_path:
+                self.datatype_converters_path = os.path.join( root_dir, registration.get( 'converters_path', 'lib/galaxy/datatypes/converters' ) )
+                if not os.path.isdir( self.datatype_converters_path ):
+                    raise ConfigurationError( "Directory does not exist: %s" % self.datatype_converters_path )
+            if not self.datatype_indexers_path:
+                self.datatype_indexers_path = os.path.join( root_dir, registration.get( 'indexers_path', 'lib/galaxy/datatypes/indexers' ) )
+                if not os.path.isdir( self.datatype_indexers_path ):
+                    raise ConfigurationError( "Directory does not exist: %s" % self.datatype_indexers_path )
+            if not self.display_applications_path:
+                self.display_applications_path = os.path.join( root_dir, registration.get( 'display_path', 'display_applications' ) )
             for elem in registration.findall( 'datatype' ):
                 try:
                     extension = elem.get( 'extension', None ) 
@@ -55,11 +67,14 @@ class Registry( object ):
                             fields = dtype.split( ':' )
                             datatype_module = fields[0]
                             datatype_class_name = fields[1]
-                            fields = datatype_module.split( '.' )
-                            module = __import__( fields.pop(0) )
-                            for mod in fields:
-                                module = getattr( module, mod )
-                            datatype_class = getattr( module, datatype_class_name )
+                            if imported_module:
+                                datatype_class = getattr( imported_module, datatype_class_name )
+                            else:
+                                fields = datatype_module.split( '.' )
+                                module = __import__( fields.pop(0) )
+                                for mod in fields:
+                                    module = getattr( module, mod )
+                                datatype_class = getattr( module, datatype_class_name )
                         elif type_extension:
                             datatype_class = self.datatypes_by_extension[type_extension].__class__
                         if make_subclass:
@@ -252,10 +267,8 @@ class Registry( object ):
                 if not included:
                     self.sniff_order.append(datatype)
         append_to_sniff_order()
-    
     def get_available_tracks(self):
         return self.available_tracks
-        
     def get_mimetype_by_extension(self, ext, default = 'application/octet-stream' ):
         """Returns a mimetype based on an extension"""
         try:
@@ -265,7 +278,6 @@ class Registry( object ):
             mimetype = default
             self.log.warning('unknown mimetype in data factory %s' % ext)
         return mimetype
-    
     def get_datatype_by_extension(self, ext ):
         """Returns a datatype based on an extension"""
         try:
@@ -273,7 +285,6 @@ class Registry( object ):
         except KeyError:
             builder = data.Text()
         return builder
-
     def change_datatype(self, data, ext, set_meta = True ):
         data.extension = ext
         # call init_meta and copy metadata from itself.  The datatype
@@ -287,7 +298,6 @@ class Registry( object ):
                 data.set_meta( overwrite = False )
                 data.set_peek()
         return data
-
     def old_change_datatype(self, data, ext):
         """Creates and returns a new datatype based on an existing data and an extension"""
         newdata = factory(ext)(id=data.id)
@@ -295,7 +305,6 @@ class Registry( object ):
             setattr(newdata, key, value)
         newdata.ext = ext
         return newdata
-
     def load_datatype_converters( self, toolbox ):
         """Adds datatype converters from self.converters to the calling app's toolbox"""     
         for elem in self.converters:
@@ -312,7 +321,6 @@ class Registry( object ):
                 self.log.debug( "Loaded converter: %s", converter.id )
             except:
                 self.log.exception( "error reading converter from path: %s" % converter_path )
-
     def load_external_metadata_tool( self, toolbox ):
         """Adds a tool which is used to set external metadata"""
         #we need to be able to add a job to the queue to set metadata. The queue will currently only accept jobs with an associated tool.
@@ -337,7 +345,6 @@ class Registry( object ):
         toolbox.tools_by_id[ set_meta_tool.id ] = set_meta_tool
         self.set_external_metadata_tool = set_meta_tool
         self.log.debug( "Loaded external metadata tool: %s", self.set_external_metadata_tool.id )
-        
     def load_datatype_indexers( self, toolbox ):
         """Adds indexers from self.indexers to the toolbox from app"""
         for elem in self.indexers:
@@ -347,7 +354,6 @@ class Registry( object ):
             toolbox.tools_by_id[indexer.id] = indexer
             self.datatype_indexers[datatype] = indexer
             self.log.debug( "Loaded indexer: %s", indexer.id )
-            
     def get_converters_by_datatype(self, ext):
         """Returns available converters by source type"""
         converters = odict()
@@ -360,7 +366,6 @@ class Registry( object ):
         if ext in self.datatype_converters.keys():
             converters.update(self.datatype_converters[ext])
         return converters
-
     def get_indexers_by_datatype( self, ext ):
         """Returns indexers based on datatype"""
         class_chain = list()
@@ -373,14 +378,12 @@ class Registry( object ):
         ext2type = lambda x: self.get_datatype_by_extension(x)
         class_chain = sorted(class_chain, lambda x,y: issubclass(ext2type(x),ext2type(y)) and -1 or 1)
         return [self.datatype_indexers[x] for x in class_chain]
-    
     def get_converter_by_target_type(self, source_ext, target_ext):
         """Returns a converter based on source and target datatypes"""
         converters = self.get_converters_by_datatype(source_ext)
         if target_ext in converters.keys():
             return converters[target_ext]
         return None
-
     def find_conversion_destination_for_dataset_by_extensions( self, dataset, accepted_formats, converter_safe = True ):
         """Returns ( target_ext, existing converted dataset )"""
         for convert_ext in self.get_converters_by_datatype( dataset.ext ):
@@ -394,10 +397,8 @@ class Registry( object ):
                     ret_data = None
                 return ( convert_ext, ret_data )
         return ( None, None )
-    
     def get_composite_extensions( self ):
         return [ ext for ( ext, d_type ) in self.datatypes_by_extension.iteritems() if d_type.composite_type is not None ]
-
     def get_upload_metadata_params( self, context, group, tool ):
         """Returns dict of case value:inputs for metadata conditional for upload tool"""
         rval = {}
@@ -413,4 +414,3 @@ class Registry( object ):
         if 'auto' not in rval and 'txt' in rval: #need to manually add 'auto' datatype
             rval[ 'auto' ] = rval[ 'txt' ]
         return rval
-
diff --git a/lib/galaxy/datatypes/sniff.py b/lib/galaxy/datatypes/sniff.py
index 379c3713add..d51929f290d 100644
--- a/lib/galaxy/datatypes/sniff.py
+++ b/lib/galaxy/datatypes/sniff.py
@@ -280,6 +280,7 @@ def guess_ext( fname, sniff_order=None, is_multi_byte=False ):
     """
     if sniff_order is None:
         datatypes_registry = registry.Registry()
+        datatypes_registry.load_datatypes()
         sniff_order = datatypes_registry.sniff_order
     for datatype in sniff_order:
         """
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 40d4695fd55..cd5d71f6190 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -25,7 +25,9 @@ if sys.version_info[:2] < ( 2, 5 ):
 
 log = logging.getLogger( __name__ )
 
-datatypes_registry = galaxy.datatypes.registry.Registry() #Default Value Required for unit tests
+datatypes_registry = galaxy.datatypes.registry.Registry()
+# Default Value Required for unit tests
+datatypes_registry.load_datatypes()
 
 class NoConverterException(Exception):
     def __init__(self, value):
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index e9aab7a3067..d0c9db07921 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -1307,7 +1307,9 @@ class DataToolParameter( ToolParameter ):
             if tool is None:
                 #This occurs for things such as unit tests
                 import galaxy.datatypes.registry
-                formats.append( galaxy.datatypes.registry.Registry().get_datatype_by_extension( extension.lower() ).__class__ )
+                datatypes_registry = galaxy.datatypes.registry.Registry()
+                datatypes_registry.load_datatypes()
+                formats.append( datatypes_registry.get_datatype_by_extension( extension.lower() ).__class__ )
             else:
                 formats.append( tool.app.datatypes_registry.get_datatype_by_extension( extension.lower() ).__class__ )
         self.formats = tuple( formats )
diff --git a/lib/galaxy/util/none_like.py b/lib/galaxy/util/none_like.py
index 67b8f3ea0f1..9ba4e1f8df1 100644
--- a/lib/galaxy/util/none_like.py
+++ b/lib/galaxy/util/none_like.py
@@ -20,7 +20,9 @@ class NoneDataset( RecursiveNone ):
     def __init__( self, datatypes_registry = None, ext = 'data', dbkey = '?' ):
         self.ext = self.extension = ext
         self.dbkey = dbkey
-        if datatypes_registry is None: datatypes_registry = Registry()
+        if datatypes_registry is None:
+            datatypes_registry = Registry()
+            datatypes_registry.load_datatypes()
         self.datatype = datatypes_registry.get_datatype_by_extension( ext )
         self._metadata = None
         self.metadata = MetadataCollection( self )
diff --git a/lib/galaxy/web/controllers/admin.py b/lib/galaxy/web/controllers/admin.py
index 6d628b77942..07bc69a6502 100644
--- a/lib/galaxy/web/controllers/admin.py
+++ b/lib/galaxy/web/controllers/admin.py
@@ -4,7 +4,7 @@ from galaxy.model.orm import *
 from galaxy.web.framework.helpers import time_ago, iff, grids
 from galaxy.tools.search import ToolBoxSearch
 from galaxy.tools import ToolSection, json_fix
-from galaxy.util import inflector
+from galaxy.util import parse_xml, inflector
 import logging
 log = logging.getLogger( __name__ )
 
@@ -874,8 +874,7 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
                             tmp_stderr.close()
                             if returncode == 0:
                                 # Load data types required by tools.
-                                # TODO: uncomment the following when we're ready...
-                                #self.__load_datatypes( trans, repo_files_dir )
+                                self.__load_datatypes( trans, repo_files_dir )
                                 # Load tools and tool data files required by them.
                                 sample_files, repository_tools_tups = self.__get_repository_tools_and_sample_files( trans, tool_path, repo_files_dir )
                                 if repository_tools_tups:
@@ -898,9 +897,8 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
                                     persisted_new_tool_section.write( new_tool_section )
                                     persisted_new_tool_section.close()
                                     # Parse the persisted tool panel section
-                                    tree = ElementTree.parse( tmp_name )
+                                    tree = parse_xml( tmp_name )
                                     root = tree.getroot()
-                                    ElementInclude.include( root )
                                     # Load the tools in the section into the tool panel.
                                     trans.app.toolbox.load_section_tag_set( root, trans.app.toolbox.tool_panel, tool_path )
                                     # Remove the temporary file
@@ -1186,35 +1184,49 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
                         datatypes_config = os.path.abspath( os.path.join( root, name ) )
                         break
         if datatypes_config:
+            imported_module = None
             # Parse datatypes_config.
-            tree = ElementTree.parse( datatypes_config )
-            root = tree.getroot()
-            ElementInclude.include( root )
-            datatype_files = root.find( 'datatype_files' )
+            tree = parse_xml( datatypes_config )
+            datatypes_config_root = tree.getroot()
+            relative_path_to_datatype_file_name = None
+            datatype_files = datatypes_config_root.find( 'datatype_files' )
+            # Currently only a single datatype_file is supported.  For example:
+            # <datatype_files>
+            #    <datatype_file name="gmap.py"/>
+            # </datatype_files>
             for elem in datatype_files.findall( 'datatype_file' ):
                 datatype_file_name = elem.get( 'name', None )
                 if datatype_file_name:
                     # Find the file in the installed repository.
-                    relative_path = None
                     for root, dirs, files in os.walk( repo_files_dir ):
                         if root.find( '.hg' ) < 0:
                             for name in files:
                                 if name == datatype_file_name:
-                                    relative_path = os.path.join( root, name )
+                                    relative_path_to_datatype_file_name = os.path.join( root, name )
                                     break
-                    relative_head, relative_tail = os.path.split( relative_path )
-                    # TODO: get the import_module by parsing the <registration><datatype> tags
-                    if datatype_file_name.find( '.' ) > 0:
-                        import_module = datatype_file_name.split( '.' )[ 0 ]
-                    else:
-                        import_module = datatype_file_name
-                    try:
-                        sys.path.insert( 0, relative_head )
-                        module = __import__( import_module )
-                        sys.path.pop( 0 )
-                    except Exception, e:
-                        log.debug( "Exception importing datatypes code file included in installed repository: %s" % str( e ) )
-                    trans.app.datatypes_registry = galaxy.datatypes.registry.Registry( trans.app.config.root, datatypes_config )
+                    break
+            if relative_path_to_datatype_file_name:
+                relative_head, relative_tail = os.path.split( relative_path_to_datatype_file_name )
+                registration = datatypes_config_root.find( 'registration' )
+                # Get the module by parsing the <datatype> tag.
+                for elem in registration.findall( 'datatype' ):
+                    # A 'type' attribute is currently required.  The attribute
+                    # should be something like: type="gmap:GmapDB".
+                    dtype = elem.get( 'type', None )
+                    if dtype:
+                        fields = dtype.split( ':' )
+                        datatype_module = fields[0]
+                        datatype_class_name = fields[1]
+                        # Since we currently support only a single datatype_file,
+                        #  we have what we need.
+                        break
+                try:
+                    sys.path.insert( 0, relative_head )
+                    imported_module = __import__( datatype_module )
+                    sys.path.pop( 0 )
+                except Exception, e:
+                    log.debug( "Exception importing datatypes code file included in installed repository: %s" % str( e ) )
+            trans.app.datatypes_registry.load_datatypes( root_dir=trans.app.config.root, config=datatypes_config, imported_module=imported_module )
     def __get_repository_tools_and_sample_files( self, trans, tool_path, repo_files_dir ):
         # The sample_files list contains all files whose name ends in .sample
         sample_files = []
diff --git a/lib/galaxy/webapps/community/app.py b/lib/galaxy/webapps/community/app.py
index 00f6f622b01..2eb4d0cc9f4 100644
--- a/lib/galaxy/webapps/community/app.py
+++ b/lib/galaxy/webapps/community/app.py
@@ -15,7 +15,8 @@ class UniverseApplication( object ):
         self.config.check()
         config.configure_logging( self.config )
         # Set up datatypes registry
-        self.datatypes_registry = galaxy.datatypes.registry.Registry( self.config.root, self.config.datatypes_config )
+        self.datatypes_registry = galaxy.datatypes.registry.Registry()
+        self.datatypes_registry.load_datatypes( self.config.root, self.config.datatypes_config )
         # Determine the database url
         if self.config.database_connection:
             db_url = self.config.database_connection
diff --git a/scripts/functional_tests.py b/scripts/functional_tests.py
index 8ebd5fefdb8..dc8fa1a754d 100644
--- a/scripts/functional_tests.py
+++ b/scripts/functional_tests.py
@@ -244,7 +244,9 @@ def main():
     else:
         # FIXME: This doesn't work at all now that toolbox requires an 'app' instance
         #        (to get at datatypes, might just pass a datatype registry directly)
-        my_app = bunch.Bunch( datatypes_registry = galaxy.datatypes.registry.Registry() )
+        datatypes_registry = galaxy.datatypes.registry.Registry()
+        datatypes_registry.load_datatypes()
+        my_app = bunch.Bunch( datatypes_registry )
         test_toolbox.toolbox = tools.ToolBox( 'tool_conf.xml.test', 'tools', my_app )
 
     # ---- Find tests ---------------------------------------------------------
diff --git a/scripts/set_metadata.py b/scripts/set_metadata.py
index 792f3c18b71..8c35ee31af2 100644
--- a/scripts/set_metadata.py
+++ b/scripts/set_metadata.py
@@ -37,7 +37,9 @@ def __main__():
     # Set up datatypes registry
     config_root = sys.argv.pop( 1 )
     datatypes_config = sys.argv.pop( 1 )
-    galaxy.model.set_datatypes_registry( galaxy.datatypes.registry.Registry( config_root, datatypes_config ) )
+    datatypes_registry = galaxy.datatypes.registry.Registry()
+    datatypes_registry.load_datatypes( root_dir=config_root, config=datatypes_config )
+    galaxy.model.set_datatypes_registry( datatypes_registry )
 
     job_metadata = sys.argv.pop( 1 )
     ext_override = dict()
diff --git a/tools/data_source/data_source.py b/tools/data_source/data_source.py
index 2d0c60545f7..fd85fc2906d 100644
--- a/tools/data_source/data_source.py
+++ b/tools/data_source/data_source.py
@@ -57,7 +57,8 @@ def __main__():
         enhanced_handling = True
         json_file = open( job_params[ 'job_config' ][ 'TOOL_PROVIDED_JOB_METADATA_FILE' ], 'w' ) #specially named file for output junk to pass onto set metadata
     
-    datatypes_registry = Registry( root_dir = job_params[ 'job_config' ][ 'GALAXY_ROOT_DIR' ], config = job_params[ 'job_config' ][ 'GALAXY_DATATYPES_CONF_FILE' ] )
+    datatypes_registry = Registry()
+    datatypes_registry.load_datatypes( root_dir = job_params[ 'job_config' ][ 'GALAXY_ROOT_DIR' ], config = job_params[ 'job_config' ][ 'GALAXY_DATATYPES_CONF_FILE' ] )
     
     URL = params.get( 'URL', None ) #using exactly URL indicates that only one dataset is being downloaded
     URL_method = params.get( 'URL_method', None )
diff --git a/tools/data_source/upload.py b/tools/data_source/upload.py
index efc2543a41d..2d08cb45451 100644
--- a/tools/data_source/upload.py
+++ b/tools/data_source/upload.py
@@ -369,7 +369,8 @@ def __main__():
     output_paths = parse_outputs( sys.argv[4:] )
     json_file = open( 'galaxy.json', 'w' )
 
-    registry = Registry( sys.argv[1], sys.argv[2] )
+    registry = Registry()
+    registry.load_datatypes( root_dir=sys.argv[1], config=sys.argv[2] )
 
     for line in open( sys.argv[3], 'r' ):
         dataset = from_json_string( line )

From 017716b4c4d6f8b3ad963ee49852a7aa1458039e Mon Sep 17 00:00:00 2001
From: Hanfei Sun <ad9075@gmail.com>
Date: Thu, 24 Nov 2011 23:56:36 +0800
Subject: [PATCH 245/362] Modify some string in Mako templetes for complete
 i18n support.

---
 locale/zh/LC_MESSAGES/ginga.mo            | Bin 9248 -> 9906 bytes
 locale/zh/LC_MESSAGES/ginga.po            |  52 ++++++++++---------
 templates/root/history_common.mako        |  38 +++++++-------
 templates/root/index.mako                 |  46 ++++++++---------
 templates/webapps/galaxy/base_panels.mako |  58 +++++++++++-----------
 5 files changed, 100 insertions(+), 94 deletions(-)

diff --git a/locale/zh/LC_MESSAGES/ginga.mo b/locale/zh/LC_MESSAGES/ginga.mo
index e1635e655ec80cf13465adcac6cf06e52f4e1d25..313becab3316482d2927e80aebaf24133df491f0 100644
GIT binary patch
delta 4702
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delta 4012
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diff --git a/locale/zh/LC_MESSAGES/ginga.po b/locale/zh/LC_MESSAGES/ginga.po
index f7f7721a399..7f13341e093 100644
--- a/locale/zh/LC_MESSAGES/ginga.po
+++ b/locale/zh/LC_MESSAGES/ginga.po
@@ -33,12 +33,10 @@ msgstr "Galaxy"
 msgid "Are you sure you want to delete the current history?"
 msgstr "确认要删除当前的历史记录吗？"
 
-
 #: templates/root/history.mako:38
 msgid "collapse all"
 msgstr "全部收缩"
 
-
 #: templates/root/index.mako:5
 msgid "Tools"
 msgstr "工具"
@@ -57,7 +55,6 @@ msgstr "ENCODE工具"
 msgid "Lift-Over"
 msgstr "版本转换"
 
-
 msgid "Text Manipulation"
 msgstr "文本操作"
 
@@ -134,7 +131,7 @@ msgid "History Item Attributes"
 msgstr "历史项目属性"
 
 #: templates/dataset/edit_attributes.mako:19
-msgid "Edit Attributes"
+msgid "Edit attributes"
 msgstr "编辑属性"
 
 #: templates/dataset/edit_attributes.mako:64
@@ -148,21 +145,21 @@ msgid ""
 "Required metadata values are missing. Some of these values may not be "
 "editable by the user. Selecting \"Auto-detect\" will attempt to fix these "
 "values."
-msgstr "所需元数据值缺失。其中一些值可能无法被用户编辑。选择“自动检测”将修正这些值。"
+msgstr "缺少所需的metadata的值。用户可能无法对这些值进行编辑。选择“自动检测”来尝试修正这些值。"
 
 #: templates/dataset/edit_attributes.mako:78
 msgid "Convert to new format"
-msgstr "转换成新格式"
+msgstr "转换为新格式"
 
 #: templates/dataset/edit_attributes.mako:84
 msgid "Convert to"
-msgstr "转换"
+msgstr "转换为"
 
 #: templates/dataset/edit_attributes.mako:95
 msgid ""
 "This will create a new dataset with the contents of this dataset converted "
 "to a new format."
-msgstr "这将创建一个新的数据集，内容是转换后的数据集。"
+msgstr "这将产生一个转换格式后的新数据集，"
 
 #: templates/dataset/edit_attributes.mako:111
 msgid "Change data type"
@@ -177,7 +174,7 @@ msgid ""
 "This will change the datatype of the existing dataset but <i>not</i> modify "
 "its contents. Use this if Galaxy has incorrectly guessed the type of your "
 "dataset."
-msgstr "这将改变已有数据集的数据类型，但是<i>不</i>改变其内容。当Galaxy不能正确判断你的数据类型时，设置该参数。"
+msgstr "这将改变已有数据集的数据类型，但<i>不</i>改变其内容。当Galaxy不能正确判断你的数据类型时，设置该参数。"
 
 #: templates/dataset/edit_attributes.mako:137
 msgid "Copy History Item"
@@ -185,19 +182,16 @@ msgstr "复制历史记录项"
 
 #: templates/history/list.mako:3
 msgid "Saved Histories"
-msgstr "保存的历史记录"
+msgstr "已保存的历史"
 
-#: templates/history/list.mako:19
-msgid "Stored Histories"
-msgstr "存储的历史记录"
 
 #: templates/history/list.mako:21 templates/root/history.mako:239
 msgid "hide deleted"
-msgstr "隐藏已删除"
+msgstr "隐藏已删除的数据"
 
 #: templates/history/list.mako:23
 msgid "show deleted"
-msgstr "显示已删除"
+msgstr "显示已删除的数据"
 
 #: templates/history/list.mako:27
 msgid "Name"
@@ -209,7 +203,7 @@ msgstr "大小"
 
 #: templates/history/list.mako:27
 msgid "Last modified"
-msgstr "最后修改"
+msgstr "最后修改时间"
 
 #: templates/history/list.mako:27
 msgid "Actions"
@@ -229,7 +223,7 @@ msgstr "删除"
 
 #: templates/history/list.mako:49
 msgid "undelete"
-msgstr "取消删除"
+msgstr "还原"
 
 #: templates/history/list.mako:55
 msgid "Action"
@@ -249,7 +243,7 @@ msgstr "删除"
 
 #: templates/history/list.mako:58
 msgid "Undelete"
-msgstr "取消删除"
+msgstr "还原"
 
 #: templates/history/list.mako:65
 msgid "You have no stored histories"
@@ -261,7 +255,7 @@ msgstr "历史记录选项"
 
 #: templates/history/options.mako:9
 msgid "You must be "
-msgstr "你必须"
+msgstr "你必须成为"
 
 #: templates/history/options.mako:9
 msgid "logged in"
@@ -290,7 +284,7 @@ msgstr "创建"
 
 #: templates/history/options.mako:18
 msgid " a new empty history"
-msgstr " 一个新的空历史记录"
+msgstr " 一个新的空白历史记录"
 
 #: templates/history/options.mako:20
 msgid "Construct workflow"
@@ -550,10 +544,10 @@ msgstr "数据安全性"
 
 
 msgid "Show Deleted Datasets"
-msgstr "显示已删除数据"
+msgstr "显示已删除的数据"
 
 msgid "Show Hidden Datasets"
-msgstr "显示隐藏数据"
+msgstr "显示隐藏的数据"
 
 msgid "Show Structure"
 msgstr "显示结构"
@@ -594,4 +588,16 @@ msgstr "用户"
 
 
 msgid "Register"
-msgstr "注册"
\ No newline at end of file
+msgstr "注册"
+
+msgid "Support"
+msgstr "技术支持"
+
+msgid "Galaxy Wiki"
+msgstr "Galaxy百科"
+
+msgid "Video tutorials (screencasts)"
+msgstr "视频教程（动画演示）"
+
+msgid "How to Cite Galaxy"
+msgstr "如何引用Galaxy"
diff --git a/templates/root/history_common.mako b/templates/root/history_common.mako
index e0585d871e3..bbd04684c58 100644
--- a/templates/root/history_common.mako
+++ b/templates/root/history_common.mako
@@ -19,7 +19,7 @@
             </div>
             <div style="float:left;" class="menubutton split popup" id="dataset-${dataset_id}-popup">
         %endif
-        <a href="${h.url_for( controller='dataset', action='display', dataset_id=dataset_id, to_ext=data.ext )}" title="Download" class="icon-button disk tooltip"></a>
+        <a href="${h.url_for( controller='dataset', action='display', dataset_id=dataset_id, to_ext=data.ext )}" title='${_("Download")}' class="icon-button disk tooltip"></a>
         %if meta_files:
             </div>
         %endif
@@ -75,7 +75,7 @@
                 ## TODO: Make these CSS, just adding a "disabled" class to the normal
                 ## links should be enough. However the number of datasets being uploaded
                 ## at a time is usually small so the impact of these images is also small.
-                <span title='Display Data' class='icon-button display_disabled tooltip'></span>
+                <span title='${_("Display Data")}' class='icon-button display_disabled tooltip'></span>
                 %if for_editing:
                     <span title='Edit Attributes' class='icon-button edit_disabled tooltip'></span>
                 %endif
@@ -98,7 +98,7 @@
                 %if data.purged:
                     <span class="icon-button display_disabled tooltip" title="Cannot display datasets removed from disk"></span>
                 %else:
-                    <a class="icon-button display tooltip" title="Display data in browser" href="${display_url}"
+                    <a class="icon-button display tooltip" title='${_("Display data in browser")}' href="${display_url}"
                     %if for_editing:
                         target="galaxy_main"
                     %endif
@@ -110,13 +110,13 @@
                     %elif data.purged:
                         <span title="Cannot edit attributes of datasets removed from disk" class="icon-button edit_disabled tooltip"></span>
                     %else:
-                        <a class="icon-button edit tooltip" title="Edit attributes" href="${h.url_for( controller='dataset', action='edit', dataset_id=dataset_id )}" target="galaxy_main"></a>
+                        <a class="icon-button edit tooltip" title='${_("Edit attributes")}' href="${h.url_for( controller='dataset', action='edit', dataset_id=dataset_id )}" target="galaxy_main"></a>
                     %endif
                 %endif
             %endif
             %if for_editing:
                 %if can_edit:
-                    <a class="icon-button delete tooltip" title="Delete" href="${h.url_for( controller='dataset', action='delete', dataset_id=dataset_id, show_deleted_on_refresh=show_deleted_on_refresh )}" id="historyItemDeleter-${dataset_id}"></a>
+                    <a class="icon-button delete tooltip" title='${_("Delete")}' href="${h.url_for( controller='dataset', action='delete', dataset_id=dataset_id, show_deleted_on_refresh=show_deleted_on_refresh )}" id="historyItemDeleter-${dataset_id}"></a>
                 %else:
                     <span title="Dataset is already deleted" class="icon-button delete_disabled tooltip"></span>
                 %endif
@@ -136,17 +136,17 @@
         %elif data_state == "queued":
             <div>${_('Job is waiting to run')}</div>
             <div>
-                <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title="View Details" class="icon-button information tooltip"></a>
+                <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title='${_("View Details")}' class="icon-button information tooltip"></a>
                 %if for_editing:
-                    <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title="Run this job again" class="icon-button arrow-circle tooltip"></a>
+                    <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title='${_("Run this job again")}' class="icon-button arrow-circle tooltip"></a>
                 %endif
             </div>
         %elif data_state == "running":
             <div>${_('Job is currently running')}</div>
             <div>
-                <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title="View Details" class="icon-button information tooltip"></a>
+                <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title='${_("View Details")}' class="icon-button information tooltip"></a>
                 %if for_editing:
-                    <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title="Run this job again" class="icon-button arrow-circle tooltip"></a>
+                    <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title='${_("Run this job again")}' class="icon-button arrow-circle tooltip"></a>
                 %endif
             </div>
         %elif data_state == "error":
@@ -163,9 +163,9 @@
                 %if data.has_data():
                     ${render_download_links( data, dataset_id )}
                 %endif
-                <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title="View Details" class="icon-button information tooltip"></a>
+                <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title='${_("View Details")}' class="icon-button information tooltip"></a>
                 %if for_editing:
-                    <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title="Run this job again" class="icon-button arrow-circle tooltip"></a>
+                    <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title='${_("Run this job again")}' class="icon-button arrow-circle tooltip"></a>
                 %endif
             </div>
         %elif data_state == "discarded":
@@ -177,9 +177,9 @@
         %elif data_state == "empty":
             <div>${_('No data: ')}<i>${data.display_info()}</i></div>
             <div>
-                <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title="View Details" class="icon-button information tooltip"></a>
+                <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title='${_("View Details")}' class="icon-button information tooltip"></a>
                 %if for_editing:
-                    <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title="Run this job again" class="icon-button arrow-circle tooltip"></a>
+                    <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title='${_("Run this job again")}' class="icon-button arrow-circle tooltip"></a>
                 %endif
             </div>
         %elif data_state in [ "ok", "failed_metadata" ]:
@@ -193,8 +193,8 @@
             %endif
             <div>
                 ${data.blurb}<br />
-                format: <span class="${data.ext}">${data.ext}</span>, 
-                database:
+                ${_("format: ")} <span class="${data.ext}">${data.ext}</span>, 
+                ${_("database: ")}
                 %if data.dbkey == '?' and can_edit:
                     <a href="${h.url_for( controller='dataset', action='edit', dataset_id=dataset_id )}" target="galaxy_main">${_(data.dbkey)}</a>
                 %else:
@@ -208,10 +208,10 @@
                 %if data.has_data():
                     ${render_download_links( data, dataset_id )}
                     
-                    <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title="View Details" class="icon-button information tooltip"></a>
+                    <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title='${_("View Details")}' class="icon-button information tooltip"></a>
                     
                     %if for_editing:
-                        <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title="Run this job again" class="icon-button arrow-circle tooltip"></a>
+                        <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title='${_("Run this job again")}' class="icon-button arrow-circle tooltip"></a>
                         %if app.config.get_bool( 'enable_tracks', False ) and data.ext in app.datatypes_registry.get_available_tracks():
                             <%
                             if data.dbkey != '?':
@@ -266,8 +266,8 @@
                         <br />
                     %endfor
                 %elif for_editing:
-                    <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title="View Details" class="icon-button information tooltip"></a>
-                    <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title="Run this job again" class="icon-button arrow-circle tooltip"></a>
+                    <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title='${_("View Details")}' class="icon-button information tooltip"></a>
+                    <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title='${_("Run this job again")}' class="icon-button arrow-circle tooltip"></a>
                 %endif
     
                 </div>
diff --git a/templates/root/index.mako b/templates/root/index.mako
index e6f28509b79..74ff48fbed8 100644
--- a/templates/root/index.mako
+++ b/templates/root/index.mako
@@ -11,71 +11,71 @@
         // Init history options.
         $("#history-options-button").css( "position", "relative" );
         make_popupmenu( $("#history-options-button"), {
-            "History Lists": null,
-            "Saved Histories": function() {
+            "${_("History Lists")}": null,
+            "${_("Saved Histories")}": function() {
                 galaxy_main.location = "${h.url_for( controller='history', action='list')}";
             },
-            "Histories Shared with Me": function() {
+            "${_("Histories Shared with Me")}": function() {
                 galaxy_main.location = "${h.url_for( controller='history', action='list_shared')}";
             },
-            "Current History": null,
-            "Create New": function() {
+            "${_("Current History")}": null,
+            "${_("Create New")}": function() {
                 galaxy_history.location = "${h.url_for( controller='root', action='history_new' )}";
             },
-            "Clone": function() {
+            "${_("Clone")}": function() {
                 galaxy_main.location = "${h.url_for( controller='history', action='clone')}";
             },
-            "Copy Datasets": function() {
+            "${_("Copy Datasets")}": function() {
                 galaxy_main.location = "${h.url_for( controller='dataset', action='copy_datasets' )}";
             },
-            "Share or Publish": function() {
+            "${_("Share or Publish")}": function() {
                 galaxy_main.location = "${h.url_for( controller='history', action='sharing' )}";
             },
-            "Extract Workflow": function() {
+            "${_("Extract Workflow")}": function() {
                 galaxy_main.location = "${h.url_for( controller='workflow', action='build_from_current_history' )}";
             },
-            "Dataset Security": function() {
+            "${_("Dataset Security")}": function() {
                 galaxy_main.location = "${h.url_for( controller='root', action='history_set_default_permissions' )}";
             },
-            "Show Deleted Datasets": function() {
+            "${_("Show Deleted Datasets")}": function() {
                 galaxy_history.location = "${h.url_for( controller='root', action='history', show_deleted=True)}";
             },
-            "Show Hidden Datasets": function() {
+            "${_("Show Hidden Datasets")}": function() {
                 galaxy_history.location = "${h.url_for( controller='root', action='history', show_hidden=True)}";
             },
-            "Purge Deleted Datasets": function() {
+            "${_("Purge Deleted Datasets")}": function() {
                 if ( confirm( "Really delete all deleted datasets permanently? This cannot be undone." ) ) {
                     galaxy_main.location = "${h.url_for( controller='history', action='purge_deleted_datasets' )}";
                 }
             },
-            "Show Structure": function() {
+            "${_("Show Structure")}": function() {
                 galaxy_main.location = "${h.url_for( controller='history', action='display_structured' )}";
             },
-            "Export to File": function() {
+            "${_("Export to File")}": function() {
                 galaxy_main.location = "${h.url_for( controller='history', action='export_archive' )}";
             },
-            "Delete": function() {
+            "${_("Delete")}": function() {
                 if ( confirm( "Really delete the current history?" ) ) {
                     galaxy_main.location = "${h.url_for( controller='history', action='delete_current' )}";
                 }
             },
-            "Delete Permanently": function() {
+            "${_("Delete Permanently")}": function() {
                 if ( confirm( "Really delete the current history permanently? This cannot be undone." ) ) {
                     galaxy_main.location = "${h.url_for( controller='history', action='delete_current', purge=True )}";
                 }
             },
-            "Other Actions": null,
-            "Import from File": function() {
+            "${_("Other Actions")}": null,
+            "${_("Import from File")}": function() {
                 galaxy_main.location = "${h.url_for( controller='history', action='import_archive' )}";
             }
         });
         
         var menu_options = {}; // Holds dictionary of { label: toggle_fn }
         
-        SHOW_TOOL = "Show Tool Search";
-        HIDE_TOOL = "Hide Tool Search";
-        SHOW_RECENT = "Show Recently Used";
-        HIDE_RECENT = "Hide Recently Used";
+        SHOW_TOOL = "${_("Show Tool Search")}";
+        HIDE_TOOL = "${_("Hide Tool Search")}";
+        SHOW_RECENT = "${_("Show Recently Used")}";
+        HIDE_RECENT = "${_("Hide Recently Used")}";
         
         var toggle_tool_search_fn = function() {
             // Show/hide menu and update vars, user preferences.
diff --git a/templates/webapps/galaxy/base_panels.mako b/templates/webapps/galaxy/base_panels.mako
index 50ef7be93bc..254312f35c1 100644
--- a/templates/webapps/galaxy/base_panels.mako
+++ b/templates/webapps/galaxy/base_panels.mako
@@ -64,32 +64,32 @@
     
 
     ## Analyze data tab.
-    ${tab( "analysis", "Analyze Data", h.url_for( controller='/root', action='index' ) )}
+    ${tab( "analysis", _("Analyze Data"), h.url_for( controller='/root', action='index' ) )}
     
     ## Workflow tab.
-    ${tab( "workflow", "Workflow", h.url_for( controller='/workflow', action='index' ) )}
+    ${tab( "workflow", _("Workflow"), h.url_for( controller='/workflow', action='index' ) )}
     
     ## 'Shared Items' or Libraries tab.
     <%
         menu_options = [ 
-                        [ 'Data Libraries', h.url_for( controller='/library', action='index') ],
+                        [ _('Data Libraries'), h.url_for( controller='/library', action='index') ],
                         None,
-                        [ 'Published Histories', h.url_for( controller='/history', action='list_published' ) ],
-                        [ 'Published Workflows', h.url_for( controller='/workflow', action='list_published' ) ]
+                        [ _('Published Histories'), h.url_for( controller='/history', action='list_published' ) ],
+                        [ _('Published Workflows'), h.url_for( controller='/workflow', action='list_published' ) ]
                        ]
         if app.config.get_bool( 'enable_tracks', False ):
-            menu_options.append( [ 'Published Visualizations', h.url_for( controller='/visualization', action='list_published' ) ] )        
+            menu_options.append( [ _('Published Visualizations'), h.url_for( controller='/visualization', action='list_published' ) ] )        
         if app.config.get_bool( 'enable_pages', False ):
-            menu_options.append( [ 'Published Pages', h.url_for( controller='/page', action='list_published' ) ] )
-        tab( "shared", "Shared Data", h.url_for( controller='/library', action='index'), menu_options=menu_options )
+            menu_options.append( [ _('Published Pages'), h.url_for( controller='/page', action='list_published' ) ] )
+        tab( "shared", _("Shared Data"), h.url_for( controller='/library', action='index'), menu_options=menu_options )
     %>
     
     ## Lab menu.
     <%
         menu_options = [
-                         [ 'Sequencing Requests', h.url_for( controller='/requests', action='index' ) ],
-                         [ 'Find Samples', h.url_for( controller='/requests', action='find_samples_index' ) ],
-                         [ 'Help', app.config.get( "lims_doc_url", "http://main.g2.bx.psu.edu/u/rkchak/p/sts" ), "galaxy_main" ]
+                         [ _('Sequencing Requests'), h.url_for( controller='/requests', action='index' ) ],
+                         [ _('Find Samples'), h.url_for( controller='/requests', action='find_samples_index' ) ],
+                         [ _('Help'), app.config.get( "lims_doc_url", "http://main.g2.bx.psu.edu/u/rkchak/p/sts" ), "galaxy_main" ]
                        ]
         tab( "lab", "Lab", None, menu_options=menu_options, visible=( trans.user and ( trans.user.requests or trans.app.security_agent.get_accessible_request_types( trans, trans.user ) ) ) )
     %>
@@ -98,10 +98,10 @@
     %if app.config.get_bool( 'enable_tracks', False ):
         <%
             menu_options = [
-                             ['New Track Browser', h.url_for( controller='/tracks', action='index' ) ],
-                             ['Saved Visualizations', h.url_for( controller='/visualization', action='list' ) ]
+                             [_('New Track Browser'), h.url_for( controller='/tracks', action='index' ) ],
+                             [_('Saved Visualizations'), h.url_for( controller='/visualization', action='list' ) ]
                            ]
-            tab( "visualization", "Visualization", h.url_for( controller='/visualization', action='list'), menu_options=menu_options )
+            tab( "visualization", _("Visualization"), h.url_for( controller='/visualization', action='list'), menu_options=menu_options )
         %>
     %endif
 
@@ -111,23 +111,23 @@
     ## Help tab.
     <%
         menu_options = [
-                            ['Support', app.config.get( "support_url", "http://wiki.g2.bx.psu.edu/Support" ), "_blank" ],
-                            ['Galaxy Wiki', app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/" ), "_blank" ],
-                            ['Video tutorials (screencasts)', app.config.get( "screencasts_url", "http://galaxycast.org" ), "_blank" ],
-                            ['How to Cite Galaxy', app.config.get( "citation_url", "http://wiki.g2.bx.psu.edu/Citing%20Galaxy" ), "_blank" ]
+                            [_('Support'), app.config.get( "support_url", "http://wiki.g2.bx.psu.edu/Support" ), "_blank" ],
+                            [_('Galaxy Wiki'), app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/" ), "_blank" ],
+                            [_('Video tutorials (screencasts)'), app.config.get( "screencasts_url", "http://galaxycast.org" ), "_blank" ],
+                            [_('How to Cite Galaxy'), app.config.get( "citation_url", "http://wiki.g2.bx.psu.edu/Citing%20Galaxy" ), "_blank" ]
                         ]
-        tab( "help", "Help", None, menu_options=menu_options)
+        tab( "help", _("Help"), None, menu_options=menu_options)
     %>
     
     ## User tabs.
     <%  
         # Menu for user who is not logged in.
-        menu_options = [ [ "Login", h.url_for( controller='/user', action='login' ), "galaxy_main" ] ]
+        menu_options = [ [ _("Login"), h.url_for( controller='/user', action='login' ), "galaxy_main" ] ]
         if app.config.allow_user_creation:
-            menu_options.append( [ "Register", h.url_for( controller='/user', action='create', cntrller='user' ), "galaxy_main" ] ) 
+            menu_options.append( [ _("Register"), h.url_for( controller='/user', action='create', cntrller='user' ), "galaxy_main" ] ) 
         extra_class = "loggedout-only"
         visible = ( trans.user == None )
-        tab( "user", "User", None, visible=visible, menu_options=menu_options )
+        tab( "user", _("User"), None, visible=visible, menu_options=menu_options )
         
         # Menu for user who is logged in.
         if trans.user:
@@ -137,9 +137,9 @@
         menu_options = [ [ '<li>Logged in as <span id="user-email">%s</span></li>' %  email ] ]
         if app.config.use_remote_user:
             if app.config.remote_user_logout_href:
-                menu_options.append( [ 'Logout', app.config.remote_user_logout_href, "_top" ] )
+                menu_options.append( [ _('Logout'), app.config.remote_user_logout_href, "_top" ] )
         else:
-            menu_options.append( [ 'Preferences', h.url_for( controller='/user', action='index', cntrller='user' ), "galaxy_main" ] )
+            menu_options.append( [ _('Preferences'), h.url_for( controller='/user', action='index', cntrller='user' ), "galaxy_main" ] )
             if app.config.get_bool( 'enable_tracks', False ):
                 menu_options.append( [ 'Custom Builds', h.url_for( controller='/user', action='dbkeys' ), "galaxy_main" ] )
             if app.config.require_login:
@@ -148,14 +148,14 @@
                 logout_url = h.url_for( controller='/user', action='logout' )
             menu_options.append( [ 'Logout', logout_url, "_top" ] )
             menu_options.append( None )
-        menu_options.append( [ 'Saved Histories', h.url_for( controller='/history', action='list' ), "galaxy_main" ] )
-        menu_options.append( [ 'Saved Datasets', h.url_for( controller='/dataset', action='list' ), "galaxy_main" ] )
+        menu_options.append( [ _('Saved Histories'), h.url_for( controller='/history', action='list' ), "galaxy_main" ] )
+        menu_options.append( [ _('Saved Datasets'), h.url_for( controller='/dataset', action='list' ), "galaxy_main" ] )
         if app.config.get_bool( 'enable_pages', False ):
-            menu_options.append( [ 'Saved Pages', h.url_for( controller='/page', action='list' ), "_top" ] )
+            menu_options.append( [ _('Saved Pages'), h.url_for( controller='/page', action='list' ), "_top" ] )
         if app.config.enable_api:
-            menu_options.append( [ 'API Keys', h.url_for( controller='/user', action='api_keys', cntrller='user' ), "galaxy_main" ] )
+            menu_options.append( [ _('API Keys'), h.url_for( controller='/user', action='api_keys', cntrller='user' ), "galaxy_main" ] )
         if app.config.use_remote_user:
-            menu_options.append( [ 'Public Name', h.url_for( controller='/user', action='edit_username', cntrller='user' ), "galaxy_main" ] )
+            menu_options.append( [ _('Public Name'), h.url_for( controller='/user', action='edit_username', cntrller='user' ), "galaxy_main" ] )
     
         extra_class = "loggedin-only"
         visible = ( trans.user != None )

From 9b8d0e0ca32d49be5e7c32829a326d9bf6640c1a Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Fri, 25 Nov 2011 09:24:58 -0500
Subject: [PATCH 246/362] Remove the old template_path setting from
 community_wsgi.ini. since it is set incorrecly and not neede anyway.

---
 community_wsgi.ini.sample | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/community_wsgi.ini.sample b/community_wsgi.ini.sample
index 55b67ce5d4c..7dff5b2da3d 100644
--- a/community_wsgi.ini.sample
+++ b/community_wsgi.ini.sample
@@ -26,9 +26,6 @@ file_path = database/community_files
 # Temporary storage for additional datasets, this should be shared through the cluster
 new_file_path = database/tmp
 
-# Where templates are stored
-template_path = lib/galaxy/webapps/community/templates
-
 # Session support (beaker)
 use_beaker_session = True
 session_type = memory

From 86fe959b0d844cf3d879bf1d0a04792cf3efec93 Mon Sep 17 00:00:00 2001
From: Richard Burhans <burhans@bx.psu.edu>
Date: Mon, 28 Nov 2011 13:13:39 -0500
Subject: [PATCH 247/362] Added "Convert CG MasterVar file to pgSnp format"
 tool to the Human Genome Variation section

---
 tool_conf.xml.sample | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index 1f12de1a36f..5f604024bc5 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -469,6 +469,7 @@
     <tool file="human_genome_variation/lps.xml" />
     <tool file="human_genome_variation/hilbertvis.xml" />
     <tool file="human_genome_variation/freebayes.xml" />
+	<tool file="human_genome_variation/master2pg.xml" />
   </section>
   <section name="Genome Diversity" id="gd">
     <tool file="genome_diversity/extract_primers.xml" />

From 57a8be43bf897a608da74f427966c488fd4123dd Mon Sep 17 00:00:00 2001
From: Richard Burhans <burhans@bx.psu.edu>
Date: Mon, 28 Nov 2011 13:15:08 -0500
Subject: [PATCH 248/362] "Convert CG MasterVar file to pgSnp format" tool and
 test data

---
 tools/human_genome_variation/master2pg.pl  | 131 +++++++++++++++++++++
 tools/human_genome_variation/master2pg.xml |  51 ++++++++
 2 files changed, 182 insertions(+)
 create mode 100755 tools/human_genome_variation/master2pg.pl
 create mode 100644 tools/human_genome_variation/master2pg.xml

diff --git a/tools/human_genome_variation/master2pg.pl b/tools/human_genome_variation/master2pg.pl
new file mode 100755
index 00000000000..6697fa20230
--- /dev/null
+++ b/tools/human_genome_variation/master2pg.pl
@@ -0,0 +1,131 @@
+#!/usr/bin/perl -w
+use strict;
+
+#convert from master variant file to pgSnp
+my $snpsOnly = 1; #flag for if doing SNPs or indels
+if (@ARGV && $ARGV[0] eq 'indel') { shift @ARGV; $snpsOnly = 0; }
+my $in = shift @ARGV;
+open(FH, $in) or die "Couldn't open input file $in, $!\n";
+
+while (<FH>) {
+   chomp;
+   if (/^#/) { next; }
+   if (/^>/) { next; } #headers
+   if (/^\s*$/) { next; } 
+   my @f = split(/\t/);
+   if (!$f[5]) { next; } #WHAT? most likely still zipped?
+   if ($f[5] =~ /(hom|het)/) { #zygosity #haploid chrX and chrY?
+      #only get snps for now
+      if ($snpsOnly && $f[6] eq 'snp') { #varType
+         my $a;
+         my $c = 2;
+         my $freq;
+         my $sc;
+         if ($f[8] eq $f[9]) { #should be homozygous?
+            $a = $f[8];
+            $c = 1;
+         }else {
+            $a = "$f[8]/$f[9]";
+         }
+         if (defined $f[10] && $c == 1) {
+            $sc = $f[10];
+         }elsif (defined $f[10] && defined $f[11] && $c == 2) {
+            $sc = "$f[10],$f[11]";
+         }
+         if (defined $f[16] && $c == 1) {
+            $freq = $f[16];
+         }elsif (defined $f[16] && defined $f[17] && $c == 2) {
+            $freq = "$f[16],$f[17]";
+         }
+         print "$f[2]\t$f[3]\t$f[4]\t$a\t$c\t$freq\t$sc\n";
+      }elsif (!$snpsOnly) {
+         if ($f[8] =~ /^\s*$/) { undef $f[8]; }
+         if ($f[9] =~ /^\s*$/) { undef $f[9]; }
+         my $a;
+         my $c = 2;
+         #do indels
+         if ($f[6] eq "ins") {
+            if (defined $f[8] && defined $f[9] && $f[8] eq $f[9]) { $a = $f[8]; $c = 1; }
+            elsif (defined $f[8] && defined $f[9] && $f[8] ne '?' && $f[9] ne '?') { 
+               $a = "$f[8]/$f[9]";
+            }elsif (!defined $f[8] && defined $f[9]) {
+               $a = "$f[9]/-";
+            }elsif (defined $f[8] && !defined $f[9]) {
+               $a = "$f[8]/-";
+            }
+         }elsif ($f[6] eq "del") {
+            if (!defined $f[8] && !defined $f[9]) {
+               $a = '-'; #homozygous deletion
+               $c = 1;
+            }elsif (!defined $f[8] && defined $f[9]) {
+               $a = "$f[9]/-";
+            }elsif (defined $f[8] && !defined $f[9]) {
+               $a = "$f[8]/-";
+            }            
+         }elsif ($f[6] eq "sub") { #multiple nt substitutions
+            if ($f[8] eq $f[9]) {
+               $a = $f[8];
+               $c = 1;
+            }else {
+               $a = "$f[8]/$f[9]";
+            }
+         }elsif ($f[6] eq "complex") { #treat same as multi-nt sub
+            if ($f[5] =~ /het-alt/ && !defined $f[8]) { $f[8] = '-'; }
+            if ($f[5] =~ /het-alt/ && !defined $f[9]) { $f[9] = '-'; }
+            if (defined $f[8] && defined $f[9] && $f[8] eq $f[9]) {
+               $c = 1;
+               $a = $f[8];
+            }elsif (defined $f[8] && defined $f[9]) {
+               $a = "$f[8]/$f[9]";
+            }
+         }
+         my $sc = '';
+         my $freq = '';
+         if (defined $f[10] && $c == 1) {
+            $sc = $f[10];
+         }elsif (defined $f[10] && defined $f[11] && $c == 2) {
+            $sc = "$f[10],$f[11]";
+         }
+         if (defined $f[16] && $c == 1) {
+            $freq = $f[16];
+         }elsif (defined $f[16] && defined $f[17] && $c == 2) {
+            $freq = "$f[16],$f[17]";
+         }
+         if ($a) {
+            print "$f[2]\t$f[3]\t$f[4]\t$a\t$c\t$freq\t$sc\n";
+         }
+      }
+   }elsif ($f[5] eq 'hap' && $f[6] eq 'snp' && $snpsOnly) {
+      my $c = 1;
+      my $freq = '';
+      if (defined $f[10]) { $freq = $f[10]; }
+      my $sc = '';
+      if (defined $f[16]) { $sc = $f[16]; }
+      if ($f[8]) {
+         print "$f[2]\t$f[3]\t$f[4]\t$f[8]\t$c\t$freq\t$sc\n";
+      }   
+   }elsif ($f[5] eq 'hap' && !$snpsOnly && $f[6] =~ /(del|ins|sub)/) {
+      if ($f[8] =~ /^\s*$/) { undef $f[8]; }
+      my $a;
+      my $c = 1;
+      #do indels
+      if ($f[6] eq "ins") {
+         $a = $f[8]; 
+      }elsif ($f[6] eq "del") {
+         $a = '-'; #deletion
+      }elsif ($f[6] eq "sub") { #multiple nt substitutions
+         $a = $f[8];
+      }
+      my $sc = '';
+      my $freq = '';
+      if (defined $f[10]) { $sc = $f[10]; }
+      if (defined $f[16]) { $freq = $f[16]; }
+      if ($a) {
+         print "$f[2]\t$f[3]\t$f[4]\t$a\t$c\t$freq\t$sc\n";
+      }
+   }
+}
+
+close FH or die "Couldn't close $in, $!\n";
+
+exit;
diff --git a/tools/human_genome_variation/master2pg.xml b/tools/human_genome_variation/master2pg.xml
new file mode 100644
index 00000000000..f17e1aab5cd
--- /dev/null
+++ b/tools/human_genome_variation/master2pg.xml
@@ -0,0 +1,51 @@
+<tool id="hgv_master2pgSnp" name="Convert CG MasterVar" version="1.0.0">
+  <description>file to pgSnp format</description>
+  <command interpreter="perl">
+    master2pg.pl $indel $input1 > $out_file1
+  </command>
+  <inputs>
+    <param format="tab" name="input1" type="data" label="Complete Genomics MasterVar file" />
+    <param name="indel" type="select" label="Convert indels">
+      <option value="" selected="true">no</option>
+      <option value="indel">yes</option>
+    </param>
+  </inputs>
+  <outputs>
+  <data format="interval" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name='input1' value='masterVarTest.txt' ftype='tab' />
+      <param name='indel' value="" />
+      <output name="output" file="masterVar_output.txt" />
+    </test>
+  </tests>
+
+  <help>
+**What it does**
+
+This converts from a Complete Genomics MasterVar file to a pgSnp format file 
+which can be viewed in browsers or used with other human variation and bed 
+operations tools.
+
+-----
+
+**Examples**
+
+- input MasterVar file::
+
+   934     2       chr1    41980   41981   hom     snp     A       G       G       76      97                      dbsnp.86:rs806721       425     1       1       1       2       -170                            ERVL-E-int:ERVL:47.4    2       1.17    N
+   935     2       chr1    41981   42198   hom     ref     =       =       =                                                                                       -170                                            1.17    N
+   1102    2       chr1    53205   53206   het-ref snp     G       C       G       93      127                     dbsnp.100:rs2854676     477     7       30      0       37      -127                                    2       1.17    N
+   etc.
+
+- output::
+
+   chr1    41980   41981   G       1       1       76
+   chr1    51672   51673   C       1       1       53
+   chr1    52237   52238   G       1       7       63
+   chr1    53205   53206   C/G     2       7,30    93,127
+   etc.
+
+</help>
+</tool>

From c1b4254ebe648fa042c0983c44353e972edc80c2 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Mon, 28 Nov 2011 13:37:10 -0500
Subject: [PATCH 249/362] Update Yogeshwar Kelkar's microsatellite tools.

---
 .../regVariation/microsatellite_birthdeath.pl | 1121 ++++++++++------
 .../microsatellite_birthdeath.xml             |   59 +-
 ...icrosatDataGenerator_interrupted_GALAXY.pl | 1161 ++++++++++-------
 ...crosatDataGenerator_interrupted_GALAXY.xml |   56 +-
 4 files changed, 1509 insertions(+), 888 deletions(-)
 mode change 100644 => 100755 tools/regVariation/microsatellite_birthdeath.pl
 mode change 100644 => 100755 tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.pl

diff --git a/tools/regVariation/microsatellite_birthdeath.pl b/tools/regVariation/microsatellite_birthdeath.pl
old mode 100644
new mode 100755
index a7562cb3ff1..dffcf700ae2
--- a/tools/regVariation/microsatellite_birthdeath.pl
+++ b/tools/regVariation/microsatellite_birthdeath.pl
@@ -11,11 +11,12 @@ use File::Temp qw/ tempfile tempdir /;
 my $tdir = tempdir( CLEANUP => 0 );
 chdir $tdir;
 my $dir = getcwd;  
-#print "current dit=$dir\n";
-
+# print "current dit=$dir\n"; 
+#<STDIN>;
 use vars qw (%treesToReject %template $printer $interr_poscord $interrcord $no_of_interruptionscord $stringfile @tags 
 $infocord $typecord $startcord $strandcord $endcord $microsatcord $motifcord $sequencepos $no_of_species 
-$gapcord %thresholdhash $tree_decipherer @sp_ident %revHash %sameHash %treesToIgnore %alternate @exactspecies @exacttags);
+$gapcord %thresholdhash $tree_decipherer @sp_ident %revHash %sameHash %treesToIgnore %alternate @exactspecies_orig @exactspecies @exacttags
+$mono_flanksimplicityRepno $di_flanksimplicityRepno $prop_of_seq_allowedtoAT $prop_of_seq_allowedtoCG);
 use FileHandle;
 use IO::Handle;                     # 5.004 or higher
 
@@ -30,14 +31,151 @@ $SIMILARITY_THRESH = $SIMILARITY_THRESH/100;
 my $EDGE_DISTANCE = 10; 
 my $COMPLEXITY_SUPPORT = 20;
 load_thresholds("9_10_12_12");
+my $FLANKINDEL_MAXTHRESH = 0.3;
+
+my $mono_flanksimplicityRepno=6;
+my $di_flanksimplicityRepno=10;
+my $prop_of_seq_allowedtoAT=0.5;
+my $prop_of_seq_allowedtoCG=0.66;
+
 #########################
+my $tspecies_set = $species_set;
+
+my %speciesReplacement = ();
+my %speciesReplacementTag = ();
+my %replacementArr= ();
+my %replacementArrTag= ();
+my %backReplacementArr= ();
+my %backReplacementArrTag= ();
+
+my $tree_definition_split = $tree_definition;
+$tree_definition_split =~ s/[\(\)]//g;
+my @gotSpecies = ($tree_definition_split =~ /(,)/g);
+# print "gotSpecies = @gotSpecies\n";
+
+if (scalar(@gotSpecies)+1 ==5){
+
+	$speciesReplacement{1}="calJac1";
+	$speciesReplacement{2}="rheMac2";
+	$speciesReplacement{3}="ponAbe2";
+	$speciesReplacement{4}="panTro2";
+	$speciesReplacement{5}="hg18";
+
+	$speciesReplacementTag{1}="M";
+	$speciesReplacementTag{2}="R";
+	$speciesReplacementTag{3}="O";
+	$speciesReplacementTag{4}="C";
+	$speciesReplacementTag{5}="H";
+	$species_set="hg18,panTro2,ponAbe2,rheMac2,calJac1";
+
+}
+if (scalar(@gotSpecies)+1 ==4){
+
+	$speciesReplacement{1}="rheMac2";
+	$speciesReplacement{2}="ponAbe2";
+	$speciesReplacement{3}="panTro2";
+	$speciesReplacement{4}="hg18";
+
+	$speciesReplacementTag{1}="R";
+	$speciesReplacementTag{2}="O";
+	$speciesReplacementTag{3}="C";
+	$speciesReplacementTag{4}="H";
+	$species_set="hg18,panTro2,ponAbe2,rheMac2";
+
+}
+
+#	$tree_definition = "((((hg18,panTro2),ponAbe2),rheMac2),calJac1)";
+my $tree_definition_copy = $tree_definition;
+my $tree_definition_orig = $tree_definition;
+my $brackets = 0;
+
+while (1){
+	#last if $tree_definition_copy !~ /\(/;
+	$brackets++;
+# print "brackets = $brackets\n";
+	last if $brackets > 6;
+	$tree_definition_copy =~ s/^\(//g;
+	$tree_definition_copy =~ s/\)$//g;
+# print "tree_definition_copy = $tree_definition_copy\n";
+	my @arr = ();
+
+	if ($tree_definition_copy =~ /^([a-zA-Z0-9_]+),([a-zA-Z0-9_\(\),]+)\)$/){
+		@arr = $tree_definition_copy =~ /^([a-zA-Z0-9_]+),([a-zA-Z0-9_\(\),]+)$/;
+# print "arr = @arr\n";
+		$tree_definition_copy = $2;
+		$replacementArr{$1} = $speciesReplacement{$brackets};
+		$backReplacementArr{$speciesReplacement{$brackets}}=$1;
+		
+		$replacementArrTag{$1} = $speciesReplacementTag{$brackets};
+		$backReplacementArrTag{$speciesReplacementTag{$brackets}}=$1;
+# print "replacing $1 with $replacementArr{$1}\n";
+		
+		$sp_ident[$brackets-1] = $1;
+	
+	}
+	elsif ($tree_definition_copy =~ /^\(([a-zA-Z0-9_\(\),]+),([a-zA-Z0-9_]+)$/){
+		@arr = $tree_definition_copy =~ /^([a-zA-Z0-9_\(\),]+),([a-zA-Z0-9_]+)$/;
+# print "arr = @arr\n";
+		$tree_definition_copy = $1;
+		$replacementArr{$2} = $speciesReplacement{$brackets};
+		$backReplacementArr{$speciesReplacement{$brackets}}=$2;
+
+		$replacementArrTag{$2} = $speciesReplacementTag{$brackets};
+		$backReplacementArrTag{$speciesReplacementTag{$brackets}}=$2;
+# print "replacing $2 with $replacementArr{$2}\n";
+
+		$sp_ident[$brackets-1] = $2;
+	}
+	elsif ($tree_definition_copy =~ /^([a-zA-Z0-9_]+),([a-zA-Z0-9_]+)$/){
+		@arr = $tree_definition_copy =~ /^([a-zA-Z0-9_]+),([a-zA-Z0-9_]+)$/;
+# print "arr = @arr .. TERMINAL\n";
+		$tree_definition_copy = $1;
+		$replacementArr{$2} = $speciesReplacement{$brackets};
+		$replacementArr{$1} = $speciesReplacement{$brackets+1};
+		$backReplacementArr{$speciesReplacement{$brackets}}=$2;
+		$backReplacementArr{$speciesReplacement{$brackets+1}}=$1;
+
+		$replacementArrTag{$1} = $speciesReplacementTag{$brackets+1};
+		$backReplacementArrTag{$speciesReplacementTag{$brackets+1}}=$1;
+
+		$replacementArrTag{$2} = $speciesReplacementTag{$brackets};
+		$backReplacementArrTag{$speciesReplacementTag{$brackets}}=$2;
+# print "replacing $1 with $replacementArr{$1}\n";
+# print "replacing $2 with $replacementArr{$2}\n";
+# print "replacing $1 with $replacementArrTag{$1}\n";
+# print "replacing $2 with $replacementArrTag{$2}\n";
+
+		$sp_ident[$brackets-1] = $2;
+		$sp_ident[$brackets] = $1;
+
+
+		last;
+
+	}
+	elsif ($tree_definition_copy =~ /^\(([a-zA-Z0-9_\(\),]+),([a-zA-Z0-9_\(\),]+)\)$/){
+		$tree_definition_copy =~ s/^\(//g;
+		$tree_definition_copy =~ s/\)$//g;
+		$brackets--;
+	}		
+}
+
+foreach my $key (keys %replacementArr){
+	my $replacement = $replacementArr{$key};
+	$tree_definition =~ s/$key/$replacement/g;
+}
+@sp_ident = reverse(@sp_ident);
+# print "modified tree_definition = $tree_definition\n";
+# print "done .. tree_definition = $tree_definition\n";
+# print "sp_ident = @sp_ident\n";
+#<STDIN>;
+
 
 my $complexity=int($COMPLEXITY_SUPPORT * (1/40));
 
 #print "complexity=$complexity\n";
 #<STDIN>;
 
-#$printer = 1;
+$printer = 1;
 
 my $rando = int(rand(1000));
 my $localdate = `date`;
@@ -54,9 +192,9 @@ my $megamatch = $randno.".megamatch.net.axt"; #"/gpfs/home/ydk104/work/rhesus_mi
 my $megamatchlck = $megamatch.".lck";
 unlink $megamatchlck;
 
-#my $selected= $orth;
+my $selected= $orth;
 #my $eventfile = $orth;
-#$selected = $selected."_SELECTED";
+ $selected = $selected."_SELECTED";
 #$selected = $selected."_".$SIMILARITY_THRESH;
 #my $runtime = $selected.".runtime";
 
@@ -66,14 +204,14 @@ $inputtags = $ARGV[3] if exists $ARGV[3] && $ARGV[3] =~ /[A-Z]:[A-Z]/;
 my @all_tags = split(/:/, $inputtags);
 my $inputsp = "hg18:panTro2:ponAbe2:rheMac2:calJac1";
 $inputsp = $ARGV[4] if exists $ARGV[4] && $ARGV[3] =~ /[0-9]+:/;
-@sp_ident = split(/:/,$inputsp);
+#@sp_ident = split(/:/,$inputsp);
 my $junkfile = $orth."_junk";
 
 my $sh = load_sameHash(1);
 my $rh = load_revHash(1);
 
 #print "inputs are : \n"; foreach(@ARGV){print $_,"\n";} 
-#open (SELECT, ">$selected") or die "Cannot open selected file: $selected: $!";
+open (SELECT, ">$selected") or die "Cannot open selected file: $selected: $!";
 open (SUMMARY, ">$summout") or die "Cannot open summout file: $summout: $!";
 #open (RUN, ">$runtime") or die "Cannot open orth file: $runtime: $!";
 #my $ctlfile = "baseml\.ctl"; #$ARGV[4];
@@ -101,23 +239,58 @@ my %allowedhash=();
 my $chromt=int(rand(10000));
 my $p_chr=$chromt;
 
+my $tree_definition_orig_copy = $tree_definition_orig;
+
 $tree_definition=~s/,/, /g;
 $tree_definition =~ s/, +/, /g;
+$tree_definition_orig=~s/,/, /g;
+$tree_definition_orig =~ s/, +/, /g;
 my @exactspeciesset_unarranged = split(/,/,$species_set);
+my @exactspeciesset_unarranged_orig = split(/,/,$tspecies_set);
 my $largesttree = "$tree_definition;";
+my $largesttree_orig = "$tree_definition_orig;";
+# print "largesttree = $largesttree\n";
+$tree_definition =~ s/\(//g;
+$tree_definition =~ s/\)//g;
 $tree_definition=~s/[\)\(, ]/\t/g;
-		
+$tree_definition =~ s/\t+/\t/g;		
+
+$tree_definition_orig =~ s/\(//g;
+$tree_definition_orig =~ s/\)//g;
+$tree_definition_orig =~s/[\)\(, ]/\t/g;
+$tree_definition_orig =~ s/\t+/\t/g;		
+# print "tree_definition = $tree_definition tree_definition_orig = $tree_definition_orig\n";
+
 my @treespecies=split(/\t+/,$tree_definition);
+my @treespecies_orig=split(/\t+/,$tree_definition_orig);
+# print "tree_definition = $tree_definition .. treespecies=@treespecies ... treespecies_orig=@treespecies_orig\n";
+#<STDIN>;
 
 foreach my $spec (@treespecies){
 	foreach my $espec (@exactspeciesset_unarranged){
+# print "spec=$spec and espec=$espec\n";
 		push @exactspecies, $spec if $spec eq $espec;
 	}
 }
-#print "exactspecies=@exactspecies\n";
+
+foreach my $spec (@treespecies_orig){
+	foreach my $espec (@exactspeciesset_unarranged_orig){
+# print "spec=$spec and espec=$espec\n";
+		push @exactspecies_orig, $spec if $spec eq $espec;
+	}
+}
+
 my $focalspec = $exactspecies[0];
-my $arranged_species_set=join(".",@exactspecies);
+my $focalspec_orig = $exactspecies_orig[0];
+# print "exactspecies=@exactspecies ... focalspec=$focalspec\n";
+# print "texactspecies=@exactspecies_orig ... focalspec_orig=$focalspec_orig\n";
+#<STDIN>;
+my $arranged_species_set = join(".",@exactspecies);
+my $arranged_species_set_orig = join(".",@exactspecies_orig);
+
 @exacttags=@exactspecies;
+my @exacttags_orig=@exactspecies_orig;
+
 foreach my $extag (@exacttags){
 	$extag =~ s/hg18/H/g;
 	$extag =~ s/panTro2/C/g;
@@ -125,15 +298,27 @@ foreach my $extag (@exacttags){
 	$extag =~ s/rheMac2/R/g;
 	$extag =~ s/calJac1/M/g;
 }
+
+foreach my $extag (@exacttags_orig){
+	$extag =~ s/hg18/H/g;
+	$extag =~ s/panTro2/C/g;
+	$extag =~ s/ponAbe2/O/g;
+	$extag =~ s/rheMac2/R/g;
+	$extag =~ s/calJac1/M/g;
+}
+
 my $chr_name = join(".",("chr".$p_chr),$arranged_species_set, "net", "axt");
 #print "sending to maftoAxt_multispecies: $maf, $tree_definition, $chr_name, $species_set .. focalspec=$focalspec \n"; 
-maftoAxt_multispecies($maf, $tree_definition, $chr_name, $species_set);
+
+maftoAxt_multispecies($maf, $tree_definition_orig_copy, $chr_name, $tspecies_set);
+#print "made files\n";
 my @filterseqfiles= ($chr_name);
-		$largesttree =~ s/hg18/H/g;
-		$largesttree =~ s/panTro2/C/g;
-		$largesttree =~ s/ponAbe2/O/g;
-		$largesttree =~ s/rheMac2/R/g;
-		$largesttree =~ s/calJac1/M/g;
+$largesttree =~ s/hg18/H/g;
+$largesttree =~ s/panTro2/C/g;
+$largesttree =~ s/ponAbe2/O/g;
+$largesttree =~ s/rheMac2/R/g;
+$largesttree =~ s/calJac1/M/g;
+#<STDIN>;
 #---------------------------------------------------------------------------
 
 my ($lagestnodes, $largestbranches) = get_nodes($largesttree); 
@@ -143,13 +328,13 @@ my @extendedtitle=();
 my $title = ();
 my $parttitle = ();
 my @titlearr = ();
-my @firsttitle=($focalspec."chrom", $focalspec."start", $focalspec."end", $focalspec."motif", $focalspec."motifsize", $focalspec."threshold");
+my @firsttitle=($focalspec_orig."chrom", $focalspec_orig."start", $focalspec_orig."end", $focalspec_orig."motif", $focalspec_orig."motifsize", $focalspec_orig."threshold");
 
 my @finames= qw(chr	start	end	motif	motifsize	microsat	mutation	mutation.position	mutation.from	mutation.to	insertion.details	deletion.details);
 
 my @fititle=();
 
-foreach my $spec (split(",",$species_set)){
+foreach my $spec (split(",",$tspecies_set)){
 	push @fititle, $spec;
 	foreach my $name (@finames){
 		push @fititle, $spec.".".$name;
@@ -167,30 +352,42 @@ push @fnames, qw(ninsertions_num ndeletions_num nmotinsertions_num nmotinsertion
 push @fnames, qw(substitutions_num bsubstitutions_num dsubstitutions_num nsubstitutions_num indels_num subs_num);
 
 my @fullnames = ();
+# print "revising\n";
+# print "H = $backReplacementArrTag{H}\n";
+# print "C = $backReplacementArrTag{C}\n";
+# print "O = $backReplacementArrTag{O}\n";
+# print "R = $backReplacementArrTag{R}\n";
+# print "M = $backReplacementArrTag{M}\n";
 
 foreach my $lnode (@$lagestnodes){
 	my @pair = @$lnode;
 	my @nodemutarr = ();
 	for my $p (@pair){
-	#	print "p = $p\n";
+# print "p = $p\n";
 		$p =~ s/[\(\), ]+//g;
-		$p =~ s/H/hg18/g;
-		$p =~ s/C/panTro2/g;
-		$p =~ s/O/ponAbe2/g;
-		$p =~ s/R/rheMac2/g;
-		$p =~ s/M/calJac1/g;
+		$p =~ s/([A-Z])/$1./g;
+		$p =~ s/\.$//g;
+		
+		$p =~ s/H/$backReplacementArrTag{H}/g;
+		$p =~ s/C/$backReplacementArrTag{C}/g;
+		$p =~ s/O/$backReplacementArrTag{O}/g;
+		$p =~ s/R/$backReplacementArrTag{R}/g;
+		$p =~ s/M/$backReplacementArrTag{M}/g;
 		foreach my $n (@fnames) {	push @fullnames, $p.".".$n;}
 	}
 }
-print SUMMARY "#",join("\t", @firsttitle, @fititle, @othertitle);
 
-print SUMMARY "\t",join("\t", @fullnames);
-#$title = $title."\t".join("\t", @fullnames);
+#print SUMMARY "#",join("\t", @firsttitle, @fititle, @othertitle);
 
-print SUMMARY "\t",join("\t", @fnames);
+#print SUMMARY "\t",join("\t", @fullnames);
+my $header = join("\t",@firsttitle, @fititle, @othertitle,  @fullnames, @fnames, "tree", "cleancase");
+# print "header= $header\n";
+#<STDIN>;
+
+#print SUMMARY "\t",join("\t", @fnames);
 #$title=  $title."\t".join("\t", @fnames);
 
-print SUMMARY "\t","tree","\t", "cleancase", "\n";
+#print SUMMARY "\t","tree","\t", "cleancase", "\n";
 #$title=  $title."\t"."tree"."\t"."cleancase". "\n";
 
 #print $title; #<STDIN>;
@@ -200,12 +397,11 @@ print SUMMARY "\t","tree","\t", "cleancase", "\n";
 for my $no (3 ... $#all_tags+1){
 #	print "no=$no\n"; #<STDIN>;
 	@tags = @all_tags[0 ... $no-1];
-	#print "tags = = @tags\n" if $printer == 1;
+# print "all_tags=>@all_tags< , tags = >@tags<\n" if $printer == 1; #<STDIN>;
 	%template=();
 	my @nextcounter = (0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0);
 	#next if scalar(@tags) < 4;
-	
-	#print "now doing tags = @tags, no = $no\n"; 
+# print "now doing tags = @tags, no = $no\n"; 
 	open (ORTH, "<$orth") or die "Cannot open orth file: $orth: $!";
 	
 #	print SUMMARY join "\t", qw (species chr start end branch motif microsat mutation position from to insertion deletion);
@@ -239,6 +435,8 @@ for my $no (3 ... $#all_tags+1){
 	#---------------------------------------------------------------------------
 	# LOADING HASH CONTAINING ALL POSSIBLE TREES:
 	$tree_decipherer = "/gpfs/home/ydk104/work/rhesus_microsat/codes/lib/tree_analysis_".join("",@tags).".txt";
+	%template=();
+	%alternate=();
 	load_allPossibleTrees($tree_decipherer, \%template, \%alternate);
 	
 	#---------------------------------------------------------------------------
@@ -263,17 +461,25 @@ for my $no (3 ... $#all_tags+1){
 #	print "no = $no\n"; #<STDIN>;
 
 	while (my $line = <ORTH>){
-		#print "line=$line\n";
-		$line =~ s/>hg18/>H/g;
-		$line =~ s/>panTro2/>C/g;
-		$line =~ s/>ponAbe2/>O/g;
-		$line =~ s/>rheMac2/>R/g;
-		$line =~ s/>calJac1/>M/g;
+	#	print "line=$line\n";
+		my $register1 = $line =~ s/>$exactspecies_orig[0]/>$replacementArrTag{$exactspecies_orig[0]}/g;
+		my $register2 = $line =~ s/>$exactspecies_orig[1]/>$replacementArrTag{$exactspecies_orig[1]}/g;
+		my $register3 = $line =~ s/>$exactspecies_orig[2]/>$replacementArrTag{$exactspecies_orig[2]}/g;
+		my $register4 = $line =~ s/>$exactspecies_orig[3]/>$replacementArrTag{$exactspecies_orig[3]}/g;
+		my $register5 = $line =~ s/>$exactspecies_orig[4]/>$replacementArrTag{$exactspecies_orig[4]}/g if exists $exactspecies_orig[4];
+		
+	#	print "line = $line\n"; <STDIN>;
+		
+		
+	#	next if $register1 + $register2 + $register3 + $register4 + $register5 > scalar(@tags);
 		my @micros = split(/>/,$line); 									# LOADING ALL THE MICROSAT ENTRIES FROM THE CLUSTER INTO @micros
 		#print "micros=",printarr(@micros),"\n"; #<STDIN>;
 		shift @micros; 													# EMPTYING THE FIRST, EMTPY ELEMENT OF THE ARRAY
+		
 		$no_of_species = adjustCoordinates($micros[0]);
+#		print "A: $no_of_species\n";
 		next if $no_of_species != $no;
+# print "no = $no ... no_of_species=$no_of_species\n";#<STDIN>;
 		$counterm++;
 		#------------------------------------------------
 		$nextcounter[0]++  if $line =~ /compound/;
@@ -351,11 +557,14 @@ for my $no (3 ... $#all_tags+1){
 		my $prevmotif = $tempfirstmotif;
 		
 		my $key = ();
-		if ($tempmicro =~ /([0-9]+)\s+($focalspec)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)/ ) {
-			$key = join("\t",$1, $2,  $4, $5);
+	#	print "searching temp micro for 0-9 $focalspec chr0-9a-zA-Z 0-9 0-9 \n";
+	#	print "tempmicro = $tempmicro .. looking for ([0-9]+)\s+($focalspec_orig)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)\n"; <STDIN>;
+		if ($tempmicro =~ /([0-9]+)\s+($focalspec_orig)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)/ ) {
+	#		print "B: $no_of_species\n";
+			$key = join("_",$2, $3,  $4, $5);
 		}
 		else{
-		#	print "counld not form  a key \n" if $printer == 1;
+# print "counld not form  a key for temp\n"; # if $printer == 1;
 			$nextcounter[7]++;
 			next;
 		}
@@ -404,8 +613,9 @@ for my $no (3 ... $#all_tags+1){
 			
 			for my $t (0 ... $#tags){								#1	DISCARDING MICROSAT CLUSTERS WHERE MICROSAT ENTRIES BELONG
 																	#2	DIFFERENT ALIGNMENT BLOCKS
-				if ($micro =~ /([0-9]+)\s+($focalspec)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)/ ) {
-					my $key2 = join("\t",$1, $2,  $4, $5);
+				if ($micro =~ /([0-9]+)\s+($focalspec_orig)\s([_0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)/ ) {
+					my $key2 = join("_",$2, $3, $4, $5);
+# print "key = $key .. key2 = $key2\n"; #<STDIN>;
 					if ($key2 ne $key){
 #						print "microsats belong to diffferent alignment blocks altogether\n" if $printer == 1;
 						$nextcounter[10]++;
@@ -413,49 +623,53 @@ for my $no (3 ... $#all_tags+1){
 					}
 				}
 				else{
-				#	print "counld not form  a key \n" if $printer == 1;
+# print "counld not form  a key for $line\n"; # if $printer == 1; 
+					#<STDIN>;
 					$nexter = 1; last;
 				}
 			}
-			
 		}
+		#print "D2: $no_of_species\n";
+
 		#####################
 		if ($nexter == 1){
-			#	print "nexting\n" if $printer == 1; 
+# print "nexting\n"; # if $printer == 1; 
 				next;
 			}
 		else{
-#			print "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n$key:\n$line\nvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv\n"  if $printer == 1;
+# print "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n$key:\n$line\nvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv\n"  if $printer == 1;
 			push (@{$orths{$key}},$line);	
 			$loaded++;
-			if ($line =~ /($focalspec)\s([a-zA-Z0-9]+)\s([0-9]+)\s([0-9]+)/ ) {
+			if ($line =~ /($focalspec_orig)\s([_a-zA-Z0-9]+)\s([0-9]+)\s([0-9]+)/ ) {
+				
 #				print "$line\n"  if $printer == 1; #if $line =~ /Contig/;
 #				print "################ ################\n" if $printer == 1;
 				push @allowedchrs, $2 if !exists $allowedhash{$2};
 				$allowedhash{$2} = 1; 
 				my $key = join("\t",$1, $2, $3, $4);
-				#print "print the shit: $key\n" if $printer  == 1;
+#				print "C: $no_of_species .. key = $key\n";#<STDIN>;
+# print "print the shit: $key\n" ; #if $printer  == 1;
 				$seen{$key} = 1;
 			}
-			else { #print "Key could not be formed in SPUT for ($org) ($title) ([0-9]+) ([0-9]+)\n";
+			else { #print "Key could not be formed in SPUT for ($focalspec_orig) (chrom) ([0-9]+) ([0-9]+)\n";
 			}
 		}
 	}
 	close ORTH;
-
-#	print "now studying where we lost microsatellites: @nextcounter\n";
+# print "now studying where we lost microsatellites: @nextcounter\n";
 	for my $reason (0 ... $#nextcounter){
-#		print $removalReasons[$reason]."\t".$nextcounter[$reason],"\n";
+		#print $removalReasons[$reason]."\t".$nextcounter[$reason],"\n";
 	}
-#	print "\ntotal number of keys formed = ", scalar(keys %orths), " = \n";
-#	print "done filtering .. counterm = $counterm and loaded = $loaded\n"; 
-
+# print "\ntotal number of keys formed = ", scalar(keys %orths), " = \n";
+# print "done filtering .. counterm = $counterm and loaded = $loaded\n"; 
 	#----------------------------------------------------------------------------------------------------------------
 	# NOW GENERATING THE ALIGNMENT FILE WITH RELELEVENT ALIGNMENTS STORED ONLY.
+# print "adding files @filterseqfiles \n";
+	#<STDIN>;
 	
 	while (1){
 		if (-e $megamatchlck){
-#			print "waiting to write into $megamatchlck\n";
+# print "waiting to write into $megamatchlck\n";
 			sleep 10;
 		}
 		else{
@@ -467,15 +681,20 @@ for my $no (3 ... $#all_tags+1){
 	
 	foreach my $seqfile (@filterseqfiles){
 		my $fullpath = $seqfile;
-		
-#		print "opening file: $fullpath\n"; 
+  		#print "opening file: $fullpath\n"; <STDIN>;
 		open (MATCH, "<$fullpath") or die "Cannot open MATCH file $fullpath: $!";
 		my $matchlines = 0;
 
 		while (my $line = <MATCH>)	{
-			if ($line =~ /($focalspec)\s([a-zA-Z0-9]+)\s([0-9]+)\s([0-9]+)/ ) {
+			#print "checking $line";
+			if ($line =~ /($focalspec_orig)\s([a-zA-Z0-9]+)\s([0-9]+)\s([0-9]+)/ ) {
 				my $key = join("\t",$1, $2, $3, $4);
+# print "key = $key\n";
+				#print "------------------------------------------------------\n";
+				#print "asking $line\n";
 				if (exists $seen{$key}){
+				
+				#print "seen $line \n"; <STDIN>;
 					while (1){
 						$matchlines++;
 						print MEGAM $line;
@@ -484,6 +703,9 @@ for my $no (3 ... $#all_tags+1){
 						last if $line !~/[0-9a-zA-Z]/;
 					}
 				}
+				else{
+# print "not seen\n";
+				}
 			}
 		}
 #		print "matchlines = $matchlines\n";
@@ -494,8 +716,9 @@ for my $no (3 ... $#all_tags+1){
 	unlink $megamatchlck;
 	close MEGAM;
 	undef %seen;
+# print "done writitn to $megamatch\n";#<STDIN>;
 	#----------------------------------------------------------------------------------------------------------------
-
+	#<STDIN>;
 	#---------------------------------------------------------------------------
 	# NOW, AFTER FILTERING MANY MICROSATS, AND LOADING THE FILTERED ONES INTO
 	# THE HASH %orths , WE GO THROUGH THE ALIGNMENT FILE, AND STUDY THE 
@@ -509,34 +732,47 @@ for my $no (3 ... $#all_tags+1){
 	my $keynotfoundcounter= 0;
 	my $dotcounter = 0;
 
+#	print "opening $megamatch\n";
+
 	open (BO, "<$megamatch") or die "Cannot open alignment file: $megamatch: $!";
+# print "doing  $megamatch\n " ;
+
+	#<STDIN>;
 	
 	while (my $line = <BO>){
-#		print "." if $dotcounter % 100 ==0;
+#		print $line; #<STDIN>;
+# print "." if $dotcounter % 100 ==0;
 #		print "\n" if $dotcounter % 5000 ==0;
-#		print "dotcounter = $dotcounter\n " if $printer == 1;
+# print "dotcounter = $dotcounter\n " if $printer == 1;
 		next if $line !~ /^[0-9]+/;
 		$dotcounter++;
 #		print colored ['green'], "~" x 60, "\n" if $printer == 1;
 #		print colored ['green'], $line;# if $printer == 1;
-		chomp $line;	
+		chomp $line;
 		my @fields2 = split(/\t/,$line);
 		my $key2 = ();
 		my $alignment_no = ();										#1 TEMPORARY
-		if ($line =~ /([0-9]+)\s+($focalspec)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)/ ) {
-			$key2 = join("\t",$1, $2,  $4, $5);
+		if ($line =~ /([0-9]+)\s+($focalspec_orig)\s([_\-s0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)/ ) {
+#			$key2 = join("\t",$1, $2,  $4, $5);
+			$key2 = join("_",$2, $3,  $4, $5);
+#			print "key = $key2\n";
+
+# print "key = $key2\n";
 			$alignment_no=$1;
 		}
 		else {print "seq line $line incompatible\n"; $keynotformedcounter++; next;}
 		
 		$no_of_species = adjustCoordinates($line);
+
 		$contignotrightcounter++  if $no_of_species != $no;
-	#	print "contignotrightcounter=$contignotrightcounter\n";
-	#	print "no_of_species=$no_of_species\n";
-	#	print "no=$no\n";
+# print "contignotrightcounter=$contignotrightcounter\n";
+# print "no_of_species=$no_of_species\n";
+# print "no=$no\n";
 		
 		next if $no_of_species != $no;
-		
+#		print "D: $no_of_species\n";
+#		print "E: $no_of_species\n";
+		#<STDIN>;
 	#	print "key = $key2\n" if $printer == 1;
 		my @clusters = ();											#1 EXTRACTING MICROSATS CORRESPONDING TO THIS 
 																	#2 ALIGNMENT BLOCK
@@ -546,7 +782,7 @@ for my $no (3 ... $#all_tags+1){
 			delete $orths{$key2};
 		}
 		else{
-			#print "orth does not exist\n";
+#			 print "orth does not exist\n";
 			$keynotfoundcounter++;
 			next;
 		}
@@ -563,8 +799,8 @@ for my $no (3 ... $#all_tags+1){
 		
 		
 		foreach my $cluster (@clusters){							#1 NOW, GOING THROUGH THE CLUSTER OF MICROSATS
-			#print "x" x 60, "\n" if $printer == 1;
-			#print colored ['red'],"cluster = $cluster\n";
+# print "x" x 60, "\n" if $printer == 1;
+#			print colored ['red'],"cluster = $cluster\n";
 			$largesttree =~ s/hg18/H/g;
 			$largesttree =~ s/panTro2/C/g;
 			$largesttree =~ s/ponAbe2/O/g;
@@ -573,6 +809,12 @@ for my $no (3 ... $#all_tags+1){
 
 			$microreadcounter++;
 			my @micros = split(/>/,$cluster);
+			
+			
+			
+			
+			
+			
 			shift @micros;
 	
 			my $edge_microsat=0;									#1 THIS WILL HAVE VALUE "1" IF MICROSAT IS FOUND
@@ -586,7 +828,7 @@ for my $no (3 ... $#all_tags+1){
 			my %microsathash=();
 			my %nonmicrosathash=();
 			my $motif=();											#1 BASIC MOTIF OF THE MICROSATELLITE.. THERE'S ONLY 1
-			#print "tags=@tags\n";
+# print "tags=@tags\n";
 			for my $i (0 ... $#tags){								#1	FINDING THE MICROSAT, AND THE ALIGNMENT SEQUENCE
 																	#2	CORRESPONDING TO THE PARTICULAR SPECIES (AS PER 
 																	#3	THE VARIABLE $TAG;
@@ -621,7 +863,7 @@ for my $no (3 ... $#all_tags+1){
 			my $extreme_end  = largest_number(@ends);			#2 MICROSAT CLUSTER ACCROSS ALL THE SPECIES IN 
 																#3 WHOM IT IS FOUND TO BE ORTHOLOGOUS.
 			
-			#print "starts=@starts... ends=@ends\n";
+#			print "starts=@starts... ends=@ends\n";
 				
 			my %up_flanks = ();									#1	CONTAINS UPSTEAM FLANKING REGIONS FOR EACH SPECIES
 			my %down_flanks = ();								#1	CONTAINS DOWNDTREAM FLANKING REGIONS FOR EACH SPECIES
@@ -656,7 +898,7 @@ for my $no (3 ... $#all_tags+1){
 																#5 FLANKING SEQUENCE OF ALL ORGS, AND STUDY IT IN 
 																#6 MORE DETAIL.
 				my $tag = $tags[$i];		
-			#	print "tag=$tag.. seqlength = ",length($sequences{$tag})," extreme_start=$extreme_start and extreme_end=$extreme_end\n";
+#				print "tag=$tag.. seqlength = ",length($sequences{$tag})," extreme_start=$extreme_start and extreme_end=$extreme_end\n";
 				my $upstream_gaps = (substr($sequences{$tag}, 0, $extreme_start) =~ s/\-/-/g);		#1	NOW MEASURING THE NUMBER OF GAPS IN THE UPSTEAM 
 																										#2	AND DOWNSTREAM SEQUENCES OF THE MICROSATs IN THIS
 																										#3	CLUSTER.
@@ -747,14 +989,21 @@ for my $no (3 ... $#all_tags+1){
 
 			next if $sequence_dissimilarity == 1;
 			my ($simplified_microsat, $Hchrom, $Hstart, $Hend, $locusmotif, $locusmotifsize) = summarize_microsat($cluster, $humseq);
-		#	print "simplified_microsat=$simplified_microsat\n"; <STDIN>;
-			my ($tree_analysis, $alternative_trees, $conformation) = treeStudy($simplified_microsat);
+#			print "simplified_microsat=$simplified_microsat\n"; 
+			my ($tree_analysis,  $conformation) = treeStudy($simplified_microsat);
+# print "tree_analysis = $tree_analysis .. conformation=$conformation\n"; 
+			#<STDIN>;
 			
+			print SELECT "\"$conformation\"\t$tree_analysis\n";
+			
+			next if $tree_analysis =~ /DISCARD/;
 			if (exists $treesToReject{$tree_analysis}){
 				$nextcounter[14]++;
 				next;
 			}
 
+#			print "F: $no_of_species\n";
+
 # 			my $adjuster=();
 # 			if ($no_of_species == 4){
 # 				my @sields = split(/\t/,$simplified_microsat);
@@ -779,7 +1028,7 @@ for my $no (3 ... $#all_tags+1){
 			if (exists $treesToIgnore{$tree_analysis}){
 				my @appendarr = ();
 
-				print SUMMARY $Hchrom,"\t",$Hstart,"\t",$Hend,"\t",$locusmotif,"\t",$locusmotifsize,"\t", $thresharr[$locusmotifsize], "\t", $simplified_microsat,"\t", $tree_analysis,"\t", join("",@tags), "\t";
+#				print SUMMARY $Hchrom,"\t",$Hstart,"\t",$Hend,"\t",$locusmotif,"\t",$locusmotifsize,"\t", $thresharr[$locusmotifsize], "\t", $simplified_microsat,"\t", $tree_analysis,"\t", join("",@tags), "\t";
 				#print "SUMMARY ",$Hchrom,"\t",$Hstart,"\t",$Hend,"\t",$locusmotif,"\t",$locusmotifsize,"\t", $thresharr[$locusmotifsize], "\t", $simplified_microsat,"\t", $tree_analysis,"\t", join("",@tags), "\t";
 #				print SELECT $Hchrom,"\t",$Hstart,"\t",$Hend,"\t","NOEVENT", "\t\t", $cluster,"\n";
 				
@@ -789,46 +1038,48 @@ for my $no (3 ... $#all_tags+1){
 					for my $p (@pair){
 						my @mutinfoarray1 = ();
 						for (1 ... 38){
-							push (@mutinfoarray1, "NA")
+#							push (@mutinfoarray1, "NA")
 						}
-						print SUMMARY join ("\t", @mutinfoarray1[0...($#mutinfoarray1)] ),"\t"; 			
+#						print SUMMARY join ("\t", @mutinfoarray1[0...($#mutinfoarray1)] ),"\t"; 			
+#						print  join ("\t", @mutinfoarray1[0...($#mutinfoarray1)] ),"\t"; 			
 					}
 	
 				}
 				for (1 ... 38){
 					push (@appendarr, "NA")
 				}
-				print SUMMARY join ("\t", @appendarr,"NULL", "NULL"),"\n"; 
+#				print SUMMARY join ("\t", @appendarr,"NULL", "NULL"),"\n"; 
+#				print  join ("\t", @appendarr,"NULL", "NULL"),"\n"; 
 		#		print "SUMMARY ",join ("\t", @appendarr,"NULL", "NULL"),"\n"; #<STDIN>;
 				next;
 			}
+#			print colored ['blue'],"cluster = $cluster\n";
 			
 			my ($mutations_array, $nodes, $branches_hash, $alivehash, $primaryalignment) = peel_onion($tree, \%sequences, \%alignment, \@tags, \%microsathash, \%nonmicrosathash, $motif, $tree_analysis, $thresholdhash{length($motif)}, \%microsatstarts);
-			
+	
 			if ($mutations_array eq "NULL"){
+			#	print "cluster = $cluster \n"; <STDIN>;
 				my @appendarr = ();
 
-				print SUMMARY $Hchrom,"\t",$Hstart,"\t",$Hend,"\t",$locusmotif,"\t",$locusmotifsize,"\t", $thresharr[$locusmotifsize],"\t",$simplified_microsat,"\t", $tree_analysis,"\t", join("",@tags), "\t";
-		#		print "SUMMARY ", $Hchrom,"\t",$Hstart,"\t",$Hend,"\t",$locusmotif,"\t",$locusmotifsize,"\t", $thresharr[$locusmotifsize],"\t",$simplified_microsat,"\t", $tree_analysis,"\t", join("",@tags), "\t"; 
-#				print SELECT $Hchrom,"\t",$Hstart,"\t",$Hend,"\t","EVENT", "\t\t", $cluster,"\n";
+			#	print SUMMARY $Hchrom,"\t",$Hstart,"\t",$Hend,"\t",$locusmotif,"\t",$locusmotifsize, "\t";
 
-				foreach my $lnode (@$lagestnodes){
-					my @pair = @$lnode;
-					my @nodemutarr = ();
-					for my $p (@pair){
-						my @mutinfoarray1 = ();
-						for (1 ... 38){
-							push (@mutinfoarray1, "NA")
-						}
-						print SUMMARY join ("\t", @mutinfoarray1[0...($#mutinfoarray1)] ),"\t"; 			
-		#				print  join ("\t", "SUMMARY", @mutinfoarray1[0...($#mutinfoarray1)] ),"\t"; 			
-					}
-	
-				}
-				for (1 ... 38){
-					push (@appendarr, "NA")
-				}
-				print SUMMARY join ("\t", @appendarr,"NULL", "NULL"),"\n"; 
+			#	foreach my $lnode (@$lagestnodes){
+			#		my @pair = @$lnode;
+			#		my @nodemutarr = ();
+			#		for my $p (@pair){
+			#			my @mutinfoarray1 = ();
+			#			for (1 ... 38){
+			#				push (@mutinfoarray1, "NA")
+			#			}
+			#			print SUMMARY join ("\t", @mutinfoarray1[0...($#mutinfoarray1)] ),"\t"; 			
+			#			print  join ("\t", @mutinfoarray1[0...($#mutinfoarray1)] ),"\t"; 			
+			#		}
+			#	}
+			#	for (1 ... 38){
+			#		push (@appendarr, "NA")
+			#	}
+			#	print SUMMARY join ("\t", @appendarr,"NULL", "NULL"),"\n"; 
+			#	print  join ("\t", @appendarr,"NULL", "NULL"),"\n"; 
 			#	print  join ("\t","SUMMARY", @appendarr,"NULL", "NULL"),"\n"; #<STDIN>;
 				next;
 			}
@@ -842,19 +1093,42 @@ for my $no (3 ... $#all_tags+1){
 			my @finalmutations_array= ();
 			@finalmutations_array = selectMutationArray($mutations_array, $newmutations_array, \@tags, $alivehash, \%alignment, $motif) if $newmutations_array ne "NULL";
 			@finalmutations_array = selectMutationArray($mutations_array, $mutations_array, \@tags, $alivehash, \%alignment, $motif) if $newmutations_array eq "NULL";
+# print "alt = $alternate{$conformation}\n";
 
-			my ($besttree, $treescore) = selectBetterTree($tree_analysis, $alternate{$tree_analysis}, \@finalmutations_array);
+			my ($besttree, $treescore) = selectBetterTree($tree_analysis, $alternate{$conformation}, \@finalmutations_array);
 			my $cleancase = "UNCLEAN";
-			
 			$cleancase = checkCleanCase($besttree, $finalalignment) if $treescore > 0 && $finalalignment ne "NULL" && $finalalignment =~ /\!/;
 			$cleancase = checkCleanCase($besttree, $primaryalignment) if $treescore > 0 && $finalalignment eq "NULL" && $primaryalignment =~ /\!/ && $primaryalignment ne "NULL";
 			$cleancase = "CLEAN" if $finalalignment eq "NULL" && $primaryalignment !~ /\!/ && $primaryalignment ne "NULL";
 			$cleancase = "CLEAN" if $finalalignment ne "NULL" && $finalalignment !~ /\!/ ;
+# print "besttree = $besttree ... cleancase=$cleancase\n"; #<STDIN>;
+
+			my @selects = ("-C","+C","-H","+H","-HC","+HC","-O","+O","-H.-C","-H.-O","-HC,+C","-HC,+H","-HC.-O","-HCO,+HC","-HCO,+O","-O.-C","-O.-H",
+			"+C.+O","+H.+C","+H.+O","+HC,-C","+HC,-H","+HC.+O","+HCO,-C","+HCO,-H","+HCO,-HC","+HCO,-O","+O.+C","+O.+H","+H.+C.+O","-H.-C.-O","+HCO","-HCO");
+			next if (oneOf(@selects, $besttree) == 0);
+			if ( ($besttree =~ /,/ || $besttree =~ /\./) && $cleancase eq "UNCLEAN"){
+				$besttree = "$besttree / $tree_analysis";				
+			}
+
 			$besttree = "NULL" if $treescore <= 0;
-			print SUMMARY $Hchrom,"\t",$Hstart,"\t",$Hend,"\t",$locusmotif,"\t",$locusmotifsize,"\t", $thresharr[$locusmotifsize],"\t",$simplified_microsat,"\t", $tree_analysis,"\t", join("",@tags), "\t";
-		#	print "SUMMARY ", $Hchrom,"\t",$Hstart,"\t",$Hend,"\t",$locusmotif,"\t",$locusmotifsize,"\t", $thresharr[$locusmotifsize],"\t",$simplified_microsat,"\t", $tree_analysis,"\t", join("",@tags), "\t";
-		
-#			print SELECT $Hchrom,"\t",$Hstart,"\t",$Hend,"\t","EVENT", "\t\t", $cluster,"\n";
+			
+			while ($besttree =~ /[A-Z][A-Z]/){
+				$besttree =~ s/([A-Z])([A-Z])/$1:$2/g;
+			}
+			
+			if ($besttree !~ /NULL/){			
+				my @elements = ($besttree =~ /([A-Z])/g);
+				
+				foreach my $ele (@elements){
+#					 print "replacing $ele with $backReplacementArrTag{$ele}\n";
+					$besttree =~ s/$ele/$backReplacementArrTag{$ele}/g if exists $backReplacementArrTag{$ele};
+				}
+			}
+			my $endendstate = $focalspec_orig.".".$Hchrom."\t".$Hstart."\t".$Hend."\t".$locusmotif."\t".$locusmotifsize."\t".$tree_analysis."\t";
+			next if $endendstate =~ /NA\tNA\tNA/;
+			
+			print SUMMARY $focalspec_orig,".",$Hchrom,"\t",$Hstart,"\t",$Hend,"\t",$locusmotif,"\t",$locusmotifsize,"\t";
+# print "SUMMARY\t", $focalspec_orig,".",$Hchrom,"\t",$Hstart,"\t",$Hend,"\t",$locusmotif,"\t",$locusmotifsize,"\t",$tree_analysis,"\t" ;
 			
 			my @mutinfoarray =();
 			
@@ -868,19 +1142,33 @@ for my $no (3 ... $#all_tags+1){
 						$mut =~ /node=([A-Z, \(\)]+)/;
 						push @nodemutarr, $mut if $p eq $1;
 					}
-#					print "from pair @pair, p=$p\n";
 					@mutinfoarray = summarizeMutations(\@nodemutarr, $besttree);
-					print SUMMARY join ("\t", @mutinfoarray[0...($#mutinfoarray-1)] ),"\t"; 			
-		#			print "SUMMARY ",join ("\t", @mutinfoarray[0...($#mutinfoarray-1)] ),"\t"; 			
+					
+				#	print SUMMARY join ("\t", @mutinfoarray[0...($#mutinfoarray-1)] ),"\t"; 			
+				#	print  join ("\t", @mutinfoarray[0...($#mutinfoarray-1)] ),"\t"; 			
 				}
-
 			}
 			
+#			print "G: $no_of_species\n";
+			
+			my @alignmentarr = ();
+			
+			foreach my $key (keys %alignment){
+				push @alignmentarr, $backReplacementArrTag{$key}.":".$alignment{$key};
+				
+			}
+#			print "alignmentarr = @alignmentarr"; <STDIN>;
+			
 			@mutinfoarray = summarizeMutations(\@finalmutations_array, $besttree);
 			print SUMMARY join ("\t", @mutinfoarray ),"\t"; 			
-			print SUMMARY  $cleancase, "\n";
-		#	print "SUMMARY ",join ("\t", @mutinfoarray,$cleancase ),"\n"; #<STDIN>; 			
-		#	print "summarized\n"; <STDIN>;
+			print SUMMARY join(",",@alignmentarr),"\n";
+#			print join("\t","--------------","\n",$besttree, join("",@tags)),"\n" if scalar(@tags) < 5;
+#			<STDIN> if scalar(@tags) < 5;
+#			print   $cleancase, "\n";
+#			print join ("\t", @mutinfoarray,$cleancase,join(",",@alignmentarr)),"\n"; #<STDIN>; 			
+# print "summarized\n"; #<STDIN>;
+	
+	
 	
 			my %indelcatch = ();
 			my %substcatch = ();
@@ -936,11 +1224,11 @@ for my $no (3 ... $#all_tags+1){
 		#	print colored ['red'], "-------------------------------------------------------------\n" if $printer == 1;
 
 		#	print colored ['red'],"finalmutations_array=\n" if $printer == 1;
-			foreach (@finalmutations_array) {
+#			foreach (@finalmutations_array) {
 #				print colored ['red'], "$_\n" if $_ =~ /type=substitution/ && $printer == 1  ;
 #				print colored ['yellow'], "$_\n" if $_ !~ /type=substitution/ && $printer == 1  ;
 				
-			}# if $line =~ /cal/;# && $line =~ /chr4/;
+#			}# if $line =~ /cal/;# && $line =~ /chr4/;
 			
 #			print colored ['red'], "-------------------------------------------------------------\n" if $printer == 1;
 #			print colored ['red'], "-------------------------------------------------------------\n" if $printer == 1;
@@ -959,20 +1247,19 @@ for my $no (3 ... $#all_tags+1){
 		}
 	}
 	close BO;
-#	print "now studying where we lost microsatellites:";
-#	print "x" x 60,"\n";
+# print "now studying where we lost microsatellites:\n";
+# print "x" x 60,"\n";
 	for my $reason (0 ... $#nextcounter){
 #		print $removalReasons[$reason]."\t".$nextcounter[$reason],"\n";
 	}
-#	print "x" x 60,"\n";
-#	print "In total we read $microreadcounter microsatellites after reading through $contigsentered contigs\n";
-#	print " we lost $keynotformedcounter contigs as they did not form the key, \n";
-#	print "$contignotrightcounter contigs as they were not of the right species configuration\n";  
-#	print "$keynotfoundcounter contigs as they did not contain the microsats\n";  
-#	print "... In total we went through a file that had $dotcounter contigs...\n";  
+# print "x" x 60,"\n";
+# print "In total we read $microreadcounter microsatellites after reading through $contigsentered contigs\n";
+# print " we lost $keynotformedcounter contigs as they did not form the key, \n";
+# print "$contignotrightcounter contigs as they were not of the right species configuration\n";  
+# print "$keynotfoundcounter contigs as they did not contain the microsats\n";  
+# print "... In total we went through a file that had $dotcounter contigs...\n";  
 #	print join ("\n","remaining orth keys = ", (keys %orths),"");
-
-
+# print "------   ------   ------   ------   ------   ------   ------   ------   ------   ------   ------   \n";
 #	print "now printing counted trees: \n";
 		if (scalar(keys %registeredTrees) > 0){
 		foreach my $keyb ( sort (keys %registeredTrees) )
@@ -984,6 +1271,8 @@ for my $no (3 ... $#all_tags+1){
 	
 }	
 
+close SUMMARY;
+
 my @summarizarr = ("+C=+C +R.+C -HCOR,+C",
 "+H=+H +R.+H -HCOR,+H",
 "-C=-C -R.-C +HCOR,-C",
@@ -1105,6 +1394,7 @@ sub baseml_parser{
 sub test_complexity{
 	my $printer = 0;
 	my $sequence = $_[0];
+	#print "sequence = $sequence\n";
 	my $COMPLEXITY_SUPPORT = $_[1];
 	my $complexity=int($COMPLEXITY_SUPPORT * (1/40));				#1	THIS IS AN ARBITRARY THRESHOLD SET FOR LOW COMPLEXITY.
 																	#2	THE INSPIRATION WAS WEB MILLER'S MAIL SENT ON 
@@ -1121,7 +1411,10 @@ sub test_complexity{
 	my $Ts = ($sequence=~ s/T/T/gi);
 	my $Gs = ($sequence=~ s/G/G/gi);
 	my $Cs = ($sequence=~ s/C/C/gi);
-	#print "seq = $sequence, As=$As, Ts=$Ts, Gs=$Gs, Cs=$Cs\n" if $printer == 1;
+	my $dashes = ($sequence=~ s/\-/-/gi);
+	$dashes = 0 if $sequence !~ /\-/;
+# print "seq = $sequence, As=$As, Ts=$Ts, Gs=$Gs, Cs=$Cs, dashes=$dashes\n";
+	return "LOW" if $dashes > length($sequence)/2;
 	
 	my $ans = ();
 
@@ -1132,13 +1425,12 @@ sub test_complexity{
 	my $lowcomplex = 0;
 	
 	foreach my $nt (@nts){
-		$lowcomplex =1 if $sequence =~ /(($nt\-*){10,})/i;
-#		print "caught with a mono of $nt : $1 in $sequence\n" if $sequence =~ /(($nt\-*){10,})/i;
-		$lowcomplex =1 if $sequence =~ /(($nt[A-Za-z]){10,})/i;
-		$lowcomplex =1 if $sequence =~ /(([A-Za-z]$nt){10,})/i;
-#		print "caught with a di with $nt : $2 in $sequence\n" if $sequence =~ /(($nt[A-Za-z]){10,})/i || $sequence =~ /(([A-Za-z]$nt){10,})/i;
+		$lowcomplex =1 if $sequence =~ /(($nt\-*){$mono_flanksimplicityRepno,})/i;
+		$lowcomplex =1 if $sequence =~ /(($nt[A-Za-z]){$di_flanksimplicityRepno,})/i;
+		$lowcomplex =1 if $sequence =~ /(([A-Za-z]$nt){$di_flanksimplicityRepno,})/i;
 		my $nont = ($sequence=~ s/$nt/$nt/gi);
-		
+		$lowcomplex = 1 if $nont > (length($sequence)  * $prop_of_seq_allowedtoAT) && ($nt =~ /[AT\-]/);
+		$lowcomplex = 1 if $nont > (length($sequence)  * $prop_of_seq_allowedtoCG) && ($nt =~ /[CG]/);
 	}
 #	print "leaving for now.. $sequence\n" if $printer == 1 && $lowcomplex == 0;
 	#<STDIN>;
@@ -1240,8 +1532,8 @@ sub load_allPossibleTrees{
 "+ + + +	+HCOR	NA",
 "+ + + _	+HCO|-R	+H.+C.+O",
 "+ + _ _	+HC	+H.+C;-O",
-"+ _ _ _	+H	+HC,-C",
-"_ + _ _	+C	+HC,-H",
+"+ _ _ _	+H	+HC,-C;+HC,-C",
+"_ + _ _	+C	+HC,-H;+HC,-H",
 "_ _ + _	+O	-HC|-H.-C",
 "_ _ + +	-HC	-H.-C",
 "+ _ _ +	+H|-C.-O	+HC,-C",
@@ -1254,37 +1546,38 @@ sub load_allPossibleTrees{
 "+ + _ +	-O	+HC") if $tree_list =~ /_HCOR\.txt/;
 
 		@trarr = ("#H C O R M	CONCLUSION	ALTERNATE",
-"+ + + + _	+HCOR	NA",
-"+ + + _ +	-R	+HCO;+HC.+O;+H.+C.+O",
 "+ + _ + +	-O	-HCO,+HC|-HCO,+HC;-HCO,(+H.+C)",
 "+ _ + + +	-C	-HC,+H;+HCO,(+H.+O)",
 "_ + + + +	-H	-HC,+C;-HCO,(+C.+O)",
-"_ _ _ _ +	-HCOR	NA",
-"_ _ _ + _	+R	-HC.-O;-H.-C.-O",
 "_ _ + _ _	+O	+HCO,-HC;+HCO,(-H.-C)",
 "_ + _ _ _	+C	+HC,-H;+HCO,(-H.-O)",
 "+ _ _ _ _	+H	+HC,-C;+HCO,(-C.-O)",
 "+ + + _ _	+HCO	+H.+C.+O",
-"+ + _ + _	-O	+R.+HC|-HCO,+HC;+H.+C.+R|-HCO,(+H.+C)",
-"+ _ + + _	-C	-HC,+H;+H.+O.+R|-HCO,(+H.+O)",
-"_ + + + _	-H	-HC,+C;+C.+O.+R|-HCO,(+C.+O)",
 "_ _ _ + +	-HCO	-HC.-O;-H.-C.-O",
-"_ _ + _ +	+O	+HCO,-HC;+HCO,(-H.-C)",
-"_ + _ _ +	+C	+HC,-H;+HCO,(-H.-O)",
-"+ _ _ _ +	+H	-HC,+H;+HCO,(-C.-O)",
-"+ + _ _ +	+HC	-R.-O|+HCO,-O|+H.+C;-HCO,+HC;-HCO,(+H.+C)",
-"+ _ + _ +	-R.-C|+HCO,-C|+H.+O	NA",
-"_ + + _ +	-R.-H|+HCO,-H|+C.+O	NA",
-"_ _ + + _	-HC	+R.+O|-HCO,+O|+HCO,-HC",
-"_ + _ + _	+R.+C|-HCO,+C|-HC,+C	+HCO,(-H.-O)",
-"+ _ _ + _	+R.+H|-C.-O	+HCO,(-C.-O)",
 "+ _ _ + +	-O.-C|-HCO,+H	+R.+H;-HCO,(+R.+H)",
 "_ + _ + +	-O.-H|-HCO,+C	+R.+C;-HCO,(+R.+C)",
 "_ + + _ _	+HCO,-H|+O.+C	NA",
 "+ _ + _ _	+HCO,-C|+O.+H	NA",
 "_ _ + + +	-HC	-H.-C|-HCO,+O",
 "+ + _ _ _	+HC	+H.+C|+HCO,-O|-HCO,+HC;-HCO,(+H.+C)",
-"+ + + + +	+HCORM	NA") if $tree_list =~ /_HCORM\.txt/;
+"+ + + + +	+HCORM	NA",
+"_ _ + _ +	DISCARD	+O;+HCO,-HC;+HCO,(-H.-C)",
+"_ + _ _ +	+C	+HC,-H;+HCO,(-H.-O)",
+"+ _ _ _ +	+H	+HC,-C;+HCO,(-C.-O)",
+"+ + _ _ +	+HC	-R.-O|+HCO,-O|+H.+C;-HCO,+HC;-HCO,(+H.+C)",
+"+ _ + _ +	DISCARD	-R.-C|+HCO,-C|+H.+O	NA",
+"_ + + _ +	DISCARD	-R.-H|+HCO,-H|+C.+O	NA",
+"_ _ _ _ +	DISCARD	-HCOR	NA",
+"_ _ _ + _	DISCARD	+R;-HC.-O;-H.-C.-O",
+"+ + _ + _	-O	+R.+HC|-HCO,+HC;+H.+C.+R|-HCO,(+H.+C)",
+"+ + + + _	+HCOR	NA",
+"+ + + _ +	DISCARD	-R;+HCO;+HC.+O;+H.+C.+O",
+"+ _ + + _	-C	-HC,+H;+H.+O.+R|-HCO,(+H.+O)",
+"_ + + + _	-H	-HC,+C;+C.+O.+R|-HCO,(+C.+O)",
+"_ _ + + _	-HC	+R.+O|-HCO,+O|+HCO,-HC",
+"_ + _ + _	+C	+R.+C|-HCO,+C|-HC,+C	+HCO,(-H.-O)",
+"+ _ _ + _	+H	+R.+H|-C.-O	+HCO,(-C.-O)"
+) if $tree_list =~ /_HCORM\.txt/;
 
 	
 	my $template_p = $_[1];
@@ -1304,6 +1597,7 @@ sub load_allPossibleTrees{
 																	#13 MENTIONED ABOVE.	
 	my @keys_array=();
 	foreach my $line (@trarr){
+#		print $line,"\n";
 		next if $line =~ /^#/;
 		chomp $line;
 		my @fields = split("\t", $line);
@@ -1311,8 +1605,9 @@ sub load_allPossibleTrees{
 #		print "loading: $fields[0]\n";
 		$template_p->{$fields[0]}[0] = $fields[1];
 		$template_p->{$fields[0]}[1] = 0;
-		$alternate_p->{$fields[1]} = $fields[2];
-		
+		$alternate_p->{$fields[0]} = $fields[2];
+#		$alternate_p->{$fields[1]} = $fields[2];
+# print "loading alternate_p $fields[1] $fields[2]\n"; #<STDIN> if $fields[1] eq "+H";
 	}
 #	print "loaded the trees with keys: @keys_array\n";
 	return $template_p, \@keys_array, $alternate_p;
@@ -1363,7 +1658,14 @@ sub checkCleanCase{
 
 sub adjustCoordinates{
 	my $line = $_[0];
-	my $no_of_species = $line =~ s/(chr[0-9a-zA-Z]+)|(Contig[0-9a-zA-Z\._\-]+)/x/g;
+	return 0 if !defined $line;
+	#print "------x------x------x------x------x------x------x------x------\n";
+	#print $line,"\n\n";
+	my $no_of_species = $line =~ s/(chr[0-9a-zA-Z]+)|(Contig[0-9a-zA-Z\._\-]+)|(scaffold[0-9a-zA-Z\._\-]+)|(supercontig[0-9a-zA-Z\._\-]+)/x/ig;
+	#print $line,"\n";
+	#print "------x------x------x------x------x------x------x------x------\n\n\n";
+#	my @got = ($line =~ s/(chr[0-9a-zA-Z]+)|(Contig[0-9a-zA-Z\._\-]+)/x/g);
+# print "line = $line\n";
 	$infocord = 2 + (4*$no_of_species) - 1;
 	$typecord = 2 + (4*$no_of_species) + 1 - 1;
 	$motifcord = 2 + (4*$no_of_species) + 2 - 1;
@@ -1376,7 +1678,8 @@ sub adjustCoordinates{
 	$interr_poscord = $microsatcord + 3;
 	$no_of_interruptionscord = $microsatcord + 4;
 	$interrcord = $microsatcord + 2;
-	#print "$line\n startcord = $startcord, and endcord = $endcord and no_of_species = $no_of_species\n" if $printer == 1;
+#	print "$line\n startcord = $startcord, and endcord = $endcord and no_of_species = $no_of_species\n" if $line !~ /calJac/i;
+	
 	return $no_of_species;
 }
 
@@ -1417,11 +1720,11 @@ sub peel_onion{
 		$node_sequences{$tag}=join ".",split(/\s*/,$nonmicrosathash->{$tag}) if $microsathash->{$tag} eq "NULL";
 		$node_alignments{$tag}=join ".",split(/\s*/,$alignment->{$tag}) ;
 		push @locus_sequences, $node_sequences{$tag};
-		#print "adding to node_seq: $tag = ",$node_alignments{$tag},"\n";
+# print "adding to node_seq: $tag = ",$node_alignments{$tag},"\n";
 	}
-
 	
-
+	#<STDIN>;
+	
 	my ($nodes_arr, $branches_hash) = get_nodes($tree);
 	my @nodes=@$nodes_arr;
 #	print "recieved nodes = " if $printer == 1; 
@@ -1457,7 +1760,7 @@ sub peel_onion{
 
 		foreach my $tag (@pair){
 #			print "$tag:  $node_alignments{$tag}\n" if $printer == 1;
-			print $node_alignments{$tag},"\n" if $printer == 1;
+#			print $node_alignments{$tag},"\n" if $printer == 1;
 			push @pair_sequences, $node_alignments{$tag};
 		}
 #		print "ppeel onion joint = $joint , pair_sequences=>@pair_sequences< , pair=>@pair<\n" if $printer == 1; 
@@ -1468,18 +1771,9 @@ sub peel_onion{
 #		print "newly added to node_sequences: $node_alignments{$joint} and list of mutations =\n", join("\n",@mutations_array),"\n" if $printer == 1;
 	}
 	
-#	print "now sending for analyze_mutations: mutation_array=@mutations_array, nodes=@nodes, branches_hash=$branches_hash, alignment=$alignment, tags=@tags, alivehash=\%alivehash, node_sequences=\%node_sequences, microsatstarts=$microsatstarts, motif=$motif\n" if $printer == 1;
-	## <STDIN> if $printer == 1;
 	
 	my $analayzed_mutations = analyze_mutations(\@mutations_array, \@nodes, $branches_hash, $alignment, \@tags, \%alivehash, \%node_sequences, $microsatstarts, $motif);
 
-#	print "returning: ", $analayzed_mutations, \@nodes, $branches_hash,"\n" if scalar @mutations_array > 0 && $printer == 1;
-#	print "returning: NULL, NULL, NULL " if scalar @mutations_array == 0 && $printer == 1;
-#	print "final node alignment = $node_alignments{$joint}\n" if $printer == 1;
-	
-	# <STDIN> if $printer == 1;
-
-
 	return ($analayzed_mutations, \@nodes, $branches_hash, \%alivehash, $node_alignments{$joint}) if scalar @mutations_array > 0;
 	return ("NULL",\@nodes,$branches_hash, \%alivehash, "NULL") if scalar @mutations_array == 0;
 }
@@ -1497,7 +1791,7 @@ sub get_nodes{
 	#$tree =~ s/ +//g;
 	$tree =~ s/\t+//g;
 	$tree=~s/;//g;
-	print "tree=$tree\n" if $printer == 1; 
+# print "tree=$tree\n" if $printer == 1; 
 	my @nodes = ();
 	my @onions=($tree);
 	my %branches=();
@@ -1509,11 +1803,11 @@ sub get_nodes{
 		$bite=~ /([ ,\(\)A-Z]+)\,\s*([ ,\(\)A-Z]+)/;
 		#$tree =~ /(\(\(\(H, C\), O\), R\))\, (M)/;
 		my @raw_nodes = ($1, $2);
-		print "raw nodes =  $1 and $2\n" if $printer == 1;
+# print "raw nodes =  $1 and $2\n" if $printer == 1;
 		push(@nodes, [@raw_nodes]);
 		foreach my $node (@raw_nodes) {push (@onions, $node) if $node =~ /,/;}
-		foreach my $node (@raw_nodes) {$branches{$node}="(".$bite.")"; print "adding to branches: $node = ($bite)\n" if $printer == 1;}
-		print "onions = @onions\n" if $printer == 1;<STDIN> if $printer == 1;
+		foreach my $node (@raw_nodes) {$branches{$node}="(".$bite.")"; }
+#		print "onions = @onions\n" if $printer == 1;<STDIN> if $printer == 1;
 	}
 	$printer = 0;
 	return \@nodes, \%branches;
@@ -1578,7 +1872,7 @@ sub analyze_mutations{
 #						print "now open_insertion=$open_insertion\n" if $printer == 1;
 						delete $mutation_hash{$posnext} if $froms_megahash{$posnext}{$local_node} eq "-";
 					}					
-					print "1 Feeding in: ", join("\t", "node=$local_node","type=insertion" ,"position=$pos", "from=", "to=", "insertion=$open_insertion", "deletion="),"\n" if $printer == 1;
+# print "1 Feeding in: ", join("\t", "node=$local_node","type=insertion" ,"position=$pos", "from=", "to=", "insertion=$open_insertion", "deletion="),"\n" if $printer == 1;
 					push (@solutions_array, join("\t", "node=$local_node","type=insertion" ,"position=$pos", "from=", "to=", "insertion=$open_insertion", "deletion="));
 				}
 				elsif ($tos_megahash{$pos}{$local_node} eq "-"){
@@ -1587,14 +1881,14 @@ sub analyze_mutations{
 					#next if exists $alivehash->{$local_node} && exists $alivehash->{$branches_hash->{$local_node}};
 					$open_deletion=$froms_megahash{$pos}{$local_node};
 					for my $posnext ($pos+1 ... $locuslength-1){
-						print "in 1st elsif studying posnext: $posnext\n" if $printer == 1;
-						print "nexting as nextpos does not exist\n" if !exists ($tos_megahash{$posnext}{$local_node}) && $printer == 1;
+# print "in 1st elsif studying posnext: $posnext\n" if $printer == 1;
+# print "nexting as nextpos does not exist\n" if !exists ($tos_megahash{$posnext}{$local_node}) && $printer == 1;
 						last if !exists ($tos_megahash{$posnext}{$local_node});
-						print "for posnext: $posnext, there exists $tos_megahash{$posnext}{$local_node}\n" if $printer == 1;
+# print "for posnext: $posnext, there exists $tos_megahash{$posnext}{$local_node}\n" if $printer == 1;
 						$open_deletion = $open_deletion.$froms_megahash{$posnext}{$local_node} if $tos_megahash{$posnext}{$local_node} eq "-";
 						delete $mutation_hash{$posnext} if $tos_megahash{$posnext}{$local_node} eq "-";
 					}					
-					print "2 Feeding in:",  join("\t", "node=$local_node","type=deletion" ,"position=$pos", "from=", "to=", "insertion=", "deletion=$open_deletion"), "\n" if $printer == 1;
+# print "2 Feeding in:",  join("\t", "node=$local_node","type=deletion" ,"position=$pos", "from=", "to=", "insertion=", "deletion=$open_deletion"), "\n" if $printer == 1;
 					push (@solutions_array, join("\t", "node=$local_node","type=deletion" ,"position=$pos", "from=", "to=", "insertion=", "deletion=$open_deletion"));
 				}
 				elsif ($tos_megahash{$pos}{$local_node} ne "-"){
@@ -1605,16 +1899,16 @@ sub analyze_mutations{
 					next if exists $microsatstarts->{$local_node} && $pos < $microsatstarts->{$local_node};
 					$open_to_substitution=$tos_megahash{$pos}{$local_node};
 					$open_from_substitution=$froms_megahash{$pos}{$local_node};
-					print "open from substitution: $open_from_substitution \n" if $printer == 1;
+# print "open from substitution: $open_from_substitution \n" if $printer == 1;
 					for my $posnext ($pos+1 ... $locuslength-1){
 						#print "in last elsif studying posnext: $posnext\n";
 						last if !exists ($tos_megahash{$posnext}{$local_node});
-						print "for posnext: $posnext, there exists $tos_megahash{$posnext}{$local_node}\n" if $printer == 1;
+# print "for posnext: $posnext, there exists $tos_megahash{$posnext}{$local_node}\n" if $printer == 1;
 						$open_to_substitution = $open_to_substitution.$tos_megahash{$posnext}{$local_node} if $tos_megahash{$posnext}{$local_node} ne "-";
 						$open_from_substitution = $open_from_substitution.$froms_megahash{$posnext}{$local_node} if $tos_megahash{$posnext}{$local_node} ne "-";
 						delete $mutation_hash{$posnext} if $tos_megahash{$posnext}{$local_node} ne "-" && $froms_megahash{$posnext}{$local_node} ;
 					}	
-					print "open from substitution: $open_from_substitution \n" if $printer == 1;
+# print "open from substitution: $open_from_substitution \n" if $printer == 1;
 					
 					#IS THE STRETCH OF SUBSTITUTION MICROSATELLITE-LIKE?
 					my @motif_parts=split(/\s*/,$motif);
@@ -1625,8 +1919,7 @@ sub analyze_mutations{
 						$left_query="(".$left_query;
 					}
 					$left_query=$left_query."?";
-				
-					print "left_quewry = $left_query\n" if $printer == 1;
+# print "left_quewry = $left_query\n" if $printer == 1;
 					#GENERATING THE FLEXIBLE RIGHT END	
 					my $right_query=();
 					for my $k (0 ... ($#motif_parts-1)) {
@@ -1634,22 +1927,22 @@ sub analyze_mutations{
 						$right_query=$right_query.")";
 					}
 					$right_query=$right_query."?";
-					print "right_query = $right_query\n" if $printer == 1;
-					print "Hence, searching for: ^$left_query($motif)+$right_query\$\n" if $printer == 1;
+# print "right_query = $right_query\n" if $printer == 1;
+# print "Hence, searching for: ^$left_query($motif)+$right_query\$\n" if $printer == 1;
 					
 					my $motifcomb=$motif x 50;
-					print "motifcomb = $motifcomb\n" if $printer == 1;
+# print "motifcomb = $motifcomb\n" if $printer == 1;
 					if ( ($motifcomb =~/$open_to_substitution/i) && (length ($open_to_substitution) >= length($motif)) ){
-						print "sequence microsat-like\n" if $printer == 1;
+# print "sequence microsat-like\n" if $printer == 1;
 						my $all_microsat_like = 0;
-						print "3 feeding in: ", join("\t", "node=$local_node","type=deletion" ,"position=$pos", "from=", "to=", "insertion=", "deletion=$open_from_substitution"), "\n" if $printer == 1;
+# print "3 feeding in: ", join("\t", "node=$local_node","type=deletion" ,"position=$pos", "from=", "to=", "insertion=", "deletion=$open_from_substitution"), "\n" if $printer == 1;
 						push (@solutions_array, join("\t", "node=$local_node","type=deletion" ,"position=$pos", "from=", "to=", "insertion=", "deletion=$open_from_substitution"));
-						print "4 feeding in: ", join("\t", "node=$local_node","type=insertion" ,"position=$pos", "from=", "to=", "insertion=$open_to_substitution", "deletion="), "\n" if $printer == 1;
+# print "4 feeding in: ", join("\t", "node=$local_node","type=insertion" ,"position=$pos", "from=", "to=", "insertion=$open_to_substitution", "deletion="), "\n" if $printer == 1;
 						push (@solutions_array, join("\t", "node=$local_node","type=insertion" ,"position=$pos", "from=", "to=", "insertion=$open_to_substitution", "deletion="));
 						
 					}
 					else{
-						print "5 feeding in: ", join("\t", "node=$local_node","type=substitution" ,"position=$pos", "from=$open_from_substitution", "to=$open_to_substitution", "insertion=", "deletion="), "\n" if $printer == 1;
+# print "5 feeding in: ", join("\t", "node=$local_node","type=substitution" ,"position=$pos", "from=$open_from_substitution", "to=$open_to_substitution", "insertion=", "deletion="), "\n" if $printer == 1;
 						push (@solutions_array, join("\t", "node=$local_node","type=substitution" ,"position=$pos", "from=$open_from_substitution", "to=$open_to_substitution", "insertion=", "deletion="));
 					}
 					#IS THE FROM-SEQUENCE MICROSATELLITE-LIKE?
@@ -1660,14 +1953,12 @@ sub analyze_mutations{
 			#<STDIN> if $printer ==1;
 		}
 	}
-
-	print "\n", "#" x 50, "\n"  if $printer == 1;
+# print "\n", "#" x 50, "\n"  if $printer == 1;
 	foreach my $tag (@$tags){
-		print "$tag: $alignment->{$tag}\n" if $printer == 1;	
+# print "$tag: $alignment->{$tag}\n" if $printer == 1;	
 	}
-	print "\n", "#" x 50, "\n" if $printer == 1;
-
-	print "returning SOLUTIONS ARRAY : \n",join("\n", @solutions_array),"\n" if $printer == 1; 
+# print "\n", "#" x 50, "\n" if $printer == 1;
+# print "returning SOLUTIONS ARRAY : \n",join("\n", @solutions_array),"\n" if $printer == 1; 
 	#print "end\n";
 	#<STDIN> if 
 	return \@solutions_array;
@@ -1681,12 +1972,12 @@ sub base_by_base_simple{
 	my $printer = 0;
 	my ($motif, $locus, $no, $pair0, $pair1, $joint) = @_;
 	my @seq_array=();
-	print "IN SUBROUTUNE base_by_base_simple.. information received = @_\n" if $printer == 1;
-	print "pair0 = $pair0 and pair1  = $pair1\n" if $printer == 1;
+# print "IN SUBROUTUNE base_by_base_simple.. information received = @_\n" if $printer == 1;
+# print "pair0 = $pair0 and pair1  = $pair1\n" if $printer == 1;
 
 	my @example=split(/\./,$locus->[0]);
-	print "example, for length = @example\n" if $printer == 1;
-	for my $i (0...$no-1){push(@seq_array, [split(/\./,$locus->[$i])]); print "for $i, from $locus->[$i],  seq_array = >@{$seq_array[$i]}<\n" if $printer == 1;}
+# print "example, for length = @example\n" if $printer == 1;
+	for my $i (0...$no-1){push(@seq_array, [split(/\./,$locus->[$i])]); }
 
 	my @compared_sequence=();
 	my @substitutions_list;
@@ -1733,7 +2024,7 @@ sub base_by_base_simple{
 			}
 		}		
 	}
-	print "returning: comared = @compared_sequence \nand substitutions list =\n", join("\n",@substitutions_list),"\n" if $printer == 1; 
+# print "returning: comared = @compared_sequence \nand substitutions list =\n", join("\n",@substitutions_list),"\n" if $printer == 1; 
 	return join(".",@compared_sequence), join(":", @substitutions_list) if scalar (@substitutions_list) > 0;
 	return join(".",@compared_sequence), "" if scalar (@substitutions_list) == 0;
 }
@@ -1741,19 +2032,18 @@ sub base_by_base_simple{
 
 sub resolve_base{
 	my $printer = 0;
-
-	print "IN SUBROUTUNE resolve_base.. information received = @_\n" if $printer == 1;
+# print "IN SUBROUTUNE resolve_base.. information received = @_\n" if $printer == 1;
 	my ($optional, $single, $singlesp, $arg) = @_;
 	my @options=split(/!/,$optional);
 	foreach my $option(@options) { 
 		$option=~s/[A-Z\(\) ,]+://g;
 		if ($option =~ /$single/i){
-			print "option = $option , returning single: $single\n" if $printer == 1;
+# print "option = $option , returning single: $single\n" if $printer == 1;
 			return $single;
 		}
 	}
-	print "returning ",$optional."!".$singlesp.":".$single. "\n" if $arg eq "keep" && $printer == 1; 
-	print "returning ",$singlesp.":".$single."!".$optional. "\n" if $arg eq "invert" && $printer == 1; 
+# print "returning ",$optional."!".$singlesp.":".$single. "\n" if $arg eq "keep" && $printer == 1; 
+# print "returning ",$singlesp.":".$single."!".$optional. "\n" if $arg eq "invert" && $printer == 1; 
 	return $optional."!".$singlesp.":".$single if $arg eq "keep";
 	return $singlesp.":".$single."!".$optional if $arg eq "invert";
 
@@ -1772,26 +2062,26 @@ sub same_length{
 	return 1;
 }
 sub treeStudy{
-	my $printer = 0;
+	my $printer = 1;
 #	print "template DEFINED.. received: @_\n" if defined %template; 
 #	print "only received = @_" if !defined %template; 
 	my $stopper = 0;
 	if (!defined %template){
 		$stopper = 1;
 		%template=();
-		print "tree decipherer = $tree_decipherer\n" if $printer == 1;
+# print "tree decipherer = $tree_decipherer\n" if $printer == 1; 
 		my ( $template_ref, $keys_array)=load_allPossibleTrees($tree_decipherer, \%template);
-		print "return = $template_ref and @{$keys_array}\n" if $printer == 1;
+# print "return = $template_ref and @{$keys_array}\n" if $printer == 1;
 		foreach my $key (@$keys_array){
-			print "addding : $template_ref->{$key} for $key\n" if $printer == 1;
+# print "addding : $template_ref->{$key} for $key\n" if $printer == 1;
 			$template{$key} = $template_ref->{$key};
 		}
 	}
-	
+#	<STDIN>;
 	for my $templet ( keys %template ) {
 	#	print "$templet => @{$template{$templet}}\n";
 	}
-	<STDIN> if !defined %template;
+#	<STDIN> if !defined %template;
 
 	my $strict = 0;
 
@@ -1881,7 +2171,7 @@ sub treeStudy{
 	chomp $line;
 	
 	my @f = split(/\t/,$line);
-	print "received array : @f.. recieved tags = @tags\n" if $printer == 1;
+# print "received array : @f.. recieved tags = @tags\n" if $printer == 1;
 	
 	# collect all motifs
 	my @motifs=();
@@ -1889,7 +2179,7 @@ sub treeStudy{
 	 @motifs = ($f[$Hmotif], $f[$Cmotif], $f[$Omotif], $f[$Rmotif]) if $tags[$#tags] =~ /R/;
 	 @motifs = ($f[$Hmotif], $f[$Cmotif], $f[$Omotif]) if $tags[$#tags] =~ /O/;
 #	print "motifs in the array = $f[$Hmotif], $f[$Cmotif], $f[$Omotif], $f[$Rmotif]\n" if $tags[$#tags] =~ /R/;;
-	print "motifs = @motifs\n" if $printer == 1;
+# print "motifs = @motifs\n" if $printer == 1;
 	my @translation = ();
 	foreach my $motif (@motifs){
 		push(@translation, "_") if $motif eq "NA";
@@ -1898,8 +2188,7 @@ sub treeStudy{
 	my $translate = join(" ", @translation);
 #	print "translate = >$translate< and analysis = $template{$translate}[0].. on the other hand, ",$template{"- - +"}[0],"\n"; 
 	my @analyses = split(/\|/,$template{$translate}[0]);
-	
-	print "motifs = @motifs, analyses = @analyses\n" if $printer == 1; 
+# print "motifs = @motifs, analyses = @analyses\n" if $printer == 1; 
 
 	if (scalar(@analyses) == 1) {
 		#print "analysis = $analyses[0]\n"; 
@@ -1909,11 +2198,12 @@ sub treeStudy{
 				$analysis =~ s/\+|\-//g;
 				my @species = split(/\s*/,$analysis);
 				my @currentMotifs = ();
-				foreach my $specie (@species){	push(@currentMotifs, $motifs[$speciesOrder{$specie}]); print "pushing into currentMotifs: $speciesOrder{$specie}: $motifs[$speciesOrder{$specie}]\n" if $printer == 1;}
-				print "current motifs = @currentMotifs and consistency? ", (consistency(@currentMotifs))," \n" if $printer == 1;
+				foreach my $specie (@species){	push(@currentMotifs, $motifs[$speciesOrder{$specie}]); #print "pushing into currentMotifs: $speciesOrder{$specie}: $motifs[$speciesOrder{$specie}]\n" if $printer == 1;
+					}
+# print "current motifs = @currentMotifs and consistency? ", (consistency(@currentMotifs))," \n" if $printer == 1;
 				$template{$translate}[1]++ if $strict == 1 && consistency(@currentMotifs) ne "NULL";
 				$template{$translate}[1]++ if $strict == 0;
-				print "adding to template $translate: $template{$translate}[1]\n" if $printer == 1;
+# print "adding to template $translate: $template{$translate}[1]\n" if $printer == 1;
 			}
 			else{
 				my $analysis = $analyses[0];
@@ -1923,32 +2213,33 @@ sub treeStudy{
 				my @complementarySpecies = ();
 				my $allSpecies = join("",@tags);
 				foreach my $specie (@species){	$allSpecies =~	s/$specie//g; }
-				foreach my $specie (split(/\s*/,$allSpecies)){	push(@currentMotifs, $motifs[$speciesOrder{$specie}]); print "pushing into currentMotifs: $speciesOrder{$specie}: $motifs[$speciesOrder{$specie}]\n" if $printer == 1;;}
-				print "current motifs = @currentMotifs and consistency? ", (consistency(@currentMotifs))," \n" if $printer == 1;
+				foreach my $specie (split(/\s*/,$allSpecies)){	push(@currentMotifs, $motifs[$speciesOrder{$specie}]); #print "pushing into currentMotifs: $speciesOrder{$specie}: $motifs[$speciesOrder{$specie}]\n" if $printer == 1;;
+					}
+# print "current motifs = @currentMotifs and consistency? ", (consistency(@currentMotifs))," \n" if $printer == 1;
 				$template{$translate}[1]=$template{$translate}[1]+1 if $strict == 1 && consistency(@currentMotifs) ne "NULL";
 				$template{$translate}[1]=$template{$translate}[1]+1  if $strict == 0;
-				print "adding to template $translate: $template{$translate}[1]\n" if $printer == 1;
+# print "adding to template $translate: $template{$translate}[1]\n" if $printer == 1;
 			}
 		}
 
 		elsif ($analyses[0] =~ /,/) {
 			my @events = split(/,/,$analyses[0]);	
-			print "events = @events \n " if $printer == 1;
+# print "events = @events \n " if $printer == 1;
 			if ($events[0] =~ /\+/){
 				my $analysis1 = $events[0];
 				$analysis1 =~ s/\+|\-//g;
 				my $analysis2 = $events[1];
 				$analysis2 =~ s/\+|\-//g;
 				my @nSpecies = split(/\s*/,$analysis2);
-				print "original anslysis = $analysis1 " if $printer == 1;
+# print "original anslysis = $analysis1 " if $printer == 1;
 				foreach my $specie (@nSpecies){ $analysis1=~ s/$specie//g;}
-				print "processed anslysis = $analysis1 \n" if $printer == 1; 
+# print "processed anslysis = $analysis1 \n" if $printer == 1; 
 				my @currentMotifs = ();
 				foreach my $specie (split(/\s*/,$analysis1)){push(@currentMotifs, $motifs[$speciesOrder{$specie}]); }
-				print "current motifs = @currentMotifs and consistency? ", (consistency(@currentMotifs))," \n" if $printer == 1;
+# print "current motifs = @currentMotifs and consistency? ", (consistency(@currentMotifs))," \n" if $printer == 1;
 				$template{$translate}[1]=$template{$translate}[1]+1 if $strict == 1 && consistency(@currentMotifs) ne "NULL";
 				$template{$translate}[1]=$template{$translate}[1]+1  if $strict == 0;
-				print "adding to template $translate: $template{$translate}[1]\n" if $printer == 1;
+# print "adding to template $translate: $template{$translate}[1]\n" if $printer == 1;
 			}
 			else{
 				my $analysis1 = $events[0];
@@ -1958,10 +2249,10 @@ sub treeStudy{
 				my @pSpecies = split(/\s*/,$analysis2);
 				my @currentMotifs = ();
 				foreach my $specie (@pSpecies){	push(@currentMotifs, $motifs[$speciesOrder{$specie}]); }
-				print "current motifs = @currentMotifs and consistency? ", (consistency(@currentMotifs))," \n" if $printer == 1;
+# print "current motifs = @currentMotifs and consistency? ", (consistency(@currentMotifs))," \n" if $printer == 1;
 				$template{$translate}[1]=$template{$translate}[1]+1 if $strict == 1 && consistency(@currentMotifs) ne "NULL";
 				$template{$translate}[1]=$template{$translate}[1]+1 if $strict == 0;
-				print "adding to template $translate: $template{$translate}[1]\n" if $printer == 1;
+# print "adding to template $translate: $template{$translate}[1]\n" if $printer == 1;
 			
 			}
 			
@@ -1969,7 +2260,7 @@ sub treeStudy{
 		elsif ($analyses[0] =~ /\./) {
 			my @events = split(/\./,$analyses[0]);	
 			foreach my $event (@events){
-				print "event = $event \n" if $printer == 1;
+# print "event = $event \n" if $printer == 1;
 				if ($event =~ /\+/){
 					my $analysis = $event;
 					$analysis =~ s/\+|\-//g;
@@ -1977,10 +2268,10 @@ sub treeStudy{
 					my @currentMotifs = ();
 					foreach my $specie (@species){	push(@currentMotifs, $motifs[$speciesOrder{$specie}]); }
 					#print consistency(@currentMotifs),"<- \n"; 
-					print "current motifs = @currentMotifs and consistency? ", (consistency(@currentMotifs))," \n" if $printer == 1;
+# print "current motifs = @currentMotifs and consistency? ", (consistency(@currentMotifs))," \n" if $printer == 1;
 					$template{$translate}[1]=$template{$translate}[1]+1 if $strict == 1 && consistency(@currentMotifs) ne "NULL";
 					$template{$translate}[1]=$template{$translate}[1]+1 if $strict == 0;
-					print "adding to template $translate: $template{$translate}[1]\n" if $printer == 1;
+# print "adding to template $translate: $template{$translate}[1]\n" if $printer == 1;
 				}
 				else{
 					my $analysis = $event;
@@ -1992,10 +2283,10 @@ sub treeStudy{
 					foreach my $specie (@species){	$allSpecies =~	s/$specie//g; }
 					foreach my $specie (split(/\s*/,$allSpecies)){	push(@currentMotifs, $motifs[$speciesOrder{$specie}]); }
 					#print consistency(@currentMotifs),"<- \n"; 
-					print "current motifs = @currentMotifs and consistency? ", (consistency(@currentMotifs))," \n" if $printer == 1;
+# print "current motifs = @currentMotifs and consistency? ", (consistency(@currentMotifs))," \n" if $printer == 1;
 					$template{$translate}[1]=$template{$translate}[1]+1 if $strict == 1 && consistency(@currentMotifs) ne "NULL";
 					$template{$translate}[1]=$template{$translate}[1]+1 if $strict == 0;
-					print "adding to template $translate: $template{$translate}[1]\n" if $printer == 1;
+# print "adding to template $translate: $template{$translate}[1]\n" if $printer == 1;
 				}
 			}	
 		
@@ -2011,24 +2302,24 @@ sub treeStudy{
 	
 	
 	for my $templet ( keys %template ) {
-	#	print "now returning: $templet\n";
 		if (@{ $template{$templet} }[1] > 0){
-			print "returning in the end: $templet and $translate\n" if $printer == 1;
+			
 			$template{$templet}[1] = 0;
-			return 	(@{$template{$templet}}[0], $translate);
+# print "now returning: @{$template{$templet}}[0], $templet\n";
+			return 	(@{$template{$templet}}[0], $templet);
 		}
 	}
 	undef %template;
-	print "sending NULL\n" if $printer == 1;
-	return ("NULL", $translate);
+# print "sending NULL\n" if $printer == 1;
+	return ("NULL", "NULL");
 	
 }
 
 
 sub consistency{
 	my @motifs = @_;
-	print "in consistency \n" if $printer == 1;
-	print "motifs sent = >",join("|",@motifs),"< \n" if $printer == 1; 
+# print "in consistency \n" if $printer == 1;
+# print "motifs sent = >",join("|",@motifs),"< \n" if $printer == 1; 
 	return $motifs[0] if scalar(@motifs) == 1;
 	my $prevmotif = shift(@motifs);
 	my $stopper = 0;
@@ -2043,14 +2334,14 @@ sub consistency{
 	return "NULL" if $stopper == 1;
 }
 sub summarize_microsat{
-	my $printer = 0;
+	my $printer = 1;
 	my $line = $_[0];	
 	my $humseq = $_[1];
 
 	my @gaps = $line =~ /[0-9]+\t[0-9]+\t[\+\-]/g;
 	my @starts = $line =~ /[0-9]+\t[\+\-]/g;
 	my @ends = $line =~ /[\+\-]\t[0-9]+/g;
-	print "starts = @starts\tends = @ends\n" if $printer == 1;
+# print "starts = @starts\tends = @ends\n" if $printer == 1;
 	for my $i (0 ... $#gaps) {$gaps[$i] =~ s/\t[0-9]+\t[\+\-]//g;}
 	for my $i (0 ... $#starts) {$starts[$i] =~ s/\t[\+\-]//g;}
 	for my $i (0 ... $#ends) {$ends[$i] =~ s/[\+\-]\t//g;}
@@ -2066,9 +2357,7 @@ sub summarize_microsat{
 	$no_of_gaps_to_end = ($humupstream_en =~ s/\-/x/g) if $humupstream_en=~/\-/;
 
 	my $locusmotif = ();
-	
-	
-	print "IN SUB SUMMARIZE_MICROSAT $line\n" if $printer == 1;
+# print "IN SUB SUMMARIZE_MICROSAT $line\n" if $printer == 1;
 	#return "NULL" if $line =~ /compound/;
 	my $Hstart = "NA";
 	my $Hend = "NA";
@@ -2114,37 +2403,35 @@ sub summarize_microsat{
 		$micro =~ s/\t\t/\t \t/g;
 		$micro =~ s/\t,/\t ,/g;
 		$micro =~ s/,\t/, \t/g;
-		print "------------------------------------------------------------------------------------------\n" if $printer == 1;
+# print "------------------------------------------------------------------------------------------\n" if $printer == 1;
 		chomp $micro;
 		if ($micro eq '0'){
 			push(@endstatement, join("\t",$exacttags[$species_counter],"NA","NA","NA","NA",0 ,"NA", "NA", 0,"NA","NA","NA", "NA" ));
 			$species_counter++;
-			print join("|","ENDSTATEMENT:",@endstatement),"\n" if $printer == 1;
+		#	print join("|","ENDSTATEMENT:",@endstatement),"\n" if $printer == 1;
 			next;
 		}
 	#		print $micro,"\n";
-		print "micro  = $micro \n" if $printer == 1;
+# print "micro  = $micro \n" if $printer == 1;
 		my @fields  = split(/\t/,$micro);
 		my $microcopy = $fields[$microsatcord];
 		$microcopy =~ s/\[|\]|-//g;
 		my $microsatlength = length($microcopy);
-		print "microsat = $fields[$microsatcord] and microsatlength = $microsatlength\n" if $printer == 1;
+# print "microsat = $fields[$microsatcord] and microsatlength = $microsatlength\n" if $printer == 1;
 #		print "sp_ident = @sp_ident.. species_no=$species_no\n";
-		$micro =~ /$sp_ident[$species_no]\s(\S+)\s([0-9]+)\s([0-9]+)/;
-		
-	
+		$micro =~ /$sp_ident[$species_no]\s([0-9a-zA-Z_]+)\s([0-9]+)\s([0-9]+)/;
+# print "$micro =~ /$sp_ident[$species_no] ([0-9a-zA-Z_]+) ([0-9]+) ([0-9]+)/\n";
 		my $sp_chr=$1;
 		my $sp_start=$2 + $fields[$startcord] - $fields[$gapcord];
 		my $sp_end= $sp_start + $microsatlength - 1;
 		
 		$species_no++;
 	
-		$micro =~ /$focalspec\s(\S+)\s([0-9]+)\s([0-9]+)/;
+		$micro =~ /$focalspec_orig\s(\S+)\s([0-9]+)\s([0-9]+)/;
 		$orthHchr=$1;
 		$Hstart=$2+$minstart-$no_of_gaps_to_start;
 		$Hend=$2+$maxend-$no_of_gaps_to_end;
-
-		print "Hstart = $Hstart = $fields[4] + $fields[$startcord] - $fields[$gapcord]\n" if $printer == 1;
+# print "Hstart = $Hstart = $fields[4] + $fields[$startcord] - $fields[$gapcord]\n" if $printer == 1;
 	
 		my $motif = $fields[$motifcord];
 		my $firstmotif = ();
@@ -2159,7 +2446,7 @@ sub summarize_microsat{
 		}
 		
 		else {$firstmotif = $motif;}
-		print "firstmotif =$firstmotif : \n" if $printer == 1;
+# print "firstmotif =$firstmotif : \n" if $printer == 1;
 		$firstmotif = allCaps($firstmotif);
 
 		if (exists $revHash{$firstmotif} && $turn == 0) {
@@ -2168,17 +2455,17 @@ sub summarize_microsat{
 		}
 		
 		elsif (exists $revHash{$firstmotif} && $turn == 1) {$firstmotif = $revHash{$firstmotif}; $turn = 1;}
-		print "changed firstmotif =$firstmotif\n" if $printer == 1;
+# print "changed firstmotif =$firstmotif\n" if $printer == 1;
 	#		<STDIN>;
 		$locusmotif = $firstmotif;
 		
 		if (scalar(@fields) > $microsatcord + 2){
-			print "fields = @fields ... interr_poscord=$interr_poscord=$fields[$interr_poscord] .. interrcord=$interrcord=$fields[$interrcord]\n" if $printer == 1; 
+# print "fields = @fields ... interr_poscord=$interr_poscord=$fields[$interr_poscord] .. interrcord=$interrcord=$fields[$interrcord]\n" if $printer == 1; 
 
 			my @interposes = ();
 			@interposes = split(",",$fields[$interr_poscord]) if $fields[$interr_poscord] =~ /,/; 
 			$interposes[0] = $fields[$interr_poscord] if $fields[$interr_poscord] !~ /,/ ;
-			print "interposes=@interposes\n" if $printer == 1;
+# print "interposes=@interposes\n" if $printer == 1;
 			my @relativeposes = (); 
 			my @interruptions = ();
 			@interruptions = split(",",$fields[$interrcord]) if $fields[$interrcord] =~ /,/; 
@@ -2196,16 +2483,16 @@ sub summarize_microsat{
 			
 				
 				my $relativepos = (100 * $interpos) / $microsatlength;
-				print "relativepos  = $relativepos ,interpos=$interpos, interruption=$interruption, interlen=$interlen \n" if $printer == 1;
+# print "relativepos  = $relativepos ,interpos=$interpos, interruption=$interruption, interlen=$interlen \n" if $printer == 1;
 				$relativepos = (100 * ($interpos-$interlen)) / $microsatlength if $relativepos > 50;
-				print "-->  = $relativepos\n" if $printer == 1;
+# print "-->  = $relativepos\n" if $printer == 1;
 				$interruption = "IND" if length($interruption) < 1;
 		
 				if ($turn == 1){
 					$fields[$microsatcord] = switch_micro($fields[$microsatcord]);
 					$interruption = switch_nucl($interruption) unless $interruption eq "IND";
 					$interpos = ($microsatlength - $interpos) - $interlen + 2;
-					print "turn interpos = $interpos for $fields[$microsatcord]\n" if $printer == 1;
+# print "turn interpos = $interpos for $fields[$microsatcord]\n" if $printer == 1;
 					$relativepos = (100 * $interpos) / $microsatlength;
 					$relativepos = (100 * ($interpos-$interlen)) / $microsatlength if $relativepos > 50;
 		
@@ -2213,7 +2500,7 @@ sub summarize_microsat{
 					$strand = '+' if $strand eq '-';
 					$strand = '-' if $strand eq '+';
 				}
-				print "final relativepos = $relativepos\n" if $printer == 1;
+# print "final relativepos = $relativepos\n" if $printer == 1;
 				push(@relativeposes, $relativepos);
 			}
 			push(@endstatement,join("\t",($exacttags[$species_counter],$sp_chr, $sp_start, $sp_end, $firstmotif,length($firstmotif),$fields[$microsatcord],$strand,$microsatlength,join(",",@interposes),join(",",@relativeposes),join(",",@interruptions), join(",",@interlens))));
@@ -2230,7 +2517,7 @@ sub summarize_microsat{
 		$locusmotif = $revHash{$locusmotif} if exists $revHash{$locusmotif};
 	
 		my $endst =  join("\t", @endstatement, $orthHchr, $Hstart, $Hend);
-		print join("\t", @endstatement, $orthHchr,  $Hstart, $Hend), "\n" if $printer == 1; 
+#		print join("\t", @endstatement, $orthHchr,  $Hstart, $Hend), "\n" if $printer == 1; 
 	
 	
 	return (join("\t", @endstatement, $orthHchr, $Hstart, $Hend), $orthHchr, $Hstart, $Hend, $locusmotif, length($locusmotif));
@@ -2267,10 +2554,10 @@ sub decipher_history{
 	my ($mutations_array, $tags_string, $nodes, $branches_hash, $tree_analysis, $confirmation_string, $alivehash) = @_;
 	my %mutations_hash=();
 	foreach my $mutation (@$mutations_array){
-		print "mutation = $mutation\n" if $printer == 1;
+# print "mutation = $mutation\n" if $printer == 1;
 		my %local = $mutation =~ /([\S ]+)=([\S ]+)/g;
 		push @{$mutations_hash{$local{"node"}}},$mutation; 
-		print "just for confirmation: $local{node} pushed as: $mutation\n" if $printer == 1;
+# print "just for confirmation: $local{node} pushed as: $mutation\n" if $printer == 1;
 	}
 	my @nodes;
 	my @birth_steps=();
@@ -2282,7 +2569,7 @@ sub decipher_history{
 	
 	for my $i (0 ... $#tags){
 		$info{$tags[$i]}=$confirmation[$i];
-		print "feeding info: $tags[$i] = $info{$tags[$i]}\n" if $printer == 1;
+# print "feeding info: $tags[$i] = $info{$tags[$i]}\n" if $printer == 1;
 	}
 	
 	for my $keys (@$nodes) {
@@ -2295,8 +2582,7 @@ sub decipher_history{
 			foreach my $copy (@copykeys){
 				$states=$states.$info{$copy};
 			}
-			
-			print "reduced key = $copykey and state = $states\n" if $printer == 1;
+# print "reduced key = $copykey and state = $states\n" if $printer == 1;
 			
 			if (exists $mutations_hash{$key}) {
 				
@@ -2313,18 +2599,18 @@ sub decipher_history{
 			}
 		}
 	}
-	print "conformation = $confirmation_string\n" if $printer == 1;
+# print "conformation = $confirmation_string\n" if $printer == 1;
 	push (@birth_steps, "NULL") if scalar(@birth_steps) == 0;
 	push (@death_steps, "NULL") if scalar(@death_steps) == 0;
-	print "birth steps = ",join("\n",@birth_steps)," and death steps = ",join("\n",@death_steps),"\n" if $printer == 1;
+# print "birth steps = ",join("\n",@birth_steps)," and death steps = ",join("\n",@death_steps),"\n" if $printer == 1;
 	return \@birth_steps, \@death_steps;
 }
 
 sub fillAlignmentGaps{
 	my $printer = 0;
-	print "received: @_\n" if $printer == 1;
+# print "received: @_\n" if $printer == 1;
 	my ($tree, $sequences, $alignment, $tagarray, $microsathash, $nonmicrosathash, $motif, $tree_analysis, $threshold, $microsatstarts) = @_;
-	print "in fillAlignmentGaps.. tree = $tree \n" if $printer == 1;
+# print "in fillAlignmentGaps.. tree = $tree \n" if $printer == 1;
 	my %sequence_hash=();
 
 	my @phases = ();
@@ -2392,12 +2678,11 @@ sub fillAlignmentGaps{
 		$node_sequences{$tag} = join ".",split(/\s*/,$node_sequences_temp{$tag});
 		$node_alignments{$tag} = join ".",split(/\s*/,$node_alignments_temp{$tag});		
 	}	
-
-	print "\n", "#" x 50, "\n" if $printer == 1;
+# print "\n", "#" x 50, "\n" if $printer == 1;
 	foreach my $tag (@tags){
-		print "$tag: $alignment->{$tag} = $node_alignments{$tag}\n" if $printer == 1;	
+# print "$tag: $alignment->{$tag} = $node_alignments{$tag}\n" if $printer == 1;	
 	}
-	print "\n", "#" x 50, "\n" if $printer == 1;
+# print "\n", "#" x 50, "\n" if $printer == 1;
 #	print "change = $change\n";
 	#<STDIN> if $concatalignment=~/\-/;
 	
@@ -2407,7 +2692,7 @@ sub fillAlignmentGaps{
 	
 	my ($nodes_arr, $branches_hash) = get_nodes($tree);
 	my @nodes=@$nodes_arr;
-	print "recieved nodes = @nodes\n" if $printer == 1; 
+# print "recieved nodes = @nodes\n" if $printer == 1; 
 	
 	
 	#POPULATE branches_hash WITH INFORMATION ABOUT LIVESTATUS
@@ -2416,13 +2701,13 @@ sub fillAlignmentGaps{
 		my $joint = "(".join(", ",@pair).")";
 		my $copykey = join "", @pair;
 		$copykey =~ s/[\W ]+//g;
-		print "for node: $keys, copykey = $copykey and joint = $joint\n" if $printer == 1;
+# print "for node: $keys, copykey = $copykey and joint = $joint\n" if $printer == 1;
 		my $livestatus = 1;
 		foreach my $copy (split(/\s*/,$copykey)){
 			$livestatus = 0 if !exists $alivehash{$copy};
 		}
 		$alivehash{$joint} = $joint if !exists $alivehash{$joint} && $livestatus == 1;
-		print "alivehash = $alivehash{$joint}\n" if exists $alivehash{$joint} && $printer == 1;
+# print "alivehash = $alivehash{$joint}\n" if exists $alivehash{$joint} && $printer == 1;
 	}
 	
 
@@ -2434,31 +2719,31 @@ sub fillAlignmentGaps{
 	my $joint = ();
 	foreach my $node (@nodes){
 		my @pair = @$node; 
-		print "now in the nodes for loop, pair = @pair\n and sequences=\n" if $printer == 1;
+# print "now in the nodes for loop, pair = @pair\n and sequences=\n" if $printer == 1;
 		$joint = "(".join(", ",@pair).")"; 	
-		print "joint = $joint \n" if $printer == 1; 
+# print "joint = $joint \n" if $printer == 1; 
 		my @pair_sequences=();
 
 		foreach my $tag (@pair){
-			print "tag = $tag: " if $printer == 1;
-			print $node_alignments{$tag},"\n" if $printer == 1;
+# print "tag = $tag: " if $printer == 1;
+#			print $node_alignments{$tag},"\n" if $printer == 1;
 			push @pair_sequences, $node_alignments{$tag};
 		}
 #		print "fillgap\n";
 		my ($compared, $substitutions_list) = base_by_base_simple($motif,\@pair_sequences, scalar(@pair_sequences), @pair, $joint);
 		$node_alignments{$joint}=$compared;
 		push(  @mutations_array,split(/:/,$substitutions_list));
-		print "newly added to node_sequences: $node_alignments{$joint} and list of mutations = @mutations_array\n" if $printer == 1;
+# print "newly added to node_sequences: $node_alignments{$joint} and list of mutations = @mutations_array\n" if $printer == 1;
 	}
-	print "now sending for analyze_mutations: mutation_array=@mutations_array, nodes=@nodes, branches_hash=$branches_hash, alignment=$alignment, tags=@tags, alivehash=%alivehash, node_sequences=\%node_sequences, microsatstarts=$microsatstarts, motif=$motif\n" if $printer == 1;
+# print "now sending for analyze_mutations: mutation_array=@mutations_array, nodes=@nodes, branches_hash=$branches_hash, alignment=$alignment, tags=@tags, alivehash=%alivehash, node_sequences=\%node_sequences, microsatstarts=$microsatstarts, motif=$motif\n" if $printer == 1;
 #	<STDIN> if $printer == 1;
 	
 	my $analayzed_mutations = analyze_mutations(\@mutations_array, \@nodes, $branches_hash, $alignment, \@tags, \%alivehash, \%node_sequences, $microsatstarts, $motif);
 
 #	print "returningt: ", $analayzed_mutations, \@nodes,"\n" if scalar @mutations_array > 0;;
 #	print "returningy: NULL, NULL, NULL " if scalar @mutations_array == 0 && $printer == 1;
-	print "final node alignment after filling for $joint= " if $printer == 1;
-	print "$node_alignments{$joint}\n" if $printer == 1;
+# print "final node alignment after filling for $joint= " if $printer == 1;
+# print "$node_alignments{$joint}\n" if $printer == 1;
 	
 
 	return 1, $analayzed_mutations, \@nodes, $branches_hash, \%alivehash, $node_alignments{$joint} if scalar @mutations_array > 0 ;
@@ -2469,21 +2754,21 @@ sub fillAlignmentGaps{
 
 sub add_mutation{
 	my $printer = 0;
-	print "IN SUBROUTUNE add_mutation.. information received = @_\n" if $printer == 1;
+# print "IN SUBROUTUNE add_mutation.. information received = @_\n" if $printer == 1;
 	my ($i , $bite, $to, $from) = @_;
-	print "bite = $bite.. all received info = ",join("^", @_),"\n" if $printer == 1;
-	print "to=$to\n" if $printer == 1;
-	print "tis split = ",join(" and ",split(/!/,$to)),"\n" if $printer == 1;
+# print "bite = $bite.. all received info = ",join("^", @_),"\n" if $printer == 1;
+# print "to=$to\n" if $printer == 1;
+# print "tis split = ",join(" and ",split(/!/,$to)),"\n" if $printer == 1;
 	my @toields = split "!",$to;
-	print "toilds  = @toields\n" if $printer == 1;
+# print "toilds  = @toields\n" if $printer == 1;
 	my @mutations=();
 	
 	foreach my $toield (@toields){
 		my @toinfo=split(":",$toield);
-		print " at toinfo=@toinfo \n" if $printer == 1;
+# print " at toinfo=@toinfo \n" if $printer == 1;
 		next if  $toinfo[1] =~ /$from/i;
 		my @mutation = @toinfo if $toinfo[1] !~ /$from/i;
-		print "adding to mutaton list: ", join(",", "node=$mutation[0]","type=substitution" ,"position=$i", "from=$from", "to=$mutation[1]", "insertion=", "deletion="),"\n" if $printer == 1;
+# print "adding to mutaton list: ", join(",", "node=$mutation[0]","type=substitution" ,"position=$i", "from=$from", "to=$mutation[1]", "insertion=", "deletion="),"\n" if $printer == 1;
 		push (@mutations, join("\t", "node=$mutation[0]","type=substitution" ,"position=$i", "from=$from", "to=$mutation[1]", "insertion=", "deletion="));
 	}
 	return @mutations;
@@ -2493,7 +2778,7 @@ sub add_mutation{
 sub add_bases{
 
 	my $printer = 0;
-	print "IN SUBROUTUNE add_bases.. information received = @_\n" if $printer == 1;
+# print "IN SUBROUTUNE add_bases.. information received = @_\n" if $printer == 1;
 	my ($optional0, $optional1, $pair0, $pair1,$joint) = @_;
 	my $total_list=();
 
@@ -2535,8 +2820,7 @@ sub add_bases{
 		}
 
 	}
-
-	print "returning ",join "!",@return_options,"\n" if $printer == 1; 
+# print "returning ",join "!",@return_options,"\n" if $printer == 1; 
 	return join "!",@return_options;
 
 }
@@ -2688,7 +2972,7 @@ sub selectMutationArray{
 	my @tags = @$tagstringpt;
 	my $alignmentln = length($alignmentpt->{$tags[0]});
 	
-	foreach my $key (keys %$alivehashpt) { push @alivehasharr, $key; print "we have alive: $key\n" if $printer == 1;}
+	foreach my $key (keys %$alivehashpt) { push @alivehasharr, $key; }
 	
 	my %newside = ();
 	my %oldside = ();
@@ -2717,8 +3001,8 @@ sub selectMutationArray{
 			 $mut =~ /node=([A-Z\(\), ]+)\stype=([a-zA-Z ]+)\sposition=([0-9 ]+)\sfrom=([a-zA-Z\- ]+)\sto=([a-zA-Z\- ]+)\sinsertion=([a-zA-Z\- ]+)\sdeletion=([a-zA-Z\- ]+)/;
 			my $node = $1;
 			next if $3 != $pos;
-			print "new mut = $mut\n" if $printer == 1;
-			print "node = $node, pos = $3 ... and alivehasharr = >@alivehasharr<\n" if $printer == 1;
+# print "new mut = $mut\n" if $printer == 1;
+# print "node = $node, pos = $3 ... and alivehasharr = >@alivehasharr<\n" if $printer == 1;
 			my $alivenode = 0;
 			foreach my $key (@alivehasharr){
 				$alivenode = 1 if $key =~ /$node/;
@@ -2734,14 +3018,14 @@ sub selectMutationArray{
 				$indel_type = "d".checkIndelType($node, $thisindel, $motif,$alignmentpt, $3, $2) if $2 eq "deletion";
 				$indel_type = $indel_type."f" if $indel_type =~ /mot/ && length($thisindel) >= length($motif);
 			}
-			print "indeltype = $indel_type\n" if $printer == 1;
+# print "indeltype = $indel_type\n" if $printer == 1;
 			my $added = 0;
 			
 			if (exists $newside{$pos} && $indel_type =~ /[a-z]+/){
-				print "we have a preexisting one for $pos\n" if $printer == 1;
+# print "we have a preexisting one for $pos\n" if $printer == 1;
 				my @preexisting = @{$newside{$pos}};
 				foreach my $pre (@preexisting){
-					print "looking at $pre\n" if $printer == 1;
+# print "looking at $pre\n" if $printer == 1;
 					next if $pre !~ /node=$node/;
 					next if $pre !~ /indeltype=([a-z]+)/;
 					my $currtype = $1;
@@ -2768,11 +3052,9 @@ sub selectMutationArray{
 					}					
 				}
 			}
-			
-			print "added = $added\n" if $printer == 1;
+# print "added = $added\n" if $printer == 1;
 			push @{$newside{$pos}}, $mut."\tindeltype=$indel_type" if $added == 0;
-
-			print "for new pos,: $pos we have: @{$newside{$pos}}\n " if $printer == 1;
+# print "for new pos,: $pos we have: @{$newside{$pos}}\n " if $printer == 1;
 		}
 	}
 	
@@ -2786,7 +3068,7 @@ sub selectMutationArray{
 			$mut =~ /node=([A-Z\(\), ]+)\ttype=([a-zA-Z ]+)\tposition=([0-9 ]+)\tfrom=([a-zA-Z\- ]+)\tto=([a-zA-Z\- ]+)\tinsertion=([a-zA-Z\- ]+)\tdeletion=([a-zA-Z\- ]+)/;
 			my $node = $1;
 			next if $3 != $pos;
-			print "old mut = $mut\n" if $printer == 1;
+# print "old mut = $mut\n" if $printer == 1;
 			my $alivenode = 0;
 			foreach my $key (@alivehasharr){
 				$alivenode = 1 if $key =~ /$node/;
@@ -2807,7 +3089,7 @@ sub selectMutationArray{
 			
 			if (exists $newside{$pos} && $indel_type =~ /[a-z]+/){
 				my @preexisting = @{$newside{$pos}};
-				print "we have a preexisting one for $pos: @preexisting\n" if $printer == 1;
+# print "we have a preexisting one for $pos: @preexisting\n" if $printer == 1;
 				next if $imp == 0;
 				
 				if (scalar(@preexisting) == 1){
@@ -2816,7 +3098,7 @@ sub selectMutationArray{
 					next if $1 eq $node;
 					
 					if (exists $oldside{$pos} || exists $commons{$foundmut}){
-						print "not replacing, but just adding\n" if $printer == 1;
+# print "not replacing, but just adding\n" if $printer == 1;
 						push @{$newside{$pos}}, $mut."\tindeltype=$indel_type";
 						push @{$oldside{$pos}}, $mut."\tindeltype=$indel_type";
 						next;
@@ -2825,26 +3107,23 @@ sub selectMutationArray{
 					delete $newside{$pos};
 					push @{$oldside{$pos}}, $mut."\tindeltype=$indel_type";
 					push @{$newside{$pos}}, $mut."\tindeltype=$indel_type";
-					print "now  new one is : @{$newside{$pos}}\n" if $printer == 1;
+# print "now  new one is : @{$newside{$pos}}\n" if $printer == 1;
 				}
-				
-				print "for pos: $pos: @{$newside{$pos}}\n" if $printer == 1;
+# print "for pos: $pos: @{$newside{$pos}}\n" if $printer == 1;
 				next;
 			}
 
 			
 			my @news = @{$newside{$pos}} if exists $newside{$pos};
-			
-			print "mut = $mut and news = @news\n" if $printer == 1; 
+# print "mut = $mut and news = @news\n" if $printer == 1; 
 			push @{$oldside{$pos}}, $mut."\tindeltype=$indel_type";
 			push @{$newside{$pos}}, $mut."\tindeltype=$indel_type";
 		}
 	}
-
-	print "in the end, our collected mutations = \n" if $printer == 1;
+# print "in the end, our collected mutations = \n" if $printer == 1;
 	my @returnarr = ();
 	foreach my $key (keys %newside) {push @returnarr,@{$newside{$key}};}
-	print join("\n", @returnarr),"\n" if $printer == 1;
+#	print join("\n", @returnarr),"\n" if $printer == 1;
 	#<STDIN>;
 	return @returnarr;
 
@@ -2863,7 +3142,7 @@ sub checkIndelType{
 	my %prephases = ();
 	my %postphases = ();
 	#print "motif = $motif\n";
-	print "IN checkIndelType ... received: @_\n" if $printer == 1;
+# print "IN checkIndelType ... received: @_\n" if $printer == 1;
 	my $concat = $motif.$motif.$motif.$motif;
 	my $motiflength = length($motif);
 	
@@ -2878,16 +3157,16 @@ sub checkIndelType{
 		push @phases, $phase;
 		$firstpass = 1 if $indel =~ /$phase/i;
 		for my $k (0 ... length($motif)-1){
-			print "at: motiflength=$motiflength , y=$y , k=$k.. for pre: $motiflength+$y-$k and post: $motiflength+$y-$k+$motiflength in $concat\n" if $printer == 1;
+# print "at: motiflength=$motiflength , y=$y , k=$k.. for pre: $motiflength+$y-$k and post: $motiflength+$y-$k+$motiflength in $concat\n" if $printer == 1;
 			my $pre = substr($concat, $motiflength+$y-$k, $k );
 			my $post = substr($concat, $motiflength+$y+$motiflength, $k);
-			print "adding to phases : $phase - $pre and $post\n" if $printer == 1;
+# print "adding to phases : $phase - $pre and $post\n" if $printer == 1;
 			push @{$prephases{$phase}} , $pre;
 			push @{$postphases{$phase}} , $post;			
 		}
 		
 	}
-	print "firstpass 1= $firstpass\n" if $printer == 1;
+# print "firstpass 1= $firstpass\n" if $printer == 1;
 	return "non" if $firstpass ==0;
 	$firstpass =0;
 	
@@ -2900,15 +3179,14 @@ sub checkIndelType{
 				
 				$firstpass = 1 if $indel =~ /($pre)?($phase)+($post)?/i && length($indel) > (3 * length($motif));
 				$firstpass = 1 if $indel =~ /^($pre)?($phase)+($post)?$/i && length($indel) < (3 * length($motif));
-				print "matched here : ($pre)?($phase)+($post)?\n" if $printer == 1;
+# print "matched here : ($pre)?($phase)+($post)?\n" if $printer == 1;
 				last if $firstpass == 1;
 			}
 			last if $firstpass == 1;
 		}
 		last if $firstpass == 1;
 	}
-	
-	print "firstpass 2= $firstpass\n" if $printer == 1;
+# print "firstpass 2= $firstpass\n" if $printer == 1;
 	return "non" if $firstpass ==0;
 	return "mot" if $firstpass ==1;	
 }
@@ -2926,10 +3204,10 @@ sub checkIndelType_ComplexAnalysis{
 	
 	my @seqs = ();
 	my $residualseq = length($motif) - length($indel);
-	print "IN COMPLEX ANALYSIS ... received: @_  .... speciesinvolved = @speciesinvolved\n" if $printer == 1;
-	print "we have position = $pos, sseq = $alignmentpt->{$speciesinvolved[0]}\n" if $printer == 1;
-	print "residualseq = $residualseq\n" if $printer == 1;
-	print "pos=$pos... got: @_\n" if $printer == 1;
+# print "IN COMPLEX ANALYSIS ... received: @_  .... speciesinvolved = @speciesinvolved\n" if $printer == 1;
+# print "we have position = $pos, sseq = $alignmentpt->{$speciesinvolved[0]}\n" if $printer == 1;
+# print "residualseq = $residualseq\n" if $printer == 1;
+# print "pos=$pos... got: @_\n" if $printer == 1;
 	foreach my $sp (@speciesinvolved){
 		my $spseq = $alignmentpt->{$sp};
 		#print "orig spseq = $spseq\n";
@@ -2946,23 +3224,21 @@ sub checkIndelType_ComplexAnalysis{
 		}
 		#print "mod spseq = $spseq\n";
 	#	$spseq=~ s/\-//g if $type !~ /deletion/;
-		
-		print "substr($spseq, $pos-($residualseq), length($indel)+$residualseq+$residualseq)\n" if $pos > 0 && $pos < (length($spseq) - length($motif))  && $printer == 1;
-		print "substr($spseq, 0, length($indel)+$residualseq)\n" if $pos == 0 && $printer == 1;
-		print "substr($spseq, $pos - $residualseq, length($indel)+$residualseq)\n" if $pos >= (length($spseq) - length($motif))  && $printer == 1;
+# print "substr($spseq, $pos-($residualseq), length($indel)+$residualseq+$residualseq)\n" if $pos > 0 && $pos < (length($spseq) - length($motif))  && $printer == 1;
+# print "substr($spseq, 0, length($indel)+$residualseq)\n" if $pos == 0 && $printer == 1;
+# print "substr($spseq, $pos - $residualseq, length($indel)+$residualseq)\n" if $pos >= (length($spseq) - length($motif))  && $printer == 1;
 		
 		$subseq = substr($spseq, $pos-($residualseq), length($indel)+$residualseq+$residualseq) if $pos > 0 && $pos < (length($spseq) - length($motif))  ;
 		$subseq = substr($spseq, 0, length($indel)+$residualseq) if $pos == 0;
 		$subseq = substr($spseq, $pos - $residualseq, length($indel)+$residualseq) if $pos >= (length($spseq) - length($motif))  ;
-		print "spseq = $spseq . subseq=$subseq . type = $type\n" if $printer == 1;
+# print "spseq = $spseq . subseq=$subseq . type = $type\n" if $printer == 1;
 		#<STDIN> if $subseq !~ /[a-z\-]/i; 
 		$subseq =~ s/\-/$indel/g if $type =~ /insertion/;
 		push @seqs, $subseq;
-		print "seqs = @seqs\n" if $printer == 1;
+# print "seqs = @seqs\n" if $printer == 1;
 	}
 	return "non" if checkIfSeqsIdentical(@seqs) eq "NO";
-	
-	print "checking for $seqs[0] \n" if $printer == 1;
+# print "checking for $seqs[0] \n" if $printer == 1;
 	
 	my @phases =();
 	my %prephases = ();
@@ -2979,13 +3255,13 @@ sub checkIndelType_ComplexAnalysis{
 		for my $k (0 ... length($motif)-1){
 			my $pre = substr($concat, $motiflength+$y-$k, $k );
 			my $post = substr($concat, $motiflength+$y+$motiflength, $k);
-			print "adding to phases : $phase - $pre and $post\n" if $printer == 1;
+# print "adding to phases : $phase - $pre and $post\n" if $printer == 1;
 			push @{$prephases{$phase}} , $pre;
 			push @{$postphases{$phase}} , $post;			
 		}
 		
 	}
-	print "firstpass 1= $firstpass.. also, res-d = ",(length($seqs[0]))%(length($motif)),"\n" if $printer == 1;
+# print "firstpass 1= $firstpass.. also, res-d = ",(length($seqs[0]))%(length($motif)),"\n" if $printer == 1;
 	return "non" if $firstpass ==0;
 	$firstpass =0;
 	foreach my $phase (@phases){
@@ -2999,7 +3275,7 @@ sub checkIndelType_ComplexAnalysis{
 				foreach my $post (@posts){
 					next if $pre !~ /\S/ && $post !~ /\S/;
 					$firstpass = 1 if ($seqs[0] =~ /^($pre)($phase)+($post)$/i || $seqs[0] =~ /^($pre)($phase)+$/i || $seqs[0] =~ /^($phase)+($post)$/i);
-					print "caught with $pre $phase $post\n" if $printer == 1;
+# print "caught with $pre $phase $post\n" if $printer == 1;
 					last if $firstpass == 1;
 				}
 				last if $firstpass == 1;
@@ -3124,9 +3400,9 @@ sub summarizeMutations{
 			$dsubstitutions++ if $myutype eq "d";
 			$nsubstitutions++ if $myutype eq "n";
 	#		print "substitution: from= $mhash{from}, to = $mhash{to}, and type = myutype\n";
-			push @substitutionsarr, "b:$mhash{position}:".$mhash{"from"}.">".$mhash{"to"} if $myutype eq "b";
-			push @substitutionsarr, "d:$mhash{position}:".$mhash{"from"}.">".$mhash{"to"} if $myutype eq "d";
-			push @substitutionsarr, "n:$mhash{position}:".$mhash{"from"}.">".$mhash{"to"} if $myutype eq "n";
+			push @substitutionsarr, "$mhash{position}:".$mhash{"from"}.">".$mhash{"to"} if $myutype eq "b";
+			push @substitutionsarr, "$mhash{position}:".$mhash{"from"}.">".$mhash{"to"} if $myutype eq "d";
+			push @substitutionsarr, "$mhash{position}:".$mhash{"from"}.">".$mhash{"to"} if $myutype eq "n";
 	#		print "substitutionsarr = @substitutionsarr\n";
 	#		<STDIN>;
 		}
@@ -3156,9 +3432,9 @@ sub summarizeMutations{
 				$nmotdeletionsf++ if $mhash{"indeltype"} =~ /dmotf/ && $myutype eq "n";
 				$nnondeletions++ if $mhash{"indeltype"} =~ /dnon/ && $myutype eq "n";
 				
-				push @deletionsarr, "b:$mhash{indeltype}:$mhash{position}:".$mhash{"deletion"} if $myutype eq "b";
-				push @deletionsarr, "d:$mhash{indeltype}:$mhash{position}:".$mhash{"deletion"} if $myutype eq "d";
-				push @deletionsarr, "n:$mhash{indeltype}:$mhash{position}:".$mhash{"deletion"} if $myutype eq "n";
+				push @deletionsarr, "$mhash{indeltype}:$mhash{position}:".$mhash{"deletion"} if $myutype eq "b";
+				push @deletionsarr, "$mhash{indeltype}:$mhash{position}:".$mhash{"deletion"} if $myutype eq "d";
+				push @deletionsarr, "$mhash{indeltype}:$mhash{position}:".$mhash{"deletion"} if $myutype eq "n";
 			}
 
 			if ($mhash{"type"} eq "insertion"){
@@ -3184,9 +3460,9 @@ sub summarizeMutations{
 				$nmotinsertionsf++ if $mhash{"indeltype"} =~ /imotf/ && $myutype eq "n";
 				$nnoninsertions++ if $mhash{"indeltype"} =~ /inon/ && $myutype eq "n";
 
-				push @insertionsarr, "b:$mhash{indeltype}:$mhash{position}:".$mhash{"insertion"} if $myutype eq "b";
-				push @insertionsarr, "d:$mhash{indeltype}:$mhash{position}:".$mhash{"insertion"} if $myutype eq "d";
-				push @insertionsarr, "n:$mhash{indeltype}:$mhash{position}:".$mhash{"insertion"} if $myutype eq "n";
+				push @insertionsarr, "$mhash{indeltype}:$mhash{position}:".$mhash{"insertion"} if $myutype eq "b";
+				push @insertionsarr, "$mhash{indeltype}:$mhash{position}:".$mhash{"insertion"} if $myutype eq "d";
+				push @insertionsarr, "$mhash{indeltype}:$mhash{position}:".$mhash{"insertion"} if $myutype eq "n";
 				
 			}
 		}
@@ -3204,21 +3480,19 @@ sub summarizeMutations{
 	#print "tree = $tree, indels = $indels, subs = $subs, bspecies = @bspecies, dspecies = @dspecies \n";
 	my @returnarray = ();
 	
-	push (@returnarray, $insertions,  $deletions,  $motinsertions, $motinsertionsf,  $motdeletions,  $motdeletionsf,  $noninsertions,  $nondeletions) ;
-	push (@returnarray, $binsertions, $bdeletions, $bmotinsertions,$bmotinsertionsf, $bmotdeletions, $bmotdeletionsf, $bnoninsertions, $bnondeletions) ;
-	push (@returnarray, $dinsertions, $ddeletions, $dmotinsertions,$dmotinsertionsf, $dmotdeletions, $dmotdeletionsf, $dnoninsertions, $dnondeletions) ;
-	push (@returnarray, $ninsertions, $ndeletions, $nmotinsertions,$nmotinsertionsf, $nmotdeletions, $nmotdeletionsf, $nnoninsertions, $nnondeletions) ;
-	push (@returnarray, $substitutions, $bsubstitutions, $dsubstitutions, $nsubstitutions, $indels, $subs) ;
+	push (@returnarray, $indels, $subs) ;
 		
 	push @returnarray, $tree;
 	
 	my @copy = @returnarray;
+	#print "\n\nreturnarray = @returnarray ... binsertions=$binsertions dinsertions=$dinsertions bsubstitutions=$bsubstitutions dsubstitutions=$dsubstitutions\n";
+	#<STDIN>;
 	return (@returnarray);
 	
 }
 
 sub selectBetterTree{
-	my $printer = 0;
+	my $printer = 1;
 	my $treestudy = $_[0];
 	my $alt = $_[1];
 	my $mutspt = $_[2];
@@ -3235,11 +3509,10 @@ sub selectBetterTree{
 #	push(@alltrees,@alternatetrees);
 	
 	my %mutspecies = ();
-	
-	print "IN selectBetterTree..treestudy=$treestudy. alt=$alt. for: @_. trees=@trees<. alternatetrees=@alternatetrees\n" if $printer == 1;
+# print "IN selectBetterTree..treestudy=$treestudy. alt=$alt. for: @_. trees=@trees<. alternatetrees=@alternatetrees\n" if $printer == 1;
 	#<STDIN>;
 	foreach my $mut (@muts){
-		print colored ['green'],"mut = $mut\n" if $printer == 1;
+#		print colored ['green'],"mut = $mut\n" if $printer == 1;
 		$mut =~ /node=([A-Z,\(\) ]+)/;
 		my $node  = $1;
 		$node =~s/[,\(\) ]+//g;
@@ -3247,35 +3520,30 @@ sub selectBetterTree{
 		#print "adding node: $node\n" if $printer == 1;
 		$mutspecies{$node} = $node;
 		
-		#foreach (@indivspecies) { 
-			#$mutspecies{$mut} = $_; #print "for $_ adding $mutspecies{$_}\n";
-		#}
-		
 	}
 	
 	my @treerecords = ();
 	my $treecount = -1;
 	foreach my $tree (@alltrees){
-		print "checking with tree $tree\n" if $printer == 1;
+# print "checking with tree $tree\n" if $printer == 1;
 		$treecount++;
 		$treerecords[$treecount] = 0;
 		my @indivspecies = ($tree =~ /[A-Z]+/g);
-		print "indivspecies=@indivspecies\n" if $printer == 1;
+# print "indivspecies=@indivspecies\n" if $printer == 1;
 		foreach my $species (@indivspecies){
-			print "checkin if exists species: $species\n" if $printer == 1;
+# print "checkin if exists species: $species\n" if $printer == 1;
 			$treerecords[$treecount]+=2 if exists $mutspecies{$species} && $mutspecies{$species} !~ /indeltype=[a-z]mot/;
 			$treerecords[$treecount]+=1.5 if exists $mutspecies{$species} && $mutspecies{$species} =~ /indeltype=[a-z]mot/;
 			$treerecords[$treecount]-- if !exists $mutspecies{$species};
 		}
-		
-		print "for tree $tree, our treecount = $treerecords[$treecount]\n" if $printer == 1;
+# print "for tree $tree, our treecount = $treerecords[$treecount]\n" if $printer == 1;
 	}
 	
 	my @best_tree = array_largest_number_arrayPosition(@treerecords);
-	print "treerecords = @treerecords. hence, best tree = @best_tree\n" if $printer == 1;
-	
+# print "treerecords = @treerecords. hence, best tree = @best_tree = $alltrees[$best_tree[0]], $treerecords[$best_tree[0]]\n" if $printer == 1;
+	#<STDIN>;	
 	return ($alltrees[$best_tree[0]], $treerecords[$best_tree[0]]) if scalar(@best_tree) == 1;
-	print "best_tree[0] = $best_tree[0], and treerecords = $treerecords[$best_tree[0]]\n" if $printer == 1;
+# print "best_tree[0] = $best_tree[0], and treerecords = $treerecords[$best_tree[0]]\n" if $printer == 1;
 	return ("NULL", -1) if $treerecords[$best_tree[0]] < 1;
 	my $rando = int(rand($#trees));
 	return ($alltrees[$rando], $treerecords[$rando]) if scalar(@best_tree) > 1;
@@ -3777,10 +4045,15 @@ sub basic_stats{
 
 sub maftoAxt_multispecies {
 	my $printer = 0;
-#	print "in maftoAxt_multispecies : got @_\n";
+	#print "in maftoAxt_multispecies : got @_\n";
 	my $fname=$_[0];
 	open(IN,"<$_[0]") or die "Cannot open $_[0]: $! \n";
 	my $treedefinition = $_[1];
+	#print "treedefinition= $treedefinition\n";
+	
+	my @treedefinitions = MakeTrees($treedefinition);
+	
+	
 	open(OUT,">$_[2]") or die "Cannot open $_[2]: $! \n";
 	my $counter = 0;
 	my $exactspeciesset = $_[3];
@@ -3788,14 +4061,28 @@ sub maftoAxt_multispecies {
 	
 	$treedefinition=~s/[\)\(, ]/\t/g;
 	my @species=split(/\t+/,$treedefinition);
-	my @exactspecies=();
+	@exactspeciesset_unarranged = @species;
+#	print "species=@species\n";
 	
-	foreach my $spec (@species){
-		foreach my $espec (@exactspeciesset_unarranged){
-			push @exactspecies, $spec if $spec eq $espec;
+	my @exactspeciesarr=();
+
+	
+	foreach my $def (@treedefinitions){
+		$def=~s/[\)\(, ]/\t/g;
+		my @specs = split(/\t+/,$def);
+		my @exactspecies=();
+		foreach my $spec (@specs){
+			foreach my $espec (@exactspeciesset_unarranged){
+			#	print "pushing >$spec< nd >$espec<\n"  if $spec eq $espec && $espec =~ /[a-zA-Z0-9]/;
+				push @exactspecies, $spec if $spec eq $espec && $espec =~ /[a-zA-Z0-9]/;
+			}
+			
 		}
+			#print "exactspecies = >@exactspecies<\n";
+			push @exactspeciesarr, [@exactspecies];
 	}
-#	print "exactspecies=@exactspecies\n";
+	#<STDIN>;
+	#print "exactspeciesarr=@exactspeciesarr\n";
 	
 	###########
 	my $select = 2;  
@@ -3806,10 +4093,15 @@ sub maftoAxt_multispecies {
 	my @allowedset = ();
 	@allowedset = split(/;/,allowedSetOfSpecies(join("_",@species))) if $select == 0;
 	@allowedset = join("_",0,@species) if $select == 1;
-	#print "species = @species , allowedset =",join("\n", @allowedset) ," \n"; 
-	@allowedset = join("_",0,@exactspecies) if $select == 2;
-	#print "allowedset = @allowedset and exactspecies = @exactspecies\n";
+	#print "species = @species , allowedset =",join("\n", @allowedset) ," \n";
 	
+	
+	foreach my $set (@exactspeciesarr){
+		my @openset = @$set;
+		push @allowedset, join("_",0,@openset) if $select == 2;
+	#	print "openset = >@openset<, allowedset = @allowedset and exactspecies = @exactspecies\n";
+	}
+#	<STDIN>;
 	my $start = 0;
 	my @sequences = ();
 	my @titles = ();
@@ -3820,8 +4112,8 @@ sub maftoAxt_multispecies {
 	while(my $line = <IN>){
 		next if $line =~ /^#/;
 		next if $line =~ /^i/;
+	#	print "$line .. species = @species\n";
 		chomp $line;
-		#print "$line";
 		my @fields = split(/\s+/,$line);
 		chomp $line;
 		if ($line =~ /^a /){
@@ -3844,13 +4136,16 @@ sub maftoAxt_multispecies {
 		}
 		
 		if (($line !~ /^a/) && ($line !~ /^s/) && ($line !~ /^#/) && ($line !~ /^i/) && ($start = 1)){
-		
+			
 			my $arranged = reorderSpecies($species_counter, @species);
+#			print "species_counter=$species_counter .. arranged = $arranged\n";
+			
 			my $stopper = 1;
 			my $arrno = 0;
 			foreach my $set (@allowedset){
+#					print "checking $set with $arranged\n";
 				if ($arranged eq $set){
-	#				print "$arranged == $set\n";
+#					print "checked $set with $arranged\n";
 					$stopper = 0; last;
 				}
 				$arrno++;
@@ -3881,6 +4176,7 @@ sub maftoAxt_multispecies {
 		}
 	}
 #	print "countermatch = $countermatch\n";
+#	<STDIN>;
 }
 
 sub reorderSpecies{
@@ -3977,8 +4273,53 @@ sub orderInfo{
 #xxxxxxx maftoAxt_multispecies xxxxxxx xxxxxxx maftoAxt_multispecies xxxxxxx xxxxxxx maftoAxt_multispecies xxxxxxx 
 
 sub printarr {
-	print ">::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::\n";
-	foreach my $line (@_) {print "$line\n";}
-	print "::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::<\n";
+# print ">::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::\n";
+#	foreach my $line (@_) {print "$line\n";}
+# print "::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::<\n";
 }
 
+sub oneOf{
+	my @arr = @_;
+	my $element = $arr[$#arr];
+	@arr = @arr[0 ... $#arr-1];
+	my $present = 0;
+	
+	foreach my $el (@arr){
+		$present = 1 if $el eq $element;		
+	}
+	return $present;
+}
+
+#xxxxxxxxxxxxxx MakeTrees xxxxxxxxxxxxxxxxxxxxxxxxxxxx  MakeTrees xxxxxxxxxxxxxxxxxxxxxxxxxxxx  MakeTrees xxxxxxxxxxxxxxxxxxxxxxxxxxxx 
+
+sub MakeTrees{
+	my $tree = $_[0];
+#	my @parts=($tree);
+	my @parts=();
+	
+#	print "parts=@parts\n";
+	
+	while (1){
+		$tree =~ s/^\(//g;
+		$tree =~ s/\)$//g;
+		my @arr = ();
+	
+		if ($tree =~ /^([a-zA-Z0-9_]+),([a-zA-Z0-9_\(\),]+)\)$/){
+			@arr = $tree =~ /^([a-zA-Z0-9_]+),([a-zA-Z0-9_\(\),]+)$/;
+			push @parts, "(".$tree.")";
+			$tree = $2;
+		}
+		elsif ($tree =~ /^\(([a-zA-Z0-9_\(\),]+),([a-zA-Z0-9_]+)$/){
+			@arr = $tree =~ /^([a-zA-Z0-9_\(\),]+),([a-zA-Z0-9_]+)$/;
+			push @parts, "(".$tree.")";
+			$tree = $1;
+		}
+		elsif ($tree =~ /^([a-zA-Z0-9_]+),([a-zA-Z0-9_]+)$/){
+			last;
+		}
+	}	
+	#print "parts=@parts\n";
+	return @parts;
+}
+
+
diff --git a/tools/regVariation/microsatellite_birthdeath.xml b/tools/regVariation/microsatellite_birthdeath.xml
index e2008abc44f..2afe6437e86 100644
--- a/tools/regVariation/microsatellite_birthdeath.xml
+++ b/tools/regVariation/microsatellite_birthdeath.xml
@@ -1,11 +1,11 @@
-<tool id="microsatellite_birthdeath" name="Identify microsatellite births and deaths" version="1.0.0">
+<tool id="microsatellite_birthdeath" name="Identify microsatellite births and deaths" version="1.0.2">
   <description> and causal mutational mechanisms from previously identified orthologous microsatellite sets</description>
   <command interpreter="perl">
       microsatellite_birthdeath.pl 
       $alignment 
       $orthfile 
       $outfile 
-      ${alignment.metadata.species} 
+	  $species
       "$tree_definition" 
       $thresholds
       $separation 
@@ -14,11 +14,17 @@
   </command>
   <inputs>
     <page>
-        <param format="maf" name="alignment" type="data" label="Select MAF alignments"/>
+        <param format="maf" name="alignment" type="data" label="Select MAF alignments that have NOT been masked for nucleotide quality"/>
         
         <param format="txt" name="orthfile" type="data" label="Select raw microsatellite data"/>
 
-    	<param name="tree_definition" size="200" type="text" value= "((((hg18,panTro2),ponAbe2),rheMac2),calJac1)" label="Tree definition of all species above whether or not selected for microsatellite extraction" 
+     <param name="species" type="select" label="Select species" display="checkboxes" multiple="true" help="NOTE: Currently users are requested to select one of these three combinations: hg18-panTro2-ponAbe2, hg18-panTro2-ponAbe2-rheMac2 or hg18-panTro2-ponAbe2-rheMac2-calJac1">
+      <options>
+        <filter type="data_meta" ref="alignment" key="species" />
+      </options>
+    </param>
+
+   	<param name="tree_definition" size="200" type="text" value= "((((hg18,panTro2),ponAbe2),rheMac2),calJac1)" label="Tree definition of all species above whether or not selected for microsatellite extraction" 
     	help="For example: ((((hg18,panTro2),ponAbe2),rheMac2),calJac1)"/>
       	
       	<param name="separation" size="10" type="integer" value="40" label="Total length of flanking DNA used for sequence-similarity comparisons among species"
@@ -38,13 +44,14 @@
   </outputs>
   <tests>
     <test>
-      <param name="alignment" value="chr22_5sp.maf"/>
-      <param name="orthfile" value="chr22_5sp.microraw.tabular"/>
+      <param name="alignment" value="regVariation/microsatellite/Galaxy17_unmasked_short.maf.gz"/>
+      <param name="orthfile" value="regVariation/microsatellite/Galaxy17_short_raw.txt"/>
       <param name="thresholds" value="9,10,12,12"/>
+      <param name="species" value="hg18,panTro2,ponAbe2,rheMac2,calJac1"/>
       <param name="tree_definition" value="((((hg18, panTro2), ponAbe2), rheMac2), calJac1)"/>
-      <param name="separation" value="40"/>
-      <param name="simthresh" value="80"/>
-      <output name="outfile" file="chr22_5sp.microtab.tabular"/>
+      <param name="separation" value="10"/>
+      <param name="simthresh" value="85"/>
+      <output name="outfile" file="regVariation/microsatellite/Galaxy17_unmasked_results.txt"/>
     </test>
   </tests>
 
@@ -56,6 +63,40 @@
 **What it does**
 
 This tool uses raw orthologous microsatellite clusters (identified by the tool "Extract orthologous microsatellites") to identify microsatellite births and deaths along individual lineages of a phylogenetic tree.
+-----
+
+.. class:: warningmark
+
+**Note**
+
+A tab-separated output table (depending on the species being considered) is generated where each row contains all information for a microsatellite locus from multiple species. 
+The table typically reads like this:
+
+hg18.chr22	16153057	16153074	A		1	ins=,imot:0:tt;dels=	,9:t>c	-panTro2	hg18:tttttttttttttttttt,ponAbe2:--tttttttttttttttt,panTro2:-----ttttctttttttt
+
+hg18.chr22	16131711	16131722	ATGC	4	NA						,2:C>T	+ponAbe2	hg18:CACGCATGCATG,ponAbe2:CATGCATGCATG,panTro2:CACGCATGCATG,rheMac2:CACGCGTGCATG
+
+Where columns list the following:
+
+1: Chromosome/scaffold/contig  of one of the species. The species chosen is the first species readable in the Newick tree submitted by the user.
+
+2: Start coordinate
+
+3: End coordinate
+
+4: Motif of microsatellite
+
+5: Motif size
+
+6: Insertion and deletion details. Insertions are separated from deletions by a ";", and individual insertions and deletions are separated from others by a comma. For the purpose of illustration, consider the first row listed above:
+"imot:0:tt", where imot/imotf again suggest insertion, the number indicates position of insertion within the microsatellite's alignment, and this is followed by identity of nucleotides that are inserted.
+
+7: Substitution details. Individual substitutions are separated by commas. Each entry contains the position of substitution event in the microsatellites' alignment, and the nature of substitution.
+
+8: Inference of birth/death event. Births are indicated by "+", and deaths by "-". Events such as "-hg18:panTro2" suggest death in the common ancestor of hg18 and panTro2, whereas events such as "-hg18.panTro2" indicate parallel, independent death events along the two lineages. Alternative interpretations of the event may also be listed, following a "/", such as:
+"+hg18.+panTro2 / +hg18:panTro2"
+
+9: Actual sequences in the alignment, separated by commas.
 
 </help>  
 
diff --git a/tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.pl b/tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.pl
old mode 100644
new mode 100755
index e33bdd8dea9..a0535c8dbdc
--- a/tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.pl
+++ b/tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.pl
@@ -6,19 +6,19 @@ use File::Basename;
 use IO::Handle;
 use Cwd;
 use File::Path;
-use File::Temp qw/ tempfile tempdir /;
-use vars qw($distance @thresholds @tags $printer $mergestarts $mergeends $mergemicros $interrtypecord $microscanned $interrcord $interr_poscord $no_of_interruptionscord $infocord $typecord $startcord $strandcord $endcord $microsatcord $motifcord $sequencepos $no_of_species $gapcord $prinkter);
+#use File::Temp qw/ tempfile tempdir /;
+use vars qw($distance @thresholds @tags $species_set @allspecies $printer $treeSpeciesNum $focalspec $mergestarts $mergeends $mergemicros $interrtypecord $microscanned $interrcord $interr_poscord $no_of_interruptionscord $infocord $typecord $startcord $strandcord $endcord $microsatcord $motifcord $sequencepos $no_of_species $gapcord $prinkter);
 
-$ENV{'PATH'} .= ':' . dirname($0);
+#$ENV{'PATH'} .= ':' . dirname($0);
 my $date = `date`;
 
-my ($mafile, $orthfile, $threshold_array,  $species_set, $tree_definition, $separation) = @ARGV;
-if (!$mafile or !$orthfile or !$threshold_array or !$separation or !$tree_definition or !$species_set) { die "missing arguments\n"; }
-
+my ($mafile, $mafile_sputt, $orthfile, $threshold_array,  $allspeciesin, $tree_definition_all, $separation) = @ARGV;
+if (!$mafile or !$mafile_sputt or !$orthfile or !$threshold_array or !$separation or !$tree_definition_all or !$allspeciesin) { die "missing arguments\n"; }
 #-------------------------------------------------------------------------------
 # WHICH SPUTNIK USED?
 my $sputnikpath = ();
-$sputnikpath = "sputnik";
+$sputnikpath = "bx-sputnik" ;
+#$sputnikpath = "/Users/ydk/work/rhesus_microsat/codes/./sputnik_Mac-PowerPC";
 #print "sputnik_Mac-PowerPC non-existant\n" if !-e $sputnikpath;
 #exit if !-e $sputnikpath;
 #$sputnikpath = "bx-sputnik" ;
@@ -29,418 +29,450 @@ $sputnikpath = "sputnik";
 #-------------------------------------------------------------------------------
 $distance = 1; #bp
 $distance++;
-#-------------------------------------------------------------------------------
-# MICROSATELLITE THRESHOLD SETTINGS (LENGTH, BP)
-$threshold_array=~ s/,/_/g;
-my @thresharr = split("_",$threshold_array);
-my @thresholds=@thresharr;
-my $mono_threshold = $thresharr[0];
-my $di_threshold = $thresharr[1];
-my $tri_threshold = $thresharr[2];
-my $tetra_threshold = $thresharr[3];
-#my $threshold_array = join("_",($mono_threshold, $di_threshold, $tri_threshold, $tetra_threshold));
-my $tdir = tempdir( CLEANUP => 0 );
-chdir $tdir;
+my @tree_definitions=MakeTrees($tree_definition_all);
+my $allspeciesset = $tree_definition_all;
+$allspeciesset =~ s/[\(\) ]+//g;
+@allspecies = split(/,/,$allspeciesset);
+
+my @outputfiles = ();
+my $round = 0;
+#my $tdir = tempdir( CLEANUP => 0 );
+#chdir $tdir;
 my $dir = getcwd;  
-#print "current dit=$dir\n";
-#-------------------------------------------------------------------------------
-# CREATE AXT FILES IN FORWARD AND REVERSE ORDERS IF NECESSARY
-my @chrfiles=();
 
-#my $mafile =  "/Users/ydk/work/rhesus_microsat/results/galay/align.txt"; #$ARGV[0];
-my $chromt=int(rand(10000));
-my $p_chr=$chromt;
+foreach my $tree_definition (@tree_definitions){
+	my @commas = ($tree_definition =~ /,/g) ;
+	#print "commas = @commas\n"; <STDIN>;
+	next if scalar(@commas) <= 1;
+	#print "species_set = $species_set\n";
+	$treeSpeciesNum = scalar(@commas) + 1;
+	$species_set = $tree_definition;
+	$species_set =~ s/[\)\( ;]+//g;
+	#print "species_set = $species_set\n"; <STDIN>;
 
-
-my @exactspeciesset_unarranged = split(/,/,$species_set);
-$tree_definition=~s/[\)\(, ]/\t/g;
-my @treespecies=split(/\t+/,$tree_definition);
-my @exactspecies=();
-
-foreach my $spec (@treespecies){
-	foreach my $espec (@exactspeciesset_unarranged){
-		push @exactspecies, $spec if $spec eq $espec;
-	}
-}
-#print "exactspecies=@exactspecies\n";
-my $focalspec = $exactspecies[0];
-my $arranged_species_set=join(".",@exactspecies);
-my $chr_name = join(".",("chr".$p_chr),$arranged_species_set, "net", "axt");
-#print "sending to maftoAxt_multispecies: $mafile, $tree_definition, $chr_name, $species_set .. focalspec=$focalspec \n"; 
-maftoAxt_multispecies($mafile, $tree_definition, $chr_name, $species_set);
-#print "done maf to axt conversion\n";
-my $reverse_chr_name = join(".",("chr".$p_chr."r"),$arranged_species_set, "net", "axt");
-artificial_axdata_inverter ($chr_name, $reverse_chr_name);
-#print "reverse_chr_name=$reverse_chr_name\n"; 
-#-------------------------------------------------------------------------------
-# FIND THE CORRESPONDING CHIMP CHROMOSOME FROM FILE ORTp_chrS.TXT
-foreach my $direct ("reverse_direction","forward_direction"){
-	$p_chr=$chromt;
-	#print "direction = $direct\n";
-	$p_chr = $p_chr."r" if $direct eq "reverse_direction";
-	$p_chr = $p_chr if $direct eq "forward_direction";
-	my $config = $species_set;
-	$config=~s/,/./g;
-	my @orgs = split(/\./,$arranged_species_set);
-	#print "ORGS= @orgs\n";
-	my @tag=@orgs;
-		
-	
-	my $tags = join(",", @tag);
-	my @tags=@tag;
-	chomp $p_chr;
-	$tags = join("_", split(/,/, $tags));
-	my $pchr = "chr".$p_chr;
-	
-	my $ptag = $orgs[0]."-".$pchr.".".join(".",@orgs[1 ... scalar(@orgs)-1])."-".$threshold_array;
-	my @sp_tags = ();
-	
-	#print "orgs=@orgs, pchr=$pchr, hence, ptag = $ptag\n";
-	foreach my $sp (@tag){
-		push(@sp_tags, ($sp.".".$ptag));
-	}
-
-	my $preptag = $orgs[0]."-".$pchr.".".join(".",@orgs[1 ... scalar(@orgs)-1]);
-	my @presp_tags = ();
-	
-	foreach my $sp (@tag){
-		push(@presp_tags, ($sp.".".$preptag));
-	}
-
-	my $resultdir = "";
-	my $orthdir = "";
-	my $filtereddir = "";
-	my $pipedir = "";
-	
-	my @title_queries = ();
-	push(@title_queries, "^[0-9]+");
-	my $sep="\\s";
-	for my $or (0 ... $#orgs){
-		my $title =  join($sep, ($orgs[$or],  "[A-Za-z]+[0-9a-zA-Z]+", "[0-9]+", "[0-9]+", "[\\-\\+]"));
-		#$title =~ s/chr\\+\\s+\+/chr/g;
-		push(@title_queries, $title);
-	}
-	my $title_query = join($sep, @title_queries);
-	#print "title_queries=@title_queries\n";
-	#print "query = >$title_query<\n"; 
-	#print "orgs = @orgs\n"; 
+	$round++;
 	#-------------------------------------------------------------------------------
-	# GET AXTNET FILES, EDIT THEM AND SPLIT THEM INTO HUMAN AND CHIMP INPUT FILES
-	my $t1input = $pchr.".".$arranged_species_set.".net.axt";
-	
-	my @t1outputs = ();
-	
-	foreach my $sp (@presp_tags){
-		push(@t1outputs, $sp."_gap_op");
-	}
-	
-	multi_species_t1($t1input,$tags,(join(",", @t1outputs)), $title_query); 
-	#print "t1outputs=@t1outputs\n";
-	#print "done t1\n";
+	# MICROSATELLITE THRESHOLD SETTINGS (LENGTH, BP)
+	$threshold_array=~ s/,/_/g;
+	my @thresharr = split("_",$threshold_array);
+	@thresholds=@thresharr;
+	#my $threshold_array = join("_",($mono_threshold, $di_threshold, $tri_threshold, $tetra_threshold));
+	#print "current dit=$dir\n";
 	#-------------------------------------------------------------------------------
-	#START T2.PL
+	# CREATE AXT FILES IN FORWARD AND REVERSE ORDERS IF NECESSARY
+	my @chrfiles=();
 	
-	my $stag  = (); my $tag1 = (); my $tag2 = ();  my $schrs = ();
+	#my $mafile =  "/Users/ydk/work/rhesus_microsat/results/galay/align.txt"; #$ARGV[0];
+	my $chromt=int(rand(10000));
+	my $p_chr=$chromt;
 	
-	for my $t (0 ... scalar(@tags)-1){
-		multi_species_t2($t1outputs[$t], $tag[$t]);		
-	}
-	#-------------------------------------------------------------------------------
-	#START T2.2.PL
 	
-	my @temp_tags = @tag;
+	my @exactspeciesset_unarranged = split(/,/,$species_set);
+	$tree_definition=~s/[\)\(, ]/\t/g;
+	my @treespecies=split(/\t+/,$tree_definition);
+	my @exactspecies=();
 	
-	foreach my $sp (@presp_tags){
-		my $t2input =  $sp."_nogap_op_unrand";
-		multi_species_t2_2($t2input, shift(@temp_tags));
-	}
-	undef (@temp_tags);
-	
-	#-------------------------------------------------------------------------------
-	#START SPUTNIK
-	
-	my @jobIDs = ();
-	@temp_tags = @tag;
-	my @sput_filelist = ();
-	
-	foreach my $sp (@presp_tags){
-		#print "sp = $sp\n";
-		my $sputnikoutput = $pipedir.$sp."_sput_op0";
-		my $sputnikinput = $pipedir.$sp."_nogap_op_unrand";
-		push(@sput_filelist, $sputnikinput);
-		my $sputnikcommand = $sputnikpath." ".$sputnikinput." > ".$sputnikoutput;
-		#print "$sputnikcommand\n";
-		my @sputnikcommand_system = $sputnikcommand;
-		system(@sputnikcommand_system);
-	}
-
-	#-------------------------------------------------------------------------------
-	#START SPUTNIK OUTPUT CORRECTOR
-	
-	foreach my $sp (@presp_tags){
-		my $corroutput = $pipedir.$sp."_sput_op1";
-		my $corrinput = $pipedir.$sp."_sput_op0";
-		sputnikoutput_corrector($corrinput,$corroutput);
-		
-		my $t4output = $pipedir.$sp."_sput_op2";
-		multi_species_t4($corroutput,$t4output);
-	
-		my $t5output = $pipedir.$sp."_sput_op3";
-		multi_species_t5($t4output,$t5output);
-		#print "done t5.pl for $sp\n";
-	
-		my $t6output = $pipedir.$sp."_sput_op4";
-		multi_species_t6($t5output,$t6output,scalar(@orgs));
-	}
-	#-------------------------------------------------------------------------------
-	#START T9.PL FOR T10.PL AND FOR INTERRUPTED HUNTING
-	
-	foreach my $sp (@presp_tags){
-		my $t9output = $pipedir.$sp."_gap_op_unrand_match";
-		my $t9sequence = $pipedir.$sp."_gap_op_unrand2";
-		my $t9micro = $pipedir.$sp."_sput_op4";
-		t9($t9micro,$t9sequence,$t9output);
-		
-		my $t9output2 = $pipedir.$sp."_nogap_op_unrand2_match";
-		my $t9sequence2 = $pipedir.$sp."_nogap_op_unrand2";
-		t9($t9micro,$t9sequence2,$t9output2);
-	}
-	#print "done both t9.pl for all orgs\n";
-
-	#-------------------------------------------------------------------------------
-	# FIND COMPOUND MICROSATELLITES
-	
-	@jobIDs = ();
-	my $species_counter = 0;
-	
-	foreach my $sp (@presp_tags){
-		my $simple_microsats=$pipedir.$sp."_sput_op4_simple";
-		my $compound_microsats=$pipedir.$sp."_sput_op4_compound";
-		my $input_micro = $pipedir.$sp."_sput_op4";
-		my $input_seq = $pipedir.$sp."_nogap_op_unrand2_match";
-		multiSpecies_compound_microsat_hunter3($input_micro,$input_seq,$simple_microsats,$compound_microsats,$orgs[$species_counter], scalar(@sp_tags), $threshold_array );
-		$species_counter++;
-	}
-	
-	#-------------------------------------------------------------------------------
-	# READING  AND FILTERING SIMPLE MICROSATELLITES
-	my $spcounter2=0;
-	foreach my $sp (@sp_tags){
-		my $presp = $presp_tags[$spcounter2];
-		$spcounter2++;
-		my $simple_microsats=$pipedir.$presp."_sput_op4_simple";
-		my $simple_filterout = $pipedir.$sp."_sput_op4_simple_filtered";
-		my $simple_residue = $pipedir.$sp."_sput_op4_simple_residue";
-		multiSpecies_filtering_interrupted_microsats($simple_microsats, $simple_filterout, $simple_residue,$threshold_array,$threshold_array,scalar(@sp_tags));
-	}
-	
-	#-------------------------------------------------------------------------------
-	# ANALYZE  COMPOUND MICROSATELLITES FOR BEING INTERRUPTED MICROSATS
-	
-	$species_counter = 0;
-	foreach my $sp (@sp_tags){
-		my $presp = $presp_tags[$species_counter];
-		my $compound_microsats = $pipedir.$presp."_sput_op4_compound";
-		my $analyzed_simple_microsats=$pipedir.$presp."_sput_op4_compound_interrupted";
-		my $analyzed_compound_microsats=$pipedir.$presp."_sput_op4_compound_pure";
-		my $seq_file = $pipedir.$presp."_nogap_op_unrand2_match";
-		multiSpecies_compound_microsat_analyzer($compound_microsats,$seq_file,$analyzed_simple_microsats,$analyzed_compound_microsats,$orgs[$species_counter], scalar(@sp_tags));
-		$species_counter++;
-	}
-	#-------------------------------------------------------------------------------
-	# REANALYZE COMPOUND MICROSATELLITES FOR PRESENCE OF SIMPLE ONES WITHIN THEM.. 
-	$species_counter = 0;
-	
-	foreach my $sp (@sp_tags){
-		my $presp = $presp_tags[$species_counter];
-		my $compound_microsats = $pipedir.$presp."_sput_op4_compound_pure";
-		my $compound_interrupted = $pipedir.$presp."_sput_op4_compound_clarifiedInterrupted";
-		my $compound_compound = $pipedir.$presp."_sput_op4_compound_compound";
-		my $seq_file = $pipedir.$presp."_nogap_op_unrand2_match";
-		multiSpecies_compoundClarifyer($compound_microsats,$seq_file,$compound_interrupted,$compound_compound,$orgs[$species_counter], scalar(@sp_tags), "2_4_6_8", "3_4_6_8", "2_4_6_8");
-		$species_counter++;
-	}
-	#-------------------------------------------------------------------------------
-	# READING  AND FILTERING SIMPLE AND COMPOUND MICROSATELLITES
-	$species_counter = 0;
-	
-	foreach my $sp (@sp_tags){
-		my $presp = $presp_tags[$species_counter];
-	
-		my $simple_microsats=$pipedir.$presp."_sput_op4_compound_clarifiedInterrupted";
-		my $simple_filterout = $pipedir.$sp."_sput_op4_compound_clarifiedInterrupted_filtered";
-		my $simple_residue = $pipedir.$sp."_sput_op4_compound_clarifiedInterrupted_residue";
-		multiSpecies_filtering_interrupted_microsats($simple_microsats, $simple_filterout, $simple_residue,$threshold_array,$threshold_array,scalar(@sp_tags));
-	
-		my $simple_microsats2 = $pipedir.$presp."_sput_op4_compound_interrupted";
-		my $simple_filterout2 = $pipedir.$sp."_sput_op4_compound_interrupted_filtered";
-		my $simple_residue2 = $pipedir.$sp."_sput_op4_compound_interrupted_residue";
-		multiSpecies_filtering_interrupted_microsats($simple_microsats2, $simple_filterout2, $simple_residue2,$threshold_array,$threshold_array,scalar(@sp_tags));
-	
-		my $compound_microsats=$pipedir.$presp."_sput_op4_compound_compound";
-		my $compound_filterout = $pipedir.$sp."_sput_op4_compound_compound_filtered";
-		my $compound_residue = $pipedir.$sp."_sput_op4_compound_compound_residue";
-		multispecies_filtering_compound_microsats($compound_microsats, $compound_filterout, $compound_residue,$threshold_array,$threshold_array,scalar(@sp_tags));
-		$species_counter++;
-	}
-	#print "done filtering both simple and compound microsatellites \n";
-	
-	#-------------------------------------------------------------------------------
-	
-	my @combinedarray = ();
-	my @combinedarray_indicators = ("mononucleotide", "dinucleotide", "trinucleotide", "tetranucleotide");
-	my @combinedarray_tags = ("mono", "di", "tri", "tetra");
-	$species_counter = 0;
-	
-	foreach my $sp (@sp_tags){
-		my $simple_interrupted = $pipedir.$sp."_simple_analyzed_simple";
-		push @{$combinedarray[$species_counter]}, $pipedir.$sp."_simple_analyzed_simple_mono", $pipedir.$sp."_simple_analyzed_simple_di", $pipedir.$sp."_simple_analyzed_simple_tri", $pipedir.$sp."_simple_analyzed_simple_tetra";
-		$species_counter++;
-	}
-	
-	#-------------------------------------------------------------------------------
-	# PUT TOGETHER THE INTERRUPTED AND SIMPLE MICROSATELLITES BASED ON THEIR MOTIF SIZE FOR FURTHER EXTENTION	
-	my $sp_counter = 0;
-	foreach my $sp (@sp_tags){	
-		my $analyzed_simple = $pipedir.$sp."_sput_op4_compound_interrupted_filtered";
-		my $clarifyed_simple = $pipedir.$sp."_sput_op4_compound_clarifiedInterrupted_filtered";
-		my $simple = $pipedir.$sp."_sput_op4_simple_filtered";
-		my $simple_analyzed_simple = $pipedir.$sp."_simple_analyzed_simple";
-		`cat $analyzed_simple $clarifyed_simple $simple > $simple_analyzed_simple`;
-		for my $i (0 ... 3){
-			`grep "$combinedarray_indicators[$i]" $simple_analyzed_simple > $combinedarray[$sp_counter][$i]`;	
+	foreach my $spec (@treespecies){
+		foreach my $espec (@exactspeciesset_unarranged){
+			push @exactspecies, $spec if $spec eq $espec;
 		}
-		$sp_counter++;		
 	}
-	#print "\ndone grouping interrupted & simple microsats based on their motif size for further extention\n";
-	
+	#print "exactspecies=@exactspecies\n";
+	$focalspec = $exactspecies[0];
+	my $arranged_species_set=join(".",@exactspecies);
+	my $chr_name = join(".",("chr".$p_chr),$arranged_species_set, "net", "axt");
+	my $chr_name_sputt = join(".",("chr".$p_chr),$arranged_species_set, "net", "axt_sputt");
+	#print "sending to maftoAxt_multispecies: $mafile, $tree_definition, $chr_name, $species_set .. focalspec=$focalspec \n"; 
+	maftoAxt_multispecies($mafile, $tree_definition, $chr_name, $species_set);
+	maftoAxt_multispecies($mafile_sputt, $tree_definition, $chr_name_sputt, $species_set);
+	#print "done maf to axt conversion\n";
+	my $reverse_chr_name = join(".",("chr".$p_chr."r"),$arranged_species_set, "net", "axt");
+	artificial_axdata_inverter ($chr_name, $reverse_chr_name);
+	#print "reverse_chr_name=$reverse_chr_name\n"; 
 	#-------------------------------------------------------------------------------
-	# BREAK CHROMOSOME INTO PARTS OF CERTAIN NO. CONTIGS EACH, FOR FUTURE SEARCHING OF INTERRUPTED MICROSATELLITES
-	# ESPECIALLY DI, TRI AND TETRANUCLEOTIDE MICROSATELLITES
-	@temp_tags = @sp_tags;
-	my $increment = 1000000;
-	my @splist = ();
-	my $targetdir = $pipedir;
-	$species_counter=0;
-	
-	foreach my $sp (@sp_tags){
-		my $presp = $presp_tags[$species_counter];
-		$species_counter++;
-		my $localtag = shift @temp_tags;
-		my $locallist = $targetdir.$localtag."_".$p_chr."_list";
-		push(@splist, $locallist);
-		my $input = $pipedir.$presp."_nogap_op_unrand2_match";
-		chromosome_unrand_breaker($input,$targetdir,$locallist,$increment, $localtag, $pchr);
-	}
-	
+	# FIND THE CORRESPONDING CHIMP CHROMOSOME FROM FILE ORTp_chrS.TXT
+	foreach my $direct ("reverse_direction","forward_direction"){
+		$p_chr=$chromt;
+		#print "direction = $direct\n";
+		$p_chr = $p_chr."r" if $direct eq "reverse_direction";
+		$p_chr = $p_chr if $direct eq "forward_direction";
+		my $config = $species_set;
+		$config=~s/,/./g;
+		my @orgs = split(/\./,$arranged_species_set);
+		#print "ORGS= @orgs\n";
+		my @tag=@orgs;
+			
+		
+		my $tags = join(",", @tag);
+		my @tags=@tag;
+		chomp $p_chr;
+		$tags = join("_", split(/,/, $tags));
+		my $pchr = "chr".$p_chr;
+		
+		my $ptag = $orgs[0]."-".$pchr.".".join(".",@orgs[1 ... scalar(@orgs)-1])."-".$threshold_array;
+		my @sp_tags = ();
+		
+#		print "$ptag _ orthfile\n"; <STDIN>;
 
-	my @unionarray = ();
-	#print "splist=@splist\n";
-	#-------------------------------------------------------------------------------
-	# FIND INTERRUPTED MICROSATELLITES
+		
+		#print "orgs=@orgs, pchr=$pchr, hence, ptag = $ptag\n";
+		foreach my $sp (@tag){
+			push(@sp_tags, ($sp.".".$ptag));
+		}
 	
-	$species_counter = 0;		
+		my $preptag = $orgs[0]."-".$pchr.".".join(".",@orgs[1 ... scalar(@orgs)-1]);
+		my @presp_tags = ();
+		
+		foreach my $sp (@tag){
+			push(@presp_tags, ($sp.".".$preptag));
+		}
 	
-	for my $i (0 .. $#combinedarray){
+		my $resultdir = "";
+		my $orthdir = "";
+		my $filtereddir = "";
+		my $pipedir = "";
+		
+		my @title_queries = ();
+		push(@title_queries, "^[0-9]+");
+		my $sep="\\s";
+		for my $or (0 ... $#orgs){
+			my $title =  join($sep, ($orgs[$or],  "[A-Za-z_]+[0-9a-zA-Z]+", "[0-9]+", "[0-9]+", "[\\-\\+]"));
+			#$title =~ s/chr\\+\\s+\+/chr/g;
+			push(@title_queries, $title);
+		}
+		my $title_query = join($sep, @title_queries);
+		#print "title_queries=@title_queries\n";
+		#print "query = >$title_query<\n"; 
+		#print "orgs = @orgs\n"; 
+		#-------------------------------------------------------------------------------
+		# GET AXTNET FILES, EDIT THEM AND SPLIT THEM INTO HUMAN AND CHIMP INPUT FILES
+		my $t1input = $pchr.".".$arranged_species_set.".net.axt";
+		
+		my @t1outputs = ();
+		
+		foreach my $sp (@presp_tags){
+			push(@t1outputs, $sp."_gap_op");
+		}
+		
+		
+		
+		multi_species_t1($t1input,$tags,(join(",", @t1outputs)), $title_query); 
+		#print "t1outputs=@t1outputs\n";
+		#print "done t1\n"; <STDIN>;
+		#-------------------------------------------------------------------------------
+		#START T2.PL
+		
+		my $stag  = (); my $tag1 = (); my $tag2 = ();  my $schrs = ();
+		
+		for my $t (0 ... scalar(@tags)-1){
+			multi_species_t2($t1outputs[$t], $tag[$t]);		
+		}
+		#-------------------------------------------------------------------------------
+		#START T2.2.PL
+		
+		my @temp_tags = @tag;
+		
+		foreach my $sp (@presp_tags){
+			my $t2input =  $sp."_nogap_op_unrand";
+			multi_species_t2_2($t2input, shift(@temp_tags));
+		}
+		undef (@temp_tags);
+		
+		#-------------------------------------------------------------------------------
+		#START SPUTNIK
+		
+		my @jobIDs = ();
+		@temp_tags = @tag;
+		my @sput_filelist = ();
+		
+		foreach my $sp (@presp_tags){
+			#print "sp = $sp\n";
+			my $sputnikoutput = $pipedir.$sp."_sput_op0";
+			my $sputnikinput = $pipedir.$sp."_nogap_op_unrand";
+			push(@sput_filelist, $sputnikinput);
+			my $sputnikcommand = $sputnikpath." ".$sputnikinput." > ".$sputnikoutput;
+			#print "$sputnikcommand\n";
+			my @sputnikcommand_system = $sputnikcommand;
+			system(@sputnikcommand_system);
+		}
+	
+		#-------------------------------------------------------------------------------
+		#START SPUTNIK OUTPUT CORRECTOR
+		
+		foreach my $sp (@presp_tags){
+			my $corroutput = $pipedir.$sp."_sput_op1";
+			my $corrinput = $pipedir.$sp."_sput_op0";
+			sputnikoutput_corrector($corrinput,$corroutput);
+			
+			my $t4output = $pipedir.$sp."_sput_op2";
+			multi_species_t4($corroutput,$t4output);
+		
+			my $t5output = $pipedir.$sp."_sput_op3";
+			multi_species_t5($t4output,$t5output);
+			#print "done t5.pl for $sp\n";
+		
+			my $t6output = $pipedir.$sp."_sput_op4";
+			multi_species_t6($t5output,$t6output,scalar(@orgs));
+		}
+		#-------------------------------------------------------------------------------
+		#START T9.PL FOR T10.PL AND FOR INTERRUPTED HUNTING
+		
+		foreach my $sp (@presp_tags){
+			my $t9output = $pipedir.$sp."_gap_op_unrand_match";
+			my $t9sequence = $pipedir.$sp."_gap_op_unrand2";
+			my $t9micro = $pipedir.$sp."_sput_op4";
+			t9($t9micro,$t9sequence,$t9output);
+			
+			my $t9output2 = $pipedir.$sp."_nogap_op_unrand2_match";
+			my $t9sequence2 = $pipedir.$sp."_nogap_op_unrand2";
+			t9($t9micro,$t9sequence2,$t9output2);
+		}
+		#print "done both t9.pl for all orgs\n";
+	
+		#-------------------------------------------------------------------------------
+		# FIND COMPOUND MICROSATELLITES
 		
 		@jobIDs = ();
-		open (JLIST1, "$splist[$i]") or die "Cannot open file $splist[$i]: $!";
+		my $species_counter = 0;
 		
-		while (my $sp1  = <JLIST1>){
-			#print "$splist[$i]: sp1=$sp1\n";
-			chomp $sp1;
+		foreach my $sp (@presp_tags){
+			my $simple_microsats=$pipedir.$sp."_sput_op4_simple";
+			my $compound_microsats=$pipedir.$sp."_sput_op4_compound";
+			my $input_micro = $pipedir.$sp."_sput_op4";
+			my $input_seq = $pipedir.$sp."_nogap_op_unrand2_match";
+			multiSpecies_compound_microsat_hunter3($input_micro,$input_seq,$simple_microsats,$compound_microsats,$orgs[$species_counter], scalar(@sp_tags), $threshold_array );
+			$species_counter++;
+		}
+		
+		#-------------------------------------------------------------------------------
+		# READING  AND FILTERING SIMPLE MICROSATELLITES
+		my $spcounter2=0;
+		foreach my $sp (@sp_tags){
+			my $presp = $presp_tags[$spcounter2];
+			$spcounter2++;
+			my $simple_microsats=$pipedir.$presp."_sput_op4_simple";
+			my $simple_filterout = $pipedir.$sp."_sput_op4_simple_filtered";
+			my $simple_residue = $pipedir.$sp."_sput_op4_simple_residue";
+			multiSpecies_filtering_interrupted_microsats($simple_microsats, $simple_filterout, $simple_residue,$threshold_array,$threshold_array,scalar(@sp_tags));
+		}
+		
+		#-------------------------------------------------------------------------------
+		# ANALYZE  COMPOUND MICROSATELLITES FOR BEING INTERRUPTED MICROSATS
+		
+		$species_counter = 0;
+		foreach my $sp (@sp_tags){
+			my $presp = $presp_tags[$species_counter];
+			my $compound_microsats = $pipedir.$presp."_sput_op4_compound";
+			my $analyzed_simple_microsats=$pipedir.$presp."_sput_op4_compound_interrupted";
+			my $analyzed_compound_microsats=$pipedir.$presp."_sput_op4_compound_pure";
+			my $seq_file = $pipedir.$presp."_nogap_op_unrand2_match";
+			multiSpecies_compound_microsat_analyzer($compound_microsats,$seq_file,$analyzed_simple_microsats,$analyzed_compound_microsats,$orgs[$species_counter], scalar(@sp_tags));
+			$species_counter++;
+		}
+		#-------------------------------------------------------------------------------
+		# REANALYZE COMPOUND MICROSATELLITES FOR PRESENCE OF SIMPLE ONES WITHIN THEM.. 
+		$species_counter = 0;
+		
+		foreach my $sp (@sp_tags){
+			my $presp = $presp_tags[$species_counter];
+			my $compound_microsats = $pipedir.$presp."_sput_op4_compound_pure";
+			my $compound_interrupted = $pipedir.$presp."_sput_op4_compound_clarifiedInterrupted";
+			my $compound_compound = $pipedir.$presp."_sput_op4_compound_compound";
+			my $seq_file = $pipedir.$presp."_nogap_op_unrand2_match";
+			multiSpecies_compoundClarifyer($compound_microsats,$seq_file,$compound_interrupted,$compound_compound,$orgs[$species_counter], scalar(@sp_tags), "2_4_6_8", "3_4_6_8", "2_4_6_8");
+			$species_counter++;
+		}
+		#-------------------------------------------------------------------------------
+		# READING  AND FILTERING SIMPLE AND COMPOUND MICROSATELLITES
+		$species_counter = 0;
+		
+		foreach my $sp (@sp_tags){
+			my $presp = $presp_tags[$species_counter];
+		
+			my $simple_microsats=$pipedir.$presp."_sput_op4_compound_clarifiedInterrupted";
+			my $simple_filterout = $pipedir.$sp."_sput_op4_compound_clarifiedInterrupted_filtered";
+			my $simple_residue = $pipedir.$sp."_sput_op4_compound_clarifiedInterrupted_residue";
+			multiSpecies_filtering_interrupted_microsats($simple_microsats, $simple_filterout, $simple_residue,$threshold_array,$threshold_array,scalar(@sp_tags));
+		
+			my $simple_microsats2 = $pipedir.$presp."_sput_op4_compound_interrupted";
+			my $simple_filterout2 = $pipedir.$sp."_sput_op4_compound_interrupted_filtered";
+			my $simple_residue2 = $pipedir.$sp."_sput_op4_compound_interrupted_residue";
+			multiSpecies_filtering_interrupted_microsats($simple_microsats2, $simple_filterout2, $simple_residue2,$threshold_array,$threshold_array,scalar(@sp_tags));
+		
+			my $compound_microsats=$pipedir.$presp."_sput_op4_compound_compound";
+			my $compound_filterout = $pipedir.$sp."_sput_op4_compound_compound_filtered";
+			my $compound_residue = $pipedir.$sp."_sput_op4_compound_compound_residue";
+			multispecies_filtering_compound_microsats($compound_microsats, $compound_filterout, $compound_residue,$threshold_array,$threshold_array,scalar(@sp_tags));
+			$species_counter++;
+		}
+		#print "done filtering both simple and compound microsatellites \n";
+		
+		#-------------------------------------------------------------------------------
+		
+		my @combinedarray = ();
+		my @combinedarray_indicators = ("mononucleotide", "dinucleotide", "trinucleotide", "tetranucleotide");
+		my @combinedarray_tags = ("mono", "di", "tri", "tetra");
+		$species_counter = 0;
+		
+		foreach my $sp (@sp_tags){
+			my $simple_interrupted = $pipedir.$sp."_simple_analyzed_simple";
+			push @{$combinedarray[$species_counter]}, $pipedir.$sp."_simple_analyzed_simple_mono", $pipedir.$sp."_simple_analyzed_simple_di", $pipedir.$sp."_simple_analyzed_simple_tri", $pipedir.$sp."_simple_analyzed_simple_tetra";
+			$species_counter++;
+		}
+		
+		#-------------------------------------------------------------------------------
+		# PUT TOGETHER THE INTERRUPTED AND SIMPLE MICROSATELLITES BASED ON THEIR MOTIF SIZE FOR FURTHER EXTENTION	
+		my $sp_counter = 0;
+		foreach my $sp (@sp_tags){	
+			my $analyzed_simple = $pipedir.$sp."_sput_op4_compound_interrupted_filtered";
+			my $clarifyed_simple = $pipedir.$sp."_sput_op4_compound_clarifiedInterrupted_filtered";
+			my $simple = $pipedir.$sp."_sput_op4_simple_filtered";
+			my $simple_analyzed_simple = $pipedir.$sp."_simple_analyzed_simple";
+			`cat $analyzed_simple $clarifyed_simple $simple > $simple_analyzed_simple`;
+			for my $i (0 ... 3){
+				`grep "$combinedarray_indicators[$i]" $simple_analyzed_simple > $combinedarray[$sp_counter][$i]`;	
+			}
+			$sp_counter++;		
+		}
+		#print "\ndone grouping interrupted & simple microsats based on their motif size for further extention\n";
+		
+		#-------------------------------------------------------------------------------
+		# BREAK CHROMOSOME INTO PARTS OF CERTAIN NO. CONTIGS EACH, FOR FUTURE SEARCHING OF INTERRUPTED MICROSATELLITES
+		# ESPECIALLY DI, TRI AND TETRANUCLEOTIDE MICROSATELLITES
+		@temp_tags = @sp_tags;
+		my $increment = 1000000;
+		my @splist = ();
+		my $targetdir = $pipedir;
+		$species_counter=0;
+		
+		foreach my $sp (@sp_tags){
+			my $presp = $presp_tags[$species_counter];
+			$species_counter++;
+			my $localtag = shift @temp_tags;
+			my $locallist = $targetdir.$localtag."_".$p_chr."_list";
+			push(@splist, $locallist);
+			my $input = $pipedir.$presp."_nogap_op_unrand2_match";
+			chromosome_unrand_breaker($input,$targetdir,$locallist,$increment, $localtag, $pchr);
+		}
+		
+	
+		my @unionarray = ();
+		#print "splist=@splist\n";
+		#-------------------------------------------------------------------------------
+		# FIND INTERRUPTED MICROSATELLITES
+		
+		$species_counter = 0;		
+		
+		for my $i (0 .. $#combinedarray){
 			
-			for my $j (0 ... $#combinedarray_tags){
-				my $interr  = $sp1."_interr_".$combinedarray_tags[$j];
-				my $simple  = $sp1."_simple_".$combinedarray_tags[$j];
-				push @{$unionarray[$i]}, $interr, $simple;	
-				multiSpecies_interruptedMicrosatHunter($combinedarray[$i][$j],$sp1,$interr ,$simple, $orgs[$species_counter], scalar(@sp_tags), "3_4_6_8"); 
-			}		
+			@jobIDs = ();
+			open (JLIST1, "$splist[$i]") or die "Cannot open file $splist[$i]: $!";
+			
+			while (my $sp1  = <JLIST1>){
+				#print "$splist[$i]: sp1=$sp1\n";
+				chomp $sp1;
+				
+				for my $j (0 ... $#combinedarray_tags){
+					my $interr  = $sp1."_interr_".$combinedarray_tags[$j];
+					my $simple  = $sp1."_simple_".$combinedarray_tags[$j];
+					push @{$unionarray[$i]}, $interr, $simple;	
+					multiSpecies_interruptedMicrosatHunter($combinedarray[$i][$j],$sp1,$interr ,$simple, $orgs[$species_counter], scalar(@sp_tags), "3_4_6_8"); 
+				}		
+			}
+			$species_counter++;
 		}
-		$species_counter++;
-	}
-	close JLIST1;	
-	#-------------------------------------------------------------------------------
-	#	REUNION AND ZIPPING BEFORE T10.PL
-	
-	my @allarray = ();
-	
-	for my $i (0 ... $#sp_tags){	
-		my $localfile = $pipedir.$sp_tags[$i]."_allmicrosats";
-		unlink $localfile if -e $localfile;
-		push(@allarray, $localfile);
-	
-		my $unfiltered_localfile= $localfile."_unfiltered";
-		my $residue_localfile= $localfile."_residue";
+		close JLIST1;	
+		#-------------------------------------------------------------------------------
+		#	REUNION AND ZIPPING BEFORE T10.PL
 		
-		unlink $unfiltered_localfile;
-		#unlink $unfiltered_localfile;
-		for my $j (0 ... $#{$unionarray[$i]}){
-			#print "listing files for species $i  and list number $j= \n$unionarray[$i][$j] \n";
-			`cat $unionarray[$i][$j] >> $unfiltered_localfile`;
-			unlink $unionarray[$i][$j];
+		my @allarray = ();
+		
+		for my $i (0 ... $#sp_tags){	
+			my $localfile = $pipedir.$sp_tags[$i]."_allmicrosats";
+			unlink $localfile if -e $localfile;
+			push(@allarray, $localfile);
+		
+			my $unfiltered_localfile= $localfile."_unfiltered";
+			my $residue_localfile= $localfile."_residue";
+			
+			unlink $unfiltered_localfile;
+			#unlink $unfiltered_localfile;
+			for my $j (0 ... $#{$unionarray[$i]}){
+				#print "listing files for species $i  and list number $j= \n$unionarray[$i][$j] \n";
+				`cat $unionarray[$i][$j] >> $unfiltered_localfile`;
+				unlink $unionarray[$i][$j];
+			}
+	
+			multiSpecies_filtering_interrupted_microsats($unfiltered_localfile, $localfile, $residue_localfile,$threshold_array,$threshold_array,scalar(@sp_tags) );
+			my $analyzed_compound = $pipedir.$sp_tags[$i]."_sput_op4_compound_compound_filtered";
+			my $simple_residue = $pipedir.$sp_tags[$i]."_sput_op4_simple_residue";
+			my $compound_residue = $pipedir.$sp_tags[$i]."_sput_op4_compound_residue";
+			
+			`cat $analyzed_compound >> $localfile`;
 		}
+		#-------------------------------------------------------------------------------
+		# MERGING MICROSATELLITES THAT ARE VERY CLOSE TO EACH OTHER, INCLUDING THOSE FOUND BY SEARCHING IN 2 OPPOSIT DIRECTIONS
+		
+		my $toescape=0;
+		
+		
+		for my $i (0 ... $#sp_tags){	
+			my $localfile = $pipedir.$sp_tags[$i]."_allmicrosats";
+			$localfile =~ /$focalspec\-(chr[0-9a-zA-Z]+)\./;
+			my $direction = $1;
+			#print "localfile = $localfile , direction = $direction\n"; 
+	#		`gzip $reverse_chr_name` if $direction =~ /chr[0-9a-zA-Z]+r/ && $switchboard{"deleting_processFiles"} != 1;
+			$toescape =1 if $direction =~ /chr[0-9a-zA-Z]+r/;
+			last if $direction =~ /chr[0-9a-zA-Z]+r/;
+			my $nogap_sequence = $pipedir.$presp_tags[$i]."_nogap_op_unrand2_match";
+			my $gap_sequence = $pipedir.$presp_tags[$i]."_gap_op_unrand_match";
+			my $reverselocal = $localfile;
+			$reverselocal =~ s/\-chr([0-9a-zA-Z]+)\./-chr$1r./g;
+			merge_interruptedMicrosats($nogap_sequence,$localfile, $reverselocal ,scalar(@sp_tags)); 
+			#-------------------------------------------------------------------------------
+			my $forward_separate = $localfile."_separate";
+			my $reverse_separate = $reverselocal."_separate";
+			my $diff = $forward_separate."_diff";
+			my $miss = $forward_separate."_miss";
+			my $common = $forward_separate."_common";
+			forward_reverse_sputoutput_comparer($nogap_sequence,$forward_separate, $reverse_separate, $diff, $miss, $common ,scalar(@sp_tags)); 
+			#-------------------------------------------------------------------------------
+			my $symmetrical_file = $localfile."_symmetrical";
+			my $merged_file = $localfile."_merged";
+			#print "cating: $merged_file $common  into -> $symmetrical_file \n"; 
+			`cat $merged_file $common > $symmetrical_file`;
+			#-------------------------------------------------------------------------------
+			my $t10output = $symmetrical_file."_fin_hit_all_2";
+			new_multispecies_t10($gap_sequence, $symmetrical_file, $t10output, join(".", @orgs));
+			#-------------------------------------------------------------------------------		
+		}
+		next if $toescape == 1;
+		#------------------------------------------------------------------------------------------------
+		# BRINGING IT ALL TOGETHER: FINDING ORTHOLOGOUS MICROSATELLITES AMONG THE SPECIES
+		
+		
+		my @micros_array = ();
+		my $sampletag = ();
+		for my $i (0 ... $#sp_tags){
+			my $finhitFile = $pipedir.$sp_tags[$i]."_allmicrosats_symmetrical_fin_hit_all_2";
+			push(@micros_array, $finhitFile);
+			$sampletag = $sp_tags[$i];
+		}
+		#$sampletag =~ s/^([A-Z]+\.)/ORTH_/;
+		#$sampletag = $sampletag."_monoThresh-".$mono_threshold."bp";
+		my $orthfiletemp = $ptag."_orthfile";
+		my $orthanswer = multiSpecies_orthFinder4($t1input, join(":",@micros_array), $orthfiletemp, join(":", @orgs), $separation);
 
-		multiSpecies_filtering_interrupted_microsats($unfiltered_localfile, $localfile, $residue_localfile,$threshold_array,$threshold_array,scalar(@sp_tags) );
-		my $analyzed_compound = $pipedir.$sp_tags[$i]."_sput_op4_compound_compound_filtered";
-		my $simple_residue = $pipedir.$sp_tags[$i]."_sput_op4_simple_residue";
-		my $compound_residue = $pipedir.$sp_tags[$i]."_sput_op4_compound_residue";
-		
-		`cat $analyzed_compound >> $localfile`;
+		my $maskedorthfiletemp = $ptag."_orthfile_masked";
+		qualityFilter ($orthfiletemp, $chr_name_sputt, $maskedorthfiletemp);
+
+		push @outputfiles , $maskedorthfiletemp;
 	}
-	#-------------------------------------------------------------------------------
-	# MERGING MICROSATELLITES THAT ARE VERY CLOSE TO EACH OTHER, INCLUDING THOSE FOUND BY SEARCHING IN 2 OPPOSIT DIRECTIONS
-	
-	my $toescape=0;
-	
-	
-	for my $i (0 ... $#sp_tags){	
-		my $localfile = $pipedir.$sp_tags[$i]."_allmicrosats";
-		$localfile =~ /$focalspec\-(chr[0-9a-zA-Z]+)\./;
-		my $direction = $1;
-		#print "localfile = $localfile , direction = $direction\n"; 
-#		`gzip $reverse_chr_name` if $direction =~ /chr[0-9a-zA-Z]+r/ && $switchboard{"deleting_processFiles"} != 1;
-		$toescape =1 if $direction =~ /chr[0-9a-zA-Z]+r/;
-		last if $direction =~ /chr[0-9a-zA-Z]+r/;
-		my $nogap_sequence = $pipedir.$presp_tags[$i]."_nogap_op_unrand2_match";
-		my $gap_sequence = $pipedir.$presp_tags[$i]."_gap_op_unrand_match";
-		my $reverselocal = $localfile;
-		$reverselocal =~ s/\-chr([0-9a-zA-Z]+)\./-chr$1r./g;
-		merge_interruptedMicrosats($nogap_sequence,$localfile, $reverselocal ,scalar(@sp_tags)); 
-		#-------------------------------------------------------------------------------
-		my $forward_separate = $localfile."_separate";
-		my $reverse_separate = $reverselocal."_separate";
-		my $diff = $forward_separate."_diff";
-		my $miss = $forward_separate."_miss";
-		my $common = $forward_separate."_common";
-		forward_reverse_sputoutput_comparer($nogap_sequence,$forward_separate, $reverse_separate, $diff, $miss, $common ,scalar(@sp_tags)); 
-		#-------------------------------------------------------------------------------
-		my $symmetrical_file = $localfile."_symmetrical";
-		my $merged_file = $localfile."_merged";
-		#print "cating: $merged_file $common  into -> $symmetrical_file \n"; 
-		`cat $merged_file $common > $symmetrical_file`;
-		#-------------------------------------------------------------------------------
-		my $t10output = $symmetrical_file."_fin_hit_all_2";
-		new_multispecies_t10($gap_sequence, $symmetrical_file, $t10output, join(".", @orgs));
-		#-------------------------------------------------------------------------------		
-	}
-	next if $toescape == 1;
-	#------------------------------------------------------------------------------------------------
-	# BRINGING IT ALL TOGETHER: FINDING ORTHOLOGOUS MICROSATELLITES AMONG THE SPECIES
-	
-	
-	my @micros_array = ();
-	my $sampletag = ();
-	for my $i (0 ... $#sp_tags){
-		my $finhitFile = $pipedir.$sp_tags[$i]."_allmicrosats_symmetrical_fin_hit_all_2";
-		push(@micros_array, $finhitFile);
-		$sampletag = $sp_tags[$i];
-	}
-	#$sampletag =~ s/^([A-Z]+\.)/ORTH_/;
-	#$sampletag = $sampletag."_monoThresh-".$mono_threshold."bp";
-	my $orthanswer = multiSpecies_orthFinder4($t1input, join(":",@micros_array), $orthfile, join(":", @orgs), $separation);
+	$date = `date`;
 }
-$date = `date`;
+
+`cat @outputfiles > $orthfile`;
+
 #print "date = $date\n";
 #remove_tree($tdir);
 #------------------------------------------------------------------------------------------------
@@ -492,10 +524,10 @@ sub maftoAxt_multispecies {
 	my $outsideSpecies=0;
 	
 	while(my $line = <IN>){
+#		print $line;
 		next if $line =~ /^#/;
 		next if $line =~ /^i/;
 		chomp $line;
-		#print "$line";
 		my @fields = split(/\s+/,$line);
 		chomp $line;
 		if ($line =~ /^a /){
@@ -503,39 +535,48 @@ sub maftoAxt_multispecies {
 		}
 		
 		if ($line =~ /^s /){
-		#	print "fields1 = $fields[1] , start = $start\n";
 		
-			foreach my $sp (@species){
+			foreach my $sp (@allspecies){
+#				print "checking species $sp\n";
 				if ($fields[1] =~ /$sp/){
 					$species_counter = $species_counter."_".$sp;
 					push(@sequences, $fields[6]);
 					my @sp_info = split(/\./,$fields[1]);
 					my $title = join(" ",@sp_info, $fields[2], ($fields[2]+$fields[3]), $fields[4]);
 					push(@titles, $title);				
-					
+#					print "species_counter = $species_counter\n";
 				}
 			}
 		}
 		
 		if (($line !~ /^a/) && ($line !~ /^s/) && ($line !~ /^#/) && ($line !~ /^i/) && ($start = 1)){
-			my $arranged = reorderSpecies($species_counter, @species);
+#			print "species_counter = $species_counter\n"; 
+			my $arranged = reorderSpecies($species_counter, @allspecies);
 			my $stopper = 1;
 			my $arrno = 0;
-			foreach my $set (@allowedset){
-				if ($arranged eq $set){
-	#				print "$arranged == $set\n";
-					$stopper = 0; last;
+			
+#			print "checking if ", scalar(@sequences), " match @exactspecies allowedset=@allowedset\n";
+			if (scalar(@sequences) == scalar(@exactspecies)){
+				foreach my $set (@allowedset){
+#					print "testing $arranged against $set\n";
+					if ($arranged eq $set){
+						$stopper = 0; last;
+					}
+					$arrno++;
 				}
-				$arrno++;
 			}
-	
+			else{
+				$stopper = 1;
+			}
+			
+			
 			if ($stopper == 0) {
-			#	print "    accepted\n";
 				@titles = split ";", orderInfo(join(";", @titles), $species_counter, $arranged) if $species_counter ne $arranged;				
 				@sequences = split ";", orderInfo(join(";", @sequences), $species_counter, $arranged) if $species_counter ne $arranged;				
 				my $filteredseq = filter_gaps(@sequences);
 				
 				if ($filteredseq ne "SHORT"){
+					#print "printing"; <STDIN>;
 					$counter++;
 					print OUT join (" ",$counter, @titles), "\n";
 					print OUT $filteredseq, "\n";
@@ -543,7 +584,7 @@ sub maftoAxt_multispecies {
 					$countermatch++;
 				}
 			}
-			else{#print "\n";
+			else{ #print "nexting\n";<STDIN>;
 			}
 	
 			@sequences = (); @titles = (); $start = 0;$species_counter = "0";
@@ -559,6 +600,7 @@ sub reorderSpecies{
 	my $currSpecies = shift (@inarr);
 	my $ordered_species = 0;
 	my @species=@inarr;
+	#print "species = @species\n";
 	foreach my $order (@species){
 		$ordered_species = $ordered_species."_".$order	if	$currSpecies=~ /$order/;
 	}
@@ -687,7 +729,7 @@ sub artificial_axdata_inverter{
 sub multi_species_t1 {
 
 	my $input1 = $_[0];
-#	print "@_\n"; #<STDIN>;
+	#print "@_\n"; <STDIN>;
 	my @tags = split(/_/, $_[1]);
 	my @outputs = split(/,/, $_[2]);
 	my $title_query = $_[3];
@@ -778,8 +820,8 @@ sub multi_species_t2{
 		my $line = $_;
 		chomp($line);
 		my @fields=split (/\t/, $line);
-	#   print $line,"\n";
-		if($fields[5] ne "chrUn_random"){
+	  #  print $line,"\n"; <STDIN>;
+		if($line !~ /random/){
 			print FILEF3 join ("\t",@fields[0 ... scalar(@fields)-2]), "\n", $fields[scalar(@fields)-1], "\n";
 			print FILEF4 join ("\t",@fields[0 ... scalar(@fields)-2]), "\t", $fields[scalar(@fields)-1], "\n";	
 		}
@@ -1061,7 +1103,7 @@ sub t9{
 		while (my $line = <IN1>){
 			chomp($line);
 			my @fields = split(/\t/,$line);
-			my $key1 = join ("_",@fields[0,1,3,4,5]);
+			my $key1 = join ("_K10K1_",@fields[0,1,3,4,5]);
 		#	print "key in t9 = $key1\n";
 			$seen{$key1}++	if ($prevkey ne $key1) ;
 			$prevkey = $key1;
@@ -1075,7 +1117,7 @@ sub t9{
 		if (-e $input1){
 			chomp($line);
 			my @fields = split(/\t/,$line);
-			my $key2 = join ("_",@fields[0,1,3,4,5]);
+			my $key2 = join ("_K10K1_",@fields[0,1,3,4,5]);
 			if (exists $seen{$key2}){
 				print OUT "$line\n"	;
 				delete $seen{$key2};
@@ -1083,6 +1125,7 @@ sub t9{
 		}
 		else {
 			print OUT "$line\n"	;		
+#			print  "$line\n"	;		
 		}
 	}
 	
@@ -1125,7 +1168,7 @@ sub multiSpecies_compound_microsat_hunter3{
 	while (my $line = <IN>){
 	#	print "$org\t(chr[0-9]+)\t([0-9]+)\t([0-9])+\t \n";
 		next if $line =~ /\t\t/;
-		if ($line =~ /^>[A-Za-z0-9]+\s+([0-9]+)\s+([a-zA-Z0-9]+)\s([a-zA-Z]+[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)\s/ ) {
+		if ($line =~ /^>[A-Za-z0-9_]+\s+([0-9]+)\s+([a-zA-Z0-9]+)\s([a-zA-Z]+[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)\s/ ) {
 			my $key = join("\t",$1, $2, $3, $4, $5);
 		#	print $key, "#-#-#-#-#-#-#-#\n";
 			push (@{$micros{$key}},$line);		
@@ -1507,7 +1550,7 @@ sub multiSpecies_compound_microsat_analyzer{
 	my $linecounter=0;
 	while (my $line = <IN>){
 		$linecounter++;
-		if ($line =~ /([0-9a-zA-Z]+)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)\s([0-9a-zA-Z]+)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)\s([0-9a-zA-Z]+)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)\s/ ) {
+		if ($line =~ /([0-9a-zA-Z]+)\s([0-9a-zA-Z_]+)\s([0-9]+)\s([0-9]+)\s([0-9a-zA-Z]+)\s([0-9a-zA-Z_]+)\s([0-9]+)\s([0-9]+)\s([0-9a-zA-Z]+)\s([0-9a-zA-Z_]+)\s([0-9]+)\s([0-9]+)\s/ ) {
 			my $key = join("\t",$1, $2, $3, $4, $5, $6, $7, $8, $9, $10, $11, $12);
 			push (@{$micros{$key}},$line);		
 			$keycounter++;
@@ -1530,14 +1573,18 @@ sub multiSpecies_compound_microsat_analyzer{
 		my %microstart=();
 		my %microend=();
 		my @sields = split(/\t/,$sine);
-		my $key = ();
-		if ($sine =~ /([0-9a-zA-Z]+)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)\s[\+|\-]\s([0-9a-zA-Z]+)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)\s[\+|\-]\s([0-9a-zA-Z]+)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)\s/ ) {
+		my $key = 0;
+		if ($sine =~ /([0-9a-zA-Z]+)\s([0-9a-zA-Z_]+)\s([0-9]+)\s([0-9]+)\s[\+|\-]\s([0-9a-zA-Z]+)\s([0-9a-zA-Z_]+)\s([0-9]+)\s([0-9]+)\s[\+|\-]\s([0-9a-zA-Z]+)\s([0-9a-zA-Z_]+)\s([0-9]+)\s([0-9]+)\s/ ) {
 			$key = join("\t",$1, $2, $3, $4, $5, $6, $7, $8, $9, $10, $11, $12);
+		#	print $sine;
+		#	print $key;
 			$keyfound++;
 		}
 		else{
 		
 		}
+		#<STDIN> if !defined $key;
+
 		if (exists $micros{$key}){
 			$keyexists++;
 			my @microstring = @{$micros{$key}};
@@ -1689,13 +1736,15 @@ sub multiSpecies_compoundClarifyer{
 	while (my $line = <IN>){
 	#	print "$org\t(chr[0-9a-zA-Z]+)\t([0-9]+)\t([0-9])+\t \n";
 		$linecounter++;
-		if ($line =~ /([a-zA-Z0-9]+)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)\s([a-zA-Z0-9]+)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)\s([a-zA-Z0-9]+)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)\s/ ) {
-			my $key = join("\t",$1, $2, $3, $4, $5, $6, $7, $8, $9, $10, $11, $12);
+		if ($line =~ /($focalspec)\s+([0-9a-zA-Z_\-]+)\s+([0-9]+)\s+([0-9]+)/ ) {
+			my $key = join("\t",$1, $2, $3, $4);
 	#		print $key, "#-#-#-#-#-#-#-#\n";
+	#		print "key = $key\n";
 			push (@{$micros{$key}},$line);	
 			$microcounter++;
 		}
-		else {print $line;}
+		else {#print $line," key not made\n"; <STDIN>;
+			}
 	}
 #	print "number of microsatellites added to hash = $microcounter\nnumber of lines scanned = $linecounter\n";
 	close IN;
@@ -1712,8 +1761,14 @@ sub multiSpecies_compoundClarifyer{
 		my %microend=();
 		my @sields = split(/\t/,$sine);
 		my $key = ();
-		if ($sine =~ /([a-z0-9A-Z]+)\s+(chr[0-9a-zA-Z]+)\s+([0-9]+)\s+([0-9]+)\s+[\+|\-]\s+([a-z0-9A-Z]+)\s+(chr[0-9a-zA-Z]+)\s+([0-9]+)\s+([0-9]+)\s+[\+|\-]\s+([a-z0-9A-Z]+)\s+(chr[0-9a-zA-Z]+)\s+([0-9]+)\s+([0-9]+)\s/ ) {
-			$key = join("\t",$1, $2, $3, $4, $5, $6, $7, $8, $9, $10, $11, $12);
+		
+#		print "sine = $sine. focalspec = $focalspec \n"; #<STDIN>;
+		
+		if ($sine =~ /($focalspec)\s+([0-9a-zA-Z_\-]+)\s+([0-9]+)\s+([0-9]+)/ ) {
+			
+#			if ($sine =~ /([a-z0-9A-Z]+)\s+([0-9a-zA-Z_]+)\s+([0-9]+)\s+([0-9]+)\s+[\+|\-]\s+([a-z0-9A-Z]+)\s+([0-9a-zA-Z_]+)\s+([0-9]+)\s+([0-9]+)\s+[\+|\-]\s+([a-z0-9A-Z]+)\s+([0-9a-zA-Z_]+)\s+([0-9]+)\s+([0-9]+)\s/ ) {
+			$key = join("\t",$1, $2, $3, $4);
+#			print "key = $key\n";
 		}
 		else{
 #			print "no key in $sine\nfor pattern ([a-z0-9A-Z]+) (chr[0-9a-zA-Z]+) ([0-9]+) ([0-9]+) [\+|\-] (a-z0-9A-Z) (chr[0-9a-zA-Z]+) ([0-9]+) ([0-9]+) [\+|\-] (a-z0-9A-Z) (chr[0-9a-zA-Z]+) ([0-9]+) ([0-9]+)   / \n"; 
@@ -1726,7 +1781,7 @@ sub multiSpecies_compoundClarifyer{
 			foreach my $line (@microstring){
 #				print "#---------#---------#---------#---------#---------#---------#---------#---------\n" if $printer == 1; 
 #				print "microsat = $line" if $printer == 1; 
-				$linecounter++;
+				$linecounter++; 
 				my $copy_line = $line;
 				my @mields = split(/\t/,$line);
 				my @fields = @mields;
@@ -1944,7 +1999,8 @@ sub multiSpecies_compoundClarifyer{
 					if ($tempfields[$startcord] != $fields[$startcord]) {
 						$leftmotif = $motields[$left_captured]; 
 #						print "$left_captured in @microields: $motields[$left_captured]\n" if $printer == 1; 
-						if ( $left_captured !~ /[0-9]+/) {print $line,"\n", $templine,"\n"; }
+						if ( $left_captured !~ /[0-9]+/) {#print $line,"\n", $templine,"\n"; 
+						}
 						 $left_trashed = length($microields[$left_captured]) - $left_bp;
 					}
 					my $rightmotif = (); my $right_trashed = ();
@@ -2689,7 +2745,7 @@ sub multiSpecies_interruptedMicrosatHunter{
 	while (my $line = <IN>){
 	#	print "$org\t(chr[0-9a-zA-Z]+)\t([0-9]+)\t([0-9])+\t \n";
 		$linecounter++;
-		if ($line =~ /^>[A-Za-z0-9]+\s+([0-9]+)\s+([0-9a-zA-Z]+)\s+(chr[0-9a-zA-Z]+)\s([0-9]+)\s+([0-9]+)\s/ ) {
+		if ($line =~ /^>[A-Za-z0-9]+\s+([0-9]+)\s+([0-9a-zA-Z]+)\s+([0-9a-zA-Z_]+)\s([0-9]+)\s+([0-9]+)\s/ ) {
 			my $key = join("\t",$1, $2, $3, $4, $5);
 		#	print $key, "#-#-#-#-#-#-#-#\n" if $prinkter == 1;
 			push (@{$micros{$key}},$line);	
@@ -2711,7 +2767,7 @@ sub multiSpecies_interruptedMicrosatHunter{
 		my %microend=();
 		my @sields = split(/\t/,$sine);
 		my $key = ();
-		if ($sine =~ /^>[A-Za-z0-9]+\s+([0-9]+)\s+([0-9a-zA-Z]+)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)\s/ ) {
+		if ($sine =~ /^>[A-Za-z0-9]+\s+([0-9]+)\s+([0-9a-zA-Z]+)\s([0-9a-zA-Z_]+)\s([0-9]+)\s([0-9]+)\s/ ) {
 			$key = join("\t",$1, $2, $3, $4, $5);
 	#		print $key, "<-<-<-<-<-<-<-<\n";		
 		}
@@ -3417,13 +3473,15 @@ sub merge_interruptedMicrosats{
 	while (my $line = <INF>){
 	#	print "$org\t(chr[0-9a-zA-Z]+)\t([0-9]+)\t([0-9])+\t \n";
 		$linecounter++;
-		if ($line =~ /^>[A-Za-z0-9]+\s+([0-9]+)\s+([0-9a-zA-Z]+)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)\s/ ) {
+		if ($line =~ /^>[A-Za-z0-9]+\s+([0-9]+)\s+([0-9a-zA-Z]+)\s([0-9a-zA-Z_]+)\s([0-9]+)\s([0-9]+)\s/ ) {
 			my $key = join("\t",$1, $2, $4, $5);
 		#	print $key, "#-#-#-#-#-#-#-#\n";
 			push (@{$fmicros{$key}},$line);	
 			$microcounter++;
 		}
-		else {print $line;}
+		else {
+			#print $line;
+		}
 	}
 #	print "number of microsatellites added to hash = $microcounter\nnumber of lines scanned = $linecounter\n";
 	close INF;
@@ -3437,13 +3495,15 @@ sub merge_interruptedMicrosats{
 	while (my $line = <INR>){
 	#	print "$org\t(chr[0-9a-zA-Z]+)\t([0-9]+)\t([0-9])+\t \n";
 		$linecounter++;
-		if ($line =~ /^>[A-Za-z0-9]+\s+([0-9]+)\s+([0-9a-zA-Z]+)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)\s/ ) {
+		if ($line =~ /^>[A-Za-z0-9]+\s+([0-9]+)\s+([0-9a-zA-Z]+)\s([0-9a-zA-Z_]+)\s([0-9]+)\s([0-9]+)\s/ ) {
 			my $key = join("\t",$1, $2, $4, $5);
 	#		print $key, "#-#-#-#-#-#-#-#\n";
 			push (@{$rmicros{$key}},$line);	
 			$microcounter++;
 		}
-		else {print "cant make key\n";}
+		else {
+			#print "cant make key\n";
+		}
 	}
 #	print "number of reverse microsatellites added to hash = $microcounter\nnumber of lines scanned = $linecounter\n";
 	close INR;
@@ -3461,7 +3521,7 @@ sub merge_interruptedMicrosats{
 	
 		my $key = ();
 	
-		if ($sine =~ /^>[A-Za-z0-9]+\s+([0-9]+)\s+([0-9a-zA-Z]+)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)\s/ ) {
+		if ($sine =~ /^>[A-Za-z0-9]+\s+([0-9]+)\s+([0-9a-zA-Z]+)\s([0-9a-zA-Z_]+)\s([0-9]+)\s([0-9]+)\s/ ) {
 			$key = join("\t",$1, $2, $4, $5);
 		#	print $key, "<-<-<-<-<-<-<-<\n";		
 		}
@@ -3493,7 +3553,7 @@ sub merge_interruptedMicrosats{
 			chomp @microstring;
 			my $clusterresult = (find_clusters(@microstring, $sields[$sequencepos])); 	
 			@sets1 = split("\=", $clusterresult);
-			my @temp = split(/_/,$sets1[0]) ; $microscanned+= scalar(@temp);
+			my @temp = split(/_X0X_/,$sets1[0]) ; $microscanned+= scalar(@temp);
 		#	print "sets = ", join("<all\nmerged>", @sets1), "\n<<-sets1\n"; <STDIN>;
 		}	#if (exists $micros{$key}){
 	
@@ -3515,7 +3575,7 @@ sub merge_interruptedMicrosats{
 	#		print "sending reversed sequence\n";
 			my $clusterresult = (find_clusters(@microstring, $rev_sequence ) ); 	
 			@sets2 = split("\=", $clusterresult);
-			my @temp = split(/_/,$sets2[0]) ; $microscanned+= scalar(@temp);
+			my @temp = split(/_X0X_/,$sets2[0]) ; $microscanned+= scalar(@temp);
 		}	#if (exists $micros{$key}){
 	
 		my @popout1 = ();
@@ -3525,10 +3585,11 @@ sub merge_interruptedMicrosats{
 			if(exists $sets1[0]) {
 				push (@popout1, $sets1[0],$sets2[1]);
 				my @forwardset = split("=", popOuter(@popout1, $rev_sequence ));#		
-				print OUTF join("\n",split("_", $forwardset[0])), "\n";
-				my @localmerged = split("_", $forwardset[1]);
+				print OUTF join("\n",split("_X0X_", $forwardset[0])), "\n";
+				my @localmerged = split("_X0X_", $forwardset[1]);
 				my $sequence = $sields[$sequencepos];
 				$sequence =~ s/ //g;
+#				print "\nforwardset = @forwardset\n";
 				for my $j (0 ... $#localmerged){
 					$localmerged[$j] = 	invert_justCoordinates ($localmerged[$j], length($sequence));
 				}
@@ -3537,10 +3598,11 @@ sub merge_interruptedMicrosats{
 				
 			}
 			else{
-				my @localmerged = split("_", $sets2[1]);
+				my @localmerged = split("_X0X_", $sets2[1]);
 				my $sequence = $sields[$sequencepos];
 				$sequence =~ s/ //g;
 				for my $j (0 ... $#localmerged){
+#					print "\nlocalmerged = @localmerged\n";
 					$localmerged[$j] = 	invert_justCoordinates ($localmerged[$j], length($sequence));
 				}
 				
@@ -3548,7 +3610,7 @@ sub merge_interruptedMicrosats{
 			}
 		}
 		elsif (exists $sets1[0]){
-			print OUTF join("\n",split("_", $sets1[0])), "\n";
+			print OUTF join("\n",split("_X0X_", $sets1[0])), "\n";
 		}
 		
 		my @reverseset= ();
@@ -3558,15 +3620,15 @@ sub merge_interruptedMicrosats{
 			#	print "popout2 = @popout2\n";
 				my @reverseset = split("=", popOuter(@popout2, $sields[$sequencepos]));
 				#print "reverseset = $reverseset[1] < --- reverseset1\n"; 
-				print OUTR join("\n",split("_", $reverseset[0])), "\n";
-				push(@merged,  (split("_", $reverseset[1])));
+				print OUTR join("\n",split("_X0X_", $reverseset[0])), "\n";
+				push(@merged,  (split("_X0X_", $reverseset[1])));
 			}
 			else{
-				push(@merged,  (split("_", $sets1[1])));
+				push(@merged,  (split("_X0X_", $sets1[1])));
 			}
 		}
 		elsif (exists $sets2[0]){
-			print OUTR join("\n",split("_", $sets2[0])), "\n";
+			print OUTR join("\n",split("_X0X_", $sets2[0])), "\n";
 		
 		}
 		
@@ -3721,7 +3783,7 @@ sub find_clusters{
 #	print join("\n",@mergedSet),"<-----mergedSet\n"  if $printer == 1;
 #<STDIN> if scalar(@mergedSet) > 0;
 #	print "EXIT: find_clusters\n";
-return (join("_",@nonmerged). "=".join("_",@mergedSet));
+return (join("_X0X_",@nonmerged). "=".join("_X0X_",@mergedSet));
 }
 
 sub custom {
@@ -3729,19 +3791,16 @@ sub custom {
 }
 
 sub popOuter {
-#	print "\nIN: popOuter @_\n";
-	my @all = split ("_",$_[0]);
+#	print "\nIN: popOuter @_\n"; <STDIN>;
+	my @all = split ("_X0X_",$_[0]);
 #	<STDIN> if !defined $_[0];
-	my @merged = split ("_",$_[1]);
+	my @merged = split ("_X0X_",$_[1]);
 	my $sequence = $_[2];
 	my $seqlen = length($sequence);
-#	print "\nIN: popOuter @_\n" if scalar(@_) != 3;
-#	<STDIN> if scalar(@_) != 3;
 	my %microstart=();
 	my %microend=();
 	my @mergedSet = ();
 	my @nonmerged = ();
-#	print "\n\n\n all = @all\n<--all\n";
 	
 	foreach my $line (@all){
 		my @fields = split(/\t/,$line);
@@ -3751,18 +3810,18 @@ sub popOuter {
 		push (@{$microend{$end}},$line);	
 	}
 	my $firstflag = 'down';
-
 	my %forPopouting = ();
 
 	while( my $line =shift(@merged)){
-#		print "\n MErgedline: $line \n" if $printer == 1;
+	#	print "\n MErgedline: $line .. startcord = $startcord  ... endcord = $endcord\n" ;
 		chomp $line;
 		my @fields = split(/\t/,$line);
 		my $start = $fields[$startcord];
 		my $end = $fields[$endcord];
 		my $startmicro = $line;
 		my $endmicro = $line;
-
+		
+		
 		delete ($microstart{$start});
 		delete ($microend{$end});
 		my $flag = 'down';	
@@ -3817,14 +3876,14 @@ sub popOuter {
     	push(@nonmerged,$microstart{$key}[0]);
 	}
 	
-	return (join("_",@nonmerged). "=".join("_",@mergedSet) );
+	return (join("_X0X_",@nonmerged). "=".join("_X0X_",@mergedSet) );
 }
 
 
 
 sub invert_justCoordinates{
 	my $microsat = $_[0];
-#	print "IN invert_justCoordinates\n" if $printer == 1;
+#	print "IN invert_justCoordinates ... @_\n" ; <STDIN>;
 	chomp $microsat;
 	my $seqLength = $_[1];
 	my @fields = split(/\t/,$microsat);
@@ -3868,7 +3927,7 @@ sub filterDuplicates_merged{
 	foreach my $micro (@merged) {
 		my @fields = split(/\t/,$micro);
 		if ($fields[3] =~ /chr[A-Z0-9a-z]+r/){
-			my $key = join("_",$fields[1], $fields[$startcord], $fields[$endcord]);
+			my $key = join("_K0K_",$fields[1], $fields[$startcord], $fields[$endcord]);
 	#		print "adding  ... \n$key\n$micro\n";
 			push(@{$revmerged{$key}}, $micro);
 		}
@@ -3880,7 +3939,7 @@ sub filterDuplicates_merged{
 #	print "\n";
 	foreach my $micro (@fmerged) {
 			my @fields = split(/\t/,$micro);
-			my $key = join("_",$fields[1], $fields[$startcord], $fields[$endcord]);
+			my $key = join("_K0K_",$fields[1], $fields[$startcord], $fields[$endcord]);
 	#		print "searching for key $key\n";
 			if (exists $revmerged{$key}){
 		#		print "deleting $revmerged{$key}[0]\n";
@@ -3998,7 +4057,7 @@ sub forward_reverse_sputoutput_comparer	{
 	my $microcounter=0;
 	while (my $line = <INF>){
 		$linecounter++;
-		if ($line =~ /([0-9a-zA-Z]+)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)\s([0-9a-zA-Z]+)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)\s([0-9a-zA-Z]+)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)\s/ ) {
+		if ($line =~ /([0-9a-zA-Z]+)\s([0-9a-zA-Z_]+)\s([0-9]+)\s([0-9]+)\s([0-9a-zA-Z]+)\s([0-9a-zA-Z_]+)\s([0-9]+)\s([0-9]+)\s([0-9a-zA-Z]+)\s([0-9a-zA-Z_]+)\s([0-9]+)\s([0-9]+)\s/ ) {
 			my $key = join("\t",$1, $3, $4, $5, $7, $8, $9, $11, $12);
 		#	print $key, "#-#-#-#-#-#-#-#\n";
 			push (@{$fmicros{$key}},$line);	
@@ -4019,7 +4078,7 @@ sub forward_reverse_sputoutput_comparer	{
 	$microcounter=0;
 	while (my $line = <INR>){
 		$linecounter++;
-		if ($line =~ /([0-9a-zA-Z]+)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)\s([0-9a-zA-Z]+)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)\s([0-9a-zA-Z]+)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)\s/ ) {
+		if ($line =~ /([0-9a-zA-Z]+)\s([0-9a-zA-Z_]+)\s([0-9]+)\s([0-9]+)\s([0-9a-zA-Z]+)\s([0-9a-zA-Z_]+)\s([0-9]+)\s([0-9]+)\s([0-9a-zA-Z]+)\s([0-9a-zA-Z_]+)\s([0-9]+)\s([0-9]+)\s/ ) {
 			my $key = join("\t",$1, $3, $4, $5, $7, $8, $9, $11, $12);
 		#	print $key, "#-#-#-#-#-#-#-#\n";
 			push (@{$rmicros{$key}},$line);	
@@ -4039,7 +4098,7 @@ sub forward_reverse_sputoutput_comparer	{
 		my %microend=();
 		my @sields = split(/\t/,$sine);
 		my $key = ();
-		if ($sine =~ /([0-9a-zA-Z]+)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)\s[\+|\-]\s([0-9a-zA-Z]+)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)\s[\+|\-]\s([0-9a-zA-Z]+)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)\s/ ) {
+		if ($sine =~ /([0-9a-zA-Z]+)\s([0-9a-zA-Z_]+)\s([0-9]+)\s([0-9]+)\s[\+|\-]\s([0-9a-zA-Z]+)\s([0-9a-zA-Z_]+)\s([0-9]+)\s([0-9]+)\s[\+|\-]\s([0-9a-zA-Z]+)\s([0-9a-zA-Z_]+)\s([0-9]+)\s([0-9]+)\s/ ) {
 			$key = join("\t",$1, $3, $4, $5, $7, $8, $9, $11, $12);
 		}
 		else {
@@ -4464,7 +4523,8 @@ sub new_multispecies_t10{
 			push (@{$seen{$key}},$line);	
 			$microcounter++;
 		}
-		else {		print "could not make ker in SPUT : \n$line \n"; 
+		else {		
+			#print "could not make ker in SPUT : \n$line \n"; 
 		}
 	}
 #	print "done hash.. linecounter = $linecounter, microcounter = $microcounter and total keys entered = ",scalar(keys %seen),"\n";
@@ -4583,6 +4643,10 @@ sub new_multispecies_t10{
 #					print "with poscounter = $poscounter\n" if $prinkter == 1;
 					my $search_result = ();
 					my $posnow  = ();
+					
+#					print "for $line, temp $temp or human_search $human_search not defined\n" if !defined $temp || !defined $human_search;
+#					<STDIN> if !defined $temp || !defined $human_search;
+					
 					while ($temp =~ /($human_search)/gi){
 						$search_result = $1;
 					#	$posnow  = pos($temp);
@@ -4590,6 +4654,8 @@ sub new_multispecies_t10{
 					}
 					
 					my @gapspos = ();
+					next if !defined $search_result;
+					
 					while($search_result =~ m/-/g) {push(@gapspos, (pos($search_result))); }
 					my $gaps  = join("__",@gapspos);
 	
@@ -4609,10 +4675,10 @@ sub new_multispecies_t10{
 		}
 	}
 	my $unusedkeys = scalar(keys %seen);
-	print INFO "in hash = $ref, looped = $ref4, captured = $ref3\n REMOVED: \nmicrosats with too long gaps = $deletes\n";
-	print INFO "exact duplicated removed = $duplicates \nmicrosats removed due to multiple microsats defined  in +-10 bp neighboring region: $neighbors \n";
-	print INFO "microsatellites too short = $tooshort\n";
-	print INFO "keysused = $keysused...starts not found = $startnotfound ... matchkeysformed=$matchkeysformed ... unusedkeys=$unusedkeys\n";
+#	print INFO "in hash = $ref, looped = $ref4, captured = $ref3\n REMOVED: \nmicrosats with too long gaps = $deletes\n";
+#	print INFO "exact duplicated removed = $duplicates \nmicrosats removed due to multiple microsats defined  in +-10 bp neighboring region: $neighbors \n";
+#	print INFO "microsatellites too short = $tooshort\n";
+#	print INFO "keysused = $keysused...starts not found = $startnotfound ... matchkeysformed=$matchkeysformed ... unusedkeys=$unusedkeys\n";
 	
 	#print  "in hash = $ref, looped = $ref4, captured = $ref3\n REMOVED: \nmicrosats with too long gaps = $deletes\n";
 	#print  "exact duplicated removed = $duplicates \nmicrosats removed due to multiple microsats defined  in +-10 bp neighboring region: $neighbors \n";
@@ -4800,9 +4866,6 @@ sub multiSpecies_orthFinder4{
 	while (my $line = <BO>){
 #		print "x" x 60, "\n" if $prinkter == 1;
 		$dotcounter++;
-		
-	
-		
 #		print "." if $dotcounter % 100 ==0;
 #		print "\n" if $dotcounter % 5000 ==0;
 		next if $line !~ /^[0-9]+/;
@@ -4861,11 +4924,11 @@ sub multiSpecies_orthFinder4{
 			if (exists $hasharr[$i]{$key2}){
 				@temparr =  @{$hasharr[$i]{$key2}};
 				
-#				print "in line $line, trying to hunt for: $tags[$i]\\s([a-zA-Z0-9])+\\s([0-9]+)\\s([0-9]+) \n" if $prinkter == 1;
-				$line =~ /$tags[$i]\s([a-zA-Z0-9]+)\s([0-9]+)\s([0-9]+)/;
+				$line =~ /$tags[$i]\s([a-zA-Z0-9_]+)\s([0-9]+)\s([0-9]+)/;
+##				print "in line $line, trying to hunt for: $tags[$i]\\s([a-zA-Z0-9_])+\\s([0-9]+)\\s([0-9]+) \n" if $prinkter == 1;
 #				print "org = $tags[$i], and chr = $1, start = $2, end =$3 \n" if $prinkter == 1; 
-				my $startkey = $1."_".$2; print "adding start key for this alignmebt block: $startkey to species $tags[$i]\n" if $prinkter == 1;
-				my $endkey = $1."_".$3; print "adding end key for this alignmebt block: $endkey to species $tags[$i]\n" if $prinkter == 1;
+				my $startkey = $1."_SK0SK_".$2; #print "adding start key for this alignmebt block: $startkey to species $tags[$i]\n" if $prinkter == 1;
+				my $endkey = $1."_EK0EK_".$3; #print "adding end key for this alignmebt block: $endkey to species $tags[$i]\n" if $prinkter == 1;
 				$contigstarts[$i]{$startkey}= $key2;
 				$contigends[$i]{$endkey}= $key2;
 #				print "confirming existance: \n" if $prinkter == 1;
@@ -4910,6 +4973,8 @@ sub multiSpecies_orthFinder4{
 			push @starthash, {%localhash};
 			my $foundclusters  =findClusters(join("!",@{$strings[$i]}), $CLUSTER_DIST);
 	
+#			print "foundclusters = $foundclusters\n";
+	
 			my @clusters = split(/_/,$foundclusters);
 			
 			my $clustno = 0;
@@ -4919,7 +4984,7 @@ sub multiSpecies_orthFinder4{
 #				print "clusters returned: @constituenst\n" if $prinkter == 1;
 			}
 	
-			@string = split("_",stringPainter(join("_",@string),$foundclusters));
+			@string = split("_S0S_",stringPainter(join("_C0C_",@string),$foundclusters));
 			
 			
 		}
@@ -4927,6 +4992,7 @@ sub multiSpecies_orthFinder4{
 	
 #		print colored ['blue'],"FINAL:\n" if $prinkter == 1;
 		my $finalclusters  =findClusters(join("!",@string), 1);
+#		print "finalclusters = $finalclusters\n";
 #		print colored ['blue'],"----------------------\n" if $prinkter == 1;
 		my @clusters = split(/,/,$finalclusters);
 #			print "@string\n" if $prinkter == 1;
@@ -5053,11 +5119,14 @@ sub multiSpecies_orthFinder4{
 		chomp $line;	
 		my @fields2 = split(/\t/,$line);
 		my $key2 = ();
-		if ($line =~ /([0-9]+)\s+($focalspec)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)/ ) {
+		if ($line =~ /([0-9]+)\s+($focalspec)\s(chr[0-9a-zA-Z_]+)\s([0-9]+)\s([0-9]+)/ ) {
 			$key2 = join("\t",$1, $2,  $4, $5);
 		}
 		
-		else {print "seq line $line incompatible\n"; next;}
+		else {
+		#	print "seq line $line incompatible\n";
+			next;
+		}
 #		print "KEY =  : $key2\n" if $prinkter == 1;
 	
 	
@@ -5071,10 +5140,10 @@ sub multiSpecies_orthFinder4{
 			@clusterscopy=@clusters;
 			for my $i (0 ... $#tags){
 	#			print "in line $line, trying to hunt for: $tags[$i]\\s([a-zA-Z0-9])+\\s([0-9]+)\\s([0-9]+) \n" if $prinkter == 1;
-				if ($line =~ /$tags[$i]\s([a-zA-Z0-9]+)\s([0-9]+)\s([0-9]+)/){
+				if ($line =~ /$tags[$i]\s([a-zA-Z0-9_]+)\s([0-9]+)\s([0-9]+)/){
 	#				print "org = $tags[$i], and chr = $1, start = $2, end =$3 \n" if $prinkter == 1; 
-					my $startkey = $1."_".$2; #print "adding start key for this alignmebt block: $startkey to species $tags[$i]\n" if $prinkter == 1;
-					my $endkey = $1."_".$3; #print "adding end key for this alignmebt block: $endkey to species $tags[$i]\n" if $prinkter == 1;
+					my $startkey = $1."_S0E_".$2; #print "adding start key for this alignmebt block: $startkey to species $tags[$i]\n" if $prinkter == 1;
+					my $endkey = $1."_S0E_".$3; #print "adding end key for this alignmebt block: $endkey to species $tags[$i]\n" if $prinkter == 1;
 					$currentcontigchrs[$i]=$1;
 					$currentcontigstarts[$i]=$2;
 					$currentcontigends[$i]=$3;			
@@ -5112,7 +5181,7 @@ sub multiSpecies_orthFinder4{
 			my $firstclusterstart = $contigclustersFirstStartOnly{$key2};
 			my $lastclusterend = $contigclustersLastEndOnly{$key2};
 					
-			my $key3 = $currentcontigchrs[$i]."_".($currentcontigstarts[$i]);
+			my $key3 = $currentcontigchrs[$i]."_S0E_".($currentcontigstarts[$i]);
 #			print  "check if exists $key3 in  contigends for $i\n" if $prinkter == 1; 
 			
 			if (exists($contigends[$i]{$key3}) && !exists $visitedcontigs{$contigends[$i]{$key3}}){
@@ -5251,7 +5320,9 @@ sub multiSpecies_orthFinder4{
 #				print "KEEY $key->$key3\n" if $prinkter == 1;
 #				print "our contigcluster = @{$contigclusters{$key}}\n----------\n" if $prinkter == 1;
 				
-				if (scalar(@{$contigclusters{$key}}) > 0) {push @pool, @{$contigclusters{$key}}; print "now pool = @pool\n" if $prinkter == 1;}
+				if (scalar(@{$contigclusters{$key}}) > 0) {push @pool, @{$contigclusters{$key}}; 
+				#	print "now pool = @pool\n" if $prinkter == 1;
+				}
 				delete $foundkeys{$key3};
 				$key=$key3;
 				$key3=$clusteringpaths{$key};
@@ -5278,7 +5349,7 @@ sub multiSpecies_orthFinder4{
 	
 }
 sub stringPainter{
-	my @string  = split(/_/,$_[0]);
+	my @string  = split(/_C0C_/,$_[0]);
 #	print $_[0], " <- in stringPainter\n";
 #	print $_[1], " <- in clusters\n";
 	
@@ -5304,7 +5375,7 @@ sub stringPainter{
 		
 	}
 #	print "@string <-done from function stringPainter\n";
-	return join("_",@string);
+	return join("_S0S_",@string);
 }
 
 sub findClusters{
@@ -5390,3 +5461,135 @@ sub findClusters{
 	return join(",",@returner);
 }
 #xxxxxxxxxxxxxx multiSpecies_orthFinder4 xxxxxxxxxxxxxx  multiSpecies_orthFinder4 xxxxxxxxxxxxxx  multiSpecies_orthFinder4 xxxxxxxxxxxxxx 
+
+#xxxxxxxxxxxxxx MakeTrees xxxxxxxxxxxxxxxxxxxxxxxxxxxx  MakeTrees xxxxxxxxxxxxxxxxxxxxxxxxxxxx  MakeTrees xxxxxxxxxxxxxxxxxxxxxxxxxxxx 
+
+sub MakeTrees{
+	my $tree = $_[0];
+	my @parts=($tree);
+#	my @parts=();
+	
+	while (1){
+		$tree =~ s/^\(//g;
+		$tree =~ s/\)$//g;
+		my @arr = ();
+	
+		if ($tree =~ /^([a-zA-Z0-9_]+),([a-zA-Z0-9_\(\),]+)\)$/){
+			@arr = $tree =~ /^([a-zA-Z0-9_]+),([a-zA-Z0-9_\(\),]+)$/;
+			$tree = $2;
+			push @parts, $tree;
+		}
+		elsif ($tree =~ /^\(([a-zA-Z0-9_\(\),]+),([a-zA-Z0-9_]+)$/){
+			@arr = $tree =~ /^([a-zA-Z0-9_\(\),]+),([a-zA-Z0-9_]+)$/;
+			$tree = $1;
+			push @parts, $tree;
+		}
+		elsif ($tree =~ /^([a-zA-Z0-9_]+),([a-zA-Z0-9_]+)$/){
+			last;
+		}
+	}	
+	return @parts;
+}
+
+#xxxxxxxxxxxxxx qualityFilter xxxxxxxxxxxxxxxxxxxxxxxxxxxx  qualityFilter xxxxxxxxxxxxxxxxxxxxxxxxxxxx  qualityFilter xxxxxxxxxxxxxxxxxxxxxxxxxxxx 
+
+sub qualityFilter{
+	my $unmaskedorthfile = $_[0];
+	my $seqfile = $_[1];
+	my $maskedorthfile = $_[2];
+	my $filteredout = $maskedorthfile."_residue";
+	open (PMORTH, "<$unmaskedorthfile") or die "Cannot open unmaskedorthfile file: $unmaskedorthfile: $!";
+
+	my %keyhash = ();
+	
+	while (my $line = <PMORTH>){
+		my $key = join("\t", $1,$2,$3,$4) if $line =~ /($focalspec)\s+([a-zA-Z0-9\-_]+)\s+([0-9]+)\s+([0-9]+)/;
+		push @{$keyhash{$key}}, $line;
+	}
+	
+	open (SEQ, "<$seqfile") or die "Cannot open seqfile file: $seqfile: $!";
+	open (MORTH, ">$maskedorthfile") or die "Cannot open maskedorthfile file: $maskedorthfile: $!";
+        open (RES, ">$filteredout") or die "Cannot open filteredout file: $filteredout: $!";
+
+
+	
+	while (my $line = <SEQ>){
+		chomp $line;
+		if ($line =~ /($focalspec)\s+([a-zA-Z0-9\-_]+)\s+([0-9]+)\s+([0-9]+)/){
+			my $key = join("\t", $1,$2,$3,$4);
+			next if !exists $keyhash{$key};
+			my @orths = @{$keyhash{$key}} if exists $keyhash{$key};
+			delete $keyhash{$key};
+			
+			my $sine = <SEQ>;
+			
+			foreach my $orth (@orths){
+				#print "-----------------------------------------------------------------\n";
+				#print $orth;
+				my $orthcopy = $orth;
+				$orth =~ s/^>//;
+				my @parts = split(/>/,$orth);
+				
+				my @starts = ();
+				my @ends = ();
+				
+				foreach my $part (@parts){
+					my $no_of_species = adjustCoordinates($part);
+					my @pields = split(/\t/,$part);
+					
+				#	print "pields = @pields .. no_of_species = $no_of_species .. startcord = $pields[$startcord]\n";
+					
+					push @starts, $pields[$startcord];
+					push @ends, $pields[$endcord];
+				}
+				
+				#print "starts = @starts ... ends = @ends\n";
+				
+				my $leftend = smallest_number(@starts)-10;
+				my $rightend = largest_number(@ends)+10;
+
+				my $maskarea = substr($sine, $leftend, $rightend-$leftend+1);
+				print RES $orth if $maskarea =~ /#/;		
+				
+				
+				next if $maskarea =~ /#/;
+				
+				print MORTH $orthcopy;
+			}
+		}
+		else{
+			next;
+		}
+		
+		
+	}
+	
+#	print "UNDONE: ", scalar(keys %keyhash),"\n";
+#	print MORTH "UNDONE: ", scalar(keys %keyhash),"\n";
+	
+}
+
+sub adjustCoordinates{
+	my $line = $_[0];
+	my $no_of_species = $line =~ s/(chr[0-9a-zA-Z]+)|(Contig[0-9a-zA-Z\._\-]+)|(scaffold[0-9a-zA-Z\._\-]+)|(supercontig[0-9a-zA-Z\._\-]+)/x/ig;
+	my @got = ($line =~ s/(chr[0-9a-zA-Z]+)|(Contig[0-9a-zA-Z\._\-]+)/x/g);
+# print "line = $line\n";
+	$infocord = 2 + (4*$no_of_species) - 1;
+	$typecord = 2 + (4*$no_of_species) + 1 - 1;
+	$motifcord = 2 + (4*$no_of_species) + 2 - 1;
+	$gapcord = $motifcord+1;
+	$startcord = $gapcord+1;
+	$strandcord = $startcord+1;
+	$endcord = $strandcord + 1;
+	$microsatcord = $endcord + 1;
+	$sequencepos = 2 + (5*$no_of_species) + 1 -1 ; 
+	$interr_poscord = $microsatcord + 3;
+	$no_of_interruptionscord = $microsatcord + 4;
+	$interrcord = $microsatcord + 2;
+#	print "$line\n startcord = $startcord, and endcord = $endcord and no_of_species = $no_of_species\n" if $line !~ /calJac/i;
+	return $no_of_species;
+}
+
+
+
+
diff --git a/tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml b/tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml
index ef2d4eca386..4a1b449222d 100644
--- a/tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml
+++ b/tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml
@@ -1,8 +1,9 @@
-<tool id="multispecies_orthologous_microsats" name="Extract orthologous microsatellites" version="1.0.1">
+<tool id="multispecies_orthologous_microsats" name="Extract orthologous microsatellites" version="1.0.2">
   <description> for multiple (>2) species alignments</description>
   <command interpreter="perl">
     multispecies_MicrosatDataGenerator_interrupted_GALAXY.pl   	
     $input1 
+    $input2
   	$out_file1 
   	$thresholds 
   	$species 
@@ -12,16 +13,17 @@
   </command>
   <inputs>
     <page>
-        <param format="maf" name="input1" type="data" label="Select MAF alignments"/>
+        <param format="maf" name="input1" type="data" label="Select unfiltered MAF alignments" help= "NOTE: Currently users are requested to select only the alignments that contain five, four or three species' genomes. )"/>
+        <param format="maf" name="input2" type="data" label="Select the filtered version of above MAF alignments" help= "NOTE: Please use the tool 'Filter nucleotides' to filter nucleotides based on quality, in multiple species. When using the Filter nucleotide tool, ensure that you click 'Select All' for the option 'Mask Species')"/>
        	<param name="separation" size="10" type="integer" value="10" label="Minimum base pair distance between adjacent microsatellite blocks"
     	help="A value of 10 means: Adjacent microsatellites separated by less than 10 base pairs will be excluded from the output."/>
     	<param name="thresholds" size="15" type="text" value="9,10,12,12" label="Minimum Threshold for the number of repeats for microsatellites"
     	help="A value of 9,10,12,12 means: All monos having fewer than 9 repeats, dis having fewer than 5 repeats, tris having fewer than 4 repeats, tetras having fewer than 3 repeats will be excluded from the output."/>
-        <param name="species" type="select" label="Select species" display="checkboxes" multiple="true" help="NOTE: Currently users are requested to select one of these three combinations: hg18-panTro2-ponAbe2, hg18-panTro2-ponAbe2-rheMac2 or hg18-panTro2-ponAbe2-rheMac2-calJac1">
-      	<options>
-        	<filter type="data_meta" ref="input1" key="species" />
-      	</options>
-    	</param>
+    <param name="species" type="select" label="Select species" display="checkboxes" multiple="true" help="NOTE: Currently users are requested to select one of these three combinations: hg18-panTro2-ponAbe2, hg18-panTro2-ponAbe2-rheMac2 or hg18-panTro2-ponAbe2-rheMac2-calJac1">
+      <options>
+        <filter type="data_meta" ref="input1" key="species" />
+      </options>
+    </param>
     	<param name="treedefinition" size="200" type="text" value = "((((hg18,panTro2),ponAbe2),rheMac2),calJac1)" label="Tree definition of all species above whether or not selected for microsatellite extraction" 
     	help="For example: ((((hg18,panTro2),ponAbe2),rheMac2),calJac1)"/>
     </page>
@@ -30,16 +32,17 @@
     <data format="txt" name="out_file1" metadata_source="input1"/>
   </outputs>
   <requirements>
-     <requirement type="binary">sputnik</requirement>
+     <requirement type="binary">bx-sputnik</requirement>
   </requirements>
   <tests>
     <test>
-      <param name="input1" value="chr22_5sp.maf"/>
+      <param name="input1" value="regVariation/microsatellite/Galaxy17_unmasked_short.maf.gz"/>
+      <param name="input2" value="regVariation/microsatellite/Galaxy17_masked_short.maf.gz"/>
       <param name="thresholds" value="9,10,12,12"/>
       <param name="species" value="hg18,panTro2,ponAbe2,rheMac2,calJac1"/>
       <param name="treedefinition" value="((((hg18, panTro2), ponAbe2), rheMac2), calJac1)"/>
       <param name="separation" value="10"/>
-      <output name="out_file1" file="chr22_5sp.microraw.tabular"/>
+      <output name="out_file1" file="regVariation/microsatellite/Galaxy17_short_raw.txt"/>
     </test>
   </tests>
 
@@ -51,6 +54,39 @@
 
 This tool finds ortholgous microsatellite blocks between aligned species
   
+-----
+
+.. class:: warningmark
+
+**Note**
+
+A non-tabular format is created in which each row contains all information pertaining to a microsatellite locus from multiple species in the alignment.
+The rows read like this:
+
+>hg18	15	hg18	chr22	16092941	16093413	panTro2	chr22	16103944	16104421	ponAbe2	chr22	13797750	13798215	rheMac2	chr10	61890946	61891409	calJac1	Contig6986	140254	140728	mononucleotide	A	0	13	+	29	aaaaa------aaaAAA	>rheMac2	15	hg18	chr22	16092941	16093413	panTro2	chr22	16103944	16104421	ponAbe2	chr22	13797750	13798215	rheMac2	chr10	61890946	61891409	calJac1	Contig6986	140254	140728	mononucleotide	A	0	13	+	29	aaaaaaaa---AAAAAA
+
+Information from each species starts with an ">" followed by the species name, for instance, ">rheMac2". Below we describe all information listed for a microsatellite sequence in each species.
+
+After the species tag the alignemnt number is listed.
+What follows is details of the alignment block from all the species, including the chromosome number, start and end coordinates in each species. For instance:
+
+hg18	chr22	16092941	16093413	panTro2	chr22	16103944	16104421	ponAbe2	chr22	13797750	13798215	rheMac2	chr10	61890946	61891409	calJac1	Contig6986	140254	140728
+
+suggests that the alignment block as five species: hg18, panTro2, ponAbe2, rheMac2 and calJac1.
+
+Then the type of microsatellite is written, for instance, "mononucleotide".
+
+Then the microsatellite motif.
+
+Then the number of gaps in the alignment, in the respective species (as noted above, rheMac2 in this case).
+
+Then the start coordinate, the strand, and the end coordinate WITHIN the alignment block.
+
+At the end is listed the microsatellite sequence.
+
+If the microsatellite contains interruptions (which are not important for this tool), then the interruptions' information will be written out after the microsatellite sequence.
+
+
 </help>  
 
 

From 6706a47f35e3fa1ba8cb6353476f62d084554513 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Mon, 28 Nov 2011 14:37:57 -0500
Subject: [PATCH 250/362] Support display of extra files/composite types in
 published items. Fixes #628

---
 lib/galaxy/web/buildapp.py            | 2 +-
 lib/galaxy/web/controllers/dataset.py | 6 +++++-
 templates/root/history_common.mako    | 2 +-
 3 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/web/buildapp.py b/lib/galaxy/web/buildapp.py
index 1f6abb828c1..6984fefc4d1 100644
--- a/lib/galaxy/web/buildapp.py
+++ b/lib/galaxy/web/buildapp.py
@@ -98,7 +98,7 @@ def app_factory( global_conf, **kwargs ):
     webapp.add_route( '/datasets/:dataset_id/display/{filename:.+?}', controller='dataset', action='display', dataset_id=None, filename=None)
     webapp.add_route( '/datasets/:dataset_id/:action/:filename', controller='dataset', action='index', dataset_id=None, filename=None)
     webapp.add_route( '/display_application/:dataset_id/:app_name/:link_name/:user_id/:app_action/:action_param', controller='dataset', action='display_application', dataset_id=None, user_id=None, app_name = None, link_name = None, app_action = None, action_param = None )
-    webapp.add_route( '/u/:username/d/:slug', controller='dataset', action='display_by_username_and_slug' )
+    webapp.add_route( '/u/:username/d/:slug/:filename', controller='dataset', action='display_by_username_and_slug', filename=None )
     webapp.add_route( '/u/:username/p/:slug', controller='page', action='display_by_username_and_slug' )
     webapp.add_route( '/u/:username/h/:slug', controller='history', action='display_by_username_and_slug' )
     webapp.add_route( '/u/:username/w/:slug', controller='workflow', action='display_by_username_and_slug' )
diff --git a/lib/galaxy/web/controllers/dataset.py b/lib/galaxy/web/controllers/dataset.py
index ae32e915d3c..ec56f9453d7 100644
--- a/lib/galaxy/web/controllers/dataset.py
+++ b/lib/galaxy/web/controllers/dataset.py
@@ -683,10 +683,14 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesHistory, UsesHist
         return self.get_ave_item_rating_data( trans.sa_session, dataset )
         
     @web.expose
-    def display_by_username_and_slug( self, trans, username, slug, preview=True ):
+    def display_by_username_and_slug( self, trans, username, slug, filename=None, preview=True ):
         """ Display dataset by username and slug; because datasets do not yet have slugs, the slug is the dataset's id. """
         dataset = self.get_dataset( trans, slug, False, True )
         if dataset:
+            # Filename used for composite types.
+            if filename:
+                return self.display( trans, dataset_id=slug, filename=filename)
+                
             truncated, dataset_data = self.get_data( dataset, preview )
             dataset.annotation = self.get_item_annotation_str( trans.sa_session, dataset.history.user, dataset )
             
diff --git a/templates/root/history_common.mako b/templates/root/history_common.mako
index bbd04684c58..a593aad1356 100644
--- a/templates/root/history_common.mako
+++ b/templates/root/history_common.mako
@@ -87,7 +87,7 @@
                         # Get URL for display only.
                         if data.history.user and data.history.user.username:
                             display_url = h.url_for( controller='dataset', action='display_by_username_and_slug',
-                                                     username=data.history.user.username, slug=dataset_id )
+                                                     username=data.history.user.username, slug=dataset_id, filename='' )
                         else:
                             # HACK: revert to for_editing display URL when there is no user/username. This should only happen when
                             # there's no user/username because dataset is being displayed by history/view after error reported.

From 0260ed36f584a1d50f2e5ab75376213a3b1d19a6 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Mon, 28 Nov 2011 16:31:04 -0500
Subject: [PATCH 251/362] Make the use of the 'require_login' config setting
 functionally correct for the tool shed, and debug it's use in the Galaxy
 framework as well.

---
 lib/galaxy/web/controllers/user.py           | 41 ++++++++-------
 lib/galaxy/web/framework/__init__.py         | 54 ++++++++++++--------
 templates/user/index.mako                    | 20 ++++----
 templates/webapps/community/base_panels.mako |  7 +--
 templates/webapps/galaxy/base_panels.mako    | 14 ++---
 5 files changed, 71 insertions(+), 65 deletions(-)

diff --git a/lib/galaxy/web/controllers/user.py b/lib/galaxy/web/controllers/user.py
index 00426878c03..bf59187026c 100644
--- a/lib/galaxy/web/controllers/user.py
+++ b/lib/galaxy/web/controllers/user.py
@@ -15,15 +15,11 @@ from galaxy.security.validate_user_input import validate_email, validate_usernam
 log = logging.getLogger( __name__ )
 
 require_login_template = """
-<h1>Welcome to Galaxy</h1>
-
 <p>
-    This installation of Galaxy has been configured such that only users who are logged in may use it.%s
+    This %s has been configured such that only users who are logged in may use it.%s
 </p>
 <p/>
 """
-require_login_nocreation_template = require_login_template % ""
-require_login_creation_template = require_login_template % "  If you don't already have an account, <a href='%s'>you may create one</a>."
 
 OPENID_PROVIDERS = { 'Google' : 'https://www.google.com/accounts/o8/id',
                      'Yahoo!' : 'http://yahoo.com',
@@ -362,15 +358,23 @@ class User( BaseUIController, UsesFormDefinitions ):
                 else:
                     refresh_frames = [ 'masthead', 'history' ]
             message, status, user, success = self.__validate_login( trans, webapp, **kwd )
-            if success and referer and not referer.startswith( trans.request.base + url_for( controller='user', action='logout' ) ):
+            if success and referer and not referer.startswith( url_for( trans.request.base + url_for( controller='user', action='logout' ) ) ):
                 redirect_url = referer
             elif success:
                 redirect_url = url_for( '/' )
         if not user and trans.app.config.require_login:
             if trans.app.config.allow_user_creation:
-                header = require_login_creation_template % web.url_for( action='create', cntrller='user' )
+                create_account_str = "  If you don't already have an account, <a href='%s'>you may create one</a>." % \
+                    web.url_for( action='create', cntrller='user', webapp=webapp )
+                if webapp == 'galaxy':
+                    header = require_login_template % ( "Galaxy instance", create_account_str )
+                else:
+                    header = require_login_template % ( "Galaxy tool shed", create_account_str )
             else:
-                header = require_login_nocreation_template
+                if webapp == 'galaxy':
+                    header = require_login_template % ( "Galaxy instance", "" )
+                else:
+                    header = require_login_template % ( "Galaxy tool shed", "" )
         return trans.fill_template( '/user/login.mako',
                                     webapp=webapp,
                                     email=email,
@@ -405,11 +409,12 @@ class User( BaseUIController, UsesFormDefinitions ):
             status = 'error'
         else:
             trans.handle_user_login( user, webapp )
-            trans.log_event( "User logged in" )
-            message = 'You are now logged in as %s.<br>You can <a target="_top" href="%s">go back to the page you were visiting</a> or <a target="_top" href="%s">go to the home page</a>.' % \
-                ( user.email, referer, url_for( '/' ) )
-            if trans.app.config.require_login:
-                message += '  <a target="_top" href="%s">Click here</a> to continue to the home page.' % web.url_for( '/static/welcome.html' )
+            if webapp == 'galaxy':
+                trans.log_event( "User logged in" )
+                message = 'You are now logged in as %s.<br>You can <a target="_top" href="%s">go back to the page you were visiting</a> or <a target="_top" href="%s">go to the home page</a>.' % \
+                    ( user.email, referer, url_for( '/' ) )
+                if trans.app.config.require_login:
+                    message += '  <a target="_top" href="%s">Click here</a> to continue to the home page.' % web.url_for( '/static/welcome.html' )
             success = True
         return ( message, status, user, success )
     @web.expose
@@ -419,10 +424,10 @@ class User( BaseUIController, UsesFormDefinitions ):
                 refresh_frames = [ 'masthead', 'history', 'tools' ]
             else:
                 refresh_frames = [ 'masthead', 'history' ]
+            # Since logging an event requires a session, we'll log prior to ending the session
+            trans.log_event( "User logged out" )
         else:
             refresh_frames = [ 'masthead' ]
-        # Since logging an event requires a session, we'll log prior to ending the session
-        trans.log_event( "User logged out" )
         trans.handle_user_logout( logout_all=logout_all )
         message = 'You have been logged out.<br>You can log in again, <a target="_top" href="%s">go back to the page you were visiting</a> or <a target="_top" href="%s">go to the home page</a>.' % \
             ( trans.request.referer, url_for( '/' ) )
@@ -471,10 +476,8 @@ class User( BaseUIController, UsesFormDefinitions ):
                                                                       cntrller,
                                                                       subscribe_checked,
                                                                       **kwd )
-                    if success and not is_admin and webapp != 'galaxy':
-                        # Must be logging into the community space webapp
-                        trans.handle_user_login( user, webapp )
-                        redirect_url = referer
+                    if webapp == 'community':
+                        redirect_url = url_for( '/' )
                     if success and not is_admin:
                         # The handle_user_login() method has a call to the history_set_default_permissions() method
                         # (needed when logging in with a history), user needs to have default permissions set before logging in
diff --git a/lib/galaxy/web/framework/__init__.py b/lib/galaxy/web/framework/__init__.py
index fbc1283264d..b2022172814 100644
--- a/lib/galaxy/web/framework/__init__.py
+++ b/lib/galaxy/web/framework/__init__.py
@@ -404,26 +404,38 @@ class GalaxyWebTransaction( base.DefaultWebTransaction ):
         # If the old session was invalid, get a new history with our new session
         if invalidate_existing_session:
             self.new_history()
-    def _ensure_logged_in_user( self, environ ):
-        allowed_paths = (
-            url_for( controller='root', action='index' ),
-            url_for( controller='root', action='tool_menu' ),
-            url_for( controller='root', action='masthead' ),
-            url_for( controller='root', action='history' ),
-            url_for( controller='user', action='login' ),
-            url_for( controller='user', action='create' ),
-            url_for( controller='user', action='reset_password' ),
-            url_for( controller='library', action='browse' )
-        )
-        display_as = url_for( controller='root', action='display_as' )
-        if self.galaxy_session.user is None:
-            if self.app.config.ucsc_display_sites and self.request.path == display_as:
-                try:
-                    host = socket.gethostbyaddr( self.environ[ 'REMOTE_ADDR' ] )[0]
-                except( socket.error, socket.herror, socket.gaierror, socket.timeout ):
-                    host = None
-                if host in UCSC_SERVERS:
-                    return
+    def _ensure_logged_in_user( self, environ, session_cookie ):
+        # The value of session_cookie can be one of 
+        # 'galaxysession' or 'galaxycommunitysession'
+        if session_cookie == 'galaxysession':
+            # TODO: re-engineer to eliminate the use of allowed_paths
+            # as maintenance overhead is far too high.
+            allowed_paths = (
+                url_for( controller='root', action='index' ),
+                url_for( controller='root', action='tool_menu' ),
+                url_for( controller='root', action='masthead' ),
+                url_for( controller='root', action='history' ),
+                url_for( controller='user', action='api_keys' ),
+                url_for( controller='user', action='create' ),
+                url_for( controller='user', action='index' ),
+                url_for( controller='user', action='login' ),
+                url_for( controller='user', action='logout' ),
+                url_for( controller='user', action='manage_user_info' ),
+                url_for( controller='user', action='set_default_permissions' ),
+                url_for( controller='user', action='reset_password' ),
+                url_for( controller='library', action='browse' ),
+                url_for( controller='history', action='list' ),
+                url_for( controller='dataset', action='list' )
+            )
+            display_as = url_for( controller='root', action='display_as' )
+            if self.galaxy_session.user is None:
+                if self.app.config.ucsc_display_sites and self.request.path == display_as:
+                    try:
+                        host = socket.gethostbyaddr( self.environ[ 'REMOTE_ADDR' ] )[0]
+                    except( socket.error, socket.herror, socket.gaierror, socket.timeout ):
+                        host = None
+                    if host in UCSC_SERVERS:
+                        return
             if self.request.path not in allowed_paths:
                 self.response.send_redirect( url_for( controller='root', action='index' ) )
     def __create_new_session( self, prev_galaxy_session=None, user_for_new_session=None ):
@@ -857,7 +869,7 @@ class GalaxyWebUITransaction( GalaxyWebTransaction ):
         if self.app.config.use_remote_user and self.galaxy_session.user.deleted:
             self.response.send_redirect( url_for( '/static/user_disabled.html' ) )
         if self.app.config.require_login:
-            self._ensure_logged_in_user( environ )
+            self._ensure_logged_in_user( environ, session_cookie )
     def get_user( self ):
         """Return the current user if logged in or None."""
         return self.galaxy_session.user
diff --git a/templates/user/index.mako b/templates/user/index.mako
index 42dec0fadab..5ae22b17848 100644
--- a/templates/user/index.mako
+++ b/templates/user/index.mako
@@ -10,25 +10,25 @@
     <p>You are currently logged in as ${trans.user.email}.</p>
     <ul>
         %if webapp == 'galaxy':
-            <li><a href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller )}">${_('Manage your information')}</a></li>
-            <li><a href="${h.url_for( controller='user', action='set_default_permissions', cntrller=cntrller )}">${_('Change default permissions')}</a> for new histories</li>
+            <li><a href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller, webapp=webapp )}">${_('Manage your information')}</a></li>
+            <li><a href="${h.url_for( controller='user', action='set_default_permissions', cntrller=cntrller, webapp=webapp )}">${_('Change default permissions')}</a> for new histories</li>
             %if trans.app.config.enable_api:
-                <li><a href="${h.url_for( controller='user', action='api_keys', cntrller=cntrller )}">${_('Manage your API keys')}</a></li>
+                <li><a href="${h.url_for( controller='user', action='api_keys', cntrller=cntrller, webapp=webapp )}">${_('Manage your API keys')}</a></li>
             %endif
             %if trans.app.config.enable_openid:
-                <li><a href="${h.url_for( controller='user', action='openid_manage', cntrller=cntrller )}">${_('Manage OpenIDs')}</a> linked to your account</li>
+                <li><a href="${h.url_for( controller='user', action='openid_manage', cntrller=cntrller, webapp=webapp )}">${_('Manage OpenIDs')}</a> linked to your account</li>
             %endif
             %if trans.app.config.use_remote_user:
                 %if trans.app.config.remote_user_logout_href:
                     <li><a href="${trans.app.config.remote_user_logout_href}" target="_top">${_('Logout')}</a></li>
                 %endif
             %else:
-                <li><a href="${h.url_for( controller='user', action='logout', logout_all=True )}" target="_top">${_('Logout')}</a> ${_('of all user sessions')}</li>
+                <li><a href="${h.url_for( controller='user', action='logout', webapp=webapp, logout_all=True )}" target="_top">${_('Logout')}</a> ${_('of all user sessions')}</li>
             %endif
         %else:
-            <li><a href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller,  webapp='community' )}">${_('Manage your information')}</a></li>
-            <li><a href="${h.url_for( controller='repository', action='manage_email_alerts', cntrller=cntrller,  webapp='community' )}">${_('Manage your email alerts')}</a></li>
-            <li><a href="${h.url_for( controller='user', action='logout', logout_all=True )}" target="_top">${_('Logout')}</a> ${_('of all user sessions')}</li>
+            <li><a href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller,  webapp=webapp )}">${_('Manage your information')}</a></li>
+            <li><a href="${h.url_for( controller='repository', action='manage_email_alerts', cntrller=cntrller,  webapp=webapp )}">${_('Manage your email alerts')}</a></li>
+            <li><a href="${h.url_for( controller='user', action='logout', webapp=webapp, logout_all=True )}" target="_top">${_('Logout')}</a> ${_('of all user sessions')}</li>
         %endif
     </ul>
     %if webapp == 'galaxy':
@@ -44,7 +44,7 @@
         <p>${n_('You are currently not logged in.')}</p>
     %endif
     <ul>
-        <li><a href="${h.url_for( action='login' )}">${_('Login')}</li>
-        <li><a href="${h.url_for( action='create', cntrller='user' )}">${_('Register')}</a></li>
+        <li><a href="${h.url_for( action='login', webapp=webapp )}">${_('Login')}</li>
+        <li><a href="${h.url_for( action='create', cntrller='user', webapp=webapp )}">${_('Register')}</a></li>
     </ul>
 %endif
diff --git a/templates/webapps/community/base_panels.mako b/templates/webapps/community/base_panels.mako
index 29a89c4bb57..056ed66ad9c 100644
--- a/templates/webapps/community/base_panels.mako
+++ b/templates/webapps/community/base_panels.mako
@@ -74,12 +74,7 @@
             %else:
                 <li>Logged in as <span id="user-email">${user_email}</span></li>
                 <li><a target="galaxy_main" href="${h.url_for( controller='/user', action='index', cntrller='user', webapp='community' )}">Preferences</a></li>
-                <%
-                    if app.config.require_login:
-                        logout_url = h.url_for( controller='/root', action='index', webapp='community', m_c='user', m_a='logout' )
-                    else:
-                        logout_url = h.url_for( controller='/user', action='logout', webapp='community' )
-                %>
+                <% logout_url = h.url_for( controller='/user', action='logout', webapp='community' ) %>
                 <li><a target="_top" href="${logout_url}">Logout</a></li>
             %endif
         </ul>
diff --git a/templates/webapps/galaxy/base_panels.mako b/templates/webapps/galaxy/base_panels.mako
index 254312f35c1..98dbfea871b 100644
--- a/templates/webapps/galaxy/base_panels.mako
+++ b/templates/webapps/galaxy/base_panels.mako
@@ -124,7 +124,7 @@
         # Menu for user who is not logged in.
         menu_options = [ [ _("Login"), h.url_for( controller='/user', action='login' ), "galaxy_main" ] ]
         if app.config.allow_user_creation:
-            menu_options.append( [ _("Register"), h.url_for( controller='/user', action='create', cntrller='user' ), "galaxy_main" ] ) 
+            menu_options.append( [ _("Register"), h.url_for( controller='/user', action='create', cntrller='user', webapp='galaxy' ), "galaxy_main" ] ) 
         extra_class = "loggedout-only"
         visible = ( trans.user == None )
         tab( "user", _("User"), None, visible=visible, menu_options=menu_options )
@@ -139,23 +139,19 @@
             if app.config.remote_user_logout_href:
                 menu_options.append( [ _('Logout'), app.config.remote_user_logout_href, "_top" ] )
         else:
-            menu_options.append( [ _('Preferences'), h.url_for( controller='/user', action='index', cntrller='user' ), "galaxy_main" ] )
+            menu_options.append( [ _('Preferences'), h.url_for( controller='/user', action='index', cntrller='user', webapp='galaxy' ), "galaxy_main" ] )
             if app.config.get_bool( 'enable_tracks', False ):
                 menu_options.append( [ 'Custom Builds', h.url_for( controller='/user', action='dbkeys' ), "galaxy_main" ] )
-            if app.config.require_login:
-                logout_url = h.url_for( controller='/root', action='index', m_c='user', m_a='logout' )
-            else:
-                logout_url = h.url_for( controller='/user', action='logout' )
-            menu_options.append( [ 'Logout', logout_url, "_top" ] )
+            menu_options.append( [ 'Logout', h.url_for( controller='/user', action='logout', webapp='galaxy' ), "_top" ] )
             menu_options.append( None )
         menu_options.append( [ _('Saved Histories'), h.url_for( controller='/history', action='list' ), "galaxy_main" ] )
         menu_options.append( [ _('Saved Datasets'), h.url_for( controller='/dataset', action='list' ), "galaxy_main" ] )
         if app.config.get_bool( 'enable_pages', False ):
             menu_options.append( [ _('Saved Pages'), h.url_for( controller='/page', action='list' ), "_top" ] )
         if app.config.enable_api:
-            menu_options.append( [ _('API Keys'), h.url_for( controller='/user', action='api_keys', cntrller='user' ), "galaxy_main" ] )
+            menu_options.append( [ _('API Keys'), h.url_for( controller='/user', action='api_keys', cntrller='user', webapp='galaxy' ), "galaxy_main" ] )
         if app.config.use_remote_user:
-            menu_options.append( [ _('Public Name'), h.url_for( controller='/user', action='edit_username', cntrller='user' ), "galaxy_main" ] )
+            menu_options.append( [ _('Public Name'), h.url_for( controller='/user', action='edit_username', cntrller='user', webapp='galaxy' ), "galaxy_main" ] )
     
         extra_class = "loggedin-only"
         visible = ( trans.user != None )

From a2f5a502db1876215929733ae2bc9940f521fb9d Mon Sep 17 00:00:00 2001
From: John Duddy <jduddy@illumina.com>
Date: Mon, 28 Nov 2011 15:37:37 -0800
Subject: [PATCH 252/362] Add merge method to SAM datatype so BWA can do
 split/merge

---
 lib/galaxy/datatypes/tabular.py | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py
index 7b1d3fccb4f..895de1b6060 100644
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -352,6 +352,22 @@ class Sam( Tabular ):
             dataset.metadata.comment_lines = comment_lines
             dataset.metadata.columns = 12
             dataset.metadata.column_types = ['str', 'int', 'str', 'int', 'int', 'str', 'str', 'int', 'int', 'str', 'str', 'str']
+355,369d354
+     def merge( split_files, output_file): 
+        """
+        Multiple SAM files may each have headers. Since the headers should all be the same, remove
+        the headers from files 1-n, keeping them in the first file only
+        """
+        cmd = 'mv %s %s' % ( split_files[0], output_file ) 
+        result = os.system(cmd)
+        if result != 0:
+            raise Exception('Result %s from %s' % (result, cmd))
+        if len(split_files) > 1:
+            cmd = 'egrep -v "^@" %s >> %s' % ( ' '.join(split_files[1:]), output_file ) 
+        result = os.system(cmd)
+        if result != 0:
+            raise Exception('Result %s from %s' % (result, cmd))
+    merge = staticmethod(merge)
 
 class Pileup( Tabular ):
     """Tab delimited data in pileup (6- or 10-column) format"""

From ce5432164b88760ae286936750b1bc3003a1bfbb Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Tue, 29 Nov 2011 08:58:45 -0500
Subject: [PATCH 253/362] Object Store: Remove some debugging statements.

---
 lib/galaxy/objectstore/__init__.py            | 15 +++++++--------
 lib/galaxy/objectstore/s3_multipart_upload.py |  4 ++--
 2 files changed, 9 insertions(+), 10 deletions(-)

diff --git a/lib/galaxy/objectstore/__init__.py b/lib/galaxy/objectstore/__init__.py
index d540451a987..dac6ee82888 100644
--- a/lib/galaxy/objectstore/__init__.py
+++ b/lib/galaxy/objectstore/__init__.py
@@ -306,7 +306,6 @@ class DiskObjectStore(ObjectStore):
             return path
         else:
             path = self._construct_path(dataset_id, **kwargs)
-        print "Checking it %s exists: %s" %(path, os.path.exists(path))
         if os.path.exists(path):
             return path
         else:
@@ -499,7 +498,7 @@ class S3ObjectStore(ObjectStore):
         except S3ResponseError, ex:
             log.error("Trouble checking existence of S3 key '%s': %s" % (rel_path, ex))
             return False
-        print "Checking if '%s' exists in S3: %s" % (rel_path, exists)
+        #print "Checking if '%s' exists in S3: %s" % (rel_path, exists)
         if rel_path[0] == '/':
             raise
         return exists
@@ -570,14 +569,14 @@ class S3ObjectStore(ObjectStore):
             if ret_code == 127:
                 self.transfer_progress = 0 # Reset transfer progress counter
                 key.get_contents_to_filename(self._get_cache_path(rel_path), cb=self._transfer_cb, num_cb=10)
-                print "(ssss1) Pulled key '%s' into cache to %s" % (rel_path, self._get_cache_path(rel_path))
+                #print "(ssss1) Pulled key '%s' into cache to %s" % (rel_path, self._get_cache_path(rel_path))
                 return True
             else:
                 ncores = multiprocessing.cpu_count()
                 url = key.generate_url(7200)
                 ret_code = subprocess.call("axel -a -n %s '%s'" % (ncores, url))
                 if ret_code == 0:
-                    print "(ssss2) Parallel pulled key '%s' into cache to %s" % (rel_path, self._get_cache_path(rel_path))
+                    #print "(ssss2) Parallel pulled key '%s' into cache to %s" % (rel_path, self._get_cache_path(rel_path))
                     return True
         except S3ResponseError, ex:
             log.error("Problem downloading key '%s' from S3 bucket '%s': %s" % (rel_path, self.bucket.name, ex))
@@ -659,7 +658,7 @@ class S3ObjectStore(ObjectStore):
     
     def create(self, dataset_id, **kwargs):
         if not self.exists(dataset_id, **kwargs):
-            print "S3 OS creating a dataset with ID %s" % dataset_id
+            #print "S3 OS creating a dataset with ID %s" % dataset_id
             # Pull out locally used fields
             extra_dir = kwargs.get('extra_dir', None)
             extra_dir_at_root = kwargs.get('extra_dir_at_root', False)
@@ -742,8 +741,8 @@ class S3ObjectStore(ObjectStore):
         # Check cache first and get file if not there
         if not self._in_cache(rel_path):
             self._pull_into_cache(rel_path)
-        else:
-            print "(cccc) Getting '%s' from cache" % self._get_cache_path(rel_path)
+        #else:
+        #    print "(cccc) Getting '%s' from cache" % self._get_cache_path(rel_path)
         # Read the file content from cache
         data_file = open(self._get_cache_path(rel_path), 'r')
         data_file.seek(start)
@@ -752,7 +751,7 @@ class S3ObjectStore(ObjectStore):
         return content
     
     def get_filename(self, dataset_id, **kwargs):
-        print "S3 get_filename for dataset: %s" % dataset_id
+        #print "S3 get_filename for dataset: %s" % dataset_id
         dir_only = kwargs.get('dir_only', False)
         rel_path = self._construct_path(dataset_id, **kwargs)
         cache_path = self._get_cache_path(rel_path)
diff --git a/lib/galaxy/objectstore/s3_multipart_upload.py b/lib/galaxy/objectstore/s3_multipart_upload.py
index 56e52b3efd8..8bfc920b4c7 100644
--- a/lib/galaxy/objectstore/s3_multipart_upload.py
+++ b/lib/galaxy/objectstore/s3_multipart_upload.py
@@ -41,7 +41,7 @@ def transfer_part(mp_id, mp_keyname, mp_bucketname, i, part):
     """Transfer a part of a multipart upload. Designed to be run in parallel.
     """
     mp = mp_from_ids(mp_id, mp_keyname, mp_bucketname)
-    print " Transferring", i, part
+    #print " Transferring", i, part
     with open(part) as t_handle:
         mp.upload_part_from_file(t_handle, i+1)
     os.remove(part)
@@ -50,7 +50,7 @@ def multipart_upload(bucket, s3_key_name, tarball, mb_size, use_rr=True):
     """Upload large files using Amazon's multipart upload functionality.
     """
     cores = multiprocessing.cpu_count()
-    print "Initiating multipart upload using %s cores" % cores
+    #print "Initiating multipart upload using %s cores" % cores
     def split_file(in_file, mb_size, split_num=5):
         prefix = os.path.join(os.path.dirname(in_file),
                               "%sS3PART" % (os.path.basename(s3_key_name)))

From fd7dfeee9a544e6c67ed4f8d4ea9bd98dd70b387 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Tue, 29 Nov 2011 11:15:10 -0500
Subject: [PATCH 254/362] Enhance the process for displaying a workflow in a
 tool shed repository so that workflows in change sets other than the
 repository tip can be viewed.

---
 .../webapps/community/controllers/common.py   | 42 +++++++++++++
 .../community/controllers/repository.py       | 41 +------------
 .../webapps/community/controllers/workflow.py | 61 ++++++++++---------
 3 files changed, 76 insertions(+), 68 deletions(-)

diff --git a/lib/galaxy/webapps/community/controllers/common.py b/lib/galaxy/webapps/community/controllers/common.py
index 71b74ae9f2d..df975bab82c 100644
--- a/lib/galaxy/webapps/community/controllers/common.py
+++ b/lib/galaxy/webapps/community/controllers/common.py
@@ -765,6 +765,48 @@ def load_tool( trans, config_file ):
             ToolClass = Tool
         return ToolClass( config_file, root, trans.app )
     return None
+def load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ):
+    repository = get_repository( trans, repository_id )
+    repo = hg.repository( get_configured_ui(), repository.repo_path )
+    tool = None
+    message = ''
+    if changeset_revision == repository.tip:
+        try:
+            tool = load_tool( trans, os.path.abspath( tool_config ) )
+        except Exception, e:
+            tool = None
+            message = "Error loading tool: %s.  Clicking <b>Reset metadata</b> may correct this error." % str( e )
+    else:
+        # Get the tool config file name from the hgweb url, something like:
+        # /repos/test/convert_chars1/file/e58dcf0026c7/convert_characters.xml
+        old_tool_config_file_name = tool_config.split( '/' )[ -1 ]
+        ctx = get_changectx_for_changeset( trans, repo, changeset_revision )
+        fctx = None
+        for filename in ctx:
+            filename_head, filename_tail = os.path.split( filename )
+            if filename_tail == old_tool_config_file_name:
+                fctx = ctx[ filename ]
+                break
+        if fctx:
+            # Write the contents of the old tool config to a temporary file.
+            fh = tempfile.NamedTemporaryFile( 'w' )
+            tmp_filename = fh.name
+            fh.close()
+            fh = open( tmp_filename, 'w' )
+            fh.write( fctx.data() )
+            fh.close()
+            try:
+                tool = load_tool( trans, tmp_filename )
+            except Exception, e:
+                tool = None
+                message = "Error loading tool: %s.  Clicking <b>Reset metadata</b> may correct this error." % str( e )
+            try:
+                os.unlink( tmp_filename )
+            except:
+                pass
+        else:
+            tool = None
+    return tool, message
 def build_changeset_revision_select_field( trans, repository, selected_value=None, add_id_to_name=True ):
     """
     Build a SelectField whose options are the changeset_revision
diff --git a/lib/galaxy/webapps/community/controllers/repository.py b/lib/galaxy/webapps/community/controllers/repository.py
index 13375d9312d..0fcaab43f68 100644
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -1905,46 +1905,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
         status = params.get( 'status', 'done' )
         webapp = params.get( 'webapp', 'community' )
         repository = get_repository( trans, repository_id )
-        repo = hg.repository( get_configured_ui(), repository.repo_path )
-        valid = True
-        if changeset_revision == repository.tip:
-            try:
-                tool = load_tool( trans, os.path.abspath( tool_config ) )
-            except Exception, e:
-                tool = None
-                valid = False
-                message = "Error loading tool: %s.  Clicking <b>Reset metadata</b> may correct this error." % str( e )
-        else:
-            # Get the tool config file name from the hgweb url, something like:
-            # /repos/test/convert_chars1/file/e58dcf0026c7/convert_characters.xml
-            old_tool_config_file_name = tool_config.split( '/' )[ -1 ]
-            ctx = get_changectx_for_changeset( trans, repo, changeset_revision )
-            fctx = None
-            for filename in ctx:
-                filename_head, filename_tail = os.path.split( filename )
-                if filename_tail == old_tool_config_file_name:
-                    fctx = ctx[ filename ]
-                    break
-            if fctx:
-                # Write the contents of the old tool config to a temporary file.
-                fh = tempfile.NamedTemporaryFile( 'w' )
-                tmp_filename = fh.name
-                fh.close()
-                fh = open( tmp_filename, 'w' )
-                fh.write( fctx.data() )
-                fh.close()
-                try:
-                    tool = load_tool( trans, tmp_filename )
-                except Exception, e:
-                    tool = None
-                    valid = False
-                    message = "Error loading tool: %s.  Clicking <b>Reset metadata</b> may correct this error." % str( e )
-                try:
-                    os.unlink( tmp_filename )
-                except:
-                    pass
-            else:
-                tool = None
+        tool, message = load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config )
         tool_state = self.__new_state( trans )
         is_malicious = change_set_is_malicious( trans, repository_id, repository.tip )
         try:
diff --git a/lib/galaxy/webapps/community/controllers/workflow.py b/lib/galaxy/webapps/community/controllers/workflow.py
index ccd7355946a..ed7d8af418e 100644
--- a/lib/galaxy/webapps/community/controllers/workflow.py
+++ b/lib/galaxy/webapps/community/controllers/workflow.py
@@ -22,13 +22,13 @@ class RepoInputDataModule( InputDataModule ):
         module.state = dict( name="Input Dataset" )
         return module
     @classmethod
-    def from_dict( Class, trans, d, tools_metadata=None, secure=True ):
+    def from_dict( Class, trans, repository_id, changeset_revision, step_dict, tools_metadata=None, secure=True ):
         module = Class( trans )
-        state = from_json_string( d[ "tool_state" ] )
+        state = from_json_string( step_dict[ "tool_state" ] )
         module.state = dict( name=state.get( "name", "Input Dataset" ) )
         return module
     @classmethod
-    def from_workflow_step( Class, trans, tools_metadata, step ):
+    def from_workflow_step( Class, trans, repository_id, changeset_revision, tools_metadata, step ):
         module = Class( trans )
         module.state = dict( name="Input Dataset" )
         if step.tool_inputs and "name" in step.tool_inputs:
@@ -39,35 +39,38 @@ class RepoToolModule( ToolModule ):
     
     type = "tool"
     
-    def __init__( self, trans, tools_metadata, tool_id ):
+    def __init__( self, trans, repository_id, changeset_revision, tools_metadata, tool_id ):
         self.trans = trans
         self.tools_metadata = tools_metadata
         self.tool_id = tool_id
         self.tool = None
+        self.errors = None
         for tool_dict in tools_metadata:
             if self.tool_id in [ tool_dict[ 'id' ], tool_dict[ 'guid' ] ]:
-                self.tool = load_tool( trans, os.path.abspath( tool_dict[ 'tool_config' ] ) )
+                self.tool, message = load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_dict[ 'tool_config' ] )
+                if message and self.tool is None:
+                    self.errors = 'unavailable'
+                break
         self.post_job_actions = {}
         self.workflow_outputs = []
         self.state = None
-        self.errors = None
     @classmethod
-    def new( Class, trans, tools_metadata, tool_id=None ):
-        module = Class( trans, tools_metadata, tool_id )
+    def new( Class, trans, repository_id, changeset_revision, tools_metadata, tool_id=None ):
+        module = Class( trans, repository_id, changeset_revision, tools_metadata, tool_id )
         module.state = module.tool.new_state( trans, all_pages=True )
         return module
     @classmethod
-    def from_dict( Class, trans, d, tools_metadata, secure=True ):
-        tool_id = d[ 'tool_id' ]
-        module = Class( trans, tools_metadata, tool_id )
+    def from_dict( Class, trans, repository_id, changeset_revision, step_dict, tools_metadata, secure=True ):
+        tool_id = step_dict[ 'tool_id' ]
+        module = Class( trans, repository_id, changeset_revision, tools_metadata, tool_id )
         module.state = DefaultToolState()
         if module.tool is not None:
-            module.state.decode( d[ "tool_state" ], module.tool, module.trans.app, secure=secure )
-        module.errors = d.get( "tool_errors", None )
+            module.state.decode( step_dict[ "tool_state" ], module.tool, module.trans.app, secure=secure )
+        module.errors = step_dict.get( "tool_errors", None )
         return module
     @classmethod
-    def from_workflow_step( Class, trans, tools_metadata, step ):
-        module = Class( trans, tools_metadata, step.tool_id )
+    def from_workflow_step( Class, trans, repository_id, changeset_revision, tools_metadata, step ):
+        module = Class( trans, repository_id, changeset_revision, tools_metadata, step.tool_id )
         module.state = DefaultToolState()
         if module.tool:
             module.state.inputs = module.tool.params_from_strings( step.tool_inputs, trans.app, ignore_errors=True )
@@ -115,18 +118,18 @@ class RepoWorkflowModuleFactory( WorkflowModuleFactory ):
     def __init__( self, module_types ):
         self.module_types = module_types
     def new( self, trans, type, tools_metadata=None, tool_id=None ):
-        """Return module for type and (optional) tool_id intialized with new / default state."""
+        """Return module for type and (optional) tool_id initialized with new / default state."""
         assert type in self.module_types
         return self.module_types[type].new( trans, tool_id )
-    def from_dict( self, trans, d, **kwargs ):
-        """Return module initialized from the data in dictionary `d`."""
-        type = d[ 'type' ]
+    def from_dict( self, trans, repository_id, changeset_revision, step_dict, **kwd ):
+        """Return module initialized from the data in dictionary `step_dict`."""
+        type = step_dict[ 'type' ]
         assert type in self.module_types
-        return self.module_types[ type ].from_dict( trans, d, **kwargs )
-    def from_workflow_step( self, trans, tools_metadata, step ):
+        return self.module_types[ type ].from_dict( trans, repository_id, changeset_revision, step_dict, **kwd )
+    def from_workflow_step( self, trans, repository_id, changeset_revision, tools_metadata, step ):
         """Return module initialized from the WorkflowStep object `step`."""
         type = step.type
-        return self.module_types[ type ].from_workflow_step( trans, tools_metadata, step )
+        return self.module_types[ type ].from_workflow_step( trans, repository_id, changeset_revision, tools_metadata, step )
 
 module_factory = RepoWorkflowModuleFactory( dict( data_input=RepoInputDataModule, tool=RepoToolModule ) )
 
@@ -153,6 +156,8 @@ class WorkflowController( BaseUIController ):
     @web.expose
     def generate_workflow_image( self, trans, repository_metadata_id, workflow_name, webapp='community' ):
         repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id )
+        repository_id = trans.security.encode_id( repository_metadata.repository_id )
+        changeset_revision = repository_metadata.changeset_revision
         metadata = repository_metadata.metadata
         workflow_name = decode( workflow_name )
         for workflow_dict in metadata[ 'workflows' ]:
@@ -162,7 +167,7 @@ class WorkflowController( BaseUIController ):
             tools_metadata = metadata[ 'tools' ]
         else:
             tools_metadata = []
-        workflow, missing_tool_tups = self.__workflow_from_dict( trans, workflow_dict, tools_metadata )
+        workflow, missing_tool_tups = self.__workflow_from_dict( trans, workflow_dict, tools_metadata, repository_id, changeset_revision )
         data = []
         canvas = svgfig.canvas( style="stroke:black; fill:none; stroke-width:1px; stroke-linejoin:round; text-anchor:left" )
         text = svgfig.SVG( "g" )
@@ -179,7 +184,7 @@ class WorkflowController( BaseUIController ):
         max_width, max_x, max_y = 0, 0, 0
         for step in workflow.steps:
             step.upgrade_messages = {}
-            module = module_factory.from_workflow_step( trans, tools_metadata, step )
+            module = module_factory.from_workflow_step( trans, repository_id, changeset_revision, tools_metadata, step )
             tool_errors = module.type == 'tool' and not module.tool
             module_data_inputs = self.__get_data_inputs( step, module )
             module_data_outputs = self.__get_data_outputs( step, module, workflow.steps )
@@ -308,11 +313,11 @@ class WorkflowController( BaseUIController ):
                 data_outputs.append( data_outputs_dict )       
                 return data_outputs
         return module.get_data_outputs()
-    def __workflow_from_dict( self, trans, data, tools_metadata ):
+    def __workflow_from_dict( self, trans, workflow_dict, tools_metadata, repository_id, changeset_revision ):
         """Creates and returns workflow object from a dictionary."""
         trans.workflow_building_mode = True
         workflow = model.Workflow()
-        workflow.name = data[ 'name' ]
+        workflow.name = workflow_dict[ 'name' ]
         workflow.has_errors = False
         steps = []
         # Keep ids for each step that we need to use to make connections.
@@ -322,12 +327,12 @@ class WorkflowController( BaseUIController ):
         # will be ( tool_id, tool_name, tool_version ).
         missing_tool_tups = []
         # First pass to build step objects and populate basic values
-        for key, step_dict in data[ 'steps' ].iteritems():
+        for key, step_dict in workflow_dict[ 'steps' ].iteritems():
             # Create the model class for the step
             step = model.WorkflowStep()
             step.name = step_dict[ 'name' ]
             step.position = step_dict[ 'position' ]
-            module = module_factory.from_dict( trans, step_dict, tools_metadata=tools_metadata, secure=False )
+            module = module_factory.from_dict( trans, repository_id, changeset_revision, step_dict, tools_metadata=tools_metadata, secure=False )
             if module.type == 'tool' and module.tool is None:
                 # A required tool is not available in the current repository.
                 step.tool_errors = 'unavailable'

From df82c9dd76f80736816c71c1fe4532ed0a860f67 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Tue, 29 Nov 2011 13:41:40 -0500
Subject: [PATCH 255/362] Updates for 'GenomeSpace import from file browser'
 tools.

---
 tools/data_source/genomespace_file_browser_prod.xml | 2 +-
 tools/data_source/genomespace_file_browser_test.xml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/data_source/genomespace_file_browser_prod.xml b/tools/data_source/genomespace_file_browser_prod.xml
index 0dbb0cb765a..8558113d7f0 100644
--- a/tools/data_source/genomespace_file_browser_prod.xml
+++ b/tools/data_source/genomespace_file_browser_prod.xml
@@ -4,7 +4,7 @@
     <command interpreter="python">genomespace_file_browser.py --json_parameter_file "${output}" --genomespace_site "prod"</command>
     <inputs action="https://dm.genomespace.org/datamanager/defaultdirectory" check_values="False" method="post"> 
         <display>go to GenomeSpace Data Manager </display>
-        <param name="appCallbackUrl" type="baseurl" value="/tool_runner?tool_id=genomespace_file_browser_dev&amp;runtool_btn=Execute" />
+        <param name="appCallbackUrl" type="baseurl" value="/tool_runner?tool_id=genomespace_file_browser_prod&amp;runtool_btn=Execute" />
         <param name="appName" type="hidden" value="Galaxy" />
     </inputs>
     <uihints minwidth="800"/>
diff --git a/tools/data_source/genomespace_file_browser_test.xml b/tools/data_source/genomespace_file_browser_test.xml
index a308f5f3480..3e1a50e3491 100644
--- a/tools/data_source/genomespace_file_browser_test.xml
+++ b/tools/data_source/genomespace_file_browser_test.xml
@@ -4,7 +4,7 @@
     <command interpreter="python">genomespace_file_browser.py --json_parameter_file "${output}" --genomespace_site "test"</command>
     <inputs action="https://dmtest.genomespace.org:8444/datamanager/defaultdirectory" check_values="False" method="post"> 
         <display>go to GenomeSpace Data Manager </display>
-        <param name="appCallbackUrl" type="baseurl" value="/tool_runner?tool_id=genomespace_file_browser_dev&amp;runtool_btn=Execute" />
+        <param name="appCallbackUrl" type="baseurl" value="/tool_runner?tool_id=genomespace_file_browser_test&amp;runtool_btn=Execute" />
         <param name="appName" type="hidden" value="Galaxy" />
     </inputs>
     <uihints minwidth="800"/>

From 76ccdfd38c3450d1319ce1aee625dc3b5b62e50a Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Tue, 29 Nov 2011 16:45:37 -0500
Subject: [PATCH 256/362] Updates for GATK tools.

---
 tools/gatk/unified_genotyper.xml | 128 +++++++++++++++++++++++--------
 tools/gatk/variant_annotator.xml | 111 +++++++++++++++++++--------
 2 files changed, 173 insertions(+), 66 deletions(-)

diff --git a/tools/gatk/unified_genotyper.xml b/tools/gatk/unified_genotyper.xml
index d9b4d45c009..726b14e160c 100644
--- a/tools/gatk/unified_genotyper.xml
+++ b/tools/gatk/unified_genotyper.xml
@@ -1,4 +1,4 @@
-<tool id="gatk_unified_genotyper" name="Unified Genotyper" version="0.0.4">
+<tool id="gatk_unified_genotyper" name="Unified Genotyper" version="0.0.5">
   <description>SNP and indel caller</description>
   <requirements>
       <requirement type="package" version="1.3">gatk</requirement>
@@ -122,7 +122,18 @@
                 --group "${group}"
             #end for
         #end if
+        #if str( $analysis_param_type.exclude_annotations ) != "None":
+            #for $annotation in str( $analysis_param_type.exclude_annotations ).split( ','):
+                --excludeAnnotation "${annotation}"
+            #end for
+        #end if
         '
+##        #if str( $analysis_param_type.snpEff_rod_bind_type.snpEff_rod_bind_type_selector ) == 'set_snpEff':
+##            -p '--annotation "SnpEff"'
+##            -d "--snpEffFile:${analysis_param_type.snpEff_rod_bind_type.snpEff_rod_name},%(file_type)s" "${analysis_param_type.snpEff_rod_bind_type.snpEff_input_rod}" "${analysis_param_type.snpEff_rod_bind_type.snpEff_input_rod.ext}" "input_snpEff_${analysis_param_type.snpEff_rod_bind_type.snpEff_rod_name}"
+##        #else:
+##            -p '--excludeAnnotation "SnpEff"'
+##        #end if
     #end if
   </command>
   <inputs>
@@ -354,42 +365,91 @@
         <param name="indelHaplotypeSize" type="integer" value="80" label="Indel haplotype size" />
         <param name="doContextDependentGapPenalties" type="boolean" truevalue="--doContextDependentGapPenalties" falsevalue="" label="Vary gap penalties by context" />
 	    <param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types">
-          <option value="ChromosomeCounts"/>
-          <option value="IndelType"/>
-          <option value="SpanningDeletions"/>
-          <option value="HardyWeinberg"/>
-          <option value="NBaseCount"/>
-          <option value="MappingQualityZero"/>
-          <option value="AlleleBalance"/>
-          <option value="BaseCounts"/>
-          <option value="LowMQ"/>
-          <option value="InbreedingCoeff"/>
-          <option value="RMSMappingQuality"/>
-          <option value="HaplotypeScore"/>
-          <option value="TechnologyComposition"/>
-          <option value="SampleList"/>
-          <option value="FisherStrand"/>
-          <option value="HomopolymerRun"/>
-          <option value="DepthOfCoverage"/>
-          <option value="SnpEff"/>
-          <option value="MappingQualityZeroFraction"/>
-          <option value="GCContent"/>
-          <option value="MappingQualityRankSumTest"/>
-          <option value="ReadPosRankSumTest"/>
-          <option value="BaseQualityRankSumTest"/>
-          <option value="QualByDepth"/>
-          <option value="SBByDepth"/>
-          <option value="ReadDepthAndAllelicFractionBySample"/>
-          <option value="AlleleBalanceBySample"/>
-          <option value="DepthPerAlleleBySample"/>
-          <option value="MappingQualityZeroBySample"/>
+          <option value="AlleleBalance" />
+          <option value="AlleleBalanceBySample" />
+          <option value="BaseCounts" />
+          <option value="BaseQualityRankSumTest" />
+          <option value="ChromosomeCounts" />
+          <option value="DepthOfCoverage" />
+          <option value="DepthPerAlleleBySample" />
+          <option value="FisherStrand" />
+          <option value="GCContent" />
+          <option value="HaplotypeScore" />
+          <option value="HardyWeinberg" />
+          <option value="HomopolymerRun" />
+          <option value="InbreedingCoeff" />
+          <option value="IndelType" />
+          <option value="LowMQ" />
+          <option value="MVLikelihoodRatio" />
+          <option value="MappingQualityRankSumTest" />
+          <option value="MappingQualityZero" />
+          <option value="MappingQualityZeroBySample" />
+          <option value="MappingQualityZeroFraction" />
+          <option value="NBaseCount" />
+          <option value="QualByDepth" />
+          <option value="RMSMappingQuality" />
+          <option value="ReadDepthAndAllelicFractionBySample" />
+          <option value="ReadPosRankSumTest" />
+          <option value="SampleList" />
+          <!-- <option value="SnpEff" /> -->
+          <option value="SpanningDeletions" />
+          <option value="TechnologyComposition" />
 	    </param>
+<!--
+        <conditional name="snpEff_rod_bind_type">
+          <param name="snpEff_rod_bind_type_selector" type="select" label="Provide a snpEff reference-ordered data file">
+            <option value="set_snpEff">Set snpEff</option>
+            <option value="exclude_snpEff" selected="True">Don't set snpEff</option>
+          </param>
+          <when value="exclude_snpEff">
+          </when>
+          <when value="set_snpEff">
+            <param name="snpEff_input_rod" type="data" format="vcf" label="ROD file" />
+            <param name="snpEff_rod_name" type="hidden" value="snpEff" label="ROD Name"/>
+          </when>
+        </conditional>
+-->
 	    <param name="group" type="select" multiple="True" display="checkboxes" label="Annotation Interfaces/Groups">
-	      <option value="Standard">Standard</option>
-	      <option value="Experimental">Experimental</option>
-	      <option value="WorkInProgress">WorkInProgress</option>
-	      <!-- <option value="none">none</option> -->
+            <option value="RodRequiringAnnotation">RodRequiringAnnotation</option>
+            <option value="Standard">Standard</option>
+            <option value="Experimental">Experimental</option>
+            <option value="WorkInProgress">WorkInProgress</option>
+            <option value="RankSumTest">RankSumTest</option>
+	        <!-- <option value="none">none</option> -->
 	    </param>
+    <!--     <param name="family_string" type="text" value="" label="Family String"/> -->
+        <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" >
+          <!-- might we want to load the available annotations from an external configuration file, since additional ones can be added to local installs? -->
+          <option value="AlleleBalance" />
+          <option value="AlleleBalanceBySample" />
+          <option value="BaseCounts" />
+          <option value="BaseQualityRankSumTest" />
+          <option value="ChromosomeCounts" />
+          <option value="DepthOfCoverage" />
+          <option value="DepthPerAlleleBySample" />
+          <option value="FisherStrand" />
+          <option value="GCContent" />
+          <option value="HaplotypeScore" />
+          <option value="HardyWeinberg" />
+          <option value="HomopolymerRun" />
+          <option value="InbreedingCoeff" />
+          <option value="IndelType" />
+          <option value="LowMQ" />
+          <option value="MVLikelihoodRatio" />
+          <option value="MappingQualityRankSumTest" />
+          <option value="MappingQualityZero" />
+          <option value="MappingQualityZeroBySample" />
+          <option value="MappingQualityZeroFraction" />
+          <option value="NBaseCount" />
+          <option value="QualByDepth" />
+          <option value="RMSMappingQuality" />
+          <option value="ReadDepthAndAllelicFractionBySample" />
+          <option value="ReadPosRankSumTest" />
+          <option value="SampleList" />
+          <!-- <option value="SnpEff" /> -->
+          <option value="SpanningDeletions" />
+          <option value="TechnologyComposition" />
+        </param>
       </when>
     </conditional>
   </inputs>
diff --git a/tools/gatk/variant_annotator.xml b/tools/gatk/variant_annotator.xml
index 9de7288c69e..f8d8509b99e 100644
--- a/tools/gatk/variant_annotator.xml
+++ b/tools/gatk/variant_annotator.xml
@@ -1,4 +1,4 @@
-<tool id="gatk_variant_annotator" name="Variant Annotator" version="0.0.3">
+<tool id="gatk_variant_annotator" name="Variant Annotator" version="0.0.4">
   <description></description>
   <requirements>
       <requirement type="package" version="1.3">gatk</requirement>
@@ -13,6 +13,7 @@
    -d "--variant" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
    -p 'java 
     -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar"
+    ##--list
     -T "VariantAnnotator"
     ##--num_threads 4 ##hard coded, for now
     -et "NO_ET" ##ET no phone home
@@ -30,6 +31,11 @@
             #end for
         #end if
     #end if
+    #if str( $exclude_annotations ) != "None":
+        #for $annotation in str( $exclude_annotations ).split( ',' ):
+            --excludeAnnotation "${annotation}"
+        #end for
+    #end if
 ##    #for $additional_annotation in $additional_annotations:
 ##        --annotation "${additional_annotation.additional_annotation_type.additional_annotation_type_selector}"
 ##        #for $name, $param in $additional_annotation.additional_annotation_type.iteritems():
@@ -55,7 +61,10 @@
     #end for
     
     #if str( $snpEff_rod_bind_type.snpEff_rod_bind_type_selector ) == 'set_snpEff':
-        -d "--snpEff:${snpEff_rod_bind_type.snpEff_rod_name},%(file_type)s" "${snpEff_rod_bind_type.snpEff_input_rod}" "${snpEff_rod_bind_type.snpEff_input_rod.ext}" "input_snpEff_${snpEff_rod_bind_type.snpEff_rod_name}"
+        -p '--annotation "SnpEff"'
+        -d "--snpEffFile:${snpEff_rod_bind_type.snpEff_rod_name},%(file_type)s" "${snpEff_rod_bind_type.snpEff_input_rod}" "${snpEff_rod_bind_type.snpEff_input_rod.ext}" "input_snpEff_${snpEff_rod_bind_type.snpEff_rod_name}"
+    #else:
+        -p '--excludeAnnotation "SnpEff"'
     #end if
     
     #for $expression in $expressions:
@@ -124,6 +133,10 @@
             --group "${group}"
         #end for
     #end if
+    #if str( $family_string ) != "":
+        --family_string "${family_string}"
+    #end if
+    --MendelViolationGenotypeQualityThreshold "${mendel_violation_genotype_quality_threshold}"
         '
   </command>
   <inputs>
@@ -166,35 +179,35 @@
       <when value="choose">
         <param name="annotations" type="select" multiple="True" display="checkboxes" label="Annotations to apply" >
           <!-- might we want to load the available annotations from an external configuration file, since additional ones can be added to local installs? -->
-          <option value="ChromosomeCounts"/>
-          <option value="IndelType"/>
-          <option value="SpanningDeletions"/>
-          <option value="HardyWeinberg"/>
-          <option value="NBaseCount"/>
-          <option value="MappingQualityZero"/>
-          <option value="AlleleBalance"/>
-          <option value="BaseCounts"/>
-          <option value="LowMQ"/>
-          <option value="InbreedingCoeff"/>
-          <option value="RMSMappingQuality"/>
-          <option value="HaplotypeScore"/>
-          <option value="TechnologyComposition"/>
-          <option value="SampleList"/>
-          <option value="FisherStrand"/>
-          <option value="HomopolymerRun"/>
-          <option value="DepthOfCoverage"/>
-          <option value="SnpEff"/>
-          <option value="MappingQualityZeroFraction"/>
-          <option value="GCContent"/>
-          <option value="MappingQualityRankSumTest"/>
-          <option value="ReadPosRankSumTest"/>
-          <option value="BaseQualityRankSumTest"/>
-          <option value="QualByDepth"/>
-          <option value="SBByDepth"/>
-          <option value="ReadDepthAndAllelicFractionBySample"/>
-          <option value="AlleleBalanceBySample"/>
-          <option value="DepthPerAlleleBySample"/>
-          <option value="MappingQualityZeroBySample"/>
+          <option value="AlleleBalance" />
+          <option value="AlleleBalanceBySample" />
+          <option value="BaseCounts" />
+          <option value="BaseQualityRankSumTest" />
+          <option value="ChromosomeCounts" />
+          <option value="DepthOfCoverage" />
+          <option value="DepthPerAlleleBySample" />
+          <option value="FisherStrand" />
+          <option value="GCContent" />
+          <option value="HaplotypeScore" />
+          <option value="HardyWeinberg" />
+          <option value="HomopolymerRun" />
+          <option value="InbreedingCoeff" />
+          <option value="IndelType" />
+          <option value="LowMQ" />
+          <option value="MVLikelihoodRatio" />
+          <option value="MappingQualityRankSumTest" />
+          <option value="MappingQualityZero" />
+          <option value="MappingQualityZeroBySample" />
+          <option value="MappingQualityZeroFraction" />
+          <option value="NBaseCount" />
+          <option value="QualByDepth" />
+          <option value="RMSMappingQuality" />
+          <option value="ReadDepthAndAllelicFractionBySample" />
+          <option value="ReadPosRankSumTest" />
+          <option value="SampleList" />
+          <option value="SnpEff" />
+          <option value="SpanningDeletions" />
+          <option value="TechnologyComposition" />
         </param>
       </when>
     </conditional>
@@ -371,7 +384,41 @@
       <option value="WorkInProgress">WorkInProgress</option>
       <option value="RankSumTest">RankSumTest</option>
     </param>
-        
+    <param name="family_string" type="text" value="" label="Family String"/>
+    <param name="mendel_violation_genotype_quality_threshold" type="float" value="0.0" label="genotype quality treshold in order to annotate mendelian violation ratio."/>
+    <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" >
+      <!-- might we want to load the available annotations from an external configuration file, since additional ones can be added to local installs? -->
+      <option value="AlleleBalance" />
+      <option value="AlleleBalanceBySample" />
+      <option value="BaseCounts" />
+      <option value="BaseQualityRankSumTest" />
+      <option value="ChromosomeCounts" />
+      <option value="DepthOfCoverage" />
+      <option value="DepthPerAlleleBySample" />
+      <option value="FisherStrand" />
+      <option value="GCContent" />
+      <option value="HaplotypeScore" />
+      <option value="HardyWeinberg" />
+      <option value="HomopolymerRun" />
+      <option value="InbreedingCoeff" />
+      <option value="IndelType" />
+      <option value="LowMQ" />
+      <option value="MVLikelihoodRatio" />
+      <option value="MappingQualityRankSumTest" />
+      <option value="MappingQualityZero" />
+      <option value="MappingQualityZeroBySample" />
+      <option value="MappingQualityZeroFraction" />
+      <option value="NBaseCount" />
+      <option value="QualByDepth" />
+      <option value="RMSMappingQuality" />
+      <option value="ReadDepthAndAllelicFractionBySample" />
+      <option value="ReadPosRankSumTest" />
+      <option value="SampleList" />
+      <option value="SnpEff" />
+      <option value="SpanningDeletions" />
+      <option value="TechnologyComposition" />
+    </param>
+    
   </inputs>
   <outputs>
     <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (Variant File)" />

From ace11b1edc0b8bf90ccc440d22c343fc51494c2a Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Tue, 29 Nov 2011 17:07:06 -0500
Subject: [PATCH 257/362] Fix tab to 4 spaces in tool_conf.xml.sample.

---
 tool_conf.xml.sample | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index 5f604024bc5..2fbde9915f7 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -469,7 +469,7 @@
     <tool file="human_genome_variation/lps.xml" />
     <tool file="human_genome_variation/hilbertvis.xml" />
     <tool file="human_genome_variation/freebayes.xml" />
-	<tool file="human_genome_variation/master2pg.xml" />
+    <tool file="human_genome_variation/master2pg.xml" />
   </section>
   <section name="Genome Diversity" id="gd">
     <tool file="genome_diversity/extract_primers.xml" />

From 023c4db69ee8e4566cb7c0c208127e60dc9c59c1 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Tue, 29 Nov 2011 17:30:14 -0500
Subject: [PATCH 258/362] Replace old filter() on tool_data_tables by param
 value hack with param.fields.path for several tools.

---
 tools/metag_tools/megablast_wrapper.xml         | 2 +-
 tools/ngs_rna/tophat_color_wrapper.xml          | 2 +-
 tools/ngs_rna/tophat_wrapper.xml                | 2 +-
 tools/ngs_simulation/ngs_simulation.xml         | 2 +-
 tools/picard/rgPicardASMetrics.xml              | 2 +-
 tools/sr_mapping/PerM.xml                       | 4 ++--
 tools/sr_mapping/bowtie_color_wrapper.xml       | 2 +-
 tools/sr_mapping/bowtie_wrapper.xml             | 3 +--
 tools/sr_mapping/bwa_color_wrapper.xml          | 2 +-
 tools/sr_mapping/bwa_wrapper.xml                | 2 +-
 tools/sr_mapping/lastz_paired_reads_wrapper.xml | 2 +-
 tools/sr_mapping/lastz_wrapper.xml              | 2 +-
 tools/sr_mapping/mosaik.xml                     | 2 +-
 13 files changed, 14 insertions(+), 15 deletions(-)

diff --git a/tools/metag_tools/megablast_wrapper.xml b/tools/metag_tools/megablast_wrapper.xml
index 92092e8d0a6..7f0a2de5058 100644
--- a/tools/metag_tools/megablast_wrapper.xml
+++ b/tools/metag_tools/megablast_wrapper.xml
@@ -2,7 +2,7 @@
     <description> compare short reads against htgs, nt, and wgs databases</description>
     <command interpreter="python">
       megablast_wrapper.py
-        --db_build="${ filter( lambda x: str( x[0] ) == str( $source_select ), $__app__.tool_data_tables[ 'blastdb' ].get_fields() )[0][-1] }"
+        --db_build="${source_select.fields.path}"
         --input=$input_query
         --word_size=$word_size
         --identity_cutoff=$iden_cutoff
diff --git a/tools/ngs_rna/tophat_color_wrapper.xml b/tools/ngs_rna/tophat_color_wrapper.xml
index f162ec959bb..8fa8b1679bb 100644
--- a/tools/ngs_rna/tophat_color_wrapper.xml
+++ b/tools/ngs_rna/tophat_color_wrapper.xml
@@ -19,7 +19,7 @@
             #if $refGenomeSource.genomeSource == "history":
                 --own-file=$refGenomeSource.ownFile
             #else:
-                --indexes-path="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'tophat_indexes_color' ].get_fields() )[0][-1] }"
+                --indexes-path="${refGenomeSource.index.fields.path}"
             #end if
 
             ## Are reads single-end or paired?
diff --git a/tools/ngs_rna/tophat_wrapper.xml b/tools/ngs_rna/tophat_wrapper.xml
index 5f7ec9b56c4..42435c707f5 100644
--- a/tools/ngs_rna/tophat_wrapper.xml
+++ b/tools/ngs_rna/tophat_wrapper.xml
@@ -17,7 +17,7 @@
             #if $refGenomeSource.genomeSource == "history":
                 --own-file=$refGenomeSource.ownFile
             #else:
-                --indexes-path="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'tophat_indexes' ].get_fields() )[0][-1] }"
+                --indexes-path="${refGenomeSource.index.fields.path}"
             #end if
 
             ## Are reads single-end or paired?
diff --git a/tools/ngs_simulation/ngs_simulation.xml b/tools/ngs_simulation/ngs_simulation.xml
index e5ea55e8372..080f047be57 100644
--- a/tools/ngs_simulation/ngs_simulation.xml
+++ b/tools/ngs_simulation/ngs_simulation.xml
@@ -4,7 +4,7 @@
   <command interpreter="python">
     ngs_simulation.py
       #if $in_type.input_type == "built-in"
-        --input="${ filter( lambda x: str( x[0] ) == str( $in_type.genome ), $__app__.tool_data_tables[ 'ngs_sim_fasta' ].get_fields() )[0][-1] }"
+        --input="${in_type.genome.fields.path}"
         --genome=$in_type.genome
       #else
         --input=$in_type.input1
diff --git a/tools/picard/rgPicardASMetrics.xml b/tools/picard/rgPicardASMetrics.xml
index dcd1f998588..76028c21e3c 100644
--- a/tools/picard/rgPicardASMetrics.xml
+++ b/tools/picard/rgPicardASMetrics.xml
@@ -6,7 +6,7 @@
 #if $genomeSource.refGenomeSource == "history":
     --ref-file "$genomeSource.ownFile"
 #else
-    --ref "${ filter( lambda x: str( x[0] ) == str( $genomeSource.index ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1] }"
+    --ref "${genomeSource.index.fields.path}"
 #end if
   </command>
   <requirements><requirement type="package">picard</requirement></requirements>
diff --git a/tools/sr_mapping/PerM.xml b/tools/sr_mapping/PerM.xml
index cc290c90f97..1b787c7d5ca 100644
--- a/tools/sr_mapping/PerM.xml
+++ b/tools/sr_mapping/PerM.xml
@@ -11,9 +11,9 @@
         $s.sourceOfRef.ref
       #else
         #if $s.space == "color"
-          "${ filter( lambda x: str( x[0] ) == str( $s.sourceOfRef.index ), $__app__.tool_data_tables[ 'perm_color_indexes' ].get_fields() )[0][-1] }"
+          "${s.sourceOfRef.index.fields.path}"
         #elif $s.space == "base"
-          "${ filter( lambda x: str( x[0] ) == str( $s.sourceOfRef.index ), $__app__.tool_data_tables[ 'perm_base_indexes' ].get_fields() )[0][-1] }"
+          "${s.sourceOfRef.index.fields.path"
         #end if
       #end if
       #if $s.mate.singleOrPairs == "single":
diff --git a/tools/sr_mapping/bowtie_color_wrapper.xml b/tools/sr_mapping/bowtie_color_wrapper.xml
index 04e2e79f52d..e607d0231b9 100644
--- a/tools/sr_mapping/bowtie_color_wrapper.xml
+++ b/tools/sr_mapping/bowtie_color_wrapper.xml
@@ -58,7 +58,7 @@
       #end if
     #else
       ##use pre-built index
-      --ref="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'bowtie_indexes_color' ].get_fields() )[0][-1] }"
+      --ref="${refGenomeSource.index.fields.path}"
     #end if
     --paired=$singlePaired.sPaired
     #if $singlePaired.sPaired == "single":
diff --git a/tools/sr_mapping/bowtie_wrapper.xml b/tools/sr_mapping/bowtie_wrapper.xml
index 8bd57c3d6ee..cb2dc9ece2c 100644
--- a/tools/sr_mapping/bowtie_wrapper.xml
+++ b/tools/sr_mapping/bowtie_wrapper.xml
@@ -61,8 +61,7 @@
         #end if
       #else
         ##use pre-built index
-        ##--ref="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] }"
-        --ref="${ refGenomeSource.index.fields.path }"
+        --ref="${refGenomeSource.index.fields.path}"
       #end if
       --paired=$singlePaired.sPaired
       #if $singlePaired.sPaired == "single":
diff --git a/tools/sr_mapping/bwa_color_wrapper.xml b/tools/sr_mapping/bwa_color_wrapper.xml
index 1a6040dde82..cfd13f1ac2d 100644
--- a/tools/sr_mapping/bwa_color_wrapper.xml
+++ b/tools/sr_mapping/bwa_color_wrapper.xml
@@ -14,7 +14,7 @@
         --dbkey=$dbkey
       #else:
         ##use precomputed indexes
-        --ref="${ filter( lambda x: str( x[0] ) == str( $genomeSource.indices ), $__app__.tool_data_tables[ 'bwa_indexes_color' ].get_fields() )[0][-1] }"
+        --ref="${genomeSource.indices.fields.path}"
         --do_not_build_index
       #end if
 
diff --git a/tools/sr_mapping/bwa_wrapper.xml b/tools/sr_mapping/bwa_wrapper.xml
index bd27181746d..aa4a97fdb07 100644
--- a/tools/sr_mapping/bwa_wrapper.xml
+++ b/tools/sr_mapping/bwa_wrapper.xml
@@ -17,7 +17,7 @@
         --dbkey=$dbkey
       #else:
         ##use precomputed indexes
-        --ref="${ filter( lambda x: str( x[0] ) == str( $genomeSource.indices ), $__app__.tool_data_tables[ 'bwa_indexes' ].get_fields() )[0][-1] }"
+        --ref="${genomeSource.indices.fields.path}"
         --do_not_build_index
       #end if
 
diff --git a/tools/sr_mapping/lastz_paired_reads_wrapper.xml b/tools/sr_mapping/lastz_paired_reads_wrapper.xml
index 9f9f0f1c9d9..2ebaf3d60ed 100644
--- a/tools/sr_mapping/lastz_paired_reads_wrapper.xml
+++ b/tools/sr_mapping/lastz_paired_reads_wrapper.xml
@@ -12,7 +12,7 @@
         --input1=$source.input1
         --ref_sequences=$input1.metadata.sequences 
       #else:
-        --input1="${ filter( lambda x: str( x[0] ) == str( $source.input1_2bit ), $__app__.tool_data_tables[ 'lastz_seqs' ].get_fields() )[0][-1] }"
+        --input1="${source.input1_2bit.fields.path}"
       #end if
       --output=$output1
       --lastz_seqs_file_dir=${GALAXY_DATA_INDEX_DIR}
diff --git a/tools/sr_mapping/lastz_wrapper.xml b/tools/sr_mapping/lastz_wrapper.xml
index 3fbddea0d0b..8885f3634bc 100644
--- a/tools/sr_mapping/lastz_wrapper.xml
+++ b/tools/sr_mapping/lastz_wrapper.xml
@@ -12,7 +12,7 @@
         --input1=$source.input1
         --ref_sequences=$input1.metadata.sequences 
       #else:
-        --input1="${ filter( lambda x: str( x[0] ) == str( $source.input1_2bit ), $__app__.tool_data_tables[ 'lastz_seqs' ].get_fields() )[0][-1] }"
+        --input1="${source.input1_2bit.fields.path}"
         --ref_sequences="None" 
       #end if
       #if $params.source_select=="pre_set":
diff --git a/tools/sr_mapping/mosaik.xml b/tools/sr_mapping/mosaik.xml
index 5a947ac1ed2..aa96a41e32b 100644
--- a/tools/sr_mapping/mosaik.xml
+++ b/tools/sr_mapping/mosaik.xml
@@ -13,7 +13,7 @@
     #end if
     MosaikBuild -fr
     #if $genomeSource.refGenomeSource == 'indexed':
-        ${ filter( lambda x: str( x[0] ) == str( $genomeSource.indexReference ), $__app__.tool_data_tables[ 'mosaik_indexes' ].get_fields() )[0][-1] }
+        ${genomeSource.indexReference.fields.path}
     #else:
         $genomeSource.historyReference
     #end if

From 8a6b0001c26ab570c52c98c99054979b6826efd5 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Tue, 29 Nov 2011 17:35:14 -0500
Subject: [PATCH 259/362] Minor fix for 04e8ed0cd930.

---
 tools/sr_mapping/PerM.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/sr_mapping/PerM.xml b/tools/sr_mapping/PerM.xml
index 1b787c7d5ca..d0b84ea11fe 100644
--- a/tools/sr_mapping/PerM.xml
+++ b/tools/sr_mapping/PerM.xml
@@ -13,7 +13,7 @@
         #if $s.space == "color"
           "${s.sourceOfRef.index.fields.path}"
         #elif $s.space == "base"
-          "${s.sourceOfRef.index.fields.path"
+          "${s.sourceOfRef.index.fields.path}"
         #end if
       #end if
       #if $s.mate.singleOrPairs == "single":

From 566fc0621c6e74be8068f30975e464166fc96eed Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 30 Nov 2011 07:29:32 -0500
Subject: [PATCH 260/362] Fix for browsing libraries, json2 wasn't being
 loaded, needed in IE for jstorage to work.

---
 templates/library/common/browse_library.mako | 1 +
 1 file changed, 1 insertion(+)

diff --git a/templates/library/common/browse_library.mako b/templates/library/common/browse_library.mako
index 44a1a9952ed..649f00159b3 100644
--- a/templates/library/common/browse_library.mako
+++ b/templates/library/common/browse_library.mako
@@ -48,6 +48,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
+    ${h.js("json2")}
     ${h.js("jstorage")}
     ${common_javascripts()}
     ${self.grid_javascripts()}

From 278d15c4f923f3f9dbf5d528c99540c01a680c91 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Wed, 30 Nov 2011 09:16:37 -0500
Subject: [PATCH 261/362] Revert 2 changes made in 5db0da0007fc in an attempt
 to correct the broken behavior of rendering Galaxy correctly when using
 apache proxying, possibly in adition to requiring users to login.

---
 lib/galaxy/web/controllers/user.py        | 2 +-
 templates/webapps/galaxy/base_panels.mako | 6 +++++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/web/controllers/user.py b/lib/galaxy/web/controllers/user.py
index bf59187026c..c4d6102a532 100644
--- a/lib/galaxy/web/controllers/user.py
+++ b/lib/galaxy/web/controllers/user.py
@@ -358,7 +358,7 @@ class User( BaseUIController, UsesFormDefinitions ):
                 else:
                     refresh_frames = [ 'masthead', 'history' ]
             message, status, user, success = self.__validate_login( trans, webapp, **kwd )
-            if success and referer and not referer.startswith( url_for( trans.request.base + url_for( controller='user', action='logout' ) ) ):
+            if success and referer and not referer.startswith( trans.request.base + url_for( controller='user', action='logout' ) ):
                 redirect_url = referer
             elif success:
                 redirect_url = url_for( '/' )
diff --git a/templates/webapps/galaxy/base_panels.mako b/templates/webapps/galaxy/base_panels.mako
index 98dbfea871b..8638779f913 100644
--- a/templates/webapps/galaxy/base_panels.mako
+++ b/templates/webapps/galaxy/base_panels.mako
@@ -142,7 +142,11 @@
             menu_options.append( [ _('Preferences'), h.url_for( controller='/user', action='index', cntrller='user', webapp='galaxy' ), "galaxy_main" ] )
             if app.config.get_bool( 'enable_tracks', False ):
                 menu_options.append( [ 'Custom Builds', h.url_for( controller='/user', action='dbkeys' ), "galaxy_main" ] )
-            menu_options.append( [ 'Logout', h.url_for( controller='/user', action='logout', webapp='galaxy' ), "_top" ] )
+            if app.config.require_login:
+                logout_url = h.url_for( controller='/root', action='index', m_c='user', m_a='logout', webapp='galaxy' )
+            else:
+                logout_url = h.url_for( controller='/user', action='logout', webapp='galaxy' )
+            menu_options.append( [ 'Logout', logout_url, "_top" ] )
             menu_options.append( None )
         menu_options.append( [ _('Saved Histories'), h.url_for( controller='/history', action='list' ), "galaxy_main" ] )
         menu_options.append( [ _('Saved Datasets'), h.url_for( controller='/dataset', action='list' ), "galaxy_main" ] )

From fddfc5b6fad9b49bf31f06ffc4decebd785369d5 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Wed, 30 Nov 2011 10:20:15 -0500
Subject: [PATCH 262/362] Fix for frames inside of frames issue introduced in
 5db0da0007fc. Seen when require_login=True.

---
 lib/galaxy/web/framework/__init__.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/web/framework/__init__.py b/lib/galaxy/web/framework/__init__.py
index b2022172814..ed8e9ba4359 100644
--- a/lib/galaxy/web/framework/__init__.py
+++ b/lib/galaxy/web/framework/__init__.py
@@ -407,6 +407,7 @@ class GalaxyWebTransaction( base.DefaultWebTransaction ):
     def _ensure_logged_in_user( self, environ, session_cookie ):
         # The value of session_cookie can be one of 
         # 'galaxysession' or 'galaxycommunitysession'
+        # Currently this method does nothing unless session_cookie is 'galaxysession'
         if session_cookie == 'galaxysession':
             # TODO: re-engineer to eliminate the use of allowed_paths
             # as maintenance overhead is far too high.
@@ -436,8 +437,8 @@ class GalaxyWebTransaction( base.DefaultWebTransaction ):
                         host = None
                     if host in UCSC_SERVERS:
                         return
-            if self.request.path not in allowed_paths:
-                self.response.send_redirect( url_for( controller='root', action='index' ) )
+                if self.request.path not in allowed_paths:
+                    self.response.send_redirect( url_for( controller='root', action='index' ) )
     def __create_new_session( self, prev_galaxy_session=None, user_for_new_session=None ):
         """
         Create a new GalaxySession for this request, possibly with a connection

From a3f8cb2efc5d6660275745e3f9c5a6bd88a1337a Mon Sep 17 00:00:00 2001
From: Richard Burhans <burhans@bx.psu.edu>
Date: Wed, 30 Nov 2011 12:05:59 -0500
Subject: [PATCH 263/362] python version of "phyloP interspecies conservation
 scores" tool

---
 tool-data/add_scores.loc.sample |  27 ++++---
 tools/evolution/add_scores.py   | 120 ++++++++++++++++++++++++++++++++
 tools/evolution/add_scores.xml  |   6 +-
 3 files changed, 136 insertions(+), 17 deletions(-)
 create mode 100755 tools/evolution/add_scores.py

diff --git a/tool-data/add_scores.loc.sample b/tool-data/add_scores.loc.sample
index 1fc798bac11..7ff12ed2225 100644
--- a/tool-data/add_scores.loc.sample
+++ b/tool-data/add_scores.loc.sample
@@ -1,21 +1,20 @@
-#This is a sample file distributed with Galaxy that enables tools to use a
-#directory of gzipped genome files for use with add_scores.  You will need to
-#supply these files and then create a add_scores.loc file similar to this one
-#(store it in this directory) that points to the directories in which those
-#files are stored.  The add_scores.loc file has this format (white space
-#characters are TAB characters):
+#This is a sample file distributed with Galaxy that lists the BigWig files
+#available for use with the add_scores (phyloP interspecies conservation
+#scores) tool.  You will need to supply these BigWig files and then create
+#an add_scores.loc file similar to this one (store it in this directory)
+#that lists their locations.  The add_scores.loc file has the following
+#format (white space characters are TAB characters):
 #
-#<build>	<file_path>
+#<build>	<BigWig_file_path>
 #
 #So, for example, if your add_scores.loc began like this:
 #
-#hg18	/galaxy/data/hg18/misc/phyloP
+#hg18	/galaxy/data/hg18/misc/phyloP44way.primate.bw
 #
-#then your /galaxy/data/hg18/misc/phyloP directory would need to contain
-#the following gzipped files, among others:
+#then your /galaxy/data/hg18/misc/ directory would need to contain a
+#BigWig file named phyloP44way.primate.bw, among others:
 #
-#-rw-r--r-- 1 g2data g2data 161981190 2010-03-19 12:48 chr10.phyloP44way.primate.wigFix.gz
-#-rw-r--r-- 1 g2data g2data     54091 2010-03-19 12:56 chr10_random.phyloP44way.primate.wigFix.gz
-#-rw-r--r-- 1 g2data g2data 158621990 2010-03-19 12:46 chr11.phyloP44way.primate.wigFix.gz
+#-rw-r--r-- 1 g2data g2data 6057387572 Nov 23 10:11 phyloP44way.primate.bw
 #
-#hg18	/galaxy/data/hg18/misc/phyloP
+#hg18	/galaxy/data/hg18/misc/phyloP44way.primate.bw
+#hg19	/galaxy/data/hg19/misc/phyloP46way.primate.bw
diff --git a/tools/evolution/add_scores.py b/tools/evolution/add_scores.py
new file mode 100755
index 00000000000..5fddbf15089
--- /dev/null
+++ b/tools/evolution/add_scores.py
@@ -0,0 +1,120 @@
+#!/usr/bin/env python
+
+import sys
+from galaxy import eggs
+import pkg_resources
+pkg_resources.require( "bx-python" )
+pkg_resources.require( "numpy" )
+from bx.bbi.bigwig_file import BigWigFile
+import os
+
+################################################################################
+
+def die( message ):
+    print >> sys.stderr, message
+    sys.exit(1)
+
+def open_or_die( filename, mode='r', message=None ):
+    if message is None:
+        message = 'Error opening {0}'.format( filename )
+    try:
+        fh = open( filename, mode )
+    except IOError, err:
+        die( '{0}: {1}'.format( message, err.strerror ) )
+    return fh
+
+################################################################################
+
+class LocationFile( object ):
+    def __init__( self, filename, comment_chars=None, delimiter='\t', key_column=0 ):
+        self.filename = filename
+        if comment_chars is None:
+            self.comment_chars = ( '#' )
+        else:
+            self.comment_chars = tuple( comment_chars )
+        self.delimiter = delimiter
+        self.key_column = key_column
+        self._map = {}
+        self._populate_map()
+
+    def _populate_map( self ):
+        try:
+            with open( self.filename ) as fh:
+                line_number = 0
+                for line in fh:
+                    line_number += 1
+                    line = line.rstrip( '\r\n' )
+                    if not line.startswith( self.comment_chars ):
+                        elems = line.split( self.delimiter )
+                        if len( elems ) <= self.key_column:
+                            die( 'Location file {0} line {1}: less than {2} columns'.format( self.filename, line_number, self.key_column + 1 ) )
+                        else:
+                            key = elems.pop( self.key_column )
+                            if key in self._map:
+                                if self._map[key] != elems:
+                                    die( 'Location file {0} line {1}: duplicate key "{2}"'.format( self.filename, line_number, key ) )
+                            else:
+                                self._map[key] = elems
+        except IOError, err:
+            die( 'Error opening location file {0}: {1}'.format( self.filename, err.strerror ) )
+
+    def get_values( self, key ):
+        if key in self._map:
+            rval = self._map[key]
+            if len( rval ) == 1:
+                return rval[0]
+            else:
+                return rval
+        else:
+            die( 'key "{0}" not found in location file {1}'.format( key, self.filename ) )
+
+################################################################################
+
+def main():
+    input_filename, output_filename, loc_filename, loc_key, chrom_col, start_col = sys.argv[1:]
+
+    # open input, output, and bigwig files
+    location_file = LocationFile( loc_filename )
+    bigwig_filename = location_file.get_values( loc_key )
+    bwfh = open_or_die( bigwig_filename, message='Error opening BigWig file {0}'.format( bigwig_filename ) )
+    bw = BigWigFile( file=bwfh )
+    ifh = open_or_die( input_filename, message='Error opening input file {0}'.format( input_filename ) )
+    ofh = open_or_die( output_filename, mode='w', message='Error opening output file {0}'.format( output_filename ) )
+
+    # make column numbers 0-based
+    chrom_col = int( chrom_col ) - 1
+    start_col = int( start_col ) - 1
+    min_cols = max( chrom_col, start_col )
+
+    # add score column to imput file
+    line_number = 0
+    for line in ifh:
+        line_number += 1
+        line = line.rstrip( '\r\n' )
+        elems = line.split( '\t' )
+        if len( elems ) > min_cols:
+            chrom = elems[chrom_col].strip()
+            # base-0 position in chrom
+            start = int( elems[start_col] )
+            score_list = bw.get( chrom, start, start + 1 )
+            score_list_len = len( score_list )
+            if score_list_len == 1:
+                beg, end, score = score_list[0]
+                score_val = '{0:1.3f}'.format( score )
+            elif score_list_len == 0:
+                score_val = 'NA'
+            else:
+                die( '{0} line {1}: chrom={2}, start={3}, score_list_len = {4}'.format( input_filename, line_number, chrom, start, score_list_len ) )
+            print >> ofh, '\t'.join( [line, score_val] )
+        else:
+            print >> ofh, line
+
+    bwfh.close()
+    ifh.close()
+    ofh.close()
+
+################################################################################
+
+if __name__ == "__main__":
+    main()
+
diff --git a/tools/evolution/add_scores.xml b/tools/evolution/add_scores.xml
index 51cd75b82fc..ffa6ecac433 100644
--- a/tools/evolution/add_scores.xml
+++ b/tools/evolution/add_scores.xml
@@ -1,8 +1,8 @@
 <tool id="hgv_add_scores" name="phyloP" version="1.0.0">
   <description>interspecies conservation scores</description>
 
-  <command>
-    add_scores $input1 ${input1.metadata.dbkey} ${input1.metadata.chromCol} ${input1.metadata.startCol} ${GALAXY_DATA_INDEX_DIR}/add_scores.loc $out_file1
+  <command interpreter="python">
+    add_scores.py "$input1" "$out_file1" "${GALAXY_DATA_INDEX_DIR}/add_scores.loc" "${input1.metadata.dbkey}" "${input1.metadata.chromCol}" "${input1.metadata.startCol}"
   </command>
 
   <inputs>
@@ -34,7 +34,7 @@
   <help>
 .. class:: warningmark
 
-This currently works only for build hg18.
+This currently works only for builds hg18 and hg19.
 
 -----
 

From 6a90bd29f605efb94584190140e10cf9257b44bd Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Wed, 30 Nov 2011 13:06:12 -0500
Subject: [PATCH 264/362] Provide chromInfo correctly during conversions of
 datasets with custom build dbkeys.

---
 lib/galaxy/tools/actions/__init__.py | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/tools/actions/__init__.py b/lib/galaxy/tools/actions/__init__.py
index 33ac4968fca..eb2050d03e3 100644
--- a/lib/galaxy/tools/actions/__init__.py
+++ b/lib/galaxy/tools/actions/__init__.py
@@ -191,7 +191,16 @@ class DefaultToolAction( object ):
             db_datasets[ "chromInfo" ] = db_dataset
             incoming[ "chromInfo" ] = db_dataset.file_name
         else:
-            incoming[ "chromInfo" ] = os.path.join( trans.app.config.tool_data_path, 'shared','ucsc','chrom', "%s.len" % input_dbkey )
+            # For custom builds, chrom info resides in converted dataset; for built-in builds, chrom info resides in tool-data/shared.
+            if trans.user and ( input_dbkey in trans.user.preferences[ 'dbkeys' ] ):
+                # Custom build.
+                custom_build_dict = from_json_string( trans.user.preferences[ 'dbkeys' ] )[ input_dbkey ]
+                build_fasta_dataset = trans.app.model.HistoryDatasetAssociation.get( custom_build_dict[ 'fasta' ] )
+                chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' ).file_name
+            else:
+                # Default to built-in build.
+                chrom_info = os.path.join( trans.app.config.tool_data_path, 'shared','ucsc','chrom', "%s.len" % input_dbkey )
+            incoming[ "chromInfo" ] = chrom_info
         inp_data.update( db_datasets )
         
         # Determine output dataset permission/roles list

From ceaa71e4e8e7f7232a99afd44225430d83e6d105 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Wed, 30 Nov 2011 13:29:21 -0500
Subject: [PATCH 265/362] Add no_options validator to built-in reference genome
 selector in GATK tools.

---
 tools/gatk/count_covariates.xml            | 1 +
 tools/gatk/depth_of_coverage.xml           | 1 +
 tools/gatk/indel_realigner.xml             | 1 +
 tools/gatk/realigner_target_creator.xml    | 1 +
 tools/gatk/table_recalibration.xml         | 1 +
 tools/gatk/unified_genotyper.xml           | 1 +
 tools/gatk/variant_annotator.xml           | 1 +
 tools/gatk/variant_apply_recalibration.xml | 1 +
 tools/gatk/variant_combine.xml             | 1 +
 tools/gatk/variant_eval.xml                | 1 +
 tools/gatk/variant_filtration.xml          | 1 +
 tools/gatk/variant_recalibrator.xml        | 1 +
 tools/gatk/variants_validate.xml           | 1 +
 13 files changed, 13 insertions(+)

diff --git a/tools/gatk/count_covariates.xml b/tools/gatk/count_covariates.xml
index 6b39c225fcb..e8a1cfdd7ac 100644
--- a/tools/gatk/count_covariates.xml
+++ b/tools/gatk/count_covariates.xml
@@ -146,6 +146,7 @@
           <options from_data_table="gatk_picard_indexes">
             <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/>
           </options>
+          <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
diff --git a/tools/gatk/depth_of_coverage.xml b/tools/gatk/depth_of_coverage.xml
index 7157a0a274b..34e7543b96c 100644
--- a/tools/gatk/depth_of_coverage.xml
+++ b/tools/gatk/depth_of_coverage.xml
@@ -194,6 +194,7 @@
           <options from_data_table="gatk_picard_indexes">
             <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...--> 
           </options>
+          <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
diff --git a/tools/gatk/indel_realigner.xml b/tools/gatk/indel_realigner.xml
index fb97635d5fe..8e89e814eb9 100644
--- a/tools/gatk/indel_realigner.xml
+++ b/tools/gatk/indel_realigner.xml
@@ -124,6 +124,7 @@
           <options from_data_table="gatk_picard_indexes">
             <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/>
           </options>
+          <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
diff --git a/tools/gatk/realigner_target_creator.xml b/tools/gatk/realigner_target_creator.xml
index 5524e906ecb..684fa186db2 100644
--- a/tools/gatk/realigner_target_creator.xml
+++ b/tools/gatk/realigner_target_creator.xml
@@ -112,6 +112,7 @@
           <options from_data_table="gatk_picard_indexes">
             <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/>
           </options>
+          <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
         </param>
       </when>
       <when value="history">
diff --git a/tools/gatk/table_recalibration.xml b/tools/gatk/table_recalibration.xml
index 2ab733cb74f..afaf93ccca1 100644
--- a/tools/gatk/table_recalibration.xml
+++ b/tools/gatk/table_recalibration.xml
@@ -129,6 +129,7 @@
           <options from_data_table="gatk_picard_indexes">
             <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/>
           </options>
+          <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
diff --git a/tools/gatk/unified_genotyper.xml b/tools/gatk/unified_genotyper.xml
index 726b14e160c..82219da40c9 100644
--- a/tools/gatk/unified_genotyper.xml
+++ b/tools/gatk/unified_genotyper.xml
@@ -154,6 +154,7 @@
           <options from_data_table="gatk_picard_indexes">
             <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...--> 
           </options>
+          <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
diff --git a/tools/gatk/variant_annotator.xml b/tools/gatk/variant_annotator.xml
index f8d8509b99e..0599d93e7b3 100644
--- a/tools/gatk/variant_annotator.xml
+++ b/tools/gatk/variant_annotator.xml
@@ -157,6 +157,7 @@
           <options from_data_table="gatk_picard_indexes">
             <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/>
           </options>
+          <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
diff --git a/tools/gatk/variant_apply_recalibration.xml b/tools/gatk/variant_apply_recalibration.xml
index 6176b03244f..606f67b41a3 100644
--- a/tools/gatk/variant_apply_recalibration.xml
+++ b/tools/gatk/variant_apply_recalibration.xml
@@ -109,6 +109,7 @@
           <options from_data_table="gatk_picard_indexes">
             <!-- <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> -->
           </options>
+          <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
diff --git a/tools/gatk/variant_combine.xml b/tools/gatk/variant_combine.xml
index fd1aa9db0b1..1d4a2d95f74 100644
--- a/tools/gatk/variant_combine.xml
+++ b/tools/gatk/variant_combine.xml
@@ -121,6 +121,7 @@
           <options from_data_table="gatk_picard_indexes">
             <!-- <filter type="data_meta" key="dbkey" ref="input_variants.input_variant" column="dbkey"/> -->
           </options>
+          <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
diff --git a/tools/gatk/variant_eval.xml b/tools/gatk/variant_eval.xml
index 773b5ee51d7..57e71966a32 100644
--- a/tools/gatk/variant_eval.xml
+++ b/tools/gatk/variant_eval.xml
@@ -160,6 +160,7 @@
           <options from_data_table="gatk_picard_indexes">
             <!-- <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/> -->
           </options>
+          <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
diff --git a/tools/gatk/variant_filtration.xml b/tools/gatk/variant_filtration.xml
index 186470ee66c..5fc1ee8da02 100644
--- a/tools/gatk/variant_filtration.xml
+++ b/tools/gatk/variant_filtration.xml
@@ -110,6 +110,7 @@
           <options from_data_table="gatk_picard_indexes">
             <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/>
           </options>
+          <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
diff --git a/tools/gatk/variant_recalibrator.xml b/tools/gatk/variant_recalibrator.xml
index 3e44b0944cd..4fefaea3ef7 100644
--- a/tools/gatk/variant_recalibrator.xml
+++ b/tools/gatk/variant_recalibrator.xml
@@ -156,6 +156,7 @@
           <options from_data_table="gatk_picard_indexes">
           <!--  <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> -->
           </options>
+          <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
diff --git a/tools/gatk/variants_validate.xml b/tools/gatk/variants_validate.xml
index 911d2533189..cb680a0ab5f 100644
--- a/tools/gatk/variants_validate.xml
+++ b/tools/gatk/variants_validate.xml
@@ -96,6 +96,7 @@
           <options from_data_table="gatk_picard_indexes">
             <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/>
           </options>
+          <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->

From 40dadf71d860ce5ef4664aaedbccd116bec6135a Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Wed, 30 Nov 2011 17:22:30 -0500
Subject: [PATCH 266/362] Fix for 2ee4a6b8419b where chromInfo from custom
 dbkeys when no custom dbkeys have been defined would cause an error.

---
 lib/galaxy/tools/actions/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/tools/actions/__init__.py b/lib/galaxy/tools/actions/__init__.py
index eb2050d03e3..4d14a9d401b 100644
--- a/lib/galaxy/tools/actions/__init__.py
+++ b/lib/galaxy/tools/actions/__init__.py
@@ -192,7 +192,7 @@ class DefaultToolAction( object ):
             incoming[ "chromInfo" ] = db_dataset.file_name
         else:
             # For custom builds, chrom info resides in converted dataset; for built-in builds, chrom info resides in tool-data/shared.
-            if trans.user and ( input_dbkey in trans.user.preferences[ 'dbkeys' ] ):
+            if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( input_dbkey in trans.user.preferences[ 'dbkeys' ] ):
                 # Custom build.
                 custom_build_dict = from_json_string( trans.user.preferences[ 'dbkeys' ] )[ input_dbkey ]
                 build_fasta_dataset = trans.app.model.HistoryDatasetAssociation.get( custom_build_dict[ 'fasta' ] )

From ddcc9806aaae991341706d6fb143a5d1f4529f22 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Wed, 30 Nov 2011 22:50:12 -0500
Subject: [PATCH 267/362] Apply HTML escaping when editing dataset name.

---
 templates/dataset/edit_attributes.mako | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/templates/dataset/edit_attributes.mako b/templates/dataset/edit_attributes.mako
index 5c5c017bf3f..8a6abebbb27 100644
--- a/templates/dataset/edit_attributes.mako
+++ b/templates/dataset/edit_attributes.mako
@@ -39,7 +39,7 @@
                     Name:
                 </label>
                 <div style="float: left; width: 250px; margin-right: 10px;">
-                    <input type="text" name="name" value="${data.get_display_name()}" size="40"/>
+                    <input type="text" name="name" value="${data.get_display_name() | h}" size="40"/>
                 </div>
                 <div style="clear: both"></div>
             </div>

From cceebe85b0c52a4b9724fbcd013b5d1a8073331e Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Thu, 1 Dec 2011 10:22:46 -0500
Subject: [PATCH 268/362] When exporting a history archive, use user dataset
 names rather than Galaxy dataset names. Fixes #680

---
 lib/galaxy/tools/imp_exp/export_history.py | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/tools/imp_exp/export_history.py b/lib/galaxy/tools/imp_exp/export_history.py
index f5fa8b9fbf7..7e078379a8c 100644
--- a/lib/galaxy/tools/imp_exp/export_history.py
+++ b/lib/galaxy/tools/imp_exp/export_history.py
@@ -10,6 +10,14 @@ from galaxy import eggs
 from galaxy.util.json import *
 import optparse, sys, os, tempfile, tarfile
 
+def get_dataset_filename( name, ext ):
+    """
+    Builds a filename for a dataset using its name an extension.
+    """
+    valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
+    base = ''.join( c in valid_chars and c or '_' for c in name )
+    return base + ".%s" % ext
+
 def create_archive( history_attrs_file, datasets_attrs_file, jobs_attrs_file, out_file, gzip=False ):
     """ Create archive from the given attribute/metadata files and save it to out_file. """
     tarfile_mode = "w"
@@ -37,7 +45,8 @@ def create_archive( history_attrs_file, datasets_attrs_file, jobs_attrs_file, ou
         # TODO: security check to ensure that files added are in Galaxy dataset directory?
         for dataset_attrs in datasets_attrs:
             dataset_file_name = dataset_attrs[ 'file_name' ] # Full file name.
-            dataset_archive_name = os.path.join( "datasets", os.path.split( dataset_file_name )[-1] )
+            dataset_archive_name = os.path.join( 'datasets', 
+                                                 get_dataset_filename( dataset_attrs[ 'name' ], dataset_attrs[ 'extension' ] ) )
             history_archive.add( dataset_file_name, arcname=dataset_archive_name )
             # Update dataset filename to be archive name.
             dataset_attrs[ 'file_name' ] = dataset_archive_name

From 46a7c4913714d639014f2c16f74430d26b2bf0b7 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Thu, 1 Dec 2011 10:57:51 -0500
Subject: [PATCH 269/362] Temporarily remove Yogeshwar's recently added
 microsatellite tools from tool_conf.xml.sample to prevent buildbot testing.

---
 tool_conf.xml.sample | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index 2fbde9915f7..e1f6667d4f9 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -192,8 +192,8 @@
     <tool file="regVariation/compute_motif_frequencies_for_all_motifs.xml" />
     <tool file="regVariation/categorize_elements_satisfying_criteria.xml" />s
     <tool file="regVariation/draw_stacked_barplots.xml" />
-    <tool file="regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml" />
-    <tool file="regVariation/microsatellite_birthdeath.xml" />
+    <!-- <tool file="regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml" />
+    <tool file="regVariation/microsatellite_birthdeath.xml" /> -->
   </section>
   <section name="Multiple regression" id="multReg">
     <tool file="regVariation/linear_regression.xml" />

From fc66cff96b64b114042e3b4a7ea4384f8398ba3d Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Thu, 1 Dec 2011 15:01:28 -0500
Subject: [PATCH 270/362] Trackster: fix bug in determining when to display
 filters.

---
 static/scripts/trackster.js | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index 80addfdfc1b..2c8e2adbb39 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -3459,13 +3459,17 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
             }
 
             // Determine if filters are available; this is based on the tiles' data.
+            // Criteria for filter to be available: (a) it is applicable to tile data and (b) filter min != filter max.
             var filters_available = false,
-                example_feature;
+                example_feature,
+                filter;
             for (var i = 0; i < tiles.length; i++) {
                 if (tiles[i].data.length) {
                     example_feature = tiles[i].data[0];
                     for (var f = 0; f < filters.length; f++) {
-                        if (filters[f].applies_to(example_feature)) {
+                        filter = filters[f];
+                        if ( filter.applies_to(example_feature) && 
+                             filter.min !== filter.max ) {
                             filters_available = true;
                             break;
                         }

From b22b2358dc8a260fea8bcaedf8e1b0dde314a49e Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Fri, 2 Dec 2011 11:10:04 -0500
Subject: [PATCH 271/362] Trackster: interpret feature track data using
 0-based, half-open coordinate system.

---
 static/scripts/trackster.js | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index 2c8e2adbb39..3941704ce9e 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -4294,6 +4294,8 @@ FeaturePositionMapper.prototype.get_feature_data = function(x, y) {
 
 /**
  * Abstract object for painting feature tracks. Subclasses must implement draw_element() for painting to work.
+ * Painter uses a 0-based, half-open coordinate system; start coordinate is closed--included--and the end is open.
+ * This coordinate system matches the BED format.
  */
 var FeaturePainter = function(data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler) {
     Painter.call(this, data, view_start, view_end, prefs, mode);
@@ -4419,7 +4421,8 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
         var 
             feature_uid = feature[0],
             feature_start = feature[1],
-            feature_end = feature[2], 
+            // -1 because end is not included in feature; see FeaturePainter documentation for details.
+            feature_end = feature[2] - 1,
             feature_name = feature[3],
             f_start = Math.floor( Math.max(0, (feature_start - tile_low) * w_scale) ),
             f_end   = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low) * w_scale)) ),
@@ -4537,7 +4540,8 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
                 for (var k = 0, k_len = feature_blocks.length; k < k_len; k++) {
                     var block = feature_blocks[k],
                         block_start = Math.floor( Math.max(0, (block[0] - tile_low) * w_scale) ),
-                        block_end = Math.ceil( Math.min(width, Math.max((block[1] - tile_low) * w_scale)) ),
+                        // -1 because end is not included in feature; see FeaturePainter documentation for details.
+                        block_end = Math.ceil( Math.min(width, Math.max((block[1] - 1 - tile_low) * w_scale)) ),
                         last_block_start, last_block_end;
 
                     // Skip drawing if block not on tile.    

From d9871a4b58c34a30768b368a8934e48b43d53b64 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Fri, 2 Dec 2011 12:32:14 -0500
Subject: [PATCH 272/362] Trackster: default to datasets in current history
 when adding tracks.

---
 lib/galaxy/web/controllers/tracks.py | 9 +++++++++
 templates/tracks/browser.mako        | 2 +-
 2 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/web/controllers/tracks.py b/lib/galaxy/web/controllers/tracks.py
index 06eed0039b5..020d4fd7e14 100644
--- a/lib/galaxy/web/controllers/tracks.py
+++ b/lib/galaxy/web/controllers/tracks.py
@@ -734,6 +734,15 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
         # Render the list view
         return self.histories_grid( trans, **kwargs )
         
+    @web.expose
+    @web.require_login( "see current history's datasets that can added to this visualization" )
+    def list_current_history_datasets( self, trans, **kwargs ):
+        """ List a history's datasets that can be added to a visualization. """
+        
+        kwargs[ 'f-history' ] = trans.security.encode_id( trans.get_history().id )
+        kwargs[ 'show_item_checkboxes' ] = 'True'
+        return self.list_history_datasets( trans, **kwargs )
+        
     @web.expose
     @web.require_login( "see a history's datasets that can added to this visualization" )
     def list_history_datasets( self, trans, **kwargs ):
diff --git a/templates/tracks/browser.mako b/templates/tracks/browser.mako
index 113bc5e1129..519bb0427b4 100644
--- a/templates/tracks/browser.mako
+++ b/templates/tracks/browser.mako
@@ -63,7 +63,7 @@ ${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.e
      */
     var add_tracks = function() {
         $.ajax({
-            url: "${h.url_for( action='list_histories' )}",
+            url: "${h.url_for( action='list_current_history_datasets' )}",
             data: { "f-dbkey": view.dbkey },
             error: function() { alert( "Grid failed" ); },
             success: function(table_html) {

From ad7d37774dd8b5721dbaa59f7e9df0b83a4e4e62 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Fri, 2 Dec 2011 13:56:45 -0500
Subject: [PATCH 273/362] (1) Fail gracefully when visualization cannot be
 saved and (2) fix bug in setting modal's minimum width.

---
 static/scripts/galaxy.panels.js | 2 +-
 templates/tracks/browser.mako   | 7 +++++--
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/static/scripts/galaxy.panels.js b/static/scripts/galaxy.panels.js
index 37adce6b7e2..bc33a9c618d 100644
--- a/static/scripts/galaxy.panels.js
+++ b/static/scripts/galaxy.panels.js
@@ -211,7 +211,7 @@ function _show_modal( title, body, buttons, extra_buttons, init_fn ) {
     }
     var body_elt = $( ".dialog-box" ).find( ".body" );
     // Clear min-width to allow for modal to take size of new body.
-    body_elt.css("min-width", "");
+    body_elt.css("min-width", "0px");
     $( ".dialog-box" ).find( ".body" ).html( body );
     if ( ! $(".dialog-box-container").is( ":visible" ) ) {
         $("#overlay").show();
diff --git a/templates/tracks/browser.mako b/templates/tracks/browser.mako
index 519bb0427b4..1be5d8c2ec4 100644
--- a/templates/tracks/browser.mako
+++ b/templates/tracks/browser.mako
@@ -230,7 +230,7 @@ ${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.e
             
             $("#save-icon").click( function() {                
                 // Show saving dialog box
-                show_modal("Saving...", "<img src='${h.url_for('/static/images/yui/rel_interstitial_loading.gif')}'/>");
+                show_modal("Saving...", "progress");
                                     
                 // Save bookmarks.
                 var bookmarks = [];
@@ -267,7 +267,10 @@ ${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.e
                         // Needed to set URL when first saving a visualization.
                         window.history.pushState({}, "", vis_info.url);
                     },
-                    error: function() { alert("Could not save visualization"); }
+                    error: function() { 
+                        show_modal( "Could Not Save", "Could not save visualization. Please try again later.", 
+                                    { "Close" : hide_modal } );
+                    }
                 });
             });
             

From abc524f5a264afb5ba9d740f9a414b4282c4eef1 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Fri, 2 Dec 2011 14:20:29 -0500
Subject: [PATCH 274/362] Trackster bug fix: add missing object reference.

---
 static/scripts/trackster.js | 1 +
 1 file changed, 1 insertion(+)

diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index 3941704ce9e..85e2d9d9599 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -2355,6 +2355,7 @@ var FeatureTrackTile = function(track, index, resolution, canvas, data, mode, me
             more_across_icon = $("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(message_div);
 
         // Set up actions for icons.
+        var tile = this;
         more_down_icon.click(function() {
             // Mark tile as stale, request more data, and redraw track.
             tile.stale = true;

From 85403d0bec0540e46c84fec4465dc429241cb204 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Fri, 2 Dec 2011 14:49:43 -0500
Subject: [PATCH 275/362] 1. Add 3 columns to the tool_shed_repository table in
 the Galaxy model / database; metadata (json), includes_datatypes (boolean)
 and update_available (boolean) 2. Add the ability to set metadata for tool
 shed repositories installed into local Galaxy instances (at time of install
 and on the Manage repository page) 3. Add the ability to view tool shed
 repository metadata (including tool guids) when managing installed tool shed
 repositories within Galaxy 4. Create a new admin_toolshed controller, and
 move all tool shed related code from the admin controller to this new
 controller

---
 lib/galaxy/model/__init__.py                  |   6 +-
 lib/galaxy/model/mapping.py                   |   3 +
 ..._add_tool_shed_repository_table_columns.py |  80 ++
 lib/galaxy/web/controllers/admin.py           | 794 +---------------
 lib/galaxy/web/controllers/admin_toolshed.py  | 889 ++++++++++++++++++
 lib/galaxy/web/controllers/workflow.py        |   4 +-
 .../community/controllers/repository.py       |  10 +-
 .../browse_repository.mako                    | 115 +--
 .../admin/tool_shed_repository/common.mako    | 171 ++++
 .../manage_repository.mako                    |  12 +-
 .../select_tool_panel_section.mako            |   2 +-
 .../view_tool_metadata.mako                   | 155 +++
 templates/webapps/community/base_panels.mako  |   3 +-
 templates/webapps/galaxy/admin/index.mako     |   4 +-
 .../webapps/galaxy/admin/tool_sheds.mako      |   8 +-
 15 files changed, 1335 insertions(+), 921 deletions(-)
 create mode 100644 lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py
 create mode 100644 lib/galaxy/web/controllers/admin_toolshed.py
 create mode 100644 templates/admin/tool_shed_repository/common.mako
 rename templates/admin/{ => tool_shed_repository}/select_tool_panel_section.mako (94%)
 create mode 100644 templates/admin/tool_shed_repository/view_tool_metadata.mako

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index cd5d71f6190..03cda106d67 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -2646,7 +2646,8 @@ class APIKeys( object ):
     pass
 
 class ToolShedRepository( object ):
-    def __init__( self, id=None, create_time=None, tool_shed=None, name=None, description=None, owner=None, changeset_revision=None, deleted=False ):
+    def __init__( self, id=None, create_time=None, tool_shed=None, name=None, description=None, owner=None,
+                  changeset_revision=None, metadata=None, includes_datatypes=False, update_available=False, deleted=False ):
         self.id = id
         self.create_time = create_time
         self.tool_shed = tool_shed
@@ -2654,6 +2655,9 @@ class ToolShedRepository( object ):
         self.description = description
         self.owner = owner
         self.changeset_revision = changeset_revision
+        self.metadata = metadata
+        self.includes_datatypes = includes_datatypes
+        self.update_available = update_available
         self.deleted = deleted
 
 ## ---- Utility methods -------------------------------------------------------
diff --git a/lib/galaxy/model/mapping.py b/lib/galaxy/model/mapping.py
index 18b235ab14f..a19a5288dbe 100644
--- a/lib/galaxy/model/mapping.py
+++ b/lib/galaxy/model/mapping.py
@@ -373,6 +373,9 @@ ToolShedRepository.table = Table( "tool_shed_repository", metadata,
     Column( "description" , TEXT ),
     Column( "owner", TrimmedString( 255 ), index=True ),
     Column( "changeset_revision", TrimmedString( 255 ), index=True ),
+    Column( "metadata", JSONType, nullable=True ),
+    Column( "includes_datatypes", Boolean, index=True, default=False ),
+    Column( "update_available", Boolean, default=False ),
     Column( "deleted", Boolean, index=True, default=False ) )
 
 Job.table = Table( "job", metadata,
diff --git a/lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py b/lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py
new file mode 100644
index 00000000000..37559bf70ee
--- /dev/null
+++ b/lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py
@@ -0,0 +1,80 @@
+"""
+Migration script to add the metadata, update_available and includes_datatypes columns to the tool_shed_repository table.
+"""
+
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+from migrate.changeset import *
+
+import datetime
+now = datetime.datetime.utcnow
+# Need our custom types, but don't import anything else from model
+from galaxy.model.custom_types import *
+
+import sys, logging
+log = logging.getLogger( __name__ )
+log.setLevel(logging.DEBUG)
+handler = logging.StreamHandler( sys.stdout )
+format = "%(name)s %(levelname)s %(asctime)s %(message)s"
+formatter = logging.Formatter( format )
+handler.setFormatter( formatter )
+log.addHandler( handler )
+
+metadata = MetaData( migrate_engine )
+db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) )
+
+def upgrade():
+    print __doc__
+    metadata.reflect()
+    ToolShedRepository_table = Table( "tool_shed_repository", metadata, autoload=True )
+    c = Column( "metadata", JSONType(), nullable=True )
+    try:
+        c.create( ToolShedRepository_table )
+        assert c is ToolShedRepository_table.c.metadata
+    except Exception, e:
+        print "Adding metadata column to the tool_shed_repository table failed: %s" % str( e )
+        log.debug( "Adding metadata column to the tool_shed_repository table failed: %s" % str( e ) )
+    c = Column( "includes_datatypes", Boolean, index=True, default=False )
+    try:
+        c.create( ToolShedRepository_table )
+        assert c is ToolShedRepository_table.c.includes_datatypes
+        if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite': 
+            default_false = "0"
+        elif migrate_engine.name == 'postgres':
+            default_false = "false"
+        db_session.execute( "UPDATE tool_shed_repository SET includes_datatypes=%s" % default_false )
+    except Exception, e:
+        print "Adding includes_datatypes column to the tool_shed_repository table failed: %s" % str( e )
+        log.debug( "Adding includes_datatypes column to the tool_shed_repository table failed: %s" % str( e ) )
+    c = Column( "update_available", Boolean, default=False )
+    try:
+        c.create( ToolShedRepository_table )
+        assert c is ToolShedRepository_table.c.update_available
+        if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite': 
+            default_false = "0"
+        elif migrate_engine.name == 'postgres':
+            default_false = "false"
+        db_session.execute( "UPDATE tool_shed_repository SET update_available=%s" % default_false )
+    except Exception, e:
+        print "Adding update_available column to the tool_shed_repository table failed: %s" % str( e )
+        log.debug( "Adding update_available column to the tool_shed_repository table failed: %s" % str( e ) )
+
+def downgrade():
+    metadata.reflect()
+    ToolShedRepository_table = Table( "tool_shed_repository", metadata, autoload=True )
+    try:
+        ToolShedRepository_table.c.metadata.drop()
+    except Exception, e:
+        print "Dropping column metadata from the tool_shed_repository table failed: %s" % str( e )
+        log.debug( "Dropping column metadata from the tool_shed_repository table failed: %s" % str( e ) )
+    try:
+        ToolShedRepository_table.c.includes_datatypes.drop()
+    except Exception, e:
+        print "Dropping column includes_datatypes from the tool_shed_repository table failed: %s" % str( e )
+        log.debug( "Dropping column includes_datatypes from the tool_shed_repository table failed: %s" % str( e ) )
+    try:
+        ToolShedRepository_table.c.update_available.drop()
+    except Exception, e:
+        print "Dropping column update_available from the tool_shed_repository table failed: %s" % str( e )
+        log.debug( "Dropping column update_available from the tool_shed_repository table failed: %s" % str( e ) )
diff --git a/lib/galaxy/web/controllers/admin.py b/lib/galaxy/web/controllers/admin.py
index 07bc69a6502..6dabc40335f 100644
--- a/lib/galaxy/web/controllers/admin.py
+++ b/lib/galaxy/web/controllers/admin.py
@@ -5,13 +5,13 @@ from galaxy.web.framework.helpers import time_ago, iff, grids
 from galaxy.tools.search import ToolBoxSearch
 from galaxy.tools import ToolSection, json_fix
 from galaxy.util import parse_xml, inflector
-import logging
-log = logging.getLogger( __name__ )
-
 from galaxy.actions.admin import AdminActions
 from galaxy.web.params import QuotaParamParser
 from galaxy.exceptions import *
 import galaxy.datatypes.registry
+import logging
+
+log = logging.getLogger( __name__ )
 
 class UserListGrid( grids.Grid ):
     class EmailColumn( grids.TextColumn ):
@@ -383,63 +383,12 @@ class QuotaListGrid( grids.Grid ):
     preserve_state = False
     use_paging = True
 
-class RepositoryListGrid( grids.Grid ):
-    class NameColumn( grids.TextColumn ):
-        def get_value( self, trans, grid, tool_shed_repository ):
-            return tool_shed_repository.name
-    class DescriptionColumn( grids.TextColumn ):
-        def get_value( self, trans, grid, tool_shed_repository ):
-            return tool_shed_repository.description
-    class OwnerColumn( grids.TextColumn ):
-        def get_value( self, trans, grid, tool_shed_repository ):
-            return tool_shed_repository.owner
-    class RevisionColumn( grids.TextColumn ):
-        def get_value( self, trans, grid, tool_shed_repository ):
-            return tool_shed_repository.changeset_revision
-    class ToolShedColumn( grids.TextColumn ):
-        def get_value( self, trans, grid, tool_shed_repository ):
-            return tool_shed_repository.tool_shed
-    # Grid definition
-    title = "Installed tool shed repositories"
-    model_class = model.ToolShedRepository
-    template='/admin/tool_shed_repository/grid.mako'
-    default_sort_key = "name"
-    columns = [
-        NameColumn( "Name",
-                    key="name",
-                    link=( lambda item: dict( operation="manage_repository", id=item.id, webapp="galaxy" ) ),
-                    attach_popup=False ),
-        DescriptionColumn( "Description" ),
-        OwnerColumn( "Owner" ),
-        RevisionColumn( "Revision" ),
-        ToolShedColumn( "Tool shed" ),
-        # Columns that are valid for filtering but are not visible.
-        grids.DeletedColumn( "Deleted",
-                             key="deleted",
-                             visible=False,
-                             filterable="advanced" )
-    ]
-    columns.append( grids.MulticolFilterColumn( "Search repository name", 
-                                                cols_to_filter=[ columns[0] ],
-                                                key="free-text-search",
-                                                visible=False,
-                                                filterable="standard" ) )
-    standard_filters = []
-    default_filter = dict( deleted="False" )
-    num_rows_per_page = 50
-    preserve_state = False
-    use_paging = True
-    def build_initial_query( self, trans, **kwd ):
-        return trans.sa_session.query( self.model_class ) \
-                               .filter( self.model_class.table.c.deleted == False )
-
 class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamParser ):
     
     user_list_grid = UserListGrid()
     role_list_grid = RoleListGrid()
     group_list_grid = GroupListGrid()
     quota_list_grid = QuotaListGrid()
-    repository_list_grid = RepositoryListGrid()
     delete_operation = grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), allow_multiple=True )
     undelete_operation = grids.GridOperation( "Undelete", condition=( lambda item: item.deleted and not item.purged ), allow_multiple=True )
     purge_operation = grids.GridOperation( "Purge", condition=( lambda item: item.deleted and not item.purged ), allow_multiple=True )
@@ -676,391 +625,6 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
         return quota, params
     @web.expose
     @web.require_admin
-    def browse_tool_shed_repository( self, trans, **kwd ):
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        status = params.get( 'status', 'done' )
-        repository = get_repository( trans, kwd[ 'id' ] )
-        relative_install_dir = self.__get_relative_install_dir( trans, repository )
-        repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, repository.name ) )
-        tool_dicts = []
-        workflow_dicts = []
-        for root, dirs, files in os.walk( repo_files_dir ):
-            if not root.find( '.hg' ) >= 0 and not root.find( 'hgrc' ) >= 0:
-                if '.hg' in dirs:
-                    # Don't visit .hg directories.
-                    dirs.remove( '.hg' )
-                if 'hgrc' in files:
-                     # Don't include hgrc files.
-                    files.remove( 'hgrc' )
-                for name in files:
-                    # Find all tool configs.
-                    if name.endswith( '.xml' ):
-                        try:
-                            full_path = os.path.abspath( os.path.join( root, name ) )
-                            tool = trans.app.toolbox.load_tool( full_path )
-                            if tool is not None:
-                                tool_config = os.path.join( root, name )
-                                # Handle tool.requirements.
-                                tool_requirements = []
-                                for tr in tool.requirements:
-                                    name=tr.name
-                                    type=tr.type
-                                    if type == 'fabfile':
-                                        version = None
-                                        fabfile = tr.fabfile
-                                        method = tr.method
-                                    else:
-                                        version = tr.version
-                                        fabfile = None
-                                        method = None
-                                    requirement_dict = dict( name=name,
-                                                             type=type,
-                                                             version=version,
-                                                             fabfile=fabfile,
-                                                             method=method )
-                                    tool_requirements.append( requirement_dict )
-                                tool_dict = dict( id=tool.id,
-                                                  old_id=tool.old_id,
-                                                  name=tool.name,
-                                                  version=tool.version,
-                                                  description=tool.description,
-                                                  requirements=tool_requirements,
-                                                  tool_config=tool_config )
-                                tool_dicts.append( tool_dict )
-                        except Exception, e:
-                            # The file is not a Galaxy tool config.
-                            pass
-                    # Find all exported workflows
-                    elif name.endswith( '.ga' ):
-                        try:
-                            full_path = os.path.abspath( os.path.join( root, name ) )
-                            # Convert workflow data from json
-                            fp = open( full_path, 'rb' )
-                            workflow_text = fp.read()
-                            fp.close()
-                            workflow_dict = from_json_string( workflow_text )
-                            if workflow_dict[ 'a_galaxy_workflow' ] == 'true':
-                                workflow_dicts.append( dict( full_path=full_path, workflow_dict=workflow_dict ) )
-                        except Exception, e:
-                            # The file is not a Galaxy workflow.
-                            pass
-        return trans.fill_template( '/admin/tool_shed_repository/browse_repository.mako',
-                                    repository=repository,
-                                    tool_dicts=tool_dicts,
-                                    workflow_dicts=workflow_dicts,
-                                    message=message,
-                                    status=status )
-    @web.expose
-    @web.require_admin
-    def browse_tool_shed_repositories( self, trans, **kwd ):
-        if 'operation' in kwd:
-            operation = kwd.pop( 'operation' ).lower()
-            if operation == "manage_repository":
-                return self.manage_tool_shed_repository( trans, **kwd )
-        # Render the list view
-        return self.repository_list_grid( trans, **kwd )
-    @web.expose
-    @web.require_admin
-    def browse_tool_sheds( self, trans, **kwd ):
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        status = params.get( 'status', 'done' )
-        return trans.fill_template( '/webapps/galaxy/admin/tool_sheds.mako',
-                                    webapp='galaxy',
-                                    message=message,
-                                    status='error' )
-    @web.expose
-    @web.require_admin
-    def find_tools_in_tool_shed( self, trans, **kwd ):
-        tool_shed_url = kwd[ 'tool_shed_url' ]
-        galaxy_url = url_for( '', qualified=True )
-        url = '%s/repository/find_tools?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, galaxy_url )
-        return trans.response.send_redirect( url )
-    @web.expose
-    @web.require_admin
-    def find_workflows_in_tool_shed( self, trans, **kwd ):
-        tool_shed_url = kwd[ 'tool_shed_url' ]
-        galaxy_url = url_for( '', qualified=True )
-        url = '%s/repository/find_workflows?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, galaxy_url )
-        return trans.response.send_redirect( url )
-    @web.expose
-    @web.require_admin
-    def browse_tool_shed( self, trans, **kwd ):
-        tool_shed_url = kwd[ 'tool_shed_url' ]
-        galaxy_url = url_for( '', qualified=True )
-        url = '%s/repository/browse_valid_repositories?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, galaxy_url )
-        return trans.response.send_redirect( url )
-    @web.expose
-    @web.require_admin
-    def install_tool_shed_repository( self, trans, **kwd ):
-        if not trans.app.toolbox.shed_tool_confs:
-            message = 'The <b>tool_config_file</b> setting in <b>universe_wsgi.ini</b> must include at least one shed tool configuration file name with a '
-            message += '<b>&lt;toolbox&gt;</b> tag that includes a <b>tool_path</b> attribute value which is a directory relative to the Galaxy installation '
-            message += 'directory in order to automatically install tools from a Galaxy tool shed (e.g., the file name <b>shed_tool_conf.xml</b> whose '
-            message += '<b>&lt;toolbox&gt;</b> tag is <b>&lt;toolbox tool_path="../shed_tools"&gt;</b>).<p/>See the '
-            message += '<a href="http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance" '
-            message += 'target="_blank">Automatic installation of Galaxy tool shed repository tools into a local Galaxy instance</a> section of the '
-            message += '<a href="http://wiki.g2.bx.psu.edu/Tool%20Shed" target="_blank">Galaxy tool shed wiki</a> for all of the details.'
-            return trans.show_error_message( message )
-        message = kwd.get( 'message', ''  )
-        status = kwd.get( 'status', 'done' )
-        tool_shed_url = kwd[ 'tool_shed_url' ]
-        repo_info_dict = kwd[ 'repo_info_dict' ]
-        new_tool_panel_section = kwd.get( 'new_tool_panel_section', '' )
-        tool_panel_section = kwd.get( 'tool_panel_section', '' )
-        if kwd.get( 'select_tool_panel_section_button', False ):
-            shed_tool_conf = kwd[ 'shed_tool_conf' ]
-            # Get the tool path.
-            for k, tool_path in trans.app.toolbox.shed_tool_confs.items():
-                if k == shed_tool_conf:
-                    break
-            if new_tool_panel_section or tool_panel_section:
-                if new_tool_panel_section:
-                    section_id = new_tool_panel_section.lower().replace( ' ', '_' )
-                    new_section_key = 'section_%s' % str( section_id )
-                    if new_section_key in trans.app.toolbox.tool_panel:
-                        # Appending a tool to an existing section in trans.app.toolbox.tool_panel
-                        log.debug( "Appending to tool panel section: %s" % new_tool_panel_section )
-                        tool_section = trans.app.toolbox.tool_panel[ new_section_key ]
-                    else:
-                        # Appending a new section to trans.app.toolbox.tool_panel
-                        log.debug( "Loading new tool panel section: %s" % new_tool_panel_section )
-                        elem = Element( 'section' )
-                        elem.attrib[ 'name' ] = new_tool_panel_section
-                        elem.attrib[ 'id' ] = section_id
-                        tool_section = ToolSection( elem )
-                        trans.app.toolbox.tool_panel[ new_section_key ] = tool_section
-                else:
-                    section_key = 'section_%s' % tool_panel_section
-                    tool_section = trans.app.toolbox.tool_panel[ section_key ]
-                # Decode the encoded repo_info_dict param value.
-                repo_info_dict = tool_shed_decode( repo_info_dict )
-                # Clone the repository to the configured location.
-                current_working_dir = os.getcwd()
-                installed_repository_names = []
-                for name, repo_info_tuple in repo_info_dict.items():
-                    description, repository_clone_url, changeset_revision = repo_info_tuple
-                    clone_dir = os.path.join( tool_path, self.__generate_tool_path( repository_clone_url, changeset_revision ) )
-                    if os.path.exists( clone_dir ):
-                        # Repository and revision has already been cloned.
-                        # TODO: implement the ability to re-install or revert an existing repository.
-                        message += 'Revision <b>%s</b> of repository <b>%s</b> was previously installed.<br/>' % ( changeset_revision, name )
-                    else:
-                        os.makedirs( clone_dir )
-                        log.debug( 'Cloning %s...' % repository_clone_url )
-                        cmd = 'hg clone %s' % repository_clone_url
-                        tmp_name = tempfile.NamedTemporaryFile().name
-                        tmp_stderr = open( tmp_name, 'wb' )
-                        os.chdir( clone_dir )
-                        proc = subprocess.Popen( args=cmd, shell=True, stderr=tmp_stderr.fileno() )
-                        returncode = proc.wait()
-                        os.chdir( current_working_dir )
-                        tmp_stderr.close()
-                        if returncode == 0:
-                            # Add a new record to the tool_shed_repository table if one doesn't
-                            # already exist.  If one exists but is marked deleted, undelete it.
-                            self.__create_or_undelete_tool_shed_repository( trans, name, description, changeset_revision, repository_clone_url )
-                            # Update the cloned repository to changeset_revision.
-                            repo_files_dir = os.path.join( clone_dir, name )
-                            log.debug( 'Updating cloned repository to revision "%s"...' % changeset_revision )
-                            cmd = 'hg update -r %s' % changeset_revision
-                            tmp_name = tempfile.NamedTemporaryFile().name
-                            tmp_stderr = open( tmp_name, 'wb' )
-                            os.chdir( repo_files_dir )
-                            proc = subprocess.Popen( cmd, shell=True, stderr=tmp_stderr.fileno() )
-                            returncode = proc.wait()
-                            os.chdir( current_working_dir )
-                            tmp_stderr.close()
-                            if returncode == 0:
-                                # Load data types required by tools.
-                                self.__load_datatypes( trans, repo_files_dir )
-                                # Load tools and tool data files required by them.
-                                sample_files, repository_tools_tups = self.__get_repository_tools_and_sample_files( trans, tool_path, repo_files_dir )
-                                if repository_tools_tups:
-                                    # Handle missing data table entries for tool parameters that are dynamically generated select lists.
-                                    repository_tools_tups = self.__handle_missing_data_table_entry( trans, tool_path, sample_files, repository_tools_tups )
-                                    # Handle missing index files for tool parameters that are dynamically generated select lists.
-                                    repository_tools_tups = self.__handle_missing_index_file( trans, tool_path, sample_files, repository_tools_tups )
-                                    # Handle tools that use fabric scripts to install dependencies.
-                                    self.__handle_tool_dependencies( current_working_dir, repo_files_dir, repository_tools_tups )
-                                    # Generate an in-memory tool conf section that includes the new tools.
-                                    new_tool_section = self.__generate_tool_panel_section( name,
-                                                                                           repository_clone_url,
-                                                                                           changeset_revision,
-                                                                                           tool_section,
-                                                                                           repository_tools_tups )
-                                    # Create a temporary file to persist the in-memory tool section
-                                    # TODO: Figure out how to do this in-memory using xml.etree.
-                                    tmp_name = tempfile.NamedTemporaryFile().name
-                                    persisted_new_tool_section = open( tmp_name, 'wb' )
-                                    persisted_new_tool_section.write( new_tool_section )
-                                    persisted_new_tool_section.close()
-                                    # Parse the persisted tool panel section
-                                    tree = parse_xml( tmp_name )
-                                    root = tree.getroot()
-                                    # Load the tools in the section into the tool panel.
-                                    trans.app.toolbox.load_section_tag_set( root, trans.app.toolbox.tool_panel, tool_path )
-                                    # Remove the temporary file
-                                    try:
-                                        os.unlink( tmp_name )
-                                    except:
-                                        pass
-                                    # Append the new section to the shed_tool_config file.
-                                    self.__add_shed_tool_conf_entry( trans, shed_tool_conf, new_tool_section )
-                                    if trans.app.toolbox_search.enabled:
-                                        # If search support for tools is enabled, index the new installed tools.
-                                        trans.app.toolbox_search = ToolBoxSearch( trans.app.toolbox )
-                                installed_repository_names.append( name )
-                            else:
-                                tmp_stderr = open( tmp_name, 'rb' )
-                                message += '%s<br/>' % tmp_stderr.read()
-                                tmp_stderr.close()
-                                status = 'error'
-                        else:
-                            tmp_stderr = open( tmp_name, 'rb' )
-                            message += '%s<br/>' % tmp_stderr.read()
-                            tmp_stderr.close()
-                            status = 'error'
-                if installed_repository_names:
-                    installed_repository_names.sort()
-                    num_repositories_installed = len( installed_repository_names )
-                    message += 'Installed %d %s and all tools were loaded into tool panel section <b>%s</b>:<br/>Installed repositories: ' % \
-                        ( num_repositories_installed, inflector.cond_plural( num_repositories_installed, 'repository' ), tool_section.name )
-                    for i, repo_name in enumerate( installed_repository_names ):
-                        if i == len( installed_repository_names ) -1:
-                            message += '%s.<br/>' % repo_name
-                        else:
-                            message += '%s, ' % repo_name
-                return trans.response.send_redirect( web.url_for( controller='admin',
-                                                                  action='browse_tool_shed_repositories',
-                                                                  message=message,
-                                                                  status=status ) )
-            else:
-                message = 'Choose the section in your tool panel to contain the installed tools.'
-                status = 'error'
-        if len( trans.app.toolbox.shed_tool_confs.keys() ) > 1:
-            shed_tool_conf_select_field = build_shed_tool_conf_select_field( trans )
-            shed_tool_conf = None
-        else:
-            shed_tool_conf = trans.app.toolbox.shed_tool_confs.keys()[0].lstrip( './' )
-            shed_tool_conf_select_field = None
-        tool_panel_section_select_field = build_tool_panel_section_select_field( trans )
-        return trans.fill_template( '/admin/select_tool_panel_section.mako',
-                                    tool_shed_url=tool_shed_url,
-                                    repo_info_dict=repo_info_dict,
-                                    shed_tool_conf=shed_tool_conf,
-                                    shed_tool_conf_select_field=shed_tool_conf_select_field,
-                                    tool_panel_section_select_field=tool_panel_section_select_field,
-                                    new_tool_panel_section=new_tool_panel_section,
-                                    message=message,
-                                    status=status )
-    @web.expose
-    @web.require_admin
-    def manage_tool_shed_repository( self, trans, **kwd ):
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        status = params.get( 'status', 'done' )
-        repository_id = params.get( 'id', None )
-        repository = get_repository( trans, repository_id )
-        description = util.restore_text( params.get( 'description', repository.description ) )
-        if params.get( 'edit_repository_button', False ):
-            if description != repository.description:
-                repository.description = description
-                trans.sa_session.add( repository )
-                trans.sa_session.flush()
-            message = "The repository information has been updated."
-        relative_install_dir = self.__get_relative_install_dir( trans, repository )
-        if relative_install_dir:
-            repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, repository.name ) )
-        else:
-            repo_files_dir = 'unknown'
-        return trans.fill_template( '/admin/tool_shed_repository/manage_repository.mako',
-                                    repository=repository,
-                                    description=description,
-                                    repo_files_dir=repo_files_dir,
-                                    message=message,
-                                    status=status )
-    @web.expose
-    @web.require_admin
-    def check_for_updates( self, trans, **kwd ):
-        # Send a request to the relevant tool shed to see if there are any updates.
-        repository = get_repository( trans, kwd[ 'id' ] )
-        tool_shed_url = get_url_from_repository_tool_shed( trans, repository )
-        url = '%s/repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \
-            ( tool_shed_url, url_for( '', qualified=True ), repository.name, repository.owner, repository.changeset_revision )
-        return trans.response.send_redirect( url )
-    @web.expose
-    @web.require_admin
-    def update_to_changeset_revision( self, trans, **kwd ):
-        """Update a cloned repository to the latest revision possible."""
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        status = params.get( 'status', 'done' )
-        tool_shed_url = kwd[ 'tool_shed_url' ]
-        name = params.get( 'name', None )
-        owner = params.get( 'owner', None )
-        changeset_revision = params.get( 'changeset_revision', None )
-        latest_changeset_revision = params.get( 'latest_changeset_revision', None )
-        repository = get_repository_by_shed_name_owner_changeset_revision( trans, tool_shed_url, name, owner, changeset_revision )
-        if changeset_revision and latest_changeset_revision:
-            if changeset_revision == latest_changeset_revision:
-                message = "The cloned tool shed repository named '%s' is current (there are no updates available)." % name
-            else:
-                current_working_dir = os.getcwd()
-                relative_install_dir = self.__get_relative_install_dir( trans, repository )
-                if relative_install_dir:
-                    # Update the cloned repository to changeset_revision.
-                    repo_files_dir = os.path.join( relative_install_dir, name )
-                    log.debug( "Updating cloned repository named '%s' from revision '%s' to revision '%s'..." % \
-                        ( name, changeset_revision, latest_changeset_revision ) )
-                    cmd = 'hg pull'
-                    tmp_name = tempfile.NamedTemporaryFile().name
-                    tmp_stderr = open( tmp_name, 'wb' )
-                    os.chdir( repo_files_dir )
-                    proc = subprocess.Popen( cmd, shell=True, stderr=tmp_stderr.fileno() )
-                    returncode = proc.wait()
-                    os.chdir( current_working_dir )
-                    tmp_stderr.close()
-                    if returncode == 0:
-                        cmd = 'hg update -r %s' % latest_changeset_revision
-                        tmp_name = tempfile.NamedTemporaryFile().name
-                        tmp_stderr = open( tmp_name, 'wb' )
-                        os.chdir( repo_files_dir )
-                        proc = subprocess.Popen( cmd, shell=True, stderr=tmp_stderr.fileno() )
-                        returncode = proc.wait()
-                        os.chdir( current_working_dir )
-                        tmp_stderr.close()
-                        if returncode == 0:
-                            # Update the repository changeset_revision in the database.
-                            repository.changeset_revision = latest_changeset_revision
-                            trans.sa_session.add( repository )
-                            trans.sa_session.flush()
-                            message = "The cloned repository named '%s' has been updated to change set revision '%s'." % \
-                                ( name, latest_changeset_revision )
-                        else:
-                            tmp_stderr = open( tmp_name, 'rb' )
-                            message = tmp_stderr.read()
-                            tmp_stderr.close()
-                            status = 'error'
-                    else:
-                        tmp_stderr = open( tmp_name, 'rb' )
-                        message = tmp_stderr.read()
-                        tmp_stderr.close()
-                        status = 'error'
-                else:
-                    message = "The directory containing the cloned repository named '%s' cannot be found." % name
-                    status = 'error'
-        else:
-            message = "The latest changeset revision could not be retrieved for the repository named '%s'." % name
-            status = 'error'
-        return trans.response.send_redirect( web.url_for( controller='admin',
-                                                          action='manage_tool_shed_repository',
-                                                          id=trans.security.encode_id( repository.id ),
-                                                          message=message,
-                                                          status=status ) )
-    @web.expose
-    @web.require_admin
     def impersonate( self, trans, email=None, **kwd ):
         if not trans.app.config.allow_user_impersonation:
             return trans.show_error_message( "User impersonation is not enabled in this instance of Galaxy." )
@@ -1079,354 +643,4 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
         if emails is None:
             emails = [ u.email for u in trans.sa_session.query( trans.app.model.User ).enable_eagerloads( False ).all() ]
         return trans.fill_template( 'admin/impersonate.mako', emails=emails, message=message, status=status )
-
-    def __get_relative_install_dir( self, trans, repository ):
-        # Get the directory where the repository is install.
-        tool_shed = self.__clean_tool_shed_url( repository.tool_shed )
-        partial_install_dir = '%s/repos/%s/%s/%s' % ( tool_shed, repository.owner, repository.name, repository.changeset_revision )
-        # Get the relative tool installation paths from each of the shed tool configs.
-        shed_tool_confs = trans.app.toolbox.shed_tool_confs
-        relative_install_dir = None
-        # The shed_tool_confs dictionary contains { shed_conf_filename : tool_path } pairs.
-        for shed_conf_filename, tool_path in shed_tool_confs.items():
-            relative_install_dir = os.path.join( tool_path, partial_install_dir )
-            if os.path.isdir( relative_install_dir ):
-                break
-        return relative_install_dir
-    def __handle_missing_data_table_entry( self, trans, tool_path, sample_files, repository_tools_tups ):
-        # Inspect each tool to see if any have input parameters that are dynamically
-        # generated select lists that require entries in the tool_data_table_conf.xml file.
-        missing_data_table_entry = False
-        for index, repository_tools_tup in enumerate( repository_tools_tups ):
-            tup_path, repository_tool = repository_tools_tup
-            if repository_tool.params_with_missing_data_table_entry:
-                missing_data_table_entry = True
-                break
-        if missing_data_table_entry:
-            # The repository must contain a tool_data_table_conf.xml.sample file that includes
-            # all required entries for all tools in the repository.
-            for sample_file in sample_files:
-                head, tail = os.path.split( sample_file )
-                if tail == 'tool_data_table_conf.xml.sample':
-                    break
-            error, correction_msg = handle_sample_tool_data_table_conf_file( trans, sample_file )
-            if error:
-                # TODO: Do more here than logging an exception.
-                log.debug( exception_msg )
-            # Reload the tool into the local list of repository_tools_tups.
-            repository_tool = trans.app.toolbox.load_tool( os.path.join( tool_path, tup_path ) )
-            repository_tools_tups[ index ] = ( tup_path, repository_tool )
-        return repository_tools_tups
-    def __handle_missing_index_file( self, trans, tool_path, sample_files, repository_tools_tups ):
-        # Inspect each tool to see if it has any input parameters that
-        # are dynamically generated select lists that depend on a .loc file.
-        missing_files_handled = []
-        for index, repository_tools_tup in enumerate( repository_tools_tups ):
-            tup_path, repository_tool = repository_tools_tup
-            params_with_missing_index_file = repository_tool.params_with_missing_index_file
-            for param in params_with_missing_index_file:
-                options = param.options
-                missing_head, missing_tail = os.path.split( options.missing_index_file )
-                if missing_tail not in missing_files_handled:
-                    # The repository must contain the required xxx.loc.sample file.
-                    for sample_file in sample_files:
-                        sample_head, sample_tail = os.path.split( sample_file )
-                        if sample_tail == '%s.sample' % missing_tail:
-                            copy_sample_loc_file( trans, sample_file )
-                            if options.tool_data_table and options.tool_data_table.missing_index_file:
-                                options.tool_data_table.handle_found_index_file( options.missing_index_file )
-                            missing_files_handled.append( missing_tail )
-                            break
-            # Reload the tool into the local list of repository_tools_tups.
-            repository_tool = trans.app.toolbox.load_tool( os.path.join( tool_path, tup_path ) )
-            repository_tools_tups[ index ] = ( tup_path, repository_tool )
-        return repository_tools_tups
-    def __handle_tool_dependencies( self, current_working_dir, repo_files_dir, repository_tools_tups ):
-        # Inspect each tool to see if it includes a "requirement" that refers to a fabric
-        # script.  For those that do, execute the fabric script to install tool dependencies.
-        for index, repository_tools_tup in enumerate( repository_tools_tups ):
-            tup_path, repository_tool = repository_tools_tup
-            for requirement in repository_tool.requirements:
-                if requirement.type == 'fabfile':
-                    log.debug( 'Executing fabric script to install dependencies for tool "%s"...' % repository_tool.name )
-                    fabfile = requirement.fabfile
-                    method = requirement.method
-                    # Find the relative path to the fabfile.
-                    relative_fabfile_path = None
-                    for root, dirs, files in os.walk( repo_files_dir ):
-                        for name in files:
-                            if name == fabfile:
-                                relative_fabfile_path = os.path.join( root, name )
-                                break
-                    if relative_fabfile_path:
-                        # cmd will look something like: fab -f fabfile.py install_bowtie
-                        cmd = 'fab -f %s %s' % ( relative_fabfile_path, method )
-                        tmp_name = tempfile.NamedTemporaryFile().name
-                        tmp_stderr = open( tmp_name, 'wb' )
-                        os.chdir( repo_files_dir )
-                        proc = subprocess.Popen( cmd, shell=True, stderr=tmp_stderr.fileno() )
-                        returncode = proc.wait()
-                        os.chdir( current_working_dir )
-                        tmp_stderr.close()
-                        if returncode != 0:
-                            # TODO: do something more here than logging the problem.
-                            tmp_stderr = open( tmp_name, 'rb' )
-                            error = tmp_stderr.read()
-                            tmp_stderr.close()
-                            log.debug( 'Problem installing dependencies for tool "%s"\n%s' % ( repository_tool.name, error ) )
-    def __load_datatypes( self, trans, repo_files_dir ):
-        # Find datatypes_conf.xml if it exists.
-        datatypes_config = None
-        for root, dirs, files in os.walk( repo_files_dir ):
-            if root.find( '.hg' ) < 0:
-                for name in files:
-                    if name == 'datatypes_conf.xml':
-                        datatypes_config = os.path.abspath( os.path.join( root, name ) )
-                        break
-        if datatypes_config:
-            imported_module = None
-            # Parse datatypes_config.
-            tree = parse_xml( datatypes_config )
-            datatypes_config_root = tree.getroot()
-            relative_path_to_datatype_file_name = None
-            datatype_files = datatypes_config_root.find( 'datatype_files' )
-            # Currently only a single datatype_file is supported.  For example:
-            # <datatype_files>
-            #    <datatype_file name="gmap.py"/>
-            # </datatype_files>
-            for elem in datatype_files.findall( 'datatype_file' ):
-                datatype_file_name = elem.get( 'name', None )
-                if datatype_file_name:
-                    # Find the file in the installed repository.
-                    for root, dirs, files in os.walk( repo_files_dir ):
-                        if root.find( '.hg' ) < 0:
-                            for name in files:
-                                if name == datatype_file_name:
-                                    relative_path_to_datatype_file_name = os.path.join( root, name )
-                                    break
-                    break
-            if relative_path_to_datatype_file_name:
-                relative_head, relative_tail = os.path.split( relative_path_to_datatype_file_name )
-                registration = datatypes_config_root.find( 'registration' )
-                # Get the module by parsing the <datatype> tag.
-                for elem in registration.findall( 'datatype' ):
-                    # A 'type' attribute is currently required.  The attribute
-                    # should be something like: type="gmap:GmapDB".
-                    dtype = elem.get( 'type', None )
-                    if dtype:
-                        fields = dtype.split( ':' )
-                        datatype_module = fields[0]
-                        datatype_class_name = fields[1]
-                        # Since we currently support only a single datatype_file,
-                        #  we have what we need.
-                        break
-                try:
-                    sys.path.insert( 0, relative_head )
-                    imported_module = __import__( datatype_module )
-                    sys.path.pop( 0 )
-                except Exception, e:
-                    log.debug( "Exception importing datatypes code file included in installed repository: %s" % str( e ) )
-            trans.app.datatypes_registry.load_datatypes( root_dir=trans.app.config.root, config=datatypes_config, imported_module=imported_module )
-    def __get_repository_tools_and_sample_files( self, trans, tool_path, repo_files_dir ):
-        # The sample_files list contains all files whose name ends in .sample
-        sample_files = []
-        # Find all special .sample files first.
-        for root, dirs, files in os.walk( repo_files_dir ):
-            if root.find( '.hg' ) < 0:
-                for name in files:
-                    if name.endswith( '.sample' ):
-                        sample_files.append( os.path.abspath( os.path.join( root, name ) ) )
-        # The repository_tools_tups list contains tuples of ( relative_path_to_tool_config, tool ) pairs
-        repository_tools_tups = []
-        for root, dirs, files in os.walk( repo_files_dir ):
-            if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0:
-                if '.hg' in dirs:
-                    dirs.remove( '.hg' )
-                if 'hgrc' in files:
-                    files.remove( 'hgrc' )
-                for name in files:
-                    # Find all tool configs.
-                    if name.endswith( '.xml' ):
-                        relative_path = os.path.join( root, name )
-                        full_path = os.path.abspath( os.path.join( root, name ) )
-                        try:
-                            repository_tool = trans.app.toolbox.load_tool( full_path )
-                            if repository_tool:
-                                # At this point, we need to lstrip tool_path from relative_path.
-                                tup_path = relative_path.replace( tool_path, '' ).lstrip( '/' )
-                                repository_tools_tups.append( ( tup_path, repository_tool ) )
-                        except Exception, e:
-                            # We have an invalid .xml file, so not a tool config.
-                            log.debug( "Ignoring invalid tool config (%s). Error: %s" % ( str( relative_path ), str( e ) ) )
-        return sample_files, repository_tools_tups
-    def __create_or_undelete_tool_shed_repository( self, trans, name, description, changeset_revision, repository_clone_url ):
-        tmp_url = self.__clean_repository_clone_url( repository_clone_url )
-        tool_shed = tmp_url.split( 'repos' )[ 0 ].rstrip( '/' )
-        owner = self.__get_repository_owner( tmp_url )
-        flush_needed = False
-        tool_shed_repository = get_repository_by_shed_name_owner_changeset_revision( trans, tool_shed, name, owner, changeset_revision )
-        if tool_shed_repository:
-            if tool_shed_repository.deleted:
-                tool_shed_repository.deleted = False
-                flush_needed = True
-        else:
-            tool_shed_repository = trans.model.ToolShedRepository( tool_shed=tool_shed,
-                                                                   name=name,
-                                                                   description=description,
-                                                                   owner=owner,
-                                                                   changeset_revision=changeset_revision )
-            flush_needed = True
-        if flush_needed:
-            trans.sa_session.add( tool_shed_repository )
-            trans.sa_session.flush()
-    def __add_shed_tool_conf_entry( self, trans, shed_tool_conf, new_tool_section ):
-        # Add an entry in the shed_tool_conf file. An entry looks something like:
-        # <section name="Filter and Sort" id="filter">
-        #    <tool file="filter/filtering.xml" guid="toolshed.g2.bx.psu.edu/repos/test/filter/1.0.2"/>
-        # </section>
-        # Make a backup of the hgweb.config file since we're going to be changing it.
-        if not os.path.exists( shed_tool_conf ):
-            output = open( shed_tool_conf, 'w' )
-            output.write( '<?xml version="1.0"?>\n' )
-            output.write( '<toolbox tool_path="%s">\n' % tool_path )
-            output.write( '</toolbox>\n' )
-            output.close()
-        self.__make_shed_tool_conf_copy( trans, shed_tool_conf )
-        tmp_fd, tmp_fname = tempfile.mkstemp()
-        new_shed_tool_conf = open( tmp_fname, 'wb' )
-        for i, line in enumerate( open( shed_tool_conf ) ):
-            if line.startswith( '</toolbox>' ):
-                # We're at the end of the original config file, so add our entry.
-                new_shed_tool_conf.write( new_tool_section )
-                new_shed_tool_conf.write( line )
-            else:
-                new_shed_tool_conf.write( line )
-        new_shed_tool_conf.close()
-        shutil.move( tmp_fname, os.path.abspath( shed_tool_conf ) )
-    def __make_shed_tool_conf_copy( self, trans, shed_tool_conf ):
-        # Make a backup of the shed_tool_conf file.
-        today = date.today()
-        backup_date = today.strftime( "%Y_%m_%d" )
-        shed_tool_conf_copy = '%s/%s_%s_backup' % ( trans.app.config.root, shed_tool_conf, backup_date )
-        shutil.copy( os.path.abspath( shed_tool_conf ), os.path.abspath( shed_tool_conf_copy ) )
-    def __clean_tool_shed_url( self, tool_shed_url ):
-        if tool_shed_url.find( ':' ) > 0:
-            # Eliminate the port, if any, since it will result in an invalid directory name.
-            return tool_shed_url.split( ':' )[ 0 ]
-        return tool_shed_url.rstrip( '/' )
-    def __clean_repository_clone_url( self, repository_clone_url ):
-        if repository_clone_url.find( '@' ) > 0:
-            # We have an url that includes an authenticated user, something like:
-            # http://test@bx.psu.edu:9009/repos/some_username/column
-            items = repository_clone_url.split( '@' )
-            tmp_url = items[ 1 ]
-        elif repository_clone_url.find( '//' ) > 0:
-            # We have an url that includes only a protocol, something like:
-            # http://bx.psu.edu:9009/repos/some_username/column
-            items = repository_clone_url.split( '//' )
-            tmp_url = items[ 1 ]
-        else:
-            tmp_url = repository_clone_url
-        return tmp_url
-    def __get_repository_owner( self, cleaned_repository_url ):
-        items = cleaned_repository_url.split( 'repos' )
-        repo_path = items[ 1 ]
-        return repo_path.lstrip( '/' ).split( '/' )[ 0 ]
-    def __generate_tool_path( self, repository_clone_url, changeset_revision ):
-        """
-        Generate a tool path that guarantees repositories with the same name will always be installed
-        in different directories.  The tool path will be of the form:
-        <tool shed url>/repos/<repository owner>/<repository name>/<changeset revision>
-        http://test@bx.psu.edu:9009/repos/test/filter
-        """
-        tmp_url = self.__clean_repository_clone_url( repository_clone_url )
-        # Now tmp_url is something like: bx.psu.edu:9009/repos/some_username/column
-        items = tmp_url.split( 'repos' )
-        tool_shed_url = items[ 0 ]
-        repo_path = items[ 1 ]
-        tool_shed_url = self.__clean_tool_shed_url( tool_shed_url )
-        return '%s/repos%s/%s' % ( tool_shed_url, repo_path, changeset_revision )
-    def __generate_tool_guid( self, repository_clone_url, tool ):
-        """
-        Generate a guid for the installed tool.  It is critical that this guid matches the guid for
-        the tool in the Galaxy tool shed from which it is being installed.  The form of the guid is    
-        <tool shed host>/repos/<repository owner>/<repository name>/<tool id>/<tool version>
-        """
-        tmp_url = self.__clean_repository_clone_url( repository_clone_url )
-        return '%s/%s/%s' % ( tmp_url, tool.id, tool.version )
-    def __generate_tool_panel_section( self, repository_name, repository_clone_url, changeset_revision, tool_section, repository_tools_tups ):
-        """
-        Write an in-memory tool panel section so we can load it into the tool panel and then
-        append it to the appropriate shed tool config.
-        TODO: re-write using ElementTree.
-        """
-        tmp_url = self.__clean_repository_clone_url( repository_clone_url )
-        section_str = ''
-        section_str += '    <section name="%s" id="%s">\n' % ( tool_section.name, tool_section.id )
-        for repository_tool_tup in repository_tools_tups:
-            tool_file_path, tool = repository_tool_tup
-            guid = self.__generate_tool_guid( repository_clone_url, tool )
-            section_str += '        <tool file="%s" guid="%s">\n' % ( tool_file_path, guid )
-            section_str += '            <tool_shed>%s</tool_shed>\n' % tmp_url.split( 'repos' )[ 0 ].rstrip( '/' )
-            section_str += '            <repository_name>%s</repository_name>\n' % repository_name
-            section_str += '            <repository_owner>%s</repository_owner>\n' % self.__get_repository_owner( tmp_url )
-            section_str += '            <changeset_revision>%s</changeset_revision>\n' % changeset_revision
-            section_str += '            <id>%s</id>\n' % tool.id
-            section_str += '            <version>%s</version>\n' % tool.version
-            section_str += '        </tool>\n'
-        section_str += '    </section>\n'
-        return section_str
-
-## ---- Utility methods -------------------------------------------------------
-
-def build_shed_tool_conf_select_field( trans ):
-    """Build a SelectField whose options are the keys in trans.app.toolbox.shed_tool_confs."""
-    options = []
-    for shed_tool_conf_filename, tool_path in trans.app.toolbox.shed_tool_confs.items():
-        options.append( ( shed_tool_conf_filename.lstrip( './' ), shed_tool_conf_filename ) )
-    select_field = SelectField( name='shed_tool_conf' )
-    for option_tup in options:
-        select_field.add_option( option_tup[0], option_tup[1] )
-    return select_field
-def build_tool_panel_section_select_field( trans ):
-    """Build a SelectField whose options are the sections of the current in-memory toolbox."""
-    options = []
-    for k, tool_section in trans.app.toolbox.tool_panel.items():
-        options.append( ( tool_section.name, tool_section.id ) )
-    select_field = SelectField( name='tool_panel_section', display='radio' )
-    for option_tup in options:
-        select_field.add_option( option_tup[0], option_tup[1] )
-    return select_field
-def get_repository( trans, id ):
-    """Get a tool_shed_repository from the database via id"""
-    return trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) )
-def get_repository_by_name_owner_changeset_revision( trans, name, owner, changeset_revision ):
-    """Get a repository from the database via name owner and changeset_revision"""
-    return trans.sa_session.query( trans.model.ToolShedRepository ) \
-                             .filter( and_( trans.model.ToolShedRepository.table.c.name == name,
-                                            trans.model.ToolShedRepository.table.c.owner == owner,
-                                            trans.model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \
-                             .first()
-def get_repository_by_shed_name_owner_changeset_revision( trans, tool_shed, name, owner, changeset_revision ):
-    if tool_shed.find( '//' ) > 0:
-        tool_shed = tool_shed.split( '//' )[1]
-    return trans.sa_session.query( trans.model.ToolShedRepository ) \
-                           .filter( and_( trans.model.ToolShedRepository.table.c.tool_shed == tool_shed,
-                                          trans.model.ToolShedRepository.table.c.name == name,
-                                          trans.model.ToolShedRepository.table.c.owner == owner,
-                                          trans.model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \
-                           .first()
-def get_url_from_repository_tool_shed( trans, repository ):
-    # The stored value of repository.tool_shed is something like:
-    # toolshed.g2.bx.psu.edu
-    # We need the URL to this tool shed, which is something like:
-    # http://toolshed.g2.bx.psu.edu/
-    for shed_name, shed_url in trans.app.tool_shed_registry.tool_sheds.items():
-        if shed_url.find( repository.tool_shed ) >= 0:
-            if shed_url.endswith( '/' ):
-                shed_url = shed_url.rstrip( '/' )
-            return shed_url
-    # The tool shed from which the repository was originally
-    # installed must no longer be configured in tool_sheds_conf.xml.
-    return None
-                                    
\ No newline at end of file
+      
\ No newline at end of file
diff --git a/lib/galaxy/web/controllers/admin_toolshed.py b/lib/galaxy/web/controllers/admin_toolshed.py
new file mode 100644
index 00000000000..e5d547d56fc
--- /dev/null
+++ b/lib/galaxy/web/controllers/admin_toolshed.py
@@ -0,0 +1,889 @@
+from galaxy.web.controllers.admin import *
+import logging
+
+log = logging.getLogger( __name__ )
+
+class RepositoryListGrid( grids.Grid ):
+    class NameColumn( grids.TextColumn ):
+        def get_value( self, trans, grid, tool_shed_repository ):
+            if tool_shed_repository.update_available:
+                return '<div class="count-box state-color-error">%s</div>' % tool_shed_repository.name
+            return tool_shed_repository.name
+    class DescriptionColumn( grids.TextColumn ):
+        def get_value( self, trans, grid, tool_shed_repository ):
+            return tool_shed_repository.description
+    class OwnerColumn( grids.TextColumn ):
+        def get_value( self, trans, grid, tool_shed_repository ):
+            return tool_shed_repository.owner
+    class RevisionColumn( grids.TextColumn ):
+        def get_value( self, trans, grid, tool_shed_repository ):
+            return tool_shed_repository.changeset_revision
+    class ToolShedColumn( grids.TextColumn ):
+        def get_value( self, trans, grid, tool_shed_repository ):
+            return tool_shed_repository.tool_shed
+    # Grid definition
+    title = "Installed tool shed repositories"
+    model_class = model.ToolShedRepository
+    template='/admin/tool_shed_repository/grid.mako'
+    default_sort_key = "name"
+    columns = [
+        NameColumn( "Name",
+                    key="name",
+                    link=( lambda item: dict( operation="manage_repository", id=item.id, webapp="galaxy" ) ),
+                    attach_popup=True ),
+        DescriptionColumn( "Description" ),
+        OwnerColumn( "Owner" ),
+        RevisionColumn( "Revision" ),
+        ToolShedColumn( "Tool shed" ),
+        # Columns that are valid for filtering but are not visible.
+        grids.DeletedColumn( "Deleted",
+                             key="deleted",
+                             visible=False,
+                             filterable="advanced" )
+    ]
+    columns.append( grids.MulticolFilterColumn( "Search repository name", 
+                                                cols_to_filter=[ columns[0] ],
+                                                key="free-text-search",
+                                                visible=False,
+                                                filterable="standard" ) )
+    operations = [ grids.GridOperation( "Get updates",
+                                        allow_multiple=False,
+                                        condition=( lambda item: not item.deleted ),
+                                        async_compatible=False ) ]
+    standard_filters = []
+    default_filter = dict( deleted="False" )
+    num_rows_per_page = 50
+    preserve_state = False
+    use_paging = True
+    def build_initial_query( self, trans, **kwd ):
+        return trans.sa_session.query( self.model_class ) \
+                               .filter( self.model_class.table.c.deleted == False )
+
+class AdminToolshed( AdminGalaxy ):
+    
+    repository_list_grid = RepositoryListGrid()
+
+    @web.expose
+    @web.require_admin
+    def browse_repository( self, trans, **kwd ):
+        params = util.Params( kwd )
+        message = util.restore_text( params.get( 'message', ''  ) )
+        status = params.get( 'status', 'done' )
+        repository = get_repository( trans, kwd[ 'id' ] )
+        return trans.fill_template( '/admin/tool_shed_repository/browse_repository.mako',
+                                    repository=repository,
+                                    message=message,
+                                    status=status )
+    @web.expose
+    @web.require_admin
+    def browse_repositories( self, trans, **kwd ):
+        if 'operation' in kwd:
+            operation = kwd.pop( 'operation' ).lower()
+            if operation == "manage_repository":
+                return self.manage_repository( trans, **kwd )
+            if operation == "get updates":
+                return self.check_for_updates( trans, **kwd )
+        kwd[ 'message' ] = 'Names of repositories for which updates are available are highlighted in red.'
+        return self.repository_list_grid( trans, **kwd )
+    @web.expose
+    @web.require_admin
+    def browse_tool_sheds( self, trans, **kwd ):
+        params = util.Params( kwd )
+        message = util.restore_text( params.get( 'message', ''  ) )
+        status = params.get( 'status', 'done' )
+        return trans.fill_template( '/webapps/galaxy/admin/tool_sheds.mako',
+                                    webapp='galaxy',
+                                    message=message,
+                                    status='error' )
+    @web.expose
+    @web.require_admin
+    def find_tools_in_tool_shed( self, trans, **kwd ):
+        tool_shed_url = kwd[ 'tool_shed_url' ]
+        galaxy_url = url_for( '', qualified=True )
+        url = '%s/repository/find_tools?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, galaxy_url )
+        return trans.response.send_redirect( url )
+    @web.expose
+    @web.require_admin
+    def find_workflows_in_tool_shed( self, trans, **kwd ):
+        tool_shed_url = kwd[ 'tool_shed_url' ]
+        galaxy_url = url_for( '', qualified=True )
+        url = '%s/repository/find_workflows?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, galaxy_url )
+        return trans.response.send_redirect( url )
+    @web.expose
+    @web.require_admin
+    def browse_tool_shed( self, trans, **kwd ):
+        tool_shed_url = kwd[ 'tool_shed_url' ]
+        galaxy_url = url_for( '', qualified=True )
+        url = '%s/repository/browse_valid_repositories?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, galaxy_url )
+        return trans.response.send_redirect( url )
+    @web.expose
+    @web.require_admin
+    def install_repository( self, trans, **kwd ):
+        if not trans.app.toolbox.shed_tool_confs:
+            message = 'The <b>tool_config_file</b> setting in <b>universe_wsgi.ini</b> must include at least one shed tool configuration file name with a '
+            message += '<b>&lt;toolbox&gt;</b> tag that includes a <b>tool_path</b> attribute value which is a directory relative to the Galaxy installation '
+            message += 'directory in order to automatically install tools from a Galaxy tool shed (e.g., the file name <b>shed_tool_conf.xml</b> whose '
+            message += '<b>&lt;toolbox&gt;</b> tag is <b>&lt;toolbox tool_path="../shed_tools"&gt;</b>).<p/>See the '
+            message += '<a href="http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance" '
+            message += 'target="_blank">Automatic installation of Galaxy tool shed repository tools into a local Galaxy instance</a> section of the '
+            message += '<a href="http://wiki.g2.bx.psu.edu/Tool%20Shed" target="_blank">Galaxy tool shed wiki</a> for all of the details.'
+            return trans.show_error_message( message )
+        message = kwd.get( 'message', ''  )
+        status = kwd.get( 'status', 'done' )
+        tool_shed_url = kwd[ 'tool_shed_url' ]
+        repo_info_dict = kwd[ 'repo_info_dict' ]
+        new_tool_panel_section = kwd.get( 'new_tool_panel_section', '' )
+        tool_panel_section = kwd.get( 'tool_panel_section', '' )
+        if kwd.get( 'select_tool_panel_section_button', False ):
+            shed_tool_conf = kwd[ 'shed_tool_conf' ]
+            # Get the tool path.
+            for k, tool_path in trans.app.toolbox.shed_tool_confs.items():
+                if k == shed_tool_conf:
+                    break
+            if new_tool_panel_section or tool_panel_section:
+                if new_tool_panel_section:
+                    section_id = new_tool_panel_section.lower().replace( ' ', '_' )
+                    new_section_key = 'section_%s' % str( section_id )
+                    if new_section_key in trans.app.toolbox.tool_panel:
+                        # Appending a tool to an existing section in trans.app.toolbox.tool_panel
+                        log.debug( "Appending to tool panel section: %s" % new_tool_panel_section )
+                        tool_section = trans.app.toolbox.tool_panel[ new_section_key ]
+                    else:
+                        # Appending a new section to trans.app.toolbox.tool_panel
+                        log.debug( "Loading new tool panel section: %s" % new_tool_panel_section )
+                        elem = Element( 'section' )
+                        elem.attrib[ 'name' ] = new_tool_panel_section
+                        elem.attrib[ 'id' ] = section_id
+                        tool_section = ToolSection( elem )
+                        trans.app.toolbox.tool_panel[ new_section_key ] = tool_section
+                else:
+                    section_key = 'section_%s' % tool_panel_section
+                    tool_section = trans.app.toolbox.tool_panel[ section_key ]
+                # Decode the encoded repo_info_dict param value.
+                repo_info_dict = tool_shed_decode( repo_info_dict )
+                # Clone the repository to the configured location.
+                current_working_dir = os.getcwd()
+                installed_repository_names = []
+                for name, repo_info_tuple in repo_info_dict.items():
+                    metadata_dict = None
+                    description, repository_clone_url, changeset_revision = repo_info_tuple
+                    clone_dir = os.path.join( tool_path, self.__generate_tool_path( repository_clone_url, changeset_revision ) )
+                    if os.path.exists( clone_dir ):
+                        # Repository and revision has already been cloned.
+                        # TODO: implement the ability to re-install or revert an existing repository.
+                        message += 'Revision <b>%s</b> of repository <b>%s</b> was previously installed.<br/>' % ( changeset_revision, name )
+                    else:
+                        os.makedirs( clone_dir )
+                        log.debug( 'Cloning %s...' % repository_clone_url )
+                        cmd = 'hg clone %s' % repository_clone_url
+                        tmp_name = tempfile.NamedTemporaryFile().name
+                        tmp_stderr = open( tmp_name, 'wb' )
+                        os.chdir( clone_dir )
+                        proc = subprocess.Popen( args=cmd, shell=True, stderr=tmp_stderr.fileno() )
+                        returncode = proc.wait()
+                        os.chdir( current_working_dir )
+                        tmp_stderr.close()
+                        if returncode == 0:
+                            # Update the cloned repository to changeset_revision.  It is imperative that the 
+                            # installed repository is updated to the desired changeset_revision before metadata
+                            # is set because the process for setting metadata uses the repository files on disk.
+                            relative_install_dir = os.path.join( clone_dir, name )
+                            log.debug( 'Updating cloned repository to revision "%s"...' % changeset_revision )
+                            cmd = 'hg update -r %s' % changeset_revision
+                            tmp_name = tempfile.NamedTemporaryFile().name
+                            tmp_stderr = open( tmp_name, 'wb' )
+                            os.chdir( relative_install_dir )
+                            proc = subprocess.Popen( cmd, shell=True, stderr=tmp_stderr.fileno() )
+                            returncode = proc.wait()
+                            os.chdir( current_working_dir )
+                            tmp_stderr.close()
+                            if returncode == 0:
+                                # Generate the metadata for the installed tool shed repository.  It is imperative that
+                                # the installed repository is updated to the desired changeset_revision before metadata
+                                # is set because the process for setting metadata uses the repository files on disk.
+                                metadata_dict = self.__generate_metadata( trans, relative_install_dir, repository_clone_url )
+                                if 'datatypes_config' in metadata_dict:
+                                    datatypes_config = os.path.abspath( metadata_dict[ 'datatypes_config' ] )
+                                    # Load data types required by tools.
+                                    self.__load_datatypes( trans, datatypes_config, relative_install_dir )
+                                if 'tools' in metadata_dict:
+                                    repository_tools_tups = []
+                                    for tool_dict in metadata_dict[ 'tools' ]:
+                                        relative_path = tool_dict[ 'tool_config' ]
+                                        tool = trans.app.toolbox.load_tool( os.path.abspath( relative_path ) )
+                                        repository_tools_tups.append( ( relative_path, tool ) )
+                                    if repository_tools_tups:
+                                        sample_files = metadata_dict.get( 'sample_files', [] )
+                                        # Handle missing data table entries for tool parameters that are dynamically generated select lists.
+                                        repository_tools_tups = self.__handle_missing_data_table_entry( trans, tool_path, sample_files, repository_tools_tups )
+                                        # Handle missing index files for tool parameters that are dynamically generated select lists.
+                                        repository_tools_tups = self.__handle_missing_index_file( trans, tool_path, sample_files, repository_tools_tups )
+                                        # Handle tools that use fabric scripts to install dependencies.
+                                        self.__handle_tool_dependencies( current_working_dir, relative_install_dir, repository_tools_tups )
+                                        # Generate an in-memory tool conf section that includes the new tools.
+                                        new_tool_section = self.__generate_tool_panel_section( name,
+                                                                                               repository_clone_url,
+                                                                                               changeset_revision,
+                                                                                               tool_section,
+                                                                                               repository_tools_tups )
+                                        # Create a temporary file to persist the in-memory tool section
+                                        # TODO: Figure out how to do this in-memory using xml.etree.
+                                        tmp_name = tempfile.NamedTemporaryFile().name
+                                        persisted_new_tool_section = open( tmp_name, 'wb' )
+                                        persisted_new_tool_section.write( new_tool_section )
+                                        persisted_new_tool_section.close()
+                                        # Parse the persisted tool panel section
+                                        tree = parse_xml( tmp_name )
+                                        root = tree.getroot()
+                                        # Load the tools in the section into the tool panel.
+                                        trans.app.toolbox.load_section_tag_set( root, trans.app.toolbox.tool_panel, tool_path )
+                                        # Remove the temporary file
+                                        try:
+                                            os.unlink( tmp_name )
+                                        except:
+                                            pass
+                                        # Append the new section to the shed_tool_config file.
+                                        self.__add_shed_tool_conf_entry( trans, shed_tool_conf, new_tool_section )
+                                        if trans.app.toolbox_search.enabled:
+                                            # If search support for tools is enabled, index the new installed tools.
+                                            trans.app.toolbox_search = ToolBoxSearch( trans.app.toolbox )
+                                # Add a new record to the tool_shed_repository table if one doesn't
+                                # already exist.  If one exists but is marked deleted, undelete it.
+                                self.__create_or_undelete_tool_shed_repository( trans,
+                                                                                name,
+                                                                                description,
+                                                                                changeset_revision,
+                                                                                repository_clone_url,
+                                                                                metadata_dict )
+                                installed_repository_names.append( name )
+                            else:
+                                tmp_stderr = open( tmp_name, 'rb' )
+                                message += '%s<br/>' % tmp_stderr.read()
+                                tmp_stderr.close()
+                                status = 'error'
+                        else:
+                            tmp_stderr = open( tmp_name, 'rb' )
+                            message += '%s<br/>' % tmp_stderr.read()
+                            tmp_stderr.close()
+                            status = 'error'
+                if installed_repository_names:
+                    installed_repository_names.sort()
+                    num_repositories_installed = len( installed_repository_names )
+                    message += 'Installed %d %s and all tools were loaded into tool panel section <b>%s</b>:<br/>Installed repositories: ' % \
+                        ( num_repositories_installed, inflector.cond_plural( num_repositories_installed, 'repository' ), tool_section.name )
+                    for i, repo_name in enumerate( installed_repository_names ):
+                        if i == len( installed_repository_names ) -1:
+                            message += '%s.<br/>' % repo_name
+                        else:
+                            message += '%s, ' % repo_name
+                return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
+                                                                  action='browse_repositories',
+                                                                  message=message,
+                                                                  status=status ) )
+            else:
+                message = 'Choose the section in your tool panel to contain the installed tools.'
+                status = 'error'
+        if len( trans.app.toolbox.shed_tool_confs.keys() ) > 1:
+            shed_tool_conf_select_field = build_shed_tool_conf_select_field( trans )
+            shed_tool_conf = None
+        else:
+            shed_tool_conf = trans.app.toolbox.shed_tool_confs.keys()[0].lstrip( './' )
+            shed_tool_conf_select_field = None
+        tool_panel_section_select_field = build_tool_panel_section_select_field( trans )
+        return trans.fill_template( '/admin/tool_shed_repository/select_tool_panel_section.mako',
+                                    tool_shed_url=tool_shed_url,
+                                    repo_info_dict=repo_info_dict,
+                                    shed_tool_conf=shed_tool_conf,
+                                    shed_tool_conf_select_field=shed_tool_conf_select_field,
+                                    tool_panel_section_select_field=tool_panel_section_select_field,
+                                    new_tool_panel_section=new_tool_panel_section,
+                                    message=message,
+                                    status=status )
+    @web.expose
+    @web.require_admin
+    def manage_repository( self, trans, **kwd ):
+        params = util.Params( kwd )
+        message = util.restore_text( params.get( 'message', ''  ) )
+        status = params.get( 'status', 'done' )
+        repository = get_repository( trans, kwd[ 'id' ] )
+        description = util.restore_text( params.get( 'description', repository.description ) )
+        relative_install_dir = self.__get_relative_install_dir( trans, repository )
+        repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, repository.name ) )
+        if params.get( 'edit_repository_button', False ):
+            if description != repository.description:
+                repository.description = description
+                trans.sa_session.add( repository )
+                trans.sa_session.flush()
+            message = "The repository information has been updated."
+        elif params.get( 'set_metadata_button', False ):
+            repository_clone_url = self.__generate_clone_url( trans, repository )
+            metadata_dict = self.__generate_metadata( trans, relative_install_dir, repository_clone_url )
+            if metadata_dict:
+                repository.metadata = metadata_dict
+                trans.sa_session.add( repository )
+                trans.sa_session.flush()
+            message = "Repository metadata has been reset."
+        return trans.fill_template( '/admin/tool_shed_repository/manage_repository.mako',
+                                    repository=repository,
+                                    description=description,
+                                    repo_files_dir=repo_files_dir,
+                                    message=message,
+                                    status=status )
+    @web.expose
+    @web.require_admin
+    def check_for_updates( self, trans, **kwd ):
+        # Send a request to the relevant tool shed to see if there are any updates.
+        repository = get_repository( trans, kwd[ 'id' ] )
+        tool_shed_url = get_url_from_repository_tool_shed( trans, repository )
+        url = '%s/repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \
+            ( tool_shed_url, url_for( '', qualified=True ), repository.name, repository.owner, repository.changeset_revision )
+        return trans.response.send_redirect( url )
+    @web.expose
+    @web.require_admin
+    def update_to_changeset_revision( self, trans, **kwd ):
+        """Update a cloned repository to the latest revision possible."""
+        params = util.Params( kwd )
+        message = util.restore_text( params.get( 'message', ''  ) )
+        status = params.get( 'status', 'done' )
+        tool_shed_url = kwd[ 'tool_shed_url' ]
+        name = params.get( 'name', None )
+        owner = params.get( 'owner', None )
+        changeset_revision = params.get( 'changeset_revision', None )
+        latest_changeset_revision = params.get( 'latest_changeset_revision', None )
+        repository = get_repository_by_shed_name_owner_changeset_revision( trans, tool_shed_url, name, owner, changeset_revision )
+        if changeset_revision and latest_changeset_revision:
+            if changeset_revision == latest_changeset_revision:
+                message = "The cloned tool shed repository named '%s' is current (there are no updates available)." % name
+            else:
+                current_working_dir = os.getcwd()
+                relative_install_dir = self.__get_relative_install_dir( trans, repository )
+                if relative_install_dir:
+                    # Update the cloned repository to changeset_revision.
+                    repo_files_dir = os.path.join( relative_install_dir, name )
+                    log.debug( "Updating cloned repository named '%s' from revision '%s' to revision '%s'..." % \
+                        ( name, changeset_revision, latest_changeset_revision ) )
+                    cmd = 'hg pull'
+                    tmp_name = tempfile.NamedTemporaryFile().name
+                    tmp_stderr = open( tmp_name, 'wb' )
+                    os.chdir( repo_files_dir )
+                    proc = subprocess.Popen( cmd, shell=True, stderr=tmp_stderr.fileno() )
+                    returncode = proc.wait()
+                    os.chdir( current_working_dir )
+                    tmp_stderr.close()
+                    if returncode == 0:
+                        cmd = 'hg update -r %s' % latest_changeset_revision
+                        tmp_name = tempfile.NamedTemporaryFile().name
+                        tmp_stderr = open( tmp_name, 'wb' )
+                        os.chdir( repo_files_dir )
+                        proc = subprocess.Popen( cmd, shell=True, stderr=tmp_stderr.fileno() )
+                        returncode = proc.wait()
+                        os.chdir( current_working_dir )
+                        tmp_stderr.close()
+                        if returncode == 0:
+                            # Update the repository changeset_revision in the database.
+                            repository.changeset_revision = latest_changeset_revision
+                            trans.sa_session.add( repository )
+                            trans.sa_session.flush()
+                            message = "The cloned repository named '%s' has been updated to change set revision '%s'." % \
+                                ( name, latest_changeset_revision )
+                        else:
+                            tmp_stderr = open( tmp_name, 'rb' )
+                            message = tmp_stderr.read()
+                            tmp_stderr.close()
+                            status = 'error'
+                    else:
+                        tmp_stderr = open( tmp_name, 'rb' )
+                        message = tmp_stderr.read()
+                        tmp_stderr.close()
+                        status = 'error'
+                else:
+                    message = "The directory containing the cloned repository named '%s' cannot be found." % name
+                    status = 'error'
+        else:
+            message = "The latest changeset revision could not be retrieved for the repository named '%s'." % name
+            status = 'error'
+        return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
+                                                          action='manage_repository',
+                                                          id=trans.security.encode_id( repository.id ),
+                                                          message=message,
+                                                          status=status ) )
+    @web.expose
+    @web.require_admin
+    def view_tool_metadata( self, trans, repository_id, tool_id, **kwd ):
+        params = util.Params( kwd )
+        message = util.restore_text( params.get( 'message', ''  ) )
+        status = params.get( 'status', 'done' )
+        webapp = params.get( 'webapp', 'community' )
+        repository = get_repository( trans, repository_id )
+        metadata = {}
+        tool = None
+        if 'tools' in repository.metadata:
+            for tool_metadata_dict in repository.metadata[ 'tools' ]:
+                if tool_metadata_dict[ 'id' ] == tool_id:
+                    metadata = tool_metadata_dict
+                    tool = trans.app.toolbox.load_tool( os.path.abspath( metadata[ 'tool_config' ] ) )
+                    break
+        return trans.fill_template( "/admin/tool_shed_repository/view_tool_metadata.mako",
+                                    repository=repository,
+                                    tool=tool,
+                                    metadata=metadata,
+                                    message=message,
+                                    status=status )
+    def __generate_metadata( self, trans, relative_install_dir, repository_clone_url ):
+        """
+        Browse the repository files on disk to generate metadata.  Since we are using disk files, it
+        is imperative that the repository is updated to the desired change set revision before metadata
+        is generated.
+        """
+        metadata_dict = {}
+        sample_files = []
+        datatypes_config = None
+        # Find datatypes_conf.xml if it exists.
+        for root, dirs, files in os.walk( relative_install_dir ):
+            if root.find( '.hg' ) < 0:
+                for name in files:
+                    if name == 'datatypes_conf.xml':
+                        relative_path = os.path.join( root, name )
+                        datatypes_config = os.path.abspath( relative_path )
+                        break
+        if datatypes_config:
+            metadata_dict[ 'datatypes_config' ] = relative_path
+            metadata_dict = self.__generate_datatypes_metadata( trans, datatypes_config, metadata_dict )
+        # Find all special .sample files.
+        for root, dirs, files in os.walk( relative_install_dir ):
+            if root.find( '.hg' ) < 0:
+                for name in files:
+                    if name.endswith( '.sample' ):
+                        sample_files.append( os.path.join( root, name ) )
+        if sample_files:
+            metadata_dict[ 'sample_files' ] = sample_files
+        # Find all tool configs and exported workflows.
+        for root, dirs, files in os.walk( relative_install_dir ):
+            if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0:
+                if '.hg' in dirs:
+                    dirs.remove( '.hg' )
+                for name in files:
+                    # Find all tool configs.
+                    if name != 'datatypes_conf.xml' and name.endswith( '.xml' ):
+                        full_path = os.path.abspath( os.path.join( root, name ) )
+                        try:
+                            tool = trans.app.toolbox.load_tool( full_path )
+                        except Exception, e:
+                            tool = None
+                        if tool is not None:
+                            tool_config = os.path.join( root, name )
+                            metadata_dict = self.__generate_tool_metadata( trans, tool_config, tool, repository_clone_url, metadata_dict )
+                    # Find all exported workflows
+                    elif name.endswith( '.ga' ):
+                        relative_path = os.path.join( root, name )
+                        fp = open( relative_path, 'rb' )
+                        workflow_text = fp.read()
+                        fp.close()
+                        exported_workflow_dict = from_json_string( workflow_text )
+                        if 'a_galaxy_workflow' in exported_workflow_dict and exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true':
+                            metadata_dict = self.__generate_workflow_metadata( trans, relative_path, exported_workflow_dict, metadata_dict )
+        return metadata_dict
+    def __generate_datatypes_metadata( self, trans, datatypes_config, metadata_dict ):
+        """
+        Update the received metadata_dict with changes that have been applied
+        to the received datatypes_config.
+        """
+        # Parse datatypes_config.
+        tree = ElementTree.parse( datatypes_config )
+        root = tree.getroot()
+        ElementInclude.include( root )
+        repository_datatype_code_files = []
+        datatype_files = root.find( 'datatype_files' )
+        if datatype_files:
+            for elem in datatype_files.findall( 'datatype_file' ):
+                name = elem.get( 'name', None )
+                repository_datatype_code_files.append( name )
+            metadata_dict[ 'datatype_files' ] = repository_datatype_code_files
+        datatypes = []
+        registration = root.find( 'registration' )
+        if registration:
+            for elem in registration.findall( 'datatype' ):
+                extension = elem.get( 'extension', None ) 
+                dtype = elem.get( 'type', None )
+                mimetype = elem.get( 'mimetype', None )
+                datatypes.append( dict( extension=extension,
+                                        dtype=dtype,
+                                        mimetype=mimetype ) )
+            metadata_dict[ 'datatypes' ] = datatypes
+        return metadata_dict
+    def __generate_tool_metadata( self, trans, tool_config, tool, repository_clone_url, metadata_dict ):
+        """
+        Update the received metadata_dict with changes that have been
+        applied to the received tool.
+        """
+        # Generate the guid
+        guid = self.__generate_tool_guid( repository_clone_url, tool )
+        # Handle tool.requirements.
+        tool_requirements = []
+        for tr in tool.requirements:
+            name=tr.name
+            type=tr.type
+            if type == 'fabfile':
+                version = None
+                fabfile = tr.fabfile
+                method = tr.method
+            else:
+                version = tr.version
+                fabfile = None
+                method = None
+            requirement_dict = dict( name=name,
+                                     type=type,
+                                     version=version,
+                                     fabfile=fabfile,
+                                     method=method )
+            tool_requirements.append( requirement_dict )
+        # Handle tool.tests.
+        tool_tests = []
+        if tool.tests:
+            for ttb in tool.tests:
+                test_dict = dict( name=ttb.name,
+                                  required_files=ttb.required_files,
+                                  inputs=ttb.inputs,
+                                  outputs=ttb.outputs )
+                tool_tests.append( test_dict )
+        tool_dict = dict( id=tool.id,
+                          guid=guid,
+                          name=tool.name,
+                          version=tool.version,
+                          description=tool.description,
+                          version_string_cmd = tool.version_string_cmd,
+                          tool_config=tool_config,
+                          requirements=tool_requirements,
+                          tests=tool_tests )
+        if 'tools' in metadata_dict:
+            metadata_dict[ 'tools' ].append( tool_dict )
+        else:
+            metadata_dict[ 'tools' ] = [ tool_dict ]
+        return metadata_dict
+    def __generate_workflow_metadata( self, trans, relative_path, exported_workflow_dict, metadata_dict ):
+        """
+        Update the received metadata_dict with changes that have been applied
+        to the received exported_workflow_dict.  Store everything in the database.
+        """
+        if 'workflows' in metadata_dict:
+            metadata_dict[ 'workflows' ].append( ( relative_path, exported_workflow_dict ) )
+        else:
+            metadata_dict[ 'workflows' ] = [ ( relative_path, exported_workflow_dict ) ]
+        return metadata_dict
+    def __get_relative_install_dir( self, trans, repository ):
+        # Get the directory where the repository is install.
+        tool_shed = self.__clean_tool_shed_url( repository.tool_shed )
+        partial_install_dir = '%s/repos/%s/%s/%s' % ( tool_shed, repository.owner, repository.name, repository.changeset_revision )
+        # Get the relative tool installation paths from each of the shed tool configs.
+        shed_tool_confs = trans.app.toolbox.shed_tool_confs
+        relative_install_dir = None
+        # The shed_tool_confs dictionary contains { shed_conf_filename : tool_path } pairs.
+        for shed_conf_filename, tool_path in shed_tool_confs.items():
+            relative_install_dir = os.path.join( tool_path, partial_install_dir )
+            if os.path.isdir( relative_install_dir ):
+                break
+        return relative_install_dir
+    def __handle_missing_data_table_entry( self, trans, tool_path, sample_files, repository_tools_tups ):
+        # Inspect each tool to see if any have input parameters that are dynamically
+        # generated select lists that require entries in the tool_data_table_conf.xml file.
+        missing_data_table_entry = False
+        for index, repository_tools_tup in enumerate( repository_tools_tups ):
+            tup_path, repository_tool = repository_tools_tup
+            if repository_tool.params_with_missing_data_table_entry:
+                missing_data_table_entry = True
+                break
+        if missing_data_table_entry:
+            # The repository must contain a tool_data_table_conf.xml.sample file that includes
+            # all required entries for all tools in the repository.
+            for sample_file in sample_files:
+                head, tail = os.path.split( sample_file )
+                if tail == 'tool_data_table_conf.xml.sample':
+                    break
+            error, correction_msg = handle_sample_tool_data_table_conf_file( trans, sample_file )
+            if error:
+                # TODO: Do more here than logging an exception.
+                log.debug( exception_msg )
+            # Reload the tool into the local list of repository_tools_tups.
+            repository_tool = trans.app.toolbox.load_tool( os.path.join( tool_path, tup_path ) )
+            repository_tools_tups[ index ] = ( tup_path, repository_tool )
+        return repository_tools_tups
+    def __handle_missing_index_file( self, trans, tool_path, sample_files, repository_tools_tups ):
+        # Inspect each tool to see if it has any input parameters that
+        # are dynamically generated select lists that depend on a .loc file.
+        missing_files_handled = []
+        for index, repository_tools_tup in enumerate( repository_tools_tups ):
+            tup_path, repository_tool = repository_tools_tup
+            params_with_missing_index_file = repository_tool.params_with_missing_index_file
+            for param in params_with_missing_index_file:
+                options = param.options
+                missing_head, missing_tail = os.path.split( options.missing_index_file )
+                if missing_tail not in missing_files_handled:
+                    # The repository must contain the required xxx.loc.sample file.
+                    for sample_file in sample_files:
+                        sample_head, sample_tail = os.path.split( sample_file )
+                        if sample_tail == '%s.sample' % missing_tail:
+                            copy_sample_loc_file( trans, sample_file )
+                            if options.tool_data_table and options.tool_data_table.missing_index_file:
+                                options.tool_data_table.handle_found_index_file( options.missing_index_file )
+                            missing_files_handled.append( missing_tail )
+                            break
+            # Reload the tool into the local list of repository_tools_tups.
+            repository_tool = trans.app.toolbox.load_tool( os.path.join( tool_path, tup_path ) )
+            repository_tools_tups[ index ] = ( tup_path, repository_tool )
+        return repository_tools_tups
+    def __handle_tool_dependencies( self, current_working_dir, repo_files_dir, repository_tools_tups ):
+        # Inspect each tool to see if it includes a "requirement" that refers to a fabric
+        # script.  For those that do, execute the fabric script to install tool dependencies.
+        for index, repository_tools_tup in enumerate( repository_tools_tups ):
+            tup_path, repository_tool = repository_tools_tup
+            for requirement in repository_tool.requirements:
+                if requirement.type == 'fabfile':
+                    log.debug( 'Executing fabric script to install dependencies for tool "%s"...' % repository_tool.name )
+                    fabfile = requirement.fabfile
+                    method = requirement.method
+                    # Find the relative path to the fabfile.
+                    relative_fabfile_path = None
+                    for root, dirs, files in os.walk( repo_files_dir ):
+                        for name in files:
+                            if name == fabfile:
+                                relative_fabfile_path = os.path.join( root, name )
+                                break
+                    if relative_fabfile_path:
+                        # cmd will look something like: fab -f fabfile.py install_bowtie
+                        cmd = 'fab -f %s %s' % ( relative_fabfile_path, method )
+                        tmp_name = tempfile.NamedTemporaryFile().name
+                        tmp_stderr = open( tmp_name, 'wb' )
+                        os.chdir( repo_files_dir )
+                        proc = subprocess.Popen( cmd, shell=True, stderr=tmp_stderr.fileno() )
+                        returncode = proc.wait()
+                        os.chdir( current_working_dir )
+                        tmp_stderr.close()
+                        if returncode != 0:
+                            # TODO: do something more here than logging the problem.
+                            tmp_stderr = open( tmp_name, 'rb' )
+                            error = tmp_stderr.read()
+                            tmp_stderr.close()
+                            log.debug( 'Problem installing dependencies for tool "%s"\n%s' % ( repository_tool.name, error ) )
+    def __load_datatypes( self, trans, datatypes_config, relative_intall_dir ):
+        imported_module = None
+        # Parse datatypes_config.
+        tree = parse_xml( datatypes_config )
+        datatypes_config_root = tree.getroot()
+        relative_path_to_datatype_file_name = None
+        datatype_files = datatypes_config_root.find( 'datatype_files' )
+        # Currently only a single datatype_file is supported.  For example:
+        # <datatype_files>
+        #    <datatype_file name="gmap.py"/>
+        # </datatype_files>
+        for elem in datatype_files.findall( 'datatype_file' ):
+            datatype_file_name = elem.get( 'name', None )
+            if datatype_file_name:
+                # Find the file in the installed repository.
+                for root, dirs, files in os.walk( relative_intall_dir ):
+                    if root.find( '.hg' ) < 0:
+                        for name in files:
+                            if name == datatype_file_name:
+                                relative_path_to_datatype_file_name = os.path.join( root, name )
+                                break
+                break
+        if relative_path_to_datatype_file_name:
+            relative_head, relative_tail = os.path.split( relative_path_to_datatype_file_name )
+            registration = datatypes_config_root.find( 'registration' )
+            # Get the module by parsing the <datatype> tag.
+            for elem in registration.findall( 'datatype' ):
+                # A 'type' attribute is currently required.  The attribute
+                # should be something like: type="gmap:GmapDB".
+                dtype = elem.get( 'type', None )
+                if dtype:
+                    fields = dtype.split( ':' )
+                    datatype_module = fields[0]
+                    datatype_class_name = fields[1]
+                    # Since we currently support only a single datatype_file,
+                    #  we have what we need.
+                    break
+            try:
+                sys.path.insert( 0, relative_head )
+                imported_module = __import__( datatype_module )
+                sys.path.pop( 0 )
+            except Exception, e:
+                log.debug( "Exception importing datatypes code file included in installed repository: %s" % str( e ) )
+        trans.app.datatypes_registry.load_datatypes( root_dir=trans.app.config.root, config=datatypes_config, imported_module=imported_module )
+    def __create_or_undelete_tool_shed_repository( self, trans, name, description, changeset_revision, repository_clone_url, metadata_dict ):
+        tmp_url = self.__clean_repository_clone_url( repository_clone_url )
+        tool_shed = tmp_url.split( 'repos' )[ 0 ].rstrip( '/' )
+        owner = self.__get_repository_owner( tmp_url )
+        includes_datatypes = 'datatypes_config' in metadata_dict
+        flush_needed = False
+        tool_shed_repository = get_repository_by_shed_name_owner_changeset_revision( trans, tool_shed, name, owner, changeset_revision )
+        if tool_shed_repository:
+            if tool_shed_repository.deleted:
+                tool_shed_repository.deleted = False
+                # Reset includes_datatypes in case metadata changed since last installed.
+                tool_shed_repository.includes_datatypes = includes_datatypes
+                flush_needed = True
+        else:
+            tool_shed_repository = trans.model.ToolShedRepository( tool_shed=tool_shed,
+                                                                   name=name,
+                                                                   description=description,
+                                                                   owner=owner,
+                                                                   changeset_revision=changeset_revision,
+                                                                   metadata=metadata_dict,
+                                                                   includes_datatypes=includes_datatypes )
+            flush_needed = True
+        if flush_needed:
+            trans.sa_session.add( tool_shed_repository )
+            trans.sa_session.flush()
+    def __add_shed_tool_conf_entry( self, trans, shed_tool_conf, new_tool_section ):
+        # Add an entry in the shed_tool_conf file. An entry looks something like:
+        # <section name="Filter and Sort" id="filter">
+        #    <tool file="filter/filtering.xml" guid="toolshed.g2.bx.psu.edu/repos/test/filter/1.0.2"/>
+        # </section>
+        # Make a backup of the hgweb.config file since we're going to be changing it.
+        if not os.path.exists( shed_tool_conf ):
+            output = open( shed_tool_conf, 'w' )
+            output.write( '<?xml version="1.0"?>\n' )
+            output.write( '<toolbox tool_path="%s">\n' % tool_path )
+            output.write( '</toolbox>\n' )
+            output.close()
+        self.__make_shed_tool_conf_copy( trans, shed_tool_conf )
+        tmp_fd, tmp_fname = tempfile.mkstemp()
+        new_shed_tool_conf = open( tmp_fname, 'wb' )
+        for i, line in enumerate( open( shed_tool_conf ) ):
+            if line.startswith( '</toolbox>' ):
+                # We're at the end of the original config file, so add our entry.
+                new_shed_tool_conf.write( new_tool_section )
+                new_shed_tool_conf.write( line )
+            else:
+                new_shed_tool_conf.write( line )
+        new_shed_tool_conf.close()
+        shutil.move( tmp_fname, os.path.abspath( shed_tool_conf ) )
+    def __make_shed_tool_conf_copy( self, trans, shed_tool_conf ):
+        # Make a backup of the shed_tool_conf file.
+        today = date.today()
+        backup_date = today.strftime( "%Y_%m_%d" )
+        shed_tool_conf_copy = '%s/%s_%s_backup' % ( trans.app.config.root, shed_tool_conf, backup_date )
+        shutil.copy( os.path.abspath( shed_tool_conf ), os.path.abspath( shed_tool_conf_copy ) )
+    def __clean_tool_shed_url( self, tool_shed_url ):
+        if tool_shed_url.find( ':' ) > 0:
+            # Eliminate the port, if any, since it will result in an invalid directory name.
+            return tool_shed_url.split( ':' )[ 0 ]
+        return tool_shed_url.rstrip( '/' )
+    def __clean_repository_clone_url( self, repository_clone_url ):
+        if repository_clone_url.find( '@' ) > 0:
+            # We have an url that includes an authenticated user, something like:
+            # http://test@bx.psu.edu:9009/repos/some_username/column
+            items = repository_clone_url.split( '@' )
+            tmp_url = items[ 1 ]
+        elif repository_clone_url.find( '//' ) > 0:
+            # We have an url that includes only a protocol, something like:
+            # http://bx.psu.edu:9009/repos/some_username/column
+            items = repository_clone_url.split( '//' )
+            tmp_url = items[ 1 ]
+        else:
+            tmp_url = repository_clone_url
+        return tmp_url
+    def __get_repository_owner( self, cleaned_repository_url ):
+        items = cleaned_repository_url.split( 'repos' )
+        repo_path = items[ 1 ]
+        return repo_path.lstrip( '/' ).split( '/' )[ 0 ]
+    def __generate_tool_path( self, repository_clone_url, changeset_revision ):
+        """
+        Generate a tool path that guarantees repositories with the same name will always be installed
+        in different directories.  The tool path will be of the form:
+        <tool shed url>/repos/<repository owner>/<repository name>/<changeset revision>
+        http://test@bx.psu.edu:9009/repos/test/filter
+        """
+        tmp_url = self.__clean_repository_clone_url( repository_clone_url )
+        # Now tmp_url is something like: bx.psu.edu:9009/repos/some_username/column
+        items = tmp_url.split( 'repos' )
+        tool_shed_url = items[ 0 ]
+        repo_path = items[ 1 ]
+        tool_shed_url = self.__clean_tool_shed_url( tool_shed_url )
+        return '%s/repos%s/%s' % ( tool_shed_url, repo_path, changeset_revision )
+    def __generate_clone_url( self, trans, repository ):
+        """Generate the URL for cloning a repository."""
+        tool_shed_url = get_url_from_repository_tool_shed( trans, repository )
+        return '%s/repos/%s/%s' % ( tool_shed_url, repository.owner, repository.name )
+    def __generate_tool_guid( self, repository_clone_url, tool ):
+        """
+        Generate a guid for the installed tool.  It is critical that this guid matches the guid for
+        the tool in the Galaxy tool shed from which it is being installed.  The form of the guid is    
+        <tool shed host>/repos/<repository owner>/<repository name>/<tool id>/<tool version>
+        """
+        tmp_url = self.__clean_repository_clone_url( repository_clone_url )
+        return '%s/%s/%s' % ( tmp_url, tool.id, tool.version )
+    def __generate_tool_panel_section( self, repository_name, repository_clone_url, changeset_revision, tool_section, repository_tools_tups ):
+        """
+        Write an in-memory tool panel section so we can load it into the tool panel and then
+        append it to the appropriate shed tool config.
+        TODO: re-write using ElementTree.
+        """
+        tmp_url = self.__clean_repository_clone_url( repository_clone_url )
+        section_str = ''
+        section_str += '    <section name="%s" id="%s">\n' % ( tool_section.name, tool_section.id )
+        for repository_tool_tup in repository_tools_tups:
+            tool_file_path, tool = repository_tool_tup
+            guid = self.__generate_tool_guid( repository_clone_url, tool )
+            section_str += '        <tool file="%s" guid="%s">\n' % ( tool_file_path, guid )
+            section_str += '            <tool_shed>%s</tool_shed>\n' % tmp_url.split( 'repos' )[ 0 ].rstrip( '/' )
+            section_str += '            <repository_name>%s</repository_name>\n' % repository_name
+            section_str += '            <repository_owner>%s</repository_owner>\n' % self.__get_repository_owner( tmp_url )
+            section_str += '            <changeset_revision>%s</changeset_revision>\n' % changeset_revision
+            section_str += '            <id>%s</id>\n' % tool.id
+            section_str += '            <version>%s</version>\n' % tool.version
+            section_str += '        </tool>\n'
+        section_str += '    </section>\n'
+        return section_str
+
+## ---- Utility methods -------------------------------------------------------
+
+def build_shed_tool_conf_select_field( trans ):
+    """Build a SelectField whose options are the keys in trans.app.toolbox.shed_tool_confs."""
+    options = []
+    for shed_tool_conf_filename, tool_path in trans.app.toolbox.shed_tool_confs.items():
+        options.append( ( shed_tool_conf_filename.lstrip( './' ), shed_tool_conf_filename ) )
+    select_field = SelectField( name='shed_tool_conf' )
+    for option_tup in options:
+        select_field.add_option( option_tup[0], option_tup[1] )
+    return select_field
+def build_tool_panel_section_select_field( trans ):
+    """Build a SelectField whose options are the sections of the current in-memory toolbox."""
+    options = []
+    for k, tool_section in trans.app.toolbox.tool_panel.items():
+        options.append( ( tool_section.name, tool_section.id ) )
+    select_field = SelectField( name='tool_panel_section', display='radio' )
+    for option_tup in options:
+        select_field.add_option( option_tup[0], option_tup[1] )
+    return select_field
+def get_repository( trans, id ):
+    """Get a tool_shed_repository from the database via id"""
+    return trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) )
+def get_repository_by_name_owner_changeset_revision( trans, name, owner, changeset_revision ):
+    """Get a repository from the database via name owner and changeset_revision"""
+    return trans.sa_session.query( trans.model.ToolShedRepository ) \
+                             .filter( and_( trans.model.ToolShedRepository.table.c.name == name,
+                                            trans.model.ToolShedRepository.table.c.owner == owner,
+                                            trans.model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \
+                             .first()
+def get_repository_by_shed_name_owner_changeset_revision( trans, tool_shed, name, owner, changeset_revision ):
+    if tool_shed.find( '//' ) > 0:
+        tool_shed = tool_shed.split( '//' )[1]
+    return trans.sa_session.query( trans.model.ToolShedRepository ) \
+                           .filter( and_( trans.model.ToolShedRepository.table.c.tool_shed == tool_shed,
+                                          trans.model.ToolShedRepository.table.c.name == name,
+                                          trans.model.ToolShedRepository.table.c.owner == owner,
+                                          trans.model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \
+                           .first()
+def get_url_from_repository_tool_shed( trans, repository ):
+    # The stored value of repository.tool_shed is something like:
+    # toolshed.g2.bx.psu.edu
+    # We need the URL to this tool shed, which is something like:
+    # http://toolshed.g2.bx.psu.edu/
+    for shed_name, shed_url in trans.app.tool_shed_registry.tool_sheds.items():
+        if shed_url.find( repository.tool_shed ) >= 0:
+            if shed_url.endswith( '/' ):
+                shed_url = shed_url.rstrip( '/' )
+            return shed_url
+    # The tool shed from which the repository was originally
+    # installed must no longer be configured in tool_sheds_conf.xml.
+    return None
diff --git a/lib/galaxy/web/controllers/workflow.py b/lib/galaxy/web/controllers/workflow.py
index 2623f279ed0..577ad81372e 100644
--- a/lib/galaxy/web/controllers/workflow.py
+++ b/lib/galaxy/web/controllers/workflow.py
@@ -1230,8 +1230,8 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
                     elif installed_repository_file:
                         # The workflow was read from a file included with an installed tool shed repository.
                         message = "Workflow <b>%s</b> imported successfully." % workflow.name
-                        return trans.response.send_redirect( web.url_for( controller='admin',
-                                                                          action='browse_tool_shed_repository',
+                        return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
+                                                                          action='browse_repository',
                                                                           id=repository_id,
                                                                           message=message,
                                                                           status=status ) )
diff --git a/lib/galaxy/webapps/community/controllers/repository.py b/lib/galaxy/webapps/community/controllers/repository.py
index 0fcaab43f68..a08b14ac597 100644
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -437,7 +437,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
                 if operation == "install":
                     galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' )
                     encoded_repo_info_dict = self.__encode_repo_info_dict( trans, webapp, util.listify( item_id ) )
-                    url = '%s/admin/install_tool_shed_repository?tool_shed_url=%s&webapp=%s&repo_info_dict=%s' % \
+                    url = '%s/admin_toolshed/install_repository?tool_shed_url=%s&webapp=%s&repo_info_dict=%s' % \
                         ( galaxy_url, url_for( '', qualified=True ), webapp, encoded_repo_info_dict )
                     return trans.response.send_redirect( url )
             else:
@@ -513,7 +513,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
                 if operation == "install":
                     galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' )
                     encoded_repo_info_dict = self.__encode_repo_info_dict( trans, webapp, util.listify( item_id ) )
-                    url = '%s/admin/install_tool_shed_repository?tool_shed_url=%s&webapp=%s&repo_info_dict=%s' % \
+                    url = '%s/admin_toolshed/install_repository?tool_shed_url=%s&webapp=%s&repo_info_dict=%s' % \
                         ( galaxy_url, url_for( '', qualified=True ), webapp, encoded_repo_info_dict )
                     return trans.response.send_redirect( url )
             else:
@@ -759,7 +759,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
         repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, changeset_revision )
         encoded_repo_info_dict = encode( repo_info_dict )
         # Redirect back to local Galaxy to perform install.
-        url = '%s/admin/install_tool_shed_repository?tool_shed_url=%s&repo_info_dict=%s' % \
+        url = '%s/admin_toolshed/install_repository?tool_shed_url=%s&repo_info_dict=%s' % \
             ( galaxy_url, url_for( '', qualified=True ), encoded_repo_info_dict )
         return trans.response.send_redirect( url )
     @web.expose
@@ -773,7 +773,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
         changeset_revision = params.get( 'changeset_revision', None )
         webapp = params.get( 'webapp', 'community' )
         # Start building up the url to redirect back to the calling Galaxy instance.
-        url = '%s/admin/update_to_changeset_revision?tool_shed_url=%s' % ( galaxy_url, url_for( '', qualified=True ) )
+        url = '%s/admin_toolshed/update_to_changeset_revision?tool_shed_url=%s' % ( galaxy_url, url_for( '', qualified=True ) )
         repository = get_repository_by_name_and_owner( trans, name, owner )
         url += '&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % \
             ( repository.name, repository.user.username, changeset_revision )
@@ -1035,7 +1035,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
         hgweb_config = "%s/hgweb.config" %  trans.app.config.root
         if repository_path.startswith( './' ):
             repository_path = repository_path.replace( './', '', 1 )
-        entry = "repos/%s/%s = %s" % ( repository.user.username, repository.name, repository_path.lstrip( './' ) )
+        entry = "repos/%s/%s = %s" % ( repository.user.username, repository.name, repository_path )
         tmp_fd, tmp_fname = tempfile.mkstemp()
         if os.path.exists( hgweb_config ):
             # Make a backup of the hgweb.config file since we're going to be changing it.
diff --git a/templates/admin/tool_shed_repository/browse_repository.mako b/templates/admin/tool_shed_repository/browse_repository.mako
index 10f3a95a8b3..2b1c7d85658 100644
--- a/templates/admin/tool_shed_repository/browse_repository.mako
+++ b/templates/admin/tool_shed_repository/browse_repository.mako
@@ -1,5 +1,6 @@
 <%inherit file="/base.mako"/>
 <%namespace file="/message.mako" import="render_msg" />
+<%namespace file="/admin/tool_shed_repository/common.mako" import="*" />
 
 <% from galaxy.web.base.controller import tool_shed_encode, tool_shed_decode %>
 
@@ -7,8 +8,8 @@
 <ul class="manage-table-actions">
     <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li>
     <div popupmenu="repository-${repository.id}-popup">
-        <a class="action-button" href="${h.url_for( controller='admin', action='manage_tool_shed_repository', id=trans.security.encode_id( repository.id ) )}">Manage repository</a>
-        <a class="action-button" href="${h.url_for( controller='admin', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get updates</a>
+        <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( repository.id ) )}">Manage repository</a>
+        <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get updates</a>
     </div>
 </ul>
 
@@ -16,112 +17,4 @@
     ${render_msg( message, status )}
 %endif
 
-<div class="toolForm">
-    <div class="toolFormTitle">Installed tool shed repository '${repository.name}'</div>
-    <div class="toolFormBody">
-
-        %if tool_dicts:
-            <div class="form-row">
-                <table width="100%">
-                    <tr bgcolor="#D8D8D8" width="100%">
-                        <td><b>Tools</b></td>
-                    </tr>
-                </table>
-            </div>
-            <div class="form-row">
-                <table class="grid">
-                    <tr>
-                        <td><b>name</b></td>
-                        <td><b>description</b></td>
-                        <td><b>version</b></td>
-                        <td><b>requirements</b></td>
-                    </tr>
-                    %for tool_dict in tool_dicts:
-                        <tr>
-                            <td>${tool_dict[ 'name' ]}</div>
-                            </td>
-                            <td>${tool_dict[ 'description' ]}</td>
-                            <td>${tool_dict[ 'version' ]}</td>
-                            <td>
-                                <%
-                                    if 'requirements' in tool_dict:
-                                        requirements = tool_dict[ 'requirements' ]
-                                    else:
-                                        requirements = None
-                                %>
-                                %if requirements:
-                                    <%
-                                        requirements_str = ''
-                                        for requirement_dict in tool_dict[ 'requirements' ]:
-                                            requirements_str += '%s (%s), ' % ( requirement_dict[ 'name' ], requirement_dict[ 'type' ] )
-                                        requirements_str = requirements_str.rstrip( ', ' )
-                                    %>
-                                    ${requirements_str}
-                                %else:
-                                    none
-                                %endif
-                            </td>
-                        </tr>
-                    %endfor
-                </table>
-            </div>
-            <div style="clear: both"></div>
-        %endif
-        %if workflow_dicts:
-            <div class="form-row">
-                <table width="100%">
-                    <tr bgcolor="#D8D8D8" width="100%">
-                        <td><b>Workflows</b></td>
-                    </tr>
-                </table>
-            </div>
-            <div style="clear: both"></div>
-            <div class="form-row">
-                <table class="grid">
-                    <tr>
-                        <td><b>name</b></td>
-                        <td><b>steps</b></td>
-                        <td><b>format-version</b></td>
-                        <td><b>annotation</b></td>
-                    </tr>
-                    <% index = 0 %>
-                    %for wf_dict in workflow_dicts:
-                        <%
-                            full_path = wf_dict[ 'full_path' ]
-                            workflow_dict = wf_dict[ 'workflow_dict' ]
-                            workflow_name = workflow_dict[ 'name' ]
-                            if 'steps' in workflow_dict:
-                                ## Initially steps were not stored in the metadata record.
-                                steps = workflow_dict[ 'steps' ]
-                            else:
-                                steps = []
-                            format_version = workflow_dict[ 'format-version' ]
-                            annotation = workflow_dict[ 'annotation' ]
-                        %>
-                        <tr>
-                            <td>
-                                <div class="menubutton" style="float: left;" id="workflow-${index}-popup">
-                                    ${workflow_name}
-                                    <div popupmenu="workflow-${index}-popup">
-                                        <a class="action-button" href="${h.url_for( controller='workflow', action='import_workflow', installed_repository_file=full_path, repository_id=trans.security.encode_id( repository.id ) )}">Import to Galaxy</a>
-                                    </div>
-                                </div>
-                            </td>
-                            <td>
-                                %if 'steps' in workflow_dict:
-                                    ${len( steps )}
-                                %else:
-                                    unknown
-                                %endif
-                            </td>
-                            <td>${format_version}</td>
-                            <td>${annotation}</td>
-                        </tr>
-                        <% index += 1 %>
-                    %endfor
-                </table>
-            </div>
-            <div style="clear: both"></div>
-        %endif
-    </div>
-</div>
+${render_metadata( repository, can_reset_metadata=False )}
diff --git a/templates/admin/tool_shed_repository/common.mako b/templates/admin/tool_shed_repository/common.mako
new file mode 100644
index 00000000000..d4455358c91
--- /dev/null
+++ b/templates/admin/tool_shed_repository/common.mako
@@ -0,0 +1,171 @@
+<%def name="render_metadata( repository, can_reset_metadata=False )">
+    <div class="toolForm">
+        <div class="toolFormTitle">Repository contents</div>
+        <div class="toolFormBody">
+            <% metadata = repository.metadata %>
+            %if metadata:
+                %if 'tools' in metadata:
+                    <div class="form-row">
+                        <table width="100%">
+                            <tr bgcolor="#D8D8D8" width="100%">
+                                <td><b>Tools</b><i> - click the name to view tool related information</i></td>
+                            </tr>
+                        </table>
+                    </div>
+                    <div class="form-row">
+                        <% tool_dicts = metadata[ 'tools' ] %>
+                        <table class="grid">
+                            <tr>
+                                <td><b>name</b></td>
+                                <td><b>description</b></td>
+                                <td><b>version</b></td>
+                                <td><b>requirements</b></td>
+                            </tr>
+                            %for tool_dict in tool_dicts:
+                                <tr>
+                                    <td>
+                                        <a class="view-info" href="${h.url_for( controller='admin_toolshed', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), tool_id=tool_dict[ 'id' ] )}">
+                                            ${tool_dict[ 'name' ]}
+                                        </a>
+                                    </td>
+                                    <td>${tool_dict[ 'description' ]}</td>
+                                    <td>${tool_dict[ 'version' ]}</td>
+                                    <td>
+                                        <%
+                                            if 'requirements' in tool_dict:
+                                                requirements = tool_dict[ 'requirements' ]
+                                            else:
+                                                requirements = None
+                                        %>
+                                        %if requirements:
+                                            <%
+                                                requirements_str = ''
+                                                for requirement_dict in tool_dict[ 'requirements' ]:
+                                                    requirements_str += '%s (%s), ' % ( requirement_dict[ 'name' ], requirement_dict[ 'type' ] )
+                                                requirements_str = requirements_str.rstrip( ', ' )
+                                            %>
+                                            ${requirements_str}
+                                        %else:
+                                            none
+                                        %endif
+                                    </td>
+                                </tr>
+                            %endfor
+                        </table>
+                    </div>
+                    <div style="clear: both"></div>
+                %endif
+                %if 'workflows' in metadata:
+                    <div class="form-row">
+                        <table width="100%">
+                            <tr bgcolor="#D8D8D8" width="100%">
+                                <td><b>Workflows</b><i> - click the name to import</i></td>
+                            </tr>
+                        </table>
+                    </div>
+                    <div style="clear: both"></div>
+                    <div class="form-row">
+                        <% workflow_tups = metadata[ 'workflows' ] %>
+                        <table class="grid">
+                            <tr>
+                                <td><b>name</b></td>
+                                <td><b>steps</b></td>
+                                <td><b>format-version</b></td>
+                                <td><b>annotation</b></td>
+                            </tr>
+                            <% index = 0 %>
+                            %for workflow_tup in workflow_tups:
+                                <%
+                                    import os.path
+                                    relative_path = workflow_tup[ 0 ]
+                                    full_path = os.path.abspath( relative_path )
+                                    workflow_dict = workflow_tup[ 1 ]
+                                    workflow_name = workflow_dict[ 'name' ]
+                                    if 'steps' in workflow_dict:
+                                        ## Initially steps were not stored in the metadata record.
+                                        steps = workflow_dict[ 'steps' ]
+                                    else:
+                                        steps = []
+                                    format_version = workflow_dict[ 'format-version' ]
+                                    annotation = workflow_dict[ 'annotation' ]
+                                %>
+                                <tr>
+                                    <td>
+                                        <div class="menubutton" style="float: left;" id="workflow-${index}-popup">
+                                            ${workflow_name}
+                                            <div popupmenu="workflow-${index}-popup">
+                                                <a class="action-button" href="${h.url_for( controller='workflow', action='import_workflow', installed_repository_file=full_path, repository_id=trans.security.encode_id( repository.id ) )}">Import to Galaxy</a>
+                                            </div>
+                                        </div>
+                                    </td>
+                                    <td>
+                                        %if steps:
+                                            ${len( steps )}
+                                        %else:
+                                            unknown
+                                        %endif
+                                    </td>
+                                    <td>${format_version}</td>
+                                    <td>${annotation}</td>
+                                </tr>
+                                <% index += 1 %>
+                            %endfor
+                        </table>
+                    </div>
+                    <div style="clear: both"></div>
+                %endif
+                %if 'datatypes' in metadata:
+                    <div class="form-row">
+                        <table width="100%">
+                            <tr bgcolor="#D8D8D8" width="100%">
+                                <td><b>Data types</b></td>
+                            </tr>
+                        </table>
+                    </div>
+                    <div style="clear: both"></div>
+                    <div class="form-row">
+                        <% datatypes_dicts = metadata[ 'datatypes' ] %>
+                        <table class="grid">
+                            <tr>
+                                <td><b>extension</b></td>
+                                <td><b>dtype</b></td>
+                                <td><b>mimetype</b></td>
+                            </tr>
+                            %for datatypes_dict in datatypes_dicts:
+                                <% 
+                                    extension = datatypes_dict[ 'extension' ]
+                                    dtype = datatypes_dict[ 'dtype' ]
+                                    mimetype = datatypes_dict[ 'mimetype' ]
+                                %>
+                                <tr>
+                                    <td>${extension}</td>
+                                    <td>${dtype}</td>
+                                    <td>
+                                        %if mimetype:
+                                            ${mimetype}
+                                        %else:
+                                            &nbsp;
+                                        %endif
+                                    </td>
+                                </tr>
+                            %endfor
+                        </table>
+                    </div>
+                    <div style="clear: both"></div>
+                %endif
+            %endif
+            %if can_reset_metadata:
+                <form name="set_metadata" action="${h.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( repository.id ) )}" method="post">
+                    <div class="form-row">
+                        <div style="float: left; width: 250px; margin-right: 10px;">
+                            <input type="submit" name="set_metadata_button" value="Reset metadata"/>
+                        </div>
+                        <div class="toolParamHelp" style="clear: both;">
+                            Inspect the repository and reset the above attributes.
+                        </div>
+                    </div>
+                </form>
+            %endif
+        </div>
+    </div>
+</%def>
diff --git a/templates/admin/tool_shed_repository/manage_repository.mako b/templates/admin/tool_shed_repository/manage_repository.mako
index 2061a8c7a5f..9eaef83d917 100644
--- a/templates/admin/tool_shed_repository/manage_repository.mako
+++ b/templates/admin/tool_shed_repository/manage_repository.mako
@@ -1,12 +1,13 @@
 <%inherit file="/base.mako"/>
 <%namespace file="/message.mako" import="render_msg" />
+<%namespace file="/admin/tool_shed_repository/common.mako" import="*" />
 
 <br/><br/>
 <ul class="manage-table-actions">
     <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li>
     <div popupmenu="repository-${repository.id}-popup">
-        <a class="action-button" href="${h.url_for( controller='admin', action='browse_tool_shed_repository', id=trans.security.encode_id( repository.id ) )}">Browse repository</a>
-        <a class="action-button" href="${h.url_for( controller='admin', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get updates</a>
+        <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='browse_repository', id=trans.security.encode_id( repository.id ) )}">Browse repository</a>
+        <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get updates</a>
     </div>
 </ul>
 
@@ -15,9 +16,9 @@
 %endif
 
 <div class="toolForm">
-    <div class="toolFormTitle">${repository.name}</div>
+    <div class="toolFormTitle">Installed tool shed repository '${repository.name}'</div>
     <div class="toolFormBody">
-        <form name="edit_repository" id="edit_repository" action="${h.url_for( controller='admin', action='manage_tool_shed_repository', id=trans.security.encode_id( repository.id ) )}" method="post" >
+        <form name="edit_repository" id="edit_repository" action="${h.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( repository.id ) )}" method="post" >
             <div class="form-row">
                 <label>Tool shed:</label>
                 ${repository.tool_shed}
@@ -55,3 +56,6 @@
         </form>
     </div>
 </div>
+<p/>
+${render_metadata( repository, can_reset_metadata=True )}
+<p/>
diff --git a/templates/admin/select_tool_panel_section.mako b/templates/admin/tool_shed_repository/select_tool_panel_section.mako
similarity index 94%
rename from templates/admin/select_tool_panel_section.mako
rename to templates/admin/tool_shed_repository/select_tool_panel_section.mako
index 1a0b90058db..bc6a940ce28 100644
--- a/templates/admin/select_tool_panel_section.mako
+++ b/templates/admin/tool_shed_repository/select_tool_panel_section.mako
@@ -25,7 +25,7 @@
 <div class="toolForm">
     <div class="toolFormTitle">Choose section to load tools into tool panel</div>
     <div class="toolFormBody">
-    <form name="select_tool_panel_section" id="select_tool_panel_section" action="${h.url_for( controller='admin', action='install_tool_shed_repository', tool_shed_url=tool_shed_url, repo_info_dict=repo_info_dict )}" method="post" >
+    <form name="select_tool_panel_section" id="select_tool_panel_section" action="${h.url_for( controller='admin_toolshed', action='install_repository', tool_shed_url=tool_shed_url, repo_info_dict=repo_info_dict )}" method="post" >
         %if shed_tool_conf_select_field:
             <div class="form-row">
                 <label>Shed tool configuration file:</label>
diff --git a/templates/admin/tool_shed_repository/view_tool_metadata.mako b/templates/admin/tool_shed_repository/view_tool_metadata.mako
new file mode 100644
index 00000000000..525e501ee84
--- /dev/null
+++ b/templates/admin/tool_shed_repository/view_tool_metadata.mako
@@ -0,0 +1,155 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+<br/><br/>
+<ul class="manage-table-actions">
+    <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li>
+    <div popupmenu="repository-${repository.id}-popup">
+        <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='browse_repository', id=trans.security.encode_id( repository.id ) )}">Browse repository</a>
+        <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( repository.id ) )}">Manage repository</a>
+        <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get updates</a>
+    </div>
+</ul>
+
+%if message:
+    ${render_msg( message, status )}
+%endif
+
+%if metadata:
+    <p/>
+    <div class="toolForm">
+        <div class="toolFormTitle">${metadata[ 'name' ]} tool metadata</div>
+        <div class="toolFormBody">
+            <div class="form-row">
+                <label>Name:</label>
+                ${metadata[ 'name' ]}
+                <div style="clear: both"></div>
+            </div>
+            %if 'description' in metadata:
+                <div class="form-row">
+                    <label>Description:</label>
+                    ${metadata[ 'description' ]}
+                    <div style="clear: both"></div>
+                </div>
+            %endif
+            %if 'id' in metadata:
+                <div class="form-row">
+                    <label>Id:</label>
+                    ${metadata[ 'id' ]}
+                    <div style="clear: both"></div>
+                </div>
+            %endif
+            %if 'guid' in metadata:
+                <div class="form-row">
+                    <label>Guid:</label>
+                    ${metadata[ 'guid' ]}
+                    <div style="clear: both"></div>
+                </div>
+            %endif
+            %if 'version' in metadata:
+                <div class="form-row">
+                    <label>Version:</label>
+                    ${metadata[ 'version' ]}
+                    <div style="clear: both"></div>
+                </div>
+            %endif
+            %if 'version_string_cmd' in metadata:
+                <div class="form-row">
+                    <label>Version command string:</label>
+                    ${metadata[ 'version_string_cmd' ]}
+                    <div style="clear: both"></div>
+                </div>
+            %endif
+            %if tool:
+                <div class="form-row">
+                    <label>Command:</label>
+                    <pre>${tool.command}</pre>
+                    <div style="clear: both"></div>
+                </div>
+                <div class="form-row">
+                    <label>Interpreter:</label>
+                    ${tool.interpreter}
+                    <div style="clear: both"></div>
+                </div>
+                <div class="form-row">
+                    <label>Is multi-byte:</label>
+                    ${tool.is_multi_byte}
+                    <div style="clear: both"></div>
+                </div>
+                <div class="form-row">
+                    <label>Forces a history refresh:</label>
+                    ${tool.force_history_refresh}
+                    <div style="clear: both"></div>
+                </div>
+                <div class="form-row">
+                    <label>Parallelism:</label>
+                    ${tool.parallelism}
+                    <div style="clear: both"></div>
+                </div>
+            %endif
+            <%
+                if 'requirements' in metadata:
+                    requirements = metadata[ 'requirements' ]
+                else:
+                    requirements = None
+            %>
+            %if requirements:
+                <%
+                    requirements_str = ''
+                    for requirement_dict in metadata[ 'requirements' ]:
+                        requirements_str += '%s (%s), ' % ( requirement_dict[ 'name' ], requirement_dict[ 'type' ] )
+                    requirements_str = requirements_str.rstrip( ', ' )
+                %>
+                <div class="form-row">
+                    <label>Requirements:</label>
+                    ${requirements_str}
+                    <div style="clear: both"></div>
+                </div>
+            %endif
+            <%
+                if 'tests' in metadata:
+                    tests = metadata[ 'tests' ]
+                else:
+                    tests = None
+            %>
+            %if tests:
+                <div class="form-row">
+                    <label>Functional tests:</label></td>
+                    <table class="grid">
+                        <tr>
+                            <td><b>name</b></td>
+                            <td><b>inputs</b></td>
+                            <td><b>outputs</b></td>
+                            <td><b>required files</b></td>
+                        </tr>
+                        %for test_dict in tests:
+                            <%
+                                inputs = test_dict[ 'inputs' ]
+                                outputs = test_dict[ 'outputs' ]
+                                required_files = test_dict[ 'required_files' ]
+                            %>
+                            <tr>
+                                <td>${test_dict[ 'name' ]}</td>
+                                <td>
+                                    %for input in inputs:
+                                        <b>${input[0]}:</b> ${input[1]}<br/>
+                                    %endfor
+                                </td>
+                                <td>
+                                    %for output in outputs:
+                                        <b>${output[0]}:</b> ${output[1]}<br/>
+                                    %endfor
+                                </td>
+                                <td>
+                                    %for required_file in required_files:
+                                        ${required_file[0]}<br/>
+                                    %endfor
+                                </td>
+                            </tr>
+                        %endfor
+                    </table>
+                </div>
+            %endif
+        </div>
+    </div>
+%endif
diff --git a/templates/webapps/community/base_panels.mako b/templates/webapps/community/base_panels.mako
index 056ed66ad9c..ec1969d5bfc 100644
--- a/templates/webapps/community/base_panels.mako
+++ b/templates/webapps/community/base_panels.mako
@@ -34,7 +34,8 @@
         <div class="submenu">
         <ul>            
             <li><a target="_blank" href="${app.config.get( "support_url", "http://wiki.g2.bx.psu.edu/Support" )}">Support</a></li>
-            <li><a target="_blank" href="${app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/" )}">Galaxy Wiki</a></li>             
+            <li><a target="_blank" href="${app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/Tool%20Shed" )}">Tool shed wiki</a></li>
+            <li><a target="_blank" href="${app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/" )}">Galaxy wiki</a></li>
             <li><a target="_blank" href="${app.config.get( "screencasts_url", "http://galaxycast.org" )}">Video tutorials (screencasts)</a></li>
             <li><a target="_blank" href="${app.config.get( "citation_url", "http://wiki.g2.bx.psu.edu/Citing%20Galaxy" )}">How to Cite Galaxy</a></li>
         </ul>
diff --git a/templates/webapps/galaxy/admin/index.mako b/templates/webapps/galaxy/admin/index.mako
index ca3e1fc9f0f..6f174bf1abb 100644
--- a/templates/webapps/galaxy/admin/index.mako
+++ b/templates/webapps/galaxy/admin/index.mako
@@ -67,7 +67,7 @@
                         <div class="toolTitle"><a href="${h.url_for( controller='admin', action='memdump' )}" target="galaxy_main">Profile memory usage</a></div>
                         <div class="toolTitle"><a href="${h.url_for( controller='admin', action='jobs' )}" target="galaxy_main">Manage jobs</a></div>
                         %if cloned_repositories:
-                            <div class="toolTitle"><a href="${h.url_for( controller='admin', action='browse_tool_shed_repositories' )}" target="galaxy_main">Manage installed tool shed repositories</a></div>
+                            <div class="toolTitle"><a href="${h.url_for( controller='admin_toolshed', action='browse_repositories' )}" target="galaxy_main">Manage installed tool shed repositories</a></div>
                         %endif
                     </div>
                 </div>
@@ -76,7 +76,7 @@
                     <div class="toolSectionTitle">Tool sheds</div>
                     <div class="toolSectionBody">
                         <div class="toolSectionBg">                        
-                            <div class="toolTitle"><a href="${h.url_for( controller='admin', action='browse_tool_sheds' )}" target="galaxy_main">Search and browse tool sheds</a></div>
+                            <div class="toolTitle"><a href="${h.url_for( controller='admin_toolshed', action='browse_tool_sheds' )}" target="galaxy_main">Search and browse tool sheds</a></div>
                         </div>
                     </div>
                 %endif
diff --git a/templates/webapps/galaxy/admin/tool_sheds.mako b/templates/webapps/galaxy/admin/tool_sheds.mako
index c3dc8217f3b..1f8143d15c6 100644
--- a/templates/webapps/galaxy/admin/tool_sheds.mako
+++ b/templates/webapps/galaxy/admin/tool_sheds.mako
@@ -22,12 +22,12 @@
                     <tr class="libraryTitle">
                         <td>
                             <div style="float: left; margin-left: 1px;" class="menubutton split popup" id="dataset-${shed_id}-popup">
-                                <a class="view-info" href="${h.url_for( controller='admin', action='browse_tool_shed', tool_shed_url=url )}">${name}</a>
+                                <a class="view-info" href="${h.url_for( controller='admin_toolshed', action='browse_tool_shed', tool_shed_url=url )}">${name}</a>
                             </div>
                             <div popupmenu="dataset-${shed_id}-popup">
-                                <a class="action-button" href="${h.url_for( controller='admin', action='browse_tool_shed', tool_shed_url=url )}">Browse valid repositories</a>
-                                <a class="action-button" href="${h.url_for( controller='admin', action='find_tools_in_tool_shed', tool_shed_url=url )}">Search for valid tools</a>
-                                <a class="action-button" href="${h.url_for( controller='admin', action='find_workflows_in_tool_shed', tool_shed_url=url )}">Search for workflows</a>
+                                <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='browse_tool_shed', tool_shed_url=url )}">Browse valid repositories</a>
+                                <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='find_tools_in_tool_shed', tool_shed_url=url )}">Search for valid tools</a>
+                                <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='find_workflows_in_tool_shed', tool_shed_url=url )}">Search for workflows</a>
                             </div>
                         </td>
                     </tr>

From 737f7c1343c504754a68dcc2eb0bd23e3fb7f58a Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Fri, 2 Dec 2011 14:50:36 -0500
Subject: [PATCH 276/362] Fix bug when displaying shared visualizations with
 single quotes.

---
 templates/visualization/display.mako | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/templates/visualization/display.mako b/templates/visualization/display.mako
index a34b132f71a..6a57ddf1b72 100644
--- a/templates/visualization/display.mako
+++ b/templates/visualization/display.mako
@@ -94,7 +94,7 @@
             view = create_visualization( container_element, "${config.get('title') | h}", 
                                          "${config.get('vis_id')}", "${config.get('dbkey')}",
                                          JSON.parse('${ h.to_json_string( config.get( 'viewport', dict() ) ) }'),
-                                         JSON.parse('${ h.to_json_string( config.get('tracks') ) }'),
+                                         JSON.parse('${ h.to_json_string( config['tracks'] ).replace("'", "\\'") }'),
                                          JSON.parse('${ h.to_json_string( config.get('bookmarks') ) }')
                                          );
             

From 5f62f4b0b5ca2785a8e6757a6e6c43207f0024a1 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Fri, 2 Dec 2011 15:19:37 -0500
Subject: [PATCH 277/362] Change column Uploaded By to be the Data type of the
 library dataset when browsing a data library.  Fixes issue #597.

---
 templates/library/common/browse_library.mako | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

diff --git a/templates/library/common/browse_library.mako b/templates/library/common/browse_library.mako
index 649f00159b3..ca9fc53d1fc 100644
--- a/templates/library/common/browse_library.mako
+++ b/templates/library/common/browse_library.mako
@@ -218,10 +218,6 @@
         
         is_admin = trans.user_is_admin() and cntrller == 'library_admin'
         
-        if ldda.user:
-            uploaded_by = ldda.user.email
-        else:
-            uploaded_by = 'anonymous'
         if ldda == library_dataset.library_dataset_dataset_association:
             current_version = True
             if is_admin:
@@ -303,7 +299,7 @@
             </td>
             % if not simple:
                 <td id="libraryItemInfo">${render_library_item_info( ldda )}</td>
-                <td>${uploaded_by}</td>
+                <td>${ldda.extension}</td>
             % endif
             <td>${ldda.create_time.strftime( "%Y-%m-%d" )}</td>
             <td>${ldda.get_size( nice_size=True )}</td>
@@ -579,10 +575,10 @@
                     </th>
                     % if not simple:
                         <th>Message</th>
-                        <th>Uploaded By</th>
+                        <th>Data type</th>
                     % endif
-                    <th>Date</th>
-                    <th>File Size</th>
+                    <th>Date uploaded</th>
+                    <th>File size</th>
                 </tr>
             </thead>
             <% row_counter = RowCounter() %>

From 4ea357be7382224ef910e529f2915aafd6b3372f Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Fri, 2 Dec 2011 16:58:15 -0500
Subject: [PATCH 278/362] Prepend user's public name to custom builds so that
 this information can be shown and used to display reference data.

---
 lib/galaxy/web/base/controller.py    | 21 ++++++++++++--
 lib/galaxy/web/controllers/tracks.py | 42 ++++++++++++++++++----------
 templates/visualization/display.mako |  2 +-
 3 files changed, 47 insertions(+), 18 deletions(-)

diff --git a/lib/galaxy/web/base/controller.py b/lib/galaxy/web/base/controller.py
index 568049e3ff1..01b64e85013 100644
--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -359,7 +359,18 @@ class UsesVisualization( SharableItemSecurity ):
                     'drawables': drawables,
                     'prefs': collection_dict.get( 'prefs', [] )
                 }
-
+                
+            def encode_dbkey( dbkey ):
+                """ 
+                Encodes dbkey as needed. For now, prepends user's public name 
+                to custom dbkey keys.
+                """
+                encoded_dbkey = dbkey
+                user = visualization.user
+                if 'dbkeys' in user.preferences and dbkey in user.preferences[ 'dbkeys' ]:
+                    encoded_dbkey = "%s:%s" % ( user.username, dbkey )
+                return encoded_dbkey
+                    
             # Set tracks.
             tracks = []
             if 'tracks' in latest_revision.config:
@@ -373,8 +384,12 @@ class UsesVisualization( SharableItemSecurity ):
                     else:
                         tracks.append( pack_collection( drawable_dict ) )
                 
-            config = { "title": visualization.title, "vis_id": trans.security.encode_id( visualization.id ),
-                        "tracks": tracks, "bookmarks": bookmarks, "chrom": "", "dbkey": visualization.dbkey }
+            config = {  "title": visualization.title, 
+                        "vis_id": trans.security.encode_id( visualization.id ),
+                        "tracks": tracks, 
+                        "bookmarks": bookmarks, 
+                        "chrom": "", 
+                        "dbkey": encode_dbkey( visualization.dbkey ) }
 
             if 'viewport' in latest_revision.config:
                 config['viewport'] = latest_revision.config['viewport']
diff --git a/lib/galaxy/web/controllers/tracks.py b/lib/galaxy/web/controllers/tracks.py
index 020d4fd7e14..93f7464a26f 100644
--- a/lib/galaxy/web/controllers/tracks.py
+++ b/lib/galaxy/web/controllers/tracks.py
@@ -189,7 +189,11 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
                 avail_genomes[key] = path
         self.available_genomes = avail_genomes
         
-    def _has_reference_data( self, trans, dbkey ):
+    def _has_reference_data( self, trans, dbkey, dbkey_owner=None ):
+        """ 
+        Returns true if there is reference data for the specified dbkey. If dbkey is custom, 
+        dbkey_owner is needed to determine if there is reference data.
+        """
         # Initialize built-in builds if necessary.
         if not self.available_genomes:
             self._init_references( trans )
@@ -198,12 +202,10 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
         if dbkey in self.available_genomes:
             # There is built-in reference data.
             return True
-            
-        # Look for key in user's custom builds.
-        # TODO: how to make this work for shared visualizations?
-        user = trans.user
-        if user and 'dbkeys' in trans.user.preferences:
-            user_keys = from_json_string( user.preferences['dbkeys'] )
+                
+        # Look for key in owner's custom builds.
+        if dbkey_owner and 'dbkeys' in dbkey_owner.preferences:
+            user_keys = from_json_string( dbkey_owner.preferences[ 'dbkeys' ] )
             if dbkey in user_keys:
                 dbkey_attributes = user_keys[ dbkey ]
                 if 'fasta' in dbkey_attributes:
@@ -211,6 +213,13 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
                     return True
                     
         return False
+        
+    def _decode_dbkey( self, dbkey ):
+        """ Decodes dbkey and returns tuple ( username, dbkey )"""
+        if ':' in dbkey:
+            return dbkey.split( ':' )
+        else:
+            return None, dbkey
     
     @web.expose
     @web.require_login()
@@ -272,7 +281,7 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
     @web.require_login()
     def browser(self, trans, id, chrom="", **kwargs):
         """
-        Display browser for the datasets listed in `dataset_ids`.
+        Display browser for the visualization denoted by id and add the datasets listed in `dataset_ids`.
         """
         vis = self.get_visualization( trans, id, check_ownership=False, check_accessible=True )
         viz_config = self.get_visualization_config( trans, vis )
@@ -356,7 +365,7 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
                 len_file = os.path.join( trans.app.config.len_file_path, "%s.len" % vis_dbkey )
             else:
                 len_file = len_ds.file_name
-
+                
         #
         # Get chroms data:
         #   (a) chrom name, len;
@@ -423,7 +432,7 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
                 
         to_sort = [{ 'chrom': chrom, 'len': length } for chrom, length in chroms.iteritems()]
         to_sort.sort(lambda a,b: cmp( split_by_number(a['chrom']), split_by_number(b['chrom']) ))
-        return { 'reference': self._has_reference_data( trans, vis_dbkey ), 'chrom_info': to_sort, 
+        return { 'reference': self._has_reference_data( trans, vis_dbkey, vis_user ), 'chrom_info': to_sort, 
                  'prev_chroms' : prev_chroms, 'next_chroms' : next_chroms, 'start_index' : start_index }
         
     @web.json
@@ -432,7 +441,14 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
         Return reference data for a build.
         """
         
-        if not self._has_reference_data( trans, dbkey ):
+        # If there is no dbkey owner, default to current user.
+        dbkey_owner, dbkey = self._decode_dbkey( dbkey )
+        if dbkey_owner:
+            dbkey_user = trans.sa_session.query( trans.app.model.User ).filter_by( username=dbkey_owner ).first()
+        else:
+            dbkey_user = trans.user
+            
+        if not self._has_reference_data( trans, dbkey, dbkey_user ):
             return None
         
         #    
@@ -444,9 +460,7 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
             twobit_file_name = self.available_genomes[dbkey]
         else:
             # From custom build.
-            # TODO: how to make this work for shared visualizations?
-            user = trans.user
-            user_keys = from_json_string( user.preferences['dbkeys'] )
+            user_keys = from_json_string( dbkey_user.preferences['dbkeys'] )
             dbkey_attributes = user_keys[ dbkey ]
             fasta_dataset = trans.app.model.HistoryDatasetAssociation.get( dbkey_attributes[ 'fasta' ] )
             error = self._convert_dataset( trans, fasta_dataset, 'twobit' )
diff --git a/templates/visualization/display.mako b/templates/visualization/display.mako
index 6a57ddf1b72..a0f100d3c6e 100644
--- a/templates/visualization/display.mako
+++ b/templates/visualization/display.mako
@@ -8,7 +8,7 @@
       <script type='text/javascript' src="${h.url_for('/static/scripts/excanvas.js')}"></script>
     <![endif]-->
     
-    ${h.js( "jquery.event.drag", "jquery.autocomplete", "jquery.mousewheel", "jquery.autocomplete", "trackster", "trackster_ui", "jquery.ui.sortable.slider", "jquery.scrollTo", "farbtastic" )}
+    ${h.js( "jquery.event.drag", "jquery.autocomplete", "jquery.mousewheel", "jquery.autocomplete", "trackster", "trackster_ui", "jquery.ui.sortable.slider", "farbtastic" )}
 </%def>
 
 <%def name="stylesheets()">

From 74799ec699ef7968fb6e130097a903a11dd44852 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Sat, 3 Dec 2011 17:06:33 -0500
Subject: [PATCH 279/362] Remove unneeded vis_id parameter from tracks/chroms
 method.

---
 lib/galaxy/web/controllers/tracks.py | 39 ++++++++++------------------
 static/scripts/trackster.js          |  3 ++-
 2 files changed, 15 insertions(+), 27 deletions(-)

diff --git a/lib/galaxy/web/controllers/tracks.py b/lib/galaxy/web/controllers/tracks.py
index 93f7464a26f..44a967cdac1 100644
--- a/lib/galaxy/web/controllers/tracks.py
+++ b/lib/galaxy/web/controllers/tracks.py
@@ -293,7 +293,7 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
         return trans.fill_template( 'tracks/browser.mako', config=viz_config, add_dataset=new_dataset )
 
     @web.json
-    def chroms( self, trans, vis_id=None, dbkey=None, num=None, chrom=None, low=None ):
+    def chroms( self, trans, dbkey=None, num=None, chrom=None, low=None ):
         """
         Returns a naturally sorted list of chroms/contigs for either a given visualization or a given dbkey.
         Use either chrom or low to specify the starting chrom in the return list.
@@ -322,25 +322,12 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
         else:
             low = 0
             
-        #
-        # Get viz, dbkey.
-        #
-            
-        # Must specify either vis_id or dbkey.
-        if not vis_id and not dbkey:
-            return trans.show_error_message("No visualization id or dbkey specified.")
-            
-        # Need to get user and dbkey in order to get chroms data.
-        if vis_id:
-            # Use user, dbkey from viz.
-            visualization = self.get_visualization( trans, vis_id, check_ownership=False, check_accessible=True )
-            visualization.config = self.get_visualization_config( trans, visualization )
-            vis_user = visualization.user
-            vis_dbkey = visualization.dbkey
+        # If there is no dbkey owner, default to current user.
+        dbkey_owner, dbkey = self._decode_dbkey( dbkey )
+        if dbkey_owner:
+            dbkey_user = trans.sa_session.query( trans.app.model.User ).filter_by( username=dbkey_owner ).first()
         else:
-            # No vis_id, so visualization is new. User is current user, dbkey must be given.
-            vis_user = trans.user
-            vis_dbkey = dbkey
+            dbkey_user = trans.user
 
         #
         # Get len file.
@@ -348,21 +335,21 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
         len_file = None
         len_ds = None
         user_keys = {}
-        if 'dbkeys' in vis_user.preferences:
-            user_keys = from_json_string( vis_user.preferences['dbkeys'] )
-            if vis_dbkey in user_keys:
-                dbkey_attributes = user_keys[ vis_dbkey ]
+        if 'dbkeys' in dbkey_user.preferences:
+            user_keys = from_json_string( dbkey_user.preferences['dbkeys'] )
+            if dbkey in user_keys:
+                dbkey_attributes = user_keys[ dbkey ]
                 if 'fasta' in dbkey_attributes:
                     build_fasta = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( dbkey_attributes[ 'fasta' ] )
                     len_file = build_fasta.get_converted_dataset( trans, 'len' ).file_name
                 # Backwards compatibility: look for len file directly.
                 elif 'len' in dbkey_attributes:
-                    len_file = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( user_keys[ vis_dbkey ][ 'len' ] ).file_name
+                    len_file = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( user_keys[ dbkey ][ 'len' ] ).file_name
 
         if not len_file:
             len_ds = trans.db_dataset_for( dbkey )
             if not len_ds:
-                len_file = os.path.join( trans.app.config.len_file_path, "%s.len" % vis_dbkey )
+                len_file = os.path.join( trans.app.config.len_file_path, "%s.len" % dbkey )
             else:
                 len_file = len_ds.file_name
                 
@@ -432,7 +419,7 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
                 
         to_sort = [{ 'chrom': chrom, 'len': length } for chrom, length in chroms.iteritems()]
         to_sort.sort(lambda a,b: cmp( split_by_number(a['chrom']), split_by_number(b['chrom']) ))
-        return { 'reference': self._has_reference_data( trans, vis_dbkey, vis_user ), 'chrom_info': to_sort, 
+        return { 'reference': self._has_reference_data( trans, dbkey, dbkey_user ), 'chrom_info': to_sort, 
                  'prev_chroms' : prev_chroms, 'next_chroms' : next_chroms, 'start_index' : start_index }
         
     @web.json
diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index 85e2d9d9599..00b618aff1c 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -1195,7 +1195,8 @@ extend( View.prototype, DrawableCollection.prototype, {
      */
     load_chroms: function(url_parms) {
         url_parms['num'] = MAX_CHROMS_SELECTABLE;
-        $.extend( url_parms, (this.vis_id !== undefined ? { vis_id: this.vis_id } : { dbkey: this.dbkey } ) );
+        url_parms['dbkey'] = this.dbkey;
+
         var 
             view = this,
             chrom_data = $.Deferred();

From 756422bcc7f10fa66a3b102b88b2cba617ff0116 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Sat, 3 Dec 2011 18:05:58 -0500
Subject: [PATCH 280/362] Trackster: decode dbkey when adding tracks.

---
 lib/galaxy/web/controllers/tracks.py | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/lib/galaxy/web/controllers/tracks.py b/lib/galaxy/web/controllers/tracks.py
index 44a967cdac1..89befdd9249 100644
--- a/lib/galaxy/web/controllers/tracks.py
+++ b/lib/galaxy/web/controllers/tracks.py
@@ -30,6 +30,13 @@ messages = Bunch(
     OK = "ok"
 )
 
+def _decode_dbkey( dbkey ):
+    """ Decodes dbkey and returns tuple ( username, dbkey )"""
+    if ':' in dbkey:
+        return dbkey.split( ':' )
+    else:
+        return None, dbkey
+
 class NameColumn( grids.TextColumn ):
     def get_value( self, trans, grid, history ):
         return history.get_display_name()
@@ -92,6 +99,7 @@ class DbKeyColumn( grids.GridColumn ):
     def filter( self, trans, user, query, dbkey ):
         """ Filter by dbkey; datasets without a dbkey are returned as well. """
         # use raw SQL b/c metadata is a BLOB
+        dbkey_user, dbkey = _decode_dbkey( dbkey )
         dbkey = dbkey.replace("'", "\\'")
         return query.filter( or_( \
                                 or_( "metadata like '%%\"dbkey\": [\"%s\"]%%'" % dbkey, "metadata like '%%\"dbkey\": \"%s\"%%'" % dbkey ), \
@@ -213,13 +221,6 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
                     return True
                     
         return False
-        
-    def _decode_dbkey( self, dbkey ):
-        """ Decodes dbkey and returns tuple ( username, dbkey )"""
-        if ':' in dbkey:
-            return dbkey.split( ':' )
-        else:
-            return None, dbkey
     
     @web.expose
     @web.require_login()
@@ -323,7 +324,7 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
             low = 0
             
         # If there is no dbkey owner, default to current user.
-        dbkey_owner, dbkey = self._decode_dbkey( dbkey )
+        dbkey_owner, dbkey = _decode_dbkey( dbkey )
         if dbkey_owner:
             dbkey_user = trans.sa_session.query( trans.app.model.User ).filter_by( username=dbkey_owner ).first()
         else:
@@ -429,7 +430,7 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
         """
         
         # If there is no dbkey owner, default to current user.
-        dbkey_owner, dbkey = self._decode_dbkey( dbkey )
+        dbkey_owner, dbkey = _decode_dbkey( dbkey )
         if dbkey_owner:
             dbkey_user = trans.sa_session.query( trans.app.model.User ).filter_by( username=dbkey_owner ).first()
         else:

From 39d74e80b3589f988e2094ce5c9ae4060846773d Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Mon, 5 Dec 2011 09:58:36 -0500
Subject: [PATCH 281/362] Fix some broken functional tests and fixes for
 deleting multiple data libraries and resetting the password for multiple
 users.  Fixes issue # 678.

---
 lib/galaxy/web/base/controller.py            |  33 +++---
 lib/galaxy/web/controllers/library_common.py | 102 ++++++++++++-------
 test/base/twilltestcase.py                   |   6 +-
 test/functional/test_library_features.py     |  10 +-
 test/functional/test_library_security.py     |  10 +-
 test/functional/test_library_templates.py    |  30 +++---
 test/functional/test_user_info.py            |   2 +-
 7 files changed, 110 insertions(+), 83 deletions(-)

diff --git a/lib/galaxy/web/base/controller.py b/lib/galaxy/web/base/controller.py
index 01b64e85013..8ff0743253c 100644
--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -5,6 +5,7 @@ import os, time, logging, re, string, sys, glob, shutil, tempfile, subprocess, b
 from datetime import date, datetime, timedelta
 from time import strftime
 from galaxy import config, tools, web, util
+from galaxy.util import inflector
 from galaxy.util.hash_util import *
 from galaxy.util.json import json_fix
 from galaxy.web import error, form, url_for
@@ -2030,28 +2031,28 @@ class Admin( object ):
     @web.require_admin
     def reset_user_password( self, trans, **kwd ):
         webapp = kwd.get( 'webapp', 'galaxy' )
-        id = kwd.get( 'id', None )
-        if not id:
-            message = "No user ids received for resetting passwords"
+        user_id = kwd.get( 'id', None )
+        if not user_id:
+            message = "No users received for resetting passwords."
             trans.response.send_redirect( web.url_for( controller='admin',
                                                        action='users',
                                                        webapp=webapp,
                                                        message=message,
                                                        status='error' ) )
-        ids = util.listify( id )
+        user_ids = util.listify( user_id )
         if 'reset_user_password_button' in kwd:
             message = ''
             status = ''
-            for user_id in ids:
+            for user_id in user_ids:
                 user = get_user( trans, user_id )
                 password = kwd.get( 'password', None )
                 confirm = kwd.get( 'confirm' , None )
                 if len( password ) < 6:
-                    message = "Please use a password of at least 6 characters"
+                    message = "Use a password of at least 6 characters."
                     status = 'error'
                     break
                 elif password != confirm:
-                    message = "Passwords do not match"
+                    message = "Passwords do not match."
                     status = 'error'
                     break
                 else:
@@ -2059,18 +2060,18 @@ class Admin( object ):
                     trans.sa_session.add( user )
                     trans.sa_session.flush()
             if not message and not status:
-                message = "Passwords reset for %d users" % len( ids )
+                message = "Passwords reset for %d %s." % ( len( user_ids ), inflector.cond_plural( len( user_ids ), 'user' ) )
                 status = 'done'
             trans.response.send_redirect( web.url_for( controller='admin',
                                                        action='users',
                                                        webapp=webapp,
                                                        message=util.sanitize_text( message ),
                                                        status=status ) )
-        users = [ get_user( trans, user_id ) for user_id in ids ]
-        if len( ids ) > 1:
-            id=','.join( id )
+        users = [ get_user( trans, user_id ) for user_id in user_ids ]
+        if len( user_ids ) > 1:
+            user_id = ','.join( user_ids )
         return trans.fill_template( '/admin/user/reset_password.mako',
-                                    id=id,
+                                    id=user_id,
                                     users=users,
                                     password='',
                                     confirm='',
@@ -2435,13 +2436,11 @@ def copy_sample_loc_file( trans, filename ):
     # overwrite it in case it contains stuff proprietary to the local instance.
     if not os.path.exists( os.path.join( tool_data_path, loc_file ) ):
         shutil.copy( os.path.abspath( filename ), os.path.join( tool_data_path, loc_file ) )
-def get_user( trans, id ):
+def get_user( trans, user_id ):
     """Get a User from the database by id."""
-    # Load user from database
-    id = trans.security.decode_id( id )
-    user = trans.sa_session.query( trans.model.User ).get( id )
+    user = trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( user_id ) )
     if not user:
-        return trans.show_error_message( "User not found for id (%s)" % str( id ) )
+        return trans.show_error_message( "User not found for id (%s)" % str( user_id ) )
     return user
 def get_user_by_username( trans, username ):
     """Get a user from the database by username"""
diff --git a/lib/galaxy/web/controllers/library_common.py b/lib/galaxy/web/controllers/library_common.py
index d464c063688..90a094d1a89 100644
--- a/lib/galaxy/web/controllers/library_common.py
+++ b/lib/galaxy/web/controllers/library_common.py
@@ -2250,6 +2250,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitions ):
         # contents will be purged.  The association between this method and the cleanup_datasets.py script
         # enables clean maintenance of libraries and library dataset disk files.  This is also why the item_types
         # are not any of the associations ( the cleanup_datasets.py script handles everything ).
+        status = kwd.get( 'status', 'done' )
         show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
         item_types = { 'library': trans.app.model.Library,
                        'folder': trans.app.model.LibraryFolder,
@@ -2264,22 +2265,36 @@ class LibraryCommon( BaseUIController, UsesFormDefinitions ):
                 item_desc = 'Dataset'
             else:
                 item_desc = item_type.capitalize()
-            try:
-                library_item = trans.sa_session.query( item_types[ item_type ] ).get( trans.security.decode_id( item_id ) )
-            except:
-                library_item = None
-            if not library_item or not ( is_admin or trans.app.security_agent.can_access_library_item( current_user_roles, library_item, trans.user ) ):
-                message = 'Invalid %s id ( %s ) specifield.' % ( item_desc, item_id )
-                status = 'error'
-            elif not ( is_admin or trans.app.security_agent.can_modify_library_item( current_user_roles, library_item ) ):
-                message = "You are not authorized to delete %s '%s'." % ( item_desc, library_item.name )
-                status = 'error'
-            else:
-                library_item.deleted = True
-                trans.sa_session.add( library_item )
+            library_item_ids = util.listify( item_id )
+            valid_items = 0
+            invalid_items = 0
+            not_authorized_items = 0
+            flush_needed = False
+            message = ''
+            for library_item_id in library_item_ids:
+                try:
+                    library_item = trans.sa_session.query( item_types[ item_type ] ).get( trans.security.decode_id( library_item_id ) )
+                except:
+                    library_item = None
+                if not library_item or not ( is_admin or trans.app.security_agent.can_access_library_item( current_user_roles, library_item, trans.user ) ):
+                    invalid_items += 1
+                elif not ( is_admin or trans.app.security_agent.can_modify_library_item( current_user_roles, library_item ) ):
+                    not_authorized_items += 1
+                else:
+                    valid_items += 1
+                    library_item.deleted = True
+                    trans.sa_session.add( library_item )
+                    flush_needed = True
+            if flush_needed:
                 trans.sa_session.flush()
-                message = util.sanitize_text( "%s '%s' has been marked deleted" % ( item_desc, library_item.name ) )
-                status = 'done'
+            if valid_items:
+                message += "%d %s marked deleted.  " % ( valid_items, inflector.cond_plural( valid_items, item_desc ) )
+            if invalid_items:
+                message += '%d invalid %s specifield.  ' % ( invalid_items, inflector.cond_plural( invalid_items, item_desc ) )
+                status = 'error'
+            if not_authorized_items:
+                message += 'You are not authorized to delete %d %s.  ' % ( not_authorized_items, inflector.cond_plural( not_authorized_items, item_desc ) )
+                status = 'error'
         if item_type == 'library':
             return trans.response.send_redirect( web.url_for( controller=cntrller,
                                                               action='browse_libraries',
@@ -2296,6 +2311,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitions ):
     @web.expose
     def undelete_library_item( self, trans, cntrller, library_id, item_id, item_type, **kwd ):
         # This action will handle undeleting all types of library items
+        status = kwd.get( 'status', 'done' )
         show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
         item_types = { 'library': trans.app.model.Library,
                        'folder': trans.app.model.LibraryFolder,
@@ -2304,31 +2320,49 @@ class LibraryCommon( BaseUIController, UsesFormDefinitions ):
         current_user_roles = trans.get_current_user_roles()
         if item_type not in item_types:
             message = 'Bad item_type specified: %s' % str( item_type )
-            status = ERROR
+            status = 'error'
         else:
             if item_type == 'library_dataset':
                 item_desc = 'Dataset'
             else:
                 item_desc = item_type.capitalize()
-            try:
-                library_item = trans.sa_session.query( item_types[ item_type ] ).get( trans.security.decode_id( item_id ) )
-            except:
-                library_item = None
-            if not library_item or not ( is_admin or trans.app.security_agent.can_access_library_item( current_user_roles, library_item, trans.user ) ):
-                message = 'Invalid %s id ( %s ) specifield.' % ( item_desc, item_id )
-                status = 'error'
-            elif library_item.purged:
-                message = '%s %s has been purged, so it cannot be undeleted' % ( item_desc, library_item.name )
-                status = ERROR
-            elif not ( is_admin or trans.app.security_agent.can_modify_library_item( current_user_roles, library_item ) ):
-                message = "You are not authorized to delete %s '%s'." % ( item_desc, library_item.name )
-                status = 'error'
-            else:
-                library_item.deleted = False
-                trans.sa_session.add( library_item )
+
+            library_item_ids = util.listify( item_id )
+            valid_items = 0
+            invalid_items = 0
+            purged_items = 0
+            not_authorized_items = 0
+            flush_needed = False
+            message = ''
+            for library_item_id in library_item_ids:
+                try:
+                    library_item = trans.sa_session.query( item_types[ item_type ] ).get( trans.security.decode_id( library_item_id ) )
+                except:
+                    library_item = None
+                if not library_item or not ( is_admin or trans.app.security_agent.can_access_library_item( current_user_roles, library_item, trans.user ) ):
+                    invalid_items += 1
+                elif library_item.purged:
+                    purged_items += 1
+                elif not ( is_admin or trans.app.security_agent.can_modify_library_item( current_user_roles, library_item ) ):
+                    not_authorized_items += 1
+                else:
+                    valid_items += 1
+                    library_item.deleted = False
+                    trans.sa_session.add( library_item )
+                    flush_needed = True
+            if flush_needed:
                 trans.sa_session.flush()
-                message = util.sanitize_text( "%s '%s' has been marked undeleted" % ( item_desc, library_item.name ) )
-                status = SUCCESS
+            if valid_items:
+                message += "%d %s marked undeleted.  " % ( valid_items, inflector.cond_plural( valid_items, item_desc ) )
+            if invalid_items:
+                message += '%d invalid %s specifield.  ' % ( invalid_items, inflector.cond_plural( invalid_items, item_desc ) )
+                status = 'error'
+            if not_authorized_items:
+                message += 'You are not authorized to undelete %d %s.  ' % ( not_authorized_items, inflector.cond_plural( not_authorized_items, item_desc ) )
+                status = 'error'  
+            if purged_items:
+                message += '%d %s marked purged, so cannot be undeleted.  ' % ( purged_items, inflector.cond_plural( purged_items, item_desc ) )
+                status = 'error'  
         if item_type == 'library':
             return trans.response.send_redirect( web.url_for( controller=cntrller,
                                                               action='browse_libraries',
diff --git a/test/base/twilltestcase.py b/test/base/twilltestcase.py
index 928c8d65fd0..fff6c754f7e 100644
--- a/test/base/twilltestcase.py
+++ b/test/base/twilltestcase.py
@@ -1224,7 +1224,7 @@ class TwillTestCase( unittest.TestCase ):
         tc.fv( "1", "password", password )
         tc.fv( "1", "confirm", password )
         tc.submit( "reset_user_password_button" )
-        self.check_page_for_string( "Passwords reset for 1 users" )
+        self.check_page_for_string( "Passwords reset for 1 user." )
         self.home()
     def mark_user_deleted( self, user_id, email='' ):
         """Mark a user as deleted"""
@@ -2278,7 +2278,7 @@ class TwillTestCase( unittest.TestCase ):
             item_desc = 'Dataset'
         else:
             item_desc = item_type.capitalize()
-        check_str = "%s '%s' has been marked deleted" % ( item_desc, item_name )
+        check_str = "marked deleted"
         self.check_page_for_string( check_str )
         self.home()
     def undelete_library_item( self, cntrller, library_id, item_id, item_name, item_type='library_dataset' ):
@@ -2290,7 +2290,7 @@ class TwillTestCase( unittest.TestCase ):
             item_desc = 'Dataset'
         else:
             item_desc = item_type.capitalize()
-        check_str = "%s '%s' has been marked undeleted" % ( item_desc, item_name )
+        check_str = "marked undeleted"
         self.check_page_for_string( check_str )
         self.home()
     def purge_library( self, library_id, library_name ):
diff --git a/test/functional/test_library_features.py b/test/functional/test_library_features.py
index 05e546efec8..8067f237fc8 100644
--- a/test/functional/test_library_features.py
+++ b/test/functional/test_library_features.py
@@ -137,7 +137,7 @@ class TestLibraryFeatures( TwillTestCase ):
         assert ldda2 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda2 from the database'
         self.browse_library( cntrller='library_admin',
                              library_id=self.security.encode_id( library1.id ),
-                             strings_displayed=[ ldda2.name, ldda2.message, admin_user.email ] )
+                             strings_displayed=[ ldda2.name, ldda2.message, 'bed' ] )
     def test_050_add_2nd_public_dataset_to_folder2( self ):
         """Testing adding a 2nd public dataset folder2"""
         # Logged in as admin_user
@@ -156,7 +156,7 @@ class TestLibraryFeatures( TwillTestCase ):
         assert ldda3 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda3 from the database'
         self.browse_library( cntrller='library_admin',
                              library_id=self.security.encode_id( library1.id ),
-                             strings_displayed=[ ldda3.name, ldda3.message, admin_user.email ] )
+                             strings_displayed=[ ldda3.name, ldda3.message, 'bed' ] )
     def test_055_copy_dataset_from_history_to_subfolder( self ):
         """Testing copying a dataset from the current history to a subfolder"""
         # logged in as admin_user
@@ -176,7 +176,7 @@ class TestLibraryFeatures( TwillTestCase ):
         assert ldda4 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda4 from the database'
         self.browse_library( cntrller='library_admin',
                              library_id=self.security.encode_id( library1.id ),
-                             strings_displayed=[ ldda4.name, ldda4.message, admin_user.email ] )
+                             strings_displayed=[ ldda4.name, ldda4.message, 'bed' ] )
     def test_060_editing_dataset_attribute_info( self ):
         """Testing editing a library dataset's attribute information"""
         # logged in as admin_user
@@ -299,11 +299,11 @@ class TestLibraryFeatures( TwillTestCase ):
         ldda_message = 'Uploaded all files in test-data/users/test1...'
         self.browse_library( 'library',
                              self.security.encode_id( library1.id ),
-                             strings_displayed=[ regular_user1.email, ldda_message, '1.fasta' ] )
+                             strings_displayed=[ 'fasta', ldda_message, '1.fasta' ] )
         ldda_message = 'Uploaded all files in test-data/users/test3.../run1'
         self.browse_library( 'library',
                              self.security.encode_id( library1.id ),
-                             strings_displayed=[ regular_user3.email, ldda_message, '2.fasta' ] )
+                             strings_displayed=[ 'fasta', ldda_message, '2.fasta' ] )
     def test_085_mark_ldda2_deleted( self ):
         """Testing marking ldda2 as deleted"""
         # Logged in as admin_user
diff --git a/test/functional/test_library_security.py b/test/functional/test_library_security.py
index 550f2089529..95994a40720 100644
--- a/test/functional/test_library_security.py
+++ b/test/functional/test_library_security.py
@@ -157,7 +157,7 @@ class TestLibrarySecurity( TwillTestCase ):
         assert ldda1 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda1 from the database'
         self.browse_library( cntrller='library_admin',
                              library_id=self.security.encode_id( library1.id ),
-                             strings_displayed=[ ldda1.name, ldda1.message, admin_user.email ] )
+                             strings_displayed=[ ldda1.name, ldda1.message, 'bed' ] )
     def test_030_access_ldda1_with_private_role_restriction( self ):
         """Testing accessing ldda1 with a private role restriction"""
         # Logged in as admin_user
@@ -262,20 +262,20 @@ class TestLibrarySecurity( TwillTestCase ):
         assert ldda2 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda2 from the database'
         self.browse_library( cntrller='library',
                              library_id=self.security.encode_id( library1.id ),
-                             strings_displayed=[ ldda2.name, ldda2.message, admin_user.email ] )
+                             strings_displayed=[ ldda2.name, ldda2.message, 'bed' ] )
     def test_045_accessing_ldda2_with_role_associated_with_group_and_users( self ):
         """Testing accessing ldda2 with a role that is associated with a group and users"""
         # Logged in as admin_user
         # admin_user should be able to see 2.bed since she is associated with role2
         self.browse_library( cntrller='library',
                              library_id=self.security.encode_id( library1.id ),
-                             strings_displayed=[ ldda2.name, ldda2.message, admin_user.email ] )
+                             strings_displayed=[ ldda2.name, ldda2.message, 'bed' ] )
         self.logout()
         # regular_user1 should be able to see 2.bed since she is associated with group_two
         self.login( email = regular_user1.email )
         self.browse_library( cntrller='library',
                              library_id=self.security.encode_id( library1.id ),
-                             strings_displayed=[ folder1.name, ldda2.name, ldda2.message, admin_user.email ] )
+                             strings_displayed=[ folder1.name, ldda2.name, ldda2.message, 'bed' ] )
         # Check the permissions on the dataset 2.bed - they are as folows:
         # DATASET_MANAGE_PERMISSIONS = test@bx.psu.edu
         # DATASET_ACCESS = Role2
@@ -356,7 +356,7 @@ class TestLibrarySecurity( TwillTestCase ):
                                      strings_displayed=[ "Upload a directory of files" ] )
         self.browse_library( cntrller='library_admin',
                              library_id=self.security.encode_id( library1.id ),
-                             strings_displayed=[ admin_user.email, ldda_message ] )
+                             strings_displayed=[ 'bed', ldda_message ] )
     def test_055_change_permissions_on_datasets_uploaded_from_library_dir( self ):
         """Testing changing the permissions on datasets uploaded from a directory from the Admin view"""
         # logged in as admin_user
diff --git a/test/functional/test_library_templates.py b/test/functional/test_library_templates.py
index a016e1afc24..f340f440d74 100644
--- a/test/functional/test_library_templates.py
+++ b/test/functional/test_library_templates.py
@@ -181,7 +181,7 @@ class TestLibraryFeatures( TwillTestCase ):
         assert ldda1 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda1 from the database'
         self.browse_library( cntrller='library_admin',
                              library_id=self.security.encode_id( library1.id ),
-                             strings_displayed=[ ldda1.name, ldda1.message, admin_user.email ] )
+                             strings_displayed=[ ldda1.name, ldda1.message, 'bed' ] )
         # Make sure the library template contents were correctly saved
         self.ldda_edit_info( 'library_admin',
                              self.security.encode_id( library1.id ),
@@ -308,7 +308,7 @@ class TestLibraryFeatures( TwillTestCase ):
         assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database'
         self.browse_library( cntrller='library_admin',
                              library_id=self.security.encode_id( library2.id ),
-                             strings_displayed=[ ldda.name, ldda.message, admin_user.email ] )
+                             strings_displayed=[ ldda.name, ldda.message, 'bed' ] )
         # Make sure the library template contents were correctly saved
         self.ldda_edit_info( 'library_admin',
                              self.security.encode_id( library2.id ),
@@ -363,8 +363,7 @@ class TestLibraryFeatures( TwillTestCase ):
                                               'Option1' ] )
     def test_100_add_ldda_to_folder3( self ):
         """
-        Testing adding a new library dataset to library3's folder,
-        making sure the SelectField setting is correct on the upload form.
+        Testing adding a new library dataset to library3's folder, making sure the SelectField setting is correct on the upload form.
         """
         filename = '3.bed'
         ldda_message = '3.bed message'
@@ -381,7 +380,7 @@ class TestLibraryFeatures( TwillTestCase ):
         assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database'
         self.browse_library( cntrller='library_admin',
                              library_id=self.security.encode_id( library3.id ),
-                             strings_displayed=[ ldda.name, ldda.message, admin_user.email ] )
+                             strings_displayed=[ ldda.name, ldda.message, 'bed' ] )
         # Make sure the library template contents were correctly saved
         self.ldda_edit_info( 'library_admin',
                              self.security.encode_id( library3.id ),
@@ -453,8 +452,7 @@ class TestLibraryFeatures( TwillTestCase ):
                                               'This text should be inherited' ] )
     def test_120_add_ldda_to_folder4( self ):
         """
-        Testing adding a new library dataset to library4's folder,
-        making sure the TextArea setting is correct on the upload form.
+        Testing adding a new library dataset to library4's folder, making sure the TextArea setting is correct on the upload form.
         """
         filename = '4.bed'
         ldda_message = '4.bed message'
@@ -471,7 +469,7 @@ class TestLibraryFeatures( TwillTestCase ):
         assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database'
         self.browse_library( cntrller='library_admin',
                              library_id=self.security.encode_id( library4.id ),
-                             strings_displayed=[ ldda.name, ldda.message, admin_user.email ] )
+                             strings_displayed=[ ldda.name, ldda.message, 'bed' ] )
         # Make sure the library template contents were correctly saved
         self.ldda_edit_info( 'library_admin',
                              self.security.encode_id( library4.id ),
@@ -519,8 +517,7 @@ class TestLibraryFeatures( TwillTestCase ):
                                               'This text should be inherited' ] )
     def test_140_add_ldda_to_folder5( self ):
         """
-        Testing adding a new library dataset to library5's folder,
-        making sure the TextField setting is correct on the upload form.
+        Testing adding a new library dataset to library5's folder, making sure the TextField setting is correct on the upload form.
         """
         # Logged in as admin_user
         filename = '5.bed'
@@ -537,7 +534,7 @@ class TestLibraryFeatures( TwillTestCase ):
         assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database'
         self.browse_library( cntrller='library_admin',
                              library_id=self.security.encode_id( library5.id ),
-                             strings_displayed=[ ldda.name, ldda.message, admin_user.email ] )
+                             strings_displayed=[ ldda.name, ldda.message, 'bed' ] )
         # Make sure the library template contents were correctly saved
         self.ldda_edit_info( 'library_admin',
                              self.security.encode_id( library5.id ),
@@ -558,9 +555,7 @@ class TestLibraryFeatures( TwillTestCase ):
                             field_default_1='%s default' % TextArea_form.name )
     def test_150_add_ldda_to_library5( self ):
         """
-        Testing adding a new library dataset to library5's folder,
-        making sure the TextField and new TextArea settings are 
-        correct on the upload form.
+        Testing adding a new library dataset to library5's folder, making sure the TextField and new TextArea settings are correct on the upload form.
         """
         filename = '6.bed'
         ldda_message = '6.bed message'
@@ -579,7 +574,7 @@ class TestLibraryFeatures( TwillTestCase ):
         assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database'
         self.browse_library( cntrller='library_admin',
                              library_id=self.security.encode_id( library5.id ),
-                             strings_displayed=[ ldda.name, ldda.message, admin_user.email ] )
+                             strings_displayed=[ ldda.name, ldda.message, 'bed' ] )
         # Make sure the library template contents were correctly saved
         self.ldda_edit_info( 'library_admin',
                              self.security.encode_id( library5.id ),
@@ -626,8 +621,7 @@ class TestLibraryFeatures( TwillTestCase ):
                                               'none' ] )
     def test_170_add_ldda_to_folder6( self ):
         """
-        Testing adding a new library dataset to library6's folder,
-        making sure the WorkflowField setting is correct on the upload form.
+        Testing adding a new library dataset to library6's folder, making sure the WorkflowField setting is correct on the upload form.
         """
         # Logged in as admin_user
         filename = '7.bed'
@@ -644,7 +638,7 @@ class TestLibraryFeatures( TwillTestCase ):
         assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database'
         self.browse_library( cntrller='library_admin',
                              library_id=self.security.encode_id( library6.id ),
-                             strings_displayed=[ ldda.name, ldda.message, admin_user.email ] )
+                             strings_displayed=[ ldda.name, ldda.message, 'bed' ] )
         # Make sure the library template contents were correctly saved
         self.ldda_edit_info( 'library_admin',
                              self.security.encode_id( library6.id ),
diff --git a/test/functional/test_user_info.py b/test/functional/test_user_info.py
index 82ca78ef953..0697475028d 100644
--- a/test/functional/test_user_info.py
+++ b/test/functional/test_user_info.py
@@ -206,7 +206,7 @@ class TestUserInfo( TwillTestCase ):
         self.edit_user_info( cntrller='user',
                              password='testuser',
                              new_password='testuser#',\
-                             strings_displayed_after_submit=[ 'The password has been changed.' ] )
+                             strings_displayed_after_submit=[ 'The password has been changed' ] )
         self.logout()
         refresh( regular_user12 )
         # Test logging in with new email and password

From 2c9babc27af16a504fdc4b7735c46c13f4cf4c94 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 5 Dec 2011 11:29:31 -0500
Subject: [PATCH 282/362] Fix for workflow multiple input regression from
 6185:07f3f601d645.

---
 lib/galaxy/web/controllers/workflow.py | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/lib/galaxy/web/controllers/workflow.py b/lib/galaxy/web/controllers/workflow.py
index 577ad81372e..bd101efe510 100644
--- a/lib/galaxy/web/controllers/workflow.py
+++ b/lib/galaxy/web/controllers/workflow.py
@@ -1432,7 +1432,7 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
                         step.upgrade_messages = {}
                         # Connections by input name
                         step.input_connections_by_name = \
-                            dict( ( conn.input_name, conn ) for conn in step.input_connections ) 
+                            dict( ( conn.input_name, conn ) for conn in step.input_connections )
                         # Extract just the arguments for this step by prefix
                         p = "%s|" % step.id
                         l = len(p)
@@ -1446,7 +1446,7 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
                                 has_upgrade_messages = True
                             # Any connected input needs to have value DummyDataset (these
                             # are not persisted so we need to do it every time)
-                            module.add_dummy_datasets( connections=step.input_connections )    
+                            module.add_dummy_datasets( connections=step.input_connections )
                             # Get the tool
                             tool = module.tool
                             # Get the state
@@ -1462,7 +1462,7 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
                             state = step.state = module.decode_runtime_state( trans, step_args.pop( "tool_state" ) )
                             step_errors = module.update_runtime_state( trans, state, step_args )
                         if step_errors:
-                            errors[step.id] = state.inputs["__errors__"] = step_errors   
+                            errors[step.id] = state.inputs["__errors__"] = step_errors
                     if 'run_workflow' in kwargs and not errors:
                         new_history = None
                         if 'new_history' in kwargs:
@@ -1486,7 +1486,7 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
                                     tool = trans.app.toolbox.tools_by_id[ step.tool_id ]
                                 except KeyError, e:
                                     # Handle the case where the workflow requires a tool not available in the local Galaxy instance.
-                                    # The id value of tools installed from a Galaxy tool shed is a guid, but these tool's old_id 
+                                    # The id value of tools installed from a Galaxy tool shed is a guid, but these tool's old_id
                                     # attribute should contain what we're looking for.
                                     for available_tool_id, available_tool in trans.app.toolbox.tools_by_id.items():
                                         if step.tool_id == available_tool.old_id:
@@ -1528,7 +1528,8 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
                         invocations.append({'outputs': outputs,
                                             'new_history': new_history})
                         trans.sa_session.flush()
-                        return trans.fill_template( "workflow/run_complete.mako",
+                if invocations:
+                    return trans.fill_template( "workflow/run_complete.mako",
                                                     workflow=stored,
                                                     invocations=invocations )
             else:
@@ -1549,7 +1550,7 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
                             has_upgrade_messages = True
                         # Any connected input needs to have value DummyDataset (these
                         # are not persisted so we need to do it every time)
-                        step.module.add_dummy_datasets( connections=step.input_connections )                  
+                        step.module.add_dummy_datasets( connections=step.input_connections )
                         # Store state with the step
                         step.state = step.module.state
                         # Error dict
@@ -1568,7 +1569,7 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
             # Render the form
             stored.annotation = self.get_item_annotation_str( trans.sa_session, trans.user, stored )
             return trans.fill_template(
-                        "workflow/run.mako", 
+                        "workflow/run.mako",
                         steps=workflow.steps,
                         workflow=stored,
                         has_upgrade_messages=has_upgrade_messages,
@@ -1580,8 +1581,8 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
         finally:
             # restore the active history
             if saved_history is not None:
-                trans.set_history(saved_history) 
-                    
+                trans.set_history(saved_history)
+
     def get_item( self, trans, id ):
         return self.get_stored_workflow( trans, id ) 
         

From d1df52946d8d78d41b840ddac68b6569759a682c Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Mon, 5 Dec 2011 11:37:46 -0500
Subject: [PATCH 283/362] Allow select_param.fields.name method of accessing
 additional attributes from dynamic options work for multiple selects.

---
 lib/galaxy/tools/__init__.py                   | 11 +++++++----
 lib/galaxy/tools/parameters/dynamic_options.py |  9 +++++++--
 2 files changed, 14 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 493d7ba86ee..3894bcc7f09 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -2190,11 +2190,14 @@ class SelectToolParameterWrapper( object ):
         Only applicable for dynamic_options selects, which have more than simple 'options' defined (name, value, selected).
         """
         def __init__( self, input, value, other_values ):
-            self.input = input
-            self.value = value
-            self.other_values = other_values
+            self._input = input
+            self._value = value
+            self._other_values = other_values
+            self._fields = {}
         def __getattr__( self, name ):
-            return self.input.options.get_field_by_name_for_value( name, self.value, None, self.other_values )
+            if name not in self._fields:
+                self._fields[ name ] = self._input.options.get_field_by_name_for_value( name, self._value, None, self._other_values )
+            return self._input.separator.join( map( str, self._fields[ name ] ) )
     
     def __init__( self, input, value, app, other_values={} ):
         self.input = input
diff --git a/lib/galaxy/tools/parameters/dynamic_options.py b/lib/galaxy/tools/parameters/dynamic_options.py
index f4b86fa772d..708eba46bbb 100644
--- a/lib/galaxy/tools/parameters/dynamic_options.py
+++ b/lib/galaxy/tools/parameters/dynamic_options.py
@@ -525,13 +525,18 @@ class DynamicOptions( object ):
         """
         Get contents of field by name for specified value.
         """
+        rval = []
         if isinstance( field_name, int ):
             field_index = field_name
         else:
             assert field_name in self.columns, "Requested '%s' column missing from column def" % field_name
             field_index = self.columns[ field_name ]
-        for fields in self.get_fields_by_value( value, trans, other_values ):
-            return fields[ field_index ]
+        if not isinstance( value, list ):
+            value = [value]
+        for val in value:
+            for fields in self.get_fields_by_value( val, trans, other_values ):
+                rval.append( fields[ field_index ] )
+        return rval
     
     def get_options( self, trans, other_values ):
         rval = []

From 7e33a879efd416987aee505d48a1bbb5372d0f91 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Mon, 5 Dec 2011 12:19:48 -0500
Subject: [PATCH 284/362] Look for datasets/indices in metadata and use if
 found rather than doing conversion.

---
 lib/galaxy/model/__init__.py         | 20 +++++++++++++++++++-
 lib/galaxy/web/controllers/tracks.py | 23 +++++++----------------
 2 files changed, 26 insertions(+), 17 deletions(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 03cda106d67..24834c2ed67 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -928,7 +928,10 @@ class DatasetInstance( object ):
             depends_list = trans.app.datatypes_registry.converter_deps[self.extension][target_ext]
         except KeyError:
             depends_list = []
-        # See if converted dataset already exists
+        # See if converted dataset already exists, either in metadata in conversions.
+        converted_dataset = self.get_metadata_dataset( trans, target_ext )
+        if converted_dataset:
+            return converted_dataset
         converted_dataset = self.get_converted_files_by_type( target_ext )
         if converted_dataset:
             return converted_dataset
@@ -958,6 +961,21 @@ class DatasetInstance( object ):
         session.add( assoc )
         session.flush()
         return None
+    def get_metadata_dataset( self, trans, dataset_ext ):
+        """ 
+        Returns an HDA that points to a metadata file which contains a 
+        converted data with the requested extension.
+        """
+        for name, value in self.metadata.items():
+            # HACK: MetadataFile objects do not have a type/ext, so need to use metadata name
+            # to determine type.
+            if dataset_ext == 'bai' and name == 'bam_index' and isinstance( value, trans.app.model.MetadataFile ):
+                # HACK: MetadataFile objects cannot be used by tools, so return 
+                # a fake HDA that points to metadata file.
+                fake_dataset = trans.app.model.Dataset( state=trans.app.model.Dataset.states.OK, 
+                                                        external_filename=value.file_name )
+                fake_hda = trans.app.model.HistoryDatasetAssociation( dataset=fake_dataset )
+                return fake_hda
     def clear_associated_files( self, metadata_safe = False, purge = False ):
         raise 'Unimplemented'
     def get_child_by_designation(self, designation):
diff --git a/lib/galaxy/web/controllers/tracks.py b/lib/galaxy/web/controllers/tracks.py
index 89befdd9249..d130c6b67d1 100644
--- a/lib/galaxy/web/controllers/tracks.py
+++ b/lib/galaxy/web/controllers/tracks.py
@@ -546,7 +546,7 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
             valid_chroms = indexer.valid_chroms()
         else:
             # Standalone data provider
-            standalone_provider = get_data_provider(data_sources['data_standalone']['name'])( dataset )
+            standalone_provider = get_data_provider( data_sources['data_standalone']['name'] )( dataset )
             kwargs = {"stats": True}
             if not standalone_provider.has_data( chrom ):
                 return messages.NO_DATA
@@ -609,16 +609,8 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
         else:
             tracks_dataset_type = data_sources['data']['name']
             data_provider_class = get_data_provider( name=tracks_dataset_type, original_dataset=dataset )
-            # HACK: Use bai from bam HDA's metadata if available. This saves 
-            # the client from waiting a long time to generate a duplicate
-            # bam via a converted dataset.
-            if dataset.ext == "bam" and dataset.metadata.get( "bam_index", None ) is not None:
-                converted_dataset = dataset.metadata.bam_index
-                deps = None
-            else:
-                # Default behavior.    
-                converted_dataset = dataset.get_converted_dataset( trans, tracks_dataset_type )
-                deps = dataset.get_converted_dataset_deps( trans, tracks_dataset_type )
+            converted_dataset = dataset.get_converted_dataset( trans, tracks_dataset_type )
+            deps = dataset.get_converted_dataset_deps( trans, tracks_dataset_type )
             data_provider = data_provider_class( converted_dataset=converted_dataset, original_dataset=dataset, dependencies=deps )
         
         # Get and return data from data_provider.
@@ -1037,16 +1029,15 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
             data_sources_dict[ source_type ] = { "name" : data_source, "message": msg }
         
         return data_sources_dict
-        
+                    
     def _convert_dataset( self, trans, dataset, target_type ):
         """
         Converts a dataset to the target_type and returns a message indicating 
         status of the conversion. None is returned to indicate that dataset
         was converted successfully. 
         """
-                
-        # Get converted dataset; this will start the conversion if 
-        # necessary.
+        
+        # Get converted dataset; this will start the conversion if necessary.
         try:
             converted_dataset = dataset.get_converted_dataset( trans, target_type )
         except NoConverterException:
@@ -1063,7 +1054,7 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
             msg = { 'kind': messages.ERROR, 'message': job.stderr }
         elif not converted_dataset or converted_dataset.state != model.Dataset.states.OK:
             msg = messages.PENDING
-            
+        
         return msg
         
 def _get_highest_priority_msg( message_list ):

From d8755293e358f46c4e0c0c2a7774c92bec5a5def Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Mon, 5 Dec 2011 12:27:54 -0500
Subject: [PATCH 285/362] GATK tools will now use their own .loc file for
 picard indexes and will also load annotations from an external file.

---
 tool-data/gatk_annotations.txt.sample         | 30 ++++++++
 tool-data/gatk_sorted_picard_index.loc.sample | 26 +++++++
 tools/gatk/unified_genotyper.xml              | 73 +++---------------
 tools/gatk/variant_annotator.xml              | 74 +++----------------
 tools/gatk/variant_recalibrator.xml           | 37 ++--------
 5 files changed, 86 insertions(+), 154 deletions(-)
 create mode 100644 tool-data/gatk_annotations.txt.sample
 create mode 100644 tool-data/gatk_sorted_picard_index.loc.sample

diff --git a/tool-data/gatk_annotations.txt.sample b/tool-data/gatk_annotations.txt.sample
new file mode 100644
index 00000000000..d089f6f3288
--- /dev/null
+++ b/tool-data/gatk_annotations.txt.sample
@@ -0,0 +1,30 @@
+#unique_id	name	gatk_value	tools_valid_for
+AlleleBalance	AlleleBalance	AlleleBalance	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+AlleleBalanceBySample	AlleleBalanceBySample	AlleleBalanceBySample	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+BaseCounts	BaseCounts	BaseCounts	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+BaseQualityRankSumTest	BaseQualityRankSumTest	BaseQualityRankSumTest	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+ChromosomeCounts	ChromosomeCounts	ChromosomeCounts	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+DepthOfCoverage	DepthOfCoverage	DepthOfCoverage	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+DepthPerAlleleBySample	DepthPerAlleleBySample	DepthPerAlleleBySample	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+FisherStrand	FisherStrand	FisherStrand	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+GCContent	GCContent	GCContent	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+HaplotypeScore	HaplotypeScore	HaplotypeScore	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+HardyWeinberg	HardyWeinberg	HardyWeinberg	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+HomopolymerRun	HomopolymerRun	HomopolymerRun	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+InbreedingCoeff	InbreedingCoeff	InbreedingCoeff	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+IndelType	IndelType	IndelType	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+LowMQ	LowMQ	LowMQ	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+MVLikelihoodRatio	MVLikelihoodRatio	MVLikelihoodRatio	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+MappingQualityRankSumTest	MappingQualityRankSumTest	MappingQualityRankSumTest	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+MappingQualityZero	MappingQualityZero	MappingQualityZero	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+MappingQualityZeroBySample	MappingQualityZeroBySample	MappingQualityZeroBySample	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+MappingQualityZeroFraction	MappingQualityZeroFraction	MappingQualityZeroFraction	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+NBaseCount	NBaseCount	NBaseCount	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+QualByDepth	QualByDepth	QualByDepth	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+RMSMappingQuality	RMSMappingQuality	RMSMappingQuality	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+ReadDepthAndAllelicFractionBySample	ReadDepthAndAllelicFractionBySample	ReadDepthAndAllelicFractionBySample	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+ReadPosRankSumTest	ReadPosRankSumTest	ReadPosRankSumTest	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+SampleList	SampleList	SampleList	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+SnpEff	SnpEff	SnpEff	VariantAnnotator,VariantRecalibrator
+SpanningDeletions	SpanningDeletions	SpanningDeletions	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+TechnologyComposition	TechnologyComposition	TechnologyComposition	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
diff --git a/tool-data/gatk_sorted_picard_index.loc.sample b/tool-data/gatk_sorted_picard_index.loc.sample
new file mode 100644
index 00000000000..d21a7b0c968
--- /dev/null
+++ b/tool-data/gatk_sorted_picard_index.loc.sample
@@ -0,0 +1,26 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Picard dict and associated files. You will need
+#to create these data files and then create a picard_index.loc file 
+#similar to this one (store it in this directory) that points to 
+#the directories in which those files are stored. The picard_index.loc 
+#file has this format (longer white space is the TAB character):
+#
+#<unique_build_id>   <dbkey>   <display_name>   <fasta_file_path>
+#
+#So, for example, if you had hg18 indexed and stored in 
+#/depot/data2/galaxy/srma/hg18/, 
+#then the srma_index.loc entry would look like this:
+#
+#hg18   hg18   hg18 Pretty   /depot/data2/galaxy/picard/hg18/hg18.fa
+#
+#and your /depot/data2/galaxy/srma/hg18/ directory
+#would contain the following three files:
+#hg18.fa
+#hg18.dict
+#hg18.fa.fai
+#
+#The dictionary file for each reference (ex. hg18.dict) must be 
+#created via Picard (http://picard.sourceforge.net). Note that
+#the dict file does not have the .fa extension although the
+#path list in the loc file does include it.
+#
diff --git a/tools/gatk/unified_genotyper.xml b/tools/gatk/unified_genotyper.xml
index 82219da40c9..9966707ee99 100644
--- a/tools/gatk/unified_genotyper.xml
+++ b/tools/gatk/unified_genotyper.xml
@@ -113,7 +113,7 @@
         --indelHaplotypeSize "${analysis_param_type.indelHaplotypeSize}"
         ${analysis_param_type.doContextDependentGapPenalties}
         #if str( $analysis_param_type.annotation ) != "None":
-            #for $annotation in str( $analysis_param_type.annotation ).split( ','):
+            #for $annotation in str( $analysis_param_type.annotation.fields.gatk_value ).split( ','):
                 --annotation "${annotation}"
             #end for
         #end if
@@ -123,7 +123,7 @@
             #end for
         #end if
         #if str( $analysis_param_type.exclude_annotations ) != "None":
-            #for $annotation in str( $analysis_param_type.exclude_annotations ).split( ','):
+            #for $annotation in str( $analysis_param_type.exclude_annotations.fields.gatk_value ).split( ','):
                 --excludeAnnotation "${annotation}"
             #end for
         #end if
@@ -366,35 +366,11 @@
         <param name="indelHaplotypeSize" type="integer" value="80" label="Indel haplotype size" />
         <param name="doContextDependentGapPenalties" type="boolean" truevalue="--doContextDependentGapPenalties" falsevalue="" label="Vary gap penalties by context" />
 	    <param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types">
-          <option value="AlleleBalance" />
-          <option value="AlleleBalanceBySample" />
-          <option value="BaseCounts" />
-          <option value="BaseQualityRankSumTest" />
-          <option value="ChromosomeCounts" />
-          <option value="DepthOfCoverage" />
-          <option value="DepthPerAlleleBySample" />
-          <option value="FisherStrand" />
-          <option value="GCContent" />
-          <option value="HaplotypeScore" />
-          <option value="HardyWeinberg" />
-          <option value="HomopolymerRun" />
-          <option value="InbreedingCoeff" />
-          <option value="IndelType" />
-          <option value="LowMQ" />
-          <option value="MVLikelihoodRatio" />
-          <option value="MappingQualityRankSumTest" />
-          <option value="MappingQualityZero" />
-          <option value="MappingQualityZeroBySample" />
-          <option value="MappingQualityZeroFraction" />
-          <option value="NBaseCount" />
-          <option value="QualByDepth" />
-          <option value="RMSMappingQuality" />
-          <option value="ReadDepthAndAllelicFractionBySample" />
-          <option value="ReadPosRankSumTest" />
-          <option value="SampleList" />
-          <!-- <option value="SnpEff" /> -->
-          <option value="SpanningDeletions" />
-          <option value="TechnologyComposition" />
+          <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
+          <options from_data_table="gatk_annotations">
+            <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
+            <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/>
+          </options>
 	    </param>
 <!--
         <conditional name="snpEff_rod_bind_type">
@@ -420,36 +396,11 @@
 	    </param>
     <!--     <param name="family_string" type="text" value="" label="Family String"/> -->
         <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" >
-          <!-- might we want to load the available annotations from an external configuration file, since additional ones can be added to local installs? -->
-          <option value="AlleleBalance" />
-          <option value="AlleleBalanceBySample" />
-          <option value="BaseCounts" />
-          <option value="BaseQualityRankSumTest" />
-          <option value="ChromosomeCounts" />
-          <option value="DepthOfCoverage" />
-          <option value="DepthPerAlleleBySample" />
-          <option value="FisherStrand" />
-          <option value="GCContent" />
-          <option value="HaplotypeScore" />
-          <option value="HardyWeinberg" />
-          <option value="HomopolymerRun" />
-          <option value="InbreedingCoeff" />
-          <option value="IndelType" />
-          <option value="LowMQ" />
-          <option value="MVLikelihoodRatio" />
-          <option value="MappingQualityRankSumTest" />
-          <option value="MappingQualityZero" />
-          <option value="MappingQualityZeroBySample" />
-          <option value="MappingQualityZeroFraction" />
-          <option value="NBaseCount" />
-          <option value="QualByDepth" />
-          <option value="RMSMappingQuality" />
-          <option value="ReadDepthAndAllelicFractionBySample" />
-          <option value="ReadPosRankSumTest" />
-          <option value="SampleList" />
-          <!-- <option value="SnpEff" /> -->
-          <option value="SpanningDeletions" />
-          <option value="TechnologyComposition" />
+          <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
+          <options from_data_table="gatk_annotations">
+            <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
+            <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/>
+          </options>
         </param>
       </when>
     </conditional>
diff --git a/tools/gatk/variant_annotator.xml b/tools/gatk/variant_annotator.xml
index 0599d93e7b3..897c1418cff 100644
--- a/tools/gatk/variant_annotator.xml
+++ b/tools/gatk/variant_annotator.xml
@@ -26,13 +26,13 @@
         --useAllAnnotations
     #else:
         #if str( $annotations_type.annotations ) != "None":
-            #for $annotation in str( $annotations_type.annotations ).split( ',' ):
+            #for $annotation in str( $annotations_type.annotations.fields.gatk_value ).split( ',' ):
                 --annotation "${annotation}"
             #end for
         #end if
     #end if
     #if str( $exclude_annotations ) != "None":
-        #for $annotation in str( $exclude_annotations ).split( ',' ):
+        #for $annotation in str( $exclude_annotations.fields.gatk_value ).split( ',' ):
             --excludeAnnotation "${annotation}"
         #end for
     #end if
@@ -179,36 +179,11 @@
       </when>
       <when value="choose">
         <param name="annotations" type="select" multiple="True" display="checkboxes" label="Annotations to apply" >
-          <!-- might we want to load the available annotations from an external configuration file, since additional ones can be added to local installs? -->
-          <option value="AlleleBalance" />
-          <option value="AlleleBalanceBySample" />
-          <option value="BaseCounts" />
-          <option value="BaseQualityRankSumTest" />
-          <option value="ChromosomeCounts" />
-          <option value="DepthOfCoverage" />
-          <option value="DepthPerAlleleBySample" />
-          <option value="FisherStrand" />
-          <option value="GCContent" />
-          <option value="HaplotypeScore" />
-          <option value="HardyWeinberg" />
-          <option value="HomopolymerRun" />
-          <option value="InbreedingCoeff" />
-          <option value="IndelType" />
-          <option value="LowMQ" />
-          <option value="MVLikelihoodRatio" />
-          <option value="MappingQualityRankSumTest" />
-          <option value="MappingQualityZero" />
-          <option value="MappingQualityZeroBySample" />
-          <option value="MappingQualityZeroFraction" />
-          <option value="NBaseCount" />
-          <option value="QualByDepth" />
-          <option value="RMSMappingQuality" />
-          <option value="ReadDepthAndAllelicFractionBySample" />
-          <option value="ReadPosRankSumTest" />
-          <option value="SampleList" />
-          <option value="SnpEff" />
-          <option value="SpanningDeletions" />
-          <option value="TechnologyComposition" />
+          <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
+          <options from_data_table="gatk_annotations">
+            <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
+            <filter type="static_value" value="VariantAnnotator" column="tools_valid_for"/>
+          </options>
         </param>
       </when>
     </conditional>
@@ -388,36 +363,11 @@
     <param name="family_string" type="text" value="" label="Family String"/>
     <param name="mendel_violation_genotype_quality_threshold" type="float" value="0.0" label="genotype quality treshold in order to annotate mendelian violation ratio."/>
     <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" >
-      <!-- might we want to load the available annotations from an external configuration file, since additional ones can be added to local installs? -->
-      <option value="AlleleBalance" />
-      <option value="AlleleBalanceBySample" />
-      <option value="BaseCounts" />
-      <option value="BaseQualityRankSumTest" />
-      <option value="ChromosomeCounts" />
-      <option value="DepthOfCoverage" />
-      <option value="DepthPerAlleleBySample" />
-      <option value="FisherStrand" />
-      <option value="GCContent" />
-      <option value="HaplotypeScore" />
-      <option value="HardyWeinberg" />
-      <option value="HomopolymerRun" />
-      <option value="InbreedingCoeff" />
-      <option value="IndelType" />
-      <option value="LowMQ" />
-      <option value="MVLikelihoodRatio" />
-      <option value="MappingQualityRankSumTest" />
-      <option value="MappingQualityZero" />
-      <option value="MappingQualityZeroBySample" />
-      <option value="MappingQualityZeroFraction" />
-      <option value="NBaseCount" />
-      <option value="QualByDepth" />
-      <option value="RMSMappingQuality" />
-      <option value="ReadDepthAndAllelicFractionBySample" />
-      <option value="ReadPosRankSumTest" />
-      <option value="SampleList" />
-      <option value="SnpEff" />
-      <option value="SpanningDeletions" />
-      <option value="TechnologyComposition" />
+      <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
+      <options from_data_table="gatk_annotations">
+        <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
+        <filter type="static_value" value="VariantAnnotator" column="tools_valid_for"/>
+      </options>
     </param>
     
   </inputs>
diff --git a/tools/gatk/variant_recalibrator.xml b/tools/gatk/variant_recalibrator.xml
index 4fefaea3ef7..427e946eb14 100644
--- a/tools/gatk/variant_recalibrator.xml
+++ b/tools/gatk/variant_recalibrator.xml
@@ -100,7 +100,7 @@
     ##start analysis specific options
     -p '
     #if str( $annotations ) != "None":
-        #for $annotation in str( $annotations ).split( ',' ):
+        #for $annotation in str( $annotations.fields.gatk_value ).split( ',' ):
             --use_annotation "${annotation}"
         #end for
     #end if
@@ -337,36 +337,11 @@
     </repeat>
     
     <param name="annotations" type="select" multiple="True" display="checkboxes" label="annotations which should used for calculations">
-      <!-- might we want to load the available annotations from an external configuration file, since additional ones can be added to local installs? -->
-      <option value="ChromosomeCounts"/>
-      <option value="IndelType"/>
-      <option value="SpanningDeletions"/>
-      <option value="HardyWeinberg"/>
-      <option value="NBaseCount"/>
-      <option value="MappingQualityZero"/>
-      <option value="AlleleBalance"/>
-      <option value="BaseCounts"/>
-      <option value="LowMQ"/>
-      <option value="InbreedingCoeff"/>
-      <option value="RMSMappingQuality"/>
-      <option value="HaplotypeScore"/>
-      <option value="TechnologyComposition"/>
-      <option value="SampleList"/>
-      <option value="FisherStrand"/>
-      <option value="HomopolymerRun"/>
-      <option value="DepthOfCoverage"/>
-      <option value="SnpEff"/>
-      <option value="MappingQualityZeroFraction"/>
-      <option value="GCContent"/>
-      <option value="MappingQualityRankSumTest"/>
-      <option value="ReadPosRankSumTest"/>
-      <option value="BaseQualityRankSumTest"/>
-      <option value="QualByDepth"/>
-      <option value="SBByDepth"/>
-      <option value="ReadDepthAndAllelicFractionBySample"/>
-      <option value="AlleleBalanceBySample"/>
-      <option value="DepthPerAlleleBySample"/>
-      <option value="MappingQualityZeroBySample"/>
+      <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
+      <options from_data_table="gatk_annotations">
+        <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
+        <filter type="static_value" value="VariantRecalibrator" column="tools_valid_for"/>
+      </options>
     </param>
     
         <param name="mode" type="select" label="Recalibration mode">

From 8de943a46a40b24e99d3a6faa97fbaa9b378ff8d Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Mon, 5 Dec 2011 12:32:02 -0500
Subject: [PATCH 286/362] Update tool data tables for GATK.

---
 tool_data_table_conf.xml.sample | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/tool_data_table_conf.xml.sample b/tool_data_table_conf.xml.sample
index 5a899e0990b..952ee2cf3e0 100644
--- a/tool_data_table_conf.xml.sample
+++ b/tool_data_table_conf.xml.sample
@@ -77,8 +77,13 @@
     </table>
     <!-- Location of Picard dict files valid for GATK -->
     <table name="gatk_picard_indexes" comment_char="#">
-        <columns>value, dbkey, name, path, tools_valid_for</columns>
-        <file path="tool-data/picard_index.loc" />
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/gatk_sorted_picard_index.loc" />
+    </table>
+    <!-- Available of GATK references -->
+    <table name="gatk_annotations" comment_char="#">
+        <columns>value, name, gatk_value, tools_valid_for</columns>
+        <file path="tool-data/gatk_annotations.txt" />
     </table>
     <!-- Location of SRMA dict file and other files -->
     <table name="srma_indexes" comment_char="#">

From 9b5e9992f0138a57416fbbd681514a9dad357ded Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Mon, 5 Dec 2011 14:55:00 -0500
Subject: [PATCH 287/362] Fedora(/RHEL/SL/CentOS) init script, thanks Brad
 Chapman!

---
 contrib/README             |   6 +++
 contrib/galaxy.fedora-init | 105 +++++++++++++++++++++++++++++++++++++
 2 files changed, 111 insertions(+)
 create mode 100644 contrib/galaxy.fedora-init

diff --git a/contrib/README b/contrib/README
index 8bd81b76e51..1bfe7741c1d 100644
--- a/contrib/README
+++ b/contrib/README
@@ -19,6 +19,12 @@ galaxy.debian-init:
     paths, and configure for start at boot with `update-rc.d galaxy defaults`.
     Also written and submitted by James Casbon.
 
+galaxy.fedora-init:
+
+    init script for Fedora/RedHat/Scientific Linux/CentOS.  Copy to
+    /etc/init.d/galaxy, modify paths, and configure for start at boot with
+    `chkconfig galaxy on`.  Written and submitted by Brad Chapman.
+
 galaxy.solaris-smf.xml:
 
     SMF Manifest for Solaris 10 and OpenSolaris.  Import with `svccfg import
diff --git a/contrib/galaxy.fedora-init b/contrib/galaxy.fedora-init
new file mode 100644
index 00000000000..58f08607b49
--- /dev/null
+++ b/contrib/galaxy.fedora-init
@@ -0,0 +1,105 @@
+#!/bin/bash
+#
+# Init file for Galaxy (http://galaxyproject.org/)
+#   Suitable for use on Fedora and derivatives (RedHat Enterprise Linux, Scientific Linux, CentOS)
+#
+# Contributed by Brad Chapman
+#
+# chkconfig: 2345 98 20
+# description: Galaxy http://galaxyproject.org/
+
+#--- config
+
+SERVICE_NAME="galaxy"
+RUN_AS="galaxy"
+RUN_IN="/path/to/galaxy-dist"
+
+#--- main actions
+
+start() {
+	echo "Starting $SERVICE_NAME... "
+	cmd="cd $RUN_IN && sh run.sh --daemon"
+	case "$(id -un)" in
+		$RUN_AS)
+			eval "$cmd"
+			;;
+		root)
+			su - $RUN_AS -c "$cmd"
+			;;
+		*)
+			echo "*** ERROR *** must be $RUN_AS or root in order to control this service" >&2
+			exit 1
+	esac
+	echo "...done."
+}
+
+stop() {
+	echo -n "Stopping $SERVICE_NAME... "
+	
+	cmd="cd $RUN_IN && sh run.sh --stop-daemon"
+
+	case "$(id -un)" in
+		$RUN_AS)
+			eval "$cmd"
+			;;
+		root)
+			su - $RUN_AS -c "$cmd"
+			;;
+		*)
+			echo "*** ERROR *** must be $RUN_AS or root in order to control this service" >&2
+			exit 1
+	esac
+	
+	echo "done."
+}
+
+status() {
+	echo -n "$SERVICE_NAME status: "
+	
+	while read pid; do
+		if [ "$(readlink -m /proc/$pid/cwd)" = "$(readlink -m $RUN_IN)" ]; then
+			echo "started"
+			return 0
+		fi
+	done < <(ps ax -o 'pid cmd' | grep -P '^\s*\d+ python ./scripts/paster.py serve' | awk '{print $1}')
+	echo "stopped"
+	return 3
+}
+
+notsupported() {
+	echo "*** ERROR*** $SERVICE_NAME: operation [$1] not supported"
+}
+
+usage() {
+	echo "Usage: $SERVICE_NAME start|stop|restart|status"
+}
+
+
+#---
+
+case "$1" in
+	start)
+		start "$@"
+		;;
+	stop)
+		stop
+		;;
+	restart|reload)
+		stop
+		start
+		;;
+	status)
+		set +e
+		status
+		exit $?
+		;;
+	'')
+		usage >&2
+		exit 1
+		;;
+	*)
+		notsupported "$1" >&2
+		usage >&2
+		exit 1
+		;;
+esac

From 2bcc5212eb281b83dea2f38ab08c81b08c8d90e2 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 5 Dec 2011 21:57:19 -0500
Subject: [PATCH 288/362] Sanitize output anytime a raw text/html dataset is
 served via dataset/display.

---
 lib/galaxy/web/controllers/dataset.py | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/lib/galaxy/web/controllers/dataset.py b/lib/galaxy/web/controllers/dataset.py
index ec56f9453d7..449bf06dd00 100644
--- a/lib/galaxy/web/controllers/dataset.py
+++ b/lib/galaxy/web/controllers/dataset.py
@@ -317,7 +317,7 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesHistory, UsesHist
         trans.response.headers["Content-Type"] = "application/octet-stream"
         trans.response.headers["Content-Disposition"] = "attachment; filename=Galaxy%s-[%s].%s" % (data.hid, fname, file_ext)
         return open(data.metadata.get(metadata_name).file_name)
-        
+
     @web.expose
     def display(self, trans, dataset_id=None, preview=False, filename=None, to_ext=None, **kwd):
         """Catches the dataset id and displays file contents as directed"""
@@ -337,10 +337,9 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesHistory, UsesHist
             raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( dataset_id ) )
         if not trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), data.dataset ):
             return trans.show_error_message( "You are not allowed to access this dataset" )
-        
+
         if data.state == trans.model.Dataset.states.UPLOAD:
             return trans.show_error_message( "Please wait until this dataset finishes uploading before attempting to view it." )
-        
         if filename and filename != "index":
             # For files in extra_files_path
             file_path = os.path.join( data.extra_files_path, filename )
@@ -357,14 +356,14 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesHistory, UsesHist
                 return open( file_path )
             else:
                 return trans.show_error_message( "Could not find '%s' on the extra files path %s." % ( filename, file_path ) )
-        
+
         trans.response.set_content_type(data.get_mime())
         trans.log_event( "Display dataset id: %s" % str( dataset_id ) )
-        
+
         if to_ext or isinstance(data.datatype, datatypes.binary.Binary): # Saving the file, or binary file
             if data.extension in composite_extensions:
                 return self.archive_composite_dataset( trans, data, **kwd )
-            else:                    
+            else:
                 trans.response.headers['Content-Length'] = int( os.stat( data.file_name ).st_size )
                 if not to_ext:
                     to_ext = data.extension
@@ -375,11 +374,13 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesHistory, UsesHist
                 return open( data.file_name )
         if not os.path.exists( data.file_name ):
             raise paste.httpexceptions.HTTPNotFound( "File Not Found (%s)." % data.file_name )
-        
         max_peek_size = 1000000 # 1 MB
         if isinstance(data.datatype, datatypes.images.Html):
             max_peek_size = 10000000 # 10 MB for html
         if not preview or isinstance(data.datatype, datatypes.images.Image) or os.stat( data.file_name ).st_size < max_peek_size:
+            if trans.response.get_content_type() == "text/html":
+                # Sanitize anytime we respond with plain text/html content.
+                return sanitize_html(open( data.file_name ).read())
             return open( data.file_name )
         else:
             trans.response.set_content_type( "text/html" )

From ba4692ac00b19ed1170b7d4176ad25ed280d71b0 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 6 Dec 2011 08:01:06 -0500
Subject: [PATCH 289/362] Small patch to sanitizer to remove javascript content
 from sanitized anchors.

---
 lib/galaxy/util/sanitize_html.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/util/sanitize_html.py b/lib/galaxy/util/sanitize_html.py
index 74e090cc81a..8a6418f0905 100644
--- a/lib/galaxy/util/sanitize_html.py
+++ b/lib/galaxy/util/sanitize_html.py
@@ -373,7 +373,9 @@ class _HTMLSanitizer(_BaseHTMLProcessor):
 
         clean_attrs = []
         for key, value in self.normalize_attrs(attrs):
-            if key in acceptable_attributes:
+            if key=="href" and value.startswith("javascript"):
+                pass
+            elif key in acceptable_attributes:
                 key=keymap.get(key,key)
                 clean_attrs.append((key,value))
             elif key=='style':
@@ -436,4 +438,4 @@ def sanitize_html(htmlSource, encoding="utf-8", type="text/html"):
     p.feed(htmlSource)
     data = p.output()
     data = data.strip().replace('\r\n', '\n')
-    return data
\ No newline at end of file
+    return data

From 6162101f90d115a4ccc1af84909b9ed6be57c300 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 6 Dec 2011 08:08:16 -0500
Subject: [PATCH 290/362] Small tweak on patch, strip first to prevent
 whitespace loophole.

---
 lib/galaxy/util/sanitize_html.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/util/sanitize_html.py b/lib/galaxy/util/sanitize_html.py
index 8a6418f0905..07720bf89aa 100644
--- a/lib/galaxy/util/sanitize_html.py
+++ b/lib/galaxy/util/sanitize_html.py
@@ -373,7 +373,7 @@ class _HTMLSanitizer(_BaseHTMLProcessor):
 
         clean_attrs = []
         for key, value in self.normalize_attrs(attrs):
-            if key=="href" and value.startswith("javascript"):
+            if key=="href" and value.strip().startswith("javascript"):
                 pass
             elif key in acceptable_attributes:
                 key=keymap.get(key,key)

From 041f54bcb188b72a2b318cfaf364b74a16f9734b Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Tue, 6 Dec 2011 08:56:21 -0500
Subject: [PATCH 291/362] Fix for data library functional test.

---
 test/functional/test_library_templates.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/functional/test_library_templates.py b/test/functional/test_library_templates.py
index f340f440d74..dad2a61f2af 100644
--- a/test/functional/test_library_templates.py
+++ b/test/functional/test_library_templates.py
@@ -403,7 +403,7 @@ class TestLibraryFeatures( TwillTestCase ):
         assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database'
         self.browse_library( cntrller='library_admin',
                              library_id=self.security.encode_id( library3.id ),
-                             strings_displayed=[ ldda.name, admin_user.email ] )
+                             strings_displayed=[ ldda.name, 'bed' ] )
         # Make sure the library template contents were correctly saved
         self.ldda_edit_info( 'library_admin',
                              self.security.encode_id( library3.id ),

From 20ae669ded10fb73320f9eb9bfcae89fecb7ba19 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 6 Dec 2011 09:15:43 -0500
Subject: [PATCH 292/362] Fix bad merge.

---
 lib/galaxy/datatypes/tabular.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py
index 7c333deff6f..72ed33e949a 100644
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -353,7 +353,7 @@ class Sam( Tabular ):
             dataset.metadata.columns = 12
             dataset.metadata.column_types = ['str', 'int', 'str', 'int', 'int', 'str', 'str', 'int', 'int', 'str', 'str', 'str']
 
-     def merge( split_files, output_file):
+    def merge( split_files, output_file):
         """
         Multiple SAM files may each have headers. Since the headers should all be the same, remove
         the headers from files 1-n, keeping them in the first file only

From 2c68904b3024e2361b82c6e5c941d40b74859f72 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Tue, 6 Dec 2011 09:34:19 -0500
Subject: [PATCH 293/362] Add automatic conversions for SAM to BAM and SAM to
 summary tree. Enable SAM datasets to be visualized in Trackster.

---
 datatypes_conf.xml.sample                     |  5 ++-
 .../bam_to_summary_tree_converter.py          | 34 ---------------
 .../bam_to_summary_tree_converter.xml         |  2 +-
 .../sam_or_bam_to_summary_tree_converter.py   | 42 +++++++++++++++++++
 .../datatypes/converters/sam_to_bam.xml       | 17 ++++++++
 .../sam_to_summary_tree_converter.xml         | 14 +++++++
 lib/galaxy/datatypes/tabular.py               |  5 ++-
 .../visualization/tracks/data_providers.py    | 13 ++++++
 8 files changed, 95 insertions(+), 37 deletions(-)
 delete mode 100644 lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.py
 create mode 100644 lib/galaxy/datatypes/converters/sam_or_bam_to_summary_tree_converter.py
 create mode 100644 lib/galaxy/datatypes/converters/sam_to_bam.xml
 create mode 100644 lib/galaxy/datatypes/converters/sam_to_summary_tree_converter.xml

diff --git a/datatypes_conf.xml.sample b/datatypes_conf.xml.sample
index 5f756eec957..11c43eedb72 100644
--- a/datatypes_conf.xml.sample
+++ b/datatypes_conf.xml.sample
@@ -139,7 +139,10 @@
     <datatype extension="qualsolid" type="galaxy.datatypes.qualityscore:QualityScoreSOLiD" display_in_upload="true"/>
     <datatype extension="qual454" type="galaxy.datatypes.qualityscore:QualityScore454" display_in_upload="true"/>
     <datatype extension="Roadmaps" type="galaxy.datatypes.assembly:Roadmaps" display_in_upload="false"/>
-    <datatype extension="sam" type="galaxy.datatypes.tabular:Sam" display_in_upload="true"/>
+    <datatype extension="sam" type="galaxy.datatypes.tabular:Sam" display_in_upload="true">
+    	<converter file="sam_to_bam.xml" target_datatype="bam"/>
+    	<converter file="sam_to_summary_tree_converter.xml" target_datatype="summary_tree"/>
+	</datatype>
     <datatype extension="scf" type="galaxy.datatypes.binary:Scf" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="Sequences" type="galaxy.datatypes.assembly:Sequences" display_in_upload="false"/>
     <datatype extension="sff" type="galaxy.datatypes.binary:Sff" mimetype="application/octet-stream" display_in_upload="true"/>
diff --git a/lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.py b/lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.py
deleted file mode 100644
index 0071b052d90..00000000000
--- a/lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.py
+++ /dev/null
@@ -1,34 +0,0 @@
-#!/usr/bin/env python
-
-from __future__ import division
-
-import sys, os
-sys.stderr = open(os.devnull, 'w')  # suppress stderr as cython produces warning on some systems:
-                                    # csamtools.so:6: RuntimeWarning: __builtin__.file size changed
-
-from galaxy import eggs
-import pkg_resources
-
-if sys.version_info[:2] == (2, 4):
-    pkg_resources.require( "ctypes" )
-pkg_resources.require( "pysam" )
-
-from pysam import csamtools
-from galaxy.visualization.tracks.summary import *
-
-def main():
-   
-    input_fname = sys.argv[1]
-    index_fname = sys.argv[2]
-    out_fname = sys.argv[3]
-    
-    bamfile = csamtools.Samfile( filename=input_fname, mode='rb', index_filename=index_fname )
-    
-    st = SummaryTree(block_size=25, levels=6, draw_cutoff=150, detail_cutoff=30)
-    for read in bamfile.fetch():
-        st.insert_range(bamfile.getrname(read.rname), read.pos, read.pos + read.rlen)
-    
-    st.write(out_fname)
-
-if __name__ == "__main__": 
-    main()
diff --git a/lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.xml b/lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.xml
index adfdb22acc8..0627dd6ff5a 100644
--- a/lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.xml
+++ b/lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.xml
@@ -1,6 +1,6 @@
 <tool id="CONVERTER_bam_to_summary_tree_0" name="Convert BAM to Summary Tree" version="1.0.0" hidden="true">
 <!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
-  <command interpreter="python">bam_to_summary_tree_converter.py $input1 $bai $output1</command>
+  <command interpreter="python">sam_or_bam_to_summary_tree_converter.py --bam $input1 $bai $output1</command>
   <inputs>
     <page>
         <param format="bam" name="input1" type="data" label="Choose BAM file"/>
diff --git a/lib/galaxy/datatypes/converters/sam_or_bam_to_summary_tree_converter.py b/lib/galaxy/datatypes/converters/sam_or_bam_to_summary_tree_converter.py
new file mode 100644
index 00000000000..4b2958a5401
--- /dev/null
+++ b/lib/galaxy/datatypes/converters/sam_or_bam_to_summary_tree_converter.py
@@ -0,0 +1,42 @@
+#!/usr/bin/env python
+
+from __future__ import division
+
+import sys, os, optparse
+sys.stderr = open(os.devnull, 'w')  # suppress stderr as cython produces warning on some systems:
+                                    # csamtools.so:6: RuntimeWarning: __builtin__.file size changed
+
+from galaxy import eggs
+import pkg_resources
+
+if sys.version_info[:2] == (2, 4):
+    pkg_resources.require( "ctypes" )
+pkg_resources.require( "pysam" )
+
+from pysam import csamtools
+from galaxy.visualization.tracks.summary import *
+
+def main():
+    parser = optparse.OptionParser()
+    parser.add_option( '-S', '--sam', action="store_true", dest="is_sam" )
+    parser.add_option( '-B', '--bam', action="store_true", dest="is_bam" )
+    options, args = parser.parse_args()
+    
+    if options.is_bam:
+        input_fname = args[0]
+        index_fname = args[1]
+        out_fname = args[2]
+        samfile = csamtools.Samfile( filename=input_fname, mode='rb', index_filename=index_fname )
+    elif options.is_sam:
+        input_fname = args[0]
+        out_fname = args[1]
+        samfile = csamtools.Samfile( filename=input_fname, mode='r' )
+    
+    st = SummaryTree(block_size=25, levels=6, draw_cutoff=150, detail_cutoff=30)
+    for read in samfile.fetch():
+        st.insert_range( samfile.getrname( read.rname ), read.pos, read.pos + read.rlen )
+    
+    st.write(out_fname)
+
+if __name__ == "__main__": 
+    main()
diff --git a/lib/galaxy/datatypes/converters/sam_to_bam.xml b/lib/galaxy/datatypes/converters/sam_to_bam.xml
new file mode 100644
index 00000000000..3b9c37c8355
--- /dev/null
+++ b/lib/galaxy/datatypes/converters/sam_to_bam.xml
@@ -0,0 +1,17 @@
+<tool id="CONVERTER_sam_to_bam" name="Convert SAM to BAM" version="1.0.0">
+    <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
+    <!-- Used on the metadata edit page. -->
+    <!-- FIXME: conversion will only work if headers for reference sequences are in input file.
+         To fix this: (a) merge sam_to_bam tool in tools with this conversion (like fasta_to_len 
+         conversion); and (b) define a datatype-specific way to set converter parameters.
+      -->
+    <command>samtools view -bS $input1 > $output 2> /dev/null </command>
+    <inputs>
+        <param name="input1" type="data" format="sam" label="SAM file"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="bam"/>
+    </outputs>
+    <help>
+    </help>
+</tool>
diff --git a/lib/galaxy/datatypes/converters/sam_to_summary_tree_converter.xml b/lib/galaxy/datatypes/converters/sam_to_summary_tree_converter.xml
new file mode 100644
index 00000000000..6dd1c50ac05
--- /dev/null
+++ b/lib/galaxy/datatypes/converters/sam_to_summary_tree_converter.xml
@@ -0,0 +1,14 @@
+<tool id="CONVERTER_sam_to_summary_tree_0" name="Convert SAM to Summary Tree" version="1.0.0" hidden="true">
+<!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
+  <command interpreter="python">sam_or_bam_to_summary_tree_converter.py --sam $input1 $output1</command>
+  <inputs>
+    <page>
+        <param format="sam" name="input1" type="data" label="Choose sam file"/>
+    </page>
+   </inputs>
+  <outputs>
+    <data format="summary_tree" name="output1"/>
+  </outputs>
+  <help>
+  </help>
+</tool>
diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py
index 72ed33e949a..2a34e3baff4 100644
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -368,7 +368,10 @@ class Sam( Tabular ):
         if result != 0:
             raise Exception('Result %s from %s' % (result, cmd))
     merge = staticmethod(merge)
-
+    
+    def get_track_type( self ):
+        return "ReadTrack", {"data": "bam", "index": "summary_tree"}
+    
 class Pileup( Tabular ):
     """Tab delimited data in pileup (6- or 10-column) format"""
     file_ext = "pileup"
diff --git a/lib/galaxy/visualization/tracks/data_providers.py b/lib/galaxy/visualization/tracks/data_providers.py
index 66b09652ece..a54d9c369b4 100644
--- a/lib/galaxy/visualization/tracks/data_providers.py
+++ b/lib/galaxy/visualization/tracks/data_providers.py
@@ -725,6 +725,18 @@ class BamDataProvider( TracksDataProvider ):
         max_low, max_high = get_bounds( results, 1, 2 )
                 
         return { 'data': results, 'message': message, 'max_low': max_low, 'max_high': max_high }
+        
+class SamDataProvider( BamDataProvider ):
+    
+    def __init__( self, converted_dataset=None, original_dataset=None, dependencies=None ):
+        """ Create SamDataProvider. """
+        
+        # HACK: to use BamDataProvider, original dataset must be BAM and 
+        # converted dataset must be BAI. Use BAI from BAM metadata.
+        if converted_dataset:
+            self.converted_dataset = converted_dataset.metadata.bam_index
+            self.original_dataset = converted_dataset
+        self.dependencies = dependencies
 
 class BBIDataProvider( TracksDataProvider ):
     """
@@ -957,6 +969,7 @@ dataset_type_name_to_data_provider = {
     "tabix": { Vcf: VcfTabixDataProvider, Bed: BedTabixDataProvider, "default" : TabixDataProvider },
     "interval_index": IntervalIndexDataProvider,
     "bai": BamDataProvider,
+    "bam": SamDataProvider,
     "summary_tree": SummaryTreeDataProvider,
     "bigwig": BigWigDataProvider,
     "bigbed": BigBedDataProvider

From 5078b6ea58c886aa13225eb04b67e17e7c42db39 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Tue, 6 Dec 2011 09:42:56 -0500
Subject: [PATCH 294/362] Update GATK tools handling annotations to allow
 manually specifying additional annotation names to apply.

---
 tools/gatk/unified_genotyper.xml    |  6 ++++++
 tools/gatk/variant_annotator.xml    | 15 +++++++--------
 tools/gatk/variant_recalibrator.xml | 17 ++++++++++++-----
 3 files changed, 25 insertions(+), 13 deletions(-)

diff --git a/tools/gatk/unified_genotyper.xml b/tools/gatk/unified_genotyper.xml
index 9966707ee99..5b1985883f8 100644
--- a/tools/gatk/unified_genotyper.xml
+++ b/tools/gatk/unified_genotyper.xml
@@ -117,6 +117,9 @@
                 --annotation "${annotation}"
             #end for
         #end if
+        #for $additional_annotation in $analysis_param_type.additional_annotations:
+            --annotation "${additional_annotation.additional_annotation_name}"
+        #end for
         #if str( $analysis_param_type.group ) != "None":
             #for $group in str( $analysis_param_type.group ).split( ','):
                 --group "${group}"
@@ -372,6 +375,9 @@
             <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/>
           </options>
 	    </param>
+        <repeat name="additional_annotations" title="Additional annotation">
+          <param name="additional_annotation_name" type="text" value="" label="Annotation name" />
+        </repeat>
 <!--
         <conditional name="snpEff_rod_bind_type">
           <param name="snpEff_rod_bind_type_selector" type="select" label="Provide a snpEff reference-ordered data file">
diff --git a/tools/gatk/variant_annotator.xml b/tools/gatk/variant_annotator.xml
index 897c1418cff..72088157d9a 100644
--- a/tools/gatk/variant_annotator.xml
+++ b/tools/gatk/variant_annotator.xml
@@ -36,14 +36,9 @@
             --excludeAnnotation "${annotation}"
         #end for
     #end if
-##    #for $additional_annotation in $additional_annotations:
-##        --annotation "${additional_annotation.additional_annotation_type.additional_annotation_type_selector}"
-##        #for $name, $param in $additional_annotation.additional_annotation_type.iteritems():
-##            #if $name not in [ "__current_case__", "additional_annotation_type_selector" ]:
-##                --${name} "${param}"
-##            #end if
-##        #end for
-##    #end for
+    #for $additional_annotation in $additional_annotations:
+        --annotation "${additional_annotation.additional_annotation_name}"
+    #end for
     ${reference_source.input_variant_bti}
    '
     
@@ -188,6 +183,10 @@
       </when>
     </conditional>
     
+    <repeat name="additional_annotations" title="Additional annotation">
+      <param name="additional_annotation_name" type="text" value="" label="Annotation name" />
+    </repeat>
+    
     <repeat name="comp_rod_bind" title="Binding for reference-ordered comparison data">
       <param name="comp_input_rod" type="data" format="vcf" label="ROD file" />
       <param name="comp_rod_name" type="text" value="Unnamed" label="ROD Name"/>
diff --git a/tools/gatk/variant_recalibrator.xml b/tools/gatk/variant_recalibrator.xml
index 427e946eb14..4fb8cdcb59d 100644
--- a/tools/gatk/variant_recalibrator.xml
+++ b/tools/gatk/variant_recalibrator.xml
@@ -104,6 +104,9 @@
             --use_annotation "${annotation}"
         #end for
     #end if
+    #for $additional_annotation in $additional_annotations:
+        --use_annotation "${additional_annotation.additional_annotation_name}"
+    #end for
     --mode "${mode}"
     '
     
@@ -344,11 +347,15 @@
       </options>
     </param>
     
-        <param name="mode" type="select" label="Recalibration mode">
-          <option value="SNP" selected="True">SNP</option>
-          <option value="INDEL">INDEL</option>
-          <option value="BOTH">BOTH</option>
-        </param>
+    <repeat name="additional_annotations" title="Additional annotation">
+      <param name="additional_annotation_name" type="text" value="" label="Annotation name" />
+    </repeat>
+    
+    <param name="mode" type="select" label="Recalibration mode">
+        <option value="SNP" selected="True">SNP</option>
+        <option value="INDEL">INDEL</option>
+        <option value="BOTH">BOTH</option>
+    </param>
     
     <conditional name="gatk_param_type">
       <param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options">

From 44344fe2e0baf7e58665609e2a3f9e0a3ed82a0f Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Tue, 6 Dec 2011 11:29:02 -0500
Subject: [PATCH 295/362] Fix the dataset controller's stderr method and add
 one for stdout.  Link to both from the dataset info page.  The functional
 tests will now provide output of these on tool test failure.  The functional
 tests can now use tool_dependency_dir as well.

---
 lib/galaxy/web/controllers/dataset.py | 20 +++++++++++++++++---
 scripts/functional_tests.py           |  4 ++++
 test/base/twilltestcase.py            |  8 ++++++++
 test/functional/test_toolbox.py       | 14 +++++++++++++-
 4 files changed, 42 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/web/controllers/dataset.py b/lib/galaxy/web/controllers/dataset.py
index 449bf06dd00..c7e86d166ff 100644
--- a/lib/galaxy/web/controllers/dataset.py
+++ b/lib/galaxy/web/controllers/dataset.py
@@ -154,10 +154,24 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesHistory, UsesHist
         hda = trans.sa_session.query( model.HistoryDatasetAssociation ).get( id )
         return trans.fill_template( "dataset/errors.mako", hda=hda )
     @web.expose
-    def stderr( self, trans, id ):
-        dataset = trans.sa_session.query( model.HistoryDatasetAssociation ).get( id )
-        job = dataset.creating_job_associations[0].job
+    def stdout( self, trans, dataset_id=None, **kwargs ):
         trans.response.set_content_type( 'text/plain' )
+        try:
+            hda = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( dataset_id ) )
+            assert hda and trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset )
+            job = hda.creating_job_associations[0].job
+        except:
+            return "Invalid dataset ID or you are not allowed to access this dataset"
+        return job.stdout
+    @web.expose
+    def stderr( self, trans, dataset_id=None, **kwargs ):
+        trans.response.set_content_type( 'text/plain' )
+        try:
+            hda = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( dataset_id ) )
+            assert hda and trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset )
+            job = hda.creating_job_associations[0].job
+        except:
+            return "Invalid dataset ID or you are not allowed to access this dataset"
         return job.stderr
     @web.expose
     def report_error( self, trans, id, email='', message="" ):
diff --git a/scripts/functional_tests.py b/scripts/functional_tests.py
index dc8fa1a754d..66f2ad682f6 100644
--- a/scripts/functional_tests.py
+++ b/scripts/functional_tests.py
@@ -58,6 +58,7 @@ def main():
     tool_path = os.environ.get( 'GALAXY_TEST_TOOL_PATH', 'tools' )
     tool_config_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', 'tool_conf.xml.sample' )
     tool_data_table_config_path = 'tool_data_table_conf.xml'
+    tool_dependency_dir = os.environ.get( 'GALAXY_TOOL_DEPENDENCY_DIR', None )
     if os.path.exists( 'tool_data_table_conf.test.xml' ):
         tool_data_table_config_path = 'tool_data_table_conf.test.xml'
     if start_server:
@@ -149,6 +150,9 @@ def main():
         if not database_connection.startswith( 'sqlite://' ):
             kwargs['database_engine_option_max_overflow'] = '20'
 
+        if tool_dependency_dir is not None:
+            kwargs['tool_dependency_dir'] = tool_dependency_dir
+
         # Build the Universe Application
         app = UniverseApplication( job_queue_workers = 5,
                                    id_secret = 'changethisinproductiontoo',
diff --git a/test/base/twilltestcase.py b/test/base/twilltestcase.py
index fff6c754f7e..c12654c5eb8 100644
--- a/test/base/twilltestcase.py
+++ b/test/base/twilltestcase.py
@@ -624,6 +624,14 @@ class TwillTestCase( unittest.TestCase ):
         fd,temp_prefix = tempfile.mkstemp(prefix='tmp',suffix=suffix)
         return temp_prefix
 
+    def get_history_dataset_stdout( self, hda_id ):
+        self.visit_page( "/datasets/%s/stdout" % hda_id )
+        return self.last_page()
+
+    def get_history_dataset_stderr( self, hda_id ):
+        self.visit_page( "/datasets/%s/stderr" % hda_id )
+        return self.last_page()
+
     def verify_dataset_correctness( self, filename, hid=None, wait=True, maxseconds=120, attributes=None ):
         """Verifies that the attributes and contents of a history item meet expectations"""
         if wait:
diff --git a/test/functional/test_toolbox.py b/test/functional/test_toolbox.py
index 1843ada7ede..4a2b53eae07 100644
--- a/test/functional/test_toolbox.py
+++ b/test/functional/test_toolbox.py
@@ -93,7 +93,19 @@ class ToolTestCase( TwillTestCase ):
             self.assertTrue( elem is not None )
             elem_hid = elem.get( 'hid' )
             elem_index += 1
-            self.verify_dataset_correctness( outfile, hid=elem_hid, maxseconds=testdef.maxseconds, attributes=attributes )
+            try:
+                self.verify_dataset_correctness( outfile, hid=elem_hid, maxseconds=testdef.maxseconds, attributes=attributes )
+            except Exception, e:
+                print '-----------'
+                print 'Job STDOUT:'
+                print '-----------'
+                print self.get_history_dataset_stdout( elem.get( 'id' ) )
+                print '-----------'
+                print 'Job STDERR:'
+                print '-----------'
+                print self.get_history_dataset_stderr( elem.get( 'id' ) )
+                print '-----------'
+                raise
         self.delete_history( id=self.security.encode_id( latest_history.id ) )
 
     def __expand_grouping( self, tool_inputs, declared_inputs, prefix='' ):

From 9943f9528ee3b0c51afa4b5e519771000cd0716f Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Tue, 6 Dec 2011 11:41:32 -0500
Subject: [PATCH 296/362] Missing template changes from the last commit.

---
 templates/show_params.mako | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/templates/show_params.mako b/templates/show_params.mako
index 9f7ad363c68..cd4e6e550d1 100644
--- a/templates/show_params.mako
+++ b/templates/show_params.mako
@@ -50,6 +50,8 @@
         <tr><td>Dbkey:</td><td>${hda.dbkey}</td></tr>
         <tr><td>Format:</td><td>${hda.ext}</td></tr>
         <tr><td>Tool Version:</td><td>${hda.tool_version}</td></tr>
+        <tr><td>Tool Standard Output:</td><td><a href="${h.url_for( controller='dataset', action='stdout')}">stdout</a></td></tr>
+        <tr><td>Tool Standard Error:</td><td><a href="${h.url_for( controller='dataset', action='stderr')}">stderr</a></td></tr>
 </table>
 <br />
 <table class="tabletip">

From 03c4fa3689cd62b4c7327d46b497f55bf95f90db Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Tue, 6 Dec 2011 11:42:12 -0500
Subject: [PATCH 297/362] The upload tool requires samtools to upload BAM
 files, the Pileup tool requires samtools <= 0.1.16.

---
 tools/data_source/upload.xml  | 3 +++
 tools/samtools/sam_pileup.xml | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/tools/data_source/upload.xml b/tools/data_source/upload.xml
index 4a459a12979..3211ff2f2b2 100644
--- a/tools/data_source/upload.xml
+++ b/tools/data_source/upload.xml
@@ -5,6 +5,9 @@
     from your computer  
   </description>
   <action module="galaxy.tools.actions.upload" class="UploadToolAction"/>
+  <requirements>
+      <requirement type="package">samtools</requirement>
+  </requirements>
   <command interpreter="python">
       upload.py $GALAXY_ROOT_DIR $GALAXY_DATATYPES_CONF_FILE $paramfile
     #set $outnum = 0
diff --git a/tools/samtools/sam_pileup.xml b/tools/samtools/sam_pileup.xml
index bdb3fe92822..e51377f5aac 100644
--- a/tools/samtools/sam_pileup.xml
+++ b/tools/samtools/sam_pileup.xml
@@ -1,7 +1,7 @@
 <tool id="sam_pileup" name="Generate pileup" version="1.1.1">
   <description>from BAM dataset</description>
   <requirements>
-    <requirement type="package">samtools</requirement>
+    <requirement type="package" version="0.1.16">samtools</requirement>
   </requirements>
   <command interpreter="python">
     sam_pileup.py

From b8a8d6feb03253392c72e8797067b138cc3d140b Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Tue, 6 Dec 2011 12:41:10 -0500
Subject: [PATCH 298/362] Add control for deleting job files after job
 completion.

---
 lib/galaxy/config.py             |  1 +
 lib/galaxy/jobs/__init__.py      | 12 ++++++++----
 lib/galaxy/jobs/runners/drmaa.py | 23 ++++++++++++++---------
 lib/galaxy/jobs/runners/pbs.py   | 23 ++++++++++++++---------
 universe_wsgi.ini.sample         |  6 ++++++
 5 files changed, 43 insertions(+), 22 deletions(-)

diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py
index f291b7c3d51..05f22990f81 100644
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -80,6 +80,7 @@ class Configuration( object ):
         self.job_queue_cleanup_interval = int( kwargs.get("job_queue_cleanup_interval", "5") )
         self.cluster_files_directory = os.path.abspath( kwargs.get( "cluster_files_directory", "database/pbs" ) )
         self.job_working_directory = resolve_path( kwargs.get( "job_working_directory", "database/job_working_directory" ), self.root )
+        self.cleanup_job = kwargs.get( "cleanup_job", "always" )
         self.outputs_to_working_directory = string_as_bool( kwargs.get( 'outputs_to_working_directory', False ) )
         self.output_size_limit = int( kwargs.get( 'output_size_limit', 0 ) )
         self.job_walltime = kwargs.get( 'job_walltime', None )
diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 98987a719be..2052754fbf8 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -482,7 +482,8 @@ class JobWrapper( object ):
         # If the job was deleted, call tool specific fail actions (used for e.g. external metadata) and clean up
         if self.tool:
             self.tool.job_failed( self, message, exception )
-        self.cleanup()
+        if self.app.config.cleanup_job == 'always':
+            self.cleanup()
 
     def change_state( self, state, info = False ):
         job = self.get_job()
@@ -525,7 +526,8 @@ class JobWrapper( object ):
         job = self.get_job()
         # if the job was deleted, don't finish it
         if job.state == job.states.DELETED:
-            self.cleanup()
+            if self.app.config.cleanup_job in ( 'always', 'onsuccess' ):
+                self.cleanup()
             return
         elif job.state == job.states.ERROR:
             # Job was deleted by an administrator
@@ -698,7 +700,8 @@ class JobWrapper( object ):
             util.umask_fix_perms( path, self.app.config.umask, 0666, self.app.config.gid )
         self.sa_session.flush()
         log.debug( 'job %d ended' % self.job_id )
-        self.cleanup()
+        if self.app.config.cleanup_job in ( 'always', 'onsuccess' ):
+            self.cleanup()
 
     def cleanup( self ):
         # remove temporary files
@@ -1045,7 +1048,8 @@ class TaskWrapper(JobWrapper):
         task = self.get_task()
         # if the job was deleted, don't finish it
         if task.state == task.states.DELETED:
-            self.cleanup()
+            if self.app.config.cleanup_job in ( 'always', 'onsuccess' ):
+                self.cleanup()
             return
         elif task.state == task.states.ERROR:
             # Job was deleted by an administrator
diff --git a/lib/galaxy/jobs/runners/drmaa.py b/lib/galaxy/jobs/runners/drmaa.py
index 54f59c50998..f46b516c3b5 100644
--- a/lib/galaxy/jobs/runners/drmaa.py
+++ b/lib/galaxy/jobs/runners/drmaa.py
@@ -137,7 +137,8 @@ class DRMAAJobRunner( BaseJobRunner ):
         # Check for deletion before we change state
         if job_wrapper.get_state() == model.Job.states.DELETED:
             log.debug( "Job %s deleted by user before it entered the queue" % job_wrapper.get_id_tag() )
-            job_wrapper.cleanup()
+            if self.app.config.cleanup_job in ( "always", "onsuccess" ):
+                job_wrapper.cleanup()
             return
 
         # Change to queued state immediately
@@ -168,8 +169,9 @@ class DRMAAJobRunner( BaseJobRunner ):
         # job was deleted while we were preparing it
         if job_wrapper.get_state() == model.Job.states.DELETED:
             log.debug( "Job %s deleted by user before it entered the queue" % job_wrapper.get_id_tag() )
-            self.cleanup( ( ofile, efile, jt.remoteCommand ) )
-            job_wrapper.cleanup()
+            if self.app.config.cleanup_job in ( "always", "onsuccess" ):
+                self.cleanup( ( ofile, efile, jt.remoteCommand ) )
+                job_wrapper.cleanup()
             return
 
         # wrapper.get_id_tag() instead of job_id for compatibility with TaskWrappers.
@@ -288,7 +290,8 @@ class DRMAAJobRunner( BaseJobRunner ):
             log.exception("Job wrapper finish method failed")
 
         # clean up the drm files
-        self.cleanup( ( ofile, efile, job_file ) )
+        if self.app.config.cleanup_job == "always" or ( not stderr and self.app.config.cleanup_job == "onsuccess" )):
+            self.cleanup( ( ofile, efile, job_file ) )
 
     def fail_job( self, drm_job_state ):
         """
@@ -296,13 +299,15 @@ class DRMAAJobRunner( BaseJobRunner ):
         """
         self.stop_job( self.sa_session.query( self.app.model.Job ).get( drm_job_state.job_wrapper.job_id ) )
         drm_job_state.job_wrapper.fail( drm_job_state.fail_message )
-        self.cleanup( ( drm_job_state.ofile, drm_job_state.efile, drm_job_state.job_file ) )
+        if self.app.config.cleanup_job == "always":
+            self.cleanup( ( drm_job_state.ofile, drm_job_state.efile, drm_job_state.job_file ) )
 
     def cleanup( self, files ):
-        if not asbool( self.app.config.get( 'debug', False ) ):
-            for file in files:
-                if os.access( file, os.R_OK ):
-                    os.unlink( file )
+        for file in files:
+            try:
+                os.unlink( file )
+            except Exception, e:
+                log.warning( "Unable to cleanup: %s" % str( e ) )  
 
     def put( self, job_wrapper ):
         """Add a job to the queue (by job identifier)"""
diff --git a/lib/galaxy/jobs/runners/pbs.py b/lib/galaxy/jobs/runners/pbs.py
index 67c88e86442..20b8f5dd0ac 100644
--- a/lib/galaxy/jobs/runners/pbs.py
+++ b/lib/galaxy/jobs/runners/pbs.py
@@ -214,7 +214,8 @@ class PBSJobRunner( BaseJobRunner ):
         # Check for deletion before we change state
         if job_wrapper.get_state() == model.Job.states.DELETED:
             log.debug( "Job %s deleted by user before it entered the PBS queue" % job_wrapper.job_id )
-            job_wrapper.cleanup()
+            if self.app.config.cleanup_job in ( "always", "onsuccess" ):
+                job_wrapper.cleanup()
             return
 
         ( pbs_server_name, runner_url ) = self.determine_pbs_server( runner_url, rewrite = True )
@@ -277,8 +278,9 @@ class PBSJobRunner( BaseJobRunner ):
         if job_wrapper.get_state() == model.Job.states.DELETED:
             log.debug( "Job %s deleted by user before it entered the PBS queue" % job_wrapper.job_id )
             pbs.pbs_disconnect(c)
-            self.cleanup( ( ofile, efile, job_file ) )
-            job_wrapper.cleanup()
+            if self.app.config.cleanup_job in ( "always", "onsuccess" ):
+                self.cleanup( ( ofile, efile, job_file ) )
+                job_wrapper.cleanup()
             return
 
         # submit
@@ -517,7 +519,8 @@ class PBSJobRunner( BaseJobRunner ):
             pbs_job_state.job_wrapper.fail("Unable to finish job", exception=True)
 
         # clean up the pbs files
-        self.cleanup( ( ofile, efile, job_file ) )
+        if self.app.config.cleanup_job == "always" or ( not stderr and self.app.config.cleanup_job == "onsuccess" )):
+            self.cleanup( ( ofile, efile, job_file ) )
 
     def fail_job( self, pbs_job_state ):
         """
@@ -526,13 +529,15 @@ class PBSJobRunner( BaseJobRunner ):
         if pbs_job_state.stop_job:
             self.stop_job( self.sa_session.query( self.app.model.Job ).get( pbs_job_state.job_wrapper.job_id ) )
         pbs_job_state.job_wrapper.fail( pbs_job_state.fail_message )
-        self.cleanup( ( pbs_job_state.ofile, pbs_job_state.efile, pbs_job_state.job_file ) )
+        if self.app.config.cleanup_job == "always":
+            self.cleanup( ( pbs_job_state.ofile, pbs_job_state.efile, pbs_job_state.job_file ) )
 
     def cleanup( self, files ):
-        if not asbool( self.app.config.get( 'debug', False ) ):
-            for file in files:
-                if os.access( file, os.R_OK ):
-                    os.unlink( file )
+        for file in files:
+            try:
+                os.unlink( file )
+            except Exception, e:
+                log.warning( "Unable to cleanup: %s" % str( e ) )
 
     def put( self, job_wrapper ):
         """Add a job to the queue (by job identifier)"""
diff --git a/universe_wsgi.ini.sample b/universe_wsgi.ini.sample
index ffe82277e35..07905f389db 100644
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -514,6 +514,12 @@ use_interactive = True
 # Galaxy server after the job completes.
 #outputs_to_working_directory = False
 
+# Clean up various bits of jobs left on the filesystem after completion.  These
+# bits include the job working directory, external metadata temporary files,
+# and DRM stdout and stderr files (if using a DRM).  Possible values are:
+# always, onsuccess, never
+#cleanup_job = always
+
 # Number of concurrent jobs to run (local job runner)
 #local_job_queue_workers = 5
 

From 7eb7dde3f5d6afefda789f89e2175f2b2118f96c Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Tue, 6 Dec 2011 13:01:03 -0500
Subject: [PATCH 299/362] Bugfix for the previous commit.

---
 lib/galaxy/jobs/__init__.py      | 2 +-
 lib/galaxy/jobs/runners/drmaa.py | 2 +-
 lib/galaxy/jobs/runners/pbs.py   | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 2052754fbf8..988d7d956a8 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -700,7 +700,7 @@ class JobWrapper( object ):
             util.umask_fix_perms( path, self.app.config.umask, 0666, self.app.config.gid )
         self.sa_session.flush()
         log.debug( 'job %d ended' % self.job_id )
-        if self.app.config.cleanup_job in ( 'always', 'onsuccess' ):
+        if self.app.config.cleanup_job == 'always' or ( not stderr and self.app.config.cleanup_job == 'onsuccess' ):
             self.cleanup()
 
     def cleanup( self ):
diff --git a/lib/galaxy/jobs/runners/drmaa.py b/lib/galaxy/jobs/runners/drmaa.py
index f46b516c3b5..e0676820ddd 100644
--- a/lib/galaxy/jobs/runners/drmaa.py
+++ b/lib/galaxy/jobs/runners/drmaa.py
@@ -290,7 +290,7 @@ class DRMAAJobRunner( BaseJobRunner ):
             log.exception("Job wrapper finish method failed")
 
         # clean up the drm files
-        if self.app.config.cleanup_job == "always" or ( not stderr and self.app.config.cleanup_job == "onsuccess" )):
+        if self.app.config.cleanup_job == "always" or ( not stderr and self.app.config.cleanup_job == "onsuccess" ):
             self.cleanup( ( ofile, efile, job_file ) )
 
     def fail_job( self, drm_job_state ):
diff --git a/lib/galaxy/jobs/runners/pbs.py b/lib/galaxy/jobs/runners/pbs.py
index 20b8f5dd0ac..4c2204323f8 100644
--- a/lib/galaxy/jobs/runners/pbs.py
+++ b/lib/galaxy/jobs/runners/pbs.py
@@ -519,7 +519,7 @@ class PBSJobRunner( BaseJobRunner ):
             pbs_job_state.job_wrapper.fail("Unable to finish job", exception=True)
 
         # clean up the pbs files
-        if self.app.config.cleanup_job == "always" or ( not stderr and self.app.config.cleanup_job == "onsuccess" )):
+        if self.app.config.cleanup_job == "always" or ( not stderr and self.app.config.cleanup_job == "onsuccess" ):
             self.cleanup( ( ofile, efile, job_file ) )
 
     def fail_job( self, pbs_job_state ):

From 44ffc80d97b755c8574981e1a16306121e683386 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Wed, 7 Dec 2011 11:31:51 -0500
Subject: [PATCH 300/362] Trackster: (a) bug fixes and refactoring and (b)
 prepartion for composite tracks.

---
 static/images/fugue/layers-stack-bw.png   | Bin 0 -> 1392 bytes
 static/images/fugue/layers-stack.png      | Bin 0 -> 664 bytes
 static/june_2007_style/blue/trackster.css |   2 +
 static/june_2007_style/trackster.css.tmpl |   6 ++
 static/scripts/trackster.js               |  95 ++++++++++++++++++----
 5 files changed, 86 insertions(+), 17 deletions(-)
 create mode 100644 static/images/fugue/layers-stack-bw.png
 create mode 100755 static/images/fugue/layers-stack.png

diff --git a/static/images/fugue/layers-stack-bw.png b/static/images/fugue/layers-stack-bw.png
new file mode 100644
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diff --git a/static/june_2007_style/blue/trackster.css b/static/june_2007_style/blue/trackster.css
index dab20f2faed..f175fb5cdbc 100644
--- a/static/june_2007_style/blue/trackster.css
+++ b/static/june_2007_style/blue/trackster.css
@@ -57,6 +57,8 @@ input{font:10px verdana;}
 .param-row{margin-top:0.2em;margin-left:1em;}
 .param-label{float:left;font-weight:bold;padding-top:0.2em;}
 .menu-button{margin:0px 4px 0px 4px;}
+.layers-stack{background:transparent url(../images/fugue/layers-stack-bw.png) no-repeat;}
+.layers-stack:hover{background:transparent url(../images/fugue/layers-stack.png) no-repeat;}
 .chevron-expand{background:transparent url(../images/fugue/chevron-expand-bw.png) no-repeat;}
 .chevron-expand:hover{background:transparent url(../images/fugue/chevron-expand.png) no-repeat;}
 .settings-icon{background:transparent url(../images/fugue/gear-bw.png) no-repeat;}
diff --git a/static/june_2007_style/trackster.css.tmpl b/static/june_2007_style/trackster.css.tmpl
index bccf5540313..672ca6ec490 100644
--- a/static/june_2007_style/trackster.css.tmpl
+++ b/static/june_2007_style/trackster.css.tmpl
@@ -298,6 +298,12 @@ input {
 .menu-button {
     margin: 0px 4px 0px 4px;
 }
+.layers-stack {
+    background: transparent url(../images/fugue/layers-stack-bw.png) no-repeat;
+}
+.layers-stack:hover {
+    background:transparent url(../images/fugue/layers-stack.png) no-repeat;
+}
 .chevron-expand {
     background: transparent url(../images/fugue/chevron-expand-bw.png) no-repeat;
 }
diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index 00b618aff1c..9d11eb4c9ae 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -376,7 +376,7 @@ var
     DATA_OK = "Ready for display",
     CACHED_TILES_FEATURE = 10,
     CACHED_TILES_LINE = 5,
-    CACHED_DATA = 5;
+    DATA_CACHE_SIZE = 20;
     
 /**
  * Round a number to a given number of decimal places.
@@ -769,6 +769,13 @@ Drawable.prototype.action_icons_def = [
 
 extend(Drawable.prototype, {
     init: function() {},
+    can_draw: function() {
+        if (this.enabled && this.content_visible) { 
+            return true;
+        }
+        
+        return false;
+    },
     request_draw: function() {},
     _draw: function() {},
     to_json: function() {},
@@ -950,6 +957,19 @@ var DrawableGroup = function(name, view, container, prefs) {
 };
 
 extend(DrawableGroup.prototype, Drawable.prototype, DrawableCollection.prototype, {
+    /*
+    action_icons_def: [
+    // Create composite track from group's tracks.
+    {
+        name: "composite-icon",
+        title: "Show composite track",
+        css_class: "layers-stack",
+        on_click_fn: function(group) {
+            group.show_composite_track();
+        }
+    }
+    ].concat(Drawable.prototype.action_icons_def),
+    */
     build_container_div: function() {
         return $("<div/>").addClass("group").attr("id", "group_" + this.id).appendTo(this.container.content_div);
     },
@@ -959,14 +979,24 @@ extend(DrawableGroup.prototype, Drawable.prototype, DrawableCollection.prototype
         this.name_div = $("<div/>").addClass("track-name").text(this.name).appendTo(header_div);
         return header_div;
     },
-    hide_contents : function () {
+    hide_contents: function () {
         this.content_div.hide();
     },
-    show_contents : function() {
+    show_contents: function() {
         // Show the contents div and labels (if present)
         this.content_div.show();
         // Request a redraw of the content
         this.request_draw();
+    },
+    update_icons: function() {
+        // TODO: only show icon for compositing if all tracks are the same type.  
+    },
+    /**
+     * Show composite track using group's tracks.
+     */
+    show_composite_track: function() {
+        this.composite_track = new CompositeTiledTrack(this.drawables, this.view, this);
+        this.composite_track.request_draw();
     }
 });
 
@@ -2532,7 +2562,7 @@ extend(Track.prototype, Drawable.prototype, {
             name: "overview_icon",
             title: "Set as overview",
             css_class: "overview-icon",
-            on_click_fn: function() {
+            on_click_fn: function(track) {
                 track.view.set_overview(track);
             }
         },
@@ -2573,6 +2603,12 @@ extend(Track.prototype, Drawable.prototype, {
         // Remove track.
         Drawable.prototype.action_icons_def[2]
     ],
+    can_draw: function() {        
+        if ( this.dataset_id && Drawable.prototype.can_draw.call(this) ) { 
+            return true;
+        }
+        return false;
+    },
     build_container_div: function () {
         return $("<div/>").addClass('track').attr("id", "track_" + this.id).css("position", "relative");
     },
@@ -2807,7 +2843,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
         //
         // Show/hide filter icon.
         //
-        if (track.filters_available > 0) {
+        if (track.filters_available) {
             track.action_icons.filters_icon.show();
         }
         else {
@@ -2855,15 +2891,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
      * can manage drawing.
      */
     _draw: function(force, clear_after) {
-        if (!this.enabled) { return; }
-
-        // TODO: There should probably be a general way to disable content drawing 
-        //       for all drawables. However the button to toggle this is currently
-        //       only present for Track instances.
-        if (!this.content_visible) { return; }
-        
-        // HACK: ReferenceTrack can draw without dataset ID, but other tracks cannot.
-        if ( !(this instanceof ReferenceTrack) && (!this.dataset_id) ) { return; }
+        if ( !this.can_draw() ) { return; }
         
         var low = this.view.low,
             high = this.view.high,
@@ -3136,6 +3164,38 @@ extend(LabelTrack.prototype, Track.prototype, {
     }
 });
 
+/**
+ * A tiled track composed of multiple other tracks.
+ */
+var CompositeTiledTrack = function(drawables, view, container) {
+    TiledTrack.call(this, "Composite Track", view, container);
+    this.drawables = drawables;
+    this.enabled = true;
+    // HACK: tile cache should be (but is not) set up in TiledTrack or earlier.
+    this.tile_cache = new Cache(CACHED_TILES_FEATURE);
+};
+extend(CompositeTiledTrack.prototype, TiledTrack.prototype, {
+    init: function() {
+        console.log("initing CompositeTiledTrack");
+        this.enabled = true;  
+    },
+    can_draw: Drawable.prototype.can_draw,
+    draw_helper: function(force, width, tile_index, resolution, parent_element, w_scale, drawn_tiles, more_tile_data) {
+        // Check tile cache, if found show existing tile in correct position
+        var 
+            key = this._gen_tile_cache_key(width, w_scale, tile_index),
+            tile = ( force ? undefined : this.tile_cache.get(key) );
+        if (tile) { 
+            this.show_tile(tile, parent_element, w_scale);
+            return tile;
+        }
+        
+        // TODO: Try to build tile.
+        
+        return tile;
+    }
+});
+
 var ReferenceTrack = function (view) {
     TiledTrack.call(this, "reference", view, { content_div: view.top_labeltrack }, {});
     
@@ -3148,7 +3208,7 @@ var ReferenceTrack = function (view) {
     this.content_div.css("border", "none");
     this.data_url = reference_url;
     this.data_url_extra_params = {dbkey: view.dbkey};
-    this.data_manager = new ReferenceTrackDataManager(CACHED_DATA, this, false);
+    this.data_manager = new ReferenceTrackDataManager(DATA_CACHE_SIZE, this, false);
     this.tile_cache = new Cache(CACHED_TILES_LINE);
 };
 extend(ReferenceTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
@@ -3157,6 +3217,7 @@ extend(ReferenceTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
         // Enable by default because there should always be data when drawing track.
         this.enabled = true;  
     },
+    can_draw: Drawable.prototype.can_draw,
     /**
      * Draw ReferenceTrack tile.
      */
@@ -3199,7 +3260,7 @@ var LineTrack = function (name, view, container, hda_ldda, dataset_id, prefs) {
     this.hda_ldda = hda_ldda;
     this.dataset_id = dataset_id;
     this.original_dataset_id = dataset_id;
-    this.data_manager = new DataManager(CACHED_DATA, this);
+    this.data_manager = new DataManager(DATA_CACHE_SIZE, this);
     this.tile_cache = new Cache(CACHED_TILES_LINE);
     this.left_offset = 0;
 
@@ -3386,7 +3447,7 @@ var FeatureTrack = function(name, view, container, hda_ldda, dataset_id, prefs,
     this.inc_slots = {};
     this.start_end_dct = {};
     this.tile_cache = new Cache(CACHED_TILES_FEATURE);
-    this.data_manager = new DataManager(20, this);
+    this.data_manager = new DataManager(DATA_CACHE_SIZE, this);
     this.left_offset = 200;
 
     // this.painter = painters.LinkedFeaturePainter;

From 0e703fc6c6f385cfd9b40e53f1a0be4b36d8c16c Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Wed, 7 Dec 2011 15:50:58 -0500
Subject: [PATCH 301/362] Trackster: enable tracks to share data managers.

---
 static/scripts/trackster.js | 42 ++++++++++++++++++-------------------
 1 file changed, 21 insertions(+), 21 deletions(-)

diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index 9d11eb4c9ae..82808637e94 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -1553,7 +1553,7 @@ extend( View.prototype, DrawableCollection.prototype, {
             view.overview_close.show();
             view.resize_window();
         };
-        this.overview_drawable.init();
+        view.overview_drawable.request_draw();
         view.has_changes = true;
     },
     /** Close and reset overview. */
@@ -2524,7 +2524,7 @@ FeatureTrackTile.prototype.predisplay_actions = function() {
  * -------> ReadTrack
  * -------> VcfTrack
  */
-var Track = function(name, view, container, prefs, data_url, data_query_wait) {
+var Track = function(name, view, container, prefs, data_manager, data_url, data_query_wait) {
     // For now, track's container is always view.
     Drawable.call(this, name, view, container, {}, "draghandle");
     
@@ -2535,9 +2535,7 @@ var Track = function(name, view, container, prefs, data_url, data_query_wait) {
     this.data_url_extra_params = {}
     this.data_query_wait = (data_query_wait ? data_query_wait : DEFAULT_DATA_QUERY_WAIT);
     this.dataset_check_url = converted_datasets_state_url;
-
-    if (!Track.id_counter) { Track.id_counter = 0; }
-    this.id = Track.id_counter++;
+    this.data_manager = (data_manager ? data_manager : new DataManager(DATA_CACHE_SIZE, this));
         
     //
     // Create content div, which is where track is displayed.
@@ -2700,7 +2698,6 @@ extend(Track.prototype, Drawable.prototype, {
         track.enabled = false;
         track.tile_cache.clear();    
         track.data_manager.clear();
-        track.initial_canvas = undefined;
         track.content_div.css("height", "auto");
         /*
         if (!track.content_div.text()) {
@@ -2767,8 +2764,8 @@ extend(Track.prototype, Drawable.prototype, {
     predraw_init: function() {}
 });
 
-var TiledTrack = function(name, view, container, prefs, filters_list, tool_dict) {
-    Track.call(this, name, view, container, prefs);
+var TiledTrack = function(name, view, container, prefs, filters_list, tool_dict, data_manager) {
+    Track.call(this, name, view, container, prefs, data_manager);
 
     var track = this,
         view = track.view;
@@ -2803,10 +2800,15 @@ var TiledTrack = function(name, view, container, prefs, filters_list, tool_dict)
 };
 extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
     /**
-     * Returns a copy of the track.
+     * Returns a copy of the track. The copy uses the same data manager so that the tracks can share data.
      */
-    copy: function(container) {        
-        return new this.constructor(this.name, this.view, container, this.hda_ldda, this.dataset_id, this.prefs, this.filters, this.tool);
+    copy: function(container) {
+        // Create copy.
+        var new_track = new this.constructor(this.name, this.view, container, this.hda_ldda, this.dataset_id, this.prefs, 
+                                             this.filters, this.tool, this.data_manager);
+        // Misc. init and return.                            
+        new_track.enabled = this.enabled;
+        return new_track;
     },
     /**
      * Convert track to JSON object.
@@ -3247,11 +3249,11 @@ extend(ReferenceTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
     }
 });
 
-var LineTrack = function (name, view, container, hda_ldda, dataset_id, prefs) {
+var LineTrack = function (name, view, container, hda_ldda, dataset_id, prefs, filters, tool, data_manager) {
     var track = this;
     this.display_modes = ["Histogram", "Line", "Filled", "Intensity"];
     this.mode = "Histogram";
-    TiledTrack.call( this, name, view, container, prefs );
+    TiledTrack.call(this, name, view, container, prefs, filters, tool, data_manager);
    
     this.min_height_px = 16; 
     this.max_height_px = 400; 
@@ -3260,7 +3262,6 @@ var LineTrack = function (name, view, container, hda_ldda, dataset_id, prefs) {
     this.hda_ldda = hda_ldda;
     this.dataset_id = dataset_id;
     this.original_dataset_id = dataset_id;
-    this.data_manager = new DataManager(DATA_CACHE_SIZE, this);
     this.tile_cache = new Cache(CACHED_TILES_LINE);
     this.left_offset = 0;
 
@@ -3400,7 +3401,7 @@ extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
     } 
 });
 
-var FeatureTrack = function(name, view, container, hda_ldda, dataset_id, prefs, filters, tool) {
+var FeatureTrack = function(name, view, container, hda_ldda, dataset_id, prefs, filters, tool, data_manager) {
     //
     // Preinitialization: do things that need to be done before calling Track and TiledTrack
     // initialization code.
@@ -3411,7 +3412,7 @@ var FeatureTrack = function(name, view, container, hda_ldda, dataset_id, prefs,
     //
     // Initialization.
     //    
-    TiledTrack.call(this, name, view, container, prefs, filters, tool);
+    TiledTrack.call(this, name, view, container, prefs, filters, tool, data_manager);
 
     // Define and restore track configuration.
     this.config = new DrawableConfig( {
@@ -3447,7 +3448,6 @@ var FeatureTrack = function(name, view, container, hda_ldda, dataset_id, prefs,
     this.inc_slots = {};
     this.start_end_dct = {};
     this.tile_cache = new Cache(CACHED_TILES_FEATURE);
-    this.data_manager = new DataManager(DATA_CACHE_SIZE, this);
     this.left_offset = 200;
 
     // this.painter = painters.LinkedFeaturePainter;
@@ -3810,8 +3810,8 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
     }
 });
 
-var VcfTrack = function(name, view, container, hda_ldda, dataset_id, prefs, filters, tool) {
-    FeatureTrack.call(this, name, view, container, hda_ldda, dataset_id, prefs, filters, tool);
+var VcfTrack = function(name, view, container, hda_ldda, dataset_id, prefs, filters, tool, data_manager) {
+    FeatureTrack.call(this, name, view, container, hda_ldda, dataset_id, prefs, filters, tool, data_manager);
     
     this.config = new DrawableConfig( {
         track: this,
@@ -3837,8 +3837,8 @@ var VcfTrack = function(name, view, container, hda_ldda, dataset_id, prefs, filt
 
 extend(VcfTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype);
 
-var ReadTrack = function (name, view, container, hda_ldda, dataset_id, prefs, filters) {
-    FeatureTrack.call(this, name, view, container, hda_ldda, dataset_id, prefs, filters);
+var ReadTrack = function (name, view, container, hda_ldda, dataset_id, prefs, filters, data_manager) {
+    FeatureTrack.call(this, name, view, container, hda_ldda, dataset_id, prefs, filters, data_manager);
     
     var 
         block_color = get_random_color(),

From 1cbb83446e90c57db93755d350a66017b2b55c1b Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Wed, 7 Dec 2011 15:52:51 -0500
Subject: [PATCH 302/362] Object Store: Allow for creation of temporary and
 working directories inside the same DiskObjectStore when they back a
 HeirarchicalObjectStore.

---
 lib/galaxy/jobs/__init__.py               |  17 ++-
 lib/galaxy/objectstore/__init__.py        | 131 ++++++++++++++++------
 lib/galaxy/tools/actions/__init__.py      |   8 +-
 lib/galaxy/tools/actions/upload_common.py |  24 ++--
 4 files changed, 127 insertions(+), 53 deletions(-)

diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index b47cb90f2a4..bbc439c8586 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -324,8 +324,20 @@ class JobWrapper( object ):
         # With job outputs in the working directory, we need the working
         # directory to be set before prepare is run, or else premature deletion
         # and job recovery fail.
-        self.working_directory = \
-            os.path.join( self.app.config.job_working_directory, str( self.job_id ) )
+        # Attempt to put the working directory in the same store as the output dataset(s)
+        store_name = None
+        da = None
+        if job.output_datasets:
+            da = job.output_datasets[0]
+        elif job.output_library_datasets:
+            da = job.output_datasets[0]
+        if da is not None:
+            store_name = self.app.object_store.store_name(da.dataset.id)
+        # Create the working dir if necessary
+        if not self.app.object_store.exists(self.job_id, base_dir='job_work', dir_only=True, extra_dir=str(self.job_id)):
+            self.app.object_store.create(self.job_id, base_dir='job_work', dir_only=True, extra_dir=str(self.job_id), store_name=store_name)
+        self.working_directory = self.app.object_store.get_filename(self.job_id, base_dir='job_work', dir_only=True, extra_dir=str(self.job_id))
+        log.debug('(%s) Working directory for job is: %s' % (self.job_id, self.working_directory))
         self.output_paths = None
         self.output_dataset_paths = None
         self.tool_provided_job_metadata = None
@@ -600,7 +612,6 @@ class JobWrapper( object ):
                 dataset.set_size()
                 # Update (non-library) job output datasets through the object store
                 if dataset not in job.output_library_datasets:
-                    print "===++=== Job finish method handing dataset '%s' to object store" % dataset.file_name
                     self.app.object_store.update_from_file(dataset.id, create=True)
                 if context['stderr']:
                     dataset.blurb = "error"
diff --git a/lib/galaxy/objectstore/__init__.py b/lib/galaxy/objectstore/__init__.py
index dac6ee82888..3927cbd01e3 100644
--- a/lib/galaxy/objectstore/__init__.py
+++ b/lib/galaxy/objectstore/__init__.py
@@ -38,11 +38,13 @@ class ObjectStore(object):
     """
     def __init__(self):
         self.running = True
+        self.extra_dirs = {}
     
     def shutdown(self):
         self.running = False
+        self.extra_dirs = {}
     
-    def exists(self, dataset_id, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None):
+    def exists(self, dataset_id, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None):
         """
         Returns True if the object identified by `dataset_id` exists in this 
         file store, False otherwise.
@@ -51,6 +53,11 @@ class ObjectStore(object):
         :type dataset_id: int
         :param dataset_id: Galaxy-assigned database ID of the dataset to be checked.
         
+        :type base_dir: string
+        :param base_dir: A key in self.extra_dirs corresponding to the base
+                         directory in which this object should be created, or
+                         None to specify the default directory.
+
         :type dir_only: bool
         :param dir_only: If True, check only the path where the file
                          identified by `dataset_id` should be located, not the
@@ -74,22 +81,36 @@ class ObjectStore(object):
                          dataset rather than the default.
         """
         raise NotImplementedError()
+
+    def store_name(self, dataset_id, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None):
+        """
+        Returns the name of the store in which the object identified by
+        `dataset_id` exists, or None if it does not exist or the store is the
+        default store.
+        """
+        return None
     
-    def file_ready(self, dataset_id, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None):
+    def file_ready(self, dataset_id, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None):
         """ A helper method that checks if a file corresponding to a dataset 
         is ready and available to be used. Return True if so, False otherwise."""
         return True
     
-    def create(self, dataset_id, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None):
+    def create(self, dataset_id, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, store_name=None):
         """
         Mark the object identified by `dataset_id` as existing in the store, but
         with no content. This method will create a proper directory structure for
         the file if the directory does not already exist.
-        See `exists` method for the description of the fields.
+        See `exists` method for the description of other fields.
+
+        :type store_name: string
+        :param store_name: Backend store in which to create the dataset, if
+                           this store contains more than one backend.  If the
+                           named backend does not exist, a backend will be
+                           chosen by the store.
         """
         raise NotImplementedError()
     
-    def empty(self, dataset_id, extra_dir=None, extra_dir_at_root=False, alt_name=None):
+    def empty(self, dataset_id, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None):
         """
         Test if the object identified by `dataset_id` has content.
         If the object does not exist raises `ObjectNotFound`.
@@ -105,7 +126,7 @@ class ObjectStore(object):
         """
         raise NotImplementedError()
     
-    def delete(self, dataset_id, entire_dir=False, extra_dir=None, extra_dir_at_root=False, alt_name=None):
+    def delete(self, dataset_id, entire_dir=False, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None):
         """
         Deletes the object identified by `dataset_id`.
         See `exists` method for the description of other fields.
@@ -115,8 +136,8 @@ class ObjectStore(object):
                            only for and in conjunction with the extra_dir option.
         """
         raise NotImplementedError()
-    
-    def get_data(self, dataset_id, start=0, count=-1, extra_dir=None, extra_dir_at_root=False, alt_name=None):
+
+    def get_data(self, dataset_id, start=0, count=-1, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None):
         """
         Fetch `count` bytes of data starting at offset `start` from the
         object identified uniquely by `dataset_id`.
@@ -131,7 +152,7 @@ class ObjectStore(object):
         """
         raise NotImplementedError()
     
-    def get_filename(self, dataset_id, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None):
+    def get_filename(self, dataset_id, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None):
         """
         Get the expected filename (including the absolute path) which can be used
         to access the contents of the object uniquely identified by `dataset_id`.
@@ -139,7 +160,7 @@ class ObjectStore(object):
         """
         raise NotImplementedError()
     
-    def update_from_file(self, dataset_id, extra_dir=None, extra_dir_at_root=False, alt_name=None, file_name=None, create=False):
+    def update_from_file(self, dataset_id, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, file_name=None, create=False):
         """
         Inform the store that the file associated with the object has been
         updated. If `file_name` is provided, update from that file instead
@@ -180,9 +201,11 @@ class DiskObjectStore(ObjectStore):
     Standard Galaxy object store, stores objects in files under a specific
     directory on disk.
     """
-    def __init__(self, config, file_path=None):
+    def __init__(self, config, file_path=None, extra_dirs=None):
         super(DiskObjectStore, self).__init__()
         self.file_path = file_path or config.file_path
+        if extra_dirs is not None:
+            self.extra_dirs = extra_dirs
     
     def _get_filename(self, dataset_id, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None):
         """Class method that returns the absolute path for the file corresponding
@@ -194,13 +217,20 @@ class DiskObjectStore(ObjectStore):
         if not os.path.exists(path):
             return self._construct_path(dataset_id, dir_only=dir_only, extra_dir=extra_dir, extra_dir_at_root=extra_dir_at_root, alt_name=alt_name)
     
-    def _construct_path(self, dataset_id, old_style=False, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None):
+    def _construct_path(self, dataset_id, old_style=False, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None):
         """ Construct the expected absolute path for accessing the object
             identified by `dataset_id`.
         
+        :type base_dir: string
+        :param base_dir: A key in self.extra_dirs corresponding to the base
+                         directory in which this object should be created, or
+                         None to specify the default directory.
+
         :type dir_only: bool
-        :param dir_only: If True, return only the absolute path where the file
-                         identified by `dataset_id` should be located
+        :param dir_only: If True, check only the path where the file
+                         identified by `dataset_id` should be located, not the
+                         dataset itself. This option applies to `extra_dir`
+                         argument as well.
         
         :type extra_dir: string
         :param extra_dir: Append the value of this parameter to the expected path
@@ -216,11 +246,14 @@ class DiskObjectStore(ObjectStore):
                          the composed directory structure does not include a hash id
                          (e.g., /files/dataset_10.dat (old) vs. /files/000/dataset_10.dat (new))
         """
+        base = self.file_path
+        if base_dir in self.extra_dirs:
+            base = self.extra_dirs.get(base_dir)
         if old_style:
             if extra_dir is not None:
-                path = os.path.join(self.file_path, extra_dir)
+                path = os.path.join(base, extra_dir)
             else:
-                path = self.file_path
+                path = base
         else:
             rel_path = os.path.join(*directory_hash_id(dataset_id))
             if extra_dir is not None:
@@ -228,11 +261,11 @@ class DiskObjectStore(ObjectStore):
                     rel_path = os.path.join(extra_dir, rel_path)
                 else:
                     rel_path = os.path.join(rel_path, extra_dir)
-            path = os.path.join(self.file_path, rel_path)
+            path = os.path.join(base, rel_path)
         if not dir_only:
             path = os.path.join(path, alt_name if alt_name else "dataset_%s.dat" % dataset_id)
         return os.path.abspath(path)
-    
+
     def exists(self, dataset_id, **kwargs):
         path = self._construct_path(dataset_id, old_style=True, **kwargs)
         # For backward compatibility, check root path first; otherwise, construct 
@@ -240,14 +273,16 @@ class DiskObjectStore(ObjectStore):
         if not os.path.exists(path):
             path = self._construct_path(dataset_id, **kwargs)
         return os.path.exists(path)
-    
+
     def create(self, dataset_id, **kwargs):
+        kwargs.pop('store_name', None)
         if not self.exists(dataset_id, **kwargs):
             # Pull out locally used fields
             extra_dir = kwargs.get('extra_dir', None)
             extra_dir_at_root = kwargs.get('extra_dir_at_root', False)
             dir_only = kwargs.get('dir_only', False)
             alt_name = kwargs.get('alt_name', None)
+            base_dir_key = kwargs.get('base_dir', None)
             # Construct hashed path
             path = os.path.join(*directory_hash_id(dataset_id))
             # Optionally append extra_dir
@@ -257,14 +292,15 @@ class DiskObjectStore(ObjectStore):
                 else:
                     path = os.path.join(path, extra_dir)
             # Combine the constructted path with the root dir for all files
-            path = os.path.join(self.file_path, path)
+            base_dir = self.extra_dirs.get(base_dir_key, self.file_path)
+            path = os.path.join(base_dir, path)
             # Create directory if it does not exist
             if not os.path.exists(path):
                 os.makedirs(path)
             if not dir_only:
                 path = os.path.join(path, alt_name if alt_name else "dataset_%s.dat" % dataset_id)
                 open(path, 'w').close() 
-    
+
     def empty(self, dataset_id, **kwargs):
         return os.path.getsize(self.get_filename(dataset_id, **kwargs)) > 0
     
@@ -290,7 +326,7 @@ class DiskObjectStore(ObjectStore):
         except OSError, ex:
             log.critical('%s delete error %s' % (self._get_filename(dataset_id, **kwargs), ex))
         return False
-    
+
     def get_data(self, dataset_id, start=0, count=-1, **kwargs):
         data_file = open(self.get_filename(dataset_id, **kwargs), 'r')
         data_file.seek(start)
@@ -463,7 +499,7 @@ class S3ObjectStore(ObjectStore):
         if not dir_only:
             rel_path = os.path.join(rel_path, alt_name if alt_name else "dataset_%s.dat" % dataset_id)
         return rel_path
-    
+
     def _get_cache_path(self, rel_path):
         return os.path.abspath(os.path.join(self.staging_path, rel_path))
     
@@ -657,6 +693,7 @@ class S3ObjectStore(ObjectStore):
             return False
     
     def create(self, dataset_id, **kwargs):
+        kwargs.pop('store_name', None)
         if not self.exists(dataset_id, **kwargs):
             #print "S3 OS creating a dataset with ID %s" % dataset_id
             # Pull out locally used fields
@@ -813,7 +850,6 @@ class S3ObjectStore(ObjectStore):
             except S3ResponseError, ex:
                 log.warning("Trouble generating URL for dataset '%s': %s" % (rel_path, ex))
         return None
-    
 
 
 class HierarchicalObjectStore(ObjectStore):
@@ -845,11 +881,19 @@ class HierarchicalObjectStore(ObjectStore):
             weight = int(elem.get('weight', 1))
             if elem.get('type', 'disk'):
                 path = None
+                extra_dirs = {}
                 for sub in elem:
-                    if sub.tag == 'path':
-                        path = sub.get('value')
-                self.backends[name] = DiskObjectStore(config, file_path=path)
-                log.debug("Loaded disk backend '%s' with weight %s and disk path '%s'" % (name, weight, path))
+                    if sub.tag == 'files_dir':
+                        path = sub.get('path')
+                    elif sub.tag == 'extra_dir':
+                        type = sub.get('type')
+                        extra_dirs[type] = sub.get('path')
+                self.backends[name] = DiskObjectStore(config, file_path=path, extra_dirs=extra_dirs)
+                log.debug("Loaded disk backend '%s' with weight %s and file_path: %s" % (name, weight, path))
+                if extra_dirs:
+                    log.debug("    Extra directories:")
+                    for type, dir in extra_dirs.items():
+                        log.debug("        %s: %s" % (type, dir))
             for i in range(0, weight):
                 # The simplest way to do weighting: add backend names to a
                 # sequence the number of times equalling weight, then randomly
@@ -860,6 +904,12 @@ class HierarchicalObjectStore(ObjectStore):
         store = self.__get_store_for(dataset_id, **kwargs)
         return store is not None
 
+    def store_name(self, dataset_id, **kwargs):
+        for name, store in self.backends.items():
+            if store.exists(dataset_id, **kwargs):
+                return name
+        return None
+
     def file_ready(self, dataset_id, **kwargs):
         store = self.__get_store_for(dataset_id, **kwargs)
         if store is not None:
@@ -867,50 +917,57 @@ class HierarchicalObjectStore(ObjectStore):
         return False
 
     def create(self, dataset_id, **kwargs):
+        store_name = kwargs.pop('store_name', None)
         if not self.exists(dataset_id, **kwargs):
-            store_name = random.choice(self.weighted_backend_names)
-            log.debug("Selected backend '%s' for creation of dataset %s" % (store_name, dataset_id))
+            if store_name is None or store_name not in self.backends:
+                store_name = random.choice(self.weighted_backend_names)
+                log.debug("Selected backend '%s' for creation of dataset %s" % (store_name, dataset_id))
+            else:
+                log.debug("Using preferred backend '%s' for creation of dataset %s" % (store_name, dataset_id))
             return self.backends[store_name].create(dataset_id, **kwargs)
 
     def empty(self, dataset_id, **kwargs):
-        store = self.__get_store_for(dataset_id, **kwargs):
+        store = self.__get_store_for(dataset_id, **kwargs)
         if store is not None:
             return store.empty(dataset_id, **kwargs)
         return True
 
     def size(self, dataset_id, **kwargs):
-        store = self.__get_store_for(dataset_id, **kwargs):
+        store = self.__get_store_for(dataset_id, **kwargs)
         if store is not None:
             return store.size(dataset_id, **kwargs)
         return 0
 
     def delete(self, dataset_id, entire_dir=False, **kwargs):
-        store = self.__get_store_for(dataset_id, **kwargs):
+        store = self.__get_store_for(dataset_id, **kwargs)
         if store is not None:
             return store.delete(dataset_id, entire_dir=entire_dir, **kwargs)
         return False
 
     def get_data(self, dataset_id, start=0, count=-1, **kwargs):
-        store = self.__get_store_for(dataset_id, **kwargs):
+        store = self.__get_store_for(dataset_id, **kwargs)
         if store is not None:
             return store.get_data(dataset_id, start=0, count=-1, **kwargs)
         raise ObjectNotFound()
 
     def get_filename(self, dataset_id, **kwargs):
-        store = self.__get_store_for(dataset_id, **kwargs):
+        store = self.__get_store_for(dataset_id, **kwargs)
         if store is not None:
             return store.get_filename(dataset_id, **kwargs)
         raise ObjectNotFound()
 
     def update_from_file(self, dataset_id, file_name=None, create=False, **kwargs):
-        store = self.__get_store_for(dataset_id, **kwargs):
+        store = self.__get_store_for(dataset_id, **kwargs)
         if store is not None:
             return store.update_from_file(dataset_id, file_name=file_name, create=create, **kwargs)
+        if create:
+            store_name = random.choice(self.weighted_backend_names)
+            return self.backends[store_name].update_from_file(dataset_id, file_name=file_name, create=create, **kwargs)
         raise ObjectNotFound()
 
     def get_object_url(self, dataset_id, **kwargs):
         # FIXME: dir_only
-        store = self.__get_store_for(dataset_id, **kwargs):
+        store = self.__get_store_for(dataset_id, **kwargs)
         if store is not None:
             return store.get_object_url(dataset_id, **kwargs)
         return None
diff --git a/lib/galaxy/tools/actions/__init__.py b/lib/galaxy/tools/actions/__init__.py
index e29c6bb60a4..84c30596931 100644
--- a/lib/galaxy/tools/actions/__init__.py
+++ b/lib/galaxy/tools/actions/__init__.py
@@ -219,6 +219,8 @@ class DefaultToolAction( object ):
         # datasets first, then create the associations
         parent_to_child_pairs = []
         child_dataset_names = set()
+        store_name = None
+        store_name_set = False  # this is needed since None is a valid value for store_name
         for name, output in tool.outputs.items():
             for filter in output.filters:
                 try:
@@ -281,7 +283,11 @@ class DefaultToolAction( object ):
                     trans.app.security_agent.set_all_dataset_permissions( data.dataset, output_permissions )
                 # Create an empty file immediately
                 # open( data.file_name, "w" ).close()
-                trans.app.object_store.create( data.id )
+                trans.app.object_store.create( data.id, store_name=store_name )
+                if not store_name_set:
+                    # Ensure all other datasets in this job are created in the same store
+                    store_name = trans.app.object_store.store_name( data.id )
+                    store_name_set = True
                 # Fix permissions
                 util.umask_fix_perms( data.file_name, trans.app.config.umask, 0666 )
                 # This may not be neccesary with the new parent/child associations
diff --git a/lib/galaxy/tools/actions/upload_common.py b/lib/galaxy/tools/actions/upload_common.py
index b0517e13c60..872a3e4ebeb 100644
--- a/lib/galaxy/tools/actions/upload_common.py
+++ b/lib/galaxy/tools/actions/upload_common.py
@@ -319,20 +319,20 @@ def create_job( trans, params, tool, json_file_path, data_list, folder=None, ret
     for name, value in tool.params_to_strings( params, trans.app ).iteritems():
         job.add_parameter( name, value )
     job.add_parameter( 'paramfile', to_json_string( json_file_path ) )
-    if folder:
-        for i, dataset in enumerate( data_list ):
+    store_name = None
+    store_name_set = False  # this is needed since None is a valid value for store_name
+    for i, dataset in enumerate( data_list ):
+        if folder:
             job.add_output_library_dataset( 'output%i' % i, dataset )
-            # Create an empty file immediately
-            if not dataset.dataset.external_filename:
-                trans.app.object_store.create( dataset.id )
-                # open( dataset.file_name, "w" ).close()
-    else:
-        for i, dataset in enumerate( data_list ):
+        else:
             job.add_output_dataset( 'output%i' % i, dataset )
-            # Create an empty file immediately
-            if not dataset.dataset.external_filename:
-                trans.app.object_store.create( dataset.id )
-                # open( dataset.file_name, "w" ).close()
+        # Create an empty file immediately
+        if not dataset.dataset.external_filename:
+            trans.app.object_store.create( dataset.dataset.id, store_name=store_name )
+            # open( dataset.file_name, "w" ).close()
+            if not store_name_set:
+                store_name = trans.app.object_store.store_name( dataset.dataset.id )
+                store_name_set = True
     job.state = job.states.NEW
     trans.sa_session.add( job )
     trans.sa_session.flush()

From 5100b0e075fe6b1d1baf5a136c5a61112b5dd0fb Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Thu, 8 Dec 2011 09:00:47 -0500
Subject: [PATCH 303/362] Trackster: standardize tile cache creation and size.

---
 static/scripts/trackster.js | 9 ++-------
 1 file changed, 2 insertions(+), 7 deletions(-)

diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index 82808637e94..f550b8c7c4e 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -374,8 +374,7 @@ var
     DATA_CANNOT_RUN_TOOL = "Tool cannot be rerun: ",
     DATA_LOADING = "Loading data...",
     DATA_OK = "Ready for display",
-    CACHED_TILES_FEATURE = 10,
-    CACHED_TILES_LINE = 5,
+    TILE_CACHE_SIZE = 10,
     DATA_CACHE_SIZE = 20;
     
 /**
@@ -2779,6 +2778,7 @@ var TiledTrack = function(name, view, container, prefs, filters_list, tool_dict,
     this.filters_available = false;
     this.filters_visible = false;
     this.tool = (tool_dict !== undefined && obj_length(tool_dict) > 0 ? new Tool(this, tool_dict) : undefined);
+    this.tile_cache = new Cache(TILE_CACHE_SIZE);
     
     if (this.header_div) {
         //
@@ -3173,8 +3173,6 @@ var CompositeTiledTrack = function(drawables, view, container) {
     TiledTrack.call(this, "Composite Track", view, container);
     this.drawables = drawables;
     this.enabled = true;
-    // HACK: tile cache should be (but is not) set up in TiledTrack or earlier.
-    this.tile_cache = new Cache(CACHED_TILES_FEATURE);
 };
 extend(CompositeTiledTrack.prototype, TiledTrack.prototype, {
     init: function() {
@@ -3211,7 +3209,6 @@ var ReferenceTrack = function (view) {
     this.data_url = reference_url;
     this.data_url_extra_params = {dbkey: view.dbkey};
     this.data_manager = new ReferenceTrackDataManager(DATA_CACHE_SIZE, this, false);
-    this.tile_cache = new Cache(CACHED_TILES_LINE);
 };
 extend(ReferenceTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
     build_header_div: function() {},
@@ -3262,7 +3259,6 @@ var LineTrack = function (name, view, container, hda_ldda, dataset_id, prefs, fi
     this.hda_ldda = hda_ldda;
     this.dataset_id = dataset_id;
     this.original_dataset_id = dataset_id;
-    this.tile_cache = new Cache(CACHED_TILES_LINE);
     this.left_offset = 0;
 
     // Define track configuration
@@ -3447,7 +3443,6 @@ var FeatureTrack = function(name, view, container, hda_ldda, dataset_id, prefs,
     this.summary_draw_height = 30;
     this.inc_slots = {};
     this.start_end_dct = {};
-    this.tile_cache = new Cache(CACHED_TILES_FEATURE);
     this.left_offset = 200;
 
     // this.painter = painters.LinkedFeaturePainter;

From 256523018fcab6ee33e7fcc2383f50d8b6a99fe0 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Thu, 8 Dec 2011 10:14:00 -0500
Subject: [PATCH 304/362] Minor Object Store bug fixes.

---
 lib/galaxy/jobs/__init__.py           | 2 +-
 lib/galaxy/web/controllers/dataset.py | 7 +++++--
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index bd2b031a355..9ad021d99b2 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -330,7 +330,7 @@ class JobWrapper( object ):
         if job.output_datasets:
             da = job.output_datasets[0]
         elif job.output_library_datasets:
-            da = job.output_datasets[0]
+            da = job.output_library_datasets[0]
         if da is not None:
             store_name = self.app.object_store.store_name(da.dataset.id)
         # Create the working dir if necessary
diff --git a/lib/galaxy/web/controllers/dataset.py b/lib/galaxy/web/controllers/dataset.py
index 2fb7f3a8c43..6f0d0d4cf9e 100644
--- a/lib/galaxy/web/controllers/dataset.py
+++ b/lib/galaxy/web/controllers/dataset.py
@@ -358,7 +358,9 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesHistory, UsesHist
         """ Primarily used for the S3ObjectStore - get the status of data transfer
         if the file is not in cache """
         data = self._check_dataset(trans, dataset_id)
-        print "dataset.py -> transfer_status: Checking transfer status for dataset %s..." % data.id
+        if isinstance( data, basestring ):
+            return data
+        log.debug( "dataset.py -> transfer_status: Checking transfer status for dataset %s..." % data.id )
         
         # Pulling files in extra_files_path into cache is not handled via this
         # method but that's primarily because those files are typically linked to
@@ -375,10 +377,11 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesHistory, UsesHist
         composite_extensions = trans.app.datatypes_registry.get_composite_extensions( )
         composite_extensions.append('html') # for archiving composite datatypes
         data = self._check_dataset(trans, dataset_id)
+        if isinstance( data, basestring ):
+            return data
         
         if filename and filename != "index":
             # For files in extra_files_path
-            file_path = os.path.join( data.extra_files_path, filename ) # remove after debugging
             file_path = trans.app.object_store.get_filename(data.id, extra_dir='dataset_%s_files' % data.id, alt_name=filename)
             if os.path.exists( file_path ):
                 if os.path.isdir( file_path ):

From 3c5c6ce091afa0d99117701015933450aad5f82b Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Thu, 8 Dec 2011 10:14:29 -0500
Subject: [PATCH 305/362] Fix for some output changes I made to functional
 tests.

---
 test/base/twilltestcase.py      | 31 +++++++++++++++++--------------
 test/functional/test_toolbox.py | 11 ++---------
 2 files changed, 19 insertions(+), 23 deletions(-)

diff --git a/test/base/twilltestcase.py b/test/base/twilltestcase.py
index c12654c5eb8..a559fa4498e 100644
--- a/test/base/twilltestcase.py
+++ b/test/base/twilltestcase.py
@@ -455,16 +455,27 @@ class TwillTestCase( unittest.TestCase ):
         self.home()
 
     # Functions associated with datasets (history items) and meta data
-    def get_job_stderr( self, id ):
-        self.visit_page( "dataset/stderr?id=%s" % id )
-        return self.last_page()
+    def _get_job_stream_output( self, hda_id, stream, format ):
+        self.visit_page( "datasets/%s/%s" % ( self.security.encode_id( hda_id ), stream ) )
+        output = self.last_page()
+        if format:
+            msg =  "---------------------- >> begin tool %s << -----------------------\n" % stream
+            msg += output + "\n"
+            msg += "----------------------- >> end tool %s << ------------------------\n" % stream
+        else:
+            msg = output
+        return msg
+
+    def get_job_stdout( self, hda_id, format=False ):
+        return self._get_job_stream_output( hda_id, 'stdout', format )
+
+    def get_job_stderr( self, hda_id, format=False ):
+        return self._get_job_stream_output( hda_id, 'stderr', format )
 
     def _assert_dataset_state( self, elem, state ):
         if elem.get( 'state' ) != state:
             errmsg = "Expecting dataset state '%s', but state is '%s'. Dataset blurb: %s\n\n" % ( state, elem.get('state'), elem.text.strip() )
-            errmsg += "---------------------- >> begin tool stderr << -----------------------\n"
-            errmsg += self.get_job_stderr( elem.get( 'id' ) ) + "\n"
-            errmsg += "----------------------- >> end tool stderr << ------------------------\n"
+            errmsg += self.get_job_stderr( elem.get( 'id' ), format=True )
             raise AssertionError( errmsg )
 
     def check_metadata_for_string( self, patt, hid=None ):
@@ -624,14 +635,6 @@ class TwillTestCase( unittest.TestCase ):
         fd,temp_prefix = tempfile.mkstemp(prefix='tmp',suffix=suffix)
         return temp_prefix
 
-    def get_history_dataset_stdout( self, hda_id ):
-        self.visit_page( "/datasets/%s/stdout" % hda_id )
-        return self.last_page()
-
-    def get_history_dataset_stderr( self, hda_id ):
-        self.visit_page( "/datasets/%s/stderr" % hda_id )
-        return self.last_page()
-
     def verify_dataset_correctness( self, filename, hid=None, wait=True, maxseconds=120, attributes=None ):
         """Verifies that the attributes and contents of a history item meet expectations"""
         if wait:
diff --git a/test/functional/test_toolbox.py b/test/functional/test_toolbox.py
index 4a2b53eae07..3ea9e92886f 100644
--- a/test/functional/test_toolbox.py
+++ b/test/functional/test_toolbox.py
@@ -96,15 +96,8 @@ class ToolTestCase( TwillTestCase ):
             try:
                 self.verify_dataset_correctness( outfile, hid=elem_hid, maxseconds=testdef.maxseconds, attributes=attributes )
             except Exception, e:
-                print '-----------'
-                print 'Job STDOUT:'
-                print '-----------'
-                print self.get_history_dataset_stdout( elem.get( 'id' ) )
-                print '-----------'
-                print 'Job STDERR:'
-                print '-----------'
-                print self.get_history_dataset_stderr( elem.get( 'id' ) )
-                print '-----------'
+                print >>sys.stderr, self.get_job_stdout( elem.get( 'id' ), format=True )
+                print >>sys.stderr, self.get_job_stderr( elem.get( 'id' ), format=True )
                 raise
         self.delete_history( id=self.security.encode_id( latest_history.id ) )
 

From 7d4b23e1d97e6097a25a13952cee8018d7f87482 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Thu, 8 Dec 2011 10:44:42 -0500
Subject: [PATCH 306/362] Update EMBOSS tools to use quotes to escape user
 specified parameters during commandline substitution. Resolves #610.

---
 tools/emboss_5/emboss_antigenic.xml      | 2 +-
 tools/emboss_5/emboss_backtranseq.xml    | 2 +-
 tools/emboss_5/emboss_banana.xml         | 2 +-
 tools/emboss_5/emboss_biosed.xml         | 2 +-
 tools/emboss_5/emboss_btwisted.xml       | 2 +-
 tools/emboss_5/emboss_cai.xml            | 2 +-
 tools/emboss_5/emboss_cai_custom.xml     | 2 +-
 tools/emboss_5/emboss_chaos.xml          | 2 +-
 tools/emboss_5/emboss_charge.xml         | 2 +-
 tools/emboss_5/emboss_checktrans.xml     | 2 +-
 tools/emboss_5/emboss_chips.xml          | 2 +-
 tools/emboss_5/emboss_cirdna.xml         | 2 +-
 tools/emboss_5/emboss_codcmp.xml         | 2 +-
 tools/emboss_5/emboss_coderet.xml        | 4 ++--
 tools/emboss_5/emboss_compseq.xml        | 2 +-
 tools/emboss_5/emboss_cpgplot.xml        | 2 +-
 tools/emboss_5/emboss_cpgreport.xml      | 2 +-
 tools/emboss_5/emboss_cusp.xml           | 2 +-
 tools/emboss_5/emboss_cutseq.xml         | 2 +-
 tools/emboss_5/emboss_dan.xml            | 4 ++--
 tools/emboss_5/emboss_degapseq.xml       | 2 +-
 tools/emboss_5/emboss_descseq.xml        | 2 +-
 tools/emboss_5/emboss_diffseq.xml        | 4 ++--
 tools/emboss_5/emboss_digest.xml         | 2 +-
 tools/emboss_5/emboss_dotmatcher.xml     | 2 +-
 tools/emboss_5/emboss_dotpath.xml        | 2 +-
 tools/emboss_5/emboss_dottup.xml         | 2 +-
 tools/emboss_5/emboss_dreg.xml           | 2 +-
 tools/emboss_5/emboss_einverted.xml      | 2 +-
 tools/emboss_5/emboss_epestfind.xml      | 4 ++--
 tools/emboss_5/emboss_equicktandem.xml   | 2 +-
 tools/emboss_5/emboss_est2genome.xml     | 4 ++--
 tools/emboss_5/emboss_etandem.xml        | 2 +-
 tools/emboss_5/emboss_extractfeat.xml    | 4 ++--
 tools/emboss_5/emboss_extractseq.xml     | 2 +-
 tools/emboss_5/emboss_freak.xml          | 2 +-
 tools/emboss_5/emboss_fuzznuc.xml        | 2 +-
 tools/emboss_5/emboss_fuzzpro.xml        | 2 +-
 tools/emboss_5/emboss_fuzztran.xml       | 2 +-
 tools/emboss_5/emboss_garnier.xml        | 2 +-
 tools/emboss_5/emboss_geecee.xml         | 2 +-
 tools/emboss_5/emboss_getorf.xml         | 4 ++--
 tools/emboss_5/emboss_helixturnhelix.xml | 2 +-
 tools/emboss_5/emboss_hmoment.xml        | 2 +-
 tools/emboss_5/emboss_iep.xml            | 2 +-
 tools/emboss_5/emboss_infoseq.xml        | 4 ++--
 tools/emboss_5/emboss_isochore.xml       | 4 ++--
 tools/emboss_5/emboss_lindna.xml         | 6 +++---
 tools/emboss_5/emboss_marscan.xml        | 2 +-
 tools/emboss_5/emboss_maskfeat.xml       | 2 +-
 tools/emboss_5/emboss_maskseq.xml        | 2 +-
 tools/emboss_5/emboss_matcher.xml        | 2 +-
 tools/emboss_5/emboss_megamerger.xml     | 2 +-
 tools/emboss_5/emboss_merger.xml         | 2 +-
 tools/emboss_5/emboss_msbar.xml          | 2 +-
 tools/emboss_5/emboss_needle.xml         | 2 +-
 tools/emboss_5/emboss_newcpgreport.xml   | 2 +-
 tools/emboss_5/emboss_newcpgseek.xml     | 2 +-
 tools/emboss_5/emboss_newseq.xml         | 2 +-
 tools/emboss_5/emboss_noreturn.xml       | 2 +-
 tools/emboss_5/emboss_notseq.xml         | 2 +-
 tools/emboss_5/emboss_nthseq.xml         | 2 +-
 tools/emboss_5/emboss_octanol.xml        | 4 ++--
 tools/emboss_5/emboss_oddcomp.xml        | 2 +-
 tools/emboss_5/emboss_palindrome.xml     | 2 +-
 tools/emboss_5/emboss_pasteseq.xml       | 2 +-
 tools/emboss_5/emboss_patmatdb.xml       | 2 +-
 tools/emboss_5/emboss_pepcoil.xml        | 2 +-
 tools/emboss_5/emboss_pepinfo.xml        | 2 +-
 tools/emboss_5/emboss_pepnet.xml         | 2 +-
 tools/emboss_5/emboss_pepstats.xml       | 2 +-
 tools/emboss_5/emboss_pepwheel.xml       | 4 ++--
 tools/emboss_5/emboss_pepwindow.xml      | 2 +-
 tools/emboss_5/emboss_pepwindowall.xml   | 2 +-
 tools/emboss_5/emboss_plotcon.xml        | 2 +-
 tools/emboss_5/emboss_plotorf.xml        | 2 +-
 tools/emboss_5/emboss_polydot.xml        | 4 ++--
 tools/emboss_5/emboss_preg.xml           | 2 +-
 tools/emboss_5/emboss_prettyplot.xml     | 6 +++---
 tools/emboss_5/emboss_prettyseq.xml      | 2 +-
 tools/emboss_5/emboss_primersearch.xml   | 2 +-
 tools/emboss_5/emboss_revseq.xml         | 2 +-
 tools/emboss_5/emboss_seqmatchall.xml    | 2 +-
 tools/emboss_5/emboss_seqret.xml         | 2 +-
 tools/emboss_5/emboss_showfeat.xml       | 6 +++---
 tools/emboss_5/emboss_shuffleseq.xml     | 2 +-
 tools/emboss_5/emboss_sigcleave.xml      | 2 +-
 tools/emboss_5/emboss_sirna.xml          | 2 +-
 tools/emboss_5/emboss_sixpack.xml        | 4 ++--
 tools/emboss_5/emboss_skipseq.xml        | 2 +-
 tools/emboss_5/emboss_splitter.xml       | 2 +-
 tools/emboss_5/emboss_supermatcher.xml   | 4 ++--
 tools/emboss_5/emboss_syco.xml           | 2 +-
 tools/emboss_5/emboss_tcode.xml          | 2 +-
 tools/emboss_5/emboss_textsearch.xml     | 4 ++--
 tools/emboss_5/emboss_tmap.xml           | 2 +-
 tools/emboss_5/emboss_tranalign.xml      | 2 +-
 tools/emboss_5/emboss_transeq.xml        | 2 +-
 tools/emboss_5/emboss_trimest.xml        | 2 +-
 tools/emboss_5/emboss_trimseq.xml        | 2 +-
 tools/emboss_5/emboss_twofeat.xml        | 6 +++---
 tools/emboss_5/emboss_union.xml          | 2 +-
 tools/emboss_5/emboss_vectorstrip.xml    | 4 ++--
 tools/emboss_5/emboss_water.xml          | 2 +-
 tools/emboss_5/emboss_wobble.xml         | 2 +-
 tools/emboss_5/emboss_wordcount.xml      | 2 +-
 tools/emboss_5/emboss_wordmatch.xml      | 4 ++--
 107 files changed, 132 insertions(+), 132 deletions(-)

diff --git a/tools/emboss_5/emboss_antigenic.xml b/tools/emboss_5/emboss_antigenic.xml
index 50dfdb53783..089bcf2b0b9 100644
--- a/tools/emboss_5/emboss_antigenic.xml
+++ b/tools/emboss_5/emboss_antigenic.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: antigenic1" name="antigenic" version="5.0.0">
   <description>Predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar.</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>antigenic -sequence $input1 -outfile $out_file1 -minlen $minlen -rformat2 $out_format1 -auto</command>
+  <command>antigenic -sequence '$input1' -outfile '$out_file1' -minlen '$minlen' -rformat2 '$out_format1' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>On query</label>
diff --git a/tools/emboss_5/emboss_backtranseq.xml b/tools/emboss_5/emboss_backtranseq.xml
index b2ba60beb62..70a9910a22e 100644
--- a/tools/emboss_5/emboss_backtranseq.xml
+++ b/tools/emboss_5/emboss_backtranseq.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: backtranseq2" name="backtranseq" version="5.0.0">
   <description>Back translate a protein sequence</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>backtranseq -sequence $input1 -outfile $out_file1 -cfile $cfile -osformat2 $out_format1 -auto</command>
+  <command>backtranseq -sequence '$input1' -outfile '$out_file1' -cfile '$cfile' -osformat2 '$out_format1' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>On query</label>
diff --git a/tools/emboss_5/emboss_banana.xml b/tools/emboss_5/emboss_banana.xml
index 9948d6f6907..4d5bc325efa 100644
--- a/tools/emboss_5/emboss_banana.xml
+++ b/tools/emboss_5/emboss_banana.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: banana3" name="banana" version="5.0.0">
   <description>Bending and curvature plot in B-DNA</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>banana -sequence $input1 -outfile $out_file1 -graph none -auto</command>
+  <command>banana -sequence '$input1' -outfile '$out_file1' -graph none -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>On query</label>
diff --git a/tools/emboss_5/emboss_biosed.xml b/tools/emboss_5/emboss_biosed.xml
index dd516869ee1..277e304e0cc 100644
--- a/tools/emboss_5/emboss_biosed.xml
+++ b/tools/emboss_5/emboss_biosed.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: biosed4" name="biosed" version="5.0.0">
   <description>Replace or delete sequence sections</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>biosed -sequence $input1 -outseq $out_file1 -target "$target" -replace "$replace" -osformat2 "$out_format1" -auto</command>
+  <command>biosed -sequence '$input1' -outseq '$out_file1' -target '$target' -replace '$replace' -osformat2 '$out_format1' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>On query</label>
diff --git a/tools/emboss_5/emboss_btwisted.xml b/tools/emboss_5/emboss_btwisted.xml
index d363ec80f77..6bdeed483dd 100644
--- a/tools/emboss_5/emboss_btwisted.xml
+++ b/tools/emboss_5/emboss_btwisted.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: btwisted5" name="btwisted" version="5.0.0">
   <description>Calculates the twisting in a B-DNA sequence</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>btwisted -sequence $input1 -outfile $out_file1 -auto</command>
+  <command>btwisted -sequence '$input1' -outfile '$out_file1' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>On query</label>
diff --git a/tools/emboss_5/emboss_cai.xml b/tools/emboss_5/emboss_cai.xml
index 0d9bb463809..9a889b8d2f4 100644
--- a/tools/emboss_5/emboss_cai.xml
+++ b/tools/emboss_5/emboss_cai.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: cai6" name="cai" version="5.0.0">
   <description>CAI codon adaptation index</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>cai -seqall $input1 -outfile $out_file1 -cfile $cfile -auto</command>
+  <command>cai -seqall '$input1' -outfile '$out_file1' -cfile '$cfile' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>On query</label>
diff --git a/tools/emboss_5/emboss_cai_custom.xml b/tools/emboss_5/emboss_cai_custom.xml
index 3e6572717f0..c40a9ba8ecb 100644
--- a/tools/emboss_5/emboss_cai_custom.xml
+++ b/tools/emboss_5/emboss_cai_custom.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: cai_custom6" name="cai custom" version="5.0.0">
   <description>CAI codon adaptation index using custom codon usage file</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>cai -seqall $input1 -outfile $out_file1 -cfile $input2 -auto</command>
+  <command>cai -seqall '$input1' -outfile '$out_file1' -cfile '$input2' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>On query</label>
diff --git a/tools/emboss_5/emboss_chaos.xml b/tools/emboss_5/emboss_chaos.xml
index 2e36f52a10a..1e600505252 100644
--- a/tools/emboss_5/emboss_chaos.xml
+++ b/tools/emboss_5/emboss_chaos.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: chaos7" name="chaos" version="5.0.0">
   <description>Create a chaos game representation plot for a sequence</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command interpreter="perl">emboss_single_outputfile_wrapper.pl chaos -sequence $input1 -graph png -goutfile $out_file1 -auto</command>
+  <command interpreter="perl">emboss_single_outputfile_wrapper.pl chaos -sequence '$input1' -graph png -goutfile '$out_file1' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>On query</label>
diff --git a/tools/emboss_5/emboss_charge.xml b/tools/emboss_5/emboss_charge.xml
index 158bbb72bb0..931187c81b0 100644
--- a/tools/emboss_5/emboss_charge.xml
+++ b/tools/emboss_5/emboss_charge.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: charge8" name="charge" version="5.0.0">
   <description>Protein charge plot</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>charge -seqall $input1 -outfile $out_file1 -window $window -auto</command>
+  <command>charge -seqall '$input1' -outfile '$out_file1' -window '$window' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>On query</label>
diff --git a/tools/emboss_5/emboss_checktrans.xml b/tools/emboss_5/emboss_checktrans.xml
index dfc6e5d74d3..cf60eedc4cb 100644
--- a/tools/emboss_5/emboss_checktrans.xml
+++ b/tools/emboss_5/emboss_checktrans.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: checktrans9" name="checktrans" version="5.0.0">
   <description>Reports STOP codons and ORF statistics of a protein</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>checktrans -sequence $input1 -outfile $out_file1 -outseq $out_file2 -osformat3 $out_format2 -outfeat $out_file3 -offormat4 $out_format3 -orfml $orfml -addlast $addlast -auto</command>
+  <command>checktrans -sequence '$input1' -outfile '$out_file1' -outseq '$out_file2' -osformat3 '$out_format2' -outfeat '$out_file3' -offormat4 '$out_format3' -orfml '$orfml' -addlast '$addlast' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>On query</label>
diff --git a/tools/emboss_5/emboss_chips.xml b/tools/emboss_5/emboss_chips.xml
index 2a280c3361c..d6e9256dfbf 100644
--- a/tools/emboss_5/emboss_chips.xml
+++ b/tools/emboss_5/emboss_chips.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: chips10" name="chips" version="5.0.0">
   <description>Codon usage statistics</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>chips -seqall $input1 -outfile $out_file1 -sum $sum -auto</command>
+  <command>chips -seqall '$input1' -outfile '$out_file1' -sum '$sum' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>On query</label>
diff --git a/tools/emboss_5/emboss_cirdna.xml b/tools/emboss_5/emboss_cirdna.xml
index ce92358d017..91bc10b9259 100644
--- a/tools/emboss_5/emboss_cirdna.xml
+++ b/tools/emboss_5/emboss_cirdna.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: cirdna11" name="cirdna" version="5.0.0">
   <description>Draws circular maps of DNA constructs</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command interpreter="perl">emboss_single_outputfile_wrapper.pl cirdna -infile $input1 -graphout png -goutfile $out_file1 -auto</command>
+  <command interpreter="perl">emboss_single_outputfile_wrapper.pl cirdna -infile '$input1' -graphout png -goutfile '$out_file1' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>On query</label>
diff --git a/tools/emboss_5/emboss_codcmp.xml b/tools/emboss_5/emboss_codcmp.xml
index 9ef6063a358..b40f1838a59 100644
--- a/tools/emboss_5/emboss_codcmp.xml
+++ b/tools/emboss_5/emboss_codcmp.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: codcmp12" name="codcmp" version="5.0.0">
   <description>Codon usage table comparison</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>codcmp -first $cfile1 -second $cfile2 -outfile $out_file1 -auto</command>
+  <command>codcmp -first '$cfile1' -second '$cfile2' -outfile '$out_file1' -auto</command>
   <inputs>
     <param name="cfile1" type="select">
       <label>Codon Usage File 1</label>
diff --git a/tools/emboss_5/emboss_coderet.xml b/tools/emboss_5/emboss_coderet.xml
index 38f3b4dc656..600b7618a13 100644
--- a/tools/emboss_5/emboss_coderet.xml
+++ b/tools/emboss_5/emboss_coderet.xml
@@ -1,8 +1,8 @@
 <tool id="EMBOSS: coderet13" name="coderet" version="5.0.0">
   <description>Extract CDS, mRNA and translations from feature tables</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <!--  <command>coderet -seqall $input1 -outfile $out_file1 -osformat2 $out_format1 -cds $cds -mrna $mrna -translation $translation -auto</command>-->
-  <command>coderet -seqall $input1 -outfile $out_file1 -auto</command>
+  <!--  <command>coderet -seqall '$input1' -outfile '$out_file1' -osformat2 '$out_format1' -cds '$cds' -mrna '$mrna' -translation '$translation' -auto</command>-->
+  <command>coderet -seqall '$input1' -outfile '$out_file1' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>On query</label>
diff --git a/tools/emboss_5/emboss_compseq.xml b/tools/emboss_5/emboss_compseq.xml
index 4d8f4323d52..e1eab02d8df 100644
--- a/tools/emboss_5/emboss_compseq.xml
+++ b/tools/emboss_5/emboss_compseq.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: compseq14" name="compseq" version="5.0.0">
   <description>Count composition of dimer/trimer/etc words in a sequence</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>compseq -sequence $input1 -outfile $out_file1 -word $word -frame $frame -auto</command>
+  <command>compseq -sequence '$input1' -outfile '$out_file1' -word '$word' -frame '$frame' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>On query</label>
diff --git a/tools/emboss_5/emboss_cpgplot.xml b/tools/emboss_5/emboss_cpgplot.xml
index be4873f5df6..d920d0defe3 100644
--- a/tools/emboss_5/emboss_cpgplot.xml
+++ b/tools/emboss_5/emboss_cpgplot.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: cpgplot15" name="cpgplot" version="5.0.0">
   <description>Plot CpG rich areas</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command interpreter="perl">emboss_cpgplot_wrapper.pl cpgplot -sequence $input1 -window $window -minlen $minlen -minpc $minpc -outfile $outfile -graph png -goutfile $goutfile -outfeat $outfeat -minoe $minoe -auto</command>
+  <command interpreter="perl">emboss_cpgplot_wrapper.pl cpgplot -sequence '$input1' -window '$window' -minlen '$minlen' -minpc '$minpc' -outfile '$outfile' -graph png -goutfile '$goutfile' -outfeat '$outfeat' -minoe '$minoe' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>On query</label>
diff --git a/tools/emboss_5/emboss_cpgreport.xml b/tools/emboss_5/emboss_cpgreport.xml
index 148ca65511f..e9fedf5c385 100644
--- a/tools/emboss_5/emboss_cpgreport.xml
+++ b/tools/emboss_5/emboss_cpgreport.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: cpgreport16" name="cpgreport" version="5.0.0">
   <description>Reports all CpG rich regions</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>cpgreport -sequence $input1 -outfile $out_file1 -outfeat $out_file2 -offormat3 $out_format2 -score $score -auto</command>
+  <command>cpgreport -sequence '$input1' -outfile '$out_file1' -outfeat '$out_file2' -offormat3 '$out_format2' -score '$score' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>On query</label>
diff --git a/tools/emboss_5/emboss_cusp.xml b/tools/emboss_5/emboss_cusp.xml
index d0f88f7c9b1..0f1b0198f65 100644
--- a/tools/emboss_5/emboss_cusp.xml
+++ b/tools/emboss_5/emboss_cusp.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: cusp17" name="cusp" version="5.0.0">
   <description>Create a codon usage table</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>cusp -sequence $input1 -outfile $out_file1 -auto</command>
+  <command>cusp -sequence '$input1' -outfile '$out_file1' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>On query</label>
diff --git a/tools/emboss_5/emboss_cutseq.xml b/tools/emboss_5/emboss_cutseq.xml
index c7f91865a5b..d0c05e3decd 100644
--- a/tools/emboss_5/emboss_cutseq.xml
+++ b/tools/emboss_5/emboss_cutseq.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: cutseq18" name="cutseq" version="5.0.0">
   <description>Removes a specified section from a sequence</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>cutseq -sequence $input1 -outseq $out_file1 -from $from -to $to -osformat2 $out_format1 -auto</command>
+  <command>cutseq -sequence '$input1' -outseq '$out_file1' -from '$from' -to '$to' -osformat2 '$out_format1' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>On query</label>
diff --git a/tools/emboss_5/emboss_dan.xml b/tools/emboss_5/emboss_dan.xml
index aa968ac0ac0..6ca845ed667 100644
--- a/tools/emboss_5/emboss_dan.xml
+++ b/tools/emboss_5/emboss_dan.xml
@@ -1,8 +1,8 @@
 <tool id="EMBOSS: dan19" name="dan" version="5.0.0">
   <description>Calculates DNA RNA/DNA melting temperature</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command interpreter="perl">emboss_single_outputfile_wrapper.pl dan -sequence $input1 -windowsize $window -goutfile $out_file1 -graph png -plot $plot1 -shiftincrement $shift -dnaconc $dnaconc
-  -saltconc $saltconc -product $product -formamide $formamide -mismatch $mismatch -prodlen $prodlen -thermo $thermo -temperature $temperature -rna $rna -outfile $out_file1 -auto</command>
+  <command interpreter="perl">emboss_single_outputfile_wrapper.pl dan -sequence '$input1' -windowsize '$window' -goutfile '$out_file1' -graph png -plot '$plot1' -shiftincrement '$shift' -dnaconc '$dnaconc'
+  -saltconc '$saltconc' -product '$product' -formamide '$formamide' -mismatch '$mismatch' -prodlen '$prodlen' -thermo '$thermo' -temperature '$temperature' -rna '$rna' -outfile '$out_file1' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>On query</label>
diff --git a/tools/emboss_5/emboss_degapseq.xml b/tools/emboss_5/emboss_degapseq.xml
index d2241b7ce54..b865fc99ee5 100644
--- a/tools/emboss_5/emboss_degapseq.xml
+++ b/tools/emboss_5/emboss_degapseq.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: degapseq20" name="degapseq" version="5.0.0">
   <description>Removes gap characters from sequences</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>degapseq -sequence $input1 -outseq $out_file1 -osformat2 $out_format1 -auto</command>
+  <command>degapseq -sequence '$input1' -outseq '$out_file1' -osformat2 '$out_format1' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>On query</label>
diff --git a/tools/emboss_5/emboss_descseq.xml b/tools/emboss_5/emboss_descseq.xml
index 6b472bf074f..dfc00ae273a 100644
--- a/tools/emboss_5/emboss_descseq.xml
+++ b/tools/emboss_5/emboss_descseq.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: descseq21" name="descseq" version="5.0.0">
   <description>Alter the name or description of a sequence</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>descseq -sequence $input1 -outseq $out_file1 -name "$seqname" -description "$desc" -append $append -osformat2 $out_format1 -auto</command>
+  <command>descseq -sequence '$input1' -outseq '$out_file1' -name '$seqname' -description '$desc' -append '$append' -osformat2 '$out_format1' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>On query</label>
diff --git a/tools/emboss_5/emboss_diffseq.xml b/tools/emboss_5/emboss_diffseq.xml
index 8b76b5f4bab..712fd2d2e03 100644
--- a/tools/emboss_5/emboss_diffseq.xml
+++ b/tools/emboss_5/emboss_diffseq.xml
@@ -1,8 +1,8 @@
 <tool id="EMBOSS: diffseq22" name="diffseq" version="5.0.0">
   <description>Find differences between nearly identical sequences</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>diffseq -asequence $input1 -bsequence $input2 -outfile $out_file1 -aoutfeat $out_file2 -boutfeat $out_file3 -wordsize $wordsize -globaldifferences $globaldifferences -rformat3
-  $out_format1 -offormat4 $out_format2 -offormat5 $out_format3 -auto</command>
+  <command>diffseq -asequence '$input1' -bsequence '$input2' -outfile '$out_file1' -aoutfeat '$out_file2' -boutfeat '$out_file3' -wordsize '$wordsize' -globaldifferences '$globaldifferences' -rformat3
+  '$out_format1' -offormat4 '$out_format2' -offormat5 '$out_format3' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequence 1</label>
diff --git a/tools/emboss_5/emboss_digest.xml b/tools/emboss_5/emboss_digest.xml
index bd1b56624a5..94219d5541c 100644
--- a/tools/emboss_5/emboss_digest.xml
+++ b/tools/emboss_5/emboss_digest.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: digest23" name="digest" version="5.0.0">
   <description>Protein proteolytic enzyme or reagent cleavage digest</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>digest -seqall $input1 -outfile $out_file1 -menu $menu -unfavoured $unfavoured -overlap $overlap -allpartials $allpartials -rformat2 $out_format1 -auto</command>
+  <command>digest -seqall '$input1' -outfile '$out_file1' -menu '$menu' -unfavoured '$unfavoured' -overlap '$overlap' -allpartials '$allpartials' -rformat2 '$out_format1' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequence</label>
diff --git a/tools/emboss_5/emboss_dotmatcher.xml b/tools/emboss_5/emboss_dotmatcher.xml
index e9233031dce..d58c20784b1 100644
--- a/tools/emboss_5/emboss_dotmatcher.xml
+++ b/tools/emboss_5/emboss_dotmatcher.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: dotmatcher24" name="dotmatcher" version="5.0.0">
   <description>Displays a thresholded dotplot of two sequences</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command interpreter="perl">emboss_single_outputfile_wrapper.pl dotmatcher -asequence $input1 -bsequence $input2 -goutfile $out_file1 -windowsize $windowsize -threshold $threshold -graph png -xygraph png
+  <command interpreter="perl">emboss_single_outputfile_wrapper.pl dotmatcher -asequence '$input1' -bsequence '$input2' -goutfile '$out_file1' -windowsize '$windowsize' -threshold '$threshold' -graph png -xygraph png
   -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_dotpath.xml b/tools/emboss_5/emboss_dotpath.xml
index 1baa769c597..044321c3706 100644
--- a/tools/emboss_5/emboss_dotpath.xml
+++ b/tools/emboss_5/emboss_dotpath.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: dotpath25" name="dotpath" version="5.0.0">
   <description>Non-overlapping wordmatch dotplot of two sequences</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command interpreter="perl">emboss_single_outputfile_wrapper.pl dotpath -asequence $input1 -bsequence $input2 -goutfile $out_file1 -wordsize $wordsize -overlaps $overlaps -boxit $boxit -graph png
+  <command interpreter="perl">emboss_single_outputfile_wrapper.pl dotpath -asequence '$input1' -bsequence '$input2' -goutfile '$out_file1' -wordsize '$wordsize' -overlaps '$overlaps' -boxit '$boxit' -graph png
   -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_dottup.xml b/tools/emboss_5/emboss_dottup.xml
index 4fbe3dd68a1..34b4578f94d 100644
--- a/tools/emboss_5/emboss_dottup.xml
+++ b/tools/emboss_5/emboss_dottup.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: dottup26" name="dottup" version="5.0.0">
   <description>Displays a wordmatch dotplot of two sequences</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command interpreter="perl">emboss_single_outputfile_wrapper.pl dottup -asequence $input1 -bsequence $input2 -goutfile $out_file1 -wordsize $wordsize -boxit $boxit -graph png  -xygraph png -auto</command>
+  <command interpreter="perl">emboss_single_outputfile_wrapper.pl dottup -asequence '$input1' -bsequence '$input2' -goutfile '$out_file1' -wordsize '$wordsize' -boxit '$boxit' -graph png  -xygraph png -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequence 1</label>
diff --git a/tools/emboss_5/emboss_dreg.xml b/tools/emboss_5/emboss_dreg.xml
index b40ca586e9d..23295a0606b 100644
--- a/tools/emboss_5/emboss_dreg.xml
+++ b/tools/emboss_5/emboss_dreg.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: dreg27" name="dreg" version="5.0.0">
   <description>Regular expression search of a nucleotide sequence</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>dreg -sequence $input1 -outfile $out_file1 -pattern "$pattern" -raccshow3 "no" -rusashow3 "no" -rdesshow3 "no" -auto</command>
+  <command>dreg -sequence '$input1' -outfile '$out_file1' -pattern '$pattern' -raccshow3 'no' -rusashow3 'no' -rdesshow3 'no' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequence 1</label>
diff --git a/tools/emboss_5/emboss_einverted.xml b/tools/emboss_5/emboss_einverted.xml
index 9e74eb570da..2ebc70aa601 100644
--- a/tools/emboss_5/emboss_einverted.xml
+++ b/tools/emboss_5/emboss_einverted.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: einverted28" name="einverted" version="5.0.0">
   <description>Finds DNA inverted repeats</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>einverted -sequence $input1 -outfile $out_file1 -gap $gap -threshold $threshold -match $match -mismatch $mismatch -maxrepeat $maxrepeat -auto</command>
+  <command>einverted -sequence '$input1' -outfile '$out_file1' -gap '$gap' -threshold '$threshold' -match '$match' -mismatch '$mismatch' -maxrepeat '$maxrepeat' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>On query</label>
diff --git a/tools/emboss_5/emboss_epestfind.xml b/tools/emboss_5/emboss_epestfind.xml
index fd23ebc6a53..9cd0d3fd98d 100644
--- a/tools/emboss_5/emboss_epestfind.xml
+++ b/tools/emboss_5/emboss_epestfind.xml
@@ -1,8 +1,8 @@
 <tool id="EMBOSS: epestfind29" name="epestfind" version="5.0.0">
   <description>Finds PEST motifs as potential proteolytic cleavage sites</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command interpreter="perl">emboss_single_outputfile_wrapper.pl epestfind -sequence $input1 -goutfile $ofile2 -outfile $ofile1 -window $window -order $order -potential $potential -poor $poor
-  -invalid $invalid -map $map -graph png -auto</command>
+  <command interpreter="perl">emboss_single_outputfile_wrapper.pl epestfind -sequence '$input1' -goutfile '$ofile2' -outfile '$ofile1' -window '$window' -order '$order' -potential '$potential' -poor '$poor'
+  -invalid '$invalid' -map '$map' -graph png -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequence</label>
diff --git a/tools/emboss_5/emboss_equicktandem.xml b/tools/emboss_5/emboss_equicktandem.xml
index 49ffe86d886..9c3ce75c9cf 100644
--- a/tools/emboss_5/emboss_equicktandem.xml
+++ b/tools/emboss_5/emboss_equicktandem.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: equicktandem31" name="equicktandem" version="5.0.0">
   <description>Finds tandem repeats</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>equicktandem -sequence $input1 -outfile $out_file1 -origfile $ofile2 -maxrepeat $maxrepeat -threshold $threshold -rformat2 $out_format1 -auto</command>
+  <command>equicktandem -sequence '$input1' -outfile '$out_file1' -origfile '$ofile2' -maxrepeat '$maxrepeat' -threshold '$threshold' -rformat2 '$out_format1' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>Sequence</label>
diff --git a/tools/emboss_5/emboss_est2genome.xml b/tools/emboss_5/emboss_est2genome.xml
index a2cff4106b1..a457ff6d45d 100644
--- a/tools/emboss_5/emboss_est2genome.xml
+++ b/tools/emboss_5/emboss_est2genome.xml
@@ -1,8 +1,8 @@
 <tool id="EMBOSS: est2genome32" name="est2genome" version="5.0.0">
   <description>Align EST and genomic DNA sequences</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>est2genome -estsequence $input1 -genomesequence $input2 -outfile $out_file1 -match $match -mismatch $mismatch -gappenalty $gappenalty -intronpenalty $intronpenalty -splicepenalty
-  $splicepenalty -minscore $minscore -reverse $reverse -splice $splice -mode $mode -best $best -shuffle $shuffle -seed $seed -align $align -width $width -auto</command>
+  <command>est2genome -estsequence '$input1' -genomesequence '$input2' -outfile '$out_file1' -match '$match' -mismatch '$mismatch' -gappenalty '$gappenalty' -intronpenalty '$intronpenalty' -splicepenalty
+  ''$splice'penalty' -minscore '$minscore' -reverse '$reverse' -splice '$splice' -mode '$mode' -best '$best' -shuffle '$shuffle' -seed '$seed' -align '$align' -width '$width' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>EST sequence(s)</label>
diff --git a/tools/emboss_5/emboss_etandem.xml b/tools/emboss_5/emboss_etandem.xml
index 4b92e125f95..21e783347cc 100644
--- a/tools/emboss_5/emboss_etandem.xml
+++ b/tools/emboss_5/emboss_etandem.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: etandem33" name="etandem" version="5.0.0">
   <description>Looks for tandem repeats in a nucleotide sequence</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>etandem -sequence $input1 -outfile $out_file1 -origfile $ofile2 -minrepeat $minrepeat -maxrepeat $maxrepeat -threshold $threshold -mismatch $mismatch -uniform $uniform -rformat2 $out_format1 -auto</command>
+  <command>etandem -sequence '$input1' -outfile '$out_file1' -origfile '$ofile2' -minrepeat '$minrepeat' -maxrepeat '$maxrepeat' -threshold '$threshold' -mismatch '$mismatch' -uniform '$uniform' -rformat2 '$out_format1' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>Sequence</label>
diff --git a/tools/emboss_5/emboss_extractfeat.xml b/tools/emboss_5/emboss_extractfeat.xml
index b8d92c325d4..efe7ddf44eb 100644
--- a/tools/emboss_5/emboss_extractfeat.xml
+++ b/tools/emboss_5/emboss_extractfeat.xml
@@ -2,8 +2,8 @@
   <!-- tool tested with documentation, functional test not designed due to empty files resulting from test input sequences -->  
   <description>Extract features from a sequence</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>extractfeat -sequence $input1 -outseq $out_file1 -before $before -after $after -source "$source" -type "$type" -sense $sense -minscore $minscore -maxscore $maxscore -tag "$tag" -value
-  "$value" -join $join -featinname $featinname -describe "$describe" -osformat2 $out_format1 -auto</command>
+  <command>extractfeat -sequence '$input1' -outseq '$out_file1' -before '$before' -after '$after' -source '$source' -type '$type' -sense '$sense' -minscore '$minscore' -maxscore '$maxscore' -tag '$tag' -value
+  '$value' -join '$join' -featinname '$featinname' -describe '$describe' -osformat2 '$out_format1' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequences</label>
diff --git a/tools/emboss_5/emboss_extractseq.xml b/tools/emboss_5/emboss_extractseq.xml
index cd5430c4384..50857f92d5f 100644
--- a/tools/emboss_5/emboss_extractseq.xml
+++ b/tools/emboss_5/emboss_extractseq.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: extractseq35" name="extractseq" version="5.0.0">
   <description>Extract regions from a sequence</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>extractseq -sequence $input1 -outseq $out_file1 -regions $regions -separate $separate -osformat2 $out_format1 -auto</command>
+  <command>extractseq -sequence '$input1' -outseq '$out_file1' -regions '$regions' -separate '$separate' -osformat2 '$out_format1' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequences</label>
diff --git a/tools/emboss_5/emboss_freak.xml b/tools/emboss_5/emboss_freak.xml
index 0c2ba29ee6b..555351bc631 100644
--- a/tools/emboss_5/emboss_freak.xml
+++ b/tools/emboss_5/emboss_freak.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: freak36" name="freak" version="5.0.0">
   <description>Residue/base frequency table or plot</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>freak -seqall $input1 -outfile $out_file1 -window $window -letters $letters -graph png -step $step -auto</command>
+  <command>freak -seqall '$input1' -outfile '$out_file1' -window '$window' -letters '$letters' -graph png -step '$step' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequences</label>
diff --git a/tools/emboss_5/emboss_fuzznuc.xml b/tools/emboss_5/emboss_fuzznuc.xml
index d2dbf7f9c29..70ed4e5ccf8 100644
--- a/tools/emboss_5/emboss_fuzznuc.xml
+++ b/tools/emboss_5/emboss_fuzznuc.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: fuzznuc37" name="fuzznuc" version="5.0.1">
   <description>Nucleic acid pattern search</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>fuzznuc -sequence $input1 -outfile $out_file1 -pattern '$pattern' -pmismatch $mismatch -complement $complement -rformat2 $out_format1 -auto</command>
+  <command>fuzznuc -sequence '$input1' -outfile '$out_file1' -pattern '$pattern' -pmismatch '$mismatch' -complement '$complement' -rformat2 '$out_format1' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>Sequences</label>
diff --git a/tools/emboss_5/emboss_fuzzpro.xml b/tools/emboss_5/emboss_fuzzpro.xml
index a4d73112c3c..a83dac7ddce 100644
--- a/tools/emboss_5/emboss_fuzzpro.xml
+++ b/tools/emboss_5/emboss_fuzzpro.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: fuzzpro38" name="fuzzpro" version="5.0.0">
   <description>Protein pattern search</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>fuzzpro -sequence $input1 -outfile $out_file1 -pattern "$pattern" -pmismatch $mismatch -rformat2 $out_format1 -auto</command>
+  <command>fuzzpro -sequence '$input1' -outfile '$out_file1' -pattern '$pattern' -pmismatch '$mismatch' -rformat2 '$out_format1' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequences</label>
diff --git a/tools/emboss_5/emboss_fuzztran.xml b/tools/emboss_5/emboss_fuzztran.xml
index 63f4e596df6..c4fcfa5f8c6 100644
--- a/tools/emboss_5/emboss_fuzztran.xml
+++ b/tools/emboss_5/emboss_fuzztran.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: fuzztran39" name="fuzztran" version="5.0.0">
   <description>Protein pattern search after translation</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>fuzztran -sequence $input1 -outfile $out_file1 -pattern "$pattern" -pmismatch $mismatch -frame $frame -table $table -rformat2 $out_format1 -auto</command>
+  <command>fuzztran -sequence '$input1' -outfile '$out_file1' -pattern '$pattern' -pmismatch '$mismatch' -frame '$frame' -table '$table' -rformat2 '$out_format1' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>Sequences</label>
diff --git a/tools/emboss_5/emboss_garnier.xml b/tools/emboss_5/emboss_garnier.xml
index cfd5ecc0093..79fbea202eb 100644
--- a/tools/emboss_5/emboss_garnier.xml
+++ b/tools/emboss_5/emboss_garnier.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: garnier40" name="garnier" version="5.0.0">
   <description>Predicts protein secondary structure</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>garnier -sequence $input1 -outfile $out_file1 -idc $idc -rformat2 $out_format1 -auto</command>
+  <command>garnier -sequence '$input1' -outfile '$out_file1' -idc '$idc' -rformat2 '$out_format1' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequences</label>
diff --git a/tools/emboss_5/emboss_geecee.xml b/tools/emboss_5/emboss_geecee.xml
index 570e8fc4a1a..6555bf07680 100644
--- a/tools/emboss_5/emboss_geecee.xml
+++ b/tools/emboss_5/emboss_geecee.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: geecee41" name="geecee" version="5.0.0">
   <description>Calculates fractional GC content of nucleic acid sequences</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>geecee -sequence $input1 -outfile $out_file1 -auto</command>
+  <command>geecee -sequence '$input1' -outfile '$out_file1' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequences</label>
diff --git a/tools/emboss_5/emboss_getorf.xml b/tools/emboss_5/emboss_getorf.xml
index 24ea0d8ebab..b18b548e0a2 100644
--- a/tools/emboss_5/emboss_getorf.xml
+++ b/tools/emboss_5/emboss_getorf.xml
@@ -1,8 +1,8 @@
 <tool id="EMBOSS: getorf42" name="getorf" version="5.0.0">
   <description>Finds and extracts open reading frames (ORFs)</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>getorf -sequence $input1 -outseq $out_file1 -table $table -minsize $minsize -maxsize $maxsize -find $find -methionine $methionine -circular $circular -reverse $reverse -flanking $flanking
-  -osformat2 $out_format1 -auto</command>
+  <command>getorf -sequence '$input1' -outseq '$out_file1' -table '$table' -minsize '$minsize' -maxsize '$maxsize' -find '$find' -methionine '$methionine' -circular '$circular' -reverse '$reverse' -flanking '$flanking'
+  -osformat2 '$out_format1' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>Sequences</label>
diff --git a/tools/emboss_5/emboss_helixturnhelix.xml b/tools/emboss_5/emboss_helixturnhelix.xml
index 519d4ed36e6..9a9e9ca0164 100644
--- a/tools/emboss_5/emboss_helixturnhelix.xml
+++ b/tools/emboss_5/emboss_helixturnhelix.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: helixturnhelix43" name="helixturnhelix" version="5.0.0">
   <description>Report nucleic acid binding motifs</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>helixturnhelix -sequence $input1 -outfile $out_file1 -mean $mean -sd $sd -minsd $minsd -eightyseven $eightyseven -rformat2 $out_format1 -auto</command>
+  <command>helixturnhelix -sequence '$input1' -outfile '$out_file1' -mean '$mean' -sd '$sd' -minsd '$minsd' -eightyseven '$eightyseven' -rformat2 '$out_format1' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequences</label>
diff --git a/tools/emboss_5/emboss_hmoment.xml b/tools/emboss_5/emboss_hmoment.xml
index 3d485a7e495..715d9d3a7c8 100644
--- a/tools/emboss_5/emboss_hmoment.xml
+++ b/tools/emboss_5/emboss_hmoment.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: hmoment44" name="hmoment" version="5.0.0">
   <description>Hydrophobic moment calculation</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>hmoment -seqall $input1 -outfile $out_file1 -window $window -aangle $aangle -graph png -auto</command>
+  <command>hmoment -seqall '$input1' -outfile '$out_file1' -window '$window' -aangle '$aangle' -graph png -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequences</label>
diff --git a/tools/emboss_5/emboss_iep.xml b/tools/emboss_5/emboss_iep.xml
index 28e513fce41..c3d76f24a61 100644
--- a/tools/emboss_5/emboss_iep.xml
+++ b/tools/emboss_5/emboss_iep.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: iep45" name="iep" version="5.0.0">
   <description>Calculates the isoelectric point of a protein</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>iep -sequence $input1 -outfile $out_file1 -step $step -amino $amino -graph png -termini $termini -auto</command>
+  <command>iep -sequence '$input1' -outfile '$out_file1' -step '$step' -amino '$amino' -graph png -termini '$termini' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequences</label>
diff --git a/tools/emboss_5/emboss_infoseq.xml b/tools/emboss_5/emboss_infoseq.xml
index 14404d24548..87a6619f9f3 100644
--- a/tools/emboss_5/emboss_infoseq.xml
+++ b/tools/emboss_5/emboss_infoseq.xml
@@ -2,8 +2,8 @@
   <!-- info contains file information always -->
   <description>Displays some simple information about sequences</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>infoseq -sequence $input1 -outfile $out_file1 -html $html_out1 -heading $heading -usa $usa -name $disname -accession $accession -gi $gi -version $version -type $type -length $length -pgc
-  $pgc -description $description -auto</command>
+  <command>infoseq -sequence '$input1' -outfile '$out_file1' -html '$html_out1' -heading '$heading' -usa '$usa' -name '$disname' -accession '$accession' -gi '$gi' -version '$version' -type '$type' -length '$length' -pgc
+  '$pgc' -description '$description' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequences</label>
diff --git a/tools/emboss_5/emboss_isochore.xml b/tools/emboss_5/emboss_isochore.xml
index a167740941b..b4e012778c9 100644
--- a/tools/emboss_5/emboss_isochore.xml
+++ b/tools/emboss_5/emboss_isochore.xml
@@ -1,8 +1,8 @@
 <tool id="EMBOSS: isochore47" name="isochore" version="5.0.0">
   <description>Plots isochores in large DNA sequences</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command interpreter="perl">emboss_single_outputfile_wrapper.pl isochore -sequence $input1 -outfile $ofile2 -goutfile $ofile1 -graph png -window $window -shift $shift -auto</command>
-  <!--  <command interpreter="perl">emboss_single_outputfile_wrapper.pl isochore -sequence $input1 -goutfile $ofile1 -graph png -window $window -shift $shift -auto</command>-->
+  <command interpreter="perl">emboss_single_outputfile_wrapper.pl isochore -sequence '$input1' -outfile '$ofile2' -goutfile '$ofile1' -graph png -window '$window' -shift '$shift' -auto</command>
+  <!--  <command interpreter="perl">emboss_single_outputfile_wrapper.pl isochore -sequence '$input1' -goutfile '$ofile1' -graph png -window '$window' -shift '$shift' -auto</command>-->
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>Sequences</label>
diff --git a/tools/emboss_5/emboss_lindna.xml b/tools/emboss_5/emboss_lindna.xml
index 7ab378709a9..1747d71b6e5 100644
--- a/tools/emboss_5/emboss_lindna.xml
+++ b/tools/emboss_5/emboss_lindna.xml
@@ -2,9 +2,9 @@
   <!-- tool produces memory error in ajmem.c -->
   <description>Draws linear maps of DNA constructs</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>lindna -infile $input1 -graphout png -goutfile $out_file1 -ruler $ruler -blocktype $blocktype -maxgroups $maxgroups -maxlabels $maxlabels -intersymbol $intersymbol -intercolour $intercolour
-  -interticks $interticks -gapsize $gapsize -ticklines $ticklines -textheight $textheight -textlength $textlength -margin $margin -tickheight $tickheight -blockheight $blockheight -rangeheight
-  $rangeheight -gapgroup $gapgroup -postext $postext -auto</command>
+  <command>lindna -infile '$input1' -graphout png -goutfile '$out_file1' -ruler '$ruler' -blocktype '$blocktype' -maxgroups '$maxgroups' -maxlabels '$maxlabels' -intersymbol '$intersymbol' -intercolour '$intercolour'
+  -interticks '$interticks' -gapsize '$gapsize' -ticklines '$ticklines' -textheight '$textheight' -textlength '$textlength' -margin '$margin' -tickheight '$tickheight' -blockheight '$blockheight' -rangeheight
+  '$rangeheight' -gapgroup '$gapgroup' -postext '$postext' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequences</label>
diff --git a/tools/emboss_5/emboss_marscan.xml b/tools/emboss_5/emboss_marscan.xml
index bd19131cc98..5d3481dc59f 100644
--- a/tools/emboss_5/emboss_marscan.xml
+++ b/tools/emboss_5/emboss_marscan.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: marscan49" name="marscan" version="5.0.0">
   <description>Finds MAR/SAR sites in nucleic sequences</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>marscan -sequence $input1 -outfile $out_file1 -rformat2 $out_format1 -auto</command>
+  <command>marscan -sequence '$input1' -outfile '$out_file1' -rformat2 '$out_format1' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequence</label>
diff --git a/tools/emboss_5/emboss_maskfeat.xml b/tools/emboss_5/emboss_maskfeat.xml
index 11ac741c30d..dc4f65c6d91 100644
--- a/tools/emboss_5/emboss_maskfeat.xml
+++ b/tools/emboss_5/emboss_maskfeat.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: maskfeat50" name="maskfeat" version="5.0.0">
   <description>Mask off features of a sequence</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>maskfeat -sequence $input1 -outseq $out_file1 -type "$type" -tolower $tolower -maskchar "$maskchar" -osformat2 $out_format1 -auto</command>
+  <command>maskfeat -sequence '$input1' -outseq '$out_file1' -type '$type' -tolower '$tolower' -maskchar '$maskchar' -osformat2 '$out_format1' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequence</label>
diff --git a/tools/emboss_5/emboss_maskseq.xml b/tools/emboss_5/emboss_maskseq.xml
index 96b4cdd9087..5fa9c9f922b 100644
--- a/tools/emboss_5/emboss_maskseq.xml
+++ b/tools/emboss_5/emboss_maskseq.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: maskseq51" name="maskseq" version="5.0.0">
   <description>Mask off regions of a sequence</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>maskseq -sequence $input1 -outseq $out_file1 -regions "$regions" -tolower $tolower -maskchar "$maskchar" -osformat2 $out_format1 -auto</command>
+  <command>maskseq -sequence '$input1' -outseq '$out_file1' -regions '$regions' -tolower '$tolower' -maskchar '$maskchar' -osformat2 '$out_format1' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequence</label>
diff --git a/tools/emboss_5/emboss_matcher.xml b/tools/emboss_5/emboss_matcher.xml
index 7a55b6c802a..caa61b9788c 100644
--- a/tools/emboss_5/emboss_matcher.xml
+++ b/tools/emboss_5/emboss_matcher.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: matcher52" name="matcher" version="5.0.0">
   <description>Finds the best local alignments between two sequences</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>matcher -asequence $input1 -bsequence $input2 -outfile $out_file1 -alternatives $alternatives -gapopen $gapopen -gapextend $gapextend -aformat3 $out_format1 -auto</command>
+  <command>matcher -asequence '$input1' -bsequence '$input2' -outfile '$out_file1' -alternatives '$alternatives' -gapopen '$gapopen' -gapextend '$gapextend' -aformat3 '$out_format1' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequence 1</label>
diff --git a/tools/emboss_5/emboss_megamerger.xml b/tools/emboss_5/emboss_megamerger.xml
index fad3be07d68..07e10d4ebc3 100644
--- a/tools/emboss_5/emboss_megamerger.xml
+++ b/tools/emboss_5/emboss_megamerger.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: megamerger53" name="megamerger" version="5.0.0">
   <description>Merge two large overlapping nucleic acid sequences</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>megamerger -asequence $input1 -bsequence $input2 -outseq $out_file1 -outfile $out_file2 -wordsize $wordsize -prefer $prefer -osformat3 $out_format1 -auto</command>
+  <command>megamerger -asequence '$input1' -bsequence '$input2' -outseq '$out_file1' -outfile '$out_file2' -wordsize '$wordsize' -prefer '$prefer' -osformat3 '$out_format1' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequence 1</label>
diff --git a/tools/emboss_5/emboss_merger.xml b/tools/emboss_5/emboss_merger.xml
index 9b10641a75c..af561d18a77 100644
--- a/tools/emboss_5/emboss_merger.xml
+++ b/tools/emboss_5/emboss_merger.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: merger54" name="merger" version="5.0.0">
   <description>Merge two overlapping nucleic acid sequences</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>merger -asequence $input1 -bsequence $input2 -outseq $out_file1 -outfile $out_file2 -gapopen $gapopen -gapextend $gapextend -osformat4 $out_format1 -aformat3 $out_format2 -auto</command>
+  <command>merger -asequence '$input1' -bsequence '$input2' -outseq '$out_file1' -outfile '$out_file2' -gapopen '$gapopen' -gapextend '$gapextend' -osformat4 '$out_format1' -aformat3 '$out_format2' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequence 1</label>
diff --git a/tools/emboss_5/emboss_msbar.xml b/tools/emboss_5/emboss_msbar.xml
index 1980f0f3a7c..ba88fcaf658 100644
--- a/tools/emboss_5/emboss_msbar.xml
+++ b/tools/emboss_5/emboss_msbar.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: msbar55" name="msbar" version="5.0.0">
   <description>Mutate sequence beyond all recognition</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>msbar -sequence $input1 -outseq $out_file1 -count $count -point $point -block $block -codon $codon -inframe $inframe -minimum $minimum -maximum $maximum -osformat2 $out_format1
+  <command>msbar -sequence '$input1' -outseq '$out_file1' -count '$count' -point '$point' -block '$block' -codon '$codon' -inframe '$inframe' -minimum '$minimum' -maximum '$maximum' -osformat2 '$out_format1'
   -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_needle.xml b/tools/emboss_5/emboss_needle.xml
index 10bfb9461b6..860646528fe 100644
--- a/tools/emboss_5/emboss_needle.xml
+++ b/tools/emboss_5/emboss_needle.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: needle56" name="needle" version="5.0.0">
   <description>Needleman-Wunsch global alignment</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>needle -asequence $input1 -bsequence $input2 -outfile $out_file1 -gapopen $gapopen -gapextend $gapextend -brief $brief -aformat3 $out_format1 -auto</command>
+  <command>needle -asequence '$input1' -bsequence '$input2' -outfile '$out_file1' -gapopen '$gapopen' -gapextend '$gapextend' -brief '$brief' -aformat3 '$out_format1' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>Sequence 1</label>
diff --git a/tools/emboss_5/emboss_newcpgreport.xml b/tools/emboss_5/emboss_newcpgreport.xml
index 868851b1a1e..c9b3bc4bb79 100644
--- a/tools/emboss_5/emboss_newcpgreport.xml
+++ b/tools/emboss_5/emboss_newcpgreport.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: newcpgreport57" name="newcpgreport" version="5.0.0">
   <description>Report CpG rich areas</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>newcpgreport -sequence $input1 -window $window -shift $shift -minlen $minlen -minpc $minpc -outfile $out_file1 -minoe $minoe -auto</command>
+  <command>newcpgreport -sequence '$input1' -window '$window' -shift '$shift' -minlen '$minlen' -minpc '$minpc' -outfile '$out_file1' -minoe '$minoe' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequence</label>
diff --git a/tools/emboss_5/emboss_newcpgseek.xml b/tools/emboss_5/emboss_newcpgseek.xml
index 8bbde6f0b7a..621748ca11e 100644
--- a/tools/emboss_5/emboss_newcpgseek.xml
+++ b/tools/emboss_5/emboss_newcpgseek.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: newcpgseek58" name="newcpgseek" version="5.0.0">
   <description>Reports CpG rich region</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>newcpgseek -sequence $input1 -outfile $out_file1 -score $score -auto</command>
+  <command>newcpgseek -sequence '$input1' -outfile '$out_file1' -score '$score' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>Sequence</label>
diff --git a/tools/emboss_5/emboss_newseq.xml b/tools/emboss_5/emboss_newseq.xml
index 99c510ca6f8..6caec610642 100644
--- a/tools/emboss_5/emboss_newseq.xml
+++ b/tools/emboss_5/emboss_newseq.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: newseq59" name="newseq" version="5.0.0">
   <description>Type in a short new sequence</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>newseq -outseq $out_file1 -name "$seqname" -description "$description" -type $type -sequence "$sequence" -osformat5 $out_format1 -auto</command>
+  <command>newseq -outseq '$out_file1' -name '$seqname' -description '$description' -type '$type' -sequence '$sequence' -osformat5 '$out_format1' -auto</command>
   <inputs>
     <param name="seqname" size="10" type="text" value="">
       <label>Name of of the sequence</label>
diff --git a/tools/emboss_5/emboss_noreturn.xml b/tools/emboss_5/emboss_noreturn.xml
index 76f9dde8070..7f38a98188c 100644
--- a/tools/emboss_5/emboss_noreturn.xml
+++ b/tools/emboss_5/emboss_noreturn.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: noreturn60" name="noreturn" version="5.0.0">
   <description>Removes carriage return from ASCII files</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>noreturn -infile $input1 -outfile $out_file1 -system $system -auto</command>
+  <command>noreturn -infile '$input1' -outfile '$out_file1' -system '$system' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>On query</label>
diff --git a/tools/emboss_5/emboss_notseq.xml b/tools/emboss_5/emboss_notseq.xml
index 783141e2272..f31952600ef 100644
--- a/tools/emboss_5/emboss_notseq.xml
+++ b/tools/emboss_5/emboss_notseq.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: notseq61" name="notseq" version="5.0.0">
   <description>Exclude a set of sequences and write out the remaining ones</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>notseq -sequence $input1 -outseq $out_file1 -exclude "$exclude" -osformat3 $out_format1 -auto</command>
+  <command>notseq -sequence '$input1' -outseq '$out_file1' -exclude '$exclude' -osformat3 '$out_format1' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>On query</label>
diff --git a/tools/emboss_5/emboss_nthseq.xml b/tools/emboss_5/emboss_nthseq.xml
index ae0d178d13a..9566447398a 100644
--- a/tools/emboss_5/emboss_nthseq.xml
+++ b/tools/emboss_5/emboss_nthseq.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: nthseq62" name="nthseq" version="5.0.0">
   <description>Writes one sequence from a multiple set of sequences</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>nthseq -sequence $input1 -outseq $out_file1 -number $number -osformat2 $out_format1 -auto</command>
+  <command>nthseq -sequence '$input1' -outseq '$out_file1' -number '$number' -osformat2 '$out_format1' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>Sequences</label>
diff --git a/tools/emboss_5/emboss_octanol.xml b/tools/emboss_5/emboss_octanol.xml
index ad389f77607..d0edb72bf0f 100644
--- a/tools/emboss_5/emboss_octanol.xml
+++ b/tools/emboss_5/emboss_octanol.xml
@@ -2,8 +2,8 @@
   <!-- graphics output with filename, no functional tests added -->  
   <description>Displays protein hydropathy</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command interpreter="perl">emboss_single_outputfile_wrapper.pl octanol -sequence $input1 -graph png -goutfile $out_file1 -width $width -octanolplot $octanolplot -interfaceplot $interfaceplot
-  -differenceplot $differenceplot -auto</command>
+  <command interpreter="perl">emboss_single_outputfile_wrapper.pl octanol -sequence '$input1' -graph png -goutfile '$out_file1' -width '$width' -octanolplot '$octanolplot' -interfaceplot '$interfaceplot'
+  -differenceplot '$differenceplot' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequences</label>
diff --git a/tools/emboss_5/emboss_oddcomp.xml b/tools/emboss_5/emboss_oddcomp.xml
index c482b44850c..acada0e7efb 100644
--- a/tools/emboss_5/emboss_oddcomp.xml
+++ b/tools/emboss_5/emboss_oddcomp.xml
@@ -2,7 +2,7 @@
   <!-- output contains file location info, commented out functional tests -->
   <description>Find protein sequence regions with a biased composition</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>oddcomp -sequence $input1 -infile $input2 -outfile $out_file1 -window $window -ignorebz $ignorebz -auto</command>
+  <command>oddcomp -sequence '$input1' -infile '$input2' -outfile '$out_file1' -window '$window' -ignorebz '$ignorebz' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequences</label>
diff --git a/tools/emboss_5/emboss_palindrome.xml b/tools/emboss_5/emboss_palindrome.xml
index 957b8be3cd2..7829ce18563 100644
--- a/tools/emboss_5/emboss_palindrome.xml
+++ b/tools/emboss_5/emboss_palindrome.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: palindrome65" name="palindrome" version="5.0.0">
   <description>Looks for inverted repeats in a nucleotide sequence</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>palindrome -sequence $input1 -outfile $out_file1 -minpallen $minpallen -maxpallen $maxpallen -gaplimit $gaplimit -nummismatches $nummismatches -overlap $overlap -auto</command>
+  <command>palindrome -sequence '$input1' -outfile '$out_file1' -minpallen '$minpallen' -maxpallen '$maxpallen' -gaplimit '$gaplimit' -nummismatches '$nummismatches' -overlap '$overlap' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>Sequences</label>
diff --git a/tools/emboss_5/emboss_pasteseq.xml b/tools/emboss_5/emboss_pasteseq.xml
index 816c36b420d..47ee4880fb7 100644
--- a/tools/emboss_5/emboss_pasteseq.xml
+++ b/tools/emboss_5/emboss_pasteseq.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: pasteseq66" name="pasteseq" version="5.0.0">
   <description>Insert one sequence into another</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>pasteseq -asequence $input2 -bsequence $input1 -outseq $out_file1 -pos $pos -osformat3 $out_format1 -auto</command>
+  <command>pasteseq -asequence '$input2' -bsequence '$input1' -outseq '$out_file1' -pos '$pos' -osformat3 '$out_format1' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>Main sequence</label>
diff --git a/tools/emboss_5/emboss_patmatdb.xml b/tools/emboss_5/emboss_patmatdb.xml
index 500e4f0d5ad..e5ed3dbed16 100644
--- a/tools/emboss_5/emboss_patmatdb.xml
+++ b/tools/emboss_5/emboss_patmatdb.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: patmatdb67" name="patmatdb" version="5.0.0">
   <description>Search a protein sequence with a motif</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>patmatdb -sequence $input1 -outfile $out_file1 -motif "$motif" -rformat3 $out_format1 -auto</command>
+  <command>patmatdb -sequence '$input1' -outfile '$out_file1' -motif '$motif' -rformat3 '$out_format1' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Main sequence</label>
diff --git a/tools/emboss_5/emboss_pepcoil.xml b/tools/emboss_5/emboss_pepcoil.xml
index a2c43a183ce..587290c100c 100644
--- a/tools/emboss_5/emboss_pepcoil.xml
+++ b/tools/emboss_5/emboss_pepcoil.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: pepcoil68" name="pepcoil" version="5.0.0">
   <description>Predicts coiled coil regions</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>pepcoil -sequence $input1 -outfile $out_file1 -window $window -coil $coil -frame $frame -other $other -auto</command>
+  <command>pepcoil -sequence '$input1' -outfile '$out_file1' -window '$window' -coil '$coil' -frame '$frame' -other '$other' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequence</label>
diff --git a/tools/emboss_5/emboss_pepinfo.xml b/tools/emboss_5/emboss_pepinfo.xml
index 72555294d36..eee364b898a 100644
--- a/tools/emboss_5/emboss_pepinfo.xml
+++ b/tools/emboss_5/emboss_pepinfo.xml
@@ -2,7 +2,7 @@
   <!-- puts file info in output files -->
   <description>Plots simple amino acid properties in parallel</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command interpreter="perl">emboss_single_outputfile_wrapper.pl pepinfo -sequence $input1 -outfile $out_file1 -goutfile $out_file2 -graph png -hwindow $hwindow $plot_type -auto</command>
+  <command interpreter="perl">emboss_single_outputfile_wrapper.pl pepinfo -sequence '$input1' -outfile '$out_file1' -goutfile '$out_file2' -graph png -hwindow '$hwindow' '$plot_type' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequence</label>
diff --git a/tools/emboss_5/emboss_pepnet.xml b/tools/emboss_5/emboss_pepnet.xml
index 77c4ed171f2..6465f4e8305 100644
--- a/tools/emboss_5/emboss_pepnet.xml
+++ b/tools/emboss_5/emboss_pepnet.xml
@@ -2,7 +2,7 @@
   <!-- graphical output file with path information -->
   <description>Displays proteins as a helical net</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>pepnet -sequence $input1 -graph png -goutfile $out_file1 -squares $squares -diamonds $diamonds -octags $octags -amphipathic $amphipathic -auto</command>
+  <command>pepnet -sequence '$input1' -graph png -goutfile '$out_file1' -squares '$squares' -diamonds '$diamonds' -octags '$octags' -amphipathic '$amphipathic' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequence</label>
diff --git a/tools/emboss_5/emboss_pepstats.xml b/tools/emboss_5/emboss_pepstats.xml
index 40c32bbe3a9..4e28604313d 100644
--- a/tools/emboss_5/emboss_pepstats.xml
+++ b/tools/emboss_5/emboss_pepstats.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: pepstats71" name="pepstats" version="5.0.0">
   <description>Protein statistics</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>pepstats -sequence $input1 -outfile $out_file1 -termini $termini -auto</command>
+  <command>pepstats -sequence '$input1' -outfile '$out_file1' -termini '$termini' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequence</label>
diff --git a/tools/emboss_5/emboss_pepwheel.xml b/tools/emboss_5/emboss_pepwheel.xml
index 748a761981a..033b653f41a 100644
--- a/tools/emboss_5/emboss_pepwheel.xml
+++ b/tools/emboss_5/emboss_pepwheel.xml
@@ -2,8 +2,8 @@
   <!-- produces png file -->
   <description>Shows protein sequences as helices</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command interpreter="perl">emboss_single_outputfile_wrapper.pl pepwheel -sequence $input1 -graph png -goutfile $out_file1 -squares $squares -diamonds $diamonds -octags $octags -amphipathic
-  $amphipathic -steps $steps -turns $turns -wheel $wheel -auto</command>
+  <command interpreter="perl">emboss_single_outputfile_wrapper.pl pepwheel -sequence '$input1' -graph png -goutfile '$out_file1' -squares '$squares' -diamonds '$diamonds' -octags '$octags' -amphipathic
+  '$amphipathic' -steps '$steps' -turns '$turns' -wheel '$wheel' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequence</label>
diff --git a/tools/emboss_5/emboss_pepwindow.xml b/tools/emboss_5/emboss_pepwindow.xml
index 60c0883eac9..c36824ffdcd 100644
--- a/tools/emboss_5/emboss_pepwindow.xml
+++ b/tools/emboss_5/emboss_pepwindow.xml
@@ -2,7 +2,7 @@
   <!-- produces png file -->
   <description>Displays protein hydropathy</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command interpreter="perl">emboss_single_outputfile_wrapper.pl pepwindow -sequence $input1 -graph png -goutfile $out_file1 -length $length -auto</command>
+  <command interpreter="perl">emboss_single_outputfile_wrapper.pl pepwindow -sequence '$input1' -graph png -goutfile '$out_file1' -length '$length' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequence</label>
diff --git a/tools/emboss_5/emboss_pepwindowall.xml b/tools/emboss_5/emboss_pepwindowall.xml
index a6f4d26398c..582b659d172 100644
--- a/tools/emboss_5/emboss_pepwindowall.xml
+++ b/tools/emboss_5/emboss_pepwindowall.xml
@@ -2,7 +2,7 @@
   <!-- produces png file -->
   <description>Displays protein hydropathy of a set of sequences</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command interpreter="perl">emboss_single_outputfile_wrapper.pl pepwindowall -sequence $input1 -graph png -goutfile $out_file1 -length $length -auto</command>
+  <command interpreter="perl">emboss_single_outputfile_wrapper.pl pepwindowall -sequence '$input1' -graph png -goutfile '$out_file1' -length '$length' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequence</label>
diff --git a/tools/emboss_5/emboss_plotcon.xml b/tools/emboss_5/emboss_plotcon.xml
index 5a44b6bf9d8..2684394e69b 100644
--- a/tools/emboss_5/emboss_plotcon.xml
+++ b/tools/emboss_5/emboss_plotcon.xml
@@ -2,7 +2,7 @@
   <!-- produces png file -->
   <description>Plot quality of conservation of a sequence alignment</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command interpreter="perl">emboss_single_outputfile_wrapper.pl plotcon -sequences $input1 -graph png -goutfile $out_file1 -winsize $winsize -auto</command>
+  <command interpreter="perl">emboss_single_outputfile_wrapper.pl plotcon -sequences '$input1' -graph png -goutfile '$out_file1' -winsize '$winsize' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequence</label>
diff --git a/tools/emboss_5/emboss_plotorf.xml b/tools/emboss_5/emboss_plotorf.xml
index 050c95fb688..ae58c813a94 100644
--- a/tools/emboss_5/emboss_plotorf.xml
+++ b/tools/emboss_5/emboss_plotorf.xml
@@ -2,7 +2,7 @@
   <!-- produces png file output -->
   <description>Plot potential open reading frames</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command interpreter="perl">emboss_single_outputfile_wrapper.pl plotorf -sequence $input1 -graph png -goutfile $out_file1 -start $start -stop $stop -auto</command>
+  <command interpreter="perl">emboss_single_outputfile_wrapper.pl plotorf -sequence '$input1' -graph png -goutfile '$out_file1' -start '$start' -stop '$stop' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>Sequence</label>
diff --git a/tools/emboss_5/emboss_polydot.xml b/tools/emboss_5/emboss_polydot.xml
index 268fa80bb9d..d9de274f4de 100644
--- a/tools/emboss_5/emboss_polydot.xml
+++ b/tools/emboss_5/emboss_polydot.xml
@@ -2,8 +2,8 @@
   <!-- produces png file, not added functional tests -->
   <description>Displays all-against-all dotplots of a set of sequences</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command interpreter="perl">emboss_single_outputfile_wrapper.pl polydot -sequence $input1 -graph png -goutfile $output2 -outfeat $output1 -wordsize $wordsize -boxit $boxit -dumpfeat yes -gap
-  $gap -auto</command>
+  <command interpreter="perl">emboss_single_outputfile_wrapper.pl polydot -sequence '$input1' -graph png -goutfile '$output2' -outfeat '$output1' -wordsize '$wordsize' -boxit '$boxit' -dumpfeat yes -gap
+  '$gap' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>Sequence</label>
diff --git a/tools/emboss_5/emboss_preg.xml b/tools/emboss_5/emboss_preg.xml
index 3e8b479d8da..dc0aa32461a 100644
--- a/tools/emboss_5/emboss_preg.xml
+++ b/tools/emboss_5/emboss_preg.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: preg78" name="preg" version="5.0.0">
   <description>Regular expression search of a protein sequence</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>preg -sequence $input1 -outfile $out_file1 -pattern "$pattern" -auto</command>
+  <command>preg -sequence '$input1' -outfile '$out_file1' -pattern '$pattern' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequence 1</label>
diff --git a/tools/emboss_5/emboss_prettyplot.xml b/tools/emboss_5/emboss_prettyplot.xml
index 3b5a8507653..498b054265b 100644
--- a/tools/emboss_5/emboss_prettyplot.xml
+++ b/tools/emboss_5/emboss_prettyplot.xml
@@ -2,9 +2,9 @@
   <!-- produces png output with file name -->
   <description>Displays aligned sequences, with colouring and boxing</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>prettyplot -sequences $input1 -graph png -goutfile $out_file1 -residuesperline $residuesperline -resbreak $resbreak -ccolours $ccolours -cidentity $cidentity -csimilarity $csimilarity
-  -cother $cother -docolour $docolour -gtitle $title -pair $pair -identity $identity -box $box -boxcol $boxcol -boxcolval $boxcolval -name $name -maxnamelen $maxnamelen -number $number -listoptions
-  $listoptions -consensus $consensus -collision $collision -alternative $alternative -showscore $showscore -portrait $portrait -auto</command>
+  <command>prettyplot -sequences '$input1' -graph png -goutfile '$out_file1' -residuesperline '$residuesperline' -resbreak '$resbreak' -ccolours '$ccolours' -cidentity '$cidentity' -csimilarity '$csimilarity'
+  -cother '$cother' -docolour '$docolour' -gtitle '$title' -pair '$pair' -identity '$identity' -box '$box' -boxcol '$box'col -boxcolval '$box'colval -name '$name' -maxnamelen '$maxnamelen' -number '$number' -listoptions
+  '$listoptions' -consensus '$consensus' -collision '$collision' -alternative '$alternative' -showscore '$showscore' -portrait '$portrait' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequence</label>
diff --git a/tools/emboss_5/emboss_prettyseq.xml b/tools/emboss_5/emboss_prettyseq.xml
index e1d59c9147c..247d448fa86 100644
--- a/tools/emboss_5/emboss_prettyseq.xml
+++ b/tools/emboss_5/emboss_prettyseq.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: prettyseq80" name="prettyseq" version="5.0.0">
   <description>Output sequence with translated ranges</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>prettyseq -sequence $input1 -outfile $out_file1 -ruler $ruler -plabel $plabel -nlabel $nlabel -width $width -auto</command>
+  <command>prettyseq -sequence '$input1' -outfile '$out_file1' -ruler '$ruler' -plabel '$plabel' -nlabel '$nlabel' -width '$width' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>Sequence</label>
diff --git a/tools/emboss_5/emboss_primersearch.xml b/tools/emboss_5/emboss_primersearch.xml
index 7687eb3dc53..3a28068f5b6 100644
--- a/tools/emboss_5/emboss_primersearch.xml
+++ b/tools/emboss_5/emboss_primersearch.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: primersearch81" name="primersearch" version="5.0.0">
   <description>Searches DNA sequences for matches with primer pairs</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>primersearch -seqall $input1 -infile $input2 -outfile $out_file1 -mismatchpercent $mismatchpercent -auto</command>
+  <command>primersearch -seqall '$input1' -infile '$input2' -outfile '$out_file1' -mismatchpercent '$mismatchpercent' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>Main sequences</label>
diff --git a/tools/emboss_5/emboss_revseq.xml b/tools/emboss_5/emboss_revseq.xml
index eaad8ae383c..485b87915b0 100644
--- a/tools/emboss_5/emboss_revseq.xml
+++ b/tools/emboss_5/emboss_revseq.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: revseq82" name="revseq" version="5.0.0">
   <description>Reverse and complement a sequence</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>revseq -sequence $input1 -outseq $out_file1 -reverse $reverse -complement $complement -osformat2 $out_format1 -auto</command>
+  <command>revseq -sequence '$input1' -outseq '$out_file1' -reverse '$reverse' -complement '$complement' -osformat2 '$out_format1' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>Sequences</label>
diff --git a/tools/emboss_5/emboss_seqmatchall.xml b/tools/emboss_5/emboss_seqmatchall.xml
index a697dcb6162..f265a55a2f0 100644
--- a/tools/emboss_5/emboss_seqmatchall.xml
+++ b/tools/emboss_5/emboss_seqmatchall.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: seqmatchall83" name="seqmatchall" version="5.0.0">
   <description>All-against-all comparison of a set of sequences</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>seqmatchall -sequence $input1 -outfile $out_file1 -wordsize $wordsize -aformat2 $out_format1 -auto</command>
+  <command>seqmatchall -sequence '$input1' -outfile '$out_file1' -wordsize '$wordsize' -aformat2 '$out_format1' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>Sequences</label>
diff --git a/tools/emboss_5/emboss_seqret.xml b/tools/emboss_5/emboss_seqret.xml
index 654603e6b97..f3d93b18b40 100644
--- a/tools/emboss_5/emboss_seqret.xml
+++ b/tools/emboss_5/emboss_seqret.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: seqret84" name="seqret" version="5.0.0">
   <description>Reads and writes sequences</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>seqret -sequence $input1 -outseq $out_file1 -feature $feature -firstonly $firstonly -osformat2 $out_format1 -auto</command>
+  <command>seqret -sequence '$input1' -outseq '$out_file1' -feature '$feature' -firstonly '$firstonly' -osformat2 '$out_format1' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequences</label>
diff --git a/tools/emboss_5/emboss_showfeat.xml b/tools/emboss_5/emboss_showfeat.xml
index 7c9394eefe0..32b93472c29 100644
--- a/tools/emboss_5/emboss_showfeat.xml
+++ b/tools/emboss_5/emboss_showfeat.xml
@@ -2,9 +2,9 @@
   <!-- tool gives memory errors -->
   <description>Show features of a sequence</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>showfeat -sequence $input1 -outfile $out_file1 -matchsource "$matchsource" -matchtype "$matchtype" -matchtag "$matchtag" -matchvalue "$matchvalue" -sort $sort -annotation "$annotation" -id
-  $id -description "$description" -scale "$scale" -width "$width" -collapse $collapse -forward $forward -reverse $reverse -unknown $unknown -strand $strand -source $source -position $position -type
-  $type -tags $tags -values $values -stricttags $stricttags -html $html_out1 -auto</command>
+  <command>showfeat -sequence '$input1' -outfile '$out_file1' -matchsource '$matchsource' -matchtype '$matchtype' -matchtag '$matchtag' -matchvalue '$matchvalue' -sort '$sort' -annotation '$annotation' -id
+  '$id' -description '$description' -scale '$scale' -width '$width' -collapse '$collapse' -forward '$forward' -reverse '$reverse' -unknown '$unknown' -strand '$strand' -source '$source' -position '$position' -type
+  '$type' -tags '$tags' -values '$values' -stricttags '$stricttags' -html '$html_out1' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequences</label>
diff --git a/tools/emboss_5/emboss_shuffleseq.xml b/tools/emboss_5/emboss_shuffleseq.xml
index fb269fb98fa..a7e9f6432ac 100644
--- a/tools/emboss_5/emboss_shuffleseq.xml
+++ b/tools/emboss_5/emboss_shuffleseq.xml
@@ -2,7 +2,7 @@
   <!-- produces random outputs each time -->
   <description>Shuffles a set of sequences maintaining composition</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>shuffleseq -sequence $input1 -outseq $out_file1 -shuffle "$shuffle" -osformat2 $out_format1 -auto</command>
+  <command>shuffleseq -sequence '$input1' -outseq '$out_file1' -shuffle '$shuffle' -osformat2 '$out_format1' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>Sequences</label>
diff --git a/tools/emboss_5/emboss_sigcleave.xml b/tools/emboss_5/emboss_sigcleave.xml
index 5c41976acde..32ade2473a6 100644
--- a/tools/emboss_5/emboss_sigcleave.xml
+++ b/tools/emboss_5/emboss_sigcleave.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: sigcleave88" name="sigcleave" version="5.0.0">
   <description>Reports protein signal cleavage sites</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>sigcleave -sequence $input1 -outfile $out_file1 -minweight "$minweight" -prokaryote $prokaryote -rformat2 $out_format1 -auto</command>
+  <command>sigcleave -sequence '$input1' -outfile '$out_file1' -minweight '$minweight' -prokaryote '$prokaryote' -rformat2 '$out_format1' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequences</label>
diff --git a/tools/emboss_5/emboss_sirna.xml b/tools/emboss_5/emboss_sirna.xml
index 3e0deab97c4..ff643d847ae 100644
--- a/tools/emboss_5/emboss_sirna.xml
+++ b/tools/emboss_5/emboss_sirna.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: sirna89" name="sirna" version="5.0.0">
   <description>Finds siRNA duplexes in mRNA</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>sirna -sequence $input1 -outfile $ofile1 -outseq $ofile2 -poliii $poliii -aa $aa -tt $tt -polybase $polybase -context $context -rformat2 $out_format1 -osformat3 $out_format2
+  <command>sirna -sequence '$input1' -outfile '$ofile1' -outseq '$ofile2' -poliii '$poliii' -aa '$aa' -tt '$tt' -polybase '$polybase' -context '$context' -rformat2 '$out_format1' -osformat3 '$out_format2'
   -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_sixpack.xml b/tools/emboss_5/emboss_sixpack.xml
index 49d3f29c6b6..a0e01bdf335 100644
--- a/tools/emboss_5/emboss_sixpack.xml
+++ b/tools/emboss_5/emboss_sixpack.xml
@@ -2,8 +2,8 @@
   <!-- tool adds file description and timestamp to output data -->
   <description>Display a DNA sequence with 6-frame translation and ORFs</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>sixpack -sequence $input1 -outfile $ofile1 -outseq $ofile2 -table $table -firstorf $firstorf -lastorf $lastorf -mstart $mstart -reverse $reverse -orfminsize $orfminsize -uppercase
-  "$uppercase" -number $number -width "$width" -length "$length" -margin "$margin" -name $disp_name -description $description -offset "$offset" -html $html_out1 -osformat $out_format2 -auto</command>
+  <command>sixpack -sequence '$input1' -outfile '$ofile1' -outseq '$ofile2' -table '$table' -firstorf '$firstorf' -lastorf '$lastorf' -mstart '$mstart' -reverse '$reverse' -orfminsize '$orfminsize' -uppercase
+  '$uppercase' -number '$number' -width '$width' -length '$length' -margin '$margin' -name '$disp_name' -description '$description' -offset '$offset' -html '$html_out1' -osformat '$out_format2' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>Sequences</label>
diff --git a/tools/emboss_5/emboss_skipseq.xml b/tools/emboss_5/emboss_skipseq.xml
index dddc257e20a..80be6a2a6d8 100644
--- a/tools/emboss_5/emboss_skipseq.xml
+++ b/tools/emboss_5/emboss_skipseq.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: skipseq91" name="skipseq" version="5.0.0">
   <description>Reads and writes sequences, skipping first few</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>skipseq -sequence $input1 -outseq $out_file1 -skip "$skip" -feature $feature -osformat2 $out_format1 -auto</command>
+  <command>skipseq -sequence '$input1' -outseq '$out_file1' -skip '$skip' -feature '$feature' -osformat2 '$out_format1' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequences</label>
diff --git a/tools/emboss_5/emboss_splitter.xml b/tools/emboss_5/emboss_splitter.xml
index c46102fe816..a3faaf4e27d 100644
--- a/tools/emboss_5/emboss_splitter.xml
+++ b/tools/emboss_5/emboss_splitter.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: splitter92" name="splitter" version="5.0.0">
   <description>Split a sequence into (overlapping) smaller sequences</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>splitter -sequence $input1 -outseq $out_file1 -size "$size" -overlap "$overlap" -addoverlap $addoverlap -osformat2 $out_format1 -auto</command>
+  <command>splitter -sequence '$input1' -outseq '$out_file1' -size '$size' -overlap '$overlap' -addoverlap '$addoverlap' -osformat2 '$out_format1' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>Sequences</label>
diff --git a/tools/emboss_5/emboss_supermatcher.xml b/tools/emboss_5/emboss_supermatcher.xml
index 5d1ccccd6a7..69a80593c4c 100644
--- a/tools/emboss_5/emboss_supermatcher.xml
+++ b/tools/emboss_5/emboss_supermatcher.xml
@@ -2,8 +2,8 @@
   <!-- puts file information in output report -->
   <description>Match large sequences against one or more other sequences</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>supermatcher -asequence $input1 -bsequence $input2 -gapopen "$gapopen" -gapextend "$gapextend" -width "$width" -wordlen "$wordlen" -outfile $ofile1 -errorfile $ofile2 -aformat3
-  $out_format1 -auto</command>
+  <command>supermatcher -asequence '$input1' -bsequence '$input2' -gapopen '$gapopen' -gapextend '$gapextend' -width '$width' -wordlen '$wordlen' -outfile '$ofile1' -errorfile '$ofile2' -aformat3
+  '$out_format1' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>Large sequences</label>
diff --git a/tools/emboss_5/emboss_syco.xml b/tools/emboss_5/emboss_syco.xml
index e5baaec51a0..15a86b74d6d 100644
--- a/tools/emboss_5/emboss_syco.xml
+++ b/tools/emboss_5/emboss_syco.xml
@@ -2,7 +2,7 @@
   <!-- graphics output -->
   <description>Synonymous codon usage Gribskov statistic plot</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command interpreter="perl">emboss_single_outputfile_wrapper.pl syco -sequence $input1 -graph png -goutfile $ofile1 -outfile $ofile2 -cfile $cfile -window "$window" -uncommon $uncommon -minimum "$minimum"
+  <command interpreter="perl">emboss_single_outputfile_wrapper.pl syco -sequence '$input1' -graph png -goutfile '$ofile1' -outfile '$ofile2' -cfile '$cfile' -window '$window' -uncommon '$uncommon' -minimum '$minimum'
   -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_tcode.xml b/tools/emboss_5/emboss_tcode.xml
index beda491636d..acf8c60c43a 100644
--- a/tools/emboss_5/emboss_tcode.xml
+++ b/tools/emboss_5/emboss_tcode.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: tcode97" name="tcode" version="5.0.0">
   <description>Fickett TESTCODE statistic to identify protein-coding DNA</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>tcode -sequence $input1 -outfile $out_file1 -window "$window" -step "$step" -rformat $out_format1 -auto</command>
+  <command>tcode -sequence '$input1' -outfile '$out_file1' -window '$window' -step '$step' -rformat '$out_format1' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequence</label>
diff --git a/tools/emboss_5/emboss_textsearch.xml b/tools/emboss_5/emboss_textsearch.xml
index 8d7839f50f1..409882c4265 100644
--- a/tools/emboss_5/emboss_textsearch.xml
+++ b/tools/emboss_5/emboss_textsearch.xml
@@ -1,8 +1,8 @@
 <tool id="EMBOSS: textsearch98" name="textsearch" version="5.0.0">
   <description>Search sequence documentation. Slow, use SRS and Entrez!</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>textsearch -sequence $input1 -outfile $out_file1 -pattern "$pattern" -casesensitive -heading $heading -usa $usa -accession $accession -name $search_name -description $description -html
-  $html_out1 -auto</command>
+  <command>textsearch -sequence '$input1' -outfile '$out_file1' -pattern '$pattern' -casesensitive -heading '$heading' -usa '$usa' -accession '$accession' -name '$search_name' -description '$description' -html
+  '$html_out1' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequence</label>
diff --git a/tools/emboss_5/emboss_tmap.xml b/tools/emboss_5/emboss_tmap.xml
index cc775ac1bd5..50abd54308d 100644
--- a/tools/emboss_5/emboss_tmap.xml
+++ b/tools/emboss_5/emboss_tmap.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: tmap99" name="tmap" version="5.0.0">
   <description>Displays membrane spanning regions</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command interpreter="perl">emboss_single_outputfile_wrapper.pl tmap -sequences $input1 -outfile $out_file1 -goutfile $out_file2 -graph png -rformat $out_format1 -auto</command>
+  <command interpreter="perl">emboss_single_outputfile_wrapper.pl tmap -sequences '$input1' -outfile '$out_file1' -goutfile '$out_file2' -graph png -rformat '$out_format1' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequence</label>
diff --git a/tools/emboss_5/emboss_tranalign.xml b/tools/emboss_5/emboss_tranalign.xml
index 5e7411567ce..a0d81a72469 100644
--- a/tools/emboss_5/emboss_tranalign.xml
+++ b/tools/emboss_5/emboss_tranalign.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: tranalign100" name="tranalign" version="5.0.0">
   <description>Align nucleic coding regions given the aligned proteins</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>tranalign -asequence $input1 -bsequence $input2 -outseq $out_file1 -table $table -osformat3 $out_format1 -auto</command>
+  <command>tranalign -asequence '$input1' -bsequence '$input2' -outseq '$out_file1' -table '$table' -osformat3 '$out_format1' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>Nucleic Sequences</label>
diff --git a/tools/emboss_5/emboss_transeq.xml b/tools/emboss_5/emboss_transeq.xml
index eeffcadc320..2fe79d8e5fe 100644
--- a/tools/emboss_5/emboss_transeq.xml
+++ b/tools/emboss_5/emboss_transeq.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: transeq101" name="transeq" version="5.0.0">
   <description>Translate nucleic acid sequences</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>transeq -sequence $input1 -outseq $out_file1 -frame $frame -table $table -regions "$regions" -trim $trim -clean $clean -alternative $alternative -osformat2 $out_format1 -auto</command>
+  <command>transeq -sequence '$input1' -outseq '$out_file1' -frame '$frame' -table '$table' -regions '$regions' -trim '$trim' -clean '$clean' -alternative '$alternative' -osformat2 '$out_format1' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>Sequences</label>
diff --git a/tools/emboss_5/emboss_trimest.xml b/tools/emboss_5/emboss_trimest.xml
index e6349807813..32acfae8987 100644
--- a/tools/emboss_5/emboss_trimest.xml
+++ b/tools/emboss_5/emboss_trimest.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: trimest102" name="trimest" version="5.0.0">
   <description>Trim poly-A tails off EST sequences</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>trimest -sequence $input1 -outseq $out_file1 -minlength "$minlength" -mismatches "$mismatches" -reverse $reverse -tolower $tolower -fiveprime $fiveprime -osformat2 $out_format1
+  <command>trimest -sequence '$input1' -outseq '$out_file1' -minlength '$minlength' -mismatches '$mismatches' -reverse '$reverse' -tolower '$tolower' -fiveprime '$fiveprime' -osformat2 '$out_format1'
   -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_trimseq.xml b/tools/emboss_5/emboss_trimseq.xml
index f9abe94f102..1e303ed985f 100644
--- a/tools/emboss_5/emboss_trimseq.xml
+++ b/tools/emboss_5/emboss_trimseq.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: trimseq103" name="trimseq" version="5.0.0">
   <description>Trim ambiguous bits off the ends of sequences</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>trimseq -sequence $input1 -outseq $out_file1 -window "$window" -percent "$percent" -strict $strict -star $star -left $left -right $right -osformat2 $out_format1 -auto</command>
+  <command>trimseq -sequence '$input1' -outseq '$out_file1' -window '$window' -percent '$percent' -strict '$strict' -star '$star' -left '$left' -right '$right' -osformat2 '$out_format1' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>Sequences</label>
diff --git a/tools/emboss_5/emboss_twofeat.xml b/tools/emboss_5/emboss_twofeat.xml
index 6ddf2057761..55159068d8e 100644
--- a/tools/emboss_5/emboss_twofeat.xml
+++ b/tools/emboss_5/emboss_twofeat.xml
@@ -1,9 +1,9 @@
 <tool id="EMBOSS: twofeat104" name="twofeat" version="5.0.0">
   <description>Finds neighbouring pairs of features in sequences</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>twofeat -sequence $input1 -outfile $out_file1 -atype "$atype" -btype "$btype" -minrange "$minrange" -maxrange "$maxrange" -asource "$asource" -asense $asense -aminscore "$aminscore"
-  -amaxscore "$amaxscore" -atag "$atag" -avalue "$avalue" -bsource "$bsource" -bsense "$bsense" -bminscore "$bminscore" -bmaxscore "$bmaxscore" -btag "$btag" -bvalue "$bvalue" -overlap $overlap
-  -rangetype $rangetype -sense $sense -order $order -twoout $twoout -typeout "$typeout" -rformat2 $out_format1 -auto</command>
+  <command>twofeat -sequence '$input1' -outfile '$out_file1' -atype '$atype' -btype '$btype' -minrange '$minrange' -maxrange '$maxrange' -asource '$asource' -asense '$asense' -aminscore '$aminscore'
+  -amaxscore '$amaxscore' -atag '$atag' -avalue '$avalue' -bsource '$bsource' -bsense '$bsense' -bminscore '$bminscore' -bmaxscore '$bmaxscore' -btag '$btag' -bvalue '$bvalue' -overlap '$overlap'
+  -rangetype '$rangetype' -sense '$sense' -order '$order' -twoout '$twoout' -typeout '$typeout' -rformat2 '$out_format1' -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
       <label>Sequences</label>
diff --git a/tools/emboss_5/emboss_union.xml b/tools/emboss_5/emboss_union.xml
index ffac0550066..d5893f01655 100644
--- a/tools/emboss_5/emboss_union.xml
+++ b/tools/emboss_5/emboss_union.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: union105" name="union" version="5.0.0">
   <description>Reads sequence fragments and builds one sequence</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>union -sequence $input1 -outseq $out_file1 -osformat2 $out_format1 -auto</command>
+  <command>union -sequence '$input1' -outseq '$out_file1' -osformat2 '$out_format1' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>Sequences</label>
diff --git a/tools/emboss_5/emboss_vectorstrip.xml b/tools/emboss_5/emboss_vectorstrip.xml
index 37be239ea82..b0df0e6e399 100644
--- a/tools/emboss_5/emboss_vectorstrip.xml
+++ b/tools/emboss_5/emboss_vectorstrip.xml
@@ -1,8 +1,8 @@
 <tool id="EMBOSS: vectorstrip106" name="vectorstrip" version="5.0.0">
   <description>Strips out DNA between a pair of vector sequences</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>vectorstrip -sequence $input1 -vectorsfile $input2 -outseq $ofile1 -outfile $ofile2 -vectorfile yes -mismatch "$mismatch" -besthits $besthits -linkera "$linkera" -linkerb
-  "$linkerb" -osformat4 $out_format1 -auto</command>
+  <command>vectorstrip -sequence '$input1' -vectorsfile '$input2' -outseq '$ofile1' -outfile '$ofile2' -vectorfile yes -mismatch '$mismatch' -besthits '$besthits' -linkera '$linkera' -linkerb
+  '$linkerb' -osformat4 '$out_format1' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>Sequences</label>
diff --git a/tools/emboss_5/emboss_water.xml b/tools/emboss_5/emboss_water.xml
index eeea0953ffe..33615d147b5 100644
--- a/tools/emboss_5/emboss_water.xml
+++ b/tools/emboss_5/emboss_water.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: water107" name="water" version="5.0.0">
   <description>Smith-Waterman local alignment</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>water -asequence $input1 -bsequence $input2 -outfile $out_file1 -gapopen "$gapopen" -gapextend "$gapextend" -brief $brief -aformat3 $out_format1 -auto</command>
+  <command>water -asequence '$input1' -bsequence '$input2' -outfile '$out_file1' -gapopen '$gapopen' -gapextend '$gapextend' -brief '$brief' -aformat3 '$out_format1' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>Sequence 1</label>
diff --git a/tools/emboss_5/emboss_wobble.xml b/tools/emboss_5/emboss_wobble.xml
index e7050ade0e3..952eae14d84 100644
--- a/tools/emboss_5/emboss_wobble.xml
+++ b/tools/emboss_5/emboss_wobble.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: wobble108" name="wobble" version="5.0.0">
   <description>Wobble base plot</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command interpreter="perl">emboss_single_outputfile_wrapper.pl wobble -sequence $input1 -graph png -goutfile $ofile1 -outfile $ofile2 -window "$window" -bases "$bases" -auto</command>
+  <command interpreter="perl">emboss_single_outputfile_wrapper.pl wobble -sequence '$input1' -graph png -goutfile '$ofile1' -outfile '$ofile2' -window '$window' -bases '$bases' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>Sequence</label>
diff --git a/tools/emboss_5/emboss_wordcount.xml b/tools/emboss_5/emboss_wordcount.xml
index 7ad5af4dfe8..f60569b8907 100644
--- a/tools/emboss_5/emboss_wordcount.xml
+++ b/tools/emboss_5/emboss_wordcount.xml
@@ -1,7 +1,7 @@
 <tool id="EMBOSS: wordcount109" name="wordcount" version="5.0.0">
   <description>Counts words of a specified size in a DNA sequence</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>wordcount -sequence $input1 -outfile $out_file1 -wordsize "$wordsize" -auto</command>
+  <command>wordcount -sequence '$input1' -outfile '$out_file1' -wordsize '$wordsize' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>Sequence</label>
diff --git a/tools/emboss_5/emboss_wordmatch.xml b/tools/emboss_5/emboss_wordmatch.xml
index e6cc78c8ba6..ecef3835fcd 100644
--- a/tools/emboss_5/emboss_wordmatch.xml
+++ b/tools/emboss_5/emboss_wordmatch.xml
@@ -1,8 +1,8 @@
 <tool id="EMBOSS: wordmatch110" name="wordmatch" version="5.0.0">
   <description>Finds all exact matches of a given size between 2 sequences</description>
   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>wordmatch -asequence $input1 -bsequence $input2 -outfile $out_file1 -aoutfeat $out_file2 -boutfeat $out_file3 -wordsize "$wordsize" -aformat3 $out_format1 -offormat4 $out_format2
-  -offormat5 $out_format3 -auto</command>
+  <command>wordmatch -asequence '$input1' -bsequence '$input2' -outfile '$out_file1' -aoutfeat '$out_file2' -boutfeat '$out_file3' -wordsize '$wordsize' -aformat3 '$out_format1' -offormat4 '$out_format2'
+  -offormat5 '$out_format3' -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
       <label>Sequence 1</label>

From b417023e9de7bfea906e6928933b1c08b241d9a5 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Thu, 8 Dec 2011 11:44:22 -0500
Subject: [PATCH 307/362] Escape backslashes and quotes in name attributes for
 UCSC external display applications which use bigDataUrls. Remove no longer
 required strip_https attribute. Resolves #627.

---
 display_applications/ucsc/bam.xml    | 6 +++---
 display_applications/ucsc/bigbed.xml | 4 ++--
 display_applications/ucsc/bigwig.xml | 4 ++--
 3 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/display_applications/ucsc/bam.xml b/display_applications/ucsc/bam.xml
index da9183a35c9..89e57598a0b 100644
--- a/display_applications/ucsc/bam.xml
+++ b/display_applications/ucsc/bam.xml
@@ -10,8 +10,8 @@
         <filter>${dataset.dbkey in $builds}</filter>
         <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
         <url>${ucsc_link}db=${qp($bam_file.dbkey)}&amp;hgt.customText=${qp($track.url)}</url>
-        <param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" strip_https="True" />
-        <param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" strip_https="True" /><!-- UCSC expects index file to exist as bam_file_name.bai -->
-        <param type="template" name="track" viewable="True" strip_https="True">track type=bam name="${bam_file.name}" bigDataUrl=${bam_file.url} db=${bam_file.dbkey}</param>
+        <param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" />
+        <param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" /><!-- UCSC expects index file to exist as bam_file_name.bai -->
+        <param type="template" name="track" viewable="True">track type="bam" name="${bam_file.name.replace( '\\', '\\\\' ).replace( '"', '\\"' )}" bigDataUrl="${bam_file.url}" db="${bam_file.dbkey}"</param>
     </dynamic_links>
 </display>
diff --git a/display_applications/ucsc/bigbed.xml b/display_applications/ucsc/bigbed.xml
index 21e08d0d9b9..59397182c6a 100644
--- a/display_applications/ucsc/bigbed.xml
+++ b/display_applications/ucsc/bigbed.xml
@@ -10,7 +10,7 @@
         <filter>${dataset.dbkey in $builds}</filter>
         <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
         <url>${ucsc_link}db=${qp($bigbed_file.dbkey)}&amp;hgt.customText=${qp($track.url)}</url>
-        <param type="data" name="bigbed_file" url="galaxy_${DATASET_HASH}.bigbed" strip_https="True" />
-        <param type="template" name="track" viewable="True" strip_https="True">track type=bigBed name="${bigbed_file.name}" bigDataUrl=${bigbed_file.url} db=${bigbed_file.dbkey}</param>
+        <param type="data" name="bigbed_file" url="galaxy_${DATASET_HASH}.bigbed" />
+        <param type="template" name="track" viewable="True">track type="bigBed" name="${bigbed_file.name.replace( '\\', '\\\\' ).replace( '"', '\\"' )}" bigDataUrl="${bigbed_file.url}" db="${bigbed_file.dbkey}"</param>
     </dynamic_links>
 </display>
diff --git a/display_applications/ucsc/bigwig.xml b/display_applications/ucsc/bigwig.xml
index e3a5f5b291a..fcb5bad369b 100644
--- a/display_applications/ucsc/bigwig.xml
+++ b/display_applications/ucsc/bigwig.xml
@@ -10,7 +10,7 @@
         <filter>${dataset.dbkey in $builds}</filter>
         <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
         <url>${ucsc_link}db=${qp($bigwig_file.dbkey)}&amp;hgt.customText=${qp($track.url)}</url>
-        <param type="data" name="bigwig_file" url="galaxy_${DATASET_HASH}.bigwig" strip_https="True" />
-        <param type="template" name="track" viewable="True" strip_https="True">track type=bigWig name="${bigwig_file.name}" bigDataUrl=${bigwig_file.url} db=${bigwig_file.dbkey}</param>
+        <param type="data" name="bigwig_file" url="galaxy_${DATASET_HASH}.bigwig" />
+        <param type="template" name="track" viewable="True">track type="bigWig" name="${bigwig_file.name.replace( '\\', '\\\\' ).replace( '"', '\\"' )}" bigDataUrl="${bigwig_file.url}" db="${bigwig_file.dbkey}"</param>
     </dynamic_links>
 </display>

From f78ae0ce62e671e2ac66c281663f713c5b5b5b0a Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Thu, 8 Dec 2011 11:49:52 -0500
Subject: [PATCH 308/362] Do not allow public user names to be changed within
 the tool shed if the user has created a tool shed repository.

---
 templates/user/info.mako     | 28 ++++++++++++++++++++++------
 templates/user/register.mako | 19 ++++++++++++++-----
 2 files changed, 36 insertions(+), 11 deletions(-)

diff --git a/templates/user/info.mako b/templates/user/info.mako
index aa9203a31a6..1c1b39096ea 100644
--- a/templates/user/info.mako
+++ b/templates/user/info.mako
@@ -21,12 +21,28 @@
             </div>
             <div class="form-row">
                 <label>Public name:</label>
-                <input type="text" name="username" size="40" value="${username}"/>
-                <div class="toolParamHelp" style="clear: both;">
-                    Your public name is an optional identifier that will be used to generate addresses for information
-                    you share publicly. Public names must be at least four characters in length and contain only lower-case
-                    letters, numbers, and the '-' character.
-                </div>
+                %if webapp == 'community':
+                    ${username}
+                    %if user.active_repositories:
+                        <div class="toolParamHelp" style="clear: both;">
+                            You cannot change your public name after you have created a repository in this tool shed.
+                        </div>
+                    %else:
+                        <div class="toolParamHelp" style="clear: both;">
+                            Your public name provides a means of identifying you publicly within this tool shed. Public
+                            names must be at least four characters in length and contain only lower-case letters, numbers,
+                            and the '-' character.  You cannot change your public name after you have created a repository
+                            in this tool shed.
+                        </div>
+                    %endif
+                %else:
+                    <input type="text" name="username" size="40" value="${username}"/>
+                    <div class="toolParamHelp" style="clear: both;">
+                        Your public name is an optional identifier that will be used to generate addresses for information
+                        you share publicly. Public names must be at least four characters in length and contain only lower-case
+                        letters, numbers, and the '-' character.
+                    </div>
+                %endif
             </div>
             <div class="form-row">
                 <input type="submit" name="login_info_button" value="Save"/>
diff --git a/templates/user/register.mako b/templates/user/register.mako
index 8b49ed559ce..c98c729c0aa 100644
--- a/templates/user/register.mako
+++ b/templates/user/register.mako
@@ -50,11 +50,20 @@
             <div class="form-row">
                 <label>Public name:</label>
                 <input type="text" name="username" size="40" value="${username}"/>
-                <div class="toolParamHelp" style="clear: both;">
-                    Your public name is an identifier that will be used to generate addresses for information
-                    you share publicly. Public names must be at least four characters in length and contain only lower-case
-                    letters, numbers, and the '-' character.
-                </div>
+                %if webapp == 'galaxy':
+                    <div class="toolParamHelp" style="clear: both;">
+                        Your public name is an identifier that will be used to generate addresses for information
+                        you share publicly. Public names must be at least four characters in length and contain only lower-case
+                        letters, numbers, and the '-' character.
+                    </div>
+                %else:
+                    <div class="toolParamHelp" style="clear: both;">
+                        Your public name provides a means of identifying you publicly within this tool shed. Public
+                        names must be at least four characters in length and contain only lower-case letters, numbers,
+                        and the '-' character.  You cannot change your public name after you have created a repository
+                        in this tool shed.
+                    </div>
+                %endif
             </div>
             %if trans.app.config.smtp_server:
                 <div class="form-row">

From d75bac750b9da309c69a6d8dae87926c03077a10 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 8 Dec 2011 12:08:53 -0500
Subject: [PATCH 309/362] Email action on job failure, resolves bb issue #600. 
 Fail/cleanup logic condensation.

---
 lib/galaxy/jobs/__init__.py | 23 ++++++++++-------------
 1 file changed, 10 insertions(+), 13 deletions(-)

diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 988d7d956a8..3b7563831ed 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -443,7 +443,7 @@ class JobWrapper( object ):
         job = self.get_job()
         self.sa_session.refresh( job )
         # if the job was deleted, don't fail it
-        if not job.state == model.Job.states.DELETED:
+        if not job.state == job.states.DELETED:
             # Check if the failure is due to an exception
             if exception:
                 # Save the traceback immediately in case we generate another
@@ -474,15 +474,18 @@ class JobWrapper( object ):
                     dataset.extension = 'data'
                 self.sa_session.add( dataset )
                 self.sa_session.flush()
-            job.state = model.Job.states.ERROR
+            job.state = job.states.ERROR
             job.command_line = self.command_line
             job.info = message
             self.sa_session.add( job )
             self.sa_session.flush()
+        #Perform email action even on failure.
+        for pja in [x for x in job.post_job_actions if x.action_type == "EmailAction"]:
+            ActionBox.execute(self.app, self.sa_session, pja.post_job_action, job)
         # If the job was deleted, call tool specific fail actions (used for e.g. external metadata) and clean up
         if self.tool:
             self.tool.job_failed( self, message, exception )
-        if self.app.config.cleanup_job == 'always':
+        if self.app.cleanup_job == 'always' or (self.app.config.cleanup_job == 'onsuccess' and job.state == job.states.DELETED):
             self.cleanup()
 
     def change_state( self, state, info = False ):
@@ -525,14 +528,9 @@ class JobWrapper( object ):
         self.sa_session.expunge_all()
         job = self.get_job()
         # if the job was deleted, don't finish it
-        if job.state == job.states.DELETED:
-            if self.app.config.cleanup_job in ( 'always', 'onsuccess' ):
-                self.cleanup()
-            return
-        elif job.state == job.states.ERROR:
-            # Job was deleted by an administrator
-            self.fail( job.info )
-            return
+        if job.state == job.states.DELETED or job.state == job.states.ERROR:
+            #ERROR at this point means the job was deleted by an administrator.
+            return self.fail( job.info )
         if stderr:
             job.state = job.states.ERROR
         else:
@@ -555,8 +553,7 @@ class JobWrapper( object ):
                     if os.path.exists( dataset_path.real_path ) and os.stat( dataset_path.real_path ).st_size > 0:
                         log.warning( "finish(): %s not found, but %s is not empty, so it will be used instead" % ( dataset_path.false_path, dataset_path.real_path ) )
                     else:
-                        self.fail( "Job %s's output dataset(s) could not be read" % job.id )
-                        return
+                        return self.fail( "Job %s's output dataset(s) could not be read" % job.id )
         job_context = ExpressionContext( dict( stdout = stdout, stderr = stderr ) )
         job_tool = self.app.toolbox.tools_by_id.get( job.tool_id, None )
         def in_directory( file, directory ):

From 5bd73b2bf248f014b5ebd7638e2d422dc5a44f70 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Thu, 8 Dec 2011 14:26:34 -0500
Subject: [PATCH 310/362] Allow tools with zero inputs. Resolves #463.

---
 lib/galaxy/tools/__init__.py  | 53 ++++++++++++++++++++---------------
 templates/root/tool_menu.mako |  2 +-
 2 files changed, 32 insertions(+), 23 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 3894bcc7f09..3d2f6b2a07b 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -386,6 +386,16 @@ class Tool:
         self.config_file = config_file
         self.tool_dir = os.path.dirname( config_file )
         self.app = app
+        #setup initial attribute values
+        self.inputs = odict()
+        self.inputs_by_page = list()
+        self.display_by_page = list()
+        self.action = '/tool_runner/index'
+        self.target = 'galaxy_main'
+        self.method = 'post'
+        self.check_values = True
+        self.nginx_upload = False
+        self.input_required = False
         # Define a place to keep track of all input parameters.  These
         # differ from the inputs dictionary in that inputs can be page
         # elements like conditionals, but input_params are basic form
@@ -565,11 +575,12 @@ class Tool:
         """
         # Load parameters (optional)
         input_elem = root.find("inputs")
+        enctypes = set()
         if input_elem:
             # Handle properties of the input form
-            self.check_values = util.string_as_bool( input_elem.get("check_values", "true") )
-            self.nginx_upload = util.string_as_bool( input_elem.get( "nginx_upload", "false" ) )
-            self.action = input_elem.get( 'action', '/tool_runner/index' )
+            self.check_values = util.string_as_bool( input_elem.get("check_values", self.check_values ) )
+            self.nginx_upload = util.string_as_bool( input_elem.get( "nginx_upload", self.nginx_upload ) )
+            self.action = input_elem.get( 'action', self.action )
             # If we have an nginx upload, save the action as a tuple instead of
             # a string. The actual action needs to get url_for run to add any
             # prefixes, and we want to avoid adding the prefix to the
@@ -582,13 +593,9 @@ class Tool:
                                      'hidden POST parameters' )
                 self.action = (self.app.config.nginx_upload_path + '?nginx_redir=',
                         urllib.unquote_plus(self.action))
-            self.target = input_elem.get( "target", "galaxy_main" )
-            self.method = input_elem.get( "method", "post" )
+            self.target = input_elem.get( "target", self.target )
+            self.method = input_elem.get( "method", self.method )
             # Parse the actual parameters
-            self.inputs = odict()
-            self.inputs_by_page = list()
-            self.display_by_page = list()
-            enctypes = set()
             # Handle multiple page case
             pages = input_elem.findall( "page" )
             for page in ( pages or [ input_elem ] ):
@@ -596,22 +603,24 @@ class Tool:
                 self.inputs_by_page.append( inputs )
                 self.inputs.update( inputs )
                 self.display_by_page.append( display )
-            self.display = self.display_by_page[0]
-            self.npages = len( self.inputs_by_page )
-            self.last_page = len( self.inputs_by_page ) - 1
-            self.has_multiple_pages = bool( self.last_page )
-            # Determine the needed enctype for the form
-            if len( enctypes ) == 0:
-                self.enctype = "application/x-www-form-urlencoded"
-            elif len( enctypes ) == 1:
-                self.enctype = enctypes.pop()
-            else:
-                raise Exception, "Conflicting required enctypes: %s" % str( enctypes )
+        else:
+            self.inputs_by_page.append( self.inputs )
+            self.display_by_page.append( None )
+        self.display = self.display_by_page[0]
+        self.npages = len( self.inputs_by_page )
+        self.last_page = len( self.inputs_by_page ) - 1
+        self.has_multiple_pages = bool( self.last_page )
+        # Determine the needed enctype for the form
+        if len( enctypes ) == 0:
+            self.enctype = "application/x-www-form-urlencoded"
+        elif len( enctypes ) == 1:
+            self.enctype = enctypes.pop()
+        else:
+            raise Exception, "Conflicting required enctypes: %s" % str( enctypes )
         # Check if the tool either has no parameters or only hidden (and
         # thus hardcoded) parameters. FIXME: hidden parameters aren't
         # parameters at all really, and should be passed in a different
         # way, making this check easier.
-        self.input_required = False
         for param in self.inputs.values():
             if not isinstance( param, ( HiddenToolParameter, BaseURLToolParameter ) ):
                 self.input_required = True
@@ -943,7 +952,7 @@ class Tool:
             return False
         # This is probably the best bet for detecting external web tools
         # right now
-        if self.action != "/tool_runner/index":
+        if self.tool_type.startswith( 'data_source' ):
             return False
         # HACK: upload is (as always) a special case becuase file parameters
         #       can't be persisted.
diff --git a/templates/root/tool_menu.mako b/templates/root/tool_menu.mako
index 7963666f649..220fb0c8522 100644
--- a/templates/root/tool_menu.mako
+++ b/templates/root/tool_menu.mako
@@ -13,7 +13,7 @@
             <div class="toolTitleNoSection">
         %endif
             <%
-                if tool.input_required:
+                if not tool.tool_type.startswith( 'data_source' ):
                     link = h.url_for( controller='tool_runner', tool_id=tool.id )
                 else:
                     link = h.url_for( tool.action, ** tool.get_static_param_values( t ) )

From 5e96e67f1d36e6ec5433a94d2c05d0a63ea6ee14 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Thu, 8 Dec 2011 16:10:18 -0500
Subject: [PATCH 311/362] Hierarchical object store sample config and
 functional test capability.

---
 hierarchical_object_store_conf.xml.sample | 13 +++++++++++++
 scripts/functional_tests.py               |  5 +++++
 2 files changed, 18 insertions(+)
 create mode 100644 hierarchical_object_store_conf.xml.sample

diff --git a/hierarchical_object_store_conf.xml.sample b/hierarchical_object_store_conf.xml.sample
new file mode 100644
index 00000000000..38e61944a9f
--- /dev/null
+++ b/hierarchical_object_store_conf.xml.sample
@@ -0,0 +1,13 @@
+<?xml version="1.0"?>
+<backends>
+    <backend name="files1" type="disk" weight="1">
+        <files_dir path="database/files1"/>
+        <extra_dir type="temp" path="database/tmp1"/>
+        <extra_dir type="job_work" path="database/job_working_directory1"/>
+    </backend>
+    <backend name="files2" type="disk" weight="1">
+        <files_dir path="database/files2"/>
+        <extra_dir type="temp" path="database/tmp2"/>
+        <extra_dir type="job_work" path="database/job_working_directory2"/>
+    </backend>
+</backends>
diff --git a/scripts/functional_tests.py b/scripts/functional_tests.py
index 66f2ad682f6..1931a4eebb2 100644
--- a/scripts/functional_tests.py
+++ b/scripts/functional_tests.py
@@ -59,6 +59,7 @@ def main():
     tool_config_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', 'tool_conf.xml.sample' )
     tool_data_table_config_path = 'tool_data_table_conf.xml'
     tool_dependency_dir = os.environ.get( 'GALAXY_TOOL_DEPENDENCY_DIR', None )
+    use_hierarchical_object_store = os.environ.get( 'GALAXY_USE_HIERARCHICAL_OBJECT_STORE', False )
     if os.path.exists( 'tool_data_table_conf.test.xml' ):
         tool_data_table_config_path = 'tool_data_table_conf.test.xml'
     if start_server:
@@ -153,6 +154,10 @@ def main():
         if tool_dependency_dir is not None:
             kwargs['tool_dependency_dir'] = tool_dependency_dir
 
+        if use_hierarchical_object_store:
+            kwargs['object_store'] = 'hierarchical'
+            kwargs['hierarchical_object_store_config_file'] = 'hierarchical_object_store_conf.xml.sample'
+
         # Build the Universe Application
         app = UniverseApplication( job_queue_workers = 5,
                                    id_secret = 'changethisinproductiontoo',

From 355f22860f1882e0261c005bfd3747a427074850 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Thu, 8 Dec 2011 16:25:08 -0500
Subject: [PATCH 312/362] UCSC BAM display will now pass the pairEndsByName
 attribute. Closes #455.

---
 display_applications/ucsc/bam.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/display_applications/ucsc/bam.xml b/display_applications/ucsc/bam.xml
index 89e57598a0b..4031e318237 100644
--- a/display_applications/ucsc/bam.xml
+++ b/display_applications/ucsc/bam.xml
@@ -12,6 +12,6 @@
         <url>${ucsc_link}db=${qp($bam_file.dbkey)}&amp;hgt.customText=${qp($track.url)}</url>
         <param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" />
         <param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" /><!-- UCSC expects index file to exist as bam_file_name.bai -->
-        <param type="template" name="track" viewable="True">track type="bam" name="${bam_file.name.replace( '\\', '\\\\' ).replace( '"', '\\"' )}" bigDataUrl="${bam_file.url}" db="${bam_file.dbkey}"</param>
+        <param type="template" name="track" viewable="True">track type="bam" name="${bam_file.name.replace( '\\', '\\\\' ).replace( '"', '\\"' )}" bigDataUrl="${bam_file.url}" db="${bam_file.dbkey}" pairEndsByName="."</param>
     </dynamic_links>
 </display>

From b8a640852e1859742c84a6272f5970464a8d8f0e Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Thu, 8 Dec 2011 16:26:34 -0500
Subject: [PATCH 313/362] Add a new installation process for managing tools
 that we will remove from the distribution over time and host in the main
 Galaxy tool shed.  This process will execute when the Galaxy server is
 started if enabled in the configuration (which should not happen until users
 running local Galaxy instances are notified).

A new tool_id_guid_map table will be populated for each installed tool.  This will enable backward compatibility for workflows that were build using tools from the current Galaxy distribution but will be installed from a tool shed in the future.
---
 lib/galaxy/app.py                             |   5 +
 lib/galaxy/config.py                          |   5 +-
 lib/galaxy/model/__init__.py                  |  11 +
 lib/galaxy/model/mapping.py                   |  13 +
 .../versions/0087_tool_id_guid_map_table.py   |  51 ++
 lib/galaxy/tools/install_manager.py           | 239 ++++++
 lib/galaxy/web/base/controller.py             |  21 +-
 lib/galaxy/web/controllers/admin_toolshed.py  | 732 +++++++++---------
 .../webapps/community/controllers/common.py   |   4 +-
 .../webapps/community/controllers/upload.py   |   6 +-
 templates/user/info.mako                      |   4 +-
 tool_shed_install.xml.sample                  | 114 +++
 universe_wsgi.ini.sample                      |  16 +
 13 files changed, 850 insertions(+), 371 deletions(-)
 create mode 100644 lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py
 create mode 100644 lib/galaxy/tools/install_manager.py
 create mode 100644 tool_shed_install.xml.sample

diff --git a/lib/galaxy/app.py b/lib/galaxy/app.py
index e58102d99d5..21a432f29b4 100644
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -54,6 +54,11 @@ class UniverseApplication( object ):
         self.toolbox = tools.ToolBox( self.config.tool_configs, self.config.tool_path, self )
         # Search support for tools
         self.toolbox_search = galaxy.tools.search.ToolBoxSearch( self.toolbox )
+        # If enabled, check for tools missing from the distribution because they
+        # have been moved to the tool shed and install all such discovered tools.
+        if self.config.get_bool( 'enable_tool_shed_install', False ):
+            from tools import install_manager
+            self.install_manager = install_manager.InstallManager( self, self.config.tool_shed_install_config, self.config.install_tool_config )
         # Load datatype converters
         self.datatypes_registry.load_datatype_converters( self.toolbox )
         # Load history import/export tools
diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py
index 05f22990f81..53f955e7c0b 100644
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -47,11 +47,14 @@ class Configuration( object ):
         self.enable_openid = string_as_bool( kwargs.get( 'enable_openid', False ) )
         self.enable_quotas = string_as_bool( kwargs.get( 'enable_quotas', False ) )
         self.tool_sheds_config = kwargs.get( 'tool_sheds_config_file', 'tool_sheds_conf.xml' )
-        self.enable_unique_workflow_defaults = string_as_bool ( kwargs.get ('enable_unique_workflow_defaults', False ) )
+        self.enable_unique_workflow_defaults = string_as_bool( kwargs.get ( 'enable_unique_workflow_defaults', False ) )
         self.tool_path = resolve_path( kwargs.get( "tool_path", "tools" ), self.root )
         self.tool_data_path = resolve_path( kwargs.get( "tool_data_path", "tool-data" ), os.getcwd() )
         self.len_file_path = kwargs.get( "len_file_path", resolve_path(os.path.join(self.tool_data_path, 'shared','ucsc','chrom'), self.root) )
         self.test_conf = resolve_path( kwargs.get( "test_conf", "" ), self.root )
+        self.enable_tool_shed_install = string_as_bool( kwargs.get ( 'enable_tool_shed_install', False ) )
+        self.tool_shed_install_config = resolve_path( kwargs.get( "tool_shed_install_config_file", "tool_shed_install.xml" ), self.root )
+        self.install_tool_config = resolve_path( kwargs.get( "install_tool_config_file", "shed_tool_conf.xml" ), self.root )
         if 'tool_config_file' in kwargs:
             tcf = kwargs[ 'tool_config_file' ]
         elif 'tool_config_files' in kwargs:
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 24834c2ed67..3e2546ee8a8 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -2678,6 +2678,17 @@ class ToolShedRepository( object ):
         self.update_available = update_available
         self.deleted = deleted
 
+class ToolIdGuidMap( object ):
+    def __init__( self, id=None, create_time=None, tool_id=None, tool_version=None, tool_shed=None, repository_owner=None, repository_name=None, guid=None ):
+        self.id = id
+        self.create_time = create_time
+        self.tool_id = tool_id
+        self.tool_version = tool_version
+        self.tool_shed = tool_shed
+        self.repository_owner = repository_owner
+        self.repository_name = repository_name
+        self.guid = guid
+
 ## ---- Utility methods -------------------------------------------------------
 
 def directory_hash_id( id ):
diff --git a/lib/galaxy/model/mapping.py b/lib/galaxy/model/mapping.py
index a19a5288dbe..ec7ded8e2b9 100644
--- a/lib/galaxy/model/mapping.py
+++ b/lib/galaxy/model/mapping.py
@@ -378,6 +378,17 @@ ToolShedRepository.table = Table( "tool_shed_repository", metadata,
     Column( "update_available", Boolean, default=False ),
     Column( "deleted", Boolean, index=True, default=False ) )
 
+ToolIdGuidMap.table = Table( "tool_id_guid_map", metadata,
+    Column( "id", Integer, primary_key=True ),
+    Column( "create_time", DateTime, default=now ),
+    Column( "update_time", DateTime, default=now, onupdate=now ),
+    Column( "tool_id", String( 255 ) ),
+    Column( "tool_version", TEXT ),
+    Column( "tool_shed", TrimmedString( 255 ) ),
+    Column( "repository_owner", TrimmedString( 255 ) ),
+    Column( "repository_name", TrimmedString( 255 ) ),
+    Column( "guid", TEXT, index=True, unique=True ) )
+
 Job.table = Table( "job", metadata,
     Column( "id", Integer, primary_key=True ),
     Column( "create_time", DateTime, default=now ),
@@ -1604,6 +1615,8 @@ assign_mapper( context, Page, Page.table,
                    
 assign_mapper( context, ToolShedRepository, ToolShedRepository.table )
 
+assign_mapper( context, ToolIdGuidMap, ToolIdGuidMap.table )
+
 # Set up proxy so that 
 #   Page.users_shared_with
 # returns a list of users that page is shared with.
diff --git a/lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py b/lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py
new file mode 100644
index 00000000000..f1480023af4
--- /dev/null
+++ b/lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py
@@ -0,0 +1,51 @@
+"""
+Migration script to create the tool_id_guid_map table.
+"""
+
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+from migrate.changeset import *
+
+import datetime
+now = datetime.datetime.utcnow
+# Need our custom types, but don't import anything else from model
+from galaxy.model.custom_types import *
+
+import sys, logging
+log = logging.getLogger( __name__ )
+log.setLevel(logging.DEBUG)
+handler = logging.StreamHandler( sys.stdout )
+format = "%(name)s %(levelname)s %(asctime)s %(message)s"
+formatter = logging.Formatter( format )
+handler.setFormatter( formatter )
+log.addHandler( handler )
+
+metadata = MetaData( migrate_engine )
+db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) )
+
+ToolIdGuidMap_table = Table( "tool_id_guid_map", metadata,
+    Column( "id", Integer, primary_key=True ),
+    Column( "create_time", DateTime, default=now ),
+    Column( "update_time", DateTime, default=now, onupdate=now ),
+    Column( "tool_id", String( 255 ) ),
+    Column( "tool_version", TEXT ),
+    Column( "tool_shed", TrimmedString( 255 ) ),
+    Column( "repository_owner", TrimmedString( 255 ) ),
+    Column( "repository_name", TrimmedString( 255 ) ),
+    Column( "guid", TEXT, index=True, unique=True ) )
+
+def upgrade():
+    print __doc__
+    metadata.reflect()
+    try:
+        ToolIdGuidMap_table.create()
+    except Exception, e:
+        log.debug( "Creating tool_id_guid_map table failed: %s" % str( e ) )
+        
+def downgrade():
+    metadata.reflect()
+    try:
+        ToolIdGuidMap_table.drop()
+    except Exception, e:
+        log.debug( "Dropping tool_id_guid_map table failed: %s" % str( e ) )
diff --git a/lib/galaxy/tools/install_manager.py b/lib/galaxy/tools/install_manager.py
new file mode 100644
index 00000000000..7c067182d85
--- /dev/null
+++ b/lib/galaxy/tools/install_manager.py
@@ -0,0 +1,239 @@
+"""
+Manage automatic installation of tools configured in tool_shed_install.xml, all of which were
+at some point included in the Galaxy distribution, but are now hosted in the main Galaxy tool
+shed.  Tools included in tool_shed_install.xml that have already been installed will not be
+re-installed.
+"""
+from galaxy import util
+from galaxy.tools import ToolSection
+from galaxy.tools.search import ToolBoxSearch
+from galaxy import model
+from galaxy.web.controllers.admin_toolshed import generate_metadata, generate_tool_panel_section, add_shed_tool_conf_entry, create_or_undelete_tool_shed_repository
+from galaxy.web.controllers.admin_toolshed import handle_missing_data_table_entry, handle_missing_index_file, handle_tool_dependencies
+from galaxy.model.orm import *
+import os, subprocess, tempfile, logging
+
+pkg_resources.require( 'elementtree' )
+from elementtree import ElementTree, ElementInclude
+from elementtree.ElementTree import Element
+
+log = logging.getLogger( __name__ )
+
+class InstallManager( object ):
+    def __init__( self, app, tool_shed_install_config, install_tool_config ):
+        """
+        Check tool settings in tool_shed_install_config and install all tools that are
+        not already installed.  The tool panel configuration file is the received
+        shed_tool_config, which defaults to shed_tool_conf.xml.
+        """
+        self.app = app
+        self.sa_session = self.app.model.context.current
+        self.install_tool_config = install_tool_config
+        # Parse shed_tool_config to get the install location (tool_path).
+        tree = util.parse_xml( install_tool_config )
+        root = tree.getroot()
+        self.tool_path = root.get( 'tool_path' )
+        self.app.toolbox.shed_tool_confs[ install_tool_config ] = self.tool_path
+        # Parse tool_shed_install_config to check each of the tools.
+        log.debug( "Parsing tool shed install configuration %s" % tool_shed_install_config )
+        self.tool_shed_install_config = tool_shed_install_config
+        tree = util.parse_xml( tool_shed_install_config )
+        root = tree.getroot()
+        self.tool_shed = root.get( 'name' )
+        log.debug( "Repositories will be installed from tool shed '%s' into configured tool_path location '%s'" % ( str( self.tool_shed ), str( self.tool_path ) ) )
+        self.repository_owner = 'devteam'
+        for elem in root:
+            if elem.tag == 'tool':
+                self.check_tool( elem )
+            elif elem.tag == 'section':
+                self.check_section( elem )
+    def check_tool( self, elem ):
+        # TODO: write this method.
+        pass
+    def check_section( self, elem ):
+        section_name = elem.get( 'name' )
+        section_id = elem.get( 'id' )
+        for repository_elem in elem:
+            name = repository_elem.get( 'name' )
+            description = repository_elem.get( 'description' )
+            changeset_revision = repository_elem.get( 'changeset_revision' )
+            installed = False
+            for tool_elem in repository_elem:
+                tool_config = tool_elem.get( 'file' )
+                tool_id = tool_elem.get( 'id' )
+                tool_version = tool_elem.get( 'version' )
+                tigm = self.__get_tool_id_guid_map_by_id_version( tool_id, tool_version )
+                if tigm:
+                    # A record exists in the tool_id_guid_map
+                    # table, so see if the tool is still installed.
+                    install_path = self.__generate_install_path( tigm )
+                    if os.path.exists( install_path ):
+                        message = "Skipping automatic install of repository '%s' because it has already been installed in location '%s'" % \
+                            ( name, install_path )
+                        log.debug( message )
+                        installed = True
+                        break
+            if not installed:
+                log.debug( "Installing repository '%s' from tool shed '%s'" % ( name, self.tool_shed ) )
+                current_working_dir = os.getcwd()
+                tool_shed_url = self.__get_url_from_tool_shed( self.tool_shed )
+                repository_clone_url = '%s/repos/devteam/%s' % ( tool_shed_url, name )
+                # Install path is of the form: <tool path><tool shed>/repos/<repository owner>/<repository name>/<changeset revision>
+                clone_dir = os.path.join( self.tool_path, self.tool_shed, 'repos/devteam', name, changeset_revision )
+                if not os.path.isdir( clone_dir ):
+                    os.makedirs( clone_dir )
+                log.debug( 'Cloning %s...' % repository_clone_url )
+                cmd = 'hg clone %s' % repository_clone_url
+                tmp_name = tempfile.NamedTemporaryFile().name
+                tmp_stderr = open( tmp_name, 'wb' )
+                os.chdir( clone_dir )
+                proc = subprocess.Popen( args=cmd, shell=True, stderr=tmp_stderr.fileno() )
+                returncode = proc.wait()
+                os.chdir( current_working_dir )
+                tmp_stderr.close()
+                if returncode == 0:
+                    # Update the cloned repository to changeset_revision.  It is imperative that the 
+                    # installed repository is updated to the desired changeset_revision before metadata
+                    # is set because the process for setting metadata uses the repository files on disk.
+                    relative_install_dir = os.path.join( clone_dir, name )
+                    log.debug( 'Updating cloned repository to revision "%s"' % changeset_revision )
+                    cmd = 'hg update -r %s' % changeset_revision
+                    tmp_name = tempfile.NamedTemporaryFile().name
+                    tmp_stderr = open( tmp_name, 'wb' )
+                    os.chdir( relative_install_dir )
+                    proc = subprocess.Popen( cmd, shell=True, stderr=tmp_stderr.fileno() )
+                    returncode = proc.wait()
+                    os.chdir( current_working_dir )
+                    tmp_stderr.close()
+                    if returncode == 0:
+                        # Generate the metadata for the installed tool shed repository.  It is imperative that
+                        # the installed repository is updated to the desired changeset_revision before metadata
+                        # is set because the process for setting metadata uses the repository files on disk.
+                        metadata_dict = generate_metadata( self.app.toolbox, relative_install_dir, repository_clone_url )
+                        if 'datatypes_config' in metadata_dict:
+                            datatypes_config = os.path.abspath( metadata_dict[ 'datatypes_config' ] )
+                            # Load data types required by tools.
+                            self.__load_datatypes( trans, datatypes_config, relative_install_dir )
+                        if 'tools' in metadata_dict:
+                            repository_tools_tups = []
+                            for tool_dict in metadata_dict[ 'tools' ]:
+                                relative_path = tool_dict[ 'tool_config' ]
+                                guid = tool_dict[ 'guid' ]
+                                tool = self.app.toolbox.load_tool( os.path.abspath( relative_path ) )
+                                repository_tools_tups.append( ( relative_path, guid, tool ) )
+                            if repository_tools_tups:
+                                sample_files = metadata_dict.get( 'sample_files', [] )
+                                # Handle missing data table entries for tool parameters that are dynamically generated select lists.
+                                repository_tools_tups = handle_missing_data_table_entry( self.app, self.tool_path, sample_files, repository_tools_tups )
+                                # Handle missing index files for tool parameters that are dynamically generated select lists.
+                                repository_tools_tups = handle_missing_index_file( self.app, self.tool_path, sample_files, repository_tools_tups )
+                                # Handle tools that use fabric scripts to install dependencies.
+                                handle_tool_dependencies( current_working_dir, relative_install_dir, repository_tools_tups )
+                                section_key = 'section_%s' % str( section_id )
+                                if section_key in self.app.toolbox.tool_panel:
+                                    # Appending a tool to an existing section in self.app.toolbox.tool_panel
+                                    log.debug( "Appending to tool panel section: %s" % section_name )
+                                    tool_section = self.app.toolbox.tool_panel[ section_key ]
+                                else:
+                                    # Appending a new section to self.app.toolbox.tool_panel
+                                    log.debug( "Loading new tool panel section: %s" % section_name )
+                                    elem = Element( 'section' )
+                                    elem.attrib[ 'name' ] = section_name
+                                    elem.attrib[ 'id' ] = section_id
+                                    tool_section = ToolSection( elem )
+                                    self.app.toolbox.tool_panel[ section_key ] = tool_section
+                                # Generate an in-memory tool conf section that includes the new tools.
+                                new_tool_section = generate_tool_panel_section( name,
+                                                                                repository_clone_url,
+                                                                                changeset_revision,
+                                                                                tool_section,
+                                                                                repository_tools_tups,
+                                                                                owner=self.repository_owner )
+                                # Create a temporary file to persist the in-memory tool section
+                                # TODO: Figure out how to do this in-memory using xml.etree.
+                                tmp_name = tempfile.NamedTemporaryFile().name
+                                persisted_new_tool_section = open( tmp_name, 'wb' )
+                                persisted_new_tool_section.write( new_tool_section )
+                                persisted_new_tool_section.close()
+                                # Parse the persisted tool panel section
+                                tree = util.parse_xml( tmp_name )
+                                root = tree.getroot()
+                                # Load the tools in the section into the tool panel.
+                                self.app.toolbox.load_section_tag_set( root, self.app.toolbox.tool_panel, self.tool_path )
+                                # Remove the temporary file
+                                try:
+                                    os.unlink( tmp_name )
+                                except:
+                                    pass
+                                # Append the new section to the shed_tool_config file.
+                                add_shed_tool_conf_entry( self.app, self.install_tool_config, new_tool_section )
+                                if self.app.toolbox_search.enabled:
+                                    # If search support for tools is enabled, index the new installed tools.
+                                    self.app.toolbox_search = ToolBoxSearch( self.app.toolbox )
+                        # Add a new record to the tool_shed_repository table if one doesn't
+                        # already exist.  If one exists but is marked deleted, undelete it.
+                        log.debug( "Adding new row to tool_shed_repository table for repository '%s'" % name )
+                        create_or_undelete_tool_shed_repository( self.app,
+                                                                 name,
+                                                                 description,
+                                                                 changeset_revision,
+                                                                 repository_clone_url,
+                                                                 metadata_dict,
+                                                                 owner=self.repository_owner )
+                        # Add a new record to the tool_id_guid_map table for each
+                        # tool in the repository if one doesn't already exist.
+                        if 'tools' in metadata_dict:
+                            tools_mapped = 0
+                            for tool_dict in metadata_dict[ 'tools' ]:
+                                tool_id = tool_dict[ 'id' ]
+                                tool_version = tool_dict[ 'version' ]
+                                guid = tool_dict[ 'guid' ]
+                                tool_id_guid_map = model.ToolIdGuidMap( tool_id=tool_id,
+                                                                        tool_version=tool_version,
+                                                                        tool_shed=self.tool_shed,
+                                                                        repository_owner=self.repository_owner,
+                                                                        repository_name=name,
+                                                                        guid=guid )
+                                self.sa_session.add( tool_id_guid_map )
+                                self.sa_session.flush()
+                                tools_mapped += 1
+                            log.debug( "Mapped tool ids to guids for %d tools included in repository '%s'." % ( tools_mapped, name ) )
+    def __generate_install_path( self, tool_id_guid_map ):
+        """
+        Generate a tool path in which a tool is or will be installed.  The tool path will be of the form:
+        <tool shed>/repos/<repository owner>/<repository name>/<changeset revision>
+        """
+        tool_shed = tool_id_guid_map.tool_shed
+        repository_name = tool_id_guid_map.repository_name
+        tool_shed_repository = self.__get_repository_by_tool_shed_name_owner( tool_shed, repository_name, self.repository_owner )
+        changeset_revision = tool_shed_repository.changeset_revision
+        return '%s/repos%s/%s/%s/%s' % ( tool_shed, self.repository_owner, repository_name, changeset_revision )
+    def __get_repository_by_tool_shed_name_owner( tool_shed, name, owner ):
+        """Get a repository from the database via tool_shed, name and owner."""
+        # CRITICAL:  this assumes that a single changeset_revision exists for each repository
+        # in the tool shed.  In other words, if a repository has multiple changset_revisions
+        # there will be problems.  We're probably safe here because only a single changeset_revision
+        # for each tool shed repository will be installed using this installation process.
+        return self.sa_session.query( self.app.model.ToolShedRepository ) \
+                              .filter( and_( self.app.model.ToolShedRepository.table.c.tool_shed == tool_shed,
+                                             self.app.model.ToolShedRepository.table.c.name == name,
+                                             self.app.model.ToolShedRepository.table.c.owner == owner ) ) \
+                              .first()
+    def __get_tool_id_guid_map_by_id_version( self, tool_id, tool_version ):
+        """Get a tool_id_guid_map from the database via tool_id and tool_version."""
+        return self.sa_session.query( self.app.model.ToolIdGuidMap ) \
+                              .filter( and_( self.app.model.ToolIdGuidMap.table.c.tool_id == tool_id,
+                                             self.app.model.ToolIdGuidMap.table.c.tool_version == tool_version ) ) \
+                              .first()
+    def __get_url_from_tool_shed( self, tool_shed ):
+        # The value of tool_shed is something like: toolshed.g2.bx.psu.edu
+        # We need the URL to this tool shed, which is something like:
+        # http://toolshed.g2.bx.psu.edu/
+        for shed_name, shed_url in self.app.tool_shed_registry.tool_sheds.items():
+            if shed_url.find( tool_shed ) >= 0:
+                if shed_url.endswith( '/' ):
+                    shed_url = shed_url.rstrip( '/' )
+                return shed_url
+        # The tool shed from which the repository was originally
+        # installed must no longer be configured in tool_sheds_conf.xml.
+        return None
diff --git a/lib/galaxy/web/base/controller.py b/lib/galaxy/web/base/controller.py
index 8ff0743253c..7eeba3d8c3f 100644
--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -12,7 +12,8 @@ from galaxy.web import error, form, url_for
 from galaxy.model.orm import *
 from galaxy.workflow.modules import *
 from galaxy.web.framework import simplejson
-from galaxy.web.form_builder import AddressField, CheckboxField, SelectField, TextArea, TextField, WorkflowField, WorkflowMappingField, HistoryField, PasswordField, build_select_field
+from galaxy.web.form_builder import AddressField, CheckboxField, SelectField, TextArea, TextField
+from galaxy.web.form_builder import WorkflowField, WorkflowMappingField, HistoryField, PasswordField, build_select_field
 from galaxy.visualization.tracks.data_providers import get_data_provider
 from galaxy.visualization.tracks.visual_analytics import get_tool_def
 from galaxy.security.validate_user_input import validate_username
@@ -2425,11 +2426,11 @@ class Admin( object ):
 
 ## ---- Utility methods -------------------------------------------------------
 
-def copy_sample_loc_file( trans, filename ):
+def copy_sample_loc_file( app, filename ):
     """Copy xxx.loc.sample to ~/tool-data/xxx.loc.sample and ~/tool-data/xxx.loc"""
     head, sample_loc_file = os.path.split( filename )
     loc_file = sample_loc_file.replace( '.sample', '' )
-    tool_data_path = os.path.abspath( trans.app.config.tool_data_path )
+    tool_data_path = os.path.abspath( app.config.tool_data_path )
     # It's ok to overwrite the .sample version of the file.
     shutil.copy( os.path.abspath( filename ), os.path.join( tool_data_path, sample_loc_file ) )
     # Only create the .loc file if it does not yet exist.  We don't  
@@ -2470,29 +2471,27 @@ def get_quota( trans, id ):
     id = trans.security.decode_id( id )
     quota = trans.sa_session.query( trans.model.Quota ).get( id )
     return quota
-def handle_sample_tool_data_table_conf_file( trans, filename ):
+def handle_sample_tool_data_table_conf_file( app, filename ):
     """
     Parse the incoming filename and add new entries to the in-memory
-    trans.app.tool_data_tables dictionary as well as appending them 
-    to the shed's tool_data_table_conf.xml file on disk.
+    app.tool_data_tables dictionary as well as appending them to the
+    shed's tool_data_table_conf.xml file on disk.
     """
-    # Parse the incoming file and add new entries to the in-memory 
-    # trans.app.tool_data_tables dictionary.
     error = False
     message = ''
     try:
-        new_table_elems = trans.app.tool_data_tables.add_new_entries_from_config_file( filename )
+        new_table_elems = app.tool_data_tables.add_new_entries_from_config_file( filename )
     except Exception, e:
         message = str( e )
         error = True
     if not error:
         # Add an entry to the end of the tool_data_table_conf.xml file.
-        tdt_config = "%s/tool_data_table_conf.xml" %  trans.app.config.root
+        tdt_config = "%s/tool_data_table_conf.xml" % app.config.root
         if os.path.exists( tdt_config ):
             # Make a backup of the file since we're going to be changing it.
             today = date.today()
             backup_date = today.strftime( "%Y_%m_%d" )
-            tdt_config_copy = '%s/tool_data_table_conf.xml_%s_backup' % ( trans.app.config.root, backup_date )
+            tdt_config_copy = '%s/tool_data_table_conf.xml_%s_backup' % ( app.config.root, backup_date )
             shutil.copy( os.path.abspath( tdt_config ), os.path.abspath( tdt_config_copy ) )
             # Write each line of the tool_data_table_conf.xml file, except the last line to a temp file.
             fh = tempfile.NamedTemporaryFile( 'wb' )
diff --git a/lib/galaxy/web/controllers/admin_toolshed.py b/lib/galaxy/web/controllers/admin_toolshed.py
index e5d547d56fc..0fd186fbe3b 100644
--- a/lib/galaxy/web/controllers/admin_toolshed.py
+++ b/lib/galaxy/web/controllers/admin_toolshed.py
@@ -201,7 +201,7 @@ class AdminToolshed( AdminGalaxy ):
                                 # Generate the metadata for the installed tool shed repository.  It is imperative that
                                 # the installed repository is updated to the desired changeset_revision before metadata
                                 # is set because the process for setting metadata uses the repository files on disk.
-                                metadata_dict = self.__generate_metadata( trans, relative_install_dir, repository_clone_url )
+                                metadata_dict = generate_metadata( trans.app.toolbox, relative_install_dir, repository_clone_url )
                                 if 'datatypes_config' in metadata_dict:
                                     datatypes_config = os.path.abspath( metadata_dict[ 'datatypes_config' ] )
                                     # Load data types required by tools.
@@ -210,22 +210,23 @@ class AdminToolshed( AdminGalaxy ):
                                     repository_tools_tups = []
                                     for tool_dict in metadata_dict[ 'tools' ]:
                                         relative_path = tool_dict[ 'tool_config' ]
+                                        guid = tool_dict[ 'guid' ]
                                         tool = trans.app.toolbox.load_tool( os.path.abspath( relative_path ) )
-                                        repository_tools_tups.append( ( relative_path, tool ) )
+                                        repository_tools_tups.append( ( relative_path, guid, tool ) )
                                     if repository_tools_tups:
                                         sample_files = metadata_dict.get( 'sample_files', [] )
                                         # Handle missing data table entries for tool parameters that are dynamically generated select lists.
-                                        repository_tools_tups = self.__handle_missing_data_table_entry( trans, tool_path, sample_files, repository_tools_tups )
+                                        repository_tools_tups = handle_missing_data_table_entry( trans.app, tool_path, sample_files, repository_tools_tups )
                                         # Handle missing index files for tool parameters that are dynamically generated select lists.
-                                        repository_tools_tups = self.__handle_missing_index_file( trans, tool_path, sample_files, repository_tools_tups )
+                                        repository_tools_tups = handle_missing_index_file( trans.app, tool_path, sample_files, repository_tools_tups )
                                         # Handle tools that use fabric scripts to install dependencies.
-                                        self.__handle_tool_dependencies( current_working_dir, relative_install_dir, repository_tools_tups )
+                                        handle_tool_dependencies( current_working_dir, relative_install_dir, repository_tools_tups )
                                         # Generate an in-memory tool conf section that includes the new tools.
-                                        new_tool_section = self.__generate_tool_panel_section( name,
-                                                                                               repository_clone_url,
-                                                                                               changeset_revision,
-                                                                                               tool_section,
-                                                                                               repository_tools_tups )
+                                        new_tool_section = generate_tool_panel_section( name,
+                                                                                        repository_clone_url,
+                                                                                        changeset_revision,
+                                                                                        tool_section,
+                                                                                        repository_tools_tups )
                                         # Create a temporary file to persist the in-memory tool section
                                         # TODO: Figure out how to do this in-memory using xml.etree.
                                         tmp_name = tempfile.NamedTemporaryFile().name
@@ -243,18 +244,18 @@ class AdminToolshed( AdminGalaxy ):
                                         except:
                                             pass
                                         # Append the new section to the shed_tool_config file.
-                                        self.__add_shed_tool_conf_entry( trans, shed_tool_conf, new_tool_section )
+                                        add_shed_tool_conf_entry( trans.app, shed_tool_conf, new_tool_section )
                                         if trans.app.toolbox_search.enabled:
                                             # If search support for tools is enabled, index the new installed tools.
                                             trans.app.toolbox_search = ToolBoxSearch( trans.app.toolbox )
                                 # Add a new record to the tool_shed_repository table if one doesn't
                                 # already exist.  If one exists but is marked deleted, undelete it.
-                                self.__create_or_undelete_tool_shed_repository( trans,
-                                                                                name,
-                                                                                description,
-                                                                                changeset_revision,
-                                                                                repository_clone_url,
-                                                                                metadata_dict )
+                                create_or_undelete_tool_shed_repository( trans.app,
+                                                                         name,
+                                                                         description,
+                                                                         changeset_revision,
+                                                                         repository_clone_url,
+                                                                         metadata_dict )
                                 installed_repository_names.append( name )
                             else:
                                 tmp_stderr = open( tmp_name, 'rb' )
@@ -317,7 +318,7 @@ class AdminToolshed( AdminGalaxy ):
             message = "The repository information has been updated."
         elif params.get( 'set_metadata_button', False ):
             repository_clone_url = self.__generate_clone_url( trans, repository )
-            metadata_dict = self.__generate_metadata( trans, relative_install_dir, repository_clone_url )
+            metadata_dict = generate_metadata( trans.app.toolbox, relative_install_dir, repository_clone_url )
             if metadata_dict:
                 repository.metadata = metadata_dict
                 trans.sa_session.add( repository )
@@ -350,7 +351,7 @@ class AdminToolshed( AdminGalaxy ):
         owner = params.get( 'owner', None )
         changeset_revision = params.get( 'changeset_revision', None )
         latest_changeset_revision = params.get( 'latest_changeset_revision', None )
-        repository = get_repository_by_shed_name_owner_changeset_revision( trans, tool_shed_url, name, owner, changeset_revision )
+        repository = get_repository_by_shed_name_owner_changeset_revision( trans.app, tool_shed_url, name, owner, changeset_revision )
         if changeset_revision and latest_changeset_revision:
             if changeset_revision == latest_changeset_revision:
                 message = "The cloned tool shed repository named '%s' is current (there are no updates available)." % name
@@ -429,147 +430,6 @@ class AdminToolshed( AdminGalaxy ):
                                     metadata=metadata,
                                     message=message,
                                     status=status )
-    def __generate_metadata( self, trans, relative_install_dir, repository_clone_url ):
-        """
-        Browse the repository files on disk to generate metadata.  Since we are using disk files, it
-        is imperative that the repository is updated to the desired change set revision before metadata
-        is generated.
-        """
-        metadata_dict = {}
-        sample_files = []
-        datatypes_config = None
-        # Find datatypes_conf.xml if it exists.
-        for root, dirs, files in os.walk( relative_install_dir ):
-            if root.find( '.hg' ) < 0:
-                for name in files:
-                    if name == 'datatypes_conf.xml':
-                        relative_path = os.path.join( root, name )
-                        datatypes_config = os.path.abspath( relative_path )
-                        break
-        if datatypes_config:
-            metadata_dict[ 'datatypes_config' ] = relative_path
-            metadata_dict = self.__generate_datatypes_metadata( trans, datatypes_config, metadata_dict )
-        # Find all special .sample files.
-        for root, dirs, files in os.walk( relative_install_dir ):
-            if root.find( '.hg' ) < 0:
-                for name in files:
-                    if name.endswith( '.sample' ):
-                        sample_files.append( os.path.join( root, name ) )
-        if sample_files:
-            metadata_dict[ 'sample_files' ] = sample_files
-        # Find all tool configs and exported workflows.
-        for root, dirs, files in os.walk( relative_install_dir ):
-            if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0:
-                if '.hg' in dirs:
-                    dirs.remove( '.hg' )
-                for name in files:
-                    # Find all tool configs.
-                    if name != 'datatypes_conf.xml' and name.endswith( '.xml' ):
-                        full_path = os.path.abspath( os.path.join( root, name ) )
-                        try:
-                            tool = trans.app.toolbox.load_tool( full_path )
-                        except Exception, e:
-                            tool = None
-                        if tool is not None:
-                            tool_config = os.path.join( root, name )
-                            metadata_dict = self.__generate_tool_metadata( trans, tool_config, tool, repository_clone_url, metadata_dict )
-                    # Find all exported workflows
-                    elif name.endswith( '.ga' ):
-                        relative_path = os.path.join( root, name )
-                        fp = open( relative_path, 'rb' )
-                        workflow_text = fp.read()
-                        fp.close()
-                        exported_workflow_dict = from_json_string( workflow_text )
-                        if 'a_galaxy_workflow' in exported_workflow_dict and exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true':
-                            metadata_dict = self.__generate_workflow_metadata( trans, relative_path, exported_workflow_dict, metadata_dict )
-        return metadata_dict
-    def __generate_datatypes_metadata( self, trans, datatypes_config, metadata_dict ):
-        """
-        Update the received metadata_dict with changes that have been applied
-        to the received datatypes_config.
-        """
-        # Parse datatypes_config.
-        tree = ElementTree.parse( datatypes_config )
-        root = tree.getroot()
-        ElementInclude.include( root )
-        repository_datatype_code_files = []
-        datatype_files = root.find( 'datatype_files' )
-        if datatype_files:
-            for elem in datatype_files.findall( 'datatype_file' ):
-                name = elem.get( 'name', None )
-                repository_datatype_code_files.append( name )
-            metadata_dict[ 'datatype_files' ] = repository_datatype_code_files
-        datatypes = []
-        registration = root.find( 'registration' )
-        if registration:
-            for elem in registration.findall( 'datatype' ):
-                extension = elem.get( 'extension', None ) 
-                dtype = elem.get( 'type', None )
-                mimetype = elem.get( 'mimetype', None )
-                datatypes.append( dict( extension=extension,
-                                        dtype=dtype,
-                                        mimetype=mimetype ) )
-            metadata_dict[ 'datatypes' ] = datatypes
-        return metadata_dict
-    def __generate_tool_metadata( self, trans, tool_config, tool, repository_clone_url, metadata_dict ):
-        """
-        Update the received metadata_dict with changes that have been
-        applied to the received tool.
-        """
-        # Generate the guid
-        guid = self.__generate_tool_guid( repository_clone_url, tool )
-        # Handle tool.requirements.
-        tool_requirements = []
-        for tr in tool.requirements:
-            name=tr.name
-            type=tr.type
-            if type == 'fabfile':
-                version = None
-                fabfile = tr.fabfile
-                method = tr.method
-            else:
-                version = tr.version
-                fabfile = None
-                method = None
-            requirement_dict = dict( name=name,
-                                     type=type,
-                                     version=version,
-                                     fabfile=fabfile,
-                                     method=method )
-            tool_requirements.append( requirement_dict )
-        # Handle tool.tests.
-        tool_tests = []
-        if tool.tests:
-            for ttb in tool.tests:
-                test_dict = dict( name=ttb.name,
-                                  required_files=ttb.required_files,
-                                  inputs=ttb.inputs,
-                                  outputs=ttb.outputs )
-                tool_tests.append( test_dict )
-        tool_dict = dict( id=tool.id,
-                          guid=guid,
-                          name=tool.name,
-                          version=tool.version,
-                          description=tool.description,
-                          version_string_cmd = tool.version_string_cmd,
-                          tool_config=tool_config,
-                          requirements=tool_requirements,
-                          tests=tool_tests )
-        if 'tools' in metadata_dict:
-            metadata_dict[ 'tools' ].append( tool_dict )
-        else:
-            metadata_dict[ 'tools' ] = [ tool_dict ]
-        return metadata_dict
-    def __generate_workflow_metadata( self, trans, relative_path, exported_workflow_dict, metadata_dict ):
-        """
-        Update the received metadata_dict with changes that have been applied
-        to the received exported_workflow_dict.  Store everything in the database.
-        """
-        if 'workflows' in metadata_dict:
-            metadata_dict[ 'workflows' ].append( ( relative_path, exported_workflow_dict ) )
-        else:
-            metadata_dict[ 'workflows' ] = [ ( relative_path, exported_workflow_dict ) ]
-        return metadata_dict
     def __get_relative_install_dir( self, trans, repository ):
         # Get the directory where the repository is install.
         tool_shed = self.__clean_tool_shed_url( repository.tool_shed )
@@ -583,87 +443,6 @@ class AdminToolshed( AdminGalaxy ):
             if os.path.isdir( relative_install_dir ):
                 break
         return relative_install_dir
-    def __handle_missing_data_table_entry( self, trans, tool_path, sample_files, repository_tools_tups ):
-        # Inspect each tool to see if any have input parameters that are dynamically
-        # generated select lists that require entries in the tool_data_table_conf.xml file.
-        missing_data_table_entry = False
-        for index, repository_tools_tup in enumerate( repository_tools_tups ):
-            tup_path, repository_tool = repository_tools_tup
-            if repository_tool.params_with_missing_data_table_entry:
-                missing_data_table_entry = True
-                break
-        if missing_data_table_entry:
-            # The repository must contain a tool_data_table_conf.xml.sample file that includes
-            # all required entries for all tools in the repository.
-            for sample_file in sample_files:
-                head, tail = os.path.split( sample_file )
-                if tail == 'tool_data_table_conf.xml.sample':
-                    break
-            error, correction_msg = handle_sample_tool_data_table_conf_file( trans, sample_file )
-            if error:
-                # TODO: Do more here than logging an exception.
-                log.debug( exception_msg )
-            # Reload the tool into the local list of repository_tools_tups.
-            repository_tool = trans.app.toolbox.load_tool( os.path.join( tool_path, tup_path ) )
-            repository_tools_tups[ index ] = ( tup_path, repository_tool )
-        return repository_tools_tups
-    def __handle_missing_index_file( self, trans, tool_path, sample_files, repository_tools_tups ):
-        # Inspect each tool to see if it has any input parameters that
-        # are dynamically generated select lists that depend on a .loc file.
-        missing_files_handled = []
-        for index, repository_tools_tup in enumerate( repository_tools_tups ):
-            tup_path, repository_tool = repository_tools_tup
-            params_with_missing_index_file = repository_tool.params_with_missing_index_file
-            for param in params_with_missing_index_file:
-                options = param.options
-                missing_head, missing_tail = os.path.split( options.missing_index_file )
-                if missing_tail not in missing_files_handled:
-                    # The repository must contain the required xxx.loc.sample file.
-                    for sample_file in sample_files:
-                        sample_head, sample_tail = os.path.split( sample_file )
-                        if sample_tail == '%s.sample' % missing_tail:
-                            copy_sample_loc_file( trans, sample_file )
-                            if options.tool_data_table and options.tool_data_table.missing_index_file:
-                                options.tool_data_table.handle_found_index_file( options.missing_index_file )
-                            missing_files_handled.append( missing_tail )
-                            break
-            # Reload the tool into the local list of repository_tools_tups.
-            repository_tool = trans.app.toolbox.load_tool( os.path.join( tool_path, tup_path ) )
-            repository_tools_tups[ index ] = ( tup_path, repository_tool )
-        return repository_tools_tups
-    def __handle_tool_dependencies( self, current_working_dir, repo_files_dir, repository_tools_tups ):
-        # Inspect each tool to see if it includes a "requirement" that refers to a fabric
-        # script.  For those that do, execute the fabric script to install tool dependencies.
-        for index, repository_tools_tup in enumerate( repository_tools_tups ):
-            tup_path, repository_tool = repository_tools_tup
-            for requirement in repository_tool.requirements:
-                if requirement.type == 'fabfile':
-                    log.debug( 'Executing fabric script to install dependencies for tool "%s"...' % repository_tool.name )
-                    fabfile = requirement.fabfile
-                    method = requirement.method
-                    # Find the relative path to the fabfile.
-                    relative_fabfile_path = None
-                    for root, dirs, files in os.walk( repo_files_dir ):
-                        for name in files:
-                            if name == fabfile:
-                                relative_fabfile_path = os.path.join( root, name )
-                                break
-                    if relative_fabfile_path:
-                        # cmd will look something like: fab -f fabfile.py install_bowtie
-                        cmd = 'fab -f %s %s' % ( relative_fabfile_path, method )
-                        tmp_name = tempfile.NamedTemporaryFile().name
-                        tmp_stderr = open( tmp_name, 'wb' )
-                        os.chdir( repo_files_dir )
-                        proc = subprocess.Popen( cmd, shell=True, stderr=tmp_stderr.fileno() )
-                        returncode = proc.wait()
-                        os.chdir( current_working_dir )
-                        tmp_stderr.close()
-                        if returncode != 0:
-                            # TODO: do something more here than logging the problem.
-                            tmp_stderr = open( tmp_name, 'rb' )
-                            error = tmp_stderr.read()
-                            tmp_stderr.close()
-                            log.debug( 'Problem installing dependencies for tool "%s"\n%s' % ( repository_tool.name, error ) )
     def __load_datatypes( self, trans, datatypes_config, relative_intall_dir ):
         imported_module = None
         # Parse datatypes_config.
@@ -708,84 +487,11 @@ class AdminToolshed( AdminGalaxy ):
             except Exception, e:
                 log.debug( "Exception importing datatypes code file included in installed repository: %s" % str( e ) )
         trans.app.datatypes_registry.load_datatypes( root_dir=trans.app.config.root, config=datatypes_config, imported_module=imported_module )
-    def __create_or_undelete_tool_shed_repository( self, trans, name, description, changeset_revision, repository_clone_url, metadata_dict ):
-        tmp_url = self.__clean_repository_clone_url( repository_clone_url )
-        tool_shed = tmp_url.split( 'repos' )[ 0 ].rstrip( '/' )
-        owner = self.__get_repository_owner( tmp_url )
-        includes_datatypes = 'datatypes_config' in metadata_dict
-        flush_needed = False
-        tool_shed_repository = get_repository_by_shed_name_owner_changeset_revision( trans, tool_shed, name, owner, changeset_revision )
-        if tool_shed_repository:
-            if tool_shed_repository.deleted:
-                tool_shed_repository.deleted = False
-                # Reset includes_datatypes in case metadata changed since last installed.
-                tool_shed_repository.includes_datatypes = includes_datatypes
-                flush_needed = True
-        else:
-            tool_shed_repository = trans.model.ToolShedRepository( tool_shed=tool_shed,
-                                                                   name=name,
-                                                                   description=description,
-                                                                   owner=owner,
-                                                                   changeset_revision=changeset_revision,
-                                                                   metadata=metadata_dict,
-                                                                   includes_datatypes=includes_datatypes )
-            flush_needed = True
-        if flush_needed:
-            trans.sa_session.add( tool_shed_repository )
-            trans.sa_session.flush()
-    def __add_shed_tool_conf_entry( self, trans, shed_tool_conf, new_tool_section ):
-        # Add an entry in the shed_tool_conf file. An entry looks something like:
-        # <section name="Filter and Sort" id="filter">
-        #    <tool file="filter/filtering.xml" guid="toolshed.g2.bx.psu.edu/repos/test/filter/1.0.2"/>
-        # </section>
-        # Make a backup of the hgweb.config file since we're going to be changing it.
-        if not os.path.exists( shed_tool_conf ):
-            output = open( shed_tool_conf, 'w' )
-            output.write( '<?xml version="1.0"?>\n' )
-            output.write( '<toolbox tool_path="%s">\n' % tool_path )
-            output.write( '</toolbox>\n' )
-            output.close()
-        self.__make_shed_tool_conf_copy( trans, shed_tool_conf )
-        tmp_fd, tmp_fname = tempfile.mkstemp()
-        new_shed_tool_conf = open( tmp_fname, 'wb' )
-        for i, line in enumerate( open( shed_tool_conf ) ):
-            if line.startswith( '</toolbox>' ):
-                # We're at the end of the original config file, so add our entry.
-                new_shed_tool_conf.write( new_tool_section )
-                new_shed_tool_conf.write( line )
-            else:
-                new_shed_tool_conf.write( line )
-        new_shed_tool_conf.close()
-        shutil.move( tmp_fname, os.path.abspath( shed_tool_conf ) )
-    def __make_shed_tool_conf_copy( self, trans, shed_tool_conf ):
-        # Make a backup of the shed_tool_conf file.
-        today = date.today()
-        backup_date = today.strftime( "%Y_%m_%d" )
-        shed_tool_conf_copy = '%s/%s_%s_backup' % ( trans.app.config.root, shed_tool_conf, backup_date )
-        shutil.copy( os.path.abspath( shed_tool_conf ), os.path.abspath( shed_tool_conf_copy ) )
     def __clean_tool_shed_url( self, tool_shed_url ):
         if tool_shed_url.find( ':' ) > 0:
             # Eliminate the port, if any, since it will result in an invalid directory name.
             return tool_shed_url.split( ':' )[ 0 ]
         return tool_shed_url.rstrip( '/' )
-    def __clean_repository_clone_url( self, repository_clone_url ):
-        if repository_clone_url.find( '@' ) > 0:
-            # We have an url that includes an authenticated user, something like:
-            # http://test@bx.psu.edu:9009/repos/some_username/column
-            items = repository_clone_url.split( '@' )
-            tmp_url = items[ 1 ]
-        elif repository_clone_url.find( '//' ) > 0:
-            # We have an url that includes only a protocol, something like:
-            # http://bx.psu.edu:9009/repos/some_username/column
-            items = repository_clone_url.split( '//' )
-            tmp_url = items[ 1 ]
-        else:
-            tmp_url = repository_clone_url
-        return tmp_url
-    def __get_repository_owner( self, cleaned_repository_url ):
-        items = cleaned_repository_url.split( 'repos' )
-        repo_path = items[ 1 ]
-        return repo_path.lstrip( '/' ).split( '/' )[ 0 ]
     def __generate_tool_path( self, repository_clone_url, changeset_revision ):
         """
         Generate a tool path that guarantees repositories with the same name will always be installed
@@ -793,7 +499,7 @@ class AdminToolshed( AdminGalaxy ):
         <tool shed url>/repos/<repository owner>/<repository name>/<changeset revision>
         http://test@bx.psu.edu:9009/repos/test/filter
         """
-        tmp_url = self.__clean_repository_clone_url( repository_clone_url )
+        tmp_url = clean_repository_clone_url( repository_clone_url )
         # Now tmp_url is something like: bx.psu.edu:9009/repos/some_username/column
         items = tmp_url.split( 'repos' )
         tool_shed_url = items[ 0 ]
@@ -804,36 +510,6 @@ class AdminToolshed( AdminGalaxy ):
         """Generate the URL for cloning a repository."""
         tool_shed_url = get_url_from_repository_tool_shed( trans, repository )
         return '%s/repos/%s/%s' % ( tool_shed_url, repository.owner, repository.name )
-    def __generate_tool_guid( self, repository_clone_url, tool ):
-        """
-        Generate a guid for the installed tool.  It is critical that this guid matches the guid for
-        the tool in the Galaxy tool shed from which it is being installed.  The form of the guid is    
-        <tool shed host>/repos/<repository owner>/<repository name>/<tool id>/<tool version>
-        """
-        tmp_url = self.__clean_repository_clone_url( repository_clone_url )
-        return '%s/%s/%s' % ( tmp_url, tool.id, tool.version )
-    def __generate_tool_panel_section( self, repository_name, repository_clone_url, changeset_revision, tool_section, repository_tools_tups ):
-        """
-        Write an in-memory tool panel section so we can load it into the tool panel and then
-        append it to the appropriate shed tool config.
-        TODO: re-write using ElementTree.
-        """
-        tmp_url = self.__clean_repository_clone_url( repository_clone_url )
-        section_str = ''
-        section_str += '    <section name="%s" id="%s">\n' % ( tool_section.name, tool_section.id )
-        for repository_tool_tup in repository_tools_tups:
-            tool_file_path, tool = repository_tool_tup
-            guid = self.__generate_tool_guid( repository_clone_url, tool )
-            section_str += '        <tool file="%s" guid="%s">\n' % ( tool_file_path, guid )
-            section_str += '            <tool_shed>%s</tool_shed>\n' % tmp_url.split( 'repos' )[ 0 ].rstrip( '/' )
-            section_str += '            <repository_name>%s</repository_name>\n' % repository_name
-            section_str += '            <repository_owner>%s</repository_owner>\n' % self.__get_repository_owner( tmp_url )
-            section_str += '            <changeset_revision>%s</changeset_revision>\n' % changeset_revision
-            section_str += '            <id>%s</id>\n' % tool.id
-            section_str += '            <version>%s</version>\n' % tool.version
-            section_str += '        </tool>\n'
-        section_str += '    </section>\n'
-        return section_str
 
 ## ---- Utility methods -------------------------------------------------------
 
@@ -841,7 +517,11 @@ def build_shed_tool_conf_select_field( trans ):
     """Build a SelectField whose options are the keys in trans.app.toolbox.shed_tool_confs."""
     options = []
     for shed_tool_conf_filename, tool_path in trans.app.toolbox.shed_tool_confs.items():
-        options.append( ( shed_tool_conf_filename.lstrip( './' ), shed_tool_conf_filename ) )
+        if shed_tool_conf_filename.startswith( './' ):
+            option_label = shed_tool_conf_filename.replace( './', '', 1 )
+        else:
+            option_label = shed_tool_conf_filename
+        options.append( ( option_label, shed_tool_conf_filename ) )
     select_field = SelectField( name='shed_tool_conf' )
     for option_tup in options:
         select_field.add_option( option_tup[0], option_tup[1] )
@@ -865,15 +545,17 @@ def get_repository_by_name_owner_changeset_revision( trans, name, owner, changes
                                             trans.model.ToolShedRepository.table.c.owner == owner,
                                             trans.model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \
                              .first()
-def get_repository_by_shed_name_owner_changeset_revision( trans, tool_shed, name, owner, changeset_revision ):
+def get_repository_by_shed_name_owner_changeset_revision( app, tool_shed, name, owner, changeset_revision ):
+    # This method is used by the InstallManager, which does not have access to trans.
+    sa_session = app.model.context.current
     if tool_shed.find( '//' ) > 0:
         tool_shed = tool_shed.split( '//' )[1]
-    return trans.sa_session.query( trans.model.ToolShedRepository ) \
-                           .filter( and_( trans.model.ToolShedRepository.table.c.tool_shed == tool_shed,
-                                          trans.model.ToolShedRepository.table.c.name == name,
-                                          trans.model.ToolShedRepository.table.c.owner == owner,
-                                          trans.model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \
-                           .first()
+    return sa_session.query( app.model.ToolShedRepository ) \
+                     .filter( and_( app.model.ToolShedRepository.table.c.tool_shed == tool_shed,
+                                    app.model.ToolShedRepository.table.c.name == name,
+                                    app.model.ToolShedRepository.table.c.owner == owner,
+                                    app.model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \
+                     .first()
 def get_url_from_repository_tool_shed( trans, repository ):
     # The stored value of repository.tool_shed is something like:
     # toolshed.g2.bx.psu.edu
@@ -887,3 +569,347 @@ def get_url_from_repository_tool_shed( trans, repository ):
     # The tool shed from which the repository was originally
     # installed must no longer be configured in tool_sheds_conf.xml.
     return None
+def generate_tool_panel_section( repository_name, repository_clone_url, changeset_revision, tool_section, repository_tools_tups, owner='' ):
+    """
+    Write an in-memory tool panel section so we can load it into the tool panel and then
+    append it to the appropriate shed tool config.
+    TODO: re-write using ElementTree.
+    """
+    tmp_url = clean_repository_clone_url( repository_clone_url )
+    if not owner:
+        owner = get_repository_owner( tmp_url )
+    section_str = ''
+    section_str += '    <section name="%s" id="%s">\n' % ( tool_section.name, tool_section.id )
+    for repository_tool_tup in repository_tools_tups:
+        tool_file_path, guid, tool = repository_tool_tup
+        section_str += '        <tool file="%s" guid="%s">\n' % ( tool_file_path, guid )
+        section_str += '            <tool_shed>%s</tool_shed>\n' % tmp_url.split( 'repos' )[ 0 ].rstrip( '/' )
+        section_str += '            <repository_name>%s</repository_name>\n' % repository_name
+        section_str += '            <repository_owner>%s</repository_owner>\n' % owner
+        section_str += '            <changeset_revision>%s</changeset_revision>\n' % changeset_revision
+        section_str += '            <id>%s</id>\n' % tool.id
+        section_str += '            <version>%s</version>\n' % tool.version
+        section_str += '        </tool>\n'
+    section_str += '    </section>\n'
+    return section_str
+def get_repository_owner( cleaned_repository_url ):
+    items = cleaned_repository_url.split( 'repos' )
+    repo_path = items[ 1 ]
+    if repo_path.startswith( '/' ):
+        repo_path = repo_path.replace( '/', '', 1 )
+    return repo_path.lstrip( '/' ).split( '/' )[ 0 ]
+def generate_tool_guid( repository_clone_url, tool ):
+    """
+    Generate a guid for the installed tool.  It is critical that this guid matches the guid for
+    the tool in the Galaxy tool shed from which it is being installed.  The form of the guid is    
+    <tool shed host>/repos/<repository owner>/<repository name>/<tool id>/<tool version>
+    """
+    tmp_url = clean_repository_clone_url( repository_clone_url )
+    return '%s/%s/%s' % ( tmp_url, tool.id, tool.version )
+def clean_repository_clone_url( repository_clone_url ):
+    if repository_clone_url.find( '@' ) > 0:
+        # We have an url that includes an authenticated user, something like:
+        # http://test@bx.psu.edu:9009/repos/some_username/column
+        items = repository_clone_url.split( '@' )
+        tmp_url = items[ 1 ]
+    elif repository_clone_url.find( '//' ) > 0:
+        # We have an url that includes only a protocol, something like:
+        # http://bx.psu.edu:9009/repos/some_username/column
+        items = repository_clone_url.split( '//' )
+        tmp_url = items[ 1 ]
+    else:
+        tmp_url = repository_clone_url
+    return tmp_url
+def generate_metadata( toolbox, relative_install_dir, repository_clone_url ):
+    """
+    Browse the repository files on disk to generate metadata.  Since we are using disk files, it
+    is imperative that the repository is updated to the desired change set revision before metadata
+    is generated.  This method is used by the InstallManager, which does not have access to trans.
+    """
+    metadata_dict = {}
+    sample_files = []
+    datatypes_config = None
+    # Find datatypes_conf.xml if it exists.
+    for root, dirs, files in os.walk( relative_install_dir ):
+        if root.find( '.hg' ) < 0:
+            for name in files:
+                if name == 'datatypes_conf.xml':
+                    relative_path = os.path.join( root, name )
+                    datatypes_config = os.path.abspath( relative_path )
+                    break
+    if datatypes_config:
+        metadata_dict[ 'datatypes_config' ] = relative_path
+        metadata_dict = generate_datatypes_metadata( datatypes_config, metadata_dict )
+    # Find all special .sample files.
+    for root, dirs, files in os.walk( relative_install_dir ):
+        if root.find( '.hg' ) < 0:
+            for name in files:
+                if name.endswith( '.sample' ):
+                    sample_files.append( os.path.join( root, name ) )
+    if sample_files:
+        metadata_dict[ 'sample_files' ] = sample_files
+    # Find all tool configs and exported workflows.
+    for root, dirs, files in os.walk( relative_install_dir ):
+        if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0:
+            if '.hg' in dirs:
+                dirs.remove( '.hg' )
+            for name in files:
+                # Find all tool configs.
+                if name != 'datatypes_conf.xml' and name.endswith( '.xml' ):
+                    full_path = os.path.abspath( os.path.join( root, name ) )
+                    try:
+                        tool = toolbox.load_tool( full_path )
+                    except Exception, e:
+                        tool = None
+                    if tool is not None:
+                        tool_config = os.path.join( root, name )
+                        metadata_dict = generate_tool_metadata( tool_config, tool, repository_clone_url, metadata_dict )
+                # Find all exported workflows
+                elif name.endswith( '.ga' ):
+                    relative_path = os.path.join( root, name )
+                    fp = open( relative_path, 'rb' )
+                    workflow_text = fp.read()
+                    fp.close()
+                    exported_workflow_dict = from_json_string( workflow_text )
+                    if 'a_galaxy_workflow' in exported_workflow_dict and exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true':
+                        metadata_dict = generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict )
+    return metadata_dict
+def generate_datatypes_metadata( datatypes_config, metadata_dict ):
+    """
+    Update the received metadata_dict with changes that have been applied
+    to the received datatypes_config.  This method is used by the InstallManager,
+    which does not have access to trans.
+    """
+    # Parse datatypes_config.
+    tree = ElementTree.parse( datatypes_config )
+    root = tree.getroot()
+    ElementInclude.include( root )
+    repository_datatype_code_files = []
+    datatype_files = root.find( 'datatype_files' )
+    if datatype_files:
+        for elem in datatype_files.findall( 'datatype_file' ):
+            name = elem.get( 'name', None )
+            repository_datatype_code_files.append( name )
+        metadata_dict[ 'datatype_files' ] = repository_datatype_code_files
+    datatypes = []
+    registration = root.find( 'registration' )
+    if registration:
+        for elem in registration.findall( 'datatype' ):
+            extension = elem.get( 'extension', None ) 
+            dtype = elem.get( 'type', None )
+            mimetype = elem.get( 'mimetype', None )
+            datatypes.append( dict( extension=extension,
+                                    dtype=dtype,
+                                    mimetype=mimetype ) )
+        metadata_dict[ 'datatypes' ] = datatypes
+    return metadata_dict
+def generate_tool_metadata( tool_config, tool, repository_clone_url, metadata_dict ):
+    """
+    Update the received metadata_dict with changes that have been
+    applied to the received tool.  This method is used by the InstallManager,
+    which does not have access to trans.
+    """
+    # Generate the guid
+    guid = generate_tool_guid( repository_clone_url, tool )
+    # Handle tool.requirements.
+    tool_requirements = []
+    for tr in tool.requirements:
+        name=tr.name
+        type=tr.type
+        if type == 'fabfile':
+            version = None
+            fabfile = tr.fabfile
+            method = tr.method
+        else:
+            version = tr.version
+            fabfile = None
+            method = None
+        requirement_dict = dict( name=name,
+                                 type=type,
+                                 version=version,
+                                 fabfile=fabfile,
+                                 method=method )
+        tool_requirements.append( requirement_dict )
+    # Handle tool.tests.
+    tool_tests = []
+    if tool.tests:
+        for ttb in tool.tests:
+            test_dict = dict( name=ttb.name,
+                              required_files=ttb.required_files,
+                              inputs=ttb.inputs,
+                              outputs=ttb.outputs )
+            tool_tests.append( test_dict )
+    tool_dict = dict( id=tool.id,
+                      guid=guid,
+                      name=tool.name,
+                      version=tool.version,
+                      description=tool.description,
+                      version_string_cmd = tool.version_string_cmd,
+                      tool_config=tool_config,
+                      requirements=tool_requirements,
+                      tests=tool_tests )
+    if 'tools' in metadata_dict:
+        metadata_dict[ 'tools' ].append( tool_dict )
+    else:
+        metadata_dict[ 'tools' ] = [ tool_dict ]
+    return metadata_dict
+def generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict ):
+    """
+    Update the received metadata_dict with changes that have been applied
+    to the received exported_workflow_dict.  Store everything in the database.
+    This method is used by the InstallManager, which does not have access to trans.
+    """
+    if 'workflows' in metadata_dict:
+        metadata_dict[ 'workflows' ].append( ( relative_path, exported_workflow_dict ) )
+    else:
+        metadata_dict[ 'workflows' ] = [ ( relative_path, exported_workflow_dict ) ]
+    return metadata_dict
+def handle_missing_data_table_entry( app, tool_path, sample_files, repository_tools_tups ):
+    """
+    Inspect each tool to see if any have input parameters that are dynamically
+    generated select lists that require entries in the tool_data_table_conf.xml file.
+    This method is used by the InstallManager, which does not have access to trans.
+    """
+    missing_data_table_entry = False
+    for index, repository_tools_tup in enumerate( repository_tools_tups ):
+        tup_path, guid, repository_tool = repository_tools_tup
+        if repository_tool.params_with_missing_data_table_entry:
+            missing_data_table_entry = True
+            break
+    if missing_data_table_entry:
+        # The repository must contain a tool_data_table_conf.xml.sample file that includes
+        # all required entries for all tools in the repository.
+        for sample_file in sample_files:
+            head, tail = os.path.split( sample_file )
+            if tail == 'tool_data_table_conf.xml.sample':
+                break
+        error, correction_msg = handle_sample_tool_data_table_conf_file( app, sample_file )
+        if error:
+            # TODO: Do more here than logging an exception.
+            log.debug( exception_msg )
+        # Reload the tool into the local list of repository_tools_tups.
+        repository_tool = app.toolbox.load_tool( os.path.join( tool_path, tup_path ) )
+        repository_tools_tups[ index ] = ( tup_path, repository_tool )
+    return repository_tools_tups
+def handle_missing_index_file( app, tool_path, sample_files, repository_tools_tups ):
+    """
+    Inspect each tool to see if it has any input parameters that
+    are dynamically generated select lists that depend on a .loc file.
+    This method is used by the InstallManager, which does not have access to trans.
+    """
+    missing_files_handled = []
+    for index, repository_tools_tup in enumerate( repository_tools_tups ):
+        tup_path, guid, repository_tool = repository_tools_tup
+        params_with_missing_index_file = repository_tool.params_with_missing_index_file
+        for param in params_with_missing_index_file:
+            options = param.options
+            missing_head, missing_tail = os.path.split( options.missing_index_file )
+            if missing_tail not in missing_files_handled:
+                # The repository must contain the required xxx.loc.sample file.
+                for sample_file in sample_files:
+                    sample_head, sample_tail = os.path.split( sample_file )
+                    if sample_tail == '%s.sample' % missing_tail:
+                        copy_sample_loc_file( app, sample_file )
+                        if options.tool_data_table and options.tool_data_table.missing_index_file:
+                            options.tool_data_table.handle_found_index_file( options.missing_index_file )
+                        missing_files_handled.append( missing_tail )
+                        break
+        # Reload the tool into the local list of repository_tools_tups.
+        repository_tool = app.toolbox.load_tool( os.path.join( tool_path, tup_path ) )
+        repository_tools_tups[ index ] = ( tup_path, guid, repository_tool )
+    return repository_tools_tups
+def handle_tool_dependencies( current_working_dir, repo_files_dir, repository_tools_tups ):
+    """
+    Inspect each tool to see if it includes a "requirement" that refers to a fabric
+    script.  For those that do, execute the fabric script to install tool dependencies.
+    This method is used by the InstallManager, which does not have access to trans.
+    """
+    for index, repository_tools_tup in enumerate( repository_tools_tups ):
+        tup_path, guid, repository_tool = repository_tools_tup
+        for requirement in repository_tool.requirements:
+            if requirement.type == 'fabfile':
+                log.debug( 'Executing fabric script to install dependencies for tool "%s"...' % repository_tool.name )
+                fabfile = requirement.fabfile
+                method = requirement.method
+                # Find the relative path to the fabfile.
+                relative_fabfile_path = None
+                for root, dirs, files in os.walk( repo_files_dir ):
+                    for name in files:
+                        if name == fabfile:
+                            relative_fabfile_path = os.path.join( root, name )
+                            break
+                if relative_fabfile_path:
+                    # cmd will look something like: fab -f fabfile.py install_bowtie
+                    cmd = 'fab -f %s %s' % ( relative_fabfile_path, method )
+                    tmp_name = tempfile.NamedTemporaryFile().name
+                    tmp_stderr = open( tmp_name, 'wb' )
+                    os.chdir( repo_files_dir )
+                    proc = subprocess.Popen( cmd, shell=True, stderr=tmp_stderr.fileno() )
+                    returncode = proc.wait()
+                    os.chdir( current_working_dir )
+                    tmp_stderr.close()
+                    if returncode != 0:
+                        # TODO: do something more here than logging the problem.
+                        tmp_stderr = open( tmp_name, 'rb' )
+                        error = tmp_stderr.read()
+                        tmp_stderr.close()
+                        log.debug( 'Problem installing dependencies for tool "%s"\n%s' % ( repository_tool.name, error ) )
+def add_shed_tool_conf_entry( app, shed_tool_conf, new_tool_section ):
+    """
+    Add an entry in the shed_tool_conf file. An entry looks something like:
+    <section name="Filter and Sort" id="filter">
+        <tool file="filter/filtering.xml" guid="toolshed.g2.bx.psu.edu/repos/test/filter/1.0.2"/>
+    </section>
+    This method is used by the InstallManager, which does not have access to trans.
+    """
+    # Make a backup of the hgweb.config file since we're going to be changing it.
+    if not os.path.exists( shed_tool_conf ):
+        output = open( shed_tool_conf, 'w' )
+        output.write( '<?xml version="1.0"?>\n' )
+        output.write( '<toolbox tool_path="%s">\n' % tool_path )
+        output.write( '</toolbox>\n' )
+        output.close()
+    # Make a backup of the shed_tool_conf file.
+    today = date.today()
+    backup_date = today.strftime( "%Y_%m_%d" )
+    shed_tool_conf_copy = '%s/%s_%s_backup' % ( app.config.root, shed_tool_conf, backup_date )
+    shutil.copy( os.path.abspath( shed_tool_conf ), os.path.abspath( shed_tool_conf_copy ) )
+    tmp_fd, tmp_fname = tempfile.mkstemp()
+    new_shed_tool_conf = open( tmp_fname, 'wb' )
+    for i, line in enumerate( open( shed_tool_conf ) ):
+        if line.startswith( '</toolbox>' ):
+            # We're at the end of the original config file, so add our entry.
+            new_shed_tool_conf.write( new_tool_section )
+            new_shed_tool_conf.write( line )
+        else:
+            new_shed_tool_conf.write( line )
+    new_shed_tool_conf.close()
+    shutil.move( tmp_fname, os.path.abspath( shed_tool_conf ) )
+def create_or_undelete_tool_shed_repository( app, name, description, changeset_revision, repository_clone_url, metadata_dict, owner='' ):
+    # This method is used by the InstallManager, which does not have access to trans.
+    sa_session = app.model.context.current
+    tmp_url = clean_repository_clone_url( repository_clone_url )
+    tool_shed = tmp_url.split( 'repos' )[ 0 ].rstrip( '/' )
+    if not owner:
+        owner = get_repository_owner( tmp_url )
+    includes_datatypes = 'datatypes_config' in metadata_dict
+    flush_needed = False
+    tool_shed_repository = get_repository_by_shed_name_owner_changeset_revision( app, tool_shed, name, owner, changeset_revision )
+    if tool_shed_repository:
+        if tool_shed_repository.deleted:
+            tool_shed_repository.deleted = False
+            # Reset includes_datatypes in case metadata changed since last installed.
+            tool_shed_repository.includes_datatypes = includes_datatypes
+            flush_needed = True
+    else:
+        tool_shed_repository = app.model.ToolShedRepository( tool_shed=tool_shed,
+                                                             name=name,
+                                                             description=description,
+                                                             owner=owner,
+                                                             changeset_revision=changeset_revision,
+                                                             metadata=metadata_dict,
+                                                             includes_datatypes=includes_datatypes )
+        flush_needed = True
+    if flush_needed:
+        sa_session.add( tool_shed_repository )
+        sa_session.flush()
diff --git a/lib/galaxy/webapps/community/controllers/common.py b/lib/galaxy/webapps/community/controllers/common.py
index df975bab82c..fec93f73879 100644
--- a/lib/galaxy/webapps/community/controllers/common.py
+++ b/lib/galaxy/webapps/community/controllers/common.py
@@ -186,7 +186,7 @@ def check_tool_input_params( trans, name, tool, sample_files, invalid_files ):
                         head, tail = os.path.split( sample_file )
                         if tail == 'tool_data_table_conf.xml.sample':
                             sample_found = True
-                            error, correction_msg = handle_sample_tool_data_table_conf_file( trans, sample_file )
+                            error, correction_msg = handle_sample_tool_data_table_conf_file( trans.app, sample_file )
                             if error:
                                 can_set_metadata = False
                                 invalid_files.append( ( tail, correction_msg ) ) 
@@ -207,7 +207,7 @@ def check_tool_input_params( trans, name, tool, sample_files, invalid_files ):
                     for sample_file in sample_files:
                         sample_head, sample_tail = os.path.split( sample_file )
                         if sample_tail == '%s.sample' % index_tail:
-                            copy_sample_loc_file( trans, sample_file )
+                            copy_sample_loc_file( trans.app, sample_file )
                             options.index_file = index_tail
                             options.missing_index_file = None
                             if options.tool_data_table:
diff --git a/lib/galaxy/webapps/community/controllers/upload.py b/lib/galaxy/webapps/community/controllers/upload.py
index bb848a766a7..e297e9ee2ed 100644
--- a/lib/galaxy/webapps/community/controllers/upload.py
+++ b/lib/galaxy/webapps/community/controllers/upload.py
@@ -129,13 +129,13 @@ class UploadController( BaseUIController ):
                         # file is being uploaded by parsing the file and adding new entries
                         # to the in-memory trans.app.tool_data_tables dictionary as well as
                         # appending them to the shed's tool_data_table_conf.xml file on disk.
-                        error, error_message = handle_sample_tool_data_table_conf_file( trans, full_path )
+                        error, error_message = handle_sample_tool_data_table_conf_file( trans.app, full_path )
                         if error:
                             message = '%s<br/>%s' % ( message, error_message )
                     if full_path.endswith( '.loc.sample' ):
                         # Handle the special case where a xxx.loc.sample file is
                         # being uploaded by copying it to ~/tool-data/xxx.loc.
-                        copy_sample_loc_file( trans, full_path )
+                        copy_sample_loc_file( trans.app, full_path )
                     # See if the content of the change set was valid.
                     admin_only = len( repository.downloadable_revisions ) != 1
                     handle_email_alerts( trans, repository, content_alert_str=content_alert_str, new_repo_alert=new_repo_alert, admin_only=admin_only )
@@ -267,7 +267,7 @@ class UploadController( BaseUIController ):
                 if filename_in_archive.endswith( '.loc.sample' ):
                     # Handle the special case where a xxx.loc.sample file is
                     # being uploaded by copying it to ~/tool-data/xxx.loc.
-                    copy_sample_loc_file( trans, filename_in_archive )
+                    copy_sample_loc_file( trans.app, filename_in_archive )
             try:
                 commands.commit( repo.ui, repo, full_path, user=trans.user.username, message=commit_message )
             except Exception, e:
diff --git a/templates/user/info.mako b/templates/user/info.mako
index 1c1b39096ea..3632e63651b 100644
--- a/templates/user/info.mako
+++ b/templates/user/info.mako
@@ -22,12 +22,14 @@
             <div class="form-row">
                 <label>Public name:</label>
                 %if webapp == 'community':
-                    ${username}
                     %if user.active_repositories:
+                        <input type="hidden" name="username" value="${username}"/>
+                        ${username}
                         <div class="toolParamHelp" style="clear: both;">
                             You cannot change your public name after you have created a repository in this tool shed.
                         </div>
                     %else:
+                        <input type="text" name="username" size="40" value="${username}"/>
                         <div class="toolParamHelp" style="clear: both;">
                             Your public name provides a means of identifying you publicly within this tool shed. Public
                             names must be at least four characters in length and contain only lower-case letters, numbers,
diff --git a/tool_shed_install.xml.sample b/tool_shed_install.xml.sample
new file mode 100644
index 00000000000..d5eb434ca7f
--- /dev/null
+++ b/tool_shed_install.xml.sample
@@ -0,0 +1,114 @@
+<?xml version="1.0"?>
+<toolshed name="toolshed.g2.bx.psu.edu">
+    <section name="EMBOSS" id="EMBOSSLite">
+        <repository name="emboss_5" description="Galaxy wrappers for EMBOSS version 5 tools" changeset_revision="PlaceHereWhenKnown">
+            <tool file="emboss_5/emboss_antigenic.xml" id="EMBOSS: antigenic1" version="5.0.0" />
+            <tool file="emboss_5/emboss_backtranseq.xml" id="EMBOSS: backtranseq2" version="5.0.0" />
+            <tool file="emboss_5/emboss_banana.xml" id="EMBOSS: banana3" version="5.0.0" />
+            <tool file="emboss_5/emboss_biosed.xml" id="EMBOSS: biosed4" version="5.0.0" />
+            <tool file="emboss_5/emboss_btwisted.xml" id="EMBOSS: btwisted5" version="5.0.0" />
+            <tool file="emboss_5/emboss_cai_custom.xml" id="EMBOSS: cai_custom6" version="5.0.0" />
+            <tool file="emboss_5/emboss_cai.xml" id="EMBOSS: cai6" version="5.0.0" />
+            <tool file="emboss_5/emboss_chaos.xml" id="EMBOSS: chaos7" version="5.0.0" />
+            <tool file="emboss_5/emboss_charge.xml" id="EMBOSS: charge8" version="5.0.0" />
+            <tool file="emboss_5/emboss_checktrans.xml" id="EMBOSS: checktrans9" version="5.0.0" />
+            <tool file="emboss_5/emboss_chips.xml" id="EMBOSS: chips10" version="5.0.0" />
+            <tool file="emboss_5/emboss_cirdna.xml" id="EMBOSS: cirdna11" version="5.0.0" />
+            <tool file="emboss_5/emboss_codcmp.xml" id="EMBOSS: codcmp12" version="5.0.0" />
+            <tool file="emboss_5/emboss_coderet.xml" id="EMBOSS: coderet13" version="5.0.0" />
+            <tool file="emboss_5/emboss_compseq.xml" id="EMBOSS: compseq14" version="5.0.0" />
+            <tool file="emboss_5/emboss_cpgplot.xml" id="EMBOSS: cpgplot15" version="5.0.0" />
+            <tool file="emboss_5/emboss_cpgreport.xml" id="EMBOSS: cpgreport16" version="5.0.0" />
+            <tool file="emboss_5/emboss_cusp.xml" id="EMBOSS: cusp17" version="5.0.0" />
+            <tool file="emboss_5/emboss_cutseq.xml" id="EMBOSS: cutseq18" version="5.0.0" />
+            <tool file="emboss_5/emboss_dan.xml" id="EMBOSS: dan19" version="5.0.0" />
+            <tool file="emboss_5/emboss_degapseq.xml" id="EMBOSS: degapseq20" version="5.0.0" />
+            <tool file="emboss_5/emboss_descseq.xml" id="EMBOSS: descseq21" version="5.0.0" />
+            <tool file="emboss_5/emboss_diffseq.xml" id="EMBOSS: diffseq22" version="5.0.0" />
+            <tool file="emboss_5/emboss_digest.xml" id="EMBOSS: digest23" version="5.0.0" />
+            <tool file="emboss_5/emboss_dotmatcher.xml" id="EMBOSS: dotmatcher24" version="5.0.0" />
+            <tool file="emboss_5/emboss_dotpath.xml" id="EMBOSS: dotpath25" version="5.0.0" />
+            <tool file="emboss_5/emboss_dottup.xml" id="EMBOSS: dottup26" version="5.0.0" />
+            <tool file="emboss_5/emboss_dreg.xml" id="EMBOSS: dreg27" version="5.0.0" />
+            <tool file="emboss_5/emboss_einverted.xml" id="EMBOSS: einverted28" version="5.0.0" />
+            <tool file="emboss_5/emboss_epestfind.xml" id="EMBOSS: epestfind29" version="5.0.0" />
+            <tool file="emboss_5/emboss_equicktandem.xml" id="EMBOSS: equicktandem31" version="5.0.0" />
+            <tool file="emboss_5/emboss_est2genome.xml" id="EMBOSS: est2genome32" version="5.0.0" />
+            <tool file="emboss_5/emboss_etandem.xml" id="EMBOSS: etandem33" version="5.0.0" />
+            <tool file="emboss_5/emboss_extractfeat.xml" id="EMBOSS: extractfeat34" version="5.0.0" />
+            <tool file="emboss_5/emboss_extractseq.xml" id="EMBOSS: extractseq35" version="5.0.0" />
+            <tool file="emboss_5/emboss_freak.xml" id="EMBOSS: freak36" version="5.0.0" />
+            <tool file="emboss_5/emboss_fuzznuc.xml" id="EMBOSS: fuzznuc37" version="5.0.0" />
+            <tool file="emboss_5/emboss_fuzzpro.xml" id="EMBOSS: fuzzpro38" version="5.0.0" />
+            <tool file="emboss_5/emboss_fuzztran.xml" id="EMBOSS: fuzztran39" version="5.0.0" />
+            <tool file="emboss_5/emboss_garnier.xml" id="EMBOSS: garnier40" version="5.0.0" />
+            <tool file="emboss_5/emboss_geecee.xml" id="EMBOSS: geecee41" version="5.0.0" />
+            <tool file="emboss_5/emboss_getorf.xml" id="EMBOSS: getorf42" version="5.0.0" />
+            <tool file="emboss_5/emboss_helixturnhelix.xml" id="EMBOSS: helixturnhelix43" version="5.0.0" />
+            <tool file="emboss_5/emboss_hmoment.xml" id="EMBOSS: hmoment44" version="5.0.0" />
+            <tool file="emboss_5/emboss_iep.xml" id="EMBOSS: iep45" version="5.0.0" />
+            <tool file="emboss_5/emboss_infoseq.xml" id="EMBOSS: infoseq46" version="5.0.0" />
+            <tool file="emboss_5/emboss_isochore.xml" id="EMBOSS: isochore47" version="5.0.0" />
+            <tool file="emboss_5/emboss_lindna.xml" id="EMBOSS: lindna48" version="5.0.0" />
+            <tool file="emboss_5/emboss_marscan.xml" id="EMBOSS: marscan49" version="5.0.0" />
+            <tool file="emboss_5/emboss_maskfeat.xml" id="EMBOSS: maskfeat50" version="5.0.0" />
+            <tool file="emboss_5/emboss_maskseq.xml" id="EMBOSS: maskseq51" version="5.0.0" />
+            <tool file="emboss_5/emboss_matcher.xml" id="EMBOSS: matcher52" version="5.0.0" />
+            <tool file="emboss_5/emboss_megamerger.xml" id="EMBOSS: megamerger53" version="5.0.0" />
+            <tool file="emboss_5/emboss_merger.xml" id="EMBOSS: merger54" version="5.0.0" />
+            <tool file="emboss_5/emboss_msbar.xml" id="EMBOSS: msbar55" version="5.0.0" />
+            <tool file="emboss_5/emboss_needle.xml" id="EMBOSS: needle56" version="5.0.0" />
+            <tool file="emboss_5/emboss_newcpgreport.xml" id="EMBOSS: newcpgreport57" version="5.0.0" />
+            <tool file="emboss_5/emboss_newcpgseek.xml" id="EMBOSS: newcpgseek58" version="5.0.0" />
+            <tool file="emboss_5/emboss_newseq.xml" id="EMBOSS: newseq59" version="5.0.0" />
+            <tool file="emboss_5/emboss_noreturn.xml" id="EMBOSS: noreturn60" version="5.0.0" />
+            <tool file="emboss_5/emboss_notseq.xml" id="EMBOSS: notseq61" version="5.0.0" />
+            <tool file="emboss_5/emboss_nthseq.xml" id="EMBOSS: nthseq62" version="5.0.0" />
+            <tool file="emboss_5/emboss_octanol.xml" id="EMBOSS: octanol63" version="5.0.0" />
+            <tool file="emboss_5/emboss_oddcomp.xml" id="EMBOSS: oddcomp64" version="5.0.0" />
+            <tool file="emboss_5/emboss_palindrome.xml" id="EMBOSS: palindrome65" version="5.0.0" />
+            <tool file="emboss_5/emboss_pasteseq.xml" id="EMBOSS: pasteseq66" version="5.0.0" />
+            <tool file="emboss_5/emboss_patmatdb.xml" id="EMBOSS: patmatdb67" version="5.0.0" />
+            <tool file="emboss_5/emboss_pepcoil.xml" id="EMBOSS: pepcoil68" version="5.0.0" />
+            <tool file="emboss_5/emboss_pepinfo.xml" id="EMBOSS: pepinfo69" version="5.0.0" />
+            <tool file="emboss_5/emboss_pepnet.xml" id="EMBOSS: pepnet70" version="5.0.0" />
+            <tool file="emboss_5/emboss_pepstats.xml" id="EMBOSS: pepstats71" version="5.0.0" />
+            <tool file="emboss_5/emboss_pepwheel.xml" id="EMBOSS: pepwheel72" version="5.0.0" />
+            <tool file="emboss_5/emboss_pepwindow.xml" id="EMBOSS: pepwindow73" version="5.0.0" />
+            <tool file="emboss_5/emboss_pepwindowall.xml" id="EMBOSS: pepwindowall74" version="5.0.0" />
+            <tool file="emboss_5/emboss_plotcon.xml" id="EMBOSS: plotcon75" version="5.0.0" />
+            <tool file="emboss_5/emboss_plotorf.xml" id="EMBOSS: plotorf76" version="5.0.0" />
+            <tool file="emboss_5/emboss_polydot.xml" id="EMBOSS: polydot77" version="5.0.0" />
+            <tool file="emboss_5/emboss_preg.xml" id="EMBOSS: preg78" version="5.0.0" />
+            <tool file="emboss_5/emboss_prettyplot.xml" id="EMBOSS: prettyplot79" version="5.0.0" />
+            <tool file="emboss_5/emboss_prettyseq.xml" id="EMBOSS: prettyseq80" version="5.0.0" />
+            <tool file="emboss_5/emboss_primersearch.xml" id="EMBOSS: primersearch81" version="5.0.0" />
+            <tool file="emboss_5/emboss_revseq.xml" id="EMBOSS: revseq82" version="5.0.0" />
+            <tool file="emboss_5/emboss_seqmatchall.xml" id="EMBOSS: seqmatchall83" version="5.0.0" />
+            <tool file="emboss_5/emboss_seqret.xml" id="EMBOSS: seqret84" version="5.0.0" />
+            <tool file="emboss_5/emboss_showfeat.xml" id="EMBOSS: showfeat85" version="5.0.0" />
+            <tool file="emboss_5/emboss_shuffleseq.xml" id="EMBOSS: shuffleseq87" version="5.0.0" />
+            <tool file="emboss_5/emboss_sigcleave.xml" id="EMBOSS: sigcleave88" version="5.0.0" />
+            <tool file="emboss_5/emboss_sirna.xml" id="EMBOSS: sirna89" version="5.0.0" />
+            <tool file="emboss_5/emboss_sixpack.xml" id="EMBOSS: sixpack90" version="5.0.0" />
+            <tool file="emboss_5/emboss_skipseq.xml" id="EMBOSS: skipseq91" version="5.0.0" />
+            <tool file="emboss_5/emboss_splitter.xml" id="EMBOSS: splitter92" version="5.0.0" />
+            <tool file="emboss_5/emboss_supermatcher.xml" id="EMBOSS: supermatcher95" version="5.0.0" />
+            <tool file="emboss_5/emboss_syco.xml" id="EMBOSS: syco96" version="5.0.0" />
+            <tool file="emboss_5/emboss_tcode.xml" id="EMBOSS: tcode97" version="5.0.0" />
+            <tool file="emboss_5/emboss_textsearch.xml" id="EMBOSS: textsearch98" version="5.0.0" />
+            <tool file="emboss_5/emboss_tmap.xml" id="EMBOSS: tmap99" version="5.0.0" />
+            <tool file="emboss_5/emboss_tranalign.xml" id="EMBOSS: tranalign100" version="5.0.0" />
+            <tool file="emboss_5/emboss_transeq.xml" id="EMBOSS: transeq101" version="5.0.0" />
+            <tool file="emboss_5/emboss_trimest.xml" id="EMBOSS: trimest102" version="5.0.0" />
+            <tool file="emboss_5/emboss_trimseq.xml" id="EMBOSS: trimseq103" version="5.0.0" />
+            <tool file="emboss_5/emboss_twofeat.xml" id="EMBOSS: twofeat104" version="5.0.0" />
+            <tool file="emboss_5/emboss_union.xml" id="EMBOSS: union105" version="5.0.0" />
+            <tool file="emboss_5/emboss_vectorstrip.xml" id="EMBOSS: vectorstrip106" version="5.0.0" />
+            <tool file="emboss_5/emboss_water.xml" id="EMBOSS: water107" version="5.0.0" />
+            <tool file="emboss_5/emboss_wobble.xml" id="EMBOSS: wobble108" version="5.0.0" />
+            <tool file="emboss_5/emboss_wordcount.xml" id="EMBOSS: wordcount109" version="5.0.0" />
+            <tool file="emboss_5/emboss_wordmatch.xml" id="EMBOSS: wordmatch110" version="5.0.0" />
+        </repository>
+    </section>
+</toolshed>
diff --git a/universe_wsgi.ini.sample b/universe_wsgi.ini.sample
index 07905f389db..3ea4e1f42b0 100644
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -131,6 +131,22 @@ paste.app_factory = galaxy.web.buildapp:app_factory
 # Other tool config files must include the tool_path as an attribute in the <toolbox> tag.
 #tool_path = tools
 
+# Enable automatic installation of tools that used to be in the Galaxy
+# distribution but are now in the main Galaxy tool shed.  The tools
+# that will be installed are configured in the config file named
+# tool_shed_install.xml, which is located in the Galaxy install directory.
+# Tools already installed will not be re-installed even if they are
+# referenced in the tool_shed_install.xml file.
+#enable_tool_shed_install = False
+#tool_shed_install_config_file = tool_shed_install.xml
+
+# CRITICAL NOTE: the location in which the tools will be installed is the
+# location pointed to by the "tool_path" attribute in the following file.
+# The default location setting in shed_tool_conf.xml ("../shed_tools") may
+# be problematic for some cluster environments, so make sure to change it
+# if appropriate or use a different file name for the setting.
+#install_tool_config_file = shed_tool_conf.xml
+
 # Directory where data used by tools is located, see the samples in that
 # directory and the wiki for help:
 # http://wiki.g2.bx.psu.edu/Admin/Data%20Integration

From cb37960b167ad870ba2e3113d913cb03e01f2f0c Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Thu, 8 Dec 2011 16:48:34 -0500
Subject: [PATCH 314/362] Clean up some debugging stuff in object store.

---
 lib/galaxy/jobs/__init__.py  |  1 -
 lib/galaxy/tools/__init__.py | 18 +-----------------
 2 files changed, 1 insertion(+), 18 deletions(-)

diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index c98cd5b9f61..938cf97041d 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -486,7 +486,6 @@ class JobWrapper( object ):
                     dataset.extension = 'data'
                 # Update (non-library) job output datasets through the object store
                 if dataset not in job.output_library_datasets:
-                    print "====== Handing failed job's dataset '%s' with name '%s' to object store" % (dataset.id, dataset.file_name)
                     self.app.object_store.update_from_file(dataset.id, create=True)
                 self.sa_session.add( dataset )
                 self.sa_session.flush()
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 67a6d4fa122..b425725216f 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1850,8 +1850,6 @@ class Tool:
                 a_files = os.listdir( temp_file_path )
                 if len( a_files ) > 0:
                     for f in a_files:
-                        # print "------ Instructing ObjectStore to update/create file: %s from %s" \
-                        #     % (hda.dataset.id, os.path.join(temp_file_path, f))
                         self.app.object_store.update_from_file(hda.dataset.id,
                             extra_dir="dataset_%d_files" % hda.dataset.id, 
                             alt_name = f,
@@ -1860,21 +1858,7 @@ class Tool:
                     # Clean up after being handled by object store. 
                     # FIXME: If the object (e.g., S3) becomes async, this will 
                     # cause issues so add it to the object store functionality?
-                    # shutil.rmtree(temp_file_path)
-
-                    # store_file_path = os.path.join( 
-                    #     os.path.join( self.app.config.file_path, *directory_hash_id( hda.dataset.id ) ), 
-                    #     "dataset_%d_files" % hda.dataset.id )
-                    # shutil.move( temp_file_path, store_file_path )
-                    # # Fix permissions
-                    # for basedir, dirs, files in os.walk( store_file_path ):
-                    #     util.umask_fix_perms( basedir, self.app.config.umask, 0777, self.app.config.gid )
-                    #     for file in files:
-                    #         path = os.path.join( basedir, file )
-                    #         # Ignore symlinks
-                    #         if os.path.islink( path ):
-                    #             continue 
-                    #         util.umask_fix_perms( path, self.app.config.umask, 0666, self.app.config.gid )
+                    shutil.rmtree(temp_file_path)
             except:
                 continue
     

From 8ac0cc4e9346fc74f846d86ea5087a26fa016141 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Thu, 8 Dec 2011 16:57:12 -0500
Subject: [PATCH 315/362] Allow not specifying a value attribute for an
 optional tool parameter. Partially resolves #661.

---
 lib/galaxy/tools/parameters/basic.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index d0c9db07921..8d98e2cc832 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -224,7 +224,7 @@ class IntegerToolParameter( TextToolParameter ):
                 int( self.value )
             except:
                 raise ValueError( "An integer is required" )
-        elif self.value is None:
+        elif self.value is None and not self.optional:
             raise ValueError( "The settings for the field named '%s' require a 'value' setting and optionally a default value which must be an integer" % self.name )
         self.min = elem.get( 'min' )
         self.max = elem.get( 'max' )
@@ -296,7 +296,7 @@ class FloatToolParameter( TextToolParameter ):
                 float( self.value )
             except:
                 raise ValueError( "A real number is required" )
-        elif self.value is None:
+        elif self.value is None and not self.optional:
             raise ValueError( "The settings for this field require a 'value' setting and optionally a default value which must be a real number" )
         if self.min:
             try:

From f686e3283188a461a8b31563966f0e2889749eb3 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Thu, 8 Dec 2011 17:34:19 -0500
Subject: [PATCH 316/362] Object store bug fix (direct filesystem access in the
 default tool action)

---
 lib/galaxy/tools/actions/__init__.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/lib/galaxy/tools/actions/__init__.py b/lib/galaxy/tools/actions/__init__.py
index 7207d2987d9..4b702e4d722 100644
--- a/lib/galaxy/tools/actions/__init__.py
+++ b/lib/galaxy/tools/actions/__init__.py
@@ -291,14 +291,11 @@ class DefaultToolAction( object ):
                     trans.sa_session.flush()
                     trans.app.security_agent.set_all_dataset_permissions( data.dataset, output_permissions )
                 # Create an empty file immediately
-                # open( data.file_name, "w" ).close()
                 trans.app.object_store.create( data.id, store_name=store_name )
                 if not store_name_set:
                     # Ensure all other datasets in this job are created in the same store
                     store_name = trans.app.object_store.store_name( data.id )
                     store_name_set = True
-                # Fix permissions
-                util.umask_fix_perms( data.file_name, trans.app.config.umask, 0666 )
                 # This may not be neccesary with the new parent/child associations
                 data.designation = name
                 # Copy metadata from one of the inputs if requested. 

From c5ce54176718c56e10c7b3f65c52f4b9056452ef Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Thu, 8 Dec 2011 17:45:48 -0500
Subject: [PATCH 317/362] Missing part of the last commit.

---
 lib/galaxy/objectstore/__init__.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/lib/galaxy/objectstore/__init__.py b/lib/galaxy/objectstore/__init__.py
index 3927cbd01e3..ec765a1baea 100644
--- a/lib/galaxy/objectstore/__init__.py
+++ b/lib/galaxy/objectstore/__init__.py
@@ -204,6 +204,7 @@ class DiskObjectStore(ObjectStore):
     def __init__(self, config, file_path=None, extra_dirs=None):
         super(DiskObjectStore, self).__init__()
         self.file_path = file_path or config.file_path
+        self.config = config
         if extra_dirs is not None:
             self.extra_dirs = extra_dirs
     
@@ -300,6 +301,7 @@ class DiskObjectStore(ObjectStore):
             if not dir_only:
                 path = os.path.join(path, alt_name if alt_name else "dataset_%s.dat" % dataset_id)
                 open(path, 'w').close() 
+                util.umask_fix_perms( path, self.config.umask, 0666 )
 
     def empty(self, dataset_id, **kwargs):
         return os.path.getsize(self.get_filename(dataset_id, **kwargs)) > 0

From 6693ec516cf1c86195e9b531823898af9d1cea86 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Thu, 8 Dec 2011 17:46:59 -0500
Subject: [PATCH 318/362] Rename HierarchicalObjectStore to
 DistributedObjectStore.

---
 ...> distributed_object_store_conf.xml.sample |  0
 lib/galaxy/config.py                          |  2 +-
 lib/galaxy/objectstore/__init__.py            | 32 +++++++++++++------
 universe_wsgi.ini.sample                      |  2 +-
 4 files changed, 24 insertions(+), 12 deletions(-)
 rename hierarchical_object_store_conf.xml.sample => distributed_object_store_conf.xml.sample (100%)

diff --git a/hierarchical_object_store_conf.xml.sample b/distributed_object_store_conf.xml.sample
similarity index 100%
rename from hierarchical_object_store_conf.xml.sample
rename to distributed_object_store_conf.xml.sample
diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py
index 3703325dfdb..eb13a62532a 100644
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -156,7 +156,7 @@ class Configuration( object ):
         self.s3_bucket = kwargs.get( 's3_bucket', None)
         self.use_reduced_redundancy = kwargs.get( 'use_reduced_redundancy', False )
         self.object_store_cache_size = float(kwargs.get( 'object_store_cache_size', -1 ))
-        self.hierarchical_object_store_config_file = kwargs.get( 'hierarchical_object_store_config_file', None )
+        self.distributed_object_store_config_file = kwargs.get( 'distributed_object_store_config_file', None )
         # Parse global_conf and save the parser
         global_conf = kwargs.get( 'global_conf', None )
         global_conf_parser = ConfigParser.ConfigParser()
diff --git a/lib/galaxy/objectstore/__init__.py b/lib/galaxy/objectstore/__init__.py
index ec765a1baea..fe65ed6683c 100644
--- a/lib/galaxy/objectstore/__init__.py
+++ b/lib/galaxy/objectstore/__init__.py
@@ -854,7 +854,7 @@ class S3ObjectStore(ObjectStore):
         return None
 
 
-class HierarchicalObjectStore(ObjectStore):
+class DistributedObjectStore(ObjectStore):
     """
     ObjectStore that defers to a list of backends, for getting objects the
     first store where the object exists is used, objects are created in a
@@ -862,22 +862,22 @@ class HierarchicalObjectStore(ObjectStore):
     """
     
     def __init__(self, config):
-        super(HierarchicalObjectStore, self).__init__()
-        assert config is not None, "hierarchical object store ('object_store = hierarchical') " \
+        super(DistributedObjectStore, self).__init__()
+        assert config is not None, "distributed object store ('object_store = distributed') " \
                                    "requires a config file, please set one in " \
-                                   "'hierarchical_object_store_config_file')"
-        self.hierarchical_config = config
+                                   "'distributed_object_store_config_file')"
+        self.distributed_config = config
         self.backends = {}
         self.weighted_backend_names = []
 
         random.seed()
 
-        self.__parse_hierarchical_config(config)
+        self.__parse_distributed_config(config)
 
-    def __parse_hierarchical_config(self, config):
-        tree = util.parse_xml(self.hierarchical_config)
+    def __parse_distributed_config(self, config):
+        tree = util.parse_xml(self.distributed_config)
         root = tree.getroot()
-        log.debug('Loading backends for hierarchical object store from %s' % self.hierarchical_config)
+        log.debug('Loading backends for distributed object store from %s' % self.distributed_config)
         for elem in [ e for e in root if e.tag == 'backend' ]:
             name = elem.get('name')
             weight = int(elem.get('weight', 1))
@@ -980,6 +980,16 @@ class HierarchicalObjectStore(ObjectStore):
                 return store
         return None
 
+class HierarchicalObjectStore(ObjectStore):
+    """
+    ObjectStore that defers to a list of backends, for getting objects the
+    first store where the object exists is used, objects are always created
+    in the first store.
+    """
+    
+    def __init__(self, backends=[]):
+        super(HierarchicalObjectStore, self).__init__()
+
 def build_object_store_from_config(config):
     """ Depending on the configuration setting, invoke the appropriate object store
     """
@@ -990,8 +1000,10 @@ def build_object_store_from_config(config):
         os.environ['AWS_ACCESS_KEY_ID'] = config.aws_access_key
         os.environ['AWS_SECRET_ACCESS_KEY'] = config.aws_secret_key
         return S3ObjectStore(config=config)
+    elif store == 'distributed':
+        return DistributedObjectStore(config.distributed_object_store_config_file)
     elif store == 'hierarchical':
-        return HierarchicalObjectStore(config.hierarchical_object_store_config_file)
+        return HierarchicalObjectStore()
 
 def convert_bytes(bytes):
     """ A helper function used for pretty printing disk usage """
diff --git a/universe_wsgi.ini.sample b/universe_wsgi.ini.sample
index 05a2f5b7f25..a28f1a3567d 100644
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -437,7 +437,7 @@ use_interactive = True
 
 # -- Beta features
 
-# Object store mode (valid options are: disk, s3, hierarchical)
+# Object store mode (valid options are: disk, s3, distributed, hierarchical)
 #object_store = s3
 #aws_access_key = <AWS access key>
 #aws_secret_key = <AWS secret key>

From 24d610dac61e9dff4b34285db3aaccd968ba1af5 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Fri, 9 Dec 2011 07:01:31 -0500
Subject: [PATCH 319/362] Job.fail() failure bugfix.

---
 lib/galaxy/jobs/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 938cf97041d..376b4e82df7 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -500,7 +500,7 @@ class JobWrapper( object ):
         # If the job was deleted, call tool specific fail actions (used for e.g. external metadata) and clean up
         if self.tool:
             self.tool.job_failed( self, message, exception )
-        if self.app.cleanup_job == 'always' or (self.app.config.cleanup_job == 'onsuccess' and job.state == job.states.DELETED):
+        if self.app.config.cleanup_job == 'always' or (self.app.config.cleanup_job == 'onsuccess' and job.state == job.states.DELETED):
             self.cleanup()
 
     def change_state( self, state, info = False ):

From 7aa4a73fc7cd1b9afd6b529324a6b0b1415f44f7 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Fri, 9 Dec 2011 09:40:40 -0500
Subject: [PATCH 320/362] Fix unit test broken by object store.

---
 lib/galaxy/model/mapping_tests.py  | 5 +++--
 lib/galaxy/objectstore/__init__.py | 9 +++++++++
 2 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/model/mapping_tests.py b/lib/galaxy/model/mapping_tests.py
index ef41b1d3b11..af7b76b0506 100644
--- a/lib/galaxy/model/mapping_tests.py
+++ b/lib/galaxy/model/mapping_tests.py
@@ -36,8 +36,9 @@ class MappingTests( unittest.TestCase ):
         assert hists[0].user == users[0]
         assert hists[1].user is None
         assert hists[1].datasets[0].metadata.chromCol == 1
-        id = hists[1].datasets[0].id
-        assert hists[1].datasets[0].file_name == os.path.join( "/tmp", *directory_hash_id( id ) ) + ( "/dataset_%d.dat" % id )
+        # The filename test has moved to objecstore
+        #id = hists[1].datasets[0].id
+        #assert hists[1].datasets[0].file_name == os.path.join( "/tmp", *directory_hash_id( id ) ) + ( "/dataset_%d.dat" % id )
         # Do an update and check
         hists[1].name = "History 2b"
         model.session.flush()
diff --git a/lib/galaxy/objectstore/__init__.py b/lib/galaxy/objectstore/__init__.py
index fe65ed6683c..5190e4d6734 100644
--- a/lib/galaxy/objectstore/__init__.py
+++ b/lib/galaxy/objectstore/__init__.py
@@ -200,6 +200,15 @@ class DiskObjectStore(ObjectStore):
     """
     Standard Galaxy object store, stores objects in files under a specific
     directory on disk.
+
+    >>> from galaxy.util.bunch import Bunch
+    >>> import tempfile
+    >>> file_path=tempfile.mkdtemp()
+    >>> s = DiskObjectStore(Bunch(umask=077), file_path=file_path)
+    >>> s.create(1)
+    >>> s.exists(1)
+    True
+    >>> assert s.get_filename(1) == file_path + '/000/dataset_1.dat'
     """
     def __init__(self, config, file_path=None, extra_dirs=None):
         super(DiskObjectStore, self).__init__()

From 2dff7eb5fd0ab467c1d706b6e27330d5af0adb44 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Fri, 9 Dec 2011 09:50:15 -0500
Subject: [PATCH 321/362] Fix variable multiple outputs
 (collect_primary_datasets) to work with ObjectStore.

---
 lib/galaxy/tools/__init__.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index b425725216f..ddf55c9090f 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1958,7 +1958,7 @@ class Tool:
                 self.sa_session.add( primary_data )
                 self.sa_session.flush()
                 # Move data from temp location to dataset location
-                shutil.move( filename, primary_data.file_name )
+                self.app.object_store.update_from_file(primary_data.dataset.id, filename, create=True)
                 primary_data.set_size()
                 primary_data.name = "%s (%s)" % ( outdata.name, designation )
                 primary_data.info = outdata.info
@@ -1970,7 +1970,7 @@ class Tool:
                 job = None
                 for assoc in outdata.creating_job_associations:
                     job = assoc.job
-                    break   
+                    break
                 if job:
                     assoc = self.app.model.JobToOutputDatasetAssociation( '__new_primary_file_%s|%s__' % ( name, designation ), primary_data )
                     assoc.job = job

From 51da674bd15a1010fdeb07296dc8d81547c7cbdf Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Fri, 9 Dec 2011 10:19:20 -0500
Subject: [PATCH 322/362] Update collect_child_datasets to work with
 ObjectStore.

---
 lib/galaxy/tools/__init__.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index ddf55c9090f..3e208cefcc8 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1890,7 +1890,7 @@ class Tool:
                                                                           sa_session=self.sa_session )
                 self.app.security_agent.copy_dataset_permissions( outdata.dataset, child_dataset.dataset )
                 # Move data from temp location to dataset location
-                shutil.move( filename, child_dataset.file_name )
+                self.app.object_store.update_from_file(child_dataset.dataset.id, filename, create=True)
                 self.sa_session.add( child_dataset )
                 self.sa_session.flush()
                 child_dataset.set_size()
@@ -1902,7 +1902,7 @@ class Tool:
                 job = None
                 for assoc in outdata.creating_job_associations:
                     job = assoc.job
-                    break   
+                    break
                 if job:
                     assoc = self.app.model.JobToOutputDatasetAssociation( '__new_child_file_%s|%s__' % ( name, designation ), child_dataset )
                     assoc.job = job

From f6d6bb332881ff650f4aa8daf9b5253cd21d027e Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Fri, 9 Dec 2011 11:10:44 -0500
Subject: [PATCH 323/362] Add __non_zero__ method to
 ToolParameterValueWrappers. Resolves #661.

---
 lib/galaxy/tools/__init__.py | 20 +++++++++++++++-----
 1 file changed, 15 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 3e208cefcc8..881389bd531 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -2141,7 +2141,14 @@ class BadValue( object ):
     def __init__( self, value ):
         self.value = value
 
-class RawObjectWrapper( object ):
+class ToolParameterValueWrapper( object ):
+    """
+    Base class for object that Wraps a Tool Parameter and Value.
+    """
+    def __nonzero__( self ):
+        return bool( self.value )
+
+class RawObjectWrapper( ToolParameterValueWrapper ):
     """
     Wraps an object so that __str__ returns module_name:class_name.
     """
@@ -2152,7 +2159,7 @@ class RawObjectWrapper( object ):
     def __getattr__( self, key ):
         return getattr( self.obj, key )
 
-class LibraryDatasetValueWrapper( object ):
+class LibraryDatasetValueWrapper( ToolParameterValueWrapper ):
     """
     Wraps an input so that __str__ gives the "param_dict" representation.
     """
@@ -2173,7 +2180,7 @@ class LibraryDatasetValueWrapper( object ):
     def __getattr__( self, key ):
         return getattr( self.value, key )
         
-class InputValueWrapper( object ):
+class InputValueWrapper( ToolParameterValueWrapper ):
     """
     Wraps an input so that __str__ gives the "param_dict" representation.
     """
@@ -2186,7 +2193,7 @@ class InputValueWrapper( object ):
     def __getattr__( self, key ):
         return getattr( self.value, key )
 
-class SelectToolParameterWrapper( object ):
+class SelectToolParameterWrapper( ToolParameterValueWrapper ):
     """
     Wraps a SelectTooParameter so that __str__ returns the selected value, but all other
     attributes are accessible.
@@ -2218,7 +2225,7 @@ class SelectToolParameterWrapper( object ):
     def __getattr__( self, key ):
         return getattr( self.input, key )
 
-class DatasetFilenameWrapper( object ):
+class DatasetFilenameWrapper( ToolParameterValueWrapper ):
     """
     Wraps a dataset so that __str__ returns the filename, but all other
     attributes are accessible.
@@ -2278,6 +2285,9 @@ class DatasetFilenameWrapper( object ):
             return self.false_path
         else:
             return getattr( self.dataset, key )
+    
+    def __nonzero__( self ):
+        return bool( self.dataset )
         
 def json_fix( val ):
     if isinstance( val, list ):

From f5f140b986531b02577aa199b35fcfab87759471 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Fri, 9 Dec 2011 14:56:58 -0500
Subject: [PATCH 324/362] Object Store: Create datasets when accessed via
 file_name.

---
 lib/galaxy/exceptions/__init__.py  |  4 ++++
 lib/galaxy/model/__init__.py       | 11 +++++++----
 lib/galaxy/objectstore/__init__.py |  6 +-----
 3 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/lib/galaxy/exceptions/__init__.py b/lib/galaxy/exceptions/__init__.py
index 0b1ea5af683..7d72df19a07 100644
--- a/lib/galaxy/exceptions/__init__.py
+++ b/lib/galaxy/exceptions/__init__.py
@@ -18,3 +18,7 @@ class ItemAccessibilityException( MessageException ):
 
 class ItemOwnershipException( MessageException ):
     pass
+
+class ObjectNotFound( Exception ):
+    """ Accessed object was not found """
+    pass
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 669e49942e4..6f1c807b45f 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -16,6 +16,7 @@ from galaxy.security import RBACAgent, get_permitted_actions
 from galaxy.util.hash_util import *
 from galaxy.web.form_builder import *
 from galaxy.model.item_attrs import UsesAnnotations, APIItem
+from galaxy.exceptions import ObjectNotFound
 from sqlalchemy.orm import object_session
 from sqlalchemy.sql.expression import func
 import os.path, os, errno, codecs, operator, socket, pexpect, logging, time, shutil
@@ -649,10 +650,12 @@ class Dataset( object ):
         if not self.external_filename:
             assert self.id is not None, "ID must be set before filename used (commit the object)"
             assert self.object_store is not None, "Object Store has not been initialized for dataset %s" % self.id
-            filename = self.object_store.get_filename( self.id )
-            if not self.object_store.exists( self.id ):
-                # Create directory if it does not exist
-                self.object_store.create( self.id, dir_only=True )
+            try:
+                filename = self.object_store.get_filename( self.id )
+            except ObjectNotFound, e:
+                # Create file if it does not exist
+                self.object_store.create( self.id )
+                filename = self.object_store.get_filename( self.id )
             return filename
         else:
             filename = self.external_filename
diff --git a/lib/galaxy/objectstore/__init__.py b/lib/galaxy/objectstore/__init__.py
index 5190e4d6734..5cab11058bd 100644
--- a/lib/galaxy/objectstore/__init__.py
+++ b/lib/galaxy/objectstore/__init__.py
@@ -18,6 +18,7 @@ from galaxy import util
 from galaxy.jobs import Sleeper
 from galaxy.model import directory_hash_id
 from galaxy.objectstore.s3_multipart_upload import multipart_upload
+from galaxy.exceptions import ObjectNotFound
 
 from boto.s3.key import Key
 from boto.s3.connection import S3Connection
@@ -27,11 +28,6 @@ log = logging.getLogger( __name__ )
 logging.getLogger('boto').setLevel(logging.INFO) # Otherwise boto is quite noisy
 
 
-class ObjectNotFound(Exception):
-    """ Accessed object was not found """
-    pass
-
-
 class ObjectStore(object):
     """
     ObjectStore abstract interface

From f93d81751d40fb921ac0d37b8df833f19716e8b5 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Fri, 9 Dec 2011 15:38:03 -0500
Subject: [PATCH 325/362] First pass on composite tracks. To facilitate
 composite tracks, draw_helper now returns jQuery Deferred objects rather than
 null when drawing cannot occur so that tile drawing can be more closely
 tracked. Current limitations of composite tracks: (a) can be created only
 inside groups; (b) only tracks of the same type can be composited; and (c) no
 normalization is done b/t tracks. Also implemented generic save/restore
 functionality. Pack JS scripts.

---
 static/scripts/packed/galaxy.panels.js |   2 +-
 static/scripts/packed/trackster.js     |   2 +-
 static/scripts/packed/trackster_ui.js  |   2 +-
 static/scripts/trackster.js            | 301 +++++++++++++++++++++----
 static/scripts/trackster_ui.js         |  82 ++-----
 templates/tracks/browser.mako          |   2 +-
 6 files changed, 287 insertions(+), 104 deletions(-)

diff --git a/static/scripts/packed/galaxy.panels.js b/static/scripts/packed/galaxy.panels.js
index e289002e659..0d70f9099c9 100644
--- a/static/scripts/packed/galaxy.panels.js
+++ b/static/scripts/packed/galaxy.panels.js
@@ -1 +1 @@
-function ensure_dd_helper(){if($("#DD-helper").length==0){$("<div id='DD-helper'/>").css({background:"white",opacity:0,zIndex:9000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}var MIN_PANEL_WIDTH=100,MAX_PANEL_WIDTH=1000;function make_left_panel(h,c,e){var g=false;var f=null;var d=function(i){var j=i;if(i<0){i=0}$(h).css("width",i);$(e).css("left",j);$(c).css("left",i+7);if(document.recalc){document.recalc()}};var a=function(){if(g){$(e).removeClass("hover");$(e).animate({left:f},"fast");$(h).css("left",-f).show().animate({left:0},"fast",function(){d(f);$(e).removeClass("hidden")});g=false}else{f=$(e).position().left;$(c).css("left",$(e).innerWidth());if(document.recalc){document.recalc()}$(e).removeClass("hover");$(h).animate({left:-f},"fast");$(e).animate({left:-1},"fast",function(){$(this).addClass("hidden")});g=true}};$(e).bind("dragstart",function(){$("#DD-helper").show()}).bind("dragend",function(){$("#DD-helper").hide()}).bind("drag",function(i,j){x=j.offsetX;x=Math.min(MAX_PANEL_WIDTH,Math.max(MIN_PANEL_WIDTH,x));if(g){$(h).css("left",0);$(e).removeClass("hidden");g=false}d(x)}).bind("dragclickonly",function(){a()}).find("div").show();var b=function(i){if((g&&i=="show")||(!g&&i=="hide")){a()}};return{force_panel:b}}function make_right_panel(a,e,h){var j=false,g=false,c=null;var d=function(k){$(a).css("width",k);$(e).css("right",k+9);$(h).css("right",k).css("left","");if(document.recalc){document.recalc()}};var i=function(){if(j){$(h).removeClass("hover");$(h).animate({right:c},"fast");$(a).css("right",-c).show().animate({right:0},"fast",function(){d(c);$(h).removeClass("hidden")});j=false}else{c=$(document).width()-$(h).position().left-$(h).outerWidth();$(e).css("right",$(h).innerWidth()+1);if(document.recalc){document.recalc()}$(h).removeClass("hover");$(a).animate({right:-c},"fast");$(h).animate({right:-1},"fast",function(){$(this).addClass("hidden")});j=true}g=false};var b=function(k){var l=$(e).width()-(j?c:0);if(l<k){if(!j){i();g=true}}else{if(g){i();g=false}}};$(h).hover(function(){$(this).addClass("hover")},function(){$(this).removeClass("hover")}).bind("dragstart",function(){$("#DD-helper").show()}).bind("dragend",function(){$("#DD-helper").hide()}).bind("drag",function(k,l){x=l.offsetX;w=$(window).width();x=Math.min(w-MIN_PANEL_WIDTH,x);x=Math.max(w-MAX_PANEL_WIDTH,x);if(j){$(a).css("right",0);$(h).removeClass("hidden");j=false}d(w-x-$(this).outerWidth())}).bind("dragclickonly",function(){i()}).find("div").show();var f=function(k){if((j&&k=="show")||(!j&&k=="hide")){i()}};return{handle_minwidth_hint:b,force_panel:f}}function hide_modal(){$(".dialog-box-container").hide(0,function(){$("#overlay").hide();$("#overlay").removeClass("modal");$(".dialog-box").find(".body").children().remove()})}function show_modal(){$("#overlay").addClass("modal");_show_modal.apply(this,arguments)}function show_message(){_show_modal.apply(this,arguments)}function _show_modal(h,c,f,d,g){if(h){$(".dialog-box").find(".title").html(h);$(".dialog-box").find(".unified-panel-header").show()}else{$(".dialog-box").find(".unified-panel-header").hide()}var a=$(".dialog-box").find(".buttons").html("");if(f){$.each(f,function(b,i){a.append($("<button/>").text(b).click(i));a.append(" ")});a.show()}else{a.hide()}var a=$(".dialog-box").find(".extra_buttons").html("");if(d){$.each(d,function(b,i){a.append($("<button/>").text(b).click(i));a.append(" ")});a.show()}else{a.hide()}if(c=="progress"){c=$("<img/>").attr("src",image_path+"/yui/rel_interstitial_loading.gif")}var e=$(".dialog-box").find(".body");e.css("min-width","");$(".dialog-box").find(".body").html(c);if(!$(".dialog-box-container").is(":visible")){$("#overlay").show();$(".dialog-box-container").show()}e.css("min-width",e.width());if(g){g()}}function show_in_overlay(c){var d=c.width||"600";var b=c.height||"400";var a=c.scroll||"auto";$("#overlay-background").bind("click.overlay",function(){hide_modal();$("#overlay-background").unbind("click.overlay")});show_modal(null,$("<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-17px;top:-15px;src='"+image_path+"/closebox.png'><iframe style='margin: 0; padding: 0;' src='"+c.url+"' width='"+d+"' height='"+b+"' scrolling='"+a+"' frameborder='0'></iframe></div>"));$("#close_button").bind("click",function(){hide_modal()})}$(function(){$(".tab").each(function(){var a=$(this).children(".submenu");if(a.length>0){if($.browser.msie){a.prepend("<iframe style=\"position: absolute; top: 0; left: 0; width: 100%; height: 100%; z-index: -1; filter:Alpha(Opacity='0');\"></iframe>")}$(this).hover(function(){a.show()},function(){a.hide()});a.click(function(){a.hide()})}})});function user_changed(a,b){if(a){$(".loggedin-only").show();$(".loggedout-only").hide();$("#user-email").text(a);if(b){$(".admin-only").show()}}else{$(".loggedin-only").hide();$(".loggedout-only").show();$(".admin-only").hide()}};
\ No newline at end of file
+function ensure_dd_helper(){if($("#DD-helper").length==0){$("<div id='DD-helper'/>").css({background:"white",opacity:0,zIndex:9000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}var MIN_PANEL_WIDTH=100,MAX_PANEL_WIDTH=1000;function make_left_panel(h,c,e){var g=false;var f=null;var d=function(i){var j=i;if(i<0){i=0}$(h).css("width",i);$(e).css("left",j);$(c).css("left",i+7);if(document.recalc){document.recalc()}};var a=function(){if(g){$(e).removeClass("hover");$(e).animate({left:f},"fast");$(h).css("left",-f).show().animate({left:0},"fast",function(){d(f);$(e).removeClass("hidden")});g=false}else{f=$(e).position().left;$(c).css("left",$(e).innerWidth());if(document.recalc){document.recalc()}$(e).removeClass("hover");$(h).animate({left:-f},"fast");$(e).animate({left:-1},"fast",function(){$(this).addClass("hidden")});g=true}};$(e).bind("dragstart",function(){$("#DD-helper").show()}).bind("dragend",function(){$("#DD-helper").hide()}).bind("drag",function(i,j){x=j.offsetX;x=Math.min(MAX_PANEL_WIDTH,Math.max(MIN_PANEL_WIDTH,x));if(g){$(h).css("left",0);$(e).removeClass("hidden");g=false}d(x)}).bind("dragclickonly",function(){a()}).find("div").show();var b=function(i){if((g&&i=="show")||(!g&&i=="hide")){a()}};return{force_panel:b}}function make_right_panel(a,e,h){var j=false,g=false,c=null;var d=function(k){$(a).css("width",k);$(e).css("right",k+9);$(h).css("right",k).css("left","");if(document.recalc){document.recalc()}};var i=function(){if(j){$(h).removeClass("hover");$(h).animate({right:c},"fast");$(a).css("right",-c).show().animate({right:0},"fast",function(){d(c);$(h).removeClass("hidden")});j=false}else{c=$(document).width()-$(h).position().left-$(h).outerWidth();$(e).css("right",$(h).innerWidth()+1);if(document.recalc){document.recalc()}$(h).removeClass("hover");$(a).animate({right:-c},"fast");$(h).animate({right:-1},"fast",function(){$(this).addClass("hidden")});j=true}g=false};var b=function(k){var l=$(e).width()-(j?c:0);if(l<k){if(!j){i();g=true}}else{if(g){i();g=false}}};$(h).hover(function(){$(this).addClass("hover")},function(){$(this).removeClass("hover")}).bind("dragstart",function(){$("#DD-helper").show()}).bind("dragend",function(){$("#DD-helper").hide()}).bind("drag",function(k,l){x=l.offsetX;w=$(window).width();x=Math.min(w-MIN_PANEL_WIDTH,x);x=Math.max(w-MAX_PANEL_WIDTH,x);if(j){$(a).css("right",0);$(h).removeClass("hidden");j=false}d(w-x-$(this).outerWidth())}).bind("dragclickonly",function(){i()}).find("div").show();var f=function(k){if((j&&k=="show")||(!j&&k=="hide")){i()}};return{handle_minwidth_hint:b,force_panel:f}}function hide_modal(){$(".dialog-box-container").hide(0,function(){$("#overlay").hide();$("#overlay").removeClass("modal");$(".dialog-box").find(".body").children().remove()})}function show_modal(){$("#overlay").addClass("modal");_show_modal.apply(this,arguments)}function show_message(){_show_modal.apply(this,arguments)}function _show_modal(h,c,f,d,g){if(h){$(".dialog-box").find(".title").html(h);$(".dialog-box").find(".unified-panel-header").show()}else{$(".dialog-box").find(".unified-panel-header").hide()}var a=$(".dialog-box").find(".buttons").html("");if(f){$.each(f,function(b,i){a.append($("<button/>").text(b).click(i));a.append(" ")});a.show()}else{a.hide()}var a=$(".dialog-box").find(".extra_buttons").html("");if(d){$.each(d,function(b,i){a.append($("<button/>").text(b).click(i));a.append(" ")});a.show()}else{a.hide()}if(c=="progress"){c=$("<img/>").attr("src",image_path+"/yui/rel_interstitial_loading.gif")}var e=$(".dialog-box").find(".body");e.css("min-width","0px");$(".dialog-box").find(".body").html(c);if(!$(".dialog-box-container").is(":visible")){$("#overlay").show();$(".dialog-box-container").show()}e.css("min-width",e.width());if(g){g()}}function show_in_overlay(c){var d=c.width||"600";var b=c.height||"400";var a=c.scroll||"auto";$("#overlay-background").bind("click.overlay",function(){hide_modal();$("#overlay-background").unbind("click.overlay")});show_modal(null,$("<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-17px;top:-15px;src='"+image_path+"/closebox.png'><iframe style='margin: 0; padding: 0;' src='"+c.url+"' width='"+d+"' height='"+b+"' scrolling='"+a+"' frameborder='0'></iframe></div>"));$("#close_button").bind("click",function(){hide_modal()})}$(function(){$(".tab").each(function(){var a=$(this).children(".submenu");if(a.length>0){if($.browser.msie){a.prepend("<iframe style=\"position: absolute; top: 0; left: 0; width: 100%; height: 100%; z-index: -1; filter:Alpha(Opacity='0');\"></iframe>")}$(this).hover(function(){a.show()},function(){a.hide()});a.click(function(){a.hide()})}})});function user_changed(a,b){if(a){$(".loggedin-only").show();$(".loggedout-only").hide();$("#user-email").text(a);if(b){$(".admin-only").show()}}else{$(".loggedin-only").hide();$(".loggedout-only").show();$(".admin-only").hide()}};
\ No newline at end of file
diff --git a/static/scripts/packed/trackster.js b/static/scripts/packed/trackster.js
index a314d9b6318..9d53b5d9bb1 100644
--- a/static/scripts/packed/trackster.js
+++ b/static/scripts/packed/trackster.js
@@ -1 +1 @@
-var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var m=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(u,t,v,r,i,s){return(Math.max(u,r)-Math.min(u,r))+(Math.max(t,i)-Math.min(t,i))+(Math.max(v,s)-Math.min(v,s))};var g,n,f,k,p,h,q,c,d,b,o,l=false;do{g=Math.random()*16777215;n=g|16711680;f=g|65280;k=g|255;d=m(n,f,k);l=true;for(var j=0;j<a.length;j++){p=a[j];h=p|16711680;q=p|65280;c=p|255;b=m(h,q,c);o=e(n,f,k,h,q,c);if((Math.abs(d-b)<125)||(o<500)){l=false;break}}}while(!l);return"#"+(16777216+g).toString(16).substr(1,6)};var trackster_module=function(f,X){var p=f("class").extend,s=f("slotting"),M=f("painters");var ae=function(af,ag){this.document=af;this.default_font=ag!==undefined?ag:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};p(ae.prototype,{load_pattern:function(af,aj){var ag=this.patterns,ah=this.dummy_context,ai=new Image();ai.src=image_path+aj;ai.onload=function(){ag[af]=ah.createPattern(ai,"repeat")}},get_pattern:function(af){return this.patterns[af]},new_canvas:function(){var af=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(af)}af.manager=this;return af}});var n={};var l=function(af,ag){n[af.attr("id")]=ag};var m=function(af,ah,aj,ai){aj=".group";var ag={};n[af.attr("id")]=ai;af.bind("drag",{handle:"."+ah,relative:true},function(ar,at){var aq=$(this);var aw=$(this).parent(),an=aw.children(),ap=n[$(this).attr("id")],am,al,au,ak,ao;al=$(this).parents(aj);if(al.length!==0){au=al.position().top;ak=au+al.outerHeight();if(at.offsetY<au){$(this).insertBefore(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable_before(ap,av);return}else{if(at.offsetY>ak){$(this).insertAfter(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable(ap);return}}}al=null;for(ao=0;ao<an.length;ao++){am=$(an.get(ao));au=am.position().top;ak=au+am.outerHeight();if(am.is(aj)&&this!==am.get(0)&&at.offsetY>=au&&at.offsetY<=ak){if(at.offsetY-au<ak-at.offsetY){am.find(".content-div").prepend(this)}else{am.find(".content-div").append(this)}if(ap.container){ap.container.remove_drawable(ap)}n[am.attr("id")].add_drawable(ap);return}}for(ao=0;ao<an.length;ao++){if(at.offsetY<$(an.get(ao)).position().top){break}}if(ao===an.length){if(this!==an.get(ao-1)){aw.append(this);n[aw.attr("id")].move_drawable(ap,ao)}}else{if(this!==an.get(ao)){$(this).insertBefore(an.get(ao));n[aw.attr("id")].move_drawable(ap,(at.deltaY>0?ao-1:ao))}}}).bind("dragstart",function(){ag["border-top"]=af.css("border-top");ag["border-bottom"]=af.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ag)})};X.moveable=m;var ad=16,H=9,E=20,T=H+2,z=100,J=12000,R=200,C=5,v=10,L=5000,w=100,o="There was an error in indexing this dataset. ",K="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",F="No data for this chrom/contig.",t="Currently indexing... please wait",x="Tool cannot be rerun: ",a="Loading data...",Y="Ready for display",d=10,u=5,B=5;function Z(ag,af){if(!af){af=0}var ah=Math.pow(10,af);return Math.round(ag*ah)/ah}var c=function(af){this.num_elements=af;this.clear()};p(c.prototype,{get:function(ag){var af=this.key_ary.indexOf(ag);if(af!==-1){if(this.obj_cache[ag].stale){this.key_ary.splice(af,1);delete this.obj_cache[ag]}else{this.move_key_to_end(ag,af)}}return this.obj_cache[ag]},set:function(ag,ah){if(!this.obj_cache[ag]){if(this.key_ary.length>=this.num_elements){var af=this.key_ary.shift();delete this.obj_cache[af]}this.key_ary.push(ag)}this.obj_cache[ag]=ah;return ah},move_key_to_end:function(ag,af){this.key_ary.splice(af,1);this.key_ary.push(ag)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var S=function(ag,af,ah){c.call(this,ag);this.track=af;this.subset=(ah!==undefined?ah:true)};p(S.prototype,c.prototype,{load_data:function(ao,aj,am,ag,al){var an=this.track.view.chrom,ai={chrom:an,low:ao,high:aj,mode:am,resolution:ag,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ai,al);if(this.track.filters_manager){var ap=[];var af=this.track.filters_manager.filters;for(var ak=0;ak<af.length;ak++){ap[ap.length]=af[ak].name}ai.filter_cols=JSON.stringify(ap)}var ah=this;return $.getJSON(this.track.data_url,ai,function(aq){ah.set_data(ao,aj,am,aq)})},get_data:function(af,aj,ak,ag,ai){var ah=this.get_data_from_cache(af,aj,ak);if(ah){return ah}ah=this.load_data(af,aj,ak,ag,ai);this.set_data(af,aj,ak,ah);return ah},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(an,ai,am,ah,al,aj){var ao=this.get_data_from_cache(an,ai,am);if(!ao){console.log("ERROR: no current data for: ",this.track,an,ai,am,ah,al);return}ao.stale=true;var ag=an;if(aj===this.DEEP_DATA_REQ){$.extend(al,{start_val:ao.data.length+1})}else{if(aj===this.BROAD_DATA_REQ){ag=(ao.max_high?ao.max_high:ao.data[ao.data.length-1][2])+1}}var af=this,ak=this.load_data(ag,ai,am,ah,al);new_data_available=$.Deferred();this.set_data(an,ai,am,new_data_available);$.when(ak).then(function(ap){if(ap.data){ap.data=ao.data.concat(ap.data);if(ap.max_low){ap.max_low=ao.max_low}if(ap.message){ap.message=ap.message.replace(/[0-9]+/,ap.data.length)}}af.set_data(an,ai,am,ap);new_data_available.resolve(ap)});return new_data_available},get_data_from_cache:function(af,ag,ah){return this.get(this.gen_key(af,ag,ah))},set_data:function(ag,ah,ai,af){return this.set(this.gen_key(ag,ah,ai),af)},gen_key:function(af,ah,ai){var ag=af+"_"+ah+"_"+ai;return ag},split_key:function(af){return af.split("_")}});var I=function(ag,af,ah){S.call(this,ag,af,ah)};p(I.prototype,S.prototype,c.prototype,{load_data:function(af,ai,aj,ag,ah){if(ag>1){return{data:null}}return S.prototype.load_data.call(this,af,ai,aj,ag,ah)}});var q=function(ai,ag,af,ah,ak){if(!q.id_counter){q.id_counter=0}this.id=q.id_counter++;this.name=ai;this.view=ag;this.container=af;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ai}],saved_values:ah,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ak;this.is_overview=false;this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=this.build_icons_div().hide();this.header_div.append(this.icons_div);this.header_div.dblclick(function(al){al.stopPropagation()});var aj=this;this.container_div.hover(function(){aj.icons_div.show()},function(){aj.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p(q.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},update_icons:function(){},set_name:function(af){this.old_name=this.name;this.name=af;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.hide(0,function(){$(this).remove();view.update_intro_div();view.has_changes=true})},build_container_div:function(){},build_header_div:function(){},build_icons_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){}});var y=function(aj,ai,ag,af,ah,ak){q.call(this,ai,ag,af,ah,ak);this.obj_type=aj;this.drawables=[]};p(y.prototype,q.prototype,{init:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af].init()}},_draw:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af]._draw()}},to_json:function(){var ag=[];for(var af=0;af<this.drawables.length;af++){ag.push(this.drawables[af].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ag}},add_drawable:function(af){this.drawables.push(af);af.container=this},add_drawable_before:function(ah,af){var ag=this.drawables.indexOf(af);if(ag!=-1){this.drawables.splice(ag,0,ah);return true}return false},remove_drawable:function(ag){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);ag.container=null;return true}return false},move_drawable:function(ag,ah){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);this.drawables.splice(ah,0,ag);return true}return false}});var Q=function(ai,ag,af,ah){y.call(this,"DrawableGroup",ai,ag,af,ah,"group-handle");this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this)};p(Q.prototype,q.prototype,y.prototype,{build_container_div:function(){return $("<div/>").addClass("group").attr("id","group_"+this.id).appendTo(this.container.content_div)},build_header_div:function(){var af=$("<div/>").addClass("track-header");af.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(af);return af},build_icons_div:function(){var af=$("<div/>").css("float","left");this.toggle_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Hide/show group content").addClass("icon-button toggle").tipsy({gravity:"s"}).appendTo(af);this.settings_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Edit settings").addClass("icon-button settings-icon").tipsy({gravity:"s"}).appendTo(af);this.remove_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Remove").addClass("icon-button remove-icon").tipsy({gravity:"s"}).appendTo(af);var ag=this;this.toggle_icon.click(function(){if(ag.content_visible){ag.toggle_icon.addClass("toggle-expand").removeClass("toggle");ag.hide_contents();ag.content_visible=false}else{ag.toggle_icon.addClass("toggle").removeClass("toggle-expand");ag.content_visible=true;ag.show_contents()}});this.settings_icon.click(function(){var aj=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ah=function(){ag.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ai=function(ak){if((ak.keyCode||ak.which)===27){aj()}else{if((ak.keyCode||ak.which)===13){ah()}}};$(window).bind("keypress.check_enter_esc",ai);show_modal("Configure Group",ag.config.build_form(),{Cancel:aj,OK:ah})});this.remove_icon.click(function(){$(".tipsy").remove();ag.remove()});return af},hide_contents:function(){this.content_div.hide()},show_contents:function(){this.content_div.show();this.request_draw()}});var ac=function(af,ai,ah,ag){y.call(this,"View");this.container=af;this.chrom=null;this.vis_id=ah;this.dbkey=ag;this.title=ai;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ae(af.get(0).ownerDocument);this.reset()};p(ac.prototype,y.prototype,{init:function(){var ah=this.container,af=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ah);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ah);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ah);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,af);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ai=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ag=function(aj){if(aj.type==="focusout"||(aj.keyCode||aj.which)===13||(aj.keyCode||aj.which)===27){if((aj.keyCode||aj.which)!==27){af.go_to($(this).val())}$(this).hide();$(this).val("");af.location_span.show();af.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ag).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tipsy({gravity:"n"}).appendTo(this.nav_controls);this.location_span.click(function(){af.location_span.hide();af.chrom_select.hide();af.nav_input.val(af.chrom+":"+af.low+"-"+af.high);af.nav_input.css("display","inline-block");af.nav_input.select();af.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tipsy({gravity:"n"}).click(function(){af.zoom_out();af.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tipsy({gravity:"n"}).click(function(){af.zoom_in();af.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){af.change_chrom(af.chrom_select.val())});this.browser_content_div.click(function(aj){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(aj){af.zoom_in(aj.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(aj,ak){this.current_x=ak.offsetX}).bind("drag",function(aj,al){var am=al.offsetX-this.current_x;this.current_x=al.offsetX;var ak=Math.round(am/af.viewport_container.width()*(af.max_high-af.max_low));af.move_delta(-ak)});this.overview_close.click(function(){af.reset_overview()});this.viewport_container.bind("draginit",function(aj,ak){if(aj.clientX>af.viewport_container.width()-16){return false}}).bind("dragstart",function(aj,ak){ak.original_low=af.low;ak.current_height=aj.clientY;ak.current_x=ak.offsetX}).bind("drag",function(al,an){var aj=$(this);var ao=an.offsetX-an.current_x;var ak=aj.scrollTop()-(al.clientY-an.current_height);aj.scrollTop(ak);an.current_height=al.clientY;an.current_x=an.offsetX;var am=Math.round(ao/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}).bind("mousewheel",function(al,an,ak,aj){if(ak){ak*=50;var am=Math.round(-ak/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}});this.top_labeltrack.bind("dragstart",function(aj,ak){return $("<div />").css({height:af.browser_content_div.height()+af.top_labeltrack.height()+af.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(an,ao){$(ao.proxy).css({left:Math.min(an.pageX,ao.startX),width:Math.abs(an.pageX-ao.startX)});var ak=Math.min(an.pageX,ao.startX)-af.container.offset().left,aj=Math.max(an.pageX,ao.startX)-af.container.offset().left,am=(af.high-af.low),al=af.viewport_container.width();af.update_location(Math.round(ak/al*am)+af.low,Math.round(aj/al*am)+af.low)}).bind("dragend",function(ao,ap){var ak=Math.min(ao.pageX,ap.startX),aj=Math.max(ao.pageX,ap.startX),am=(af.high-af.low),al=af.viewport_container.width(),an=af.low;af.low=Math.round(ak/al*am)+an;af.high=Math.round(aj/al*am)+an;$(ap.proxy).remove();af.request_redraw()});this.add_label_track(new ab(this,{content_div:this.top_labeltrack}));this.add_label_track(new ab(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){af.resize_window()});$(document).bind("redraw",function(){af.redraw()});this.reset();$(window).trigger("resize")},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},update_location:function(af,ag){this.location_span.text(commatize(af)+" - "+commatize(ag));this.nav_input.val(this.chrom+":"+commatize(af)+"-"+commatize(ag))},load_chroms:function(ah){ah.num=w;$.extend(ah,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var af=this,ag=$.Deferred();$.ajax({url:chrom_url,data:ah,dataType:"json",success:function(aj){if(aj.chrom_info.length===0){alert("Invalid chromosome: "+ah.chrom);return}if(aj.reference){af.add_label_track(new A(af))}af.chrom_data=aj.chrom_info;var am='<option value="">Select Chrom/Contig</option>';for(var al=0,ai=af.chrom_data.length;al<ai;al++){var ak=af.chrom_data[al].chrom;am+='<option value="'+ak+'">'+ak+"</option>"}if(aj.prev_chroms){am+='<option value="previous">Previous '+w+"</option>"}if(aj.next_chroms){am+='<option value="next">Next '+w+"</option>"}af.chrom_select.html(am);af.chrom_start_index=aj.start_index;ag.resolve(aj)},error:function(){alert("Could not load chroms for this dbkey:",af.dbkey)}});return ag},change_chrom:function(ak,ag,am){if(!ak||ak==="None"){return}var ah=this;if(ak==="previous"){ah.load_chroms({low:this.chrom_start_index-w});return}if(ak==="next"){ah.load_chroms({low:this.chrom_start_index+w});return}var al=$.grep(ah.chrom_data,function(an,ao){return an.chrom===ak})[0];if(al===undefined){ah.load_chroms({chrom:ak},function(){ah.change_chrom(ak,ag,am)});return}else{if(ak!==ah.chrom){ah.chrom=ak;ah.chrom_select.val(ah.chrom);ah.max_high=al.len-1;ah.reset();ah.request_redraw(true);for(var aj=0,af=ah.drawables.length;aj<af;aj++){var ai=ah.drawables[aj];if(ai.init){ai.init()}}}if(ag!==undefined&&am!==undefined){ah.low=Math.max(ag,0);ah.high=Math.min(am,ah.max_high)}ah.reset_overview();ah.request_redraw()}},go_to:function(aj){aj=aj.replace(/ |,/g,"");var an=this,af,ai,ag=aj.split(":"),al=ag[0],am=ag[1];if(am!==undefined){try{var ak=am.split("-");af=parseInt(ak[0],10);ai=parseInt(ak[1],10)}catch(ah){return false}}an.change_chrom(al,af,ai)},move_fraction:function(ah){var af=this;var ag=af.high-af.low;this.move_delta(ah*ag)},move_delta:function(ah){var af=this;var ag=af.high-af.low;if(af.low-ah<af.max_low){af.low=af.max_low;af.high=af.max_low+ag}else{if(af.high-ah>af.max_high){af.high=af.max_high;af.low=af.max_high-ag}else{af.high-=ah;af.low-=ah}}af.request_redraw()},add_drawable:function(af){y.prototype.add_drawable.call(this,af);af.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(af){af.view=this;af.init();this.label_tracks.push(af)},remove_drawable:function(ah,ag){y.prototype.remove_drawable.call(this,ah);if(ag){var af=this;ah.container_div.hide(0,function(){$(this).remove();af.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(an,af,am,ag){var al=this,aj=(ag?[ag]:al.drawables),ah;var ag;for(var ak=0;ak<aj.length;ak++){ag=aj[ak];ah=-1;for(var ai=0;ai<al.tracks_to_be_redrawn.length;ai++){if(al.tracks_to_be_redrawn[ai][0]===ag){ah=ai;break}}if(ah<0){al.tracks_to_be_redrawn.push([ag,af,am])}else{al.tracks_to_be_redrawn[ak][1]=af;al.tracks_to_be_redrawn[ak][2]=am}}requestAnimationFrame(function(){al._redraw(an)})},_redraw:function(ap){var am=this.low,ai=this.high;if(am<this.max_low){am=this.max_low}if(ai>this.max_high){ai=this.max_high}var ao=this.high-this.low;if(this.high!==0&&ao<this.min_separation){ai=am+this.min_separation}this.low=Math.floor(am);this.high=Math.ceil(ai);this.resolution=Math.pow(C,Math.ceil(Math.log((this.high-this.low)/R)/Math.log(C)));this.zoom_res=Math.pow(v,Math.max(0,Math.ceil(Math.log(this.resolution,v)/Math.log(v))));var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var al=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var aq=13;this.overview_box.css({left:af,width:Math.max(aq,al)}).show();if(al<aq){this.overview_box.css("left",af-(aq-al)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:al})}this.update_location(this.low,this.high);if(!ap){var ah,ag,an;for(var aj=0,ak=this.tracks_to_be_redrawn.length;aj<ak;aj++){ah=this.tracks_to_be_redrawn[aj][0];ag=this.tracks_to_be_redrawn[aj][1];an=this.tracks_to_be_redrawn[aj][2];if(ah){ah._draw(ag,an)}}this.tracks_to_be_redrawn=[];for(aj=0,ak=this.label_tracks.length;aj<ak;aj++){this.label_tracks[aj]._draw()}}},zoom_in:function(ag,ah){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ai=this.high-this.low,aj=ai/2+this.low,af=(ai/this.zoom_factor)/2;if(ag){aj=ag/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(aj-af);this.high=Math.round(aj+af);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ag=this.high-this.low,ah=ag/2+this.low,af=(ag*this.zoom_factor)/2;this.low=Math.round(ah-af);this.high=Math.round(ah+af);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ah.dataset_id){return}this.overview_viewport.find(".track").remove()}var ag=ah.copy({content_div:this.overview_viewport}),af=this;ag.header_div.hide();ag.is_overview=true;af.overview_drawable=ag;this.overview_drawable.postdraw_actions=function(){af.overview_highlight.show().height(af.overview_drawable.content_div.height());af.overview_viewport.height(af.overview_drawable.content_div.height()+af.overview_box.outerHeight());af.overview_close.show();af.resize_window()};this.overview_drawable.init();af.has_changes=true},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var r=function(ah,al){this.track=ah;this.name=al.name;this.params=[];var at=al.params;for(var ai=0;ai<at.length;ai++){var an=at[ai],ag=an.name,ar=an.label,aj=unescape(an.html),au=an.value,ap=an.type;if(ap==="number"){this.params[this.params.length]=new g(ag,ar,aj,au,an.min,an.max)}else{if(ap=="select"){this.params[this.params.length]=new O(ag,ar,aj,au)}else{console.log("WARNING: unrecognized tool parameter type:",ag,ap)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aw){aw.stopPropagation()}).click(function(aw){aw.stopPropagation()}).bind("dblclick",function(aw){aw.stopPropagation()});var aq=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ao=this.params;var am=this;$.each(this.params,function(ax,aA){var az=$("<div>").addClass("param-row").appendTo(am.parent_div);var aw=$("<div>").addClass("param-label").text(aA.label).appendTo(az);var ay=$("<div/>").addClass("slider").html(aA.html).appendTo(az);ay.find(":input").val(aA.value);$("<div style='clear: both;'/>").appendTo(az)});this.parent_div.find("input").click(function(){$(this).select()});var av=$("<div>").addClass("param-row").appendTo(this.parent_div);var ak=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(av);var af=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(av);var am=this;af.click(function(){am.run_on_region()});ak.click(function(){am.run_on_dataset()})};p(r.prototype,{get_param_values_dict:function(){var af={};this.parent_div.find(":input").each(function(){var ag=$(this).attr("name"),ah=$(this).val();af[ag]=JSON.stringify(ah)});return af},get_param_values:function(){var ag=[];var af={};this.parent_div.find(":input").each(function(){var ah=$(this).attr("name"),ai=$(this).val();if(ah){ag[ag.length]=ai}});return ag},run_on_dataset:function(){var af=this;af.run({dataset_id:this.track.original_dataset_id,tool_id:af.name},null,function(ag){show_modal(af.name+" is Running",af.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ag={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},aj=this.track,ah=ag.tool_id+aj.tool_region_and_parameters_str(ag.chrom,ag.low,ag.high),af;if(aj.container===view){var ai=new Q(this.name,this.track.view,this.track.container);aj.container.add_drawable(ai);aj.container.remove_drawable(aj);ai.add_drawable(aj);aj.container_div.appendTo(ai.content_div);af=ai}else{af=aj.container}var ak=new aj.constructor(ah,view,af,"hda");ak.init_for_tool_data();ak.change_mode(aj.mode);af.add_drawable(ak);ak.content_div.text("Starting job.");this.run(ag,ak,function(al){ak.dataset_id=al.dataset_id;ak.content_div.text("Running job.");ak.init()})},run:function(ag,ah,ai){$.extend(ag,this.get_param_values_dict());var af=function(){$.getJSON(rerun_tool_url,ag,function(aj){if(aj==="no converter"){ah.container_div.addClass("error");ah.content_div.text(K)}else{if(aj.error){ah.container_div.addClass("error");ah.content_div.text(x+aj.message)}else{if(aj==="pending"){ah.container_div.addClass("pending");ah.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(af,2000)}else{ai(aj)}}}})};af()}});var O=function(ag,af,ah,ai){this.name=ag;this.label=af;this.html=ah;this.value=ai};var g=function(ah,ag,aj,ak,ai,af){O.call(this,ah,ag,aj,ak);this.min=ai;this.max=af};var h=function(ag,af,ah,ai){this.name=ag;this.index=af;this.tool_id=ah;this.tool_exp_name=ai};var V=function(ag,af,ah,ai){h.call(this,ag,af,ah,ai);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};p(V.prototype,{applies_to:function(af){if(af.length>this.index){return true}return false},keep:function(af){if(!this.applies_to(af)){return true}var ag=af[this.index];return(isNaN(ag)||(ag>=this.low&&ag<=this.high))},update_attrs:function(ag){var af=false;if(!this.applies_to(ag)){return af}if(ag[this.index]<this.min){this.min=Math.floor(ag[this.index]);af=true}if(ag[this.index]>this.max){this.max=Math.ceil(ag[this.index]);af=true}return af},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var ah=function(ak,ai){var aj=ai-ak;return(aj<=2?0.01:1)};var ag=this.slider.slider("option","min"),af=this.slider.slider("option","max");if(this.min<ag||this.max>af){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ah(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var aa=function(aq,ay){this.track=aq;this.filters=[];for(var at=0;at<ay.length;at++){var au=ay[at],az=au.name,af=au.type,ah=au.index,ax=au.tool_id,aw=au.tool_exp_name;if(af==="int"||af==="float"){this.filters[at]=new V(az,ah,ax,aw)}else{console.log("ERROR: unsupported filter: ",az,af)}}var ai=function(aA,aB,aC){aA.click(function(){var aD=aB.text();max=parseFloat(aC.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aC.slider("option","values")){input_size=2*input_size+1;multi_value=true}aB.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aD).appendTo(aB).focus().select().click(function(aE){aE.stopPropagation()}).blur(function(){$(this).remove();aB.text(aD)}).keyup(function(aI){if(aI.keyCode===27){$(this).trigger("blur")}else{if(aI.keyCode===13){var aG=aC.slider("option","min"),aE=aC.slider("option","max"),aH=function(aJ){return(isNaN(aJ)||aJ>aE||aJ<aG)},aF=$(this).val();if(!multi_value){aF=parseFloat(aF);if(aH(aF)){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}else{aF=aF.split("-");aF=[parseFloat(aF[0]),parseFloat(aF[1])];if(aH(aF[0])||aH(aF[1])){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}aC.slider((multi_value?"values":"value"),aF)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aA){aA.stopPropagation()}).click(function(aA){aA.stopPropagation()}).bind("dblclick",function(aA){aA.stopPropagation()}).bind("keydown",function(aA){aA.stopPropagation()});var av=$("<div/>").addClass("sliders").appendTo(this.parent_div);var an=this;$.each(this.filters,function(aD,aF){aF.container=$("<div/>").addClass("filter-row slider-row").appendTo(av);var aE=$("<div/>").addClass("elt-label").appendTo(aF.container);var aC=$("<span/>").addClass("slider-name").text(aF.name+"  ").appendTo(aE);var aB=$("<span/>");var aH=$("<span/>").addClass("slider-value").appendTo(aE).append("[").append(aB).append("]");var aA=$("<div/>").addClass("slider").appendTo(aF.container);aF.control_element=$("<div/>").attr("id",aF.name+"-filter-control").appendTo(aA);var aG=[0,0];aF.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aJ,aK){var aI=aK.values;aB.text(aI[0]+"-"+aI[1]);aF.low=aI[0];aF.high=aI[1];an.track.request_draw(true,true)},change:function(aI,aJ){aF.control_element.slider("option","slide").call(aF.control_element,aI,aJ)}});aF.slider=aF.control_element;aF.slider_label=aB;ai(aH,aB,aF.control_element);$("<div style='clear: both;'/>").appendTo(aF.container)});if(this.filters.length!==0){var ak=$("<div/>").addClass("param-row").appendTo(av);var am=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ak);var ag=this;am.click(function(){ag.run_on_dataset()})}var ap=$("<div/>").addClass("display-controls").appendTo(this.parent_div),ar,al,ao,aj={Transparency:function(aA){an.alpha_filter=aA},Height:function(aA){an.height_filter=aA}};$.each(aj,function(aC,aB){ar=$("<div/>").addClass("filter-row").appendTo(ap),al=$("<span/>").addClass("elt-label").text(aC+":").appendTo(ar),ao=$("<select/>").attr("name",aC+"_dropdown").css("float","right").appendTo(ar);$("<option/>").attr("value",-1).text("== None ==").appendTo(ao);for(var aA=0;aA<an.filters.length;aA++){$("<option/>").attr("value",aA).text(an.filters[aA].name).appendTo(ao)}ao.change(function(){$(this).children("option:selected").each(function(){var aD=parseInt($(this).val());aj[aC]((aD>=0?an.filters[aD]:null));an.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(ar)});$("<div style='clear: both;'/>").appendTo(this.parent_div)};p(aa.prototype,{reset_filters:function(){for(var af=0;af<this.filters.length;af++){filter=this.filters[af];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var an=function(ar,ap,aq){if(!(ap in ar)){ar[ap]=aq}return ar[ap]};var ah={},af,ag,ai;for(var aj=0;aj<this.filters.length;aj++){af=this.filters[aj];if(af.tool_id){if(af.min!=af.low){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" >= "+af.low}if(af.max!=af.high){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" <= "+af.high}}}var al=[];for(var ao in ah){al[al.length]=[ao,ah[ao]]}var am=al.length;(function ak(aw,at){var aq=at[0],ar=aq[0],av=aq[1],au="("+av.join(") and (")+")",ap={cond:au,input:aw,target_dataset_id:aw,tool_id:ar},at=at.slice(1);$.getJSON(run_tool_url,ap,function(ax){if(ax.error){show_modal("Filter Dataset","Error running tool "+ar,{Close:hide_modal})}else{if(at.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ak(ax.dataset_id,at)}}})})(this.track.dataset_id,al)}});var D=function(af,ag){M.Scaler.call(this,ag);this.filter=af};D.prototype.gen_val=function(af){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(af[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var G=function(af){this.track=af.track;this.params=af.params;this.values={};this.restore_values((af.saved_values?af.saved_values:{}));this.onchange=af.onchange};p(G.prototype,{restore_values:function(af){var ag=this;$.each(this.params,function(ah,ai){if(af[ai.key]!==undefined){ag.values[ai.key]=af[ai.key]}else{ag.values[ai.key]=ai.default_value}})},build_form:function(){var ai=this;var af=$("<div />");var ah;function ag(am,aj){for(var ao=0;ao<am.length;ao++){ah=am[ao];if(ah.hidden){continue}var ak="param_"+ao;var at=ai.values[ah.key];var av=$("<div class='form-row' />").appendTo(aj);av.append($("<label />").attr("for",ak).text(ah.label+":"));if(ah.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ak).attr("name",ak).attr("checked",at))}else{if(ah.type==="text"){av.append($('<input type="text"/>').attr("id",ak).val(at).click(function(){$(this).select()}))}else{if(ah.type=="select"){var aq=$("<select />").attr("id",ak);for(var an=0;an<ah.options.length;an++){$("<option/>").text(ah.options[an].label).attr("value",ah.options[an].value).appendTo(aq)}aq.val(at);av.append(aq)}else{if(ah.type==="color"){var ap=$("<input />").attr("id",ak).attr("name",ak).val(at);var ar=$("<div class='tipsy tipsy-west' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ar);var au=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:ap,color:at});$("<div />").append(ap).append(ar).appendTo(av).bind("click",function(aw){ar.css({left:$(this).position().left+$(ap).width()+5,top:$(this).position().top-($(ar).height()/2)+($(ap).height()/2)}).show();$(document).bind("click.color-picker",function(){ar.hide();$(document).unbind("click.color-picker")});aw.stopPropagation()})}else{av.append($("<input />").attr("id",ak).attr("name",ak).val(at))}}}}if(ah.help){av.append($("<div class='help'/>").text(ah.help))}}}ag(this.params,af);return af},update_from_form:function(af){var ah=this;var ag=false;$.each(this.params,function(ai,ak){if(!ak.hidden){var al="param_"+ai;var aj=af.find("#"+al).val();if(ak.type==="float"){aj=parseFloat(aj)}else{if(ak.type==="int"){aj=parseInt(aj)}else{if(ak.type==="bool"){aj=af.find("#"+al).is(":checked")}}}if(aj!==ah.values[ak.key]){ah.values[ak.key]=aj;ag=true}}});if(ag){this.onchange()}}});var b=function(af,ai,ah,ag,aj){this.track=af;this.index=ai;this.low=ai*R*ah;this.high=(ai+1)*R*ah;this.resolution=ah;this.canvas=$("<div class='track-tile'/>").append(ag);this.data=aj;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(af,ai,ah,ag,aj,ak){b.call(this,af,ai,ah,ag,aj);this.max_val=ak};p(k.prototype,b.prototype);var P=function(ah,am,ai,ag,ak,al,ap,an){b.call(this,ah,am,ai,ag,ak);this.mode=al;this.message=ap;this.feature_mapper=an;if(this.message){var ag=this.canvas.children()[0],ao=$("<div/>").addClass("tile-message").text(this.message).css({height:E-1,width:ag.width}).prependTo(this.canvas),aj=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ao),af=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ao);aj.click(function(){tile.stale=true;ah.data_manager.get_more_data(tile.low,tile.high,ah.mode,tile.resolution,{},ah.data_manager.DEEP_DATA_REQ);ah.request_draw()}).dblclick(function(aq){aq.stopPropagation()});af.click(function(){tile.stale=true;ah.data_manager.get_more_data(tile.low,tile.high,ah.mode,tile.resolution,{},ah.data_manager.BROAD_DATA_REQ);ah.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}};p(P.prototype,b.prototype);P.prototype.predisplay_actions=function(){var ag=this,af={};if(ag.mode!=="Pack"){return}$(this.canvas).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).siblings(".feature-popup").remove()}).mousemove(function(ar){if(!this.hovered){return}var am=$(this).offset(),aq=ar.pageX-am.left,ap=ar.pageY-am.top,aw=ag.feature_mapper.get_feature_data(aq,ap),an=(aw?aw[0]:null);$(this).siblings(".feature-popup").each(function(){if(!an||$(this).attr("id")!==an.toString()){$(this).remove()}});if(aw){var ai=af[an];if(!ai){var an=aw[0],at={name:aw[3],start:aw[1],end:aw[2],strand:aw[4]},al=ag.track.filters_manager.filters,ak;for(var ao=0;ao<al.length;ao++){ak=al[ao];at[ak.name]=aw[ak.index]}var ai=$("<div/>").attr("id",an).addClass("feature-popup"),ax=$("<table/>"),av,au,ay;for(av in at){au=at[av];ay=$("<tr/>").appendTo(ax);$("<th/>").appendTo(ay).text(av);$("<td/>").attr("align","left").appendTo(ay).text(typeof(au)=="number"?Z(au,2):au)}ai.append($("<div class='feature-popup-inner'>").append(ax));af[an]=ai}ai.appendTo($(ag.canvas).parent());var aj=aq+parseInt(ag.canvas.css("left"))-ai.width()/2,ah=ap+parseInt(ag.canvas.css("top"))+7;ai.css("left",aj+"px").css("top",ah+"px")}else{if(!ar.isPropagationStopped()){ar.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ar)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var i=function(ai,ag,af,ah,aj,ak){q.call(this,ai,ag,af,{},"draghandle");this.data_url=(aj?aj:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ak?ak:L);this.dataset_check_url=converted_datasets_state_url;if(!i.id_counter){i.id_counter=0}this.id=i.id_counter++;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};p(i.prototype,q.prototype,{build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var af=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(af)}this.name_div=$("<div/>").addClass("track-name").appendTo(af).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return af},build_icons_div:function(){var aj=$("<div/>").css("float","left");this.mode_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Set display mode").addClass("icon-button chevron-expand").tipsy({gravity:"s"}).appendTo(aj);this.toggle_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Hide/show track content").addClass("icon-button toggle").tipsy({gravity:"s"}).appendTo(aj);this.settings_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Edit settings").addClass("icon-button settings-icon").tipsy({gravity:"s"}).appendTo(aj);this.overview_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Set as overview").addClass("icon-button overview-icon").tipsy({gravity:"s"}).appendTo(aj);this.filters_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Filters").addClass("icon-button filters-icon").tipsy({gravity:"s"}).appendTo(aj).hide();this.tools_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Tools").addClass("icon-button tools-icon").tipsy({gravity:"s"}).appendTo(aj).hide();this.remove_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Remove").addClass("icon-button remove-icon").tipsy({gravity:"s"}).appendTo(aj);var ag=this;if(ag.display_modes!==undefined){var al=(ag.config&&ag.config.values.mode?ag.config.values.mode:ag.display_modes[0]);ag.mode=al;this.mode_icon.attr("title","Set display mode (now: "+ag.mode+")");var ai={};for(var ah=0,af=ag.display_modes.length;ah<af;ah++){var ak=ag.display_modes[ah];ai[ak]=function(am){return function(){ag.change_mode(am);ag.icons_div.show();ag.container_div.mouseleave(function(){ag.icons_div.hide()})}}(ak)}make_popupmenu(this.mode_icon,ai)}this.toggle_icon.click(function(){if(ag.content_visible){ag.toggle_icon.addClass("toggle-expand").removeClass("toggle");ag.hide_contents();ag.content_visible=false}else{ag.toggle_icon.addClass("toggle").removeClass("toggle-expand");ag.content_visible=true;ag.show_contents()}});this.settings_icon.click(function(){var ao=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},am=function(){ag.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},an=function(ap){if((ap.keyCode||ap.which)===27){ao()}else{if((ap.keyCode||ap.which)===13){am()}}};$(window).bind("keypress.check_enter_esc",an);show_modal("Configure Track",ag.config.build_form(),{Cancel:ao,OK:am})});this.overview_icon.click(function(){ag.view.set_overview(ag)});this.filters_icon.click(function(){ag.filters_div.toggle();ag.filters_manager.reset_filters()});this.tools_icon.click(function(){ag.dynamic_tool_div.toggle();if(ag.dynamic_tool_div.is(":visible")){ag.set_name(ag.name+ag.tool_region_and_parameters_str())}else{ag.revert_name()}$(".tipsy").remove()});this.remove_icon.click(function(){$(".tipsy").remove();ag.remove()});return aj},hide_contents:function(){this.content_div.children().remove();this.content_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.content_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof ab){return"LabelTrack"}else{if(this instanceof A){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof W){return"ReadTrack"}else{if(this instanceof U){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}return""},init:function(){var af=this;af.enabled=false;af.tile_cache.clear();af.data_manager.clear();af.initial_canvas=undefined;af.content_div.css("height","auto");af.container_div.removeClass("nodata error pending");if(!af.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:af.hda_ldda,dataset_id:af.dataset_id,chrom:af.view.chrom},function(ag){if(!ag||ag==="error"||ag.kind==="error"){af.container_div.addClass("error");af.content_div.text(o);if(ag.message){var ah=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})});af.content_div.append(ah)}}else{if(ag==="no converter"){af.container_div.addClass("error");af.content_div.text(K)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){af.container_div.addClass("nodata");af.content_div.text(F)}else{if(ag==="pending"){af.container_div.addClass("pending");af.content_div.text(t);setTimeout(function(){af.init()},af.data_query_wait)}else{if(ag.status==="data"){if(ag.valid_chroms){af.valid_chroms=ag.valid_chroms;af.update_icons()}af.content_div.text(Y);if(af.view.chrom){af.content_div.text("");af.content_div.css("height",af.height_px+"px");af.enabled=true;$.when(af.predraw_init()).done(function(){af.container_div.removeClass("nodata error pending");af.request_draw()})}}}}}}});this.update_icons()},predraw_init:function(){}});var N=function(aj,ah,ag,ai,al,ak){i.call(this,aj,ah,ag,ai);var af=this,ah=af.view;m(af.container_div,af.drag_handle_class,".group",af);this.filters_manager=new aa(this,(al!==undefined?al:{}));this.filters_available=false;this.filters_visible=false;this.tool=(ak!==undefined&&obj_length(ak)>0?new r(this,ak):undefined);if(this.header_div){if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}};p(N.prototype,q.prototype,i.prototype,{copy:function(af){return new this.constructor(this.name,this.view,af,this.hda_ldda,this.dataset_id,this.prefs,this.filters,this.tool)},to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ag){var af=this;af.mode=ag;af.config.values.mode=ag;af.tile_cache.clear();af.request_draw();this.mode_icon.attr("title","Set display mode (now: "+af.mode+")");return af},update_icons:function(){var af=this;if(af.filters_available>0){af.filters_icon.show()}else{af.filters_icon.hide()}if(af.tool){af.tools_icon.show()}else{af.tools_icon.hide()}},_gen_tile_cache_key:function(ag,ah,af){return ag+"_"+ah+"_"+af},request_draw:function(ag,af){this.view.request_redraw(false,ag,af,this)},_draw:function(ah,ap){if(!this.enabled){return}if(!this.content_visible){return}if(!(this instanceof A)&&(!this.dataset_id)){return}var ao=this.view.low,al=this.view.high,am=al-ao,ai=this.view.container.width(),at=ai/am,ak=this.view.resolution,ar=this.content_div;if(this.is_overview){ao=this.view.max_low;al=this.view.max_high;ak=Math.pow(C,Math.ceil(Math.log((view.max_high-view.max_low)/R)/Math.log(C)));at=ai/(view.max_high-view.max_low)}if(!ap){this.content_div.children().addClass("remove")}this.max_height=0;var ag=Math.floor(ao/ak/R);var an=true;var aq=[];var af=0;while((ag*R*ak)<al){tile=this.draw_helper(ah,ai,ag,ak,ar,at);if(tile){aq.push(tile)}else{an=false}ag+=1;af++}if(!ap){this.content_div.children(".remove").remove()}var aj=this;if(an){aj.postdraw_actions(aq,ai,at,ap)}},postdraw_actions:function(aj,ak,al,af){var ah=this;var ai=false;for(var ag=0;ag<aj.length;ag++){if(aj[ag].message){ai=true;break}}if(ai){for(var ag=0;ag<aj.length;ag++){tile=aj[ag];if(!tile.message){tile.canvas.css("padding-top",E)}}}},draw_helper:function(ag,ah,ai,al,ar,aw,at,am){var aj=this,aq=this._gen_tile_cache_key(ah,aw,ai),an=ai*R*al,av=an+R*al;var ao=(ag?undefined:aj.tile_cache.get(aq));if(ao){aj.show_tile(ao,ar,aw);return ao}var ap=function(ax){return("isResolved" in ax)};var ak=true;var af=aj.data_manager.get_data(an,av,aj.mode,al,aj.data_url_extra_params);if(ap(af)){ak=false}var au;if(view.reference_track&&aw>view.canvas_manager.char_width_px){au=view.reference_track.data_manager.get_data(an,av,aj.mode,al,view.reference_track.data_url_extra_params);if(ap(au)){ak=false}}if(ak){p(af,am);var ao=aj.draw_tile(af,aj.mode,al,ai,aw,au);if(ao!==undefined){aj.tile_cache.set(aq,ao);aj.show_tile(ao,ar,aw)}return ao}$.when(af,au).then(function(){view.request_redraw(false,false,false,aj)});return null},show_tile:function(ah,aj,ak){var ag=this,af=ah.canvas;ah.predisplay_actions();var ai=(ah.low-(this.is_overview?this.view.max_low:this.view.low))*ak;if(this.left_offset){ai-=this.left_offset}af.css({position:"absolute",top:0,left:ai,height:""});if(af.hasClass("remove")){af.removeClass("remove")}else{aj.append(af)}ag.max_height=Math.max(ag.max_height,af.height());ag.content_div.css("height",ag.max_height+"px");aj.children().css("height",ag.max_height+"px")},_get_tile_bounds:function(af,ag){var ai=af*R*ag,aj=R*ag,ah=(ai+aj<=this.view.max_high?ai+aj:this.view.max_high);return[ai,ah]},tool_region_and_parameters_str:function(ah,af,ai){var ag=this,aj=(ah!==undefined&&af!==undefined&&ai!==undefined?ah+":"+af+"-"+ai:"all");return" - region=["+aj+"], parameters=["+ag.tool.get_param_values().join(", ")+"]"},init_for_tool_data:function(){this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.predraw_init=function(){var ag=this;var af=function(){if(ag.data_manager.size()===0){setTimeout(af,300)}else{ag.data_url=default_data_url;ag.data_query_wait=L;ag.dataset_state_url=converted_datasets_state_url;$.getJSON(ag.dataset_state_url,{dataset_id:ag.dataset_id,hda_ldda:ag.hda_ldda},function(ah){})}};af()}}});var ab=function(ag,af){i.call(this,"label",ag,af,false,{});this.container_div.addClass("label-track")};p(ab.prototype,i.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ah=this.view,ai=ah.high-ah.low,al=Math.floor(Math.pow(10,Math.floor(Math.log(ai)/Math.log(10)))),af=Math.floor(ah.low/al)*al,aj=this.view.container.width(),ag=$("<div style='position: relative; height: 1.3em;'></div>");while(af<ah.high){var ak=(af-ah.low)/ai*aj;ag.append($("<div class='label'>"+commatize(af)+"</div>").css({position:"absolute",left:ak-1}));af+=al}this.content_div.children(":first").remove();this.content_div.append(ag)}});var A=function(af){N.call(this,"reference",af,{content_div:af.top_labeltrack},{});af.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:af.dbkey};this.data_manager=new I(B,this,false);this.tile_cache=new c(u)};p(A.prototype,q.prototype,N.prototype,{build_header_div:function(){},init:function(){this.enabled=true},draw_tile:function(ap,al,ak,ag,aq){var aj=this,ah=R*ak;if(aq>this.view.canvas_manager.char_width_px){if(ap.data===null){aj.content_div.css("height","0px");return}var ai=this.view.canvas_manager.new_canvas();var ao=ai.getContext("2d");ai.width=Math.ceil(ah*aq+aj.left_offset);ai.height=aj.height_px;ao.font=ao.canvas.manager.default_font;ao.textAlign="center";ap=ap.data;for(var am=0,an=ap.length;am<an;am++){var af=Math.round(am*aq);ao.fillText(ap[am],af+aj.left_offset,10)}return new b(aj,ag,ak,ai,ap)}this.content_div.css("height","0px")}});var j=function(ak,ai,ah,al,af,aj){var ag=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";N.call(this,ak,ai,ah,aj);this.min_height_px=16;this.max_height_px=400;this.height_px=32;this.hda_ldda=al;this.dataset_id=af;this.original_dataset_id=af;this.data_manager=new S(B,this);this.tile_cache=new c(u);this.left_offset=0;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:aj,onchange:function(){ag.set_name(ag.prefs.name);ag.vertical_range=ag.prefs.max_value-ag.prefs.min_value;$("#linetrack_"+ag.dataset_id+"_minval").text(ag.prefs.min_value);$("#linetrack_"+ag.dataset_id+"_maxval").text(ag.prefs.max_value);ag.tile_cache.clear();ag.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};p(j.prototype,q.prototype,N.prototype,{add_resize_handle:function(){var af=this;var ai=false;var ah=false;var ag=$("<div class='track-resize'>");$(af.container_div).hover(function(){if(af.content_visible){ai=true;ag.show()}},function(){ai=false;if(!ah){ag.hide()}});ag.hide().bind("dragstart",function(aj,ak){ah=true;ak.original_height=$(af.content_div).height()}).bind("drag",function(ak,al){var aj=Math.min(Math.max(al.original_height+al.deltaY,af.min_height_px),af.max_height_px);$(af.content_div).css("height",aj);af.height_px=aj;af.request_draw(true)}).bind("dragend",function(aj,ak){af.tile_cache.clear();ah=false;if(!ai){ag.hide()}af.config.values.height=af.height_px}).appendTo(af.container_div)},predraw_init:function(){var af=this;af.vertical_range=undefined;return $.getJSON(af.data_url,{stats:true,chrom:af.view.chrom,low:null,high:null,hda_ldda:af.hda_ldda,dataset_id:af.dataset_id},function(ag){af.container_div.addClass("line-track");var aj=ag.data;if(isNaN(parseFloat(af.prefs.min_value))||isNaN(parseFloat(af.prefs.max_value))){var ah=aj.min;var al=aj.max;ah=Math.floor(Math.min(0,Math.max(ah,aj.mean-2*aj.sd)));al=Math.ceil(Math.max(0,Math.min(al,aj.mean+2*aj.sd)));af.prefs.min_value=ah;af.prefs.max_value=al;$("#track_"+af.dataset_id+"_minval").val(af.prefs.min_value);$("#track_"+af.dataset_id+"_maxval").val(af.prefs.max_value)}af.vertical_range=af.prefs.max_value-af.prefs.min_value;af.total_frequency=aj.total_frequency;af.container_div.find(".yaxislabel").remove();var ak=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_minval").text(Z(af.prefs.min_value,3));var ai=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_maxval").text(Z(af.prefs.max_value,3));ai.css({position:"absolute",top:"24px",left:"10px"});ai.prependTo(af.container_div);ak.css({position:"absolute",bottom:"2px",left:"10px"});ak.prependTo(af.container_div)})},draw_tile:function(ar,ak,aj,ah,aq){if(this.vertical_range===undefined){return}var af=this._get_tile_bounds(ah,aj),al=af[0],ap=af[1],ag=Math.ceil((ap-al)*aq),an=this.height_px;var ai=this.view.canvas_manager.new_canvas();ai.width=ag,ai.height=an;var ao=ai.getContext("2d");var am=new M.LinePainter(ar.data,al,ap,this.prefs,ak);am.draw(ao,ag,an);return new b(this.track,ah,aj,ai,ar.data)}});var e=function(af,al,ag,ak,an,am,ai,aj){var ah=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];N.call(this,af,al,ag,am,ai,aj);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:am,onchange:function(){ah.set_name(ah.prefs.name);ah.tile_cache.clear();ah.set_painter_from_config();ah.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=ak;this.dataset_id=an;this.original_dataset_id=an;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new S(20,this);this.left_offset=200;this.set_painter_from_config()};p(e.prototype,q.prototype,N.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style=="arcs"){this.painter=M.ArcLinkedFeaturePainter}else{this.painter=M.LinkedFeaturePainter}},postdraw_actions:function(av,af,aw,au){N.prototype.postdraw_actions.call(this,av,au);var ai=this;if(au){var ak=ai.content_div.children();var al=false;for(var aj=ak.length-1,ap=0;aj>=ap;aj--){var ah=$(ak[aj]);if(al){ah.remove()}else{if(ah.children().length!==0){al=true}}}}if(ai.mode=="Histogram"){var ao=-1;for(var aj=0;aj<av.length;aj++){var at=av[aj].max_val;if(at>ao){ao=at}}for(var aj=0;aj<av.length;aj++){var ar=av[aj];if(ar.max_val!==ao){ar.canvas.remove();ai.draw_helper(true,af,ar.index,ar.resolution,ar.canvas.parent(),aw,[],{max:ao})}}}if(ai.filters_manager){var ag=ai.filters_manager.filters;for(var an=0;an<ag.length;an++){ag[an].update_ui_elt()}var am=false,aq;for(var aj=0;aj<av.length;aj++){if(av[aj].data.length){aq=av[aj].data[0];for(var an=0;an<ag.length;an++){if(ag[an].applies_to(aq)){am=true;break}}}}if(ai.filters_available!==am){ai.filters_available=am;if(!ai.filters_available){ai.filters_div.hide()}ai.update_icons()}}},update_auto_mode:function(af){var af;if(this.mode=="Auto"){if(af=="no_detail"){af="feature spans"}else{if(af=="summary_tree"){af="coverage histogram"}}this.mode_icon.attr("title","Set display mode (now: Auto/"+af+")")}},incremental_slots:function(aj,ag,ai){var ah=this.view.canvas_manager.dummy_context,af=this.inc_slots[aj];if(!af||(af.mode!==ai)){af=new (s.FeatureSlotter)(aj,ai==="Pack",z,function(ak){return ah.measureText(ak)});af.mode=ai;this.inc_slots[aj]=af}return af.slot_features(ag)},get_summary_tree_data:function(aj,am,ah,av){if(av>ah-am){av=ah-am}var aq=Math.floor((ah-am)/av),au=[],ai=0;var ak=0,al=0,ap,at=0,an=[],ar,ao;var ag=function(ay,ax,az,aw){ay[0]=ax+az*aw;ay[1]=ax+(az+1)*aw};while(at<av&&ak!==aj.length){var af=false;for(;at<av&&!af;at++){ag(an,am,at,aq);for(al=ak;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){af=true;break}}if(af){break}}data_start_index=al;au[au.length]=ar=[an[0],0];for(;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){ar[1]++}else{break}}if(ar[1]>ai){ai=ar[1]}at++}return{max:ai,delta:aq,data:au}},draw_tile:function(au,ax,aB,aF,ap,ai){var ay=this,ak=ay._get_tile_bounds(aF,aB),aI=ak[0],ag=ak[1],aw=ag-aI,az=Math.ceil(aw*ap),aO=25,aj=this.left_offset,av,al;if(ax==="Auto"){if(au.dataset_type==="summary_tree"){ax=au.dataset_type}else{if(au.extra_info==="no_detail"||ay.is_overview){ax="no_detail"}else{var aN=au.data;if(this.view.high-this.view.low>J){ax="Squish"}else{ax="Pack"}}}this.update_auto_mode(ax)}if(ax==="summary_tree"||ax==="Histogram"){al=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var af=$("<div />").addClass("yaxislabel");af.text(au.max);af.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});af.prependTo(this.container_div);var ah=this.view.canvas_manager.new_canvas();ah.width=az+aj;ah.height=al+T;if(au.dataset_type!="summary_tree"){var aq=this.get_summary_tree_data(au.data,aI,ag,200);if(au.max){aq.max=au.max}au=aq}var aK=new M.SummaryTreePainter(au,aI,ag,this.prefs);var aA=ah.getContext("2d");aA.translate(aj,T);aK.draw(aA,az,al);return new k(ay,aF,aB,ah,au.data,au.max)}var av,an=1;if(ax==="no_detail"||ax==="Squish"||ax==="Pack"){an=this.incremental_slots(ap,au.data,ax);av=this.inc_slots[ap].slots}var ao=[];if(au.data){var ar=this.filters_manager.filters;for(var aC=0,aE=au.data.length;aC<aE;aC++){var am=au.data[aC];var aD=false;var at;for(var aH=0,aM=ar.length;aH<aM;aH++){at=ar[aH];at.update_attrs(am);if(!at.keep(am)){aD=true;break}}if(!aD){ao.push(am)}}}var aL=(this.filters_manager.alpha_filter?new D(this.filters_manager.alpha_filter):null);var aJ=(this.filters_manager.height_filter?new D(this.filters_manager.height_filter):null);var aK=new (this.painter)(ao,aI,ag,this.prefs,ax,aL,aJ,ai);var al=Math.max(ad,aK.get_required_height(an,az));var ah=this.view.canvas_manager.new_canvas();var aG=null;ah.width=az+aj;ah.height=al;var aA=ah.getContext("2d");aA.fillStyle=this.prefs.block_color;aA.font=aA.canvas.manager.default_font;aA.textAlign="right";this.container_div.find(".yaxislabel").remove();if(au.data){aA.translate(aj,0);aG=aK.draw(aA,az,al,av);aG.translation=-aj}return new P(ay,aF,aB,ah,au.data,ax,au.message,aG)}});var U=function(ak,ah,ag,am,af,aj,al,ai){e.call(this,ak,ah,ag,am,af,aj,al,ai);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:aj,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter};p(U.prototype,q.prototype,N.prototype,e.prototype);var W=function(af,ak,ag,aj,an,am,ah){e.call(this,af,ak,ag,aj,an,am,ah);var ai=get_random_color(),al=get_random_color([ai,"#ffffff"]);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ai},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:al},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:am,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter;this.update_icons()};p(W.prototype,q.prototype,N.prototype,e.prototype);X.View=ac;X.DrawableGroup=Q;X.LineTrack=j;X.FeatureTrack=e;X.ReadTrack=W;X.VcfTrack=U};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(F,G){for(var E=0;E<=z;E++){var C=false,H=h[E];if(H!==undefined){for(var B=0,D=H.length;B<D;B++){var i=H[B];if(G>i[0]&&F<i[1]){C=true;break}}}if(!C){return E}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(i,x){var u=i("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y<E;y++,A+=J,G+=H){if(y%2!==0){continue}I.fillRect(A,G,D,1)}};var q=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var d=function(y){this.default_val=(y?y:1)};d.prototype.gen_val=function(y){return this.default_val};var l=function(A,C,y,z,B){this.data=A;this.view_start=C;this.view_end=y;this.prefs=u({},this.default_prefs,z);this.mode=B};l.prototype.default_prefs={};var v=function(A,C,y,z,B){l.call(this,A,C,y,z,B)};v.prototype.default_prefs={show_counts:false};v.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var b=function(y,C,E,F,A){l.call(this,y,C,E,F,A);if(this.prefs.min_value===undefined){var G=Infinity;for(var z=0,B=this.data.length;z<B;z++){G=Math.min(G,this.data[z][1])}this.prefs.min_value=G}if(this.prefs.max_value===undefined){var D=-Infinity;for(var z=0,B=this.data.length;z<B;z++){D=Math.max(D,this.data[z][1])}this.prefs.max_value=D}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var m=function(y){this.feature_positions={};this.slot_height=y;this.translation=0;this.y_translation=0};m.prototype.map_feature_data=function(z,B,y,A){if(!this.feature_positions[B]){this.feature_positions[B]=[]}this.feature_positions[B].push({data:z,x_start:y,x_end:A})};m.prototype.get_feature_data=function(z,D){var C=Math.floor((D-this.y_translation)/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var o=function(A,D,y,z,C,E,B){l.call(this,A,D,y,z,C);this.alpha_scaler=(E?E:new d());this.height_scaler=(B?B:new d())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(A,z){var y=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){y=A*y_scale}return y+this.get_top_padding(z)+this.get_bottom_padding(z)},get_top_padding:function(y){return 0},get_bottom_padding:function(y){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(K,I,G,F){var Q=this.data,D=this.view_start,M=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var H=this.view_end-this.view_start,E=I/H,L=this.get_row_height(),P=new m(L),B;for(var N=0,O=Q.length;N<O;N++){var A=Q[N],C=A[0],J=A[1],y=A[2],z=(F&&F[C]!==undefined?F[C]:null);if((J<M&&y>D)&&(this.mode=="Dense"||z!==null)){B=this.draw_element(K,this.mode,A,z,D,M,E,L,I);P.map_feature_data(A,z,B[0],B[1])}}K.restore();P.y_translation=this.get_top_padding(I);return P},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.");return[0,0]}});var c=10,h=3,k=5,w=10,f=1,s=9,e=3,a=9,j=2,g="#ccc";var r=function(A,D,y,z,C,E,B){o.call(this,A,D,y,z,C,E,B);this.draw_background_connector=true;this.draw_individual_connectors=false};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=c}else{if(z==="no_detail"){y=h}else{if(z==="Squish"){y=k}else{y=w}}}return y},draw_element:function(M,D,X,H,O,aj,an,ap,y){var T=X[0],al=X[1],ad=X[2],Q=X[3],ae=Math.floor(Math.max(0,(al-O)*an)),N=Math.ceil(Math.min(y,Math.max(0,(ad-O)*an))),ac=ae,ao=N,aa=(D==="Dense"?0:(0+H))*ap+this.get_top_padding(y),L,ah,R=null,ar=null,B=this.prefs.block_color,ag=this.prefs.label_color;M.globalAlpha=this.alpha_scaler.gen_val(X);if(D==="Dense"){H=1}if(D==="no_detail"){M.fillStyle=B;M.fillRect(ae,aa+5,N-ae,f)}else{var K=X[4],Z=X[5],af=X[6],C=X[7],V=true;if(Z&&af){R=Math.floor(Math.max(0,(Z-O)*an));ar=Math.ceil(Math.min(y,Math.max(0,(af-O)*an)))}var am,U;if(D==="Squish"){am=1;U=e;V=false}else{if(D==="Dense"){am=5;U=s}else{am=5;U=a}}if(!C){M.fillStyle=B;M.fillRect(ae,aa+1,N-ae,U);if(K&&V){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}M.fillRect(ae,aa+1,N-ae,U)}}else{var J,W;if(D==="Squish"||D==="Dense"){J=aa+Math.floor(e/2)+1;W=1}else{if(K){J=aa;W=U}else{J+=(e/2)+1;W=1}}if(this.draw_background_connector){if(D==="Squish"||D==="Dense"){M.fillStyle=g}else{if(K){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand")}}}else{M.fillStyle=g}}M.fillRect(ae,J,N-ae,W)}var E;for(var ak=0,A=C.length;ak<A;ak++){var F=C[ak],z=Math.floor(Math.max(0,(F[0]-O)*an)),Y=Math.ceil(Math.min(y,Math.max((F[1]-O)*an))),S,ab;if(z>Y){continue}M.fillStyle=B;M.fillRect(z,aa+(U-am)/2+1,Y-z,am);if(R!==undefined&&af>Z&&!(z>ar||Y<R)){var ai=Math.max(z,R),I=Math.min(Y,ar);M.fillRect(ai,aa+1,I-ai,U);if(C.length==1&&D=="Pack"){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}if(ai+14<I){ai+=2;I-=2}M.fillRect(ai,aa+1,I-ai,U)}}if(this.draw_individual_connectors&&S){this.draw_connector(M,S,ab,z,Y,aa)}S=z;ab=Y}if(D==="Pack"){M.globalAlpha=1;M.fillStyle="white";var G=this.height_scaler.gen_val(X),P=Math.ceil(U*G),aq=Math.round((U-P)/2);if(G!==1){M.fillRect(ae,J+1,N-ae,aq);M.fillRect(ae,J+U-aq+1,N-ae,aq)}}}M.globalAlpha=1;if(D==="Pack"&&al>O){M.fillStyle=ag;if(O===0&&ae-M.measureText(Q).width<0){M.textAlign="left";M.fillText(Q,N+j,aa+8);ao+=M.measureText(Q).width+j}else{M.textAlign="right";M.fillText(Q,ae-j,aa+8);ac-=M.measureText(Q).width+j}}}M.globalAlpha=1;return[ac,ao]}});var t=function(B,E,y,A,D,F,C,z){o.call(this,B,E,y,A,D,F,C);this.ref_seq=(z?z.data:null)};u(t.prototype,o.prototype,{get_row_height:function(){var y,z=this.mode;if(z==="Dense"){y=c}else{if(z==="Squish"){y=k}else{y=w;if(this.prefs.show_insertions){y*=2}}}return y},draw_read:function(K,A,ag,V,L,aa,ad,C,B,M){K.textAlign="center";var J=this,R=[L,aa],Z=0,W=0,D=0,F=K.canvas.manager.char_width_px,y=(B==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var O=[];if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){D=Math.round(ag/2)}if(!C){C=[[0,M.length]]}for(var G=0,I=C.length;G<I;G++){var z=C[G],E="MIDNSHP=X"[z[0]],S=z[1];if(E==="H"||E==="S"){Z-=S}var U=ad+Z,Y=Math.floor(Math.max(0,(U-L)*ag)),ab=Math.floor(Math.max(0,(U+S-L)*ag));if(Y===ab){ab+=1}switch(E){case"H":break;case"S":case"M":case"=":if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(D>0){K.fillStyle=y;K.fillRect(Y-D,V+1,ab-Y,9);K.fillStyle=g;for(var af=0,H=N.length;af<H;af++){if(this.prefs.show_differences&&this.ref_seq){var P=this.ref_seq[U-L+af];if(!P||P.toLowerCase()===N[af].toLowerCase()){continue}}if(U+af>=L&&U+af<=aa){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X,V+9)}}}else{K.fillStyle=y;K.fillRect(Y,V+4,ab-Y,e)}}W+=S;Z+=S;break;case"N":K.fillStyle=g;K.fillRect(Y-D,V+5,ab-Y,1);Z+=S;break;case"D":K.fillStyle="red";K.fillRect(Y-D,V+4,ab-Y,3);Z+=S;break;case"P":break;case"I":var ah=Y-D;if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(this.prefs.show_insertions){var T=Y-(ab-Y)/2;if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){K.fillStyle="yellow";K.fillRect(T-D,V-9,ab-Y,9);O[O.length]={type:"triangle",data:[ah,V+4,5]};K.fillStyle=g;switch(compute_overlap([U,U+S],R)){case (OVERLAP_START):N=N.slice(L-U);break;case (OVERLAP_END):N=N.slice(0,U-aa);break;case (CONTAINED_BY):break;case (CONTAINS):N=N.slice(L-U,U-aa);break}for(var af=0,H=N.length;af<H;af++){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X-(ab-Y)/2,V)}}else{K.fillStyle="yellow";K.fillRect(T,V+(this.mode!=="Dense"?2:5),ab-Y,(A!=="Dense"?e:s))}}else{if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){O.push({type:"text",data:[N.length,ah,V+9]})}else{}}}W+=S;break;case"X":W+=S;break}}K.fillStyle="yellow";var Q,ai,ae;for(var ac=0;ac<O.length;ac++){Q=O[ac];ai=Q.type;ae=Q.data;if(ai==="text"){K.save();K.font="bold "+K.font;K.fillText(ae[0],ae[1],ae[2]);K.restore()}else{if(ai=="triangle"){q(K,ae[0],ae[1],ae[2])}}}},draw_element:function(R,M,E,B,U,z,I,S,P){var H=E[0],Q=E[1],A=E[2],J=E[3],D=Math.floor(Math.max(0,(Q-U)*I)),F=Math.ceil(Math.min(P,Math.max(0,(A-U)*I))),C=(M==="Dense"?0:(0+B))*S,G=this.prefs.label_color,O=0;if((M==="Pack"||this.mode==="Auto")&&I>R.canvas.manager.char_width_px){var O=Math.round(I/2)}if(E[5] instanceof Array){var N=Math.floor(Math.max(0,(E[4][0]-U)*I)),L=Math.ceil(Math.min(P,Math.max(0,(E[4][1]-U)*I))),K=Math.floor(Math.max(0,(E[5][0]-U)*I)),y=Math.ceil(Math.min(P,Math.max(0,(E[5][1]-U)*I)));if(E[4][1]>=U&&E[4][0]<=z&&E[4][2]){this.draw_read(R,M,I,C,U,z,E[4][0],E[4][2],E[4][3],E[4][4])}if(E[5][1]>=U&&E[5][0]<=z&&E[5][2]){this.draw_read(R,M,I,C,U,z,E[5][0],E[5][2],E[5][3],E[5][4])}if(K>L){R.fillStyle=g;p(R,L-O,C+5,K-O,C+5)}}else{this.draw_read(R,M,I,C,U,z,Q,E[4],E[5],E[6])}if(M==="Pack"&&Q>U&&J!=="."){R.fillStyle=this.prefs.label_color;var T=1;if(T===0&&D-R.measureText(J).width<0){R.textAlign="left";R.fillText(J,F+j-O,C+8)}else{R.textAlign="right";R.fillText(J,D-j-O,C+8)}}return[0,0]}});var n=function(A,D,y,z,C,E,B){r.call(this,A,D,y,z,C,E,B);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};u(n.prototype,o.prototype,r.prototype,{calculate_longest_feature_length:function(){var z=0;for(var C=0,y=this.data.length;C<y;C++){var B=this.data[C],A=B[1],D=B[2];z=Math.max(z,D-A)}return z},get_top_padding:function(z){var y=this.view_end-this.view_start,A=z/y;return Math.min(128,Math.ceil((this.longest_feature_length/2)*A))},draw_connector:function(G,B,F,H,E,D){var y=(F+H)/2,C=H-y;var A=Math.PI,z=0;if(C>0){G.beginPath();G.arc(y,D,H-y,Math.PI,0);G.stroke()}}});x.Scaler=d;x.SummaryTreePainter=v;x.LinePainter=b;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.ArcLinkedFeaturePainter=n};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window);
\ No newline at end of file
+var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var m=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(u,t,v,r,i,s){return(Math.max(u,r)-Math.min(u,r))+(Math.max(t,i)-Math.min(t,i))+(Math.max(v,s)-Math.min(v,s))};var g,n,f,k,p,h,q,c,d,b,o,l=false;do{g=Math.random()*16777215;n=g|16711680;f=g|65280;k=g|255;d=m(n,f,k);l=true;for(var j=0;j<a.length;j++){p=a[j];h=p|16711680;q=p|65280;c=p|255;b=m(h,q,c);o=e(n,f,k,h,q,c);if((Math.abs(d-b)<125)||(o<500)){l=false;break}}}while(!l);return"#"+(16777216+g).toString(16).substr(1,6)};var trackster_module=function(e,X){var p=e("class").extend,s=e("slotting"),L=e("painters");var ae=function(af,ag){this.document=af;this.default_font=ag!==undefined?ag:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};p(ae.prototype,{load_pattern:function(af,aj){var ag=this.patterns,ah=this.dummy_context,ai=new Image();ai.src=image_path+aj;ai.onload=function(){ag[af]=ah.createPattern(ai,"repeat")}},get_pattern:function(af){return this.patterns[af]},new_canvas:function(){var af=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(af)}af.manager=this;return af}});var n={};var l=function(af,ag){n[af.attr("id")]=ag};var m=function(af,ah,aj,ai){aj=".group";var ag={};n[af.attr("id")]=ai;af.bind("drag",{handle:"."+ah,relative:true},function(ar,at){var aq=$(this);var aw=$(this).parent(),an=aw.children(),ap=n[$(this).attr("id")],am,al,au,ak,ao;al=$(this).parents(aj);if(al.length!==0){au=al.position().top;ak=au+al.outerHeight();if(at.offsetY<au){$(this).insertBefore(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable_before(ap,av);return}else{if(at.offsetY>ak){$(this).insertAfter(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable(ap);return}}}al=null;for(ao=0;ao<an.length;ao++){am=$(an.get(ao));au=am.position().top;ak=au+am.outerHeight();if(am.is(aj)&&this!==am.get(0)&&at.offsetY>=au&&at.offsetY<=ak){if(at.offsetY-au<ak-at.offsetY){am.find(".content-div").prepend(this)}else{am.find(".content-div").append(this)}if(ap.container){ap.container.remove_drawable(ap)}n[am.attr("id")].add_drawable(ap);return}}for(ao=0;ao<an.length;ao++){if(at.offsetY<$(an.get(ao)).position().top){break}}if(ao===an.length){if(this!==an.get(ao-1)){aw.append(this);n[aw.attr("id")].move_drawable(ap,ao)}}else{if(this!==an.get(ao)){$(this).insertBefore(an.get(ao));n[aw.attr("id")].move_drawable(ap,(at.deltaY>0?ao-1:ao))}}}).bind("dragstart",function(){ag["border-top"]=af.css("border-top");ag["border-bottom"]=af.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ag)})};X.moveable=m;var ad=16,F=9,C=20,T=F+2,y=100,I=12000,Q=200,A=5,u=10,K=5000,v=100,o="There was an error in indexing this dataset. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",D="No data for this chrom/contig.",t="Currently indexing... please wait",w="Tool cannot be rerun: ",a="Loading data...",Y="Ready for display",R=10,H=20;function Z(ag,af){if(!af){af=0}var ah=Math.pow(10,af);return Math.round(ag*ah)/ah}var c=function(af){this.num_elements=af;this.clear()};p(c.prototype,{get:function(ag){var af=this.key_ary.indexOf(ag);if(af!==-1){if(this.obj_cache[ag].stale){this.key_ary.splice(af,1);delete this.obj_cache[ag]}else{this.move_key_to_end(ag,af)}}return this.obj_cache[ag]},set:function(ag,ah){if(!this.obj_cache[ag]){if(this.key_ary.length>=this.num_elements){var af=this.key_ary.shift();delete this.obj_cache[af]}this.key_ary.push(ag)}this.obj_cache[ag]=ah;return ah},move_key_to_end:function(ag,af){this.key_ary.splice(af,1);this.key_ary.push(ag)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var S=function(ag,af,ah){c.call(this,ag);this.track=af;this.subset=(ah!==undefined?ah:true)};p(S.prototype,c.prototype,{load_data:function(ao,aj,am,ag,al){var an=this.track.view.chrom,ai={chrom:an,low:ao,high:aj,mode:am,resolution:ag,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ai,al);if(this.track.filters_manager){var ap=[];var af=this.track.filters_manager.filters;for(var ak=0;ak<af.length;ak++){ap[ap.length]=af[ak].name}ai.filter_cols=JSON.stringify(ap)}var ah=this;return $.getJSON(this.track.data_url,ai,function(aq){ah.set_data(ao,aj,am,aq)})},get_data:function(af,aj,ak,ag,ai){var ah=this.get_data_from_cache(af,aj,ak);if(ah){return ah}ah=this.load_data(af,aj,ak,ag,ai);this.set_data(af,aj,ak,ah);return ah},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(an,ai,am,ah,al,aj){var ao=this.get_data_from_cache(an,ai,am);if(!ao){console.log("ERROR: no current data for: ",this.track,an,ai,am,ah,al);return}ao.stale=true;var ag=an;if(aj===this.DEEP_DATA_REQ){$.extend(al,{start_val:ao.data.length+1})}else{if(aj===this.BROAD_DATA_REQ){ag=(ao.max_high?ao.max_high:ao.data[ao.data.length-1][2])+1}}var af=this,ak=this.load_data(ag,ai,am,ah,al);new_data_available=$.Deferred();this.set_data(an,ai,am,new_data_available);$.when(ak).then(function(ap){if(ap.data){ap.data=ao.data.concat(ap.data);if(ap.max_low){ap.max_low=ao.max_low}if(ap.message){ap.message=ap.message.replace(/[0-9]+/,ap.data.length)}}af.set_data(an,ai,am,ap);new_data_available.resolve(ap)});return new_data_available},get_data_from_cache:function(af,ag,ah){return this.get(this.gen_key(af,ag,ah))},set_data:function(ag,ah,ai,af){return this.set(this.gen_key(ag,ah,ai),af)},gen_key:function(af,ah,ai){var ag=af+"_"+ah+"_"+ai;return ag},split_key:function(af){return af.split("_")}});var G=function(ag,af,ah){S.call(this,ag,af,ah)};p(G.prototype,S.prototype,c.prototype,{load_data:function(af,ai,aj,ag,ah){if(ag>1){return{data:null}}return S.prototype.load_data.call(this,af,ai,aj,ag,ah)}});var q=function(ai,ag,af,ah,ak){if(!q.id_counter){q.id_counter=0}this.id=q.id_counter++;this.name=ai;this.view=ag;this.container=af;this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ai}],saved_values:ah,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ak;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(al){al.stopPropagation()});var aj=this;this.container_div.hover(function(){aj.icons_div.show()},function(){aj.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};q.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(af){if(af.content_visible){af.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");af.hide_contents();af.content_visible=false}else{af.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");af.content_visible=true;af.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ag){var ai=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(){ag.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ah=function(aj){if((aj.keyCode||aj.which)===27){ai()}else{if((aj.keyCode||aj.which)===13){af()}}};$(window).bind("keypress.check_enter_esc",ah);show_modal("Configure",ag.config.build_form(),{Cancel:ai,OK:af})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(af){$(".tipsy").remove();af.remove()}}];p(q.prototype,{init:function(){},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},from_dict:function(af){},update_icons:function(){},set_name:function(af){this.old_name=this.name;this.name=af;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.hide(0,function(){$(this).remove();view.update_intro_div();view.has_changes=true})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ag,ak,aj,ai,af){var ah=this;this.action_icons[ag]=$("<a/>").attr("href","javascript:void(0);").attr("title",ak).addClass("icon-button").addClass(aj).tipsy({gravity:"s"}).click(function(){ai(ah)}).appendTo(this.icons_div)},build_action_icons:function(af){var ah;for(var ag=0;ag<af.length;ag++){ah=af[ag];this.add_action_icon(ah.name,ah.title,ah.css_class,ah.on_click_fn,ah.prepend)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){}});var x=function(aj,ai,ag,af,ah,ak){q.call(this,ai,ag,af,ah,ak);this.obj_type=aj;this.drawables=[]};p(x.prototype,q.prototype,{init:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af].init()}},_draw:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af]._draw()}},to_dict:function(){var ag=[];for(var af=0;af<this.drawables.length;af++){ag.push(this.drawables[af].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ag}},from_dict:function(al,af){var ak=new this.constructor(al.name,view,af,al.prefs,view.viewport_container,view);var ag,aj,ai;for(var ah=0;ah<al.drawables.length;ah++){ag=al.drawables[ah];aj=ag.obj_type;if(!aj){aj=ag.track_type}ai=addable_objects[aj].prototype.from_dict(ag,ak);ak.add_drawable(ai)}return ak},add_drawable:function(af){this.drawables.push(af);af.container=this},add_drawable_before:function(ah,af){var ag=this.drawables.indexOf(af);if(ag!=-1){this.drawables.splice(ag,0,ah);return true}return false},remove_drawable:function(ag){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);ag.container=null;return true}return false},move_drawable:function(ag,ah){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);this.drawables.splice(ah,0,ag);return true}return false}});var P=function(ai,ag,af,ah){x.call(this,"DrawableGroup",ai,ag,af,ah,"group-handle");this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this)};p(P.prototype,q.prototype,x.prototype,{action_icons_def:[{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(af){af.show_composite_track()}}].concat(q.prototype.action_icons_def),build_container_div:function(){return $("<div/>").addClass("group").attr("id","group_"+this.id).appendTo(this.container.content_div)},build_header_div:function(){var af=$("<div/>").addClass("track-header");af.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(af);return af},hide_contents:function(){this.content_div.hide()},show_contents:function(){this.content_div.show();this.request_draw()},update_icons:function(){var af=true,ah=this.drawables[0].get_type();for(var ag=0;ag<this.drawables.length;ag++){if(this.drawables[ag].get_type()!==ah){af=false;break}}if(af){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tipsy").remove()}},show_composite_track:function(){var af=new h("Composite Track",this.view,this,this.drawables);this.add_drawable(af);af.request_draw()},add_drawable:function(af){x.prototype.add_drawable.call(this,af);this.update_icons()},remove_drawable:function(af){x.prototype.remove_drawable.call(this,af);this.update_icons()},from_dict:function(ai,af){var ah=x.prototype.from_dict.call(this,ai,af);for(var ag=0;ag<ah.drawables.length;ag++){ah.content_div.append(ah.drawables[ag].container_div)}return ah}});var ac=function(af,ai,ah,ag){x.call(this,"View");this.container=af;this.chrom=null;this.vis_id=ah;this.dbkey=ag;this.title=ai;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ae(af.get(0).ownerDocument);this.reset()};p(ac.prototype,x.prototype,{init:function(){var ah=this.container,af=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ah);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ah);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ah);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,af);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ai=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ag=function(aj){if(aj.type==="focusout"||(aj.keyCode||aj.which)===13||(aj.keyCode||aj.which)===27){if((aj.keyCode||aj.which)!==27){af.go_to($(this).val())}$(this).hide();$(this).val("");af.location_span.show();af.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ag).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tipsy({gravity:"n"}).appendTo(this.nav_controls);this.location_span.click(function(){af.location_span.hide();af.chrom_select.hide();af.nav_input.val(af.chrom+":"+af.low+"-"+af.high);af.nav_input.css("display","inline-block");af.nav_input.select();af.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tipsy({gravity:"n"}).click(function(){af.zoom_out();af.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tipsy({gravity:"n"}).click(function(){af.zoom_in();af.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){af.change_chrom(af.chrom_select.val())});this.browser_content_div.click(function(aj){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(aj){af.zoom_in(aj.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(aj,ak){this.current_x=ak.offsetX}).bind("drag",function(aj,al){var am=al.offsetX-this.current_x;this.current_x=al.offsetX;var ak=Math.round(am/af.viewport_container.width()*(af.max_high-af.max_low));af.move_delta(-ak)});this.overview_close.click(function(){af.reset_overview()});this.viewport_container.bind("draginit",function(aj,ak){if(aj.clientX>af.viewport_container.width()-16){return false}}).bind("dragstart",function(aj,ak){ak.original_low=af.low;ak.current_height=aj.clientY;ak.current_x=ak.offsetX}).bind("drag",function(al,an){var aj=$(this);var ao=an.offsetX-an.current_x;var ak=aj.scrollTop()-(al.clientY-an.current_height);aj.scrollTop(ak);an.current_height=al.clientY;an.current_x=an.offsetX;var am=Math.round(ao/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}).bind("mousewheel",function(al,an,ak,aj){if(ak){ak*=50;var am=Math.round(-ak/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}});this.top_labeltrack.bind("dragstart",function(aj,ak){return $("<div />").css({height:af.browser_content_div.height()+af.top_labeltrack.height()+af.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(an,ao){$(ao.proxy).css({left:Math.min(an.pageX,ao.startX),width:Math.abs(an.pageX-ao.startX)});var ak=Math.min(an.pageX,ao.startX)-af.container.offset().left,aj=Math.max(an.pageX,ao.startX)-af.container.offset().left,am=(af.high-af.low),al=af.viewport_container.width();af.update_location(Math.round(ak/al*am)+af.low,Math.round(aj/al*am)+af.low)}).bind("dragend",function(ao,ap){var ak=Math.min(ao.pageX,ap.startX),aj=Math.max(ao.pageX,ap.startX),am=(af.high-af.low),al=af.viewport_container.width(),an=af.low;af.low=Math.round(ak/al*am)+an;af.high=Math.round(aj/al*am)+an;$(ap.proxy).remove();af.request_redraw()});this.add_label_track(new ab(this,{content_div:this.top_labeltrack}));this.add_label_track(new ab(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){af.resize_window()});$(document).bind("redraw",function(){af.redraw()});this.reset();$(window).trigger("resize")},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},update_location:function(af,ag){this.location_span.text(commatize(af)+" - "+commatize(ag));this.nav_input.val(this.chrom+":"+commatize(af)+"-"+commatize(ag))},load_chroms:function(ah){ah.num=v;ah.dbkey=this.dbkey;var af=this,ag=$.Deferred();$.ajax({url:chrom_url,data:ah,dataType:"json",success:function(aj){if(aj.chrom_info.length===0){alert("Invalid chromosome: "+ah.chrom);return}if(aj.reference){af.add_label_track(new z(af))}af.chrom_data=aj.chrom_info;var am='<option value="">Select Chrom/Contig</option>';for(var al=0,ai=af.chrom_data.length;al<ai;al++){var ak=af.chrom_data[al].chrom;am+='<option value="'+ak+'">'+ak+"</option>"}if(aj.prev_chroms){am+='<option value="previous">Previous '+v+"</option>"}if(aj.next_chroms){am+='<option value="next">Next '+v+"</option>"}af.chrom_select.html(am);af.chrom_start_index=aj.start_index;ag.resolve(aj)},error:function(){alert("Could not load chroms for this dbkey:",af.dbkey)}});return ag},change_chrom:function(ak,ag,am){if(!ak||ak==="None"){return}var ah=this;if(ak==="previous"){ah.load_chroms({low:this.chrom_start_index-v});return}if(ak==="next"){ah.load_chroms({low:this.chrom_start_index+v});return}var al=$.grep(ah.chrom_data,function(an,ao){return an.chrom===ak})[0];if(al===undefined){ah.load_chroms({chrom:ak},function(){ah.change_chrom(ak,ag,am)});return}else{if(ak!==ah.chrom){ah.chrom=ak;ah.chrom_select.val(ah.chrom);ah.max_high=al.len-1;ah.reset();ah.request_redraw(true);for(var aj=0,af=ah.drawables.length;aj<af;aj++){var ai=ah.drawables[aj];if(ai.init){ai.init()}}}if(ag!==undefined&&am!==undefined){ah.low=Math.max(ag,0);ah.high=Math.min(am,ah.max_high)}ah.reset_overview();ah.request_redraw()}},go_to:function(aj){aj=aj.replace(/ |,/g,"");var an=this,af,ai,ag=aj.split(":"),al=ag[0],am=ag[1];if(am!==undefined){try{var ak=am.split("-");af=parseInt(ak[0],10);ai=parseInt(ak[1],10)}catch(ah){return false}}an.change_chrom(al,af,ai)},move_fraction:function(ah){var af=this;var ag=af.high-af.low;this.move_delta(ah*ag)},move_delta:function(ah){var af=this;var ag=af.high-af.low;if(af.low-ah<af.max_low){af.low=af.max_low;af.high=af.max_low+ag}else{if(af.high-ah>af.max_high){af.high=af.max_high;af.low=af.max_high-ag}else{af.high-=ah;af.low-=ah}}af.request_redraw()},add_drawable:function(af){x.prototype.add_drawable.call(this,af);af.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(af){af.view=this;af.init();this.label_tracks.push(af)},remove_drawable:function(ah,ag){x.prototype.remove_drawable.call(this,ah);if(ag){var af=this;ah.container_div.hide(0,function(){$(this).remove();af.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(an,af,am,ag){var al=this,aj=(ag?[ag]:al.drawables),ah;var ag;for(var ak=0;ak<aj.length;ak++){ag=aj[ak];ah=-1;for(var ai=0;ai<al.tracks_to_be_redrawn.length;ai++){if(al.tracks_to_be_redrawn[ai][0]===ag){ah=ai;break}}if(ah<0){al.tracks_to_be_redrawn.push([ag,af,am])}else{al.tracks_to_be_redrawn[ak][1]=af;al.tracks_to_be_redrawn[ak][2]=am}}requestAnimationFrame(function(){al._redraw(an)})},_redraw:function(ap){var am=this.low,ai=this.high;if(am<this.max_low){am=this.max_low}if(ai>this.max_high){ai=this.max_high}var ao=this.high-this.low;if(this.high!==0&&ao<this.min_separation){ai=am+this.min_separation}this.low=Math.floor(am);this.high=Math.ceil(ai);this.resolution=Math.pow(A,Math.ceil(Math.log((this.high-this.low)/Q)/Math.log(A)));this.zoom_res=Math.pow(u,Math.max(0,Math.ceil(Math.log(this.resolution,u)/Math.log(u))));var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var al=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var aq=13;this.overview_box.css({left:af,width:Math.max(aq,al)}).show();if(al<aq){this.overview_box.css("left",af-(aq-al)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:al})}this.update_location(this.low,this.high);if(!ap){var ah,ag,an;for(var aj=0,ak=this.tracks_to_be_redrawn.length;aj<ak;aj++){ah=this.tracks_to_be_redrawn[aj][0];ag=this.tracks_to_be_redrawn[aj][1];an=this.tracks_to_be_redrawn[aj][2];if(ah){ah._draw(ag,an)}}this.tracks_to_be_redrawn=[];for(aj=0,ak=this.label_tracks.length;aj<ak;aj++){this.label_tracks[aj]._draw()}}},zoom_in:function(ag,ah){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ai=this.high-this.low,aj=ai/2+this.low,af=(ai/this.zoom_factor)/2;if(ag){aj=ag/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(aj-af);this.high=Math.round(aj+af);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ag=this.high-this.low,ah=ag/2+this.low,af=(ag*this.zoom_factor)/2;this.low=Math.round(ah-af);this.high=Math.round(ah+af);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ah.dataset_id){return}this.overview_viewport.find(".track").remove()}var ag=ah.copy({content_div:this.overview_viewport}),af=this;ag.header_div.hide();ag.is_overview=true;af.overview_drawable=ag;this.overview_drawable.postdraw_actions=function(){af.overview_highlight.show().height(af.overview_drawable.content_div.height());af.overview_viewport.height(af.overview_drawable.content_div.height()+af.overview_box.outerHeight());af.overview_close.show();af.resize_window()};af.overview_drawable.request_draw();af.has_changes=true},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var r=function(ah,al){this.track=ah;this.name=al.name;this.params=[];var at=al.params;for(var ai=0;ai<at.length;ai++){var an=at[ai],ag=an.name,ar=an.label,aj=unescape(an.html),au=an.value,ap=an.type;if(ap==="number"){this.params[this.params.length]=new f(ag,ar,aj,au,an.min,an.max)}else{if(ap=="select"){this.params[this.params.length]=new N(ag,ar,aj,au)}else{console.log("WARNING: unrecognized tool parameter type:",ag,ap)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aw){aw.stopPropagation()}).click(function(aw){aw.stopPropagation()}).bind("dblclick",function(aw){aw.stopPropagation()});var aq=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ao=this.params;var am=this;$.each(this.params,function(ax,aA){var az=$("<div>").addClass("param-row").appendTo(am.parent_div);var aw=$("<div>").addClass("param-label").text(aA.label).appendTo(az);var ay=$("<div/>").addClass("slider").html(aA.html).appendTo(az);ay.find(":input").val(aA.value);$("<div style='clear: both;'/>").appendTo(az)});this.parent_div.find("input").click(function(){$(this).select()});var av=$("<div>").addClass("param-row").appendTo(this.parent_div);var ak=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(av);var af=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(av);var am=this;af.click(function(){am.run_on_region()});ak.click(function(){am.run_on_dataset()})};p(r.prototype,{get_param_values_dict:function(){var af={};this.parent_div.find(":input").each(function(){var ag=$(this).attr("name"),ah=$(this).val();af[ag]=JSON.stringify(ah)});return af},get_param_values:function(){var ag=[];var af={};this.parent_div.find(":input").each(function(){var ah=$(this).attr("name"),ai=$(this).val();if(ah){ag[ag.length]=ai}});return ag},run_on_dataset:function(){var af=this;af.run({dataset_id:this.track.original_dataset_id,tool_id:af.name},null,function(ag){show_modal(af.name+" is Running",af.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ag={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},aj=this.track,ah=ag.tool_id+aj.tool_region_and_parameters_str(ag.chrom,ag.low,ag.high),af;if(aj.container===view){var ai=new P(this.name,this.track.view,this.track.container);aj.container.add_drawable(ai);aj.container.remove_drawable(aj);ai.add_drawable(aj);aj.container_div.appendTo(ai.content_div);af=ai}else{af=aj.container}var ak=new aj.constructor(ah,view,af,"hda");ak.init_for_tool_data();ak.change_mode(aj.mode);af.add_drawable(ak);ak.content_div.text("Starting job.");this.run(ag,ak,function(al){ak.dataset_id=al.dataset_id;ak.content_div.text("Running job.");ak.init()})},run:function(ag,ah,ai){$.extend(ag,this.get_param_values_dict());var af=function(){$.getJSON(rerun_tool_url,ag,function(aj){if(aj==="no converter"){ah.container_div.addClass("error");ah.content_div.text(J)}else{if(aj.error){ah.container_div.addClass("error");ah.content_div.text(w+aj.message)}else{if(aj==="pending"){ah.container_div.addClass("pending");ah.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(af,2000)}else{ai(aj)}}}})};af()}});var N=function(ag,af,ah,ai){this.name=ag;this.label=af;this.html=ah;this.value=ai};var f=function(ah,ag,aj,ak,ai,af){N.call(this,ah,ag,aj,ak);this.min=ai;this.max=af};var g=function(ag,af,ah,ai){this.name=ag;this.index=af;this.tool_id=ah;this.tool_exp_name=ai};var V=function(ag,af,ah,ai){g.call(this,ag,af,ah,ai);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};p(V.prototype,{applies_to:function(af){if(af.length>this.index){return true}return false},keep:function(af){if(!this.applies_to(af)){return true}var ag=af[this.index];return(isNaN(ag)||(ag>=this.low&&ag<=this.high))},update_attrs:function(ag){var af=false;if(!this.applies_to(ag)){return af}if(ag[this.index]<this.min){this.min=Math.floor(ag[this.index]);af=true}if(ag[this.index]>this.max){this.max=Math.ceil(ag[this.index]);af=true}return af},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var ah=function(ak,ai){var aj=ai-ak;return(aj<=2?0.01:1)};var ag=this.slider.slider("option","min"),af=this.slider.slider("option","max");if(this.min<ag||this.max>af){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ah(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var aa=function(aq,ay){this.track=aq;this.filters=[];for(var at=0;at<ay.length;at++){var au=ay[at],az=au.name,af=au.type,ah=au.index,ax=au.tool_id,aw=au.tool_exp_name;if(af==="int"||af==="float"){this.filters[at]=new V(az,ah,ax,aw)}else{console.log("ERROR: unsupported filter: ",az,af)}}var ai=function(aA,aB,aC){aA.click(function(){var aD=aB.text();max=parseFloat(aC.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aC.slider("option","values")){input_size=2*input_size+1;multi_value=true}aB.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aD).appendTo(aB).focus().select().click(function(aE){aE.stopPropagation()}).blur(function(){$(this).remove();aB.text(aD)}).keyup(function(aI){if(aI.keyCode===27){$(this).trigger("blur")}else{if(aI.keyCode===13){var aG=aC.slider("option","min"),aE=aC.slider("option","max"),aH=function(aJ){return(isNaN(aJ)||aJ>aE||aJ<aG)},aF=$(this).val();if(!multi_value){aF=parseFloat(aF);if(aH(aF)){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}else{aF=aF.split("-");aF=[parseFloat(aF[0]),parseFloat(aF[1])];if(aH(aF[0])||aH(aF[1])){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}aC.slider((multi_value?"values":"value"),aF)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aA){aA.stopPropagation()}).click(function(aA){aA.stopPropagation()}).bind("dblclick",function(aA){aA.stopPropagation()}).bind("keydown",function(aA){aA.stopPropagation()});var av=$("<div/>").addClass("sliders").appendTo(this.parent_div);var an=this;$.each(this.filters,function(aD,aF){aF.container=$("<div/>").addClass("filter-row slider-row").appendTo(av);var aE=$("<div/>").addClass("elt-label").appendTo(aF.container);var aC=$("<span/>").addClass("slider-name").text(aF.name+"  ").appendTo(aE);var aB=$("<span/>");var aH=$("<span/>").addClass("slider-value").appendTo(aE).append("[").append(aB).append("]");var aA=$("<div/>").addClass("slider").appendTo(aF.container);aF.control_element=$("<div/>").attr("id",aF.name+"-filter-control").appendTo(aA);var aG=[0,0];aF.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aJ,aK){var aI=aK.values;aB.text(aI[0]+"-"+aI[1]);aF.low=aI[0];aF.high=aI[1];an.track.request_draw(true,true)},change:function(aI,aJ){aF.control_element.slider("option","slide").call(aF.control_element,aI,aJ)}});aF.slider=aF.control_element;aF.slider_label=aB;ai(aH,aB,aF.control_element);$("<div style='clear: both;'/>").appendTo(aF.container)});if(this.filters.length!==0){var ak=$("<div/>").addClass("param-row").appendTo(av);var am=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ak);var ag=this;am.click(function(){ag.run_on_dataset()})}var ap=$("<div/>").addClass("display-controls").appendTo(this.parent_div),ar,al,ao,aj={Transparency:function(aA){an.alpha_filter=aA},Height:function(aA){an.height_filter=aA}};$.each(aj,function(aC,aB){ar=$("<div/>").addClass("filter-row").appendTo(ap),al=$("<span/>").addClass("elt-label").text(aC+":").appendTo(ar),ao=$("<select/>").attr("name",aC+"_dropdown").css("float","right").appendTo(ar);$("<option/>").attr("value",-1).text("== None ==").appendTo(ao);for(var aA=0;aA<an.filters.length;aA++){$("<option/>").attr("value",aA).text(an.filters[aA].name).appendTo(ao)}ao.change(function(){$(this).children("option:selected").each(function(){var aD=parseInt($(this).val());aj[aC]((aD>=0?an.filters[aD]:null));an.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(ar)});$("<div style='clear: both;'/>").appendTo(this.parent_div)};p(aa.prototype,{reset_filters:function(){for(var af=0;af<this.filters.length;af++){filter=this.filters[af];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var an=function(ar,ap,aq){if(!(ap in ar)){ar[ap]=aq}return ar[ap]};var ah={},af,ag,ai;for(var aj=0;aj<this.filters.length;aj++){af=this.filters[aj];if(af.tool_id){if(af.min!=af.low){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" >= "+af.low}if(af.max!=af.high){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" <= "+af.high}}}var al=[];for(var ao in ah){al[al.length]=[ao,ah[ao]]}var am=al.length;(function ak(aw,at){var aq=at[0],ar=aq[0],av=aq[1],au="("+av.join(") and (")+")",ap={cond:au,input:aw,target_dataset_id:aw,tool_id:ar},at=at.slice(1);$.getJSON(run_tool_url,ap,function(ax){if(ax.error){show_modal("Filter Dataset","Error running tool "+ar,{Close:hide_modal})}else{if(at.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ak(ax.dataset_id,at)}}})})(this.track.dataset_id,al)}});var B=function(af,ag){L.Scaler.call(this,ag);this.filter=af};B.prototype.gen_val=function(af){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(af[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var E=function(af){this.track=af.track;this.params=af.params;this.values={};this.restore_values((af.saved_values?af.saved_values:{}));this.onchange=af.onchange};p(E.prototype,{restore_values:function(af){var ag=this;$.each(this.params,function(ah,ai){if(af[ai.key]!==undefined){ag.values[ai.key]=af[ai.key]}else{ag.values[ai.key]=ai.default_value}})},build_form:function(){var ai=this;var af=$("<div />");var ah;function ag(am,aj){for(var ao=0;ao<am.length;ao++){ah=am[ao];if(ah.hidden){continue}var ak="param_"+ao;var at=ai.values[ah.key];var av=$("<div class='form-row' />").appendTo(aj);av.append($("<label />").attr("for",ak).text(ah.label+":"));if(ah.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ak).attr("name",ak).attr("checked",at))}else{if(ah.type==="text"){av.append($('<input type="text"/>').attr("id",ak).val(at).click(function(){$(this).select()}))}else{if(ah.type=="select"){var aq=$("<select />").attr("id",ak);for(var an=0;an<ah.options.length;an++){$("<option/>").text(ah.options[an].label).attr("value",ah.options[an].value).appendTo(aq)}aq.val(at);av.append(aq)}else{if(ah.type==="color"){var ap=$("<input />").attr("id",ak).attr("name",ak).val(at);var ar=$("<div class='tipsy tipsy-west' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ar);var au=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:ap,color:at});$("<div />").append(ap).append(ar).appendTo(av).bind("click",function(aw){ar.css({left:$(this).position().left+$(ap).width()+5,top:$(this).position().top-($(ar).height()/2)+($(ap).height()/2)}).show();$(document).bind("click.color-picker",function(){ar.hide();$(document).unbind("click.color-picker")});aw.stopPropagation()})}else{av.append($("<input />").attr("id",ak).attr("name",ak).val(at))}}}}if(ah.help){av.append($("<div class='help'/>").text(ah.help))}}}ag(this.params,af);return af},update_from_form:function(af){var ah=this;var ag=false;$.each(this.params,function(ai,ak){if(!ak.hidden){var al="param_"+ai;var aj=af.find("#"+al).val();if(ak.type==="float"){aj=parseFloat(aj)}else{if(ak.type==="int"){aj=parseInt(aj)}else{if(ak.type==="bool"){aj=af.find("#"+al).is(":checked")}}}if(aj!==ah.values[ak.key]){ah.values[ak.key]=aj;ag=true}}});if(ag){this.onchange()}}});var b=function(af,ai,ah,ag,aj){this.track=af;this.index=ai;this.low=ai*Q*ah;this.high=(ai+1)*Q*ah;this.resolution=ah;this.html_elt=$("<div class='track-tile'/>").append(ag);this.data=aj;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(af,ai,ah,ag,aj,ak){b.call(this,af,ai,ah,ag,aj);this.max_val=ak};p(k.prototype,b.prototype);var O=function(ah,am,ai,ag,ak,al,aq,ao){b.call(this,ah,am,ai,ag,ak);this.mode=al;this.message=aq;this.feature_mapper=ao;if(this.message){var ag=this.html_elt.children()[0],ap=$("<div/>").addClass("tile-message").text(this.message).css({height:C-1,width:ag.width}).prependTo(this.html_elt),aj=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ap),af=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ap);var an=this;aj.click(function(){an.stale=true;ah.data_manager.get_more_data(an.low,an.high,ah.mode,an.resolution,{},ah.data_manager.DEEP_DATA_REQ);ah.request_draw()}).dblclick(function(ar){ar.stopPropagation()});af.click(function(){an.stale=true;ah.data_manager.get_more_data(an.low,an.high,ah.mode,an.resolution,{},ah.data_manager.BROAD_DATA_REQ);ah.request_draw()}).dblclick(function(ar){ar.stopPropagation()})}};p(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var ag=this,af={};if(ag.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).siblings(".feature-popup").remove()}).mousemove(function(ar){if(!this.hovered){return}var am=$(this).offset(),aq=ar.pageX-am.left,ap=ar.pageY-am.top,aw=ag.feature_mapper.get_feature_data(aq,ap),an=(aw?aw[0]:null);$(this).siblings(".feature-popup").each(function(){if(!an||$(this).attr("id")!==an.toString()){$(this).remove()}});if(aw){var ai=af[an];if(!ai){var an=aw[0],at={name:aw[3],start:aw[1],end:aw[2],strand:aw[4]},al=ag.track.filters_manager.filters,ak;for(var ao=0;ao<al.length;ao++){ak=al[ao];at[ak.name]=aw[ak.index]}var ai=$("<div/>").attr("id",an).addClass("feature-popup"),ax=$("<table/>"),av,au,ay;for(av in at){au=at[av];ay=$("<tr/>").appendTo(ax);$("<th/>").appendTo(ay).text(av);$("<td/>").attr("align","left").appendTo(ay).text(typeof(au)=="number"?Z(au,2):au)}ai.append($("<div class='feature-popup-inner'>").append(ax));af[an]=ai}ai.appendTo($(ag.html_elt).parent());var aj=aq+parseInt(ag.html_elt.css("left"))-ai.width()/2,ah=ap+parseInt(ag.html_elt.css("top"))+7;ai.css("left",aj+"px").css("top",ah+"px")}else{if(!ar.isPropagationStopped()){ar.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ar)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var i=function(ai,ag,af,ah,ak,aj,al){q.call(this,ai,ag,af,{},"draghandle");this.data_url=(aj?aj:default_data_url);this.data_url_extra_params={};this.data_query_wait=(al?al:K);this.dataset_check_url=converted_datasets_state_url;this.data_manager=(ak?ak:new S(H,this));this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div)}};p(i.prototype,q.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},q.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(af){af.view.set_overview(af)}},q.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(af){af.filters_div.toggle();af.filters_manager.reset_filters()}},{name:"tools_icon",title:"Tools",css_class:"tools-icon",on_click_fn:function(af){af.dynamic_tool_div.toggle();if(af.dynamic_tool_div.is(":visible")){af.set_name(af.name+af.tool_region_and_parameters_str())}else{af.revert_name()}$(".tipsy").remove()}},q.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&q.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var af=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(af)}this.name_div=$("<div/>").addClass("track-name").appendTo(af).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return af},build_action_icons:function(){q.prototype.build_action_icons.call(this,this.action_icons_def);var ag=this;if(ag.display_modes!==undefined){var ak=(ag.config&&ag.config.values.mode?ag.config.values.mode:ag.display_modes[0]);ag.mode=ak;this.action_icons.mode_icon.attr("title","Set display mode (now: "+ag.mode+")");var ai={};for(var ah=0,af=ag.display_modes.length;ah<af;ah++){var aj=ag.display_modes[ah];ai[aj]=function(al){return function(){ag.change_mode(al);ag.icons_div.show();ag.container_div.mouseleave(function(){ag.icons_div.hide()})}}(aj)}make_popupmenu(this.action_icons.mode_icon,ai)}},hide_contents:function(){this.content_div.children().remove();this.content_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.content_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof ab){return"LabelTrack"}else{if(this instanceof z){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof W){return"ReadTrack"}else{if(this instanceof U){return"VcfTrack"}else{if(this instanceof h){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},init:function(){var af=this;af.enabled=false;af.tile_cache.clear();af.data_manager.clear();af.content_div.css("height","auto");af.container_div.removeClass("nodata error pending");if(!af.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:af.hda_ldda,dataset_id:af.dataset_id,chrom:af.view.chrom},function(ag){if(!ag||ag==="error"||ag.kind==="error"){af.container_div.addClass("error");af.content_div.text(o);if(ag.message){var ah=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})});af.content_div.append(ah)}}else{if(ag==="no converter"){af.container_div.addClass("error");af.content_div.text(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){af.container_div.addClass("nodata");af.content_div.text(D)}else{if(ag==="pending"){af.container_div.addClass("pending");af.content_div.text(t);setTimeout(function(){af.init()},af.data_query_wait)}else{if(ag.status==="data"){if(ag.valid_chroms){af.valid_chroms=ag.valid_chroms;af.update_icons()}af.content_div.text(Y);if(af.view.chrom){af.content_div.text("");af.content_div.css("height",af.height_px+"px");af.enabled=true;$.when(af.predraw_init()).done(function(){af.container_div.removeClass("nodata error pending");af.request_draw()})}}}}}}});this.update_icons()},predraw_init:function(){}});var M=function(aj,ah,ag,ai,am,al,ak){i.call(this,aj,ah,ag,ai,ak);var af=this,ah=af.view;m(af.container_div,af.drag_handle_class,".group",af);this.filters_manager=new aa(this,(am!==undefined?am:{}));this.filters_available=false;this.filters_visible=false;this.tool=(al!==undefined&&obj_length(al)>0?new r(this,al):undefined);this.tile_cache=new c(R);if(this.header_div){if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}};p(M.prototype,q.prototype,i.prototype,{copy:function(af){var ag=new this.constructor(this.name,this.view,af,this.hda_ldda,this.dataset_id,this.prefs,this.filters,this.tool,this.data_manager);ag.enabled=this.enabled;return ag},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},from_dict:function(ah,ag){var af=new this.constructor(ah.name,view,ag,ah.hda_ldda,ah.dataset_id,ah.prefs,ah.filters,ah.tool);if(ah.mode){af.change_mode(ah.mode)}return af},change_mode:function(ag){var af=this;af.mode=ag;af.config.values.mode=ag;af.tile_cache.clear();af.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+af.mode+")");return af},update_icons:function(){var af=this;if(af.filters_available){af.action_icons.filters_icon.show()}else{af.action_icons.filters_icon.hide()}if(af.tool){af.action_icons.tools_icon.show()}else{af.action_icons.tools_icon.hide()}},_gen_tile_cache_key:function(ag,ah,af){return ag+"_"+ah+"_"+af},request_draw:function(ag,af){this.view.request_redraw(false,ag,af,this)},_draw:function(ah,ar){if(!this.can_draw()){return}var ap=this.view.low,al=this.view.high,an=al-ap,ai=this.view.container.width(),av=ai/an,ak=this.view.resolution,au=this.content_div;if(this.is_overview){ap=this.view.max_low;al=this.view.max_high;ak=Math.pow(A,Math.ceil(Math.log((view.max_high-view.max_low)/Q)/Math.log(A)));av=ai/(view.max_high-view.max_low)}if(!ar){this.content_div.children().addClass("remove")}this.max_height=0;var ag=Math.floor(ap/ak/Q);var ao=true;var at=[];var af=0;var am=function(aw){return("track" in aw)};while((ag*Q*ak)<al){var aq=this.draw_helper(ah,ai,ag,ak,au,av);if(am(aq)){at.push(aq)}else{ao=false}ag+=1;af++}if(!ar){this.content_div.children(".remove").remove()}var aj=this;if(ao){aj.postdraw_actions(at,ai,av,ar)}},postdraw_actions:function(aj,ak,al,af){var ah=this;var ai=false;for(var ag=0;ag<aj.length;ag++){if(aj[ag].message){ai=true;break}}if(ai){for(var ag=0;ag<aj.length;ag++){tile=aj[ag];if(!tile.message){tile.html_elt.css("padding-top",C)}}}},draw_helper:function(af,aq,au,ar,ai,aj,al,an){var ap=this,ax=this._gen_tile_cache_key(aq,aj,au),av=au*Q*ar,ag=av+Q*ar;var aw=(af?undefined:ap.tile_cache.get(ax));if(aw){ap.show_tile(aw,ai,aj);return aw}var am=function(ay){return("isResolved" in ay)};var ao=true;var at=ap.data_manager.get_data(av,ag,ap.mode,ar,ap.data_url_extra_params);if(am(at)){ao=false}var ak;if(view.reference_track&&aj>view.canvas_manager.char_width_px){ak=view.reference_track.data_manager.get_data(av,ag,ap.mode,ar,view.reference_track.data_url_extra_params);if(am(ak)){ao=false}}if(ao){p(at,an);var aw=ap.draw_tile(at,ap.mode,ar,au,aj,ak);if(aw!==undefined){ap.tile_cache.set(ax,aw);ap.show_tile(aw,ai,aj)}return aw}var ah=$.Deferred();$.when(at,ak).then(function(){view.request_redraw(false,false,false,ap);ah.resolve()});return ah},draw_tile:function(af,aj,ai,ag,ak,ah){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ah,aj,ak){var ag=this,af=ah.html_elt;ah.predisplay_actions();var ai=(ah.low-(this.is_overview?this.view.max_low:this.view.low))*ak;if(this.left_offset){ai-=this.left_offset}af.css({position:"absolute",top:0,left:ai,height:""});if(af.hasClass("remove")){af.removeClass("remove")}else{aj.append(af)}ag.max_height=Math.max(ag.max_height,af.height());ag.content_div.css("height",ag.max_height+"px");aj.children().css("height",ag.max_height+"px")},_get_tile_bounds:function(af,ag){var ai=af*Q*ag,aj=Q*ag,ah=(ai+aj<=this.view.max_high?ai+aj:this.view.max_high);return[ai,ah]},tool_region_and_parameters_str:function(ah,af,ai){var ag=this,aj=(ah!==undefined&&af!==undefined&&ai!==undefined?ah+":"+af+"-"+ai:"all");return" - region=["+aj+"], parameters=["+ag.tool.get_param_values().join(", ")+"]"},init_for_tool_data:function(){this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.predraw_init=function(){var ag=this;var af=function(){if(ag.data_manager.size()===0){setTimeout(af,300)}else{ag.data_url=default_data_url;ag.data_query_wait=K;ag.dataset_state_url=converted_datasets_state_url;$.getJSON(ag.dataset_state_url,{dataset_id:ag.dataset_id,hda_ldda:ag.hda_ldda},function(ah){})}};af()}}});var ab=function(ag,af){i.call(this,"label",ag,af,false,{});this.container_div.addClass("label-track")};p(ab.prototype,i.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ah=this.view,ai=ah.high-ah.low,al=Math.floor(Math.pow(10,Math.floor(Math.log(ai)/Math.log(10)))),af=Math.floor(ah.low/al)*al,aj=this.view.container.width(),ag=$("<div style='position: relative; height: 1.3em;'></div>");while(af<ah.high){var ak=(af-ah.low)/ai*aj;ag.append($("<div class='label'>"+commatize(af)+"</div>").css({position:"absolute",left:ak-1}));af+=al}this.content_div.children(":first").remove();this.content_div.append(ag)}});var h=function(ai,ah,ag,af){this.display_modes=["Histogram","Line","Filled","Intensity"];M.call(this,ai,ah,ag);this.drawables=[];if(af){var al=[],ak;for(var aj=0;aj<af.length;aj++){ak=af[aj];al.push(ak.dataset_id);this.drawables[aj]=ak.copy()}this.enabled=true}this.update_icons();this.obj_type="CompositeTrack"};p(h.prototype,M.prototype,{to_dict:x.prototype.to_dict,add_drawable:x.prototype.add_drawable,from_dict:function(al,af){var ak=new this.constructor(al.name,view,af,al.prefs,view.viewport_container,view);var ag,aj,ai;for(var ah=0;ah<al.drawables.length;ah++){ag=al.drawables[ah];aj=ag.obj_type;if(!aj){aj=ag.track_type}ai=addable_objects[aj].prototype.from_dict(ag);ak.add_drawable(ai)}return ak},change_mode:function(af){M.prototype.change_mode.call(this,af);for(var ag=0;ag<this.drawables.length;ag++){this.drawables[ag].change_mode(af)}},init:function(){this.enabled=true;this.request_draw()},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide()},can_draw:q.prototype.can_draw,draw_helper:function(ag,av,ay,aw,aj,an,ao,aq){var aD=this._gen_tile_cache_key(av,an,ay),aC=(ag?undefined:this.tile_cache.get(aD));if(aC){this.show_tile(aC,aj,an);return aC}var ah,ak=$("<div/>"),al,aA=[],at=[],ai=true;for(var ax=0;ax<this.drawables.length;ax++){al=this.drawables[ax].draw_helper(ag,av,ay,aw,ak,an,ao,aq);if(al instanceof b){aA.push(al)}else{at.push(al);ai=false}}if(ai){var am=aA[0].html_elt.find("canvas"),aB=am.clone(),ar=am.get(0).getContext("2d"),ap=aB.get(0).getContext("2d"),az=ar.getImageData(0,0,ar.canvas.width,ar.canvas.height);ap.putImageData(az,0,0);ap.globalCompositeOperation="darker";var af;for(var ax=1;ax<aA.length;ax++){af=aA[ax].html_elt.find("canvas").get(0);ap.drawImage(af,0,0)}aC=new b(this,ay,aw,aB);this.tile_cache.set(aD,aC);this.show_tile(aC,aj,an)}else{var au=this;$.when.apply($,at).then(function(){au.request_draw()})}return aC}});var z=function(af){M.call(this,"reference",af,{content_div:af.top_labeltrack},{});af.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:af.dbkey};this.data_manager=new G(H,this,false)};p(z.prototype,q.prototype,M.prototype,{build_header_div:function(){},init:function(){this.enabled=true},can_draw:q.prototype.can_draw,draw_tile:function(ap,al,ak,ag,aq){var aj=this,ah=Q*ak;if(aq>this.view.canvas_manager.char_width_px){if(ap.data===null){aj.content_div.css("height","0px");return}var ai=this.view.canvas_manager.new_canvas();var ao=ai.getContext("2d");ai.width=Math.ceil(ah*aq+aj.left_offset);ai.height=aj.height_px;ao.font=ao.canvas.manager.default_font;ao.textAlign="center";ap=ap.data;for(var am=0,an=ap.length;am<an;am++){var af=Math.round(am*aq);ao.fillText(ap[am],af+aj.left_offset,10)}return new b(aj,ag,ak,ai,ap)}this.content_div.css("height","0px")}});var j=function(af,am,ag,al,ao,an,aj,ak,ah){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";M.call(this,af,am,ag,an,aj,ak,ah);this.min_height_px=16;this.max_height_px=400;this.height_px=32;this.hda_ldda=al;this.dataset_id=ao;this.original_dataset_id=ao;this.left_offset=0;this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:an,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.dataset_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.dataset_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};p(j.prototype,q.prototype,M.prototype,{add_resize_handle:function(){var af=this;var ai=false;var ah=false;var ag=$("<div class='track-resize'>");$(af.container_div).hover(function(){if(af.content_visible){ai=true;ag.show()}},function(){ai=false;if(!ah){ag.hide()}});ag.hide().bind("dragstart",function(aj,ak){ah=true;ak.original_height=$(af.content_div).height()}).bind("drag",function(ak,al){var aj=Math.min(Math.max(al.original_height+al.deltaY,af.min_height_px),af.max_height_px);$(af.content_div).css("height",aj);af.height_px=aj;af.request_draw(true)}).bind("dragend",function(aj,ak){af.tile_cache.clear();ah=false;if(!ai){ag.hide()}af.config.values.height=af.height_px}).appendTo(af.container_div)},predraw_init:function(){var af=this;af.vertical_range=undefined;return $.getJSON(af.data_url,{stats:true,chrom:af.view.chrom,low:null,high:null,hda_ldda:af.hda_ldda,dataset_id:af.dataset_id},function(ag){af.container_div.addClass("line-track");var aj=ag.data;if(isNaN(parseFloat(af.prefs.min_value))||isNaN(parseFloat(af.prefs.max_value))){var ah=aj.min;var al=aj.max;ah=Math.floor(Math.min(0,Math.max(ah,aj.mean-2*aj.sd)));al=Math.ceil(Math.max(0,Math.min(al,aj.mean+2*aj.sd)));af.prefs.min_value=ah;af.prefs.max_value=al;$("#track_"+af.dataset_id+"_minval").val(af.prefs.min_value);$("#track_"+af.dataset_id+"_maxval").val(af.prefs.max_value)}af.vertical_range=af.prefs.max_value-af.prefs.min_value;af.total_frequency=aj.total_frequency;af.container_div.find(".yaxislabel").remove();var ak=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_minval").text(Z(af.prefs.min_value,3));var ai=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_maxval").text(Z(af.prefs.max_value,3));ai.css({position:"absolute",top:"24px",left:"10px"});ai.prependTo(af.container_div);ak.css({position:"absolute",bottom:"2px",left:"10px"});ak.prependTo(af.container_div)})},draw_tile:function(ar,ak,aj,ah,aq){if(this.vertical_range===undefined){return}var af=this._get_tile_bounds(ah,aj),al=af[0],ap=af[1],ag=Math.ceil((ap-al)*aq),an=this.height_px;var ai=this.view.canvas_manager.new_canvas();ai.width=ag,ai.height=an;var ao=ai.getContext("2d");var am=new L.LinePainter(ar.data,al,ap,this.prefs,ak);am.draw(ao,ag,an);return new b(this.track,ah,aj,ai,ar.data)}});var d=function(af,am,ag,al,ao,an,aj,ak,ah){var ai=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];M.call(this,af,am,ag,an,aj,ak,ah);this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:an,onchange:function(){ai.set_name(ai.prefs.name);ai.tile_cache.clear();ai.set_painter_from_config();ai.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=al;this.dataset_id=ao;this.original_dataset_id=ao;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};p(d.prototype,q.prototype,M.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style=="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(at,an,aj,ah){M.prototype.postdraw_actions.call(this,at,ah);var am=this;if(ah){var ax=am.content_div.children();var aw=false;for(var ap=ax.length-1,aq=0;ap>=aq;ap--){var ai=$(ax[ap]);if(aw){ai.remove()}else{if(ai.children().length!==0){aw=true}}}}if(am.mode=="Histogram"){var ag=-1;for(var ap=0;ap<at.length;ap++){var ao=at[ap].max_val;if(ao>ag){ag=ao}}for(var ap=0;ap<at.length;ap++){var av=at[ap];if(av.max_val!==ag){av.html_elt.remove();am.draw_helper(true,an,av.index,av.resolution,av.html_elt.parent(),aj,[],{max:ag})}}}if(am.filters_manager){var ak=am.filters_manager.filters;for(var ar=0;ar<ak.length;ar++){ak[ar].update_ui_elt()}var au=false,af,al;for(var ap=0;ap<at.length;ap++){if(at[ap].data.length){af=at[ap].data[0];for(var ar=0;ar<ak.length;ar++){al=ak[ar];if(al.applies_to(af)&&al.min!==al.max){au=true;break}}}}if(am.filters_available!==au){am.filters_available=au;if(!am.filters_available){am.filters_div.hide()}am.update_icons()}}},update_auto_mode:function(af){var af;if(this.mode=="Auto"){if(af=="no_detail"){af="feature spans"}else{if(af=="summary_tree"){af="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+af+")")}},incremental_slots:function(aj,ag,ai){var ah=this.view.canvas_manager.dummy_context,af=this.inc_slots[aj];if(!af||(af.mode!==ai)){af=new (s.FeatureSlotter)(aj,ai==="Pack",y,function(ak){return ah.measureText(ak)});af.mode=ai;this.inc_slots[aj]=af}return af.slot_features(ag)},get_summary_tree_data:function(aj,am,ah,av){if(av>ah-am){av=ah-am}var aq=Math.floor((ah-am)/av),au=[],ai=0;var ak=0,al=0,ap,at=0,an=[],ar,ao;var ag=function(ay,ax,az,aw){ay[0]=ax+az*aw;ay[1]=ax+(az+1)*aw};while(at<av&&ak!==aj.length){var af=false;for(;at<av&&!af;at++){ag(an,am,at,aq);for(al=ak;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){af=true;break}}if(af){break}}data_start_index=al;au[au.length]=ar=[an[0],0];for(;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){ar[1]++}else{break}}if(ar[1]>ai){ai=ar[1]}at++}return{max:ai,delta:aq,data:au}},draw_tile:function(au,ax,aB,aF,ap,ai){var ay=this,ak=ay._get_tile_bounds(aF,aB),aI=ak[0],ag=ak[1],aw=ag-aI,az=Math.ceil(aw*ap),aO=25,aj=this.left_offset,av,al;if(ax==="Auto"){if(au.dataset_type==="summary_tree"){ax=au.dataset_type}else{if(au.extra_info==="no_detail"||ay.is_overview){ax="no_detail"}else{var aN=au.data;if(this.view.high-this.view.low>I){ax="Squish"}else{ax="Pack"}}}this.update_auto_mode(ax)}if(ax==="summary_tree"||ax==="Histogram"){al=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var af=$("<div />").addClass("yaxislabel");af.text(au.max);af.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});af.prependTo(this.container_div);var ah=this.view.canvas_manager.new_canvas();ah.width=az+aj;ah.height=al+T;if(au.dataset_type!="summary_tree"){var aq=this.get_summary_tree_data(au.data,aI,ag,200);if(au.max){aq.max=au.max}au=aq}var aK=new L.SummaryTreePainter(au,aI,ag,this.prefs);var aA=ah.getContext("2d");aA.translate(aj,T);aK.draw(aA,az,al);return new k(ay,aF,aB,ah,au.data,au.max)}var av,an=1;if(ax==="no_detail"||ax==="Squish"||ax==="Pack"){an=this.incremental_slots(ap,au.data,ax);av=this.inc_slots[ap].slots}var ao=[];if(au.data){var ar=this.filters_manager.filters;for(var aC=0,aE=au.data.length;aC<aE;aC++){var am=au.data[aC];var aD=false;var at;for(var aH=0,aM=ar.length;aH<aM;aH++){at=ar[aH];at.update_attrs(am);if(!at.keep(am)){aD=true;break}}if(!aD){ao.push(am)}}}var aL=(this.filters_manager.alpha_filter?new B(this.filters_manager.alpha_filter):null);var aJ=(this.filters_manager.height_filter?new B(this.filters_manager.height_filter):null);var aK=new (this.painter)(ao,aI,ag,this.prefs,ax,aL,aJ,ai);var al=Math.max(ad,aK.get_required_height(an,az));var ah=this.view.canvas_manager.new_canvas();var aG=null;ah.width=az+aj;ah.height=al;var aA=ah.getContext("2d");aA.fillStyle=this.prefs.block_color;aA.font=aA.canvas.manager.default_font;aA.textAlign="right";this.container_div.find(".yaxislabel").remove();if(au.data){aA.translate(aj,0);aG=aK.draw(aA,az,al,av);aG.translation=-aj}return new O(ay,aF,aB,ah,au.data,ax,au.message,aG)}});var U=function(af,al,ag,ak,an,am,ai,aj,ah){d.call(this,af,al,ag,ak,an,am,ai,aj,ah);this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:am,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter};p(U.prototype,q.prototype,M.prototype,d.prototype);var W=function(af,al,ag,ak,ao,an,ai,ah){d.call(this,af,al,ag,ak,ao,an,ai,ah);var aj=get_random_color(),am=get_random_color([aj,"#ffffff"]);this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:aj},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:am},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:an,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter;this.update_icons()};p(W.prototype,q.prototype,M.prototype,d.prototype);X.View=ac;X.DrawableGroup=P;X.LineTrack=j;X.FeatureTrack=d;X.ReadTrack=W;X.VcfTrack=U;X.CompositeTrack=h};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(F,G){for(var E=0;E<=z;E++){var C=false,H=h[E];if(H!==undefined){for(var B=0,D=H.length;B<D;B++){var i=H[B];if(G>i[0]&&F<i[1]){C=true;break}}}if(!C){return E}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(i,x){var u=i("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y<E;y++,A+=J,G+=H){if(y%2!==0){continue}I.fillRect(A,G,D,1)}};var q=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var d=function(y){this.default_val=(y?y:1)};d.prototype.gen_val=function(y){return this.default_val};var l=function(A,C,y,z,B){this.data=A;this.view_start=C;this.view_end=y;this.prefs=u({},this.default_prefs,z);this.mode=B};l.prototype.default_prefs={};var v=function(A,C,y,z,B){l.call(this,A,C,y,z,B)};v.prototype.default_prefs={show_counts:false};v.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var b=function(y,C,E,F,A){l.call(this,y,C,E,F,A);if(this.prefs.min_value===undefined){var G=Infinity;for(var z=0,B=this.data.length;z<B;z++){G=Math.min(G,this.data[z][1])}this.prefs.min_value=G}if(this.prefs.max_value===undefined){var D=-Infinity;for(var z=0,B=this.data.length;z<B;z++){D=Math.max(D,this.data[z][1])}this.prefs.max_value=D}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var m=function(y){this.feature_positions={};this.slot_height=y;this.translation=0;this.y_translation=0};m.prototype.map_feature_data=function(z,B,y,A){if(!this.feature_positions[B]){this.feature_positions[B]=[]}this.feature_positions[B].push({data:z,x_start:y,x_end:A})};m.prototype.get_feature_data=function(z,D){var C=Math.floor((D-this.y_translation)/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var o=function(A,D,y,z,C,E,B){l.call(this,A,D,y,z,C);this.alpha_scaler=(E?E:new d());this.height_scaler=(B?B:new d())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(A,z){var y=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){y=A*y_scale}return y+this.get_top_padding(z)+this.get_bottom_padding(z)},get_top_padding:function(y){return 0},get_bottom_padding:function(y){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(K,I,G,F){var Q=this.data,D=this.view_start,M=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var H=this.view_end-this.view_start,E=I/H,L=this.get_row_height(),P=new m(L),B;for(var N=0,O=Q.length;N<O;N++){var A=Q[N],C=A[0],J=A[1],y=A[2],z=(F&&F[C]!==undefined?F[C]:null);if((J<M&&y>D)&&(this.mode=="Dense"||z!==null)){B=this.draw_element(K,this.mode,A,z,D,M,E,L,I);P.map_feature_data(A,z,B[0],B[1])}}K.restore();P.y_translation=this.get_top_padding(I);return P},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.");return[0,0]}});var c=10,h=3,k=5,w=10,f=1,s=9,e=3,a=9,j=2,g="#ccc";var r=function(A,D,y,z,C,E,B){o.call(this,A,D,y,z,C,E,B);this.draw_background_connector=true;this.draw_individual_connectors=false};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=c}else{if(z==="no_detail"){y=h}else{if(z==="Squish"){y=k}else{y=w}}}return y},draw_element:function(M,D,X,H,O,aj,an,ap,y){var T=X[0],al=X[1],ad=X[2]-1,Q=X[3],ae=Math.floor(Math.max(0,(al-O)*an)),N=Math.ceil(Math.min(y,Math.max(0,(ad-O)*an))),ac=ae,ao=N,aa=(D==="Dense"?0:(0+H))*ap+this.get_top_padding(y),L,ah,R=null,ar=null,B=this.prefs.block_color,ag=this.prefs.label_color;M.globalAlpha=this.alpha_scaler.gen_val(X);if(D==="Dense"){H=1}if(D==="no_detail"){M.fillStyle=B;M.fillRect(ae,aa+5,N-ae,f)}else{var K=X[4],Z=X[5],af=X[6],C=X[7],V=true;if(Z&&af){R=Math.floor(Math.max(0,(Z-O)*an));ar=Math.ceil(Math.min(y,Math.max(0,(af-O)*an)))}var am,U;if(D==="Squish"){am=1;U=e;V=false}else{if(D==="Dense"){am=5;U=s}else{am=5;U=a}}if(!C){M.fillStyle=B;M.fillRect(ae,aa+1,N-ae,U);if(K&&V){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}M.fillRect(ae,aa+1,N-ae,U)}}else{var J,W;if(D==="Squish"||D==="Dense"){J=aa+Math.floor(e/2)+1;W=1}else{if(K){J=aa;W=U}else{J+=(e/2)+1;W=1}}if(this.draw_background_connector){if(D==="Squish"||D==="Dense"){M.fillStyle=g}else{if(K){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand")}}}else{M.fillStyle=g}}M.fillRect(ae,J,N-ae,W)}var E;for(var ak=0,A=C.length;ak<A;ak++){var F=C[ak],z=Math.floor(Math.max(0,(F[0]-O)*an)),Y=Math.ceil(Math.min(y,Math.max((F[1]-1-O)*an))),S,ab;if(z>Y){continue}M.fillStyle=B;M.fillRect(z,aa+(U-am)/2+1,Y-z,am);if(R!==undefined&&af>Z&&!(z>ar||Y<R)){var ai=Math.max(z,R),I=Math.min(Y,ar);M.fillRect(ai,aa+1,I-ai,U);if(C.length==1&&D=="Pack"){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}if(ai+14<I){ai+=2;I-=2}M.fillRect(ai,aa+1,I-ai,U)}}if(this.draw_individual_connectors&&S){this.draw_connector(M,S,ab,z,Y,aa)}S=z;ab=Y}if(D==="Pack"){M.globalAlpha=1;M.fillStyle="white";var G=this.height_scaler.gen_val(X),P=Math.ceil(U*G),aq=Math.round((U-P)/2);if(G!==1){M.fillRect(ae,J+1,N-ae,aq);M.fillRect(ae,J+U-aq+1,N-ae,aq)}}}M.globalAlpha=1;if(D==="Pack"&&al>O){M.fillStyle=ag;if(O===0&&ae-M.measureText(Q).width<0){M.textAlign="left";M.fillText(Q,N+j,aa+8);ao+=M.measureText(Q).width+j}else{M.textAlign="right";M.fillText(Q,ae-j,aa+8);ac-=M.measureText(Q).width+j}}}M.globalAlpha=1;return[ac,ao]}});var t=function(B,E,y,A,D,F,C,z){o.call(this,B,E,y,A,D,F,C);this.ref_seq=(z?z.data:null)};u(t.prototype,o.prototype,{get_row_height:function(){var y,z=this.mode;if(z==="Dense"){y=c}else{if(z==="Squish"){y=k}else{y=w;if(this.prefs.show_insertions){y*=2}}}return y},draw_read:function(K,A,ag,V,L,aa,ad,C,B,M){K.textAlign="center";var J=this,R=[L,aa],Z=0,W=0,D=0,F=K.canvas.manager.char_width_px,y=(B==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var O=[];if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){D=Math.round(ag/2)}if(!C){C=[[0,M.length]]}for(var G=0,I=C.length;G<I;G++){var z=C[G],E="MIDNSHP=X"[z[0]],S=z[1];if(E==="H"||E==="S"){Z-=S}var U=ad+Z,Y=Math.floor(Math.max(0,(U-L)*ag)),ab=Math.floor(Math.max(0,(U+S-L)*ag));if(Y===ab){ab+=1}switch(E){case"H":break;case"S":case"M":case"=":if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(D>0){K.fillStyle=y;K.fillRect(Y-D,V+1,ab-Y,9);K.fillStyle=g;for(var af=0,H=N.length;af<H;af++){if(this.prefs.show_differences&&this.ref_seq){var P=this.ref_seq[U-L+af];if(!P||P.toLowerCase()===N[af].toLowerCase()){continue}}if(U+af>=L&&U+af<=aa){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X,V+9)}}}else{K.fillStyle=y;K.fillRect(Y,V+4,ab-Y,e)}}W+=S;Z+=S;break;case"N":K.fillStyle=g;K.fillRect(Y-D,V+5,ab-Y,1);Z+=S;break;case"D":K.fillStyle="red";K.fillRect(Y-D,V+4,ab-Y,3);Z+=S;break;case"P":break;case"I":var ah=Y-D;if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(this.prefs.show_insertions){var T=Y-(ab-Y)/2;if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){K.fillStyle="yellow";K.fillRect(T-D,V-9,ab-Y,9);O[O.length]={type:"triangle",data:[ah,V+4,5]};K.fillStyle=g;switch(compute_overlap([U,U+S],R)){case (OVERLAP_START):N=N.slice(L-U);break;case (OVERLAP_END):N=N.slice(0,U-aa);break;case (CONTAINED_BY):break;case (CONTAINS):N=N.slice(L-U,U-aa);break}for(var af=0,H=N.length;af<H;af++){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X-(ab-Y)/2,V)}}else{K.fillStyle="yellow";K.fillRect(T,V+(this.mode!=="Dense"?2:5),ab-Y,(A!=="Dense"?e:s))}}else{if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){O.push({type:"text",data:[N.length,ah,V+9]})}else{}}}W+=S;break;case"X":W+=S;break}}K.fillStyle="yellow";var Q,ai,ae;for(var ac=0;ac<O.length;ac++){Q=O[ac];ai=Q.type;ae=Q.data;if(ai==="text"){K.save();K.font="bold "+K.font;K.fillText(ae[0],ae[1],ae[2]);K.restore()}else{if(ai=="triangle"){q(K,ae[0],ae[1],ae[2])}}}},draw_element:function(R,M,E,B,U,z,I,S,P){var H=E[0],Q=E[1],A=E[2],J=E[3],D=Math.floor(Math.max(0,(Q-U)*I)),F=Math.ceil(Math.min(P,Math.max(0,(A-U)*I))),C=(M==="Dense"?0:(0+B))*S,G=this.prefs.label_color,O=0;if((M==="Pack"||this.mode==="Auto")&&I>R.canvas.manager.char_width_px){var O=Math.round(I/2)}if(E[5] instanceof Array){var N=Math.floor(Math.max(0,(E[4][0]-U)*I)),L=Math.ceil(Math.min(P,Math.max(0,(E[4][1]-U)*I))),K=Math.floor(Math.max(0,(E[5][0]-U)*I)),y=Math.ceil(Math.min(P,Math.max(0,(E[5][1]-U)*I)));if(E[4][1]>=U&&E[4][0]<=z&&E[4][2]){this.draw_read(R,M,I,C,U,z,E[4][0],E[4][2],E[4][3],E[4][4])}if(E[5][1]>=U&&E[5][0]<=z&&E[5][2]){this.draw_read(R,M,I,C,U,z,E[5][0],E[5][2],E[5][3],E[5][4])}if(K>L){R.fillStyle=g;p(R,L-O,C+5,K-O,C+5)}}else{this.draw_read(R,M,I,C,U,z,Q,E[4],E[5],E[6])}if(M==="Pack"&&Q>U&&J!=="."){R.fillStyle=this.prefs.label_color;var T=1;if(T===0&&D-R.measureText(J).width<0){R.textAlign="left";R.fillText(J,F+j-O,C+8)}else{R.textAlign="right";R.fillText(J,D-j-O,C+8)}}return[0,0]}});var n=function(A,D,y,z,C,E,B){r.call(this,A,D,y,z,C,E,B);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};u(n.prototype,o.prototype,r.prototype,{calculate_longest_feature_length:function(){var z=0;for(var C=0,y=this.data.length;C<y;C++){var B=this.data[C],A=B[1],D=B[2];z=Math.max(z,D-A)}return z},get_top_padding:function(z){var y=this.view_end-this.view_start,A=z/y;return Math.min(128,Math.ceil((this.longest_feature_length/2)*A))},draw_connector:function(G,B,F,H,E,D){var y=(F+H)/2,C=H-y;var A=Math.PI,z=0;if(C>0){G.beginPath();G.arc(y,D,H-y,Math.PI,0);G.stroke()}}});x.Scaler=d;x.SummaryTreePainter=v;x.LinePainter=b;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.ArcLinkedFeaturePainter=n};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window);
\ No newline at end of file
diff --git a/static/scripts/packed/trackster_ui.js b/static/scripts/packed/trackster_ui.js
index ce85fac69fc..483ca3f230d 100644
--- a/static/scripts/packed/trackster_ui.js
+++ b/static/scripts/packed/trackster_ui.js
@@ -1 +1 @@
-var add_bookmark=function(b,a){var g=$("#bookmarks-container"),d=$("<div/>").addClass("bookmark").appendTo(g),c=$("<div/>").addClass("delete-icon-container").appendTo(d).click(function(){d.slideUp("fast");d.remove();view.has_changes=true;return false}),e=$("<a href=''/>").addClass("icon-button delete").appendTo(c),f=$("<div/>").addClass("position").appendTo(d),h=$("<a href=''/>").text(b).appendTo(f).click(function(){view.go_to(b);return false});annotation_div=get_editable_text_elt(a,true).addClass("annotation").appendTo(d);view.has_changes=true;return d};var addable_objects={LineTrack:LineTrack,FeatureTrack:FeatureTrack,VcfTrack:VcfTrack,ReadTrack:ReadTrack,DrawableGroup:DrawableGroup};var track_from_dict=function(c,b){var a=new addable_objects[c.track_type](c.name,view,b,c.hda_ldda,c.dataset_id,c.prefs,c.filters,c.tool);if(c.mode){a.change_mode(c.mode)}return a};var drawable_collection_from_dict=function(f,a){var e=new addable_objects[f.obj_type](f.name,view,a,f.prefs,view.viewport_container,view);for(var d=0;d<f.drawables.length;d++){var b=f.drawables[d],c;if(b.track_type){c=track_from_dict(b,e)}else{c=drawable_collection_from_dict(b)}e.add_drawable(c);e.content_div.append(c.container_div)}return e};var drawable_from_dict=function(b,a){return(b.track_type?track_from_dict(b,a):drawable_collection_from_dict(b,a))};var create_visualization=function(b,e,g,c,a,d,f){view=new View(b,e,g,c);view.editor=true;$.when(view.load_chroms_deferred).then(function(){if(a){var k=a.chrom,p=a.start,h=a.end,m=a.overview;if(k&&(p!==undefined)&&h){view.change_chrom(k,p,h)}}if(d){var o;for(var j=0;j<d.length;j++){o=d[j];view.add_drawable(drawable_from_dict(o,view))}}view.update_intro_div();var n;for(var j=0;j<view.drawables.length;j++){if(view.drawables[j].name===m){view.set_overview(view.drawables[j]);break}}if(f){var l;for(var j=0;j<f.length;j++){l=f[j];add_bookmark(l.position,l.annotation)}}view.has_changes=false});return view};var init_keyboard_nav=function(a){$(document).keydown(function(b){if($(b.srcElement).is(":input")){return}switch(b.which){case 37:a.move_fraction(0.25);break;case 38:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTop(a.viewport_container.scrollTop()-20);break;case 39:a.move_fraction(-0.25);break;case 40:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTop(a.viewport_container.scrollTop()+20);break}})};
\ No newline at end of file
+var add_bookmark=function(b,a){var g=$("#bookmarks-container"),d=$("<div/>").addClass("bookmark").appendTo(g),c=$("<div/>").addClass("delete-icon-container").appendTo(d).click(function(){d.slideUp("fast");d.remove();view.has_changes=true;return false}),e=$("<a href=''/>").addClass("icon-button delete").appendTo(c),f=$("<div/>").addClass("position").appendTo(d),h=$("<a href=''/>").text(b).appendTo(f).click(function(){view.go_to(b);return false});annotation_div=get_editable_text_elt(a,true).addClass("annotation").appendTo(d);view.has_changes=true;return d};var addable_objects={LineTrack:LineTrack,FeatureTrack:FeatureTrack,VcfTrack:VcfTrack,ReadTrack:ReadTrack,CompositeTrack:CompositeTrack,DrawableGroup:DrawableGroup};var create_visualization=function(b,e,g,c,a,d,f){view=new View(b,e,g,c);view.editor=true;$.when(view.load_chroms_deferred).then(function(){if(a){var q=a.chrom,h=a.start,n=a.end,k=a.overview;if(q&&(h!==undefined)&&n){view.change_chrom(q,h,n)}}if(d){var l,j,m;for(var o=0;o<d.length;o++){l=d[o];j=l.obj_type;if(!j){j=l.track_type}m=addable_objects[j].prototype.from_dict(l,view);view.add_drawable(m)}}view.update_intro_div();var r;for(var o=0;o<view.drawables.length;o++){if(view.drawables[o].name===k){view.set_overview(view.drawables[o]);break}}if(f){var p;for(var o=0;o<f.length;o++){p=f[o];add_bookmark(p.position,p.annotation)}}view.has_changes=false});return view};var init_keyboard_nav=function(a){$(document).keydown(function(b){if($(b.srcElement).is(":input")){return}switch(b.which){case 37:a.move_fraction(0.25);break;case 38:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTop(a.viewport_container.scrollTop()-20);break;case 39:a.move_fraction(-0.25);break;case 40:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTop(a.viewport_container.scrollTop()+20);break}})};
\ No newline at end of file
diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index f550b8c7c4e..6af99254d3b 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -777,7 +777,15 @@ extend(Drawable.prototype, {
     },
     request_draw: function() {},
     _draw: function() {},
-    to_json: function() {},
+    /** 
+     * Returns representation of object in a dictionary for easy saving. 
+     * Use from_dict to recreate object.
+     */
+    to_dict: function() {},
+    /**
+     * Restore object from a dictionary created by to_dict()
+     */
+    from_dict: function(object_dict) {},
     update_icons: function() {},
     /**
      * Set drawable name.
@@ -878,21 +886,44 @@ extend(DrawableCollection.prototype, Drawable.prototype, {
             this.drawables[i]._draw();
         }
     },
-    /**
-     * Returns jsonified representation of collection.
+    /** 
+     * Returns representation of object in a dictionary for easy saving. 
+     * Use from_dict to recreate object.
      */
-    to_json: function() {
-        var jsonified_drawables = [];
+    to_dict: function() {
+        var dictified_drawables = [];
         for (var i = 0; i < this.drawables.length; i++) {
-            jsonified_drawables.push(this.drawables[i].to_json());
+            dictified_drawables.push(this.drawables[i].to_dict());
         }
         return {
             name: this.name,
             prefs: this.prefs,
             obj_type: this.obj_type,
-            drawables: jsonified_drawables
+            drawables: dictified_drawables
             };
     },
+    /**
+     * Restore object from a dictionary created by to_dict()
+     */
+    from_dict: function(collection_dict, container) {
+        var collection = new this.constructor( collection_dict.name, view, 
+                                               container, collection_dict.prefs, 
+                                               view.viewport_container, view);
+       var drawable_dict,
+           drawable_type,
+           drawable;
+        for (var i = 0; i < collection_dict.drawables.length; i++) {
+            drawable_dict = collection_dict.drawables[i];
+            drawable_type = drawable_dict['obj_type'];
+            // For backward compatibility:
+            if (!drawable_type) {
+                drawable_type = drawable_dict['track_type']; 
+            }
+            drawable = addable_objects[ drawable_type ].prototype.from_dict( drawable_dict, collection );
+            collection.add_drawable( drawable );
+        }
+        return collection;
+    },
     /**
      * Add a drawable to the end of the collection.
      */
@@ -956,11 +987,10 @@ var DrawableGroup = function(name, view, container, prefs) {
 };
 
 extend(DrawableGroup.prototype, Drawable.prototype, DrawableCollection.prototype, {
-    /*
     action_icons_def: [
     // Create composite track from group's tracks.
     {
-        name: "composite-icon",
+        name: "composite_icon",
         title: "Show composite track",
         css_class: "layers-stack",
         on_click_fn: function(group) {
@@ -968,7 +998,6 @@ extend(DrawableGroup.prototype, Drawable.prototype, DrawableCollection.prototype
         }
     }
     ].concat(Drawable.prototype.action_icons_def),
-    */
     build_container_div: function() {
         return $("<div/>").addClass("group").attr("id", "group_" + this.id).appendTo(this.container.content_div);
     },
@@ -988,14 +1017,51 @@ extend(DrawableGroup.prototype, Drawable.prototype, DrawableCollection.prototype
         this.request_draw();
     },
     update_icons: function() {
-        // TODO: only show icon for compositing if all tracks are the same type.  
+        // Only show composite icon if all tracks are the same type.
+        var can_composite = true,
+            a_type = this.drawables[0].get_type();
+        for (var i = 0; i < this.drawables.length; i++) {
+            if ( this.drawables[i].get_type() !== a_type ) {
+                can_composite = false;
+                break;
+            }
+        }
+        
+        if (can_composite) {
+            this.action_icons.composite_icon.show();
+        }
+        else {
+            this.action_icons.composite_icon.hide();
+            $(".tipsy").remove();
+        }        
     },
     /**
-     * Show composite track using group's tracks.
+     * Add composite track to group that includes all of group's tracks.
      */
     show_composite_track: function() {
-        this.composite_track = new CompositeTiledTrack(this.drawables, this.view, this);
-        this.composite_track.request_draw();
+        var composite_track = new CompositeTrack("Composite Track", this.view, this, this.drawables);
+        this.add_drawable(composite_track);
+        composite_track.request_draw();
+    },
+    add_drawable: function(drawable) {
+        DrawableCollection.prototype.add_drawable.call(this, drawable);
+        this.update_icons();
+    },
+    remove_drawable: function(drawable) {
+        DrawableCollection.prototype.remove_drawable.call(this, drawable);
+        this.update_icons();
+    },
+    /**
+     * Restore object from a dictionary created by to_dict()
+     */
+    from_dict: function(collection_dict, container) {
+        var group = DrawableCollection.prototype.from_dict.call(this, collection_dict, container);
+        
+        // Add drawables to group's content div to make them visible.
+        for (var i = 0; i < group.drawables.length; i++) {
+            group.content_div.append(group.drawables[i].container_div);   
+        }
+        return group;
     }
 });
 
@@ -2537,10 +2603,10 @@ var Track = function(name, view, container, prefs, data_manager, data_url, data_
     this.data_manager = (data_manager ? data_manager : new DataManager(DATA_CACHE_SIZE, this));
         
     //
-    // Create content div, which is where track is displayed.
+    // Create content div, which is where track is displayed, and add to container if available.
     //
     this.content_div = $("<div class='track-content'>").appendTo(this.container_div);
-    this.container.content_div.append(this.container_div);
+    if (this.container) { this.container.content_div.append(this.container_div); }
 };
 
 extend(Track.prototype, Drawable.prototype, {
@@ -2684,6 +2750,9 @@ extend(Track.prototype, Drawable.prototype, {
         else if (this instanceof VcfTrack) {
             return "VcfTrack";
         }
+        else if (this instanceof CompositeTrack) {
+            return "CompositeTrack";
+        }
         else if (this instanceof FeatureTrack) {
             return "FeatureTrack";
         }
@@ -2810,10 +2879,11 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
         new_track.enabled = this.enabled;
         return new_track;
     },
-    /**
-     * Convert track to JSON object.
+    /** 
+     * Returns representation of object in a dictionary for easy saving. 
+     * Use from_dict to recreate object.
      */
-    to_json: function() {
+    to_dict: function() {
         return {
             "track_type": this.get_type(),
             "name": this.name,
@@ -2823,14 +2893,26 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
             "mode": this.mode,
         };
     },
+    /**
+     * Restore object from a dictionary created by to_dict()
+     */
+    from_dict: function(track_dict, container) {
+        var track = new this.constructor( 
+                            track_dict.name, view, container, track_dict.hda_ldda, track_dict.dataset_id,
+                            track_dict.prefs, track_dict.filters, track_dict.tool);
+        if (track_dict.mode) {
+            track.change_mode(track_dict.mode);
+        }
+        return track;
+    },
     /**
      * Change track's mode.
      */
-    change_mode: function(name) {
+    change_mode: function(new_mode) {
         var track = this;
         // TODO: is it necessary to store the mode in two places (.mode and track_config)?
-        track.mode = name;
-        track.config.values['mode'] = name;
+        track.mode = new_mode;
+        track.config.values['mode'] = new_mode;
         track.tile_cache.clear();
         track.request_draw();
         this.action_icons.mode_icon.attr("title", "Set display mode (now: " + track.mode + ")");
@@ -2932,11 +3014,12 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
         var all_tiles_drawn = true;
         var drawn_tiles = [];
         var tile_count = 0;
+        var is_tile = function(o) { return ('track' in o) };
         // Draw or fetch and show tiles.
         while ( ( tile_index * DENSITY * resolution ) < high ) {
-            tile = this.draw_helper( force, width, tile_index, resolution, parent_element, w_scale );
-            if ( tile ) {
-                drawn_tiles.push( tile );
+            var draw_result = this.draw_helper( force, width, tile_index, resolution, parent_element, w_scale );
+            if ( is_tile(draw_result) ) {
+                drawn_tiles.push( draw_result );
             } else {
                 all_tiles_drawn = false;
             }
@@ -2982,8 +3065,8 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
         }        
     },
     /**
-     * Handle a single tile, either from cache or by setting up a deferred
-     * operation and then requesting another redraw
+     * Retrieves from cache, draws, or sets up drawing for a single tile. Returns either a Tile object or a 
+     * jQuery.Deferred object that is fulfilled when tile can be drawn again.
      */ 
     draw_helper: function(force, width, tile_index, resolution, parent_element, w_scale, drawn_tiles, more_tile_data) {
         var track = this,
@@ -3001,7 +3084,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
         // Helper to determine if object is jQuery deferred
         var is_deferred = function ( d ) {
             return ( 'isResolved' in d );
-        }
+        };
         
         // Flag to track whether we can draw everything now 
         var can_draw_now = true
@@ -3034,13 +3117,27 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
         }
          
         // Can't draw now, so trigger another redraw when the data is ready
+        var can_draw = $.Deferred();
         $.when( tile_data, seq_data ).then( function() {
             view.request_redraw(false, false, false, track);
+            can_draw.resolve();
         });
         
-        // Indicate to caller that this tile could not be drawn
-        return null;
-    }, 
+        // Returned Deferred is resolved when tile can be drawn.
+        return can_draw;
+    },
+    /**
+     * Draw a track tile.
+     * @param result result from server
+     * @param mode mode to draw in
+     * @param resolution view resolution
+     * @param tile_index index of tile to be drawn
+     * @param w_scale pixels per base
+     * @param ref_seq reference sequence data
+     */
+    draw_tile: function(result, mode, resolution, tile_index, w_scale, ref_seq) {
+        console.log("Warning: TiledTrack.draw_tile() not implemented.")
+    },
     /**
      * Show track tile and perform associated actions. Showing tile may actually move
      * an existing tile rather than reshowing it.
@@ -3169,15 +3266,81 @@ extend(LabelTrack.prototype, Track.prototype, {
 /**
  * A tiled track composed of multiple other tracks.
  */
-var CompositeTiledTrack = function(drawables, view, container) {
-    TiledTrack.call(this, "Composite Track", view, container);
-    this.drawables = drawables;
-    this.enabled = true;
+var CompositeTrack = function(name, view, container, drawables) {
+    // HACK: modes should be static class vars for most tracks and should update as
+    // needed for CompositeTracks
+    this.display_modes = ["Histogram", "Line", "Filled", "Intensity"];
+    TiledTrack.call(this, name, view, container);
+    
+    // Init drawables; each drawable is a copy so that config/preferences 
+    // are independent of each other.
+    this.drawables = [];
+    if (drawables) {
+        var 
+            ids = [],
+            drawable;
+        for (var i = 0; i < drawables.length; i++) {
+            drawable = drawables[i];
+            ids.push(drawable.dataset_id);
+            this.drawables[i] = drawable.copy();
+        }
+        this.enabled = true;
+    }
+    
+    this.update_icons();
+    
+    // HACK: needed for saving object for now. Need to generalize get_type() to all Drawables and use
+    // that for object type.
+    this.obj_type = "CompositeTrack";
 };
-extend(CompositeTiledTrack.prototype, TiledTrack.prototype, {
+
+extend(CompositeTrack.prototype, TiledTrack.prototype, {
+    // HACK: CompositeTrack should inherit from DrawableCollection as well.
+    /** 
+     * Returns representation of object in a dictionary for easy saving. 
+     * Use from_dict to recreate object.
+     */
+    to_dict: DrawableCollection.prototype.to_dict,
+    add_drawable: DrawableCollection.prototype.add_drawable,
+    /**
+     * Restore object from a dictionary created by to_dict()
+     */
+    // TODO: unify with DrawableCollection.prototype.from_dict?
+    from_dict: function(collection_dict, container) {
+        var collection = new this.constructor( collection_dict.name, view, 
+                                               container, collection_dict.prefs, 
+                                               view.viewport_container, view);
+       var drawable_dict,
+           drawable_type,
+           drawable;
+        for (var i = 0; i < collection_dict.drawables.length; i++) {
+            drawable_dict = collection_dict.drawables[i];
+            drawable_type = drawable_dict['obj_type'];
+            // For backward compatibility:
+            if (!drawable_type) {
+                drawable_type = drawable_dict['track_type']; 
+            }
+            // No container for tracks so that it is not made visible.
+            drawable = addable_objects[ drawable_type ].prototype.from_dict( drawable_dict );
+            collection.add_drawable( drawable );
+        }
+        return collection;
+    },
+    change_mode: function(new_mode) {
+        TiledTrack.prototype.change_mode.call(this, new_mode);
+        for (var i = 0; i < this.drawables.length; i++) {
+            this.drawables[i].change_mode(new_mode);
+        }
+    },
     init: function() {
-        console.log("initing CompositeTiledTrack");
-        this.enabled = true;  
+        // FIXME: probably should enable based on whether/how many drawaables are enabled.
+        this.enabled = true;
+        this.request_draw();
+    },
+    update_icons: function() {
+        // For now, hide filters and tool.
+        this.action_icons.filters_icon.hide();
+        this.action_icons.tools_icon.hide();  
     },
     can_draw: Drawable.prototype.can_draw,
     draw_helper: function(force, width, tile_index, resolution, parent_element, w_scale, drawn_tiles, more_tile_data) {
@@ -3190,7 +3353,62 @@ extend(CompositeTiledTrack.prototype, TiledTrack.prototype, {
             return tile;
         }
         
-        // TODO: Try to build tile.
+        // Get/build tiles.
+        // FIXME: using very naive and simple approach for building tiles.
+        //        issues not addressed include:
+        //        (a) choosing tile size;
+        //        (b) any kind of normalization.
+        var 
+            drawable,
+            dummy_parent = $("<div/>"),
+            draw_result,
+            tiles = [],
+            deferreds = [],
+            can_draw = true;
+        for (var i = 0; i < this.drawables.length; i++) {
+            // Build drawable tile and show it.
+            draw_result = this.drawables[i].draw_helper(force, width, tile_index, resolution, dummy_parent, 
+                                                        w_scale, drawn_tiles, more_tile_data);
+            if (draw_result instanceof Tile) {
+                tiles.push(draw_result);
+            }
+            else {
+                deferreds.push(draw_result);
+                can_draw = false;
+            }
+        }
+        
+        if (can_draw) {
+            // Build composite tile by compositing canvases.
+            
+            // Copy first canvas.
+            var src_canvas = tiles[0].html_elt.find("canvas"), 
+                cmp_canvas = src_canvas.clone(), 
+                src_ctx = src_canvas.get(0).getContext("2d"),
+                cmp_ctx = cmp_canvas.get(0).getContext("2d"),
+                imageData = src_ctx.getImageData(0, 0, src_ctx.canvas.width, src_ctx.canvas.height);
+                
+            cmp_ctx.putImageData(imageData, 0, 0);
+              
+            // Composite additional canvases.
+            cmp_ctx.globalCompositeOperation = "darker";
+            var another_canvas;
+            for (var i = 1; i < tiles.length; i++) {
+                another_canvas = tiles[i].html_elt.find("canvas").get(0);
+                cmp_ctx.drawImage(another_canvas, 0, 0);
+            }
+            
+            tile = new Tile(this, tile_index, resolution, cmp_canvas);
+            this.tile_cache.set(key, tile);
+            this.show_tile(tile, parent_element, w_scale);
+        }
+        else {
+            // Wait until tiles can be drawn, then try again.
+            var track = this;
+            $.when.apply($, deferreds).then(function() {
+                track.request_draw(); 
+            });
+        }
         
         return tile;
     }
@@ -3865,13 +4083,13 @@ var ReadTrack = function (name, view, container, hda_ldda, dataset_id, prefs, fi
 extend(ReadTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype);
 
 // Exports
-
 exports.View = View;
 exports.DrawableGroup = DrawableGroup;
 exports.LineTrack = LineTrack;
 exports.FeatureTrack = FeatureTrack;
 exports.ReadTrack = ReadTrack;
 exports.VcfTrack = VcfTrack;
+exports.CompositeTrack = CompositeTrack;
 
 // End trackster_module encapsulation
 };
@@ -5008,9 +5226,6 @@ extend(ArcLinkedFeaturePainter.prototype, FeaturePainter.prototype, LinkedFeatur
     }
 });
 
-
-
-
 exports.Scaler = Scaler;
 exports.SummaryTreePainter = SummaryTreePainter;
 exports.LinePainter = LinePainter;
diff --git a/static/scripts/trackster_ui.js b/static/scripts/trackster_ui.js
index 1183a377f5e..6b2c5fc975f 100644
--- a/static/scripts/trackster_ui.js
+++ b/static/scripts/trackster_ui.js
@@ -31,59 +31,18 @@ var add_bookmark = function(position, annotation) {
 /**
  * Objects that can be added to a view.
  */
-var addable_objects = { "LineTrack": LineTrack, "FeatureTrack": FeatureTrack, "VcfTrack": VcfTrack, "ReadTrack": ReadTrack, "DrawableGroup": DrawableGroup };
-
-/**
- * Decode a track from a dictionary.
- */
-var track_from_dict = function(track_dict, container) {
-    var track = new addable_objects[track_dict.track_type]( 
-                        track_dict.name, view, container, track_dict.hda_ldda, track_dict.dataset_id,
-                        track_dict.prefs, track_dict.filters, track_dict.tool);
-    if (track_dict.mode) {
-        track.change_mode(track_dict.mode);
-    }
-    return track;
-};
-
-/**
- * Decode a drawable collection from a dictionary.
- */
-var drawable_collection_from_dict = function(collection_dict, container) {
-    var collection = new addable_objects[collection_dict.obj_type](collection_dict.name, view, container, collection_dict.prefs, view.viewport_container, view);
-    for (var i = 0; i < collection_dict.drawables.length; i++) {
-        var 
-            drawable_dict = collection_dict.drawables[i],
-            drawable;
-        if (drawable_dict['track_type']) {
-            drawable = track_from_dict(drawable_dict, collection);
-        }
-        else {
-            drawable = drawable_collection_from_dict(drawable_dict);
-        }
-        collection.add_drawable(drawable);
-        // HACK: move track from view to collection's content_div. 
-        // FIX: Tracks should be able to be be added to arbitrary containers; 
-        // every moveable should have a container_div, and every container should have 
-        // a content_div (though perhaps name changes are needed).
-        collection.content_div.append(drawable.container_div);
-    }
-    return collection;
-};
-
-/**
- * Decode a drawable from a dict.
- */
-var drawable_from_dict = function(drawable_dict, container) {
-    return (drawable_dict['track_type'] ? 
-            track_from_dict(drawable_dict, container) :
-            drawable_collection_from_dict(drawable_dict, container));
-};
+var addable_objects = { 
+    "LineTrack": LineTrack,
+    "FeatureTrack": FeatureTrack,
+    "VcfTrack": VcfTrack,
+    "ReadTrack": ReadTrack,
+    "CompositeTrack": CompositeTrack,
+    "DrawableGroup": DrawableGroup };
 
 /**
  * Create a complete Trackster visualization. Returns view.
  */
-var create_visualization = function(parent_elt, title, id, dbkey, viewport_config, tracks_config, bookmarks_config) {
+var create_visualization = function(parent_elt, title, id, dbkey, viewport_config, drawables_config, bookmarks_config) {
     
     // Create view.
     view = new View(parent_elt, title, id, dbkey);
@@ -95,7 +54,7 @@ var create_visualization = function(parent_elt, title, id, dbkey, viewport_confi
                 chrom = viewport_config.chrom,
                 start = viewport_config.start,
                 end = viewport_config.end,
-                overview_track_name = viewport_config.overview;
+                overview_drawable_name = viewport_config.overview;
         
             if (chrom && (start !== undefined) && end) {
                 view.change_chrom(chrom, start, end);
@@ -103,11 +62,20 @@ var create_visualization = function(parent_elt, title, id, dbkey, viewport_confi
         }
         
         // Add drawables to view.
-        if (tracks_config) {
-            var track_config;
-            for (var i = 0; i < tracks_config.length; i++) {
-                track_config = tracks_config[i];
-                view.add_drawable( drawable_from_dict(track_config, view) );
+        if (drawables_config) {
+            // FIXME: can from_dict() be used to create view and add drawables?
+            var drawable_config,
+                drawable_type,
+                drawable;
+            for (var i = 0; i < drawables_config.length; i++) {
+                drawable_config = drawables_config[i];
+                drawable_type = drawable_config['obj_type'];
+                // For backward compatibility:
+                if (!drawable_type) {
+                    drawable_type = drawable_config['track_type']; 
+                }
+                drawable = addable_objects[ drawable_type ].prototype.from_dict( drawable_config, view );
+                view.add_drawable( drawable );
             }
         }
         
@@ -115,9 +83,9 @@ var create_visualization = function(parent_elt, title, id, dbkey, viewport_confi
         view.update_intro_div();
         
         // Set overview.
-        var overview_track;
+        var overview_drawable;
         for (var i = 0; i < view.drawables.length; i++) {
-            if (view.drawables[i].name === overview_track_name) {
+            if (view.drawables[i].name === overview_drawable_name) {
                 view.set_overview(view.drawables[i]);
                 break;
             }
diff --git a/templates/tracks/browser.mako b/templates/tracks/browser.mako
index 1be5d8c2ec4..d8d44cef881 100644
--- a/templates/tracks/browser.mako
+++ b/templates/tracks/browser.mako
@@ -244,7 +244,7 @@ ${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.e
                 // FIXME: give unique IDs to Drawables and save overview as ID.
                 var overview_track_name = (view.overview_drawable ? view.overview_drawable.name : null);
                 var payload = { 
-                    'view': view.to_json(), 
+                    'view': view.to_dict(), 
                     'viewport': { 'chrom': view.chrom, 'start': view.low , 'end': view.high, 'overview': overview_track_name },
                     'bookmarks': bookmarks
                 };

From b8be0448de485f5ccbd55a4f5a88f3f803d5c7be Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Fri, 9 Dec 2011 17:03:33 -0500
Subject: [PATCH 326/362] Trackster: fix bugs in e1da72b42db7 that prevented
 adding tracks.

---
 static/scripts/trackster_ui.js | 22 ++++++++++++++--------
 templates/tracks/browser.mako  |  4 ++--
 2 files changed, 16 insertions(+), 10 deletions(-)

diff --git a/static/scripts/trackster_ui.js b/static/scripts/trackster_ui.js
index 6b2c5fc975f..d1a169c886b 100644
--- a/static/scripts/trackster_ui.js
+++ b/static/scripts/trackster_ui.js
@@ -28,6 +28,19 @@ var add_bookmark = function(position, annotation) {
     return new_bookmark;
 };
 
+/**
+ * Create object from a dictionary.
+ */
+var object_from_dict = function(track_dict, container) {
+    var
+       drawable_type = track_dict['obj_type'];
+    // For backward compatibility:
+    if (!drawable_type) {
+        drawable_type = track_dict['track_type']; 
+    }
+    return addable_objects[ drawable_type ].prototype.from_dict(track_dict, container);
+};
+
 /**
  * Objects that can be added to a view.
  */
@@ -68,14 +81,7 @@ var create_visualization = function(parent_elt, title, id, dbkey, viewport_confi
                 drawable_type,
                 drawable;
             for (var i = 0; i < drawables_config.length; i++) {
-                drawable_config = drawables_config[i];
-                drawable_type = drawable_config['obj_type'];
-                // For backward compatibility:
-                if (!drawable_type) {
-                    drawable_type = drawable_config['track_type']; 
-                }
-                drawable = addable_objects[ drawable_type ].prototype.from_dict( drawable_config, view );
-                view.add_drawable( drawable );
+                view.add_drawable( object_from_dict( drawables_config[i], view ) );
             }
         }
         
diff --git a/templates/tracks/browser.mako b/templates/tracks/browser.mako
index d8d44cef881..7342ab99973 100644
--- a/templates/tracks/browser.mako
+++ b/templates/tracks/browser.mako
@@ -100,7 +100,7 @@ ${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.e
                                                    [ arguments[0] ]
                                                    );
                                  for (var i= 0; i < track_defs.length; i++) {
-                                     view.add_drawable( track_from_dict(track_defs[i], view) ); 
+                                     view.add_drawable( object_from_dict(track_defs[i], view) ); 
                                  }
                             });
                             hide_modal();
@@ -214,7 +214,7 @@ ${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.e
                     url: "${h.url_for( action='add_track_async' )}",
                     data: { hda_id: "${add_dataset}" },
                     dataType: "json",
-                    success: function(track_data) { view.add_drawable( track_from_dict(track_data, view) ) }
+                    success: function(track_data) { view.add_drawable( object_from_dict(track_data, view) ) }
                 });
                 
             %endif

From b466b2fa14a6ebbd9714232f6c3a7ef650944f4a Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Sat, 10 Dec 2011 10:35:31 -0500
Subject: [PATCH 327/362] Trackster bug fixes for random color generation and
 LineTrack display in line and intensity modes.

---
 static/scripts/trackster.js | 51 ++++++++++++++++++++++++-------------
 1 file changed, 34 insertions(+), 17 deletions(-)

diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index 6af99254d3b..f13f2c5d1b3 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -120,31 +120,34 @@ var get_random_color = function(colors) {
     var new_color, nr, ng, nb,
         other_color, or, og, ob,
         n_brightness, o_brightness,
-        diff, ok = false;
+        diff, ok = false,
+        num_tries = 0;
     do {
         // New color is never white b/c random in [0,1)
-        new_color = Math.random() * 0xffffff;
-        nr = new_color | 0xff0000;
-        ng = new_color | 0x00ff00;
-        nb = new_color | 0x0000ff;
+        new_color = Math.round( Math.random() * 0xffffff );
+        nr = ( new_color & 0xff0000 ) >> 16;
+        ng = ( new_color & 0x00ff00 ) >> 8;
+        nb = new_color & 0x0000ff;
         n_brightness = brightness(nr, ng, nb);
         ok = true;
         for (var i = 0; i < colors.length; i++) {
             other_color = colors[i];
-            or = other_color | 0xff0000;
-            og = other_color | 0x00ff00;
-            ob = other_color | 0x0000ff;
+            or = ( other_color & 0xff0000 ) >> 16;
+            og = ( other_color & 0x00ff00 ) >> 8;
+            ob = other_color & 0x0000ff;
             o_brightness = brightness(or, og, ob);
             diff = difference(nr, ng, nb, or, og, ob);
-            // Thresholds for brightness difference and color difference
-            // are from W3C link above.
-            if ( ( Math.abs(n_brightness - o_brightness) < 125 ) ||
-                 ( diff < 500 ) ) {
+            // These thresholds may need to be adjusted. Brightness difference range is 125; 
+            // color difference range is 500.
+            if ( ( Math.abs(n_brightness - o_brightness) < 40 ) ||
+                 ( diff < 200 ) ) {
                 ok = false;
                 break;         
             }
         }
-    } while (!ok);
+        
+        num_tries++
+    } while (!ok && num_tries <= 10 );
     
     // Add 0x1000000 to left pad number with 0s.
     return '#' + ( 0x1000000 + new_color ).toString(16).substr(1,6);
@@ -4445,8 +4448,17 @@ LinePainter.prototype.draw = function(ctx, width, height) {
     } else {
         delta_x_px = 10;
     }
+    
+    // Extract RGB from preference color.
+    var
+        pref_color = parseInt( this.prefs.color.slice(1), 16 ),
+        pref_r = (pref_color & 0xff0000) >> 16,
+        pref_g = (pref_color & 0x00ff00) >> 8,
+        pref_b = pref_color & 0x0000ff;
+    
+    // Paint track.
     for (var i = 0, len = data.length; i < len; i++) {
-        ctx.fillStyle = this.prefs.color;
+        ctx.fillStyle = ctx.strokeStyle = this.prefs.color;
         x_scaled = Math.round((data[i][0] - view_start) * w_scale);
         y = data[i][1];
         var top_overflow = false, bot_overflow = false;
@@ -4469,9 +4481,14 @@ LinePainter.prototype.draw = function(ctx, width, height) {
             // y becomes the bar height in pixels, which is the negated for canvas coords
             y = Math.round( y / vertical_range * height_px );
             ctx.fillRect(x_scaled, y_zero, delta_x_px, - y );
-        } else if (mode === "Intensity" ) {
-            y = 255 - Math.floor( (y - min_value) / vertical_range * 255 );
-            ctx.fillStyle = "rgb(" +y+ "," +y+ "," +y+ ")";
+        } else if (mode === "Intensity") {
+            var 
+                saturation = (y - min_value) / vertical_range,
+                // Range is [pref_color, 255] where saturation = 0 --> 255 and saturation = 1 --> pref color
+                new_r = Math.round( pref_r + (255 - pref_r) * (1 - saturation) ),
+                new_g = Math.round( pref_g + (255 - pref_g) * (1 - saturation) ),
+                new_b = Math.round( pref_b + (255 - pref_b) * (1 - saturation) );
+            ctx.fillStyle = "rgb(" + new_r + "," + new_g + "," + new_b + ")";
             ctx.fillRect(x_scaled, 0, delta_x_px, height_px);
         } else {
             // console.log(y, track.min_value, track.vertical_range, (y - track.min_value) / track.vertical_range * track.height_px);

From e310624be13591e36b071ac62272724604378f1f Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Sat, 10 Dec 2011 12:25:44 -0500
Subject: [PATCH 328/362] Trackster: (a) fix small bug in drawing composite
 tracks and (b) pass canvas in as argument to draw_tile.

---
 static/scripts/trackster.js | 21 ++++++++++-----------
 1 file changed, 10 insertions(+), 11 deletions(-)

diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index f13f2c5d1b3..28d16358173 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -3110,7 +3110,8 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
         // If we can draw now, do so.
         if ( can_draw_now ) {
             extend( tile_data, more_tile_data );
-            var tile = track.draw_tile(tile_data, track.mode, resolution, tile_index, w_scale, seq_data);
+            var canvas = this.view.canvas_manager.new_canvas();
+            var tile = track.draw_tile(tile_data, canvas, track.mode, resolution, tile_index, w_scale, seq_data);
             // Don't cache, show if no tile.
             if (tile !== undefined) {
                 track.tile_cache.set(key, tile);
@@ -3132,13 +3133,14 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
     /**
      * Draw a track tile.
      * @param result result from server
+     * @param canvas canvas to draw on
      * @param mode mode to draw in
      * @param resolution view resolution
      * @param tile_index index of tile to be drawn
      * @param w_scale pixels per base
      * @param ref_seq reference sequence data
      */
-    draw_tile: function(result, mode, resolution, tile_index, w_scale, ref_seq) {
+    draw_tile: function(result, canvas, mode, resolution, tile_index, w_scale, ref_seq) {
         console.log("Warning: TiledTrack.draw_tile() not implemented.")
     },
     /**
@@ -3411,6 +3413,7 @@ extend(CompositeTrack.prototype, TiledTrack.prototype, {
             $.when.apply($, deferreds).then(function() {
                 track.request_draw(); 
             });
+            tile = {};
         }
         
         return tile;
@@ -3441,7 +3444,7 @@ extend(ReferenceTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
     /**
      * Draw ReferenceTrack tile.
      */
-    draw_tile: function(seq, mode, resolution, tile_index, w_scale) {
+    draw_tile: function(seq, canvas, mode, resolution, tile_index, w_scale) {
         var track = this,
             tile_length = DENSITY * resolution;
         
@@ -3450,7 +3453,6 @@ extend(ReferenceTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
                 track.content_div.css("height", "0px");
                 return;
             }
-            var canvas = this.view.canvas_manager.new_canvas();
             var ctx = canvas.getContext("2d");
             canvas.width = Math.ceil(tile_length * w_scale + track.left_offset);
             canvas.height = track.height_px;
@@ -3592,7 +3594,7 @@ extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
     /**
      * Draw LineTrack tile.
      */
-    draw_tile: function(result, mode, resolution, tile_index, w_scale) {
+    draw_tile: function(result, canvas, mode, resolution, tile_index, w_scale) {
         if (this.vertical_range === undefined) {
             return;
         }
@@ -3604,8 +3606,7 @@ extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
             width = Math.ceil( (tile_high - tile_low) * w_scale ),
             height = this.height_px;
         
-        // Create canvas
-        var canvas = this.view.canvas_manager.new_canvas();
+        // Canvas setup.
         canvas.width = width,
         canvas.height = height;
         
@@ -3883,13 +3884,14 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
     /**
      * Draw FeatureTrack tile.
      * @param result result from server
+     * @param canvas canvas to draw on
      * @param mode mode to draw in
      * @param resolution view resolution
      * @param tile_index index of tile to be drawn
      * @param w_scale pixels per base
      * @param ref_seq reference sequence data
      */
-    draw_tile: function(result, mode, resolution, tile_index, w_scale, ref_seq) {
+    draw_tile: function(result, canvas, mode, resolution, tile_index, w_scale, ref_seq) {
         var track = this,
             tile_bounds = track._get_tile_bounds(tile_index, resolution),
             tile_low = tile_bounds[0],
@@ -3942,8 +3944,6 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
             max_label.text(result.max);
             max_label.css({ position: "absolute", top: "24px", left: "10px", color: this.prefs.label_color });
             max_label.prependTo(this.container_div);
-            // Create canvas
-            var canvas = this.view.canvas_manager.new_canvas();
             canvas.width = width + left_offset;
             // Extra padding at top of summary tree
             canvas.height = required_height + SUMMARY_TREE_TOP_PADDING;
@@ -4002,7 +4002,6 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
         // HACK: ref_seq will only be defined for ReadTracks, and only the ReadPainter accepts that argument
         var painter = new (this.painter)(filtered, tile_low, tile_high, this.prefs, mode, filter_alpha_scaler, filter_height_scaler, ref_seq);
         var required_height = Math.max(MIN_TRACK_HEIGHT, painter.get_required_height(slots_required,width));
-        var canvas = this.view.canvas_manager.new_canvas();
         var feature_mapper = null;
         
         canvas.width = width + left_offset;

From 72795a888cedf65de9504945532e1e76e20aeb75 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Mon, 12 Dec 2011 13:26:58 -0500
Subject: [PATCH 329/362] Trackster: remove unused parameter from draw_helper
 function.

---
 static/scripts/trackster.js | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index 28d16358173..e5522c34ff3 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -3071,7 +3071,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
      * Retrieves from cache, draws, or sets up drawing for a single tile. Returns either a Tile object or a 
      * jQuery.Deferred object that is fulfilled when tile can be drawn again.
      */ 
-    draw_helper: function(force, width, tile_index, resolution, parent_element, w_scale, drawn_tiles, more_tile_data) {
+    draw_helper: function(force, width, tile_index, resolution, parent_element, w_scale, more_tile_data) {
         var track = this,
             key = this._gen_tile_cache_key(width, w_scale, tile_index),
             tile_low = tile_index * DENSITY * resolution,
@@ -3348,7 +3348,7 @@ extend(CompositeTrack.prototype, TiledTrack.prototype, {
         this.action_icons.tools_icon.hide();  
     },
     can_draw: Drawable.prototype.can_draw,
-    draw_helper: function(force, width, tile_index, resolution, parent_element, w_scale, drawn_tiles, more_tile_data) {
+    draw_helper: function(force, width, tile_index, resolution, parent_element, w_scale, more_tile_data) {
         // Check tile cache, if found show existing tile in correct position
         var 
             key = this._gen_tile_cache_key(width, w_scale, tile_index),
@@ -3373,7 +3373,7 @@ extend(CompositeTrack.prototype, TiledTrack.prototype, {
         for (var i = 0; i < this.drawables.length; i++) {
             // Build drawable tile and show it.
             draw_result = this.drawables[i].draw_helper(force, width, tile_index, resolution, dummy_parent, 
-                                                        w_scale, drawn_tiles, more_tile_data);
+                                                        w_scale, more_tile_data);
             if (draw_result instanceof Tile) {
                 tiles.push(draw_result);
             }
@@ -3722,7 +3722,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
                 var tile = tiles[i];
                 if (tile.max_val !== global_max) {
                     tile.html_elt.remove();
-                    track.draw_helper(true, width, tile.index, tile.resolution, tile.html_elt.parent(), w_scale, [], { max: global_max });
+                    track.draw_helper(true, width, tile.index, tile.resolution, tile.html_elt.parent(), w_scale, { max: global_max });
                 }
             }
         }                

From ca3219e25f852aee7170152e1c57831b1beba74d Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Mon, 12 Dec 2011 15:58:36 -0500
Subject: [PATCH 330/362] Trackster: more memory-efficent drawing of composite
 tracks. Composite tracks are now drawn and composited on a single tile rather
 than compositing using multiple tiles. Currently only LineTracks are
 supported.

---
 static/scripts/trackster.js | 185 +++++++++++++++++++++---------------
 1 file changed, 110 insertions(+), 75 deletions(-)

diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index e5522c34ff3..aac82f6c5bb 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -3109,9 +3109,20 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
                 
         // If we can draw now, do so.
         if ( can_draw_now ) {
-            extend( tile_data, more_tile_data );
-            var canvas = this.view.canvas_manager.new_canvas();
+            // Set up and draw tile.
+            extend(tile_data, more_tile_data);
+            var 
+                canvas = track.view.canvas_manager.new_canvas(),
+                tile_bounds = track._get_tile_bounds(tile_index, resolution),
+                tile_low = tile_bounds[0],
+                tile_high = tile_bounds[1],
+                width = Math.ceil( (tile_high - tile_low) * w_scale ),
+                height = track.get_canvas_height(tile_data);
+            
+            canvas.width = width;
+            canvas.height = height;
             var tile = track.draw_tile(tile_data, canvas, track.mode, resolution, tile_index, w_scale, seq_data);
+            
             // Don't cache, show if no tile.
             if (tile !== undefined) {
                 track.tile_cache.set(key, tile);
@@ -3130,6 +3141,13 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
         // Returned Deferred is resolved when tile can be drawn.
         return can_draw;
     },
+    /**
+     * Returns canvas height needed to display data; return value is an integer that denotes the
+     * number of pixels required.
+     */
+    get_canvas_height: function(data) {
+        return this.height_px;
+    },
     /**
      * Draw a track tile.
      * @param result result from server
@@ -3141,7 +3159,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
      * @param ref_seq reference sequence data
      */
     draw_tile: function(result, canvas, mode, resolution, tile_index, w_scale, ref_seq) {
-        console.log("Warning: TiledTrack.draw_tile() not implemented.")
+        console.log("Warning: TiledTrack.draw_tile() not implemented.");
     },
     /**
      * Show track tile and perform associated actions. Showing tile may actually move
@@ -3349,74 +3367,94 @@ extend(CompositeTrack.prototype, TiledTrack.prototype, {
     },
     can_draw: Drawable.prototype.can_draw,
     draw_helper: function(force, width, tile_index, resolution, parent_element, w_scale, more_tile_data) {
-        // Check tile cache, if found show existing tile in correct position
-        var 
+        // FIXME: this function is similar to TiledTrack.draw_helper -- can the two be merged/refactored?
+        var track = this,
             key = this._gen_tile_cache_key(width, w_scale, tile_index),
-            tile = ( force ? undefined : this.tile_cache.get(key) );
+            tile_low = tile_index * DENSITY * resolution,
+            tile_high = tile_low + DENSITY * resolution;
+                       
+        // Check tile cache, if found show existing tile in correct position
+        var tile = (force ? undefined : track.tile_cache.get(key));
         if (tile) { 
-            this.show_tile(tile, parent_element, w_scale);
+            track.show_tile(tile, parent_element, w_scale);
             return tile;
         }
-        
-        // Get/build tiles.
-        // FIXME: using very naive and simple approach for building tiles.
-        //        issues not addressed include:
-        //        (a) choosing tile size;
-        //        (b) any kind of normalization.
-        var 
-            drawable,
-            dummy_parent = $("<div/>"),
-            draw_result,
-            tiles = [],
-            deferreds = [],
-            can_draw = true;
-        for (var i = 0; i < this.drawables.length; i++) {
-            // Build drawable tile and show it.
-            draw_result = this.drawables[i].draw_helper(force, width, tile_index, resolution, dummy_parent, 
-                                                        w_scale, more_tile_data);
-            if (draw_result instanceof Tile) {
-                tiles.push(draw_result);
-            }
-            else {
-                deferreds.push(draw_result);
-                can_draw = false;
-            }
-        }
-        
-        if (can_draw) {
-            // Build composite tile by compositing canvases.
-            
-            // Copy first canvas.
-            var src_canvas = tiles[0].html_elt.find("canvas"), 
-                cmp_canvas = src_canvas.clone(), 
-                src_ctx = src_canvas.get(0).getContext("2d"),
-                cmp_ctx = cmp_canvas.get(0).getContext("2d"),
-                imageData = src_ctx.getImageData(0, 0, src_ctx.canvas.width, src_ctx.canvas.height);
                 
-            cmp_ctx.putImageData(imageData, 0, 0);
-              
-            // Composite additional canvases.
-            cmp_ctx.globalCompositeOperation = "darker";
-            var another_canvas;
-            for (var i = 1; i < tiles.length; i++) {
-                another_canvas = tiles[i].html_elt.find("canvas").get(0);
-                cmp_ctx.drawImage(another_canvas, 0, 0);
+        // Helper to determine if object is jQuery deferred
+        var is_deferred = function ( d ) {
+            return ( 'isResolved' in d );
+        };
+        
+        // Try to get drawables' data.
+        var all_data = [],
+            track,
+            // Flag to track whether we can draw everything now 
+            can_draw_now = true,
+            tile_data,
+            seq_data;
+        for (var i = 0; i < this.drawables.length; i++) {
+            track = this.drawables[i];
+            // Get the track data, maybe a deferred.
+            tile_data = track.data_manager.get_data( tile_low, tile_high, track.mode, resolution, track.data_url_extra_params );
+            if ( is_deferred( tile_data ) ) {
+                can_draw_now = false;
+            }
+            all_data.push(tile_data);
+
+            // Get seq data if needed, maybe a deferred.
+            seq_data = null;
+            if ( view.reference_track && w_scale > view.canvas_manager.char_width_px ) {
+                seq_data = view.reference_track.data_manager.get_data(tile_low, tile_high, track.mode, resolution, view.reference_track.data_url_extra_params)
+                if ( is_deferred( seq_data ) ) {
+                    can_draw_now = false;
+                }
+            }
+            all_data.push(seq_data);
+        }
+                
+        // If we can draw now, do so.
+        if ( can_draw_now ) {
+            // Set up and draw tile.
+            extend(tile_data, more_tile_data);
+            var 
+                canvas = track.view.canvas_manager.new_canvas(),
+                tile_bounds = track._get_tile_bounds(tile_index, resolution),
+                tile_low = tile_bounds[0],
+                tile_high = tile_bounds[1],
+                width = Math.ceil( (tile_high - tile_low) * w_scale ),
+                height = track.get_canvas_height(tile_data);
+            
+            // FIXME: 
+            // (a) right now, only LineTracks respect width/height setting and do not set it in draw_tile; 
+            // however, other track types be modified to work this way. This is necessary b/c setting the width/height 
+            // clears the canvas and hence prevents non-compliant tracks from being used in CompositeTracks.
+            // (b) need to normalize across tracks before displaying, e.g. set LineTracks' min/max appropriately.
+            canvas.width = width;
+            canvas.height = height;
+            var all_data_index = 0
+            for (var i = 0; i < this.drawables.length; i++, all_data_index += 2) {
+                track = this.drawables[i];
+                tile_data = all_data[ all_data_index ];
+                seq_data = all_data[ all_data_index + 1 ];
+                tile = track.draw_tile(tile_data, canvas, track.mode, resolution, tile_index, w_scale, seq_data);
             }
             
-            tile = new Tile(this, tile_index, resolution, cmp_canvas);
-            this.tile_cache.set(key, tile);
-            this.show_tile(tile, parent_element, w_scale);
-        }
-        else {
-            // Wait until tiles can be drawn, then try again.
-            var track = this;
-            $.when.apply($, deferreds).then(function() {
-                track.request_draw(); 
-            });
-            tile = {};
+            // Don't cache, show if no tile.
+            track.tile_cache.set(key, tile);
+            track.show_tile(tile, parent_element, w_scale);
+            return tile;
         }
+         
+        // Can't draw now, so trigger another redraw when the data is ready
+        var can_draw = $.Deferred(),
+            track = this;
+        $.when.apply($, all_data).then(function() {
+            view.request_redraw(false, false, false, track);
+            can_draw.resolve();
+        });
         
-        return tile;
+        // Returned Deferred that is resolved when tile can be drawn.
+        return can_draw;
     }
 });
 
@@ -3595,28 +3633,25 @@ extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
      * Draw LineTrack tile.
      */
     draw_tile: function(result, canvas, mode, resolution, tile_index, w_scale) {
+        // FIXME: is this needed?
         if (this.vertical_range === undefined) {
             return;
         }
-        
+
+        // Paint onto canvas.        
         var 
+            ctx = canvas.getContext("2d"),
             tile_bounds = this._get_tile_bounds(tile_index, resolution),
             tile_low = tile_bounds[0],
             tile_high = tile_bounds[1],
-            width = Math.ceil( (tile_high - tile_low) * w_scale ),
-            height = this.height_px;
-        
-        // Canvas setup.
-        canvas.width = width,
-        canvas.height = height;
-        
-        // Paint line onto full canvas
-        var ctx = canvas.getContext("2d");
-        var painter = new painters.LinePainter(result.data, tile_low, tile_high, this.prefs, mode);
-        painter.draw(ctx, width, height);
+            painter = new painters.LinePainter(result.data, tile_low, tile_high, this.prefs, mode);
+        // HACK: this is needed for compositing tracks. This should be a config setting somewhere; also,
+        // "darker" may not be included in future canvas implementations.
+        ctx.globalCompositeOperation = "darker";
+        painter.draw(ctx, canvas.width, canvas.height);
         
         return new Tile(this.track, tile_index, resolution, canvas, result.data);
-    } 
+    }
 });
 
 var FeatureTrack = function(name, view, container, hda_ldda, dataset_id, prefs, filters, tool, data_manager) {

From c4d1fb23baec4da01912ff0e93041eaa279f7b39 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Mon, 12 Dec 2011 21:40:37 -0500
Subject: [PATCH 331/362] If there is no env.sh in a tool dependency directory,
 but there is a subdirectory named 'bin', add the bin directory to $PATH.

---
 lib/galaxy/tools/__init__.py      |  4 +++-
 lib/galaxy/tools/deps/__init__.py |  5 +++++
 lib/galaxy/tools/deps/tests.py    | 17 ++++++++---------
 3 files changed, 16 insertions(+), 10 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 881389bd531..c74290718be 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1754,8 +1754,10 @@ class Tool:
             log.debug( "Dependency %s", requirement.name )
             if requirement.type == 'package':
                 script_file, base_path, version = self.app.toolbox.dependency_manager.find_dep( requirement.name, requirement.version )
-                if script_file is None:
+                if script_file is None and base_path is None:
                     log.warn( "Failed to resolve dependency on '%s', ignoring", requirement.name )
+                elif script_file is None:
+                    commands.append( 'PACKAGE_BASE=%s; export PACKAGE_BASE; PATH="%s/bin:$PATH"; export PATH' % ( base_path, base_path ) )
                 else:
                     commands.append( 'PACKAGE_BASE=%s; export PACKAGE_BASE; . %s' % ( base_path, script_file ) )
         return commands
diff --git a/lib/galaxy/tools/deps/__init__.py b/lib/galaxy/tools/deps/__init__.py
index 4f26d2ad3b2..b15bf6e45b5 100644
--- a/lib/galaxy/tools/deps/__init__.py
+++ b/lib/galaxy/tools/deps/__init__.py
@@ -47,6 +47,8 @@ class DependencyManager( object ):
             script = os.path.join( path, 'env.sh' )
             if os.path.exists( script ):
                 return script, path, version
+            elif os.path.exists( os.path.join( path, 'bin' ) ):
+                return None, path, version
         else:
             return None, None, None
     def _find_dep_default( self, name ):
@@ -55,9 +57,12 @@ class DependencyManager( object ):
             path = os.path.join( base_path, name, 'default' )
             if os.path.islink( path ):
                 real_path = os.path.realpath( path )
+                real_bin = os.path.join( real_path, 'bin' )
                 real_version = os.path.basename( real_path )
                 script = os.path.join( real_path, 'env.sh' )
                 if os.path.exists( script ):
                     return script, real_path, real_version
+                elif os.path.exists( os.path.join( real_path, 'bin' ) ):
+                    return None, real_path, real_version
         else:
             return None, None, None
diff --git a/lib/galaxy/tools/deps/tests.py b/lib/galaxy/tools/deps/tests.py
index ccd1beaf2c7..92bb693ec40 100644
--- a/lib/galaxy/tools/deps/tests.py
+++ b/lib/galaxy/tools/deps/tests.py
@@ -14,20 +14,19 @@ def test():
     # Setup directories
     base_path = tempfile.mkdtemp()
     # mkdir( base_path )
-    for name, version in [ ( "dep1", "1.0" ), ( "dep1", "2.0" ), ( "dep2", "1.0" ) ]:
-        p = os.path.join( base_path, name, version ) 
+    for name, version, sub in [ ( "dep1", "1.0", "env.sh" ), ( "dep1", "2.0", "bin" ), ( "dep2", "1.0", None ) ]:
+        if sub == "bin":
+            p = os.path.join( base_path, name, version, "bin" ) 
+        else:
+            p = os.path.join( base_path, name, version ) 
         try:
             makedirs( p )
         except:
             pass
-        touch( os.path.join( p, "env.sh" ) )
+        if sub == "env.sh":
+            touch( os.path.join( p, "env.sh" ) )
 
     dm = galaxy.tools.deps.DependencyManager( [ base_path ] )
 
+    print dm.find_dep( "dep1", "1.0" )
     print dm.find_dep( "dep1", "2.0" )
-
-    
-
-
-
-

From b08ea5e6ff724b9db3dd5b5b8a97427f7c7d5ffc Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Mon, 12 Dec 2011 23:26:59 -0500
Subject: [PATCH 332/362] Better queries for the job queue, especially when
 checking the user job count.

---
 lib/galaxy/jobs/__init__.py | 29 ++++++++++++-----------------
 1 file changed, 12 insertions(+), 17 deletions(-)

diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 376b4e82df7..a4b49678dc6 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -2,7 +2,6 @@ import logging, threading, sys, os, time, traceback, shutil
 
 import galaxy
 from galaxy import util, model
-from galaxy.model.orm import lazyload
 from galaxy.datatypes.tabular import *
 from galaxy.datatypes.interval import *
 # tabular/interval imports appear to be unused.  Clean up?
@@ -114,7 +113,7 @@ class JobQueue( object ):
             else:
                 log.debug( "no runner: %s is still in new state, adding to the jobs queue" %job.id )
                 self.queue.put( ( job.id, job.tool_id ) )
-        for job in self.sa_session.query( model.Job ).options( lazyload( "external_output_metadata" ), lazyload( "parameters" ) ).filter( ( model.Job.state == model.Job.states.RUNNING ) | ( model.Job.state == model.Job.states.QUEUED ) ):
+        for job in self.sa_session.query( model.Job ).enable_eagerloads( False ).filter( ( model.Job.state == model.Job.states.RUNNING ) | ( model.Job.state == model.Job.states.QUEUED ) ):
             if job.tool_id not in self.app.toolbox.tools_by_id:
                 log.warning( "Tool '%s' removed from tool config, unable to recover job: %s" % ( job.tool_id, job.id ) )
                 JobWrapper( job, self ).fail( 'This tool was disabled before the job completed.  Please contact your Galaxy administrator, or' )
@@ -161,8 +160,7 @@ class JobQueue( object ):
             # Clear the session so we get fresh states for job and all datasets
             self.sa_session.expunge_all()
             # Fetch all new jobs
-            jobs_to_check = self.sa_session.query( model.Job ) \
-                                .options( lazyload( "external_output_metadata" ), lazyload( "parameters" ) ) \
+            jobs_to_check = self.sa_session.query( model.Job ).enable_eagerloads( False ) \
                                 .filter( model.Job.state == model.Job.states.NEW ).all()
         else:
             # Get job objects and append to watch queue for any which were
@@ -264,21 +262,19 @@ class JobQueue( object ):
         if not self.app.config.user_job_limit:
             return JOB_READY
         if job.user:
-            user_jobs = self.sa_session.query( model.Job ) \
-                            .options( lazyload( "external_output_metadata" ), lazyload( "parameters" ) ) \
-                            .filter( and_( model.Job.user_id == job.user.id,
-                                           or_( model.Job.state == model.Job.states.RUNNING,
-                                                model.Job.state == model.Job.states.QUEUED ) ) ).all()
+            count = self.sa_session.query( model.Job ).enable_eagerloads( False ) \
+                        .filter( and_( model.Job.user_id == job.user.id,
+                                       or_( model.Job.state == model.Job.states.RUNNING,
+                                            model.Job.state == model.Job.states.QUEUED ) ) ).count()
         elif job.galaxy_session:
-            user_jobs = self.sa_session.query( model.Job ) \
-                            .options( lazyload( "external_output_metadata" ), lazyload( "parameters" ) ) \
-                            .filter( and_( model.Job.session_id == job.galaxy_session.id,
-                                           or_( model.Job.state == model.Job.states.RUNNING,
-                                                model.Job.state == model.Job.states.QUEUED ) ) ).all()
+            count = self.sa_session.query( model.Job ).enable_eagerloads( False ) \
+                        .filter( and_( model.Job.session_id == job.galaxy_session.id,
+                                       or_( model.Job.state == model.Job.states.RUNNING,
+                                            model.Job.state == model.Job.states.QUEUED ) ) ).count()
         else:
             log.warning( 'Job %s is not associated with a user or session so job concurrency limit cannot be checked.' % job.id )
             return JOB_READY
-        if len( user_jobs ) >= self.app.config.user_job_limit:
+        if count >= self.app.config.user_job_limit:
             return JOB_WAIT
         return JOB_READY
 
@@ -1245,8 +1241,7 @@ class JobStopQueue( object ):
             # Clear the session so we get fresh states for job and all datasets
             self.sa_session.expunge_all()
             # Fetch all new jobs
-            newly_deleted_jobs = self.sa_session.query( model.Job ) \
-                                     .options( lazyload( "external_output_metadata" ), lazyload( "parameters" ) ) \
+            newly_deleted_jobs = self.sa_session.query( model.Job ).enable_eagerloads( False ) \
                                      .filter( model.Job.state == model.Job.states.DELETED_NEW ).all()
             for job in newly_deleted_jobs:
                 jobs_to_check.append( ( job, None ) )

From 445d8494accf98aa5b164969de41107339e38620 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Tue, 13 Dec 2011 00:45:52 -0500
Subject: [PATCH 333/362] Fix extra files display with object store and the
 distributed object store config.

---
 lib/galaxy/objectstore/__init__.py    | 10 +++++-----
 lib/galaxy/web/controllers/dataset.py |  2 +-
 scripts/functional_tests.py           |  8 ++++----
 3 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/lib/galaxy/objectstore/__init__.py b/lib/galaxy/objectstore/__init__.py
index 5cab11058bd..901525d2004 100644
--- a/lib/galaxy/objectstore/__init__.py
+++ b/lib/galaxy/objectstore/__init__.py
@@ -868,10 +868,10 @@ class DistributedObjectStore(ObjectStore):
     
     def __init__(self, config):
         super(DistributedObjectStore, self).__init__()
-        assert config is not None, "distributed object store ('object_store = distributed') " \
-                                   "requires a config file, please set one in " \
-                                   "'distributed_object_store_config_file')"
-        self.distributed_config = config
+        self.distributed_config = config.distributed_object_store_config_file
+        assert self.distributed_config is not None, "distributed object store ('object_store = distributed') " \
+                                                    "requires a config file, please set one in " \
+                                                    "'distributed_object_store_config_file')"
         self.backends = {}
         self.weighted_backend_names = []
 
@@ -1006,7 +1006,7 @@ def build_object_store_from_config(config):
         os.environ['AWS_SECRET_ACCESS_KEY'] = config.aws_secret_key
         return S3ObjectStore(config=config)
     elif store == 'distributed':
-        return DistributedObjectStore(config.distributed_object_store_config_file)
+        return DistributedObjectStore(config=config)
     elif store == 'hierarchical':
         return HierarchicalObjectStore()
 
diff --git a/lib/galaxy/web/controllers/dataset.py b/lib/galaxy/web/controllers/dataset.py
index 6f0d0d4cf9e..70c1464b9e0 100644
--- a/lib/galaxy/web/controllers/dataset.py
+++ b/lib/galaxy/web/controllers/dataset.py
@@ -382,7 +382,7 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesHistory, UsesHist
         
         if filename and filename != "index":
             # For files in extra_files_path
-            file_path = trans.app.object_store.get_filename(data.id, extra_dir='dataset_%s_files' % data.id, alt_name=filename)
+            file_path = trans.app.object_store.get_filename(data.dataset.id, extra_dir='dataset_%s_files' % data.dataset.id, alt_name=filename)
             if os.path.exists( file_path ):
                 if os.path.isdir( file_path ):
                     return trans.show_error_message( "Directory listing is not allowed." ) #TODO: Reconsider allowing listing of directories?
diff --git a/scripts/functional_tests.py b/scripts/functional_tests.py
index 1931a4eebb2..b504b1ce68a 100644
--- a/scripts/functional_tests.py
+++ b/scripts/functional_tests.py
@@ -59,7 +59,7 @@ def main():
     tool_config_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', 'tool_conf.xml.sample' )
     tool_data_table_config_path = 'tool_data_table_conf.xml'
     tool_dependency_dir = os.environ.get( 'GALAXY_TOOL_DEPENDENCY_DIR', None )
-    use_hierarchical_object_store = os.environ.get( 'GALAXY_USE_HIERARCHICAL_OBJECT_STORE', False )
+    use_distributed_object_store = os.environ.get( 'GALAXY_USE_DISTRIBUTED_OBJECT_STORE', False )
     if os.path.exists( 'tool_data_table_conf.test.xml' ):
         tool_data_table_config_path = 'tool_data_table_conf.test.xml'
     if start_server:
@@ -154,9 +154,9 @@ def main():
         if tool_dependency_dir is not None:
             kwargs['tool_dependency_dir'] = tool_dependency_dir
 
-        if use_hierarchical_object_store:
-            kwargs['object_store'] = 'hierarchical'
-            kwargs['hierarchical_object_store_config_file'] = 'hierarchical_object_store_conf.xml.sample'
+        if use_distributed_object_store:
+            kwargs['object_store'] = 'distributed'
+            kwargs['distributed_object_store_config_file'] = 'distributed_object_store_conf.xml.sample'
 
         # Build the Universe Application
         app = UniverseApplication( job_queue_workers = 5,

From 0694081273f57de202acac0fe09278171bdd3a87 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Tue, 13 Dec 2011 09:44:50 -0500
Subject: [PATCH 334/362] Enhance the tool shed repository installation process
 so that repository tools can be loaded into the tool panel outside of any
 sections.  Enhance the install manager to use this enhancement.  Create a new
 shed_util module that contains common mentods used between the install
 manager and the admin_toolshed controller, and modify these components to
 import these common methods.  Significant code cleanup and miscellaneous bug
 fixes included as well.

---
 lib/galaxy/tools/install_manager.py           | 301 ++++-----
 lib/galaxy/util/shed_util.py                  | 548 +++++++++++++++++
 lib/galaxy/web/base/controller.py             |   2 +-
 lib/galaxy/web/controllers/admin_toolshed.py  | 581 ++----------------
 .../select_tool_panel_section.mako            |  57 +-
 5 files changed, 747 insertions(+), 742 deletions(-)
 create mode 100644 lib/galaxy/util/shed_util.py

diff --git a/lib/galaxy/tools/install_manager.py b/lib/galaxy/tools/install_manager.py
index 7c067182d85..d0fc86df465 100644
--- a/lib/galaxy/tools/install_manager.py
+++ b/lib/galaxy/tools/install_manager.py
@@ -4,18 +4,7 @@ at some point included in the Galaxy distribution, but are now hosted in the mai
 shed.  Tools included in tool_shed_install.xml that have already been installed will not be
 re-installed.
 """
-from galaxy import util
-from galaxy.tools import ToolSection
-from galaxy.tools.search import ToolBoxSearch
-from galaxy import model
-from galaxy.web.controllers.admin_toolshed import generate_metadata, generate_tool_panel_section, add_shed_tool_conf_entry, create_or_undelete_tool_shed_repository
-from galaxy.web.controllers.admin_toolshed import handle_missing_data_table_entry, handle_missing_index_file, handle_tool_dependencies
-from galaxy.model.orm import *
-import os, subprocess, tempfile, logging
-
-pkg_resources.require( 'elementtree' )
-from elementtree import ElementTree, ElementInclude
-from elementtree.ElementTree import Element
+from galaxy.util.shed_util import *
 
 log = logging.getLogger( __name__ )
 
@@ -39,192 +28,110 @@ class InstallManager( object ):
         self.tool_shed_install_config = tool_shed_install_config
         tree = util.parse_xml( tool_shed_install_config )
         root = tree.getroot()
-        self.tool_shed = root.get( 'name' )
+        self.tool_shed = clean_tool_shed_url( root.get( 'name' ) )
         log.debug( "Repositories will be installed from tool shed '%s' into configured tool_path location '%s'" % ( str( self.tool_shed ), str( self.tool_path ) ) )
         self.repository_owner = 'devteam'
         for elem in root:
-            if elem.tag == 'tool':
-                self.check_tool( elem )
+            if elem.tag == 'repository':
+                self.install_repository( elem )
             elif elem.tag == 'section':
-                self.check_section( elem )
-    def check_tool( self, elem ):
-        # TODO: write this method.
-        pass
-    def check_section( self, elem ):
-        section_name = elem.get( 'name' )
-        section_id = elem.get( 'id' )
-        for repository_elem in elem:
-            name = repository_elem.get( 'name' )
-            description = repository_elem.get( 'description' )
-            changeset_revision = repository_elem.get( 'changeset_revision' )
-            installed = False
-            for tool_elem in repository_elem:
-                tool_config = tool_elem.get( 'file' )
-                tool_id = tool_elem.get( 'id' )
-                tool_version = tool_elem.get( 'version' )
-                tigm = self.__get_tool_id_guid_map_by_id_version( tool_id, tool_version )
-                if tigm:
-                    # A record exists in the tool_id_guid_map
-                    # table, so see if the tool is still installed.
-                    install_path = self.__generate_install_path( tigm )
-                    if os.path.exists( install_path ):
-                        message = "Skipping automatic install of repository '%s' because it has already been installed in location '%s'" % \
-                            ( name, install_path )
-                        log.debug( message )
-                        installed = True
-                        break
-            if not installed:
-                log.debug( "Installing repository '%s' from tool shed '%s'" % ( name, self.tool_shed ) )
-                current_working_dir = os.getcwd()
-                tool_shed_url = self.__get_url_from_tool_shed( self.tool_shed )
-                repository_clone_url = '%s/repos/devteam/%s' % ( tool_shed_url, name )
-                # Install path is of the form: <tool path><tool shed>/repos/<repository owner>/<repository name>/<changeset revision>
-                clone_dir = os.path.join( self.tool_path, self.tool_shed, 'repos/devteam', name, changeset_revision )
-                if not os.path.isdir( clone_dir ):
-                    os.makedirs( clone_dir )
-                log.debug( 'Cloning %s...' % repository_clone_url )
-                cmd = 'hg clone %s' % repository_clone_url
-                tmp_name = tempfile.NamedTemporaryFile().name
-                tmp_stderr = open( tmp_name, 'wb' )
-                os.chdir( clone_dir )
-                proc = subprocess.Popen( args=cmd, shell=True, stderr=tmp_stderr.fileno() )
-                returncode = proc.wait()
-                os.chdir( current_working_dir )
-                tmp_stderr.close()
+                self.install_section( elem )
+    def install_repository( self, elem, section_name='', section_id='' ):
+        # Install a single repository into the tool config.  If outside of any sections, the entry looks something like:
+        # <repository name="cut_wrapper" description="Galaxy wrapper for the Cut tool" changeset_revision="f3ed6cfe6402">
+        #    <tool id="Cut1" version="1.0.1" />
+        # </repository>
+        name = elem.get( 'name' )
+        description = elem.get( 'description' )
+        changeset_revision = elem.get( 'changeset_revision' )
+        # Install path is of the form: <tool path>/<tool shed>/repos/<repository owner>/<repository name>/<changeset revision>
+        clone_dir = os.path.join( self.tool_path, self.tool_shed, 'repos', self.repository_owner, name, changeset_revision )
+        if self.__isinstalled( elem, clone_dir ):
+            log.debug( "Skipping automatic install of repository '%s' because it has already been installed in location '%s'" % ( name, clone_dir ) )
+        else:
+            if section_name and section_id:
+                section_key = 'section_%s' % str( section_id )
+                if section_key in self.app.toolbox.tool_panel:
+                    # Appending a tool to an existing section in self.app.toolbox.tool_panel
+                    log.debug( "Appending to tool panel section: %s" % section_name )
+                    tool_section = self.app.toolbox.tool_panel[ section_key ]
+                else:
+                    # Appending a new section to self.app.toolbox.tool_panel
+                    log.debug( "Loading new tool panel section: %s" % section_name )
+                    new_section_elem = Element( 'section' )
+                    new_section_elem.attrib[ 'name' ] = section_name
+                    new_section_elem.attrib[ 'id' ] = section_id
+                    tool_section = ToolSection( new_section_elem )
+                    self.app.toolbox.tool_panel[ section_key ] = tool_section
+            else:
+                tool_section = None
+            current_working_dir = os.getcwd()
+            tool_shed_url = self.__get_url_from_tool_shed( self.tool_shed )
+            repository_clone_url = os.path.join( tool_shed_url, 'repos', self.repository_owner, name )
+            relative_install_dir = os.path.join( clone_dir, name )
+            returncode, tmp_name = clone_repository( name, clone_dir, current_working_dir, repository_clone_url )
+            if returncode == 0:
+                returncode, tmp_name = update_repository( current_working_dir, relative_install_dir, changeset_revision )
                 if returncode == 0:
-                    # Update the cloned repository to changeset_revision.  It is imperative that the 
-                    # installed repository is updated to the desired changeset_revision before metadata
-                    # is set because the process for setting metadata uses the repository files on disk.
-                    relative_install_dir = os.path.join( clone_dir, name )
-                    log.debug( 'Updating cloned repository to revision "%s"' % changeset_revision )
-                    cmd = 'hg update -r %s' % changeset_revision
-                    tmp_name = tempfile.NamedTemporaryFile().name
-                    tmp_stderr = open( tmp_name, 'wb' )
-                    os.chdir( relative_install_dir )
-                    proc = subprocess.Popen( cmd, shell=True, stderr=tmp_stderr.fileno() )
-                    returncode = proc.wait()
-                    os.chdir( current_working_dir )
-                    tmp_stderr.close()
-                    if returncode == 0:
-                        # Generate the metadata for the installed tool shed repository.  It is imperative that
-                        # the installed repository is updated to the desired changeset_revision before metadata
-                        # is set because the process for setting metadata uses the repository files on disk.
-                        metadata_dict = generate_metadata( self.app.toolbox, relative_install_dir, repository_clone_url )
-                        if 'datatypes_config' in metadata_dict:
-                            datatypes_config = os.path.abspath( metadata_dict[ 'datatypes_config' ] )
-                            # Load data types required by tools.
-                            self.__load_datatypes( trans, datatypes_config, relative_install_dir )
-                        if 'tools' in metadata_dict:
-                            repository_tools_tups = []
-                            for tool_dict in metadata_dict[ 'tools' ]:
-                                relative_path = tool_dict[ 'tool_config' ]
-                                guid = tool_dict[ 'guid' ]
-                                tool = self.app.toolbox.load_tool( os.path.abspath( relative_path ) )
-                                repository_tools_tups.append( ( relative_path, guid, tool ) )
-                            if repository_tools_tups:
-                                sample_files = metadata_dict.get( 'sample_files', [] )
-                                # Handle missing data table entries for tool parameters that are dynamically generated select lists.
-                                repository_tools_tups = handle_missing_data_table_entry( self.app, self.tool_path, sample_files, repository_tools_tups )
-                                # Handle missing index files for tool parameters that are dynamically generated select lists.
-                                repository_tools_tups = handle_missing_index_file( self.app, self.tool_path, sample_files, repository_tools_tups )
-                                # Handle tools that use fabric scripts to install dependencies.
-                                handle_tool_dependencies( current_working_dir, relative_install_dir, repository_tools_tups )
-                                section_key = 'section_%s' % str( section_id )
-                                if section_key in self.app.toolbox.tool_panel:
-                                    # Appending a tool to an existing section in self.app.toolbox.tool_panel
-                                    log.debug( "Appending to tool panel section: %s" % section_name )
-                                    tool_section = self.app.toolbox.tool_panel[ section_key ]
-                                else:
-                                    # Appending a new section to self.app.toolbox.tool_panel
-                                    log.debug( "Loading new tool panel section: %s" % section_name )
-                                    elem = Element( 'section' )
-                                    elem.attrib[ 'name' ] = section_name
-                                    elem.attrib[ 'id' ] = section_id
-                                    tool_section = ToolSection( elem )
-                                    self.app.toolbox.tool_panel[ section_key ] = tool_section
-                                # Generate an in-memory tool conf section that includes the new tools.
-                                new_tool_section = generate_tool_panel_section( name,
-                                                                                repository_clone_url,
-                                                                                changeset_revision,
-                                                                                tool_section,
-                                                                                repository_tools_tups,
-                                                                                owner=self.repository_owner )
-                                # Create a temporary file to persist the in-memory tool section
-                                # TODO: Figure out how to do this in-memory using xml.etree.
-                                tmp_name = tempfile.NamedTemporaryFile().name
-                                persisted_new_tool_section = open( tmp_name, 'wb' )
-                                persisted_new_tool_section.write( new_tool_section )
-                                persisted_new_tool_section.close()
-                                # Parse the persisted tool panel section
-                                tree = util.parse_xml( tmp_name )
-                                root = tree.getroot()
-                                # Load the tools in the section into the tool panel.
-                                self.app.toolbox.load_section_tag_set( root, self.app.toolbox.tool_panel, self.tool_path )
-                                # Remove the temporary file
-                                try:
-                                    os.unlink( tmp_name )
-                                except:
-                                    pass
-                                # Append the new section to the shed_tool_config file.
-                                add_shed_tool_conf_entry( self.app, self.install_tool_config, new_tool_section )
-                                if self.app.toolbox_search.enabled:
-                                    # If search support for tools is enabled, index the new installed tools.
-                                    self.app.toolbox_search = ToolBoxSearch( self.app.toolbox )
-                        # Add a new record to the tool_shed_repository table if one doesn't
-                        # already exist.  If one exists but is marked deleted, undelete it.
-                        log.debug( "Adding new row to tool_shed_repository table for repository '%s'" % name )
-                        create_or_undelete_tool_shed_repository( self.app,
-                                                                 name,
-                                                                 description,
-                                                                 changeset_revision,
-                                                                 repository_clone_url,
-                                                                 metadata_dict,
-                                                                 owner=self.repository_owner )
-                        # Add a new record to the tool_id_guid_map table for each
-                        # tool in the repository if one doesn't already exist.
-                        if 'tools' in metadata_dict:
-                            tools_mapped = 0
-                            for tool_dict in metadata_dict[ 'tools' ]:
-                                tool_id = tool_dict[ 'id' ]
-                                tool_version = tool_dict[ 'version' ]
-                                guid = tool_dict[ 'guid' ]
-                                tool_id_guid_map = model.ToolIdGuidMap( tool_id=tool_id,
-                                                                        tool_version=tool_version,
-                                                                        tool_shed=self.tool_shed,
-                                                                        repository_owner=self.repository_owner,
-                                                                        repository_name=name,
-                                                                        guid=guid )
+                    metadata_dict = load_repository_contents( self.app,
+                                                              name,
+                                                              description,
+                                                              self.repository_owner,
+                                                              changeset_revision,
+                                                              repository_clone_url,
+                                                              self.install_tool_config, 
+                                                              self.tool_path,
+                                                              tool_section,
+                                                              relative_install_dir,
+                                                              current_working_dir,
+                                                              tmp_name )
+                    # Add a new record to the tool_id_guid_map table for each
+                    # tool in the repository if one doesn't already exist.
+                    if 'tools' in metadata_dict:
+                        tools_mapped = 0
+                        for tool_dict in metadata_dict[ 'tools' ]:
+                            flush_needed = False
+                            tool_id = tool_dict[ 'id' ]
+                            tool_version = tool_dict[ 'version' ]
+                            guid = tool_dict[ 'guid' ]
+                            tool_id_guid_map = get_tool_id_guid_map( self.app, tool_id, tool_version, self.tool_shed, self.repository_owner, name )
+                            if tool_id_guid_map:
+                                if tool_id_guid_map.guid != guid:
+                                    tool_id_guid_map.guid = guid
+                                    flush_needed = True
+                            else:
+                                tool_id_guid_map = self.app.model.ToolIdGuidMap( tool_id=tool_id,
+                                                                                 tool_version=tool_version,
+                                                                                 tool_shed=self.tool_shed,
+                                                                                 repository_owner=self.repository_owner,
+                                                                                 repository_name=name,
+                                                                                 guid=guid )
+                                flush_needed = True
+                            if flush_needed:
                                 self.sa_session.add( tool_id_guid_map )
                                 self.sa_session.flush()
                                 tools_mapped += 1
-                            log.debug( "Mapped tool ids to guids for %d tools included in repository '%s'." % ( tools_mapped, name ) )
-    def __generate_install_path( self, tool_id_guid_map ):
-        """
-        Generate a tool path in which a tool is or will be installed.  The tool path will be of the form:
-        <tool shed>/repos/<repository owner>/<repository name>/<changeset revision>
-        """
-        tool_shed = tool_id_guid_map.tool_shed
-        repository_name = tool_id_guid_map.repository_name
-        tool_shed_repository = self.__get_repository_by_tool_shed_name_owner( tool_shed, repository_name, self.repository_owner )
-        changeset_revision = tool_shed_repository.changeset_revision
-        return '%s/repos%s/%s/%s/%s' % ( tool_shed, self.repository_owner, repository_name, changeset_revision )
-    def __get_repository_by_tool_shed_name_owner( tool_shed, name, owner ):
-        """Get a repository from the database via tool_shed, name and owner."""
-        # CRITICAL:  this assumes that a single changeset_revision exists for each repository
-        # in the tool shed.  In other words, if a repository has multiple changset_revisions
-        # there will be problems.  We're probably safe here because only a single changeset_revision
-        # for each tool shed repository will be installed using this installation process.
-        return self.sa_session.query( self.app.model.ToolShedRepository ) \
-                              .filter( and_( self.app.model.ToolShedRepository.table.c.tool_shed == tool_shed,
-                                             self.app.model.ToolShedRepository.table.c.name == name,
-                                             self.app.model.ToolShedRepository.table.c.owner == owner ) ) \
-                              .first()
-    def __get_tool_id_guid_map_by_id_version( self, tool_id, tool_version ):
-        """Get a tool_id_guid_map from the database via tool_id and tool_version."""
-        return self.sa_session.query( self.app.model.ToolIdGuidMap ) \
-                              .filter( and_( self.app.model.ToolIdGuidMap.table.c.tool_id == tool_id,
-                                             self.app.model.ToolIdGuidMap.table.c.tool_version == tool_version ) ) \
-                              .first()
+                        log.debug( "Mapped tool ids to guids for %d tools included in repository '%s'." % ( tools_mapped, name ) )
+                else:
+                    tmp_stderr = open( tmp_name, 'rb' )
+                    log.debug( "Error updating repository '%s': %s" % ( name, tmp_stderr.read() ) )
+                    tmp_stderr.close()
+            else:
+                tmp_stderr = open( tmp_name, 'rb' )
+                log.debug( "Error cloning repository '%s': %s" % ( name, tmp_stderr.read() ) )
+                tmp_stderr.close()
+    def install_section( self, elem ):
+        # Install 1 or more repositories into a section in the tool config.  An entry looks something like:
+        # <section name="EMBOSS" id="EMBOSSLite">
+        #    <repository name="emboss_5" description="Galaxy wrappers for EMBOSS version 5 tools" changeset_revision="bdd88ae5d0ac">
+        #        <tool file="emboss_5/emboss_antigenic.xml" id="EMBOSS: antigenic1" version="5.0.0" />
+        #        ...
+        #    </repository>
+        # </section>
+        section_name = elem.get( 'name' )
+        section_id = elem.get( 'id' )
+        for repository_elem in elem:
+            self.install_repository( repository_elem, section_name=section_name, section_id=section_id )
     def __get_url_from_tool_shed( self, tool_shed ):
         # The value of tool_shed is something like: toolshed.g2.bx.psu.edu
         # We need the URL to this tool shed, which is something like:
@@ -237,3 +144,17 @@ class InstallManager( object ):
         # The tool shed from which the repository was originally
         # installed must no longer be configured in tool_sheds_conf.xml.
         return None
+    def __isinstalled( self, repository_elem, clone_dir ):
+        name = repository_elem.get( 'name' )
+        installed = False
+        for tool_elem in repository_elem:
+            tool_config = tool_elem.get( 'file' )
+            tool_id = tool_elem.get( 'id' )
+            tool_version = tool_elem.get( 'version' )
+            tigm = get_tool_id_guid_map( self.app, tool_id, tool_version, self.tool_shed, self.repository_owner, name )
+            if tigm:
+                # A record exists in the tool_id_guid_map table, so see if the repository is installed.
+                if os.path.exists( clone_dir ):
+                    installed = True
+                    break
+        return installed
diff --git a/lib/galaxy/util/shed_util.py b/lib/galaxy/util/shed_util.py
new file mode 100644
index 00000000000..f699e291c43
--- /dev/null
+++ b/lib/galaxy/util/shed_util.py
@@ -0,0 +1,548 @@
+import os, tempfile, shutil, subprocess, logging
+from datetime import date, datetime, timedelta
+from time import strftime
+from galaxy import util
+from galaxy.tools import ToolSection
+from galaxy.tools.search import ToolBoxSearch
+from galaxy.model.orm import *
+
+pkg_resources.require( 'elementtree' )
+from elementtree import ElementTree, ElementInclude
+from elementtree.ElementTree import Element, SubElement, tostring
+
+log = logging.getLogger( __name__ )
+
+def add_shed_tool_conf_entry( app, shed_tool_conf, tool_panel_entry ):
+    """
+    Add an entry in the shed_tool_conf file. An entry looks something like:
+    <section name="Filter and Sort" id="filter">
+        <tool file="filter/filtering.xml" guid="toolshed.g2.bx.psu.edu/repos/test/filter/1.0.2"/>
+    </section>
+    This method is used by the InstallManager, which does not have access to trans.
+    """
+    # Make a backup of the hgweb.config file since we're going to be changing it.
+    if not os.path.exists( shed_tool_conf ):
+        output = open( shed_tool_conf, 'w' )
+        output.write( '<?xml version="1.0"?>\n' )
+        output.write( '<toolbox tool_path="%s">\n' % tool_path )
+        output.write( '</toolbox>\n' )
+        output.close()
+    # Make a backup of the shed_tool_conf file.
+    today = date.today()
+    backup_date = today.strftime( "%Y_%m_%d" )
+    shed_tool_conf_copy = '%s/%s_%s_backup' % ( app.config.root, shed_tool_conf, backup_date )
+    shutil.copy( os.path.abspath( shed_tool_conf ), os.path.abspath( shed_tool_conf_copy ) )
+    tmp_fd, tmp_fname = tempfile.mkstemp()
+    new_shed_tool_conf = open( tmp_fname, 'wb' )
+    for i, line in enumerate( open( shed_tool_conf ) ):
+        if line.startswith( '</toolbox>' ):
+            # We're at the end of the original config file, so add our entry.
+            new_shed_tool_conf.write( '    ' )
+            new_shed_tool_conf.write( tostring( pretty_print_xml( tool_panel_entry ) ) )
+            new_shed_tool_conf.write( line )
+        else:
+            new_shed_tool_conf.write( line )
+    new_shed_tool_conf.close()
+    shutil.move( tmp_fname, os.path.abspath( shed_tool_conf ) )
+def clean_repository_clone_url( repository_clone_url ):
+    if repository_clone_url.find( '@' ) > 0:
+        # We have an url that includes an authenticated user, something like:
+        # http://test@bx.psu.edu:9009/repos/some_username/column
+        items = repository_clone_url.split( '@' )
+        tmp_url = items[ 1 ]
+    elif repository_clone_url.find( '//' ) > 0:
+        # We have an url that includes only a protocol, something like:
+        # http://bx.psu.edu:9009/repos/some_username/column
+        items = repository_clone_url.split( '//' )
+        tmp_url = items[ 1 ]
+    else:
+        tmp_url = repository_clone_url
+    return tmp_url
+def clean_tool_shed_url( tool_shed_url ):
+    if tool_shed_url.find( ':' ) > 0:
+        # Eliminate the port, if any, since it will result in an invalid directory name.
+        return tool_shed_url.split( ':' )[ 0 ]
+    return tool_shed_url.rstrip( '/' )
+def clone_repository( name, clone_dir, current_working_dir, repository_clone_url ):
+    log.debug( "Installing repository '%s'" % name )
+    os.makedirs( clone_dir )
+    log.debug( 'Cloning %s' % repository_clone_url )
+    cmd = 'hg clone %s' % repository_clone_url
+    tmp_name = tempfile.NamedTemporaryFile().name
+    tmp_stderr = open( tmp_name, 'wb' )
+    os.chdir( clone_dir )
+    proc = subprocess.Popen( args=cmd, shell=True, stderr=tmp_stderr.fileno() )
+    returncode = proc.wait()
+    os.chdir( current_working_dir )
+    tmp_stderr.close()
+    return returncode, tmp_name
+def create_or_undelete_tool_shed_repository( app, name, description, changeset_revision, repository_clone_url, metadata_dict, owner='' ):
+    # This method is used by the InstallManager, which does not have access to trans.
+    sa_session = app.model.context.current
+    tmp_url = clean_repository_clone_url( repository_clone_url )
+    tool_shed = tmp_url.split( 'repos' )[ 0 ].rstrip( '/' )
+    if not owner:
+        owner = get_repository_owner( tmp_url )
+    includes_datatypes = 'datatypes_config' in metadata_dict
+    flush_needed = False
+    tool_shed_repository = get_repository_by_shed_name_owner_changeset_revision( app, tool_shed, name, owner, changeset_revision )
+    if tool_shed_repository:
+        if tool_shed_repository.deleted:
+            tool_shed_repository.deleted = False
+            # Reset includes_datatypes in case metadata changed since last installed.
+            tool_shed_repository.includes_datatypes = includes_datatypes
+            flush_needed = True
+    else:
+        tool_shed_repository = app.model.ToolShedRepository( tool_shed=tool_shed,
+                                                             name=name,
+                                                             description=description,
+                                                             owner=owner,
+                                                             changeset_revision=changeset_revision,
+                                                             metadata=metadata_dict,
+                                                             includes_datatypes=includes_datatypes )
+        flush_needed = True
+    if flush_needed:
+        sa_session.add( tool_shed_repository )
+        sa_session.flush()
+def generate_datatypes_metadata( datatypes_config, metadata_dict ):
+    """
+    Update the received metadata_dict with changes that have been applied
+    to the received datatypes_config.  This method is used by the InstallManager,
+    which does not have access to trans.
+    """
+    # Parse datatypes_config.
+    tree = ElementTree.parse( datatypes_config )
+    root = tree.getroot()
+    ElementInclude.include( root )
+    repository_datatype_code_files = []
+    datatype_files = root.find( 'datatype_files' )
+    if datatype_files:
+        for elem in datatype_files.findall( 'datatype_file' ):
+            name = elem.get( 'name', None )
+            repository_datatype_code_files.append( name )
+        metadata_dict[ 'datatype_files' ] = repository_datatype_code_files
+    datatypes = []
+    registration = root.find( 'registration' )
+    if registration:
+        for elem in registration.findall( 'datatype' ):
+            extension = elem.get( 'extension', None ) 
+            dtype = elem.get( 'type', None )
+            mimetype = elem.get( 'mimetype', None )
+            datatypes.append( dict( extension=extension,
+                                    dtype=dtype,
+                                    mimetype=mimetype ) )
+        metadata_dict[ 'datatypes' ] = datatypes
+    return metadata_dict
+def generate_metadata( toolbox, relative_install_dir, repository_clone_url ):
+    """
+    Browse the repository files on disk to generate metadata.  Since we are using disk files, it
+    is imperative that the repository is updated to the desired change set revision before metadata
+    is generated.  This method is used by the InstallManager, which does not have access to trans.
+    """
+    metadata_dict = {}
+    sample_files = []
+    datatypes_config = None
+    # Find datatypes_conf.xml if it exists.
+    for root, dirs, files in os.walk( relative_install_dir ):
+        if root.find( '.hg' ) < 0:
+            for name in files:
+                if name == 'datatypes_conf.xml':
+                    relative_path = os.path.join( root, name )
+                    datatypes_config = os.path.abspath( relative_path )
+                    break
+    if datatypes_config:
+        metadata_dict[ 'datatypes_config' ] = relative_path
+        metadata_dict = generate_datatypes_metadata( datatypes_config, metadata_dict )
+    # Find all special .sample files.
+    for root, dirs, files in os.walk( relative_install_dir ):
+        if root.find( '.hg' ) < 0:
+            for name in files:
+                if name.endswith( '.sample' ):
+                    sample_files.append( os.path.join( root, name ) )
+    if sample_files:
+        metadata_dict[ 'sample_files' ] = sample_files
+    # Find all tool configs and exported workflows.
+    for root, dirs, files in os.walk( relative_install_dir ):
+        if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0:
+            if '.hg' in dirs:
+                dirs.remove( '.hg' )
+            for name in files:
+                # Find all tool configs.
+                if name != 'datatypes_conf.xml' and name.endswith( '.xml' ):
+                    full_path = os.path.abspath( os.path.join( root, name ) )
+                    try:
+                        tool = toolbox.load_tool( full_path )
+                    except Exception, e:
+                        tool = None
+                    if tool is not None:
+                        tool_config = os.path.join( root, name )
+                        metadata_dict = generate_tool_metadata( tool_config, tool, repository_clone_url, metadata_dict )
+                # Find all exported workflows
+                elif name.endswith( '.ga' ):
+                    relative_path = os.path.join( root, name )
+                    fp = open( relative_path, 'rb' )
+                    workflow_text = fp.read()
+                    fp.close()
+                    exported_workflow_dict = from_json_string( workflow_text )
+                    if 'a_galaxy_workflow' in exported_workflow_dict and exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true':
+                        metadata_dict = generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict )
+    return metadata_dict
+def generate_tool_guid( repository_clone_url, tool ):
+    """
+    Generate a guid for the installed tool.  It is critical that this guid matches the guid for
+    the tool in the Galaxy tool shed from which it is being installed.  The form of the guid is    
+    <tool shed host>/repos/<repository owner>/<repository name>/<tool id>/<tool version>
+    """
+    tmp_url = clean_repository_clone_url( repository_clone_url )
+    return '%s/%s/%s' % ( tmp_url, tool.id, tool.version )
+def generate_tool_metadata( tool_config, tool, repository_clone_url, metadata_dict ):
+    """
+    Update the received metadata_dict with changes that have been
+    applied to the received tool.  This method is used by the InstallManager,
+    which does not have access to trans.
+    """
+    # Generate the guid
+    guid = generate_tool_guid( repository_clone_url, tool )
+    # Handle tool.requirements.
+    tool_requirements = []
+    for tr in tool.requirements:
+        name=tr.name
+        type=tr.type
+        if type == 'fabfile':
+            version = None
+            fabfile = tr.fabfile
+            method = tr.method
+        else:
+            version = tr.version
+            fabfile = None
+            method = None
+        requirement_dict = dict( name=name,
+                                 type=type,
+                                 version=version,
+                                 fabfile=fabfile,
+                                 method=method )
+        tool_requirements.append( requirement_dict )
+    # Handle tool.tests.
+    tool_tests = []
+    if tool.tests:
+        for ttb in tool.tests:
+            test_dict = dict( name=ttb.name,
+                              required_files=ttb.required_files,
+                              inputs=ttb.inputs,
+                              outputs=ttb.outputs )
+            tool_tests.append( test_dict )
+    tool_dict = dict( id=tool.id,
+                      guid=guid,
+                      name=tool.name,
+                      version=tool.version,
+                      description=tool.description,
+                      version_string_cmd = tool.version_string_cmd,
+                      tool_config=tool_config,
+                      requirements=tool_requirements,
+                      tests=tool_tests )
+    if 'tools' in metadata_dict:
+        metadata_dict[ 'tools' ].append( tool_dict )
+    else:
+        metadata_dict[ 'tools' ] = [ tool_dict ]
+    return metadata_dict
+def generate_tool_panel_elem_list( repository_name, repository_clone_url, changeset_revision, repository_tools_tups, tool_section=None, owner='' ):
+    """Generate a list of ElementTree Element objects for each section or list of tools."""
+    elem_list = []
+    tmp_url = clean_repository_clone_url( repository_clone_url )
+    if not owner:
+        owner = get_repository_owner( tmp_url )
+    if tool_section:
+        root_elem = Element( 'section' )
+        root_elem.attrib[ 'name' ] = tool_section.name
+        root_elem.attrib[ 'id' ] = tool_section.id
+    for repository_tool_tup in repository_tools_tups:
+        tool_file_path, guid, tool = repository_tool_tup
+        if tool_section:
+            tool_elem = SubElement( root_elem, 'tool' )
+        else:
+            tool_elem = Element( 'tool' )
+        tool_elem.attrib[ 'file' ] = tool_file_path
+        tool_elem.attrib[ 'guid' ] = guid
+        tool_shed_elem = SubElement( tool_elem, 'tool_shed' )
+        tool_shed_elem.text = tmp_url.split( 'repos' )[ 0 ].rstrip( '/' )
+        repository_name_elem = SubElement( tool_elem, 'repository_name' )
+        repository_name_elem.text = repository_name
+        repository_owner_elem = SubElement( tool_elem, 'repository_owner' )
+        repository_owner_elem.text = owner
+        changeset_revision_elem = SubElement( tool_elem, 'changeset_revision' )
+        changeset_revision_elem.text = changeset_revision
+        id_elem = SubElement( tool_elem, 'id' )
+        id_elem.text = tool.id
+        version_elem = SubElement( tool_elem, 'version' )
+        version_elem.text = tool.version
+    if tool_section:
+        elem_list.append( root_elem )
+    else:
+        elem_list.append( tool_elem )
+    return elem_list
+def generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict ):
+    """
+    Update the received metadata_dict with changes that have been applied
+    to the received exported_workflow_dict.  Store everything in the database.
+    This method is used by the InstallManager, which does not have access to trans.
+    """
+    if 'workflows' in metadata_dict:
+        metadata_dict[ 'workflows' ].append( ( relative_path, exported_workflow_dict ) )
+    else:
+        metadata_dict[ 'workflows' ] = [ ( relative_path, exported_workflow_dict ) ]
+    return metadata_dict
+def get_repository_by_shed_name_owner_changeset_revision( app, tool_shed, name, owner, changeset_revision ):
+    # This method is used by the InstallManager, which does not have access to trans.
+    sa_session = app.model.context.current
+    if tool_shed.find( '//' ) > 0:
+        tool_shed = tool_shed.split( '//' )[1]
+    return sa_session.query( app.model.ToolShedRepository ) \
+                     .filter( and_( app.model.ToolShedRepository.table.c.tool_shed == tool_shed,
+                                    app.model.ToolShedRepository.table.c.name == name,
+                                    app.model.ToolShedRepository.table.c.owner == owner,
+                                    app.model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \
+                     .first()
+def get_repository_owner( cleaned_repository_url ):
+    items = cleaned_repository_url.split( 'repos' )
+    repo_path = items[ 1 ]
+    if repo_path.startswith( '/' ):
+        repo_path = repo_path.replace( '/', '', 1 )
+    return repo_path.lstrip( '/' ).split( '/' )[ 0 ]
+def get_tool_id_guid_map( app, tool_id, version, tool_shed, repository_owner, repository_name ):
+    # This method is used by the InstallManager, which does not have access to trans.
+    sa_session = app.model.context.current
+    return sa_session.query( app.model.ToolIdGuidMap ) \
+                     .filter( and_( app.model.ToolIdGuidMap.table.c.tool_id == tool_id,
+                                    app.model.ToolIdGuidMap.table.c.tool_version == version,
+                                    app.model.ToolIdGuidMap.table.c.tool_shed == tool_shed,
+                                    app.model.ToolIdGuidMap.table.c.repository_owner == repository_owner,
+                                    app.model.ToolIdGuidMap.table.c.repository_name == repository_name ) ) \
+                     .first()
+def handle_missing_data_table_entry( app, tool_path, sample_files, repository_tools_tups ):
+    """
+    Inspect each tool to see if any have input parameters that are dynamically
+    generated select lists that require entries in the tool_data_table_conf.xml file.
+    This method is used by the InstallManager, which does not have access to trans.
+    """
+    missing_data_table_entry = False
+    for index, repository_tools_tup in enumerate( repository_tools_tups ):
+        tup_path, guid, repository_tool = repository_tools_tup
+        if repository_tool.params_with_missing_data_table_entry:
+            missing_data_table_entry = True
+            break
+    if missing_data_table_entry:
+        # The repository must contain a tool_data_table_conf.xml.sample file that includes
+        # all required entries for all tools in the repository.
+        for sample_file in sample_files:
+            head, tail = os.path.split( sample_file )
+            if tail == 'tool_data_table_conf.xml.sample':
+                break
+        error, correction_msg = handle_sample_tool_data_table_conf_file( app, sample_file )
+        if error:
+            # TODO: Do more here than logging an exception.
+            log.debug( exception_msg )
+        # Reload the tool into the local list of repository_tools_tups.
+        repository_tool = app.toolbox.load_tool( os.path.join( tool_path, tup_path ) )
+        repository_tools_tups[ index ] = ( tup_path, repository_tool )
+    return repository_tools_tups
+def handle_missing_index_file( app, tool_path, sample_files, repository_tools_tups ):
+    """
+    Inspect each tool to see if it has any input parameters that
+    are dynamically generated select lists that depend on a .loc file.
+    This method is used by the InstallManager, which does not have access to trans.
+    """
+    missing_files_handled = []
+    for index, repository_tools_tup in enumerate( repository_tools_tups ):
+        tup_path, guid, repository_tool = repository_tools_tup
+        params_with_missing_index_file = repository_tool.params_with_missing_index_file
+        for param in params_with_missing_index_file:
+            options = param.options
+            missing_head, missing_tail = os.path.split( options.missing_index_file )
+            if missing_tail not in missing_files_handled:
+                # The repository must contain the required xxx.loc.sample file.
+                for sample_file in sample_files:
+                    sample_head, sample_tail = os.path.split( sample_file )
+                    if sample_tail == '%s.sample' % missing_tail:
+                        copy_sample_loc_file( app, sample_file )
+                        if options.tool_data_table and options.tool_data_table.missing_index_file:
+                            options.tool_data_table.handle_found_index_file( options.missing_index_file )
+                        missing_files_handled.append( missing_tail )
+                        break
+        # Reload the tool into the local list of repository_tools_tups.
+        repository_tool = app.toolbox.load_tool( os.path.join( tool_path, tup_path ) )
+        repository_tools_tups[ index ] = ( tup_path, guid, repository_tool )
+    return repository_tools_tups
+def handle_tool_dependencies( current_working_dir, repo_files_dir, repository_tools_tups ):
+    """
+    Inspect each tool to see if it includes a "requirement" that refers to a fabric
+    script.  For those that do, execute the fabric script to install tool dependencies.
+    This method is used by the InstallManager, which does not have access to trans.
+    """
+    for index, repository_tools_tup in enumerate( repository_tools_tups ):
+        tup_path, guid, repository_tool = repository_tools_tup
+        for requirement in repository_tool.requirements:
+            if requirement.type == 'fabfile':
+                log.debug( 'Executing fabric script to install dependencies for tool "%s"...' % repository_tool.name )
+                fabfile = requirement.fabfile
+                method = requirement.method
+                # Find the relative path to the fabfile.
+                relative_fabfile_path = None
+                for root, dirs, files in os.walk( repo_files_dir ):
+                    for name in files:
+                        if name == fabfile:
+                            relative_fabfile_path = os.path.join( root, name )
+                            break
+                if relative_fabfile_path:
+                    # cmd will look something like: fab -f fabfile.py install_bowtie
+                    cmd = 'fab -f %s %s' % ( relative_fabfile_path, method )
+                    tmp_name = tempfile.NamedTemporaryFile().name
+                    tmp_stderr = open( tmp_name, 'wb' )
+                    os.chdir( repo_files_dir )
+                    proc = subprocess.Popen( cmd, shell=True, stderr=tmp_stderr.fileno() )
+                    returncode = proc.wait()
+                    os.chdir( current_working_dir )
+                    tmp_stderr.close()
+                    if returncode != 0:
+                        # TODO: do something more here than logging the problem.
+                        tmp_stderr = open( tmp_name, 'rb' )
+                        error = tmp_stderr.read()
+                        tmp_stderr.close()
+                        log.debug( 'Problem installing dependencies for tool "%s"\n%s' % ( repository_tool.name, error ) )
+def load_datatypes( app, datatypes_config, relative_intall_dir ):
+    # This method is used by the InstallManager, which does not have access to trans.
+    imported_module = None
+    # Parse datatypes_config.
+    tree = parse_xml( datatypes_config )
+    datatypes_config_root = tree.getroot()
+    relative_path_to_datatype_file_name = None
+    datatype_files = datatypes_config_root.find( 'datatype_files' )
+    # Currently only a single datatype_file is supported.  For example:
+    # <datatype_files>
+    #    <datatype_file name="gmap.py"/>
+    # </datatype_files>
+    for elem in datatype_files.findall( 'datatype_file' ):
+        datatype_file_name = elem.get( 'name', None )
+        if datatype_file_name:
+            # Find the file in the installed repository.
+            for root, dirs, files in os.walk( relative_intall_dir ):
+                if root.find( '.hg' ) < 0:
+                    for name in files:
+                        if name == datatype_file_name:
+                            relative_path_to_datatype_file_name = os.path.join( root, name )
+                            break
+            break
+    if relative_path_to_datatype_file_name:
+        relative_head, relative_tail = os.path.split( relative_path_to_datatype_file_name )
+        registration = datatypes_config_root.find( 'registration' )
+        # Get the module by parsing the <datatype> tag.
+        for elem in registration.findall( 'datatype' ):
+            # A 'type' attribute is currently required.  The attribute
+            # should be something like: type="gmap:GmapDB".
+            dtype = elem.get( 'type', None )
+            if dtype:
+                fields = dtype.split( ':' )
+                datatype_module = fields[0]
+                datatype_class_name = fields[1]
+                # Since we currently support only a single datatype_file,
+                #  we have what we need.
+                break
+        try:
+            sys.path.insert( 0, relative_head )
+            imported_module = __import__( datatype_module )
+            sys.path.pop( 0 )
+        except Exception, e:
+            log.debug( "Exception importing datatypes code file included in installed repository: %s" % str( e ) )
+    app.datatypes_registry.load_datatypes( root_dir=app.config.root, config=datatypes_config, imported_module=imported_module )
+def load_repository_contents( app, name, description, owner, changeset_revision, repository_clone_url, shed_tool_conf, 
+                              tool_path, tool_section, relative_install_dir, current_working_dir, tmp_name ):
+    # This method is used by the InstallManager, which does not have access to trans.
+    # Generate the metadata for the installed tool shed repository.  It is imperative that
+    # the installed repository is updated to the desired changeset_revision before metadata
+    # is set because the process for setting metadata uses the repository files on disk.
+    metadata_dict = generate_metadata( app.toolbox, relative_install_dir, repository_clone_url )
+    if 'datatypes_config' in metadata_dict:
+        datatypes_config = os.path.abspath( metadata_dict[ 'datatypes_config' ] )
+        # Load data types required by tools.
+        load_datatypes( app, datatypes_config, relative_install_dir )
+    if 'tools' in metadata_dict:
+        repository_tools_tups = []
+        for tool_dict in metadata_dict[ 'tools' ]:
+            relative_path = tool_dict[ 'tool_config' ]
+            guid = tool_dict[ 'guid' ]
+            tool = app.toolbox.load_tool( os.path.abspath( relative_path ) )
+            repository_tools_tups.append( ( relative_path, guid, tool ) )
+        if repository_tools_tups:
+            sample_files = metadata_dict.get( 'sample_files', [] )
+            # Handle missing data table entries for tool parameters that are dynamically generated select lists.
+            repository_tools_tups = handle_missing_data_table_entry( app, tool_path, sample_files, repository_tools_tups )
+            # Handle missing index files for tool parameters that are dynamically generated select lists.
+            repository_tools_tups = handle_missing_index_file( app, tool_path, sample_files, repository_tools_tups )
+            # Handle tools that use fabric scripts to install dependencies.
+            handle_tool_dependencies( current_working_dir, relative_install_dir, repository_tools_tups )
+            # Generate a new entry for the tool config.
+            elem_list = generate_tool_panel_elem_list( name,
+                                                       repository_clone_url,
+                                                       changeset_revision,
+                                                       repository_tools_tups,
+                                                       tool_section=tool_section,
+                                                       owner=owner )
+            if tool_section:
+                for section_elem in elem_list:
+                    # Load the section into the tool panel.
+                    app.toolbox.load_section_tag_set( section_elem, app.toolbox.tool_panel, tool_path )
+            else:
+                # Load the tools into the tool panel outside of any sections.
+                for tool_elem in elem_list:
+                    guid = tool_elem.get( 'guid' )
+                    app.toolbox.load_tool_tag_set( tool_elem, app.toolbox.tool_panel, tool_path=tool_path, guid=guid )
+            # Remove the temporary file
+            try:
+                os.unlink( tmp_name )
+            except:
+                pass
+            for elem_entry in elem_list:
+                # Append the new entry (either section or list of tools) to the shed_tool_config file.
+                add_shed_tool_conf_entry( app, shed_tool_conf, elem_entry )
+            if app.toolbox_search.enabled:
+                # If search support for tools is enabled, index the new installed tools.
+                app.toolbox_search = ToolBoxSearch( app.toolbox )
+    # Add a new record to the tool_shed_repository table if one doesn't
+    # already exist.  If one exists but is marked deleted, undelete it.
+    log.debug( "Adding new row to tool_shed_repository table for repository '%s'" % name )
+    create_or_undelete_tool_shed_repository( app,
+                                             name,
+                                             description,
+                                             changeset_revision,
+                                             repository_clone_url,
+                                             metadata_dict )
+    return metadata_dict
+def pretty_print_xml( elem, level=0 ):
+    pad = '    '
+    i = "\n" + level * pad
+    if len( elem ):
+        if not elem.text or not elem.text.strip():
+            elem.text = i + pad + pad
+        if not elem.tail or not elem.tail.strip():
+            elem.tail = i
+        for e in elem:
+            pretty_print_xml( e, level + 1 )
+        if not elem.tail or not elem.tail.strip():
+            elem.tail = i
+    else:
+        if level and ( not elem.tail or not elem.tail.strip() ):
+            elem.tail = i + pad
+    return elem
+def update_repository( current_working_dir, relative_install_dir, changeset_revision ):
+    # Update the cloned repository to changeset_revision.  It is imperative that the 
+    # installed repository is updated to the desired changeset_revision before metadata
+    # is set because the process for setting metadata uses the repository files on disk.
+    log.debug( 'Updating cloned repository to revision "%s"' % changeset_revision )
+    cmd = 'hg update -r %s' % changeset_revision
+    tmp_name = tempfile.NamedTemporaryFile().name
+    tmp_stderr = open( tmp_name, 'wb' )
+    os.chdir( relative_install_dir )
+    proc = subprocess.Popen( cmd, shell=True, stderr=tmp_stderr.fileno() )
+    returncode = proc.wait()
+    os.chdir( current_working_dir )
+    tmp_stderr.close()
+    return returncode, tmp_name
diff --git a/lib/galaxy/web/base/controller.py b/lib/galaxy/web/base/controller.py
index 7eeba3d8c3f..96674e9c96e 100644
--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -24,7 +24,7 @@ from Cheetah.Template import Template
 
 pkg_resources.require( 'elementtree' )
 from elementtree import ElementTree, ElementInclude
-from elementtree.ElementTree import Element
+from elementtree.ElementTree import Element, SubElement, tostring
 
 log = logging.getLogger( __name__ )
 
diff --git a/lib/galaxy/web/controllers/admin_toolshed.py b/lib/galaxy/web/controllers/admin_toolshed.py
index 0fd186fbe3b..816a8228b4e 100644
--- a/lib/galaxy/web/controllers/admin_toolshed.py
+++ b/lib/galaxy/web/controllers/admin_toolshed.py
@@ -1,5 +1,5 @@
 from galaxy.web.controllers.admin import *
-import logging
+from galaxy.util.shed_util import *
 
 log = logging.getLogger( __name__ )
 
@@ -159,131 +159,68 @@ class AdminToolshed( AdminGalaxy ):
                 else:
                     section_key = 'section_%s' % tool_panel_section
                     tool_section = trans.app.toolbox.tool_panel[ section_key ]
-                # Decode the encoded repo_info_dict param value.
-                repo_info_dict = tool_shed_decode( repo_info_dict )
-                # Clone the repository to the configured location.
-                current_working_dir = os.getcwd()
-                installed_repository_names = []
-                for name, repo_info_tuple in repo_info_dict.items():
-                    metadata_dict = None
-                    description, repository_clone_url, changeset_revision = repo_info_tuple
-                    clone_dir = os.path.join( tool_path, self.__generate_tool_path( repository_clone_url, changeset_revision ) )
-                    if os.path.exists( clone_dir ):
-                        # Repository and revision has already been cloned.
-                        # TODO: implement the ability to re-install or revert an existing repository.
-                        message += 'Revision <b>%s</b> of repository <b>%s</b> was previously installed.<br/>' % ( changeset_revision, name )
-                    else:
-                        os.makedirs( clone_dir )
-                        log.debug( 'Cloning %s...' % repository_clone_url )
-                        cmd = 'hg clone %s' % repository_clone_url
-                        tmp_name = tempfile.NamedTemporaryFile().name
-                        tmp_stderr = open( tmp_name, 'wb' )
-                        os.chdir( clone_dir )
-                        proc = subprocess.Popen( args=cmd, shell=True, stderr=tmp_stderr.fileno() )
-                        returncode = proc.wait()
-                        os.chdir( current_working_dir )
-                        tmp_stderr.close()
+            else:
+                tool_section = None
+            # Decode the encoded repo_info_dict param value.
+            repo_info_dict = tool_shed_decode( repo_info_dict )
+            # Clone the repository to the configured location.
+            current_working_dir = os.getcwd()
+            installed_repository_names = []
+            for name, repo_info_tuple in repo_info_dict.items():
+                description, repository_clone_url, changeset_revision = repo_info_tuple
+                clone_dir = os.path.join( tool_path, self.__generate_tool_path( repository_clone_url, changeset_revision ) )
+                relative_install_dir = os.path.join( clone_dir, name )
+                if os.path.exists( clone_dir ):
+                    # Repository and revision has already been cloned.
+                    # TODO: implement the ability to re-install or revert an existing repository.
+                    message += 'Revision <b>%s</b> of repository <b>%s</b> was previously installed.<br/>' % ( changeset_revision, name )
+                else:
+                    returncode, tmp_name = clone_repository( name, clone_dir, current_working_dir, repository_clone_url )
+                    if returncode == 0:
+                        returncode, tmp_name = update_repository( current_working_dir, relative_install_dir, changeset_revision )
                         if returncode == 0:
-                            # Update the cloned repository to changeset_revision.  It is imperative that the 
-                            # installed repository is updated to the desired changeset_revision before metadata
-                            # is set because the process for setting metadata uses the repository files on disk.
-                            relative_install_dir = os.path.join( clone_dir, name )
-                            log.debug( 'Updating cloned repository to revision "%s"...' % changeset_revision )
-                            cmd = 'hg update -r %s' % changeset_revision
-                            tmp_name = tempfile.NamedTemporaryFile().name
-                            tmp_stderr = open( tmp_name, 'wb' )
-                            os.chdir( relative_install_dir )
-                            proc = subprocess.Popen( cmd, shell=True, stderr=tmp_stderr.fileno() )
-                            returncode = proc.wait()
-                            os.chdir( current_working_dir )
-                            tmp_stderr.close()
-                            if returncode == 0:
-                                # Generate the metadata for the installed tool shed repository.  It is imperative that
-                                # the installed repository is updated to the desired changeset_revision before metadata
-                                # is set because the process for setting metadata uses the repository files on disk.
-                                metadata_dict = generate_metadata( trans.app.toolbox, relative_install_dir, repository_clone_url )
-                                if 'datatypes_config' in metadata_dict:
-                                    datatypes_config = os.path.abspath( metadata_dict[ 'datatypes_config' ] )
-                                    # Load data types required by tools.
-                                    self.__load_datatypes( trans, datatypes_config, relative_install_dir )
-                                if 'tools' in metadata_dict:
-                                    repository_tools_tups = []
-                                    for tool_dict in metadata_dict[ 'tools' ]:
-                                        relative_path = tool_dict[ 'tool_config' ]
-                                        guid = tool_dict[ 'guid' ]
-                                        tool = trans.app.toolbox.load_tool( os.path.abspath( relative_path ) )
-                                        repository_tools_tups.append( ( relative_path, guid, tool ) )
-                                    if repository_tools_tups:
-                                        sample_files = metadata_dict.get( 'sample_files', [] )
-                                        # Handle missing data table entries for tool parameters that are dynamically generated select lists.
-                                        repository_tools_tups = handle_missing_data_table_entry( trans.app, tool_path, sample_files, repository_tools_tups )
-                                        # Handle missing index files for tool parameters that are dynamically generated select lists.
-                                        repository_tools_tups = handle_missing_index_file( trans.app, tool_path, sample_files, repository_tools_tups )
-                                        # Handle tools that use fabric scripts to install dependencies.
-                                        handle_tool_dependencies( current_working_dir, relative_install_dir, repository_tools_tups )
-                                        # Generate an in-memory tool conf section that includes the new tools.
-                                        new_tool_section = generate_tool_panel_section( name,
-                                                                                        repository_clone_url,
-                                                                                        changeset_revision,
-                                                                                        tool_section,
-                                                                                        repository_tools_tups )
-                                        # Create a temporary file to persist the in-memory tool section
-                                        # TODO: Figure out how to do this in-memory using xml.etree.
-                                        tmp_name = tempfile.NamedTemporaryFile().name
-                                        persisted_new_tool_section = open( tmp_name, 'wb' )
-                                        persisted_new_tool_section.write( new_tool_section )
-                                        persisted_new_tool_section.close()
-                                        # Parse the persisted tool panel section
-                                        tree = parse_xml( tmp_name )
-                                        root = tree.getroot()
-                                        # Load the tools in the section into the tool panel.
-                                        trans.app.toolbox.load_section_tag_set( root, trans.app.toolbox.tool_panel, tool_path )
-                                        # Remove the temporary file
-                                        try:
-                                            os.unlink( tmp_name )
-                                        except:
-                                            pass
-                                        # Append the new section to the shed_tool_config file.
-                                        add_shed_tool_conf_entry( trans.app, shed_tool_conf, new_tool_section )
-                                        if trans.app.toolbox_search.enabled:
-                                            # If search support for tools is enabled, index the new installed tools.
-                                            trans.app.toolbox_search = ToolBoxSearch( trans.app.toolbox )
-                                # Add a new record to the tool_shed_repository table if one doesn't
-                                # already exist.  If one exists but is marked deleted, undelete it.
-                                create_or_undelete_tool_shed_repository( trans.app,
-                                                                         name,
-                                                                         description,
-                                                                         changeset_revision,
-                                                                         repository_clone_url,
-                                                                         metadata_dict )
-                                installed_repository_names.append( name )
-                            else:
-                                tmp_stderr = open( tmp_name, 'rb' )
-                                message += '%s<br/>' % tmp_stderr.read()
-                                tmp_stderr.close()
-                                status = 'error'
+                            owner = get_repository_owner( clean_repository_clone_url( repository_clone_url ) )
+                            metadata_dict = load_repository_contents( trans.app,
+                                                                      name,
+                                                                      description,
+                                                                      owner,
+                                                                      changeset_revision,
+                                                                      repository_clone_url,
+                                                                      shed_tool_conf, 
+                                                                      tool_path,
+                                                                      tool_section,
+                                                                      relative_install_dir,
+                                                                      current_working_dir,
+                                                                      tmp_name )
+                            installed_repository_names.append( name )
                         else:
                             tmp_stderr = open( tmp_name, 'rb' )
                             message += '%s<br/>' % tmp_stderr.read()
                             tmp_stderr.close()
                             status = 'error'
-                if installed_repository_names:
-                    installed_repository_names.sort()
-                    num_repositories_installed = len( installed_repository_names )
+                    else:
+                        tmp_stderr = open( tmp_name, 'rb' )
+                        message += '%s<br/>' % tmp_stderr.read()
+                        tmp_stderr.close()
+                        status = 'error'
+            if installed_repository_names:
+                installed_repository_names.sort()
+                num_repositories_installed = len( installed_repository_names )
+                if tool_section:
                     message += 'Installed %d %s and all tools were loaded into tool panel section <b>%s</b>:<br/>Installed repositories: ' % \
                         ( num_repositories_installed, inflector.cond_plural( num_repositories_installed, 'repository' ), tool_section.name )
-                    for i, repo_name in enumerate( installed_repository_names ):
-                        if i == len( installed_repository_names ) -1:
-                            message += '%s.<br/>' % repo_name
-                        else:
-                            message += '%s, ' % repo_name
-                return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
-                                                                  action='browse_repositories',
-                                                                  message=message,
-                                                                  status=status ) )
-            else:
-                message = 'Choose the section in your tool panel to contain the installed tools.'
-                status = 'error'
+                else:
+                    message += 'Installed %d %s and all tools were loaded into the tool panel outside of any sections.<br/>Installed repositories: ' % \
+                        ( num_repositories_installed, inflector.cond_plural( num_repositories_installed, 'repository' ) )
+                for i, repo_name in enumerate( installed_repository_names ):
+                    if i == len( installed_repository_names ) -1:
+                        message += '%s.<br/>' % repo_name
+                    else:
+                        message += '%s, ' % repo_name
+            return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
+                                                              action='browse_repositories',
+                                                              message=message,
+                                                              status=status ) )
         if len( trans.app.toolbox.shed_tool_confs.keys() ) > 1:
             shed_tool_conf_select_field = build_shed_tool_conf_select_field( trans )
             shed_tool_conf = None
@@ -432,7 +369,7 @@ class AdminToolshed( AdminGalaxy ):
                                     status=status )
     def __get_relative_install_dir( self, trans, repository ):
         # Get the directory where the repository is install.
-        tool_shed = self.__clean_tool_shed_url( repository.tool_shed )
+        tool_shed = clean_tool_shed_url( repository.tool_shed )
         partial_install_dir = '%s/repos/%s/%s/%s' % ( tool_shed, repository.owner, repository.name, repository.changeset_revision )
         # Get the relative tool installation paths from each of the shed tool configs.
         shed_tool_confs = trans.app.toolbox.shed_tool_confs
@@ -443,55 +380,6 @@ class AdminToolshed( AdminGalaxy ):
             if os.path.isdir( relative_install_dir ):
                 break
         return relative_install_dir
-    def __load_datatypes( self, trans, datatypes_config, relative_intall_dir ):
-        imported_module = None
-        # Parse datatypes_config.
-        tree = parse_xml( datatypes_config )
-        datatypes_config_root = tree.getroot()
-        relative_path_to_datatype_file_name = None
-        datatype_files = datatypes_config_root.find( 'datatype_files' )
-        # Currently only a single datatype_file is supported.  For example:
-        # <datatype_files>
-        #    <datatype_file name="gmap.py"/>
-        # </datatype_files>
-        for elem in datatype_files.findall( 'datatype_file' ):
-            datatype_file_name = elem.get( 'name', None )
-            if datatype_file_name:
-                # Find the file in the installed repository.
-                for root, dirs, files in os.walk( relative_intall_dir ):
-                    if root.find( '.hg' ) < 0:
-                        for name in files:
-                            if name == datatype_file_name:
-                                relative_path_to_datatype_file_name = os.path.join( root, name )
-                                break
-                break
-        if relative_path_to_datatype_file_name:
-            relative_head, relative_tail = os.path.split( relative_path_to_datatype_file_name )
-            registration = datatypes_config_root.find( 'registration' )
-            # Get the module by parsing the <datatype> tag.
-            for elem in registration.findall( 'datatype' ):
-                # A 'type' attribute is currently required.  The attribute
-                # should be something like: type="gmap:GmapDB".
-                dtype = elem.get( 'type', None )
-                if dtype:
-                    fields = dtype.split( ':' )
-                    datatype_module = fields[0]
-                    datatype_class_name = fields[1]
-                    # Since we currently support only a single datatype_file,
-                    #  we have what we need.
-                    break
-            try:
-                sys.path.insert( 0, relative_head )
-                imported_module = __import__( datatype_module )
-                sys.path.pop( 0 )
-            except Exception, e:
-                log.debug( "Exception importing datatypes code file included in installed repository: %s" % str( e ) )
-        trans.app.datatypes_registry.load_datatypes( root_dir=trans.app.config.root, config=datatypes_config, imported_module=imported_module )
-    def __clean_tool_shed_url( self, tool_shed_url ):
-        if tool_shed_url.find( ':' ) > 0:
-            # Eliminate the port, if any, since it will result in an invalid directory name.
-            return tool_shed_url.split( ':' )[ 0 ]
-        return tool_shed_url.rstrip( '/' )
     def __generate_tool_path( self, repository_clone_url, changeset_revision ):
         """
         Generate a tool path that guarantees repositories with the same name will always be installed
@@ -504,7 +392,7 @@ class AdminToolshed( AdminGalaxy ):
         items = tmp_url.split( 'repos' )
         tool_shed_url = items[ 0 ]
         repo_path = items[ 1 ]
-        tool_shed_url = self.__clean_tool_shed_url( tool_shed_url )
+        tool_shed_url = clean_tool_shed_url( tool_shed_url )
         return '%s/repos%s/%s' % ( tool_shed_url, repo_path, changeset_revision )
     def __generate_clone_url( self, trans, repository ):
         """Generate the URL for cloning a repository."""
@@ -545,17 +433,6 @@ def get_repository_by_name_owner_changeset_revision( trans, name, owner, changes
                                             trans.model.ToolShedRepository.table.c.owner == owner,
                                             trans.model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \
                              .first()
-def get_repository_by_shed_name_owner_changeset_revision( app, tool_shed, name, owner, changeset_revision ):
-    # This method is used by the InstallManager, which does not have access to trans.
-    sa_session = app.model.context.current
-    if tool_shed.find( '//' ) > 0:
-        tool_shed = tool_shed.split( '//' )[1]
-    return sa_session.query( app.model.ToolShedRepository ) \
-                     .filter( and_( app.model.ToolShedRepository.table.c.tool_shed == tool_shed,
-                                    app.model.ToolShedRepository.table.c.name == name,
-                                    app.model.ToolShedRepository.table.c.owner == owner,
-                                    app.model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \
-                     .first()
 def get_url_from_repository_tool_shed( trans, repository ):
     # The stored value of repository.tool_shed is something like:
     # toolshed.g2.bx.psu.edu
@@ -569,347 +446,3 @@ def get_url_from_repository_tool_shed( trans, repository ):
     # The tool shed from which the repository was originally
     # installed must no longer be configured in tool_sheds_conf.xml.
     return None
-def generate_tool_panel_section( repository_name, repository_clone_url, changeset_revision, tool_section, repository_tools_tups, owner='' ):
-    """
-    Write an in-memory tool panel section so we can load it into the tool panel and then
-    append it to the appropriate shed tool config.
-    TODO: re-write using ElementTree.
-    """
-    tmp_url = clean_repository_clone_url( repository_clone_url )
-    if not owner:
-        owner = get_repository_owner( tmp_url )
-    section_str = ''
-    section_str += '    <section name="%s" id="%s">\n' % ( tool_section.name, tool_section.id )
-    for repository_tool_tup in repository_tools_tups:
-        tool_file_path, guid, tool = repository_tool_tup
-        section_str += '        <tool file="%s" guid="%s">\n' % ( tool_file_path, guid )
-        section_str += '            <tool_shed>%s</tool_shed>\n' % tmp_url.split( 'repos' )[ 0 ].rstrip( '/' )
-        section_str += '            <repository_name>%s</repository_name>\n' % repository_name
-        section_str += '            <repository_owner>%s</repository_owner>\n' % owner
-        section_str += '            <changeset_revision>%s</changeset_revision>\n' % changeset_revision
-        section_str += '            <id>%s</id>\n' % tool.id
-        section_str += '            <version>%s</version>\n' % tool.version
-        section_str += '        </tool>\n'
-    section_str += '    </section>\n'
-    return section_str
-def get_repository_owner( cleaned_repository_url ):
-    items = cleaned_repository_url.split( 'repos' )
-    repo_path = items[ 1 ]
-    if repo_path.startswith( '/' ):
-        repo_path = repo_path.replace( '/', '', 1 )
-    return repo_path.lstrip( '/' ).split( '/' )[ 0 ]
-def generate_tool_guid( repository_clone_url, tool ):
-    """
-    Generate a guid for the installed tool.  It is critical that this guid matches the guid for
-    the tool in the Galaxy tool shed from which it is being installed.  The form of the guid is    
-    <tool shed host>/repos/<repository owner>/<repository name>/<tool id>/<tool version>
-    """
-    tmp_url = clean_repository_clone_url( repository_clone_url )
-    return '%s/%s/%s' % ( tmp_url, tool.id, tool.version )
-def clean_repository_clone_url( repository_clone_url ):
-    if repository_clone_url.find( '@' ) > 0:
-        # We have an url that includes an authenticated user, something like:
-        # http://test@bx.psu.edu:9009/repos/some_username/column
-        items = repository_clone_url.split( '@' )
-        tmp_url = items[ 1 ]
-    elif repository_clone_url.find( '//' ) > 0:
-        # We have an url that includes only a protocol, something like:
-        # http://bx.psu.edu:9009/repos/some_username/column
-        items = repository_clone_url.split( '//' )
-        tmp_url = items[ 1 ]
-    else:
-        tmp_url = repository_clone_url
-    return tmp_url
-def generate_metadata( toolbox, relative_install_dir, repository_clone_url ):
-    """
-    Browse the repository files on disk to generate metadata.  Since we are using disk files, it
-    is imperative that the repository is updated to the desired change set revision before metadata
-    is generated.  This method is used by the InstallManager, which does not have access to trans.
-    """
-    metadata_dict = {}
-    sample_files = []
-    datatypes_config = None
-    # Find datatypes_conf.xml if it exists.
-    for root, dirs, files in os.walk( relative_install_dir ):
-        if root.find( '.hg' ) < 0:
-            for name in files:
-                if name == 'datatypes_conf.xml':
-                    relative_path = os.path.join( root, name )
-                    datatypes_config = os.path.abspath( relative_path )
-                    break
-    if datatypes_config:
-        metadata_dict[ 'datatypes_config' ] = relative_path
-        metadata_dict = generate_datatypes_metadata( datatypes_config, metadata_dict )
-    # Find all special .sample files.
-    for root, dirs, files in os.walk( relative_install_dir ):
-        if root.find( '.hg' ) < 0:
-            for name in files:
-                if name.endswith( '.sample' ):
-                    sample_files.append( os.path.join( root, name ) )
-    if sample_files:
-        metadata_dict[ 'sample_files' ] = sample_files
-    # Find all tool configs and exported workflows.
-    for root, dirs, files in os.walk( relative_install_dir ):
-        if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0:
-            if '.hg' in dirs:
-                dirs.remove( '.hg' )
-            for name in files:
-                # Find all tool configs.
-                if name != 'datatypes_conf.xml' and name.endswith( '.xml' ):
-                    full_path = os.path.abspath( os.path.join( root, name ) )
-                    try:
-                        tool = toolbox.load_tool( full_path )
-                    except Exception, e:
-                        tool = None
-                    if tool is not None:
-                        tool_config = os.path.join( root, name )
-                        metadata_dict = generate_tool_metadata( tool_config, tool, repository_clone_url, metadata_dict )
-                # Find all exported workflows
-                elif name.endswith( '.ga' ):
-                    relative_path = os.path.join( root, name )
-                    fp = open( relative_path, 'rb' )
-                    workflow_text = fp.read()
-                    fp.close()
-                    exported_workflow_dict = from_json_string( workflow_text )
-                    if 'a_galaxy_workflow' in exported_workflow_dict and exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true':
-                        metadata_dict = generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict )
-    return metadata_dict
-def generate_datatypes_metadata( datatypes_config, metadata_dict ):
-    """
-    Update the received metadata_dict with changes that have been applied
-    to the received datatypes_config.  This method is used by the InstallManager,
-    which does not have access to trans.
-    """
-    # Parse datatypes_config.
-    tree = ElementTree.parse( datatypes_config )
-    root = tree.getroot()
-    ElementInclude.include( root )
-    repository_datatype_code_files = []
-    datatype_files = root.find( 'datatype_files' )
-    if datatype_files:
-        for elem in datatype_files.findall( 'datatype_file' ):
-            name = elem.get( 'name', None )
-            repository_datatype_code_files.append( name )
-        metadata_dict[ 'datatype_files' ] = repository_datatype_code_files
-    datatypes = []
-    registration = root.find( 'registration' )
-    if registration:
-        for elem in registration.findall( 'datatype' ):
-            extension = elem.get( 'extension', None ) 
-            dtype = elem.get( 'type', None )
-            mimetype = elem.get( 'mimetype', None )
-            datatypes.append( dict( extension=extension,
-                                    dtype=dtype,
-                                    mimetype=mimetype ) )
-        metadata_dict[ 'datatypes' ] = datatypes
-    return metadata_dict
-def generate_tool_metadata( tool_config, tool, repository_clone_url, metadata_dict ):
-    """
-    Update the received metadata_dict with changes that have been
-    applied to the received tool.  This method is used by the InstallManager,
-    which does not have access to trans.
-    """
-    # Generate the guid
-    guid = generate_tool_guid( repository_clone_url, tool )
-    # Handle tool.requirements.
-    tool_requirements = []
-    for tr in tool.requirements:
-        name=tr.name
-        type=tr.type
-        if type == 'fabfile':
-            version = None
-            fabfile = tr.fabfile
-            method = tr.method
-        else:
-            version = tr.version
-            fabfile = None
-            method = None
-        requirement_dict = dict( name=name,
-                                 type=type,
-                                 version=version,
-                                 fabfile=fabfile,
-                                 method=method )
-        tool_requirements.append( requirement_dict )
-    # Handle tool.tests.
-    tool_tests = []
-    if tool.tests:
-        for ttb in tool.tests:
-            test_dict = dict( name=ttb.name,
-                              required_files=ttb.required_files,
-                              inputs=ttb.inputs,
-                              outputs=ttb.outputs )
-            tool_tests.append( test_dict )
-    tool_dict = dict( id=tool.id,
-                      guid=guid,
-                      name=tool.name,
-                      version=tool.version,
-                      description=tool.description,
-                      version_string_cmd = tool.version_string_cmd,
-                      tool_config=tool_config,
-                      requirements=tool_requirements,
-                      tests=tool_tests )
-    if 'tools' in metadata_dict:
-        metadata_dict[ 'tools' ].append( tool_dict )
-    else:
-        metadata_dict[ 'tools' ] = [ tool_dict ]
-    return metadata_dict
-def generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict ):
-    """
-    Update the received metadata_dict with changes that have been applied
-    to the received exported_workflow_dict.  Store everything in the database.
-    This method is used by the InstallManager, which does not have access to trans.
-    """
-    if 'workflows' in metadata_dict:
-        metadata_dict[ 'workflows' ].append( ( relative_path, exported_workflow_dict ) )
-    else:
-        metadata_dict[ 'workflows' ] = [ ( relative_path, exported_workflow_dict ) ]
-    return metadata_dict
-def handle_missing_data_table_entry( app, tool_path, sample_files, repository_tools_tups ):
-    """
-    Inspect each tool to see if any have input parameters that are dynamically
-    generated select lists that require entries in the tool_data_table_conf.xml file.
-    This method is used by the InstallManager, which does not have access to trans.
-    """
-    missing_data_table_entry = False
-    for index, repository_tools_tup in enumerate( repository_tools_tups ):
-        tup_path, guid, repository_tool = repository_tools_tup
-        if repository_tool.params_with_missing_data_table_entry:
-            missing_data_table_entry = True
-            break
-    if missing_data_table_entry:
-        # The repository must contain a tool_data_table_conf.xml.sample file that includes
-        # all required entries for all tools in the repository.
-        for sample_file in sample_files:
-            head, tail = os.path.split( sample_file )
-            if tail == 'tool_data_table_conf.xml.sample':
-                break
-        error, correction_msg = handle_sample_tool_data_table_conf_file( app, sample_file )
-        if error:
-            # TODO: Do more here than logging an exception.
-            log.debug( exception_msg )
-        # Reload the tool into the local list of repository_tools_tups.
-        repository_tool = app.toolbox.load_tool( os.path.join( tool_path, tup_path ) )
-        repository_tools_tups[ index ] = ( tup_path, repository_tool )
-    return repository_tools_tups
-def handle_missing_index_file( app, tool_path, sample_files, repository_tools_tups ):
-    """
-    Inspect each tool to see if it has any input parameters that
-    are dynamically generated select lists that depend on a .loc file.
-    This method is used by the InstallManager, which does not have access to trans.
-    """
-    missing_files_handled = []
-    for index, repository_tools_tup in enumerate( repository_tools_tups ):
-        tup_path, guid, repository_tool = repository_tools_tup
-        params_with_missing_index_file = repository_tool.params_with_missing_index_file
-        for param in params_with_missing_index_file:
-            options = param.options
-            missing_head, missing_tail = os.path.split( options.missing_index_file )
-            if missing_tail not in missing_files_handled:
-                # The repository must contain the required xxx.loc.sample file.
-                for sample_file in sample_files:
-                    sample_head, sample_tail = os.path.split( sample_file )
-                    if sample_tail == '%s.sample' % missing_tail:
-                        copy_sample_loc_file( app, sample_file )
-                        if options.tool_data_table and options.tool_data_table.missing_index_file:
-                            options.tool_data_table.handle_found_index_file( options.missing_index_file )
-                        missing_files_handled.append( missing_tail )
-                        break
-        # Reload the tool into the local list of repository_tools_tups.
-        repository_tool = app.toolbox.load_tool( os.path.join( tool_path, tup_path ) )
-        repository_tools_tups[ index ] = ( tup_path, guid, repository_tool )
-    return repository_tools_tups
-def handle_tool_dependencies( current_working_dir, repo_files_dir, repository_tools_tups ):
-    """
-    Inspect each tool to see if it includes a "requirement" that refers to a fabric
-    script.  For those that do, execute the fabric script to install tool dependencies.
-    This method is used by the InstallManager, which does not have access to trans.
-    """
-    for index, repository_tools_tup in enumerate( repository_tools_tups ):
-        tup_path, guid, repository_tool = repository_tools_tup
-        for requirement in repository_tool.requirements:
-            if requirement.type == 'fabfile':
-                log.debug( 'Executing fabric script to install dependencies for tool "%s"...' % repository_tool.name )
-                fabfile = requirement.fabfile
-                method = requirement.method
-                # Find the relative path to the fabfile.
-                relative_fabfile_path = None
-                for root, dirs, files in os.walk( repo_files_dir ):
-                    for name in files:
-                        if name == fabfile:
-                            relative_fabfile_path = os.path.join( root, name )
-                            break
-                if relative_fabfile_path:
-                    # cmd will look something like: fab -f fabfile.py install_bowtie
-                    cmd = 'fab -f %s %s' % ( relative_fabfile_path, method )
-                    tmp_name = tempfile.NamedTemporaryFile().name
-                    tmp_stderr = open( tmp_name, 'wb' )
-                    os.chdir( repo_files_dir )
-                    proc = subprocess.Popen( cmd, shell=True, stderr=tmp_stderr.fileno() )
-                    returncode = proc.wait()
-                    os.chdir( current_working_dir )
-                    tmp_stderr.close()
-                    if returncode != 0:
-                        # TODO: do something more here than logging the problem.
-                        tmp_stderr = open( tmp_name, 'rb' )
-                        error = tmp_stderr.read()
-                        tmp_stderr.close()
-                        log.debug( 'Problem installing dependencies for tool "%s"\n%s' % ( repository_tool.name, error ) )
-def add_shed_tool_conf_entry( app, shed_tool_conf, new_tool_section ):
-    """
-    Add an entry in the shed_tool_conf file. An entry looks something like:
-    <section name="Filter and Sort" id="filter">
-        <tool file="filter/filtering.xml" guid="toolshed.g2.bx.psu.edu/repos/test/filter/1.0.2"/>
-    </section>
-    This method is used by the InstallManager, which does not have access to trans.
-    """
-    # Make a backup of the hgweb.config file since we're going to be changing it.
-    if not os.path.exists( shed_tool_conf ):
-        output = open( shed_tool_conf, 'w' )
-        output.write( '<?xml version="1.0"?>\n' )
-        output.write( '<toolbox tool_path="%s">\n' % tool_path )
-        output.write( '</toolbox>\n' )
-        output.close()
-    # Make a backup of the shed_tool_conf file.
-    today = date.today()
-    backup_date = today.strftime( "%Y_%m_%d" )
-    shed_tool_conf_copy = '%s/%s_%s_backup' % ( app.config.root, shed_tool_conf, backup_date )
-    shutil.copy( os.path.abspath( shed_tool_conf ), os.path.abspath( shed_tool_conf_copy ) )
-    tmp_fd, tmp_fname = tempfile.mkstemp()
-    new_shed_tool_conf = open( tmp_fname, 'wb' )
-    for i, line in enumerate( open( shed_tool_conf ) ):
-        if line.startswith( '</toolbox>' ):
-            # We're at the end of the original config file, so add our entry.
-            new_shed_tool_conf.write( new_tool_section )
-            new_shed_tool_conf.write( line )
-        else:
-            new_shed_tool_conf.write( line )
-    new_shed_tool_conf.close()
-    shutil.move( tmp_fname, os.path.abspath( shed_tool_conf ) )
-def create_or_undelete_tool_shed_repository( app, name, description, changeset_revision, repository_clone_url, metadata_dict, owner='' ):
-    # This method is used by the InstallManager, which does not have access to trans.
-    sa_session = app.model.context.current
-    tmp_url = clean_repository_clone_url( repository_clone_url )
-    tool_shed = tmp_url.split( 'repos' )[ 0 ].rstrip( '/' )
-    if not owner:
-        owner = get_repository_owner( tmp_url )
-    includes_datatypes = 'datatypes_config' in metadata_dict
-    flush_needed = False
-    tool_shed_repository = get_repository_by_shed_name_owner_changeset_revision( app, tool_shed, name, owner, changeset_revision )
-    if tool_shed_repository:
-        if tool_shed_repository.deleted:
-            tool_shed_repository.deleted = False
-            # Reset includes_datatypes in case metadata changed since last installed.
-            tool_shed_repository.includes_datatypes = includes_datatypes
-            flush_needed = True
-    else:
-        tool_shed_repository = app.model.ToolShedRepository( tool_shed=tool_shed,
-                                                             name=name,
-                                                             description=description,
-                                                             owner=owner,
-                                                             changeset_revision=changeset_revision,
-                                                             metadata=metadata_dict,
-                                                             includes_datatypes=includes_datatypes )
-        flush_needed = True
-    if flush_needed:
-        sa_session.add( tool_shed_repository )
-        sa_session.flush()
diff --git a/templates/admin/tool_shed_repository/select_tool_panel_section.mako b/templates/admin/tool_shed_repository/select_tool_panel_section.mako
index bc6a940ce28..bf8665af822 100644
--- a/templates/admin/tool_shed_repository/select_tool_panel_section.mako
+++ b/templates/admin/tool_shed_repository/select_tool_panel_section.mako
@@ -23,39 +23,42 @@
 <br/>
 
 <div class="toolForm">
-    <div class="toolFormTitle">Choose section to load tools into tool panel</div>
+    <div class="toolFormTitle">Choose tool panel section to contain installed tools (optional)</div>
     <div class="toolFormBody">
-    <form name="select_tool_panel_section" id="select_tool_panel_section" action="${h.url_for( controller='admin_toolshed', action='install_repository', tool_shed_url=tool_shed_url, repo_info_dict=repo_info_dict )}" method="post" >
-        %if shed_tool_conf_select_field:
+        <form name="select_tool_panel_section" id="select_tool_panel_section" action="${h.url_for( controller='admin_toolshed', action='install_repository', tool_shed_url=tool_shed_url, repo_info_dict=repo_info_dict )}" method="post" >
+            %if shed_tool_conf_select_field:
+                <div class="form-row">
+                    <label>Shed tool configuration file:</label>
+                    ${shed_tool_conf_select_field.get_html()}
+                    <div class="toolParamHelp" style="clear: both;">
+                        Your Galaxy instance is configured with ${len( shed_tool_conf_select_field.options )} shed tool configuration files, 
+                        so choose one in which to configure the installed tools.
+                    </div>
+                </div>
+                <div style="clear: both"></div>
+            %else:
+                <input type="hidden" name="shed_tool_conf" value="${shed_tool_conf}"/>
+            %endif
             <div class="form-row">
-                <label>Shed tool configuration file:</label>
-                ${shed_tool_conf_select_field.get_html()}
+                <label>Add new tool panel section:</label>
+                <input name="new_tool_panel_section" type="textfield" value="${new_tool_panel_section}" size="40"/>
                 <div class="toolParamHelp" style="clear: both;">
-                    Your Galaxy instance is configured with ${len( shed_tool_conf_select_field.options )} shed tool configuration files, 
-                    so choose one in which to configure the installed tools.
+                    Add a new tool panel section contain the installed tools (optional).
                 </div>
             </div>
-            <div style="clear: both"></div>
-        %else:
-            <input type="hidden" name="shed_tool_conf" value="${shed_tool_conf}"/>
-        %endif
-        <div class="form-row">
-            <label>Add new tool panel section:</label>
-            <input name="new_tool_panel_section" type="textfield" value="${new_tool_panel_section}" size="40"/>
-            <div class="toolParamHelp" style="clear: both;">
-                Add a new tool panel section or choose an existing section in your tool panel below to contain the installed tools.
+            <div class="form-row">
+                <label>Select existing tool panel section:</label>
+                ${tool_panel_section_select_field.get_html()}
+                <div class="toolParamHelp" style="clear: both;">
+                    Choose an existing section in your tool panel to contain the installed tools (optional).  
+                </div>
             </div>
-        </div>
-        <div class="form-row">
-            <label>Select existing tool panel section:</label>
-            ${tool_panel_section_select_field.get_html()}
-            <div class="toolParamHelp" style="clear: both;">
-                Choose an existing section in your tool panel to contain the installed tools.
+            <div class="form-row">
+                <input type="submit" name="select_tool_panel_section_button" value="Install"/>
+                <div class="toolParamHelp" style="clear: both;">
+                    Clicking <b>Install</b> without selecting a tool panel section will load the installed tools into the tool panel outside of any sections.
+                </div>
             </div>
-        </div>
-        <div class="form-row">
-            <input type="submit" name="select_tool_panel_section_button" value="Install"/>
-        </div>
-    </form>
+        </form>
     </div>
 </div>

From 2351c4aaca14f2fc386c031a6e6dcf56791046b4 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Tue, 13 Dec 2011 09:45:49 -0500
Subject: [PATCH 335/362] Add EBI ENA SRA tool contributed by Iain Cleland.

---
 tool_conf.xml.main            |  1 +
 tool_conf.xml.sample          |  1 +
 tools/data_source/ebi_sra.xml | 15 +++++++++++++++
 3 files changed, 17 insertions(+)
 create mode 100644 tools/data_source/ebi_sra.xml

diff --git a/tool_conf.xml.main b/tool_conf.xml.main
index 2d4ec0dfec6..a1606baff73 100644
--- a/tool_conf.xml.main
+++ b/tool_conf.xml.main
@@ -5,6 +5,7 @@
     <tool file="data_source/ucsc_tablebrowser.xml" />
     <tool file="data_source/ucsc_tablebrowser_archaea.xml" />
     <tool file="data_source/bx_browser.xml" />
+    <tool file="data_source/ebi_sra.xml"/>
     <tool file="data_source/biomart.xml" />
     <tool file="data_source/gramene_mart.xml" />
     <tool file="data_source/flymine.xml" />
diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index e1f6667d4f9..5405c591cb7 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -6,6 +6,7 @@
     <tool file="data_source/ucsc_tablebrowser_test.xml" />
     <tool file="data_source/ucsc_tablebrowser_archaea.xml" />
     <tool file="data_source/bx_browser.xml" />
+    <tool file="data_source/ebi_sra.xml"/>
     <tool file="data_source/microbial_import.xml" />
     <tool file="data_source/biomart.xml" />
     <tool file="data_source/biomart_test.xml" />
diff --git a/tools/data_source/ebi_sra.xml b/tools/data_source/ebi_sra.xml
new file mode 100644
index 00000000000..6009b4cf4c1
--- /dev/null
+++ b/tools/data_source/ebi_sra.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0"?>
+<tool name="EBI SRA" id="ebi_sra_main" tool_type="data_source" version="1.0.0">
+    <description>ENA SRA</description>
+    <!-- This paython script imports the file into Galaxy -->
+    <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
+    <!-- The URL where Galaxy will forwars the user when this tool is accessed from the Get Data menu -->
+    <inputs action="http://www.ebi.ac.uk/ena/" check_values="false" method="get"> 
+        <display>go to EBI SRA server $GALAXY_URL</display>
+    </inputs>
+    <uihints minwidth="800"/>
+    <outputs>
+        <data name="output" format="fastq"/>
+    </outputs>
+    <options sanitize="False" refresh="True"/>
+</tool>

From f4f8260616071b8c29c332b6181782c935ed998c Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 13 Dec 2011 10:42:38 -0500
Subject: [PATCH 336/362] Fix default static wrapping to work with favicon.ico
 and robots.txt (and other static files that may need to be mapped to / in the
 future)

---
 lib/galaxy/web/buildapp.py                    |  1 +
 lib/galaxy/web/framework/middleware/static.py | 10 ++++++++--
 universe_wsgi.ini.sample                      |  1 +
 3 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/web/buildapp.py b/lib/galaxy/web/buildapp.py
index 6984fefc4d1..b7e7f0a213b 100644
--- a/lib/galaxy/web/buildapp.py
+++ b/lib/galaxy/web/buildapp.py
@@ -251,6 +251,7 @@ def wrap_in_static( app, global_conf, **local_conf ):
     urlmap["/static/scripts"] = Static( conf.get( "static_scripts_dir" ), cache_time )
     urlmap["/static/style"] = Static( conf.get( "static_style_dir" ), cache_time )
     urlmap["/favicon.ico"] = Static( conf.get( "static_favicon_dir" ), cache_time )
+    urlmap["/robots.txt"] = Static( conf.get( "static_robots_txt" ), cache_time )
     # URL mapper becomes the root webapp
     return urlmap
     
diff --git a/lib/galaxy/web/framework/middleware/static.py b/lib/galaxy/web/framework/middleware/static.py
index 7fd9467c216..917c371cd7e 100644
--- a/lib/galaxy/web/framework/middleware/static.py
+++ b/lib/galaxy/web/framework/middleware/static.py
@@ -19,6 +19,12 @@ class CacheableStaticURLParser( StaticURLParser ):
     def __call__( self, environ, start_response ):
         path_info = environ.get('PATH_INFO', '')
         if not path_info:
+            #See if this is a static file hackishly mapped.
+            if os.path.exists(self.directory) and os.path.isfile(self.directory):
+                app = fileapp.FileApp(self.directory)
+                if self.cache_seconds:
+                    app.cache_control( max_age = int( self.cache_seconds ) )
+                return app(environ, start_response)
             return self.add_slash(environ, start_response)
         if path_info == '/':
             # @@: This should obviously be configurable
@@ -45,6 +51,6 @@ class CacheableStaticURLParser( StaticURLParser ):
         if self.cache_seconds:
             app.cache_control( max_age = int( self.cache_seconds ) )
         return app(environ, start_response)
-        
+
 def make_static( global_conf, document_root, cache_seconds=None ):
-    return CacheableStaticURLParser( document_root, cache_seconds )
\ No newline at end of file
+    return CacheableStaticURLParser( document_root, cache_seconds )
diff --git a/universe_wsgi.ini.sample b/universe_wsgi.ini.sample
index a28f1a3567d..eea8a875f31 100644
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -247,6 +247,7 @@ static_images_dir = %(here)s/static/images
 static_favicon_dir = %(here)s/static/favicon.ico
 static_scripts_dir = %(here)s/static/scripts/
 static_style_dir = %(here)s/static/june_2007_style/blue
+static_robots_txt = %(here)s/static/robots.txt
 
 # -- Advanced proxy features
 

From 36a3d6bd8d11382522af90ce8880e33b2f06ddf1 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 13 Dec 2011 11:04:07 -0500
Subject: [PATCH 337/362] Provide default for robots.txt being pulled from
 config.

---
 lib/galaxy/web/buildapp.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/web/buildapp.py b/lib/galaxy/web/buildapp.py
index b7e7f0a213b..68d2552fdde 100644
--- a/lib/galaxy/web/buildapp.py
+++ b/lib/galaxy/web/buildapp.py
@@ -251,7 +251,7 @@ def wrap_in_static( app, global_conf, **local_conf ):
     urlmap["/static/scripts"] = Static( conf.get( "static_scripts_dir" ), cache_time )
     urlmap["/static/style"] = Static( conf.get( "static_style_dir" ), cache_time )
     urlmap["/favicon.ico"] = Static( conf.get( "static_favicon_dir" ), cache_time )
-    urlmap["/robots.txt"] = Static( conf.get( "static_robots_txt" ), cache_time )
+    urlmap["/robots.txt"] = Static( conf.get( "static_robots_txt", 'static/robots.txt'), cache_time )
     # URL mapper becomes the root webapp
     return urlmap
     

From 99c74099002abb21c1c127c297091a2e2fe439cc Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Wed, 14 Dec 2011 09:37:45 -0500
Subject: [PATCH 338/362] Update EBI SRA tool's input action.

---
 tools/data_source/ebi_sra.xml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tools/data_source/ebi_sra.xml b/tools/data_source/ebi_sra.xml
index 6009b4cf4c1..a9052faa6c9 100644
--- a/tools/data_source/ebi_sra.xml
+++ b/tools/data_source/ebi_sra.xml
@@ -1,10 +1,10 @@
 <?xml version="1.0"?>
-<tool name="EBI SRA" id="ebi_sra_main" tool_type="data_source" version="1.0.0">
+<tool name="EBI SRA" id="ebi_sra_main" tool_type="data_source" version="1.0.1">
     <description>ENA SRA</description>
     <!-- This paython script imports the file into Galaxy -->
     <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
-    <!-- The URL where Galaxy will forwars the user when this tool is accessed from the Get Data menu -->
-    <inputs action="http://www.ebi.ac.uk/ena/" check_values="false" method="get"> 
+    <!-- The URL where Galaxy will forwards the user when this tool is accessed from the Get Data menu -->
+    <inputs action="http://www.ebi.ac.uk/ena/data/search" check_values="false" method="get">
         <display>go to EBI SRA server $GALAXY_URL</display>
     </inputs>
     <uihints minwidth="800"/>

From 04ed63efb3b307a3810632994a4c570f1ac4f453 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Wed, 14 Dec 2011 10:18:43 -0500
Subject: [PATCH 339/362] 1. Add a new UpdateManager for use with tool shed
 repositories installed into a local Galaxy instance.  The UpdateManager will
 poll all appropriate tool sheds to see if updates are available for each of
 the installed repositories.  Polling occurs when the Galaxy server is
 started.  In addition, a config setting tells the UpdateManager to poll after
 the configured number of hours have passed.  If updates are available for an
 installed repository, a table column is updated, and the repository name is
 highlighted in red, alerting the Galaxy admin that updates are available for
 that repository.

2. Add a new ToolIdGuidMap grid that displays all of the mappings between tool ids whose tools used to be in the distribution and guids, which is the new tool id for tools that are installed with repositories from tool sheds.

3. Add a new column named installed_changeset_revsion to the tool_shed_repository table.  This column is set when the repository is installed and remains static thereafter.

4. Move several tool shed related components to a new ~/lib/galaxy/tool_shed directory in the code base.
---
 lib/galaxy/app.py                             |  11 +-
 lib/galaxy/config.py                          |  11 +-
 lib/galaxy/model/__init__.py                  |   3 +-
 lib/galaxy/model/mapping.py                   |   1 +
 ..._add_installed_changeset_revison_column.py |  63 +++++++++++
 lib/galaxy/tool_shed/__init__.py              |   3 +
 .../{tools => tool_shed}/install_manager.py   |   0
 .../tool_shed_registry.py                     |   0
 lib/galaxy/tool_shed/update_manager.py        |  67 +++++++++++
 lib/galaxy/util/shed_util.py                  |  40 ++++++-
 lib/galaxy/web/controllers/admin_toolshed.py  | 105 +++++++++++-------
 .../community/controllers/repository.py       |  28 ++++-
 universe_wsgi.ini.sample                      |   7 ++
 13 files changed, 281 insertions(+), 58 deletions(-)
 create mode 100644 lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py
 create mode 100644 lib/galaxy/tool_shed/__init__.py
 rename lib/galaxy/{tools => tool_shed}/install_manager.py (100%)
 rename lib/galaxy/{tools => tool_shed}/tool_shed_registry.py (100%)
 create mode 100644 lib/galaxy/tool_shed/update_manager.py

diff --git a/lib/galaxy/app.py b/lib/galaxy/app.py
index 91da12ad198..408de19658d 100644
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -3,7 +3,7 @@ import sys, os, atexit
 from galaxy import config, jobs, util, tools, web
 import galaxy.tools.search
 import galaxy.tools.data
-import galaxy.tools.tool_shed_registry
+import galaxy.tool_shed.tool_shed_registry
 from galaxy.web import security
 import galaxy.model
 import galaxy.datatypes.registry
@@ -28,7 +28,7 @@ class UniverseApplication( object ):
         galaxy.model.set_datatypes_registry( self.datatypes_registry )
         # Set up the tool sheds registry
         if os.path.isfile( self.config.tool_sheds_config ):
-            self.tool_shed_registry = galaxy.tools.tool_shed_registry.Registry( self.config.root, self.config.tool_sheds_config )
+            self.tool_shed_registry = galaxy.tool_shed.tool_shed_registry.Registry( self.config.root, self.config.tool_sheds_config )
         else:
             self.tool_shed_registry = None
         # Determine the database url
@@ -61,8 +61,13 @@ class UniverseApplication( object ):
         # If enabled, check for tools missing from the distribution because they
         # have been moved to the tool shed and install all such discovered tools.
         if self.config.get_bool( 'enable_tool_shed_install', False ):
-            from tools import install_manager
+            from tool_shed import install_manager
             self.install_manager = install_manager.InstallManager( self, self.config.tool_shed_install_config, self.config.install_tool_config )
+        # If enabled, poll respective tool sheds to see if updates are
+        # available for any installed tool shed repositories.
+        if self.config.get_bool( 'enable_tool_shed_check', False ):
+            from tool_shed import update_manager
+            self.update_manager = update_manager.UpdateManager( self )
         # Load datatype converters
         self.datatypes_registry.load_datatype_converters( self.toolbox )
         # Load history import/export tools
diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py
index eb13a62532a..7df465e839f 100644
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -47,12 +47,12 @@ class Configuration( object ):
         self.enable_openid = string_as_bool( kwargs.get( 'enable_openid', False ) )
         self.enable_quotas = string_as_bool( kwargs.get( 'enable_quotas', False ) )
         self.tool_sheds_config = kwargs.get( 'tool_sheds_config_file', 'tool_sheds_conf.xml' )
-        self.enable_unique_workflow_defaults = string_as_bool( kwargs.get ( 'enable_unique_workflow_defaults', False ) )
+        self.enable_unique_workflow_defaults = string_as_bool( kwargs.get( 'enable_unique_workflow_defaults', False ) )
         self.tool_path = resolve_path( kwargs.get( "tool_path", "tools" ), self.root )
         self.tool_data_path = resolve_path( kwargs.get( "tool_data_path", "tool-data" ), os.getcwd() )
         self.len_file_path = kwargs.get( "len_file_path", resolve_path(os.path.join(self.tool_data_path, 'shared','ucsc','chrom'), self.root) )
         self.test_conf = resolve_path( kwargs.get( "test_conf", "" ), self.root )
-        self.enable_tool_shed_install = string_as_bool( kwargs.get ( 'enable_tool_shed_install', False ) )
+        self.enable_tool_shed_install = string_as_bool( kwargs.get( 'enable_tool_shed_install', False ) )
         self.tool_shed_install_config = resolve_path( kwargs.get( "tool_shed_install_config_file", "tool_shed_install.xml" ), self.root )
         self.install_tool_config = resolve_path( kwargs.get( "install_tool_config_file", "shed_tool_conf.xml" ), self.root )
         if 'tool_config_file' in kwargs:
@@ -63,6 +63,13 @@ class Configuration( object ):
             tcf = 'tool_conf.xml'
         self.tool_configs = [ resolve_path( p, self.root ) for p in listify( tcf ) ] 
         self.tool_data_table_config_path = resolve_path( kwargs.get( 'tool_data_table_config_path', 'tool_data_table_conf.xml' ), self.root )
+        self.enable_tool_shed_check = string_as_bool( kwargs.get( 'enable_tool_shed_check', False ) )
+        try:
+            self.hours_between_check = int( kwargs.get( 'hours_between_check', 12 ) )
+            if self.hours_between_check < 1 or self.hours_between_check > 24:
+                self.hours_between_check = 12
+        except:
+            self.hours_between_check = 12
         self.tool_secret = kwargs.get( "tool_secret", "" )
         self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" )
         self.set_metadata_externally = string_as_bool( kwargs.get( "set_metadata_externally", "False" ) )
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 6f1c807b45f..2072c9156a6 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -2660,7 +2660,7 @@ class APIKeys( object ):
     pass
 
 class ToolShedRepository( object ):
-    def __init__( self, id=None, create_time=None, tool_shed=None, name=None, description=None, owner=None,
+    def __init__( self, id=None, create_time=None, tool_shed=None, name=None, description=None, owner=None, installed_changeset_revision=None,
                   changeset_revision=None, metadata=None, includes_datatypes=False, update_available=False, deleted=False ):
         self.id = id
         self.create_time = create_time
@@ -2668,6 +2668,7 @@ class ToolShedRepository( object ):
         self.name = name
         self.description = description
         self.owner = owner
+        self.installed_changeset_revision = installed_changeset_revision
         self.changeset_revision = changeset_revision
         self.metadata = metadata
         self.includes_datatypes = includes_datatypes
diff --git a/lib/galaxy/model/mapping.py b/lib/galaxy/model/mapping.py
index 699f6c1367b..3e71f0975a1 100644
--- a/lib/galaxy/model/mapping.py
+++ b/lib/galaxy/model/mapping.py
@@ -372,6 +372,7 @@ ToolShedRepository.table = Table( "tool_shed_repository", metadata,
     Column( "name", TrimmedString( 255 ), index=True ),
     Column( "description" , TEXT ),
     Column( "owner", TrimmedString( 255 ), index=True ),
+    Column( "installed_changeset_revision", TrimmedString( 255 ) ),
     Column( "changeset_revision", TrimmedString( 255 ), index=True ),
     Column( "metadata", JSONType, nullable=True ),
     Column( "includes_datatypes", Boolean, index=True, default=False ),
diff --git a/lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py b/lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py
new file mode 100644
index 00000000000..ca8c28dd1ee
--- /dev/null
+++ b/lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py
@@ -0,0 +1,63 @@
+"""
+Migration script to add the installed_changeset_revision column to the tool_shed_repository table.
+"""
+
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+from migrate.changeset import *
+
+import datetime
+now = datetime.datetime.utcnow
+# Need our custom types, but don't import anything else from model
+from galaxy.model.custom_types import *
+
+import sys, logging
+log = logging.getLogger( __name__ )
+log.setLevel(logging.DEBUG)
+handler = logging.StreamHandler( sys.stdout )
+format = "%(name)s %(levelname)s %(asctime)s %(message)s"
+formatter = logging.Formatter( format )
+handler.setFormatter( formatter )
+log.addHandler( handler )
+
+metadata = MetaData( migrate_engine )
+db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) )
+
+def upgrade():
+    print __doc__
+    metadata.reflect()
+    ToolShedRepository_table = Table( "tool_shed_repository", metadata, autoload=True )
+    col = Column( "installed_changeset_revision", TrimmedString( 255 ) )
+    try:
+        col.create( ToolShedRepository_table )
+        assert col is ToolShedRepository_table.c.installed_changeset_revision
+    except Exception, e:
+        print "Adding installed_changeset_revision column to the tool_shed_repository table failed: %s" % str( e )
+        log.debug( "Adding installed_changeset_revision column to the tool_shed_repository table failed: %s" % str( e ) )
+    # Update each row by setting the value of installed_changeset_revison to be the value of changeset_revision.
+    # This will be problematic if the value of changeset_revision was updated to something other than the value
+    # that it was when the repository was installed (because the install path determined in real time will attempt to
+    # find the repository using the updated changeset_revison instead of the required installed_changeset_revision),
+    # but at the time this script was written, this scenario is extremely unlikely.
+    cmd = "SELECT id AS id, " \
+        + "installed_changeset_revision AS installed_changeset_revision, " \
+        + "changeset_revision AS changeset_revision " \
+        + "FROM tool_shed_repository;"
+    tool_shed_repositories = db_session.execute( cmd ).fetchall()
+    update_count = 0
+    for row in tool_shed_repositories:
+        cmd = "UPDATE tool_shed_repository " \
+            + "SET installed_changeset_revision = '%s' "  % row.changeset_revision \
+            + "WHERE changeset_revision = '%s';" % row.changeset_revision
+        db_session.execute( cmd )
+        update_count += 1
+    print "Updated the installed_changeset_revision column for ", update_count, " rows in the tool_shed_repository table.  "
+def downgrade():
+    metadata.reflect()
+    ToolShedRepository_table = Table( "tool_shed_repository", metadata, autoload=True )
+    try:
+        ToolShedRepository_table.c.installed_changeset_revision.drop()
+    except Exception, e:
+        print "Dropping column installed_changeset_revision from the tool_shed_repository table failed: %s" % str( e )
+        log.debug( "Dropping column installed_changeset_revision from the tool_shed_repository table failed: %s" % str( e ) )
diff --git a/lib/galaxy/tool_shed/__init__.py b/lib/galaxy/tool_shed/__init__.py
new file mode 100644
index 00000000000..422c3577184
--- /dev/null
+++ b/lib/galaxy/tool_shed/__init__.py
@@ -0,0 +1,3 @@
+"""
+Classes encapsulating the relationships between Galaxy and Galaxy tool sheds.
+"""
\ No newline at end of file
diff --git a/lib/galaxy/tools/install_manager.py b/lib/galaxy/tool_shed/install_manager.py
similarity index 100%
rename from lib/galaxy/tools/install_manager.py
rename to lib/galaxy/tool_shed/install_manager.py
diff --git a/lib/galaxy/tools/tool_shed_registry.py b/lib/galaxy/tool_shed/tool_shed_registry.py
similarity index 100%
rename from lib/galaxy/tools/tool_shed_registry.py
rename to lib/galaxy/tool_shed/tool_shed_registry.py
diff --git a/lib/galaxy/tool_shed/update_manager.py b/lib/galaxy/tool_shed/update_manager.py
new file mode 100644
index 00000000000..f1d75471d4a
--- /dev/null
+++ b/lib/galaxy/tool_shed/update_manager.py
@@ -0,0 +1,67 @@
+"""
+Determine if installed tool shed repositories have updates available in their respective tool sheds.
+"""
+import threading, urllib2, logging
+from galaxy.util import string_as_bool
+from galaxy.util.shed_util import *
+
+log = logging.getLogger( __name__ )
+
+class UpdateManager( object ):
+    def __init__( self, app ):
+        """
+        Check tool settings in tool_shed_install_config and install all tools that are
+        not already installed.  The tool panel configuration file is the received
+        shed_tool_config, which defaults to shed_tool_conf.xml.
+        """
+        self.app = app
+        self.sa_session = self.app.model.context.current
+        # Ideally only one Galaxy server process
+        # should be able to check for repository updates.
+        self.running = True
+        self.sleeper = Sleeper()
+        self.restarter = threading.Thread( target=self.__restarter )
+        self.restarter.start()
+        self.seconds_to_sleep = app.config.hours_between_check * 3600
+    def __restarter( self ):
+        log.info( 'Update manager restarter starting up...' )
+        while self.running:
+            flush_needed = False
+            for repository in self.sa_session.query( self.app.model.ToolShedRepository ) \
+                                             .filter( and_( self.app.model.ToolShedRepository.table.c.update_available == False,
+                                                            self.app.model.ToolShedRepository.table.c.deleted == False ) ):
+                if self.check_for_update( repository ):
+                    repository.update_available = True
+                    self.sa_session.add( repository )
+                    flush_needed = True
+            if flush_needed:
+                self.sa_session.flush()
+            self.sleeper.sleep( self.seconds_to_sleep )
+        log.info( 'Transfer job restarter shutting down...' )
+    def check_for_update( self, repository ):
+        tool_shed_url = get_url_from_repository_tool_shed( self.app, repository )
+        url = '%s/repository/check_for_updates?name=%s&owner=%s&changeset_revision=%s&webapp=update_manager' % \
+            ( tool_shed_url, repository.name, repository.owner, repository.changeset_revision )
+        response = urllib2.urlopen( url )
+        text = response.read()
+        response.close()
+        return string_as_bool( text )
+    def shutdown( self ):
+        self.running = False
+        self.sleeper.wake()
+
+class Sleeper( object ):
+    """
+    Provides a 'sleep' method that sleeps for a number of seconds *unless*
+    the notify method is called (from a different thread).
+    """
+    def __init__( self ):
+        self.condition = threading.Condition()
+    def sleep( self, seconds ):
+        self.condition.acquire()
+        self.condition.wait( seconds )
+        self.condition.release()
+    def wake( self ):
+        self.condition.acquire()
+        self.condition.notify()
+        self.condition.release()
diff --git a/lib/galaxy/util/shed_util.py b/lib/galaxy/util/shed_util.py
index f699e291c43..32bb25ba663 100644
--- a/lib/galaxy/util/shed_util.py
+++ b/lib/galaxy/util/shed_util.py
@@ -65,7 +65,8 @@ def clean_tool_shed_url( tool_shed_url ):
     return tool_shed_url.rstrip( '/' )
 def clone_repository( name, clone_dir, current_working_dir, repository_clone_url ):
     log.debug( "Installing repository '%s'" % name )
-    os.makedirs( clone_dir )
+    if not os.path.exists( clone_dir ):
+        os.makedirs( clone_dir )
     log.debug( 'Cloning %s' % repository_clone_url )
     cmd = 'hg clone %s' % repository_clone_url
     tmp_name = tempfile.NamedTemporaryFile().name
@@ -88,15 +89,18 @@ def create_or_undelete_tool_shed_repository( app, name, description, changeset_r
     tool_shed_repository = get_repository_by_shed_name_owner_changeset_revision( app, tool_shed, name, owner, changeset_revision )
     if tool_shed_repository:
         if tool_shed_repository.deleted:
-            tool_shed_repository.deleted = False
-            # Reset includes_datatypes in case metadata changed since last installed.
+            tool_shed_repository.description = description
+            tool_shed_repository.changeset_revision = changeset_revision
+            tool_shed_repository.metadata = metadata_dict
             tool_shed_repository.includes_datatypes = includes_datatypes
+            tool_shed_repository.deleted = False
             flush_needed = True
     else:
         tool_shed_repository = app.model.ToolShedRepository( tool_shed=tool_shed,
                                                              name=name,
                                                              description=description,
                                                              owner=owner,
+                                                             installed_changeset_revision=changeset_revision,
                                                              changeset_revision=changeset_revision,
                                                              metadata=metadata_dict,
                                                              includes_datatypes=includes_datatypes )
@@ -318,6 +322,20 @@ def get_tool_id_guid_map( app, tool_id, version, tool_shed, repository_owner, re
                                     app.model.ToolIdGuidMap.table.c.repository_owner == repository_owner,
                                     app.model.ToolIdGuidMap.table.c.repository_name == repository_name ) ) \
                      .first()
+def get_url_from_repository_tool_shed( app, repository ):
+    """
+    This method is used by the UpdateManager, which does not have access to trans.
+    The stored value of repository.tool_shed is something like: toolshed.g2.bx.psu.edu
+    We need the URL to this tool shed, which is something like: http://toolshed.g2.bx.psu.edu/
+    """
+    for shed_name, shed_url in app.tool_shed_registry.tool_sheds.items():
+        if shed_url.find( repository.tool_shed ) >= 0:
+            if shed_url.endswith( '/' ):
+                shed_url = shed_url.rstrip( '/' )
+            return shed_url
+    # The tool shed from which the repository was originally
+    # installed must no longer be configured in tool_sheds_conf.xml.
+    return None
 def handle_missing_data_table_entry( app, tool_path, sample_files, repository_tools_tups ):
     """
     Inspect each tool to see if any have input parameters that are dynamically
@@ -532,7 +550,19 @@ def pretty_print_xml( elem, level=0 ):
         if level and ( not elem.tail or not elem.tail.strip() ):
             elem.tail = i + pad
     return elem
-def update_repository( current_working_dir, relative_install_dir, changeset_revision ):
+def pull_repository( current_working_dir, repo_files_dir, name ):
+    # Pull the latest possible contents to the repository.
+    log.debug( "Pulling latest updates to the repository named '%s'" % name )
+    cmd = 'hg pull'
+    tmp_name = tempfile.NamedTemporaryFile().name
+    tmp_stderr = open( tmp_name, 'wb' )
+    os.chdir( repo_files_dir )
+    proc = subprocess.Popen( cmd, shell=True, stderr=tmp_stderr.fileno() )
+    returncode = proc.wait()
+    os.chdir( current_working_dir )
+    tmp_stderr.close()
+    return returncode, tmp_name
+def update_repository( current_working_dir, repo_files_dir, changeset_revision ):
     # Update the cloned repository to changeset_revision.  It is imperative that the 
     # installed repository is updated to the desired changeset_revision before metadata
     # is set because the process for setting metadata uses the repository files on disk.
@@ -540,7 +570,7 @@ def update_repository( current_working_dir, relative_install_dir, changeset_revi
     cmd = 'hg update -r %s' % changeset_revision
     tmp_name = tempfile.NamedTemporaryFile().name
     tmp_stderr = open( tmp_name, 'wb' )
-    os.chdir( relative_install_dir )
+    os.chdir( repo_files_dir )
     proc = subprocess.Popen( cmd, shell=True, stderr=tmp_stderr.fileno() )
     returncode = proc.wait()
     os.chdir( current_working_dir )
diff --git a/lib/galaxy/web/controllers/admin_toolshed.py b/lib/galaxy/web/controllers/admin_toolshed.py
index 816a8228b4e..94c5e280c2c 100644
--- a/lib/galaxy/web/controllers/admin_toolshed.py
+++ b/lib/galaxy/web/controllers/admin_toolshed.py
@@ -3,6 +3,55 @@ from galaxy.util.shed_util import *
 
 log = logging.getLogger( __name__ )
 
+class ToolIdGuidMapGrid( grids.Grid ):
+    class ToolIdColumn( grids.TextColumn ):
+        def get_value( self, trans, grid, tool_id_guid_map ):
+            return tool_id_guid_map.tool_id
+    class ToolVersionColumn( grids.TextColumn ):
+        def get_value( self, trans, grid, tool_id_guid_map ):
+            return tool_id_guid_map.tool_version
+    class ToolGuidColumn( grids.TextColumn ):
+        def get_value( self, trans, grid, tool_id_guid_map ):
+            return tool_id_guid_map.guid
+    class ToolShedColumn( grids.TextColumn ):
+        def get_value( self, trans, grid, tool_id_guid_map ):
+            return tool_id_guid_map.tool_shed
+    class RepositoryNameColumn( grids.TextColumn ):
+        def get_value( self, trans, grid, tool_id_guid_map ):
+            return tool_id_guid_map.repository_name
+    class RepositoryOwnerColumn( grids.TextColumn ):
+        def get_value( self, trans, grid, tool_id_guid_map ):
+            return tool_id_guid_map.repository_owner
+    # Grid definition
+    title = "Map tool id to guid"
+    model_class = model.ToolIdGuidMap
+    template='/admin/tool_shed_repository/grid.mako'
+    default_sort_key = "tool_id"
+    columns = [
+        ToolIdColumn( "Tool id" ),
+        ToolVersionColumn( "Version" ),
+        ToolGuidColumn( "Guid" ),
+        ToolShedColumn( "Tool shed" ),
+        RepositoryNameColumn( "Repository name" ),
+        RepositoryOwnerColumn( "Repository owner" )
+    ]
+    columns.append( grids.MulticolFilterColumn( "Search repository name", 
+                                                cols_to_filter=[ columns[0], columns[2], columns[4], columns[5] ],
+                                                key="free-text-search",
+                                                visible=False,
+                                                filterable="standard" ) )
+    global_actions = [
+        grids.GridAction( "Manage installed tool shed repositories", dict( controller='admin_toolshed', action='browse_repositories' ) )
+    ]
+    operations = []
+    standard_filters = []
+    default_filter = {}
+    num_rows_per_page = 50
+    preserve_state = False
+    use_paging = True
+    def build_initial_query( self, trans, **kwd ):
+        return trans.sa_session.query( self.model_class )
+
 class RepositoryListGrid( grids.Grid ):
     class NameColumn( grids.TextColumn ):
         def get_value( self, trans, grid, tool_shed_repository ):
@@ -46,6 +95,9 @@ class RepositoryListGrid( grids.Grid ):
                                                 key="free-text-search",
                                                 visible=False,
                                                 filterable="standard" ) )
+    global_actions = [
+        grids.GridAction( "View tool id guid map", dict( controller='admin_toolshed', action='browse_tool_id_guid_map' ) )
+    ]
     operations = [ grids.GridOperation( "Get updates",
                                         allow_multiple=False,
                                         condition=( lambda item: not item.deleted ),
@@ -62,7 +114,12 @@ class RepositoryListGrid( grids.Grid ):
 class AdminToolshed( AdminGalaxy ):
     
     repository_list_grid = RepositoryListGrid()
+    tool_id_guid_map_grid = ToolIdGuidMapGrid()
 
+    @web.expose
+    @web.require_admin
+    def browse_tool_id_guid_map( self, trans, **kwd ):
+        return self.tool_id_guid_map_grid( trans, **kwd )
     @web.expose
     @web.require_admin
     def browse_repository( self, trans, **kwd ):
@@ -272,7 +329,7 @@ class AdminToolshed( AdminGalaxy ):
     def check_for_updates( self, trans, **kwd ):
         # Send a request to the relevant tool shed to see if there are any updates.
         repository = get_repository( trans, kwd[ 'id' ] )
-        tool_shed_url = get_url_from_repository_tool_shed( trans, repository )
+        tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository )
         url = '%s/repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \
             ( tool_shed_url, url_for( '', qualified=True ), repository.name, repository.owner, repository.changeset_revision )
         return trans.response.send_redirect( url )
@@ -296,30 +353,14 @@ class AdminToolshed( AdminGalaxy ):
                 current_working_dir = os.getcwd()
                 relative_install_dir = self.__get_relative_install_dir( trans, repository )
                 if relative_install_dir:
-                    # Update the cloned repository to changeset_revision.
                     repo_files_dir = os.path.join( relative_install_dir, name )
-                    log.debug( "Updating cloned repository named '%s' from revision '%s' to revision '%s'..." % \
-                        ( name, changeset_revision, latest_changeset_revision ) )
-                    cmd = 'hg pull'
-                    tmp_name = tempfile.NamedTemporaryFile().name
-                    tmp_stderr = open( tmp_name, 'wb' )
-                    os.chdir( repo_files_dir )
-                    proc = subprocess.Popen( cmd, shell=True, stderr=tmp_stderr.fileno() )
-                    returncode = proc.wait()
-                    os.chdir( current_working_dir )
-                    tmp_stderr.close()
+                    returncode, tmp_name = pull_repository( current_working_dir, repo_files_dir, name )
                     if returncode == 0:
-                        cmd = 'hg update -r %s' % latest_changeset_revision
-                        tmp_name = tempfile.NamedTemporaryFile().name
-                        tmp_stderr = open( tmp_name, 'wb' )
-                        os.chdir( repo_files_dir )
-                        proc = subprocess.Popen( cmd, shell=True, stderr=tmp_stderr.fileno() )
-                        returncode = proc.wait()
-                        os.chdir( current_working_dir )
-                        tmp_stderr.close()
+                        returncode, tmp_name = update_repository( current_working_dir, repo_files_dir, latest_changeset_revision )
                         if returncode == 0:
                             # Update the repository changeset_revision in the database.
                             repository.changeset_revision = latest_changeset_revision
+                            repository.update_available = False
                             trans.sa_session.add( repository )
                             trans.sa_session.flush()
                             message = "The cloned repository named '%s' has been updated to change set revision '%s'." % \
@@ -370,7 +411,7 @@ class AdminToolshed( AdminGalaxy ):
     def __get_relative_install_dir( self, trans, repository ):
         # Get the directory where the repository is install.
         tool_shed = clean_tool_shed_url( repository.tool_shed )
-        partial_install_dir = '%s/repos/%s/%s/%s' % ( tool_shed, repository.owner, repository.name, repository.changeset_revision )
+        partial_install_dir = '%s/repos/%s/%s/%s' % ( tool_shed, repository.owner, repository.name, repository.installed_changeset_revision )
         # Get the relative tool installation paths from each of the shed tool configs.
         shed_tool_confs = trans.app.toolbox.shed_tool_confs
         relative_install_dir = None
@@ -396,7 +437,7 @@ class AdminToolshed( AdminGalaxy ):
         return '%s/repos%s/%s' % ( tool_shed_url, repo_path, changeset_revision )
     def __generate_clone_url( self, trans, repository ):
         """Generate the URL for cloning a repository."""
-        tool_shed_url = get_url_from_repository_tool_shed( trans, repository )
+        tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository )
         return '%s/repos/%s/%s' % ( tool_shed_url, repository.owner, repository.name )
 
 ## ---- Utility methods -------------------------------------------------------
@@ -426,23 +467,3 @@ def build_tool_panel_section_select_field( trans ):
 def get_repository( trans, id ):
     """Get a tool_shed_repository from the database via id"""
     return trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) )
-def get_repository_by_name_owner_changeset_revision( trans, name, owner, changeset_revision ):
-    """Get a repository from the database via name owner and changeset_revision"""
-    return trans.sa_session.query( trans.model.ToolShedRepository ) \
-                             .filter( and_( trans.model.ToolShedRepository.table.c.name == name,
-                                            trans.model.ToolShedRepository.table.c.owner == owner,
-                                            trans.model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \
-                             .first()
-def get_url_from_repository_tool_shed( trans, repository ):
-    # The stored value of repository.tool_shed is something like:
-    # toolshed.g2.bx.psu.edu
-    # We need the URL to this tool shed, which is something like:
-    # http://toolshed.g2.bx.psu.edu/
-    for shed_name, shed_url in trans.app.tool_shed_registry.tool_sheds.items():
-        if shed_url.find( repository.tool_shed ) >= 0:
-            if shed_url.endswith( '/' ):
-                shed_url = shed_url.rstrip( '/' )
-            return shed_url
-    # The tool shed from which the repository was originally
-    # installed must no longer be configured in tool_sheds_conf.xml.
-    return None
diff --git a/lib/galaxy/webapps/community/controllers/repository.py b/lib/galaxy/webapps/community/controllers/repository.py
index a08b14ac597..43712752bda 100644
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -764,22 +764,32 @@ class RepositoryController( BaseUIController, ItemRatings ):
         return trans.response.send_redirect( url )
     @web.expose
     def check_for_updates( self, trans, **kwd ):
+        # Handle a request from a local Galaxy instance.  If the request originated with the
+        # Galaxy instances' UpdateManager, the value of 'webapp' will be 'update_manager'.
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
-        galaxy_url = kwd[ 'galaxy_url' ]
+        # If the request originated with the UpdateManager, it will not include a galaxy_url.
+        galaxy_url = kwd.get( 'galaxy_url', '' )
         name = params.get( 'name', None )
         owner = params.get( 'owner', None )
         changeset_revision = params.get( 'changeset_revision', None )
         webapp = params.get( 'webapp', 'community' )
-        # Start building up the url to redirect back to the calling Galaxy instance.
-        url = '%s/admin_toolshed/update_to_changeset_revision?tool_shed_url=%s' % ( galaxy_url, url_for( '', qualified=True ) )
         repository = get_repository_by_name_and_owner( trans, name, owner )
-        url += '&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % \
-            ( repository.name, repository.user.username, changeset_revision )
+        from_update_manager = webapp == 'update_manager'
+        if from_update_manager:
+            update = 'true'
+            no_update = 'false'
+        else:
+            # Start building up the url to redirect back to the calling Galaxy instance.
+            url = '%s/admin_toolshed/update_to_changeset_revision?tool_shed_url=%s' % ( galaxy_url, url_for( '', qualified=True ) )
+            url += '&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % \
+                ( repository.name, repository.user.username, changeset_revision )
         if changeset_revision == repository.tip:
             # If changeset_revision is the repository tip, then
             # we know there are no additional updates for the tools.
+            if from_update_manager:
+                return no_update
             url += repository.tip
         else:
             repository_metadata = get_repository_metadata_by_changeset_revision( trans, 
@@ -788,6 +798,8 @@ class RepositoryController( BaseUIController, ItemRatings ):
             if repository_metadata:
                 # If changeset_revision is in the repository_metadata table for this
                 # repository, then we know there are no additional updates for the tools.
+                if from_update_manager:
+                    return no_update
                 url += changeset_revision
             else:
                 # The changeset_revision column in the repository_metadata table has been
@@ -836,15 +848,21 @@ class RepositoryController( BaseUIController, ItemRatings ):
                             if tool_guids == metadata_tool_guids:
                                 # We've found the repository_metadata record whose changeset_revision
                                 # value has been updated.
+                                if from_update_manager:
+                                    return update
                                 url += repository_metadata.changeset_revision
                                 found = True
                                 break
                         if not found:
                             # There must be a problem in the data, so we'll just send back the received changeset_revision.
                             log.debug( "Possible data corruption - updated repository_metadata cannot be found for repository id %d." % repository.id )
+                            if from_update_manager:
+                                return no_update
                             url += changeset_revision
                     else:
                         # There are not tools in the changeset_revision, so no tool updates are possible.
+                        if from_update_manager:
+                            return no_update
                         url += changeset_revision
         return trans.response.send_redirect( url )
     @web.expose
diff --git a/universe_wsgi.ini.sample b/universe_wsgi.ini.sample
index eea8a875f31..5995273c374 100644
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -147,6 +147,13 @@ paste.app_factory = galaxy.web.buildapp:app_factory
 # if appropriate or use a different file name for the setting.
 #install_tool_config_file = shed_tool_conf.xml
 
+# Enable automatic polling of relative tool sheds to see if any updates
+# are available for installed repositories.  Ideally only one Galaxy 
+# server process should be able to check for repository updates.  The
+# setting for hours_between_check should be an integer between 1 and 24.
+#enable_tool_shed_check = False
+#hours_between_check = 12
+
 # Directory where data used by tools is located, see the samples in that
 # directory and the wiki for help:
 # http://wiki.g2.bx.psu.edu/Admin/Data%20Integration

From a5e1ef2b6ea193ca5cc890f2265af8fca9a59e8c Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Wed, 14 Dec 2011 15:25:03 -0500
Subject: [PATCH 340/362] Trackster: small fixes so that ReferenceTracks are
 compatible with changes in 09c6c980e463

---
 static/scripts/trackster.js | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index aac82f6c5bb..6e639091813 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -3017,7 +3017,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
         var all_tiles_drawn = true;
         var drawn_tiles = [];
         var tile_count = 0;
-        var is_tile = function(o) { return ('track' in o) };
+        var is_tile = function(o) { return (o && 'track' in o) };
         // Draw or fetch and show tiles.
         while ( ( tile_index * DENSITY * resolution ) < high ) {
             var draw_result = this.draw_helper( force, width, tile_index, resolution, parent_element, w_scale );
@@ -3116,7 +3116,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
                 tile_bounds = track._get_tile_bounds(tile_index, resolution),
                 tile_low = tile_bounds[0],
                 tile_high = tile_bounds[1],
-                width = Math.ceil( (tile_high - tile_low) * w_scale ),
+                width = Math.ceil( (tile_high - tile_low) * w_scale ) + track.left_offset,
                 height = track.get_canvas_height(tile_data);
             
             canvas.width = width;
@@ -3483,17 +3483,14 @@ extend(ReferenceTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
      * Draw ReferenceTrack tile.
      */
     draw_tile: function(seq, canvas, mode, resolution, tile_index, w_scale) {
-        var track = this,
-            tile_length = DENSITY * resolution;
+        var track = this;
         
         if (w_scale > this.view.canvas_manager.char_width_px) {
             if (seq.data === null) {
                 track.content_div.css("height", "0px");
                 return;
             }
-            var ctx = canvas.getContext("2d");
-            canvas.width = Math.ceil(tile_length * w_scale + track.left_offset);
-            canvas.height = track.height_px;
+            var ctx = canvas.getContext("2d");            
             ctx.font = ctx.canvas.manager.default_font;
             ctx.textAlign = "center";
             seq = seq.data;

From c18c8a1901062742b644eb720dfe51af93d7c4b2 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Wed, 14 Dec 2011 17:36:18 -0500
Subject: [PATCH 341/362] Trackster: make FeatureTracks compatible with
 09c6c980e463 in preparation for enabling FeatureTracks in composite tracks.

---
 static/scripts/trackster.js | 134 ++++++++++++++++++++----------------
 1 file changed, 74 insertions(+), 60 deletions(-)

diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index 6e639091813..e49f9ff25f7 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -3111,17 +3111,27 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
         if ( can_draw_now ) {
             // Set up and draw tile.
             extend(tile_data, more_tile_data);
+            
+            // HACK: this is FeatureTrack-specific.
+            // If track mode is Auto, determine mode and update.
+            var mode = track.mode;
+            if (mode === "Auto") {
+                mode = track.get_mode(tile_data);
+                track.update_auto_mode(mode);
+            }
+            
+            // Draw canvas.
             var 
                 canvas = track.view.canvas_manager.new_canvas(),
                 tile_bounds = track._get_tile_bounds(tile_index, resolution),
                 tile_low = tile_bounds[0],
                 tile_high = tile_bounds[1],
                 width = Math.ceil( (tile_high - tile_low) * w_scale ) + track.left_offset,
-                height = track.get_canvas_height(tile_data);
+                height = track.get_canvas_height(tile_data, mode, w_scale, width);
             
             canvas.width = width;
             canvas.height = height;
-            var tile = track.draw_tile(tile_data, canvas, track.mode, resolution, tile_index, w_scale, seq_data);
+            var tile = track.draw_tile(tile_data, canvas, mode, resolution, tile_index, w_scale, seq_data);
             
             // Don't cache, show if no tile.
             if (tile !== undefined) {
@@ -3145,7 +3155,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
      * Returns canvas height needed to display data; return value is an integer that denotes the
      * number of pixels required.
      */
-    get_canvas_height: function(data) {
+    get_canvas_height: function(result, mode, w_scale, canvas_width) {
         return this.height_px;
     },
     /**
@@ -3416,13 +3426,14 @@ extend(CompositeTrack.prototype, TiledTrack.prototype, {
         if ( can_draw_now ) {
             // Set up and draw tile.
             extend(tile_data, more_tile_data);
+            
             var 
                 canvas = track.view.canvas_manager.new_canvas(),
                 tile_bounds = track._get_tile_bounds(tile_index, resolution),
                 tile_low = tile_bounds[0],
                 tile_high = tile_bounds[1],
                 width = Math.ceil( (tile_high - tile_low) * w_scale ),
-                height = track.get_canvas_height(tile_data);
+                height = track.get_canvas_height(tile_data, mode, w_scale, width);
             
             // FIXME: 
             // (a) right now, only LineTracks respect width/height setting and do not set it in draw_tile; 
@@ -3913,6 +3924,58 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
         }
         return {max: max_count, delta: bin_size, data: bins};
     },
+    /**
+     * Returns appropriate display mode based on data.
+     */
+    get_mode: function(data) {
+        if (data.dataset_type === "summary_tree") {
+            mode = "summary_tree";
+        } 
+        // HACK: use no_detail mode track is in overview to prevent overview from being too large.
+        else if (data.extra_info === "no_detail" || this.is_overview) {
+            mode = "no_detail";
+        } 
+        else {
+            // Choose b/t Squish and Pack.
+            // Proxy measures for using Squish: 
+            // (a) error message re: limiting number of features shown; 
+            // (b) X number of features shown;
+            // (c) size of view shown.
+            // TODO: cannot use (a) and (b) because it requires coordinating mode across tiles;
+            // fix this so that tiles are redrawn as necessary to use the same mode.
+            //if ( (result.message && result.message.match(/^Only the first [\d]+/)) ||
+            //     (result.data && result.data.length > 2000) ||
+            //var data = result.data;
+            // if ( (data.length && data.length < 4) ||
+            //      (this.view.high - this.view.low > MIN_SQUISH_VIEW_WIDTH) ) {
+            if ( this.view.high - this.view.low > MIN_SQUISH_VIEW_WIDTH ) {
+                mode = "Squish";
+            } else {
+                mode = "Pack";
+            }
+        }
+        return mode;
+    },
+    /**
+     * Returns canvas height needed to display data; return value is an integer that denotes the
+     * number of pixels required.
+     */
+    get_canvas_height: function(result, mode, w_scale, canvas_width) {
+        if (mode === "summary_tree" || mode === "Histogram") {
+            // Extra padding at top of summary tree so label does not overlap data.
+            return this.summary_draw_height + SUMMARY_TREE_TOP_PADDING;
+        }
+        else {
+            var rows_required = 1;
+            if (mode === "no_detail" || mode === "Squish" || mode === "Pack") {
+                var rows_required = this.incremental_slots(w_scale, result.data, mode);
+            }
+            // HACK: use dummy painter to get required height. Painter should be extended so that get_required_height
+            // works as a static function.
+            var dummy_painter = new (this.painter)(null, null, null, this.prefs, mode);
+            return Math.max(MIN_TRACK_HEIGHT, dummy_painter.get_required_height(rows_required, canvas_width) );
+        }
+    },
     /**
      * Draw FeatureTrack tile.
      * @param result result from server
@@ -3925,50 +3988,14 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
      */
     draw_tile: function(result, canvas, mode, resolution, tile_index, w_scale, ref_seq) {
         var track = this,
-            tile_bounds = track._get_tile_bounds(tile_index, resolution),
+            tile_bounds = this._get_tile_bounds(tile_index, resolution),
             tile_low = tile_bounds[0],
             tile_high = tile_bounds[1],
-            tile_span = tile_high - tile_low,
-            width = Math.ceil(tile_span * w_scale),
             min_height = 25,
-            left_offset = this.left_offset,
-            slots,
-            required_height;
-            
-        // Set display mode if Auto.
-        if (mode === "Auto") {
-            if (result.dataset_type === "summary_tree") {
-                mode = result.dataset_type;
-            } 
-            // HACK: use no_detail mode track is in overview to prevent overview from being too large.
-            else if (result.extra_info === "no_detail" || track.is_overview) {
-                mode = "no_detail";
-            } 
-            else {
-                // Choose b/t Squish and Pack.
-                // Proxy measures for using Squish: 
-                // (a) error message re: limiting number of features shown; 
-                // (b) X number of features shown;
-                // (c) size of view shown.
-                // TODO: cannot use (a) and (b) because it requires coordinating mode across tiles;
-                // fix this so that tiles are redrawn as necessary to use the same mode.
-                //if ( (result.message && result.message.match(/^Only the first [\d]+/)) ||
-                //     (result.data && result.data.length > 2000) ||
-                var data = result.data;
-                // if ( (data.length && data.length < 4) ||
-                //      (this.view.high - this.view.low > MIN_SQUISH_VIEW_WIDTH) ) {
-                if ( this.view.high - this.view.low > MIN_SQUISH_VIEW_WIDTH ) {
-                    mode = "Squish";
-                } else {
-                    mode = "Pack";
-                }
-            }
-            this.update_auto_mode( mode );
-        }
+            left_offset = this.left_offset;
         
         // Drawing the summary tree (feature coverage histogram)
         if (mode === "summary_tree" || mode === "Histogram") {
-            required_height = this.summary_draw_height;
             // Add label to container div showing maximum count
             // TODO: this shouldn't be done at the tile level
             this.container_div.find(".yaxislabel").remove();
@@ -3976,9 +4003,6 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
             max_label.text(result.max);
             max_label.css({ position: "absolute", top: "24px", left: "10px", color: this.prefs.label_color });
             max_label.prependTo(this.container_div);
-            canvas.width = width + left_offset;
-            // Extra padding at top of summary tree
-            canvas.height = required_height + SUMMARY_TREE_TOP_PADDING;
             
             // Get summary tree data if necessary and set max if there is one.
             if (result.dataset_type != "summary_tree") {
@@ -3993,18 +4017,11 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
             var ctx = canvas.getContext("2d");
             // Deal with left_offset by translating.
             ctx.translate(left_offset, SUMMARY_TREE_TOP_PADDING);
-            painter.draw(ctx, width, required_height);
+            painter.draw(ctx, canvas.width, canvas.height);
             return new SummaryTreeTile(track, tile_index, resolution, canvas, result.data, result.max);
         }
 
-        // Start dealing with row-by-row tracks
-        
-        // If working with a mode where slotting is necessary, update the incremental slotting
-        var slots, slots_required = 1;
-        if ( mode === "no_detail" || mode === "Squish" || mode === "Pack" ) {
-            slots_required = this.incremental_slots(w_scale, result.data, mode);
-            slots = this.inc_slots[w_scale].slots;
-        }
+        // Handle row-by-row tracks
 
         // Filter features.
         var filtered = [];
@@ -4028,16 +4045,12 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
             }
         }        
         
-        // Create painter, and canvas of sufficient size to contain all features.
+        // Create painter.
         var filter_alpha_scaler = (this.filters_manager.alpha_filter ? new FilterScaler(this.filters_manager.alpha_filter) : null);
         var filter_height_scaler = (this.filters_manager.height_filter ? new FilterScaler(this.filters_manager.height_filter) : null);
         // HACK: ref_seq will only be defined for ReadTracks, and only the ReadPainter accepts that argument
         var painter = new (this.painter)(filtered, tile_low, tile_high, this.prefs, mode, filter_alpha_scaler, filter_height_scaler, ref_seq);
-        var required_height = Math.max(MIN_TRACK_HEIGHT, painter.get_required_height(slots_required,width));
         var feature_mapper = null;
-        
-        canvas.width = width + left_offset;
-        canvas.height = required_height;
 
         // console.log(( tile_low - this.view.low ) * w_scale, tile_index, w_scale);
         var ctx = canvas.getContext("2d");
@@ -4048,8 +4061,9 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
         
         if (result.data) {
             // Draw features.
+            slots = this.inc_slots[w_scale].slots;
             ctx.translate(left_offset, 0);
-            feature_mapper = painter.draw(ctx, width, required_height, slots);
+            feature_mapper = painter.draw(ctx, canvas.width, canvas.height, slots);
             feature_mapper.translation = -left_offset;
         }
         

From 9be08bebdd8634adeb6465a81e8db28b7ff946f2 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Thu, 15 Dec 2011 10:49:40 -0500
Subject: [PATCH 342/362] Reset repository metadata for installed tool shed
 repositories when a new update to the repository contents has been pulled
 from the tool shed.

---
 lib/galaxy/tool_shed/install_manager.py      | 25 +++---
 lib/galaxy/util/shed_util.py                 | 87 ++++++++++----------
 lib/galaxy/web/controllers/admin_toolshed.py | 51 ++++++++----
 3 files changed, 89 insertions(+), 74 deletions(-)

diff --git a/lib/galaxy/tool_shed/install_manager.py b/lib/galaxy/tool_shed/install_manager.py
index d0fc86df465..1f182f98c7c 100644
--- a/lib/galaxy/tool_shed/install_manager.py
+++ b/lib/galaxy/tool_shed/install_manager.py
@@ -73,18 +73,19 @@ class InstallManager( object ):
             if returncode == 0:
                 returncode, tmp_name = update_repository( current_working_dir, relative_install_dir, changeset_revision )
                 if returncode == 0:
-                    metadata_dict = load_repository_contents( self.app,
-                                                              name,
-                                                              description,
-                                                              self.repository_owner,
-                                                              changeset_revision,
-                                                              repository_clone_url,
-                                                              self.install_tool_config, 
-                                                              self.tool_path,
-                                                              tool_section,
-                                                              relative_install_dir,
-                                                              current_working_dir,
-                                                              tmp_name )
+                    metadata_dict = load_repository_contents( app=self.app,
+                                                              name=name,
+                                                              description=description,
+                                                              owner=self.repository_owner,
+                                                              changeset_revision=changeset_revision,
+                                                              tool_path=self.tool_path,
+                                                              repository_clone_url=repository_clone_url,
+                                                              relative_install_dir=relative_install_dir,
+                                                              current_working_dir=current_working_dir,
+                                                              tmp_name=tmp_name,
+                                                              tool_section=tool_section,
+                                                              shed_tool_conf=self.install_tool_config,
+                                                              new_install=True )
                     # Add a new record to the tool_id_guid_map table for each
                     # tool in the repository if one doesn't already exist.
                     if 'tools' in metadata_dict:
diff --git a/lib/galaxy/util/shed_util.py b/lib/galaxy/util/shed_util.py
index 32bb25ba663..1ac108ab04c 100644
--- a/lib/galaxy/util/shed_util.py
+++ b/lib/galaxy/util/shed_util.py
@@ -2,6 +2,7 @@ import os, tempfile, shutil, subprocess, logging
 from datetime import date, datetime, timedelta
 from time import strftime
 from galaxy import util
+from galaxy.util.json import *
 from galaxy.tools import ToolSection
 from galaxy.tools.search import ToolBoxSearch
 from galaxy.model.orm import *
@@ -77,7 +78,7 @@ def clone_repository( name, clone_dir, current_working_dir, repository_clone_url
     os.chdir( current_working_dir )
     tmp_stderr.close()
     return returncode, tmp_name
-def create_or_undelete_tool_shed_repository( app, name, description, changeset_revision, repository_clone_url, metadata_dict, owner='' ):
+def create_or_update_tool_shed_repository( app, name, description, changeset_revision, repository_clone_url, metadata_dict, owner='' ):
     # This method is used by the InstallManager, which does not have access to trans.
     sa_session = app.model.context.current
     tmp_url = clean_repository_clone_url( repository_clone_url )
@@ -85,16 +86,13 @@ def create_or_undelete_tool_shed_repository( app, name, description, changeset_r
     if not owner:
         owner = get_repository_owner( tmp_url )
     includes_datatypes = 'datatypes_config' in metadata_dict
-    flush_needed = False
     tool_shed_repository = get_repository_by_shed_name_owner_changeset_revision( app, tool_shed, name, owner, changeset_revision )
     if tool_shed_repository:
-        if tool_shed_repository.deleted:
-            tool_shed_repository.description = description
-            tool_shed_repository.changeset_revision = changeset_revision
-            tool_shed_repository.metadata = metadata_dict
-            tool_shed_repository.includes_datatypes = includes_datatypes
-            tool_shed_repository.deleted = False
-            flush_needed = True
+        tool_shed_repository.description = description
+        tool_shed_repository.changeset_revision = changeset_revision
+        tool_shed_repository.metadata = metadata_dict
+        tool_shed_repository.includes_datatypes = includes_datatypes
+        tool_shed_repository.deleted = False
     else:
         tool_shed_repository = app.model.ToolShedRepository( tool_shed=tool_shed,
                                                              name=name,
@@ -104,10 +102,8 @@ def create_or_undelete_tool_shed_repository( app, name, description, changeset_r
                                                              changeset_revision=changeset_revision,
                                                              metadata=metadata_dict,
                                                              includes_datatypes=includes_datatypes )
-        flush_needed = True
-    if flush_needed:
-        sa_session.add( tool_shed_repository )
-        sa_session.flush()
+    sa_session.add( tool_shed_repository )
+    sa_session.flush()
 def generate_datatypes_metadata( datatypes_config, metadata_dict ):
     """
     Update the received metadata_dict with changes that have been applied
@@ -471,12 +467,17 @@ def load_datatypes( app, datatypes_config, relative_intall_dir ):
         except Exception, e:
             log.debug( "Exception importing datatypes code file included in installed repository: %s" % str( e ) )
     app.datatypes_registry.load_datatypes( root_dir=app.config.root, config=datatypes_config, imported_module=imported_module )
-def load_repository_contents( app, name, description, owner, changeset_revision, repository_clone_url, shed_tool_conf, 
-                              tool_path, tool_section, relative_install_dir, current_working_dir, tmp_name ):
+def load_repository_contents( app, name, description, owner, changeset_revision, tool_path, repository_clone_url, relative_install_dir,
+                              current_working_dir, tmp_name, tool_section=None, shed_tool_conf=None, new_install=True ):
     # This method is used by the InstallManager, which does not have access to trans.
     # Generate the metadata for the installed tool shed repository.  It is imperative that
     # the installed repository is updated to the desired changeset_revision before metadata
-    # is set because the process for setting metadata uses the repository files on disk.
+    # is set because the process for setting metadata uses the repository files on disk.  This
+    # method is called when new tools have been installed (in which case values should be received
+    # for tool_section and shed_tool_conf, and new_install should be left at it's default value)
+    # and when updates have been pulled to previously installed repositories (in which case the
+    # default value None is set for tool_section and shed_tool_conf, and the value of new_install
+    # is passed as False).
     metadata_dict = generate_metadata( app.toolbox, relative_install_dir, repository_clone_url )
     if 'datatypes_config' in metadata_dict:
         datatypes_config = os.path.abspath( metadata_dict[ 'datatypes_config' ] )
@@ -497,42 +498,38 @@ def load_repository_contents( app, name, description, owner, changeset_revision,
             repository_tools_tups = handle_missing_index_file( app, tool_path, sample_files, repository_tools_tups )
             # Handle tools that use fabric scripts to install dependencies.
             handle_tool_dependencies( current_working_dir, relative_install_dir, repository_tools_tups )
-            # Generate a new entry for the tool config.
-            elem_list = generate_tool_panel_elem_list( name,
-                                                       repository_clone_url,
-                                                       changeset_revision,
-                                                       repository_tools_tups,
-                                                       tool_section=tool_section,
-                                                       owner=owner )
-            if tool_section:
-                for section_elem in elem_list:
-                    # Load the section into the tool panel.
-                    app.toolbox.load_section_tag_set( section_elem, app.toolbox.tool_panel, tool_path )
-            else:
-                # Load the tools into the tool panel outside of any sections.
-                for tool_elem in elem_list:
-                    guid = tool_elem.get( 'guid' )
-                    app.toolbox.load_tool_tag_set( tool_elem, app.toolbox.tool_panel, tool_path=tool_path, guid=guid )
+            if new_install:
+                # Generate a new entry for the tool config.
+                elem_list = generate_tool_panel_elem_list( name,
+                                                           repository_clone_url,
+                                                           changeset_revision,
+                                                           repository_tools_tups,
+                                                           tool_section=tool_section,
+                                                           owner=owner )
+                if tool_section:
+                    for section_elem in elem_list:
+                        # Load the section into the tool panel.
+                        app.toolbox.load_section_tag_set( section_elem, app.toolbox.tool_panel, tool_path )
+                else:
+                    # Load the tools into the tool panel outside of any sections.
+                    for tool_elem in elem_list:
+                        guid = tool_elem.get( 'guid' )
+                        app.toolbox.load_tool_tag_set( tool_elem, app.toolbox.tool_panel, tool_path=tool_path, guid=guid )
+                for elem_entry in elem_list:
+                    # Append the new entry (either section or list of tools) to the shed_tool_config file.
+                    add_shed_tool_conf_entry( app, shed_tool_conf, elem_entry )
+            if app.toolbox_search.enabled:
+                # If search support for tools is enabled, index the new installed tools.
+                app.toolbox_search = ToolBoxSearch( app.toolbox )
             # Remove the temporary file
             try:
                 os.unlink( tmp_name )
             except:
                 pass
-            for elem_entry in elem_list:
-                # Append the new entry (either section or list of tools) to the shed_tool_config file.
-                add_shed_tool_conf_entry( app, shed_tool_conf, elem_entry )
-            if app.toolbox_search.enabled:
-                # If search support for tools is enabled, index the new installed tools.
-                app.toolbox_search = ToolBoxSearch( app.toolbox )
     # Add a new record to the tool_shed_repository table if one doesn't
     # already exist.  If one exists but is marked deleted, undelete it.
-    log.debug( "Adding new row to tool_shed_repository table for repository '%s'" % name )
-    create_or_undelete_tool_shed_repository( app,
-                                             name,
-                                             description,
-                                             changeset_revision,
-                                             repository_clone_url,
-                                             metadata_dict )
+    log.debug( "Adding new row (or updating an existing row) for repository '%s' in the tool_shed_repository table." % name )
+    create_or_update_tool_shed_repository( app, name, description, changeset_revision, repository_clone_url, metadata_dict )
     return metadata_dict
 def pretty_print_xml( elem, level=0 ):
     pad = '    '
diff --git a/lib/galaxy/web/controllers/admin_toolshed.py b/lib/galaxy/web/controllers/admin_toolshed.py
index 94c5e280c2c..a5dc6b2bcda 100644
--- a/lib/galaxy/web/controllers/admin_toolshed.py
+++ b/lib/galaxy/web/controllers/admin_toolshed.py
@@ -237,18 +237,19 @@ class AdminToolshed( AdminGalaxy ):
                         returncode, tmp_name = update_repository( current_working_dir, relative_install_dir, changeset_revision )
                         if returncode == 0:
                             owner = get_repository_owner( clean_repository_clone_url( repository_clone_url ) )
-                            metadata_dict = load_repository_contents( trans.app,
-                                                                      name,
-                                                                      description,
-                                                                      owner,
-                                                                      changeset_revision,
-                                                                      repository_clone_url,
-                                                                      shed_tool_conf, 
-                                                                      tool_path,
-                                                                      tool_section,
-                                                                      relative_install_dir,
-                                                                      current_working_dir,
-                                                                      tmp_name )
+                            metadata_dict = load_repository_contents( app=trans.app,
+                                                                      name=name,
+                                                                      description=description,
+                                                                      owner=owner,
+                                                                      changeset_revision=changeset_revision,
+                                                                      tool_path=tool_path,
+                                                                      repository_clone_url=repository_clone_url,
+                                                                      relative_install_dir=relative_install_dir,
+                                                                      current_working_dir=current_working_dir,
+                                                                      tmp_name=tmp_name,
+                                                                      tool_section=tool_section,
+                                                                      shed_tool_conf=shed_tool_conf,
+                                                                      new_install=True )
                             installed_repository_names.append( name )
                         else:
                             tmp_stderr = open( tmp_name, 'rb' )
@@ -302,7 +303,7 @@ class AdminToolshed( AdminGalaxy ):
         status = params.get( 'status', 'done' )
         repository = get_repository( trans, kwd[ 'id' ] )
         description = util.restore_text( params.get( 'description', repository.description ) )
-        relative_install_dir = self.__get_relative_install_dir( trans, repository )
+        tool_path, relative_install_dir = self.__get_tool_path_and_relative_install_dir( trans, repository )
         repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, repository.name ) )
         if params.get( 'edit_repository_button', False ):
             if description != repository.description:
@@ -351,13 +352,28 @@ class AdminToolshed( AdminGalaxy ):
                 message = "The cloned tool shed repository named '%s' is current (there are no updates available)." % name
             else:
                 current_working_dir = os.getcwd()
-                relative_install_dir = self.__get_relative_install_dir( trans, repository )
+                tool_path, relative_install_dir = self.__get_tool_path_and_relative_install_dir( trans, repository )
                 if relative_install_dir:
                     repo_files_dir = os.path.join( relative_install_dir, name )
                     returncode, tmp_name = pull_repository( current_working_dir, repo_files_dir, name )
                     if returncode == 0:
                         returncode, tmp_name = update_repository( current_working_dir, repo_files_dir, latest_changeset_revision )
                         if returncode == 0:
+                            # Update the repository metadata.
+                            repository_clone_url = os.path.join( tool_shed_url, 'repos', owner, name )
+                            metadata_dict = load_repository_contents( app=trans.app,
+                                                                      name=name,
+                                                                      description=repository.description,
+                                                                      owner=owner,
+                                                                      changeset_revision=changeset_revision,
+                                                                      tool_path=tool_path,
+                                                                      repository_clone_url=repository_clone_url,
+                                                                      relative_install_dir=relative_install_dir,
+                                                                      current_working_dir=current_working_dir,
+                                                                      tmp_name=tmp_name,
+                                                                      tool_section=None,
+                                                                      shed_tool_conf=None,
+                                                                      new_install=False )
                             # Update the repository changeset_revision in the database.
                             repository.changeset_revision = latest_changeset_revision
                             repository.update_available = False
@@ -408,8 +424,9 @@ class AdminToolshed( AdminGalaxy ):
                                     metadata=metadata,
                                     message=message,
                                     status=status )
-    def __get_relative_install_dir( self, trans, repository ):
-        # Get the directory where the repository is install.
+    def __get_tool_path_and_relative_install_dir( self, trans, repository ):
+        # Return both the tool_path configured in the relative shed_tool_conf and
+        # the relative path to the directory where the repository is installed.
         tool_shed = clean_tool_shed_url( repository.tool_shed )
         partial_install_dir = '%s/repos/%s/%s/%s' % ( tool_shed, repository.owner, repository.name, repository.installed_changeset_revision )
         # Get the relative tool installation paths from each of the shed tool configs.
@@ -420,7 +437,7 @@ class AdminToolshed( AdminGalaxy ):
             relative_install_dir = os.path.join( tool_path, partial_install_dir )
             if os.path.isdir( relative_install_dir ):
                 break
-        return relative_install_dir
+        return tool_path, relative_install_dir
     def __generate_tool_path( self, repository_clone_url, changeset_revision ):
         """
         Generate a tool path that guarantees repositories with the same name will always be installed

From 299fbf242f8bd0a628e6d19790a601c4b287e8dc Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Thu, 15 Dec 2011 16:21:39 -0500
Subject: [PATCH 343/362] Custom builds: (a) reinstitute support for len
 files/len entries and (b) improve UI so that it is easy to specify build
 definition and help is accurate.

---
 lib/galaxy/web/controllers/user.py |  51 ++++++++++-
 templates/user/dbkeys.mako         | 133 +++++++++++++++++++++++------
 2 files changed, 152 insertions(+), 32 deletions(-)

diff --git a/lib/galaxy/web/controllers/user.py b/lib/galaxy/web/controllers/user.py
index c4d6102a532..2b98d08245d 100644
--- a/lib/galaxy/web/controllers/user.py
+++ b/lib/galaxy/web/controllers/user.py
@@ -1198,14 +1198,57 @@ class User( BaseUIController, UsesFormDefinitions ):
             # Add new custom build.
             name = kwds.get('name', '')
             key = kwds.get('key', '')
-            dataset_id = kwds.get('dataset_id', '')
-            if not name or not key or not dataset_id:
+            
+            # Look for build's chrom info in len_file and len_text.
+            len_file = kwds.get( 'len_file', None )
+            if getattr( len_file, "file", None ): # Check if it's a FieldStorage object
+                len_text = len_file.file.read()
+            else:
+                len_text = kwds.get( 'len_text', None )
+            
+            if not len_text:
+                # Using FASTA from history.
+                dataset_id = kwds.get('dataset_id', '')
+                
+            if not name or not key or not ( len_text or dataset_id ):
                 message = "You must specify values for all the fields."
             elif key in dbkeys:
                 message = "There is already a custom build with that key. Delete it first if you want to replace it."
             else:
-                dataset_id = trans.security.decode_id( dataset_id )
-                dbkeys[key] = { "name": name, "fasta": dataset_id }
+                # Have everything needed; create new build.
+                build_dict = { "name": name }
+                if len_text:
+                    # Create new len file
+                    new_len = trans.app.model.HistoryDatasetAssociation( extension="len", create_dataset=True, sa_session=trans.sa_session )
+                    trans.sa_session.add( new_len )
+                    new_len.name = name
+                    new_len.visible = False
+                    new_len.state = trans.app.model.Job.states.OK
+                    new_len.info = "custom build .len file"
+                    trans.sa_session.flush()
+                    counter = 0
+                    f = open(new_len.file_name, "w")
+                    # LEN files have format:
+                    #   <chrom_name><tab><chrom_length>
+                    for line in len_text.split("\n"):
+                        lst = line.strip().rsplit(None, 1) # Splits at the last whitespace in the line
+                        if not lst or len(lst) < 2:
+                            lines_skipped += 1
+                            continue
+                        chrom, length = lst[0], lst[1]
+                        try:
+                            length = int(length)
+                        except ValueError:
+                            lines_skipped += 1
+                            continue
+                        counter += 1
+                        f.write("%s\t%s\n" % (chrom, length))
+                    f.close()
+                    build_dict.update( { "len": new_len.id, "count": counter } )
+                else:
+                    dataset_id = trans.security.decode_id( dataset_id )
+                    build_dict[ "fasta" ] = dataset_id
+                dbkeys[key] = build_dict
         # Save builds.
         # TODO: use database table to save builds.
         user.preferences['dbkeys'] = to_json_string(dbkeys)
diff --git a/templates/user/dbkeys.mako b/templates/user/dbkeys.mako
index d0c6878b824..a94bd2da215 100644
--- a/templates/user/dbkeys.mako
+++ b/templates/user/dbkeys.mako
@@ -40,6 +40,15 @@
             padding: 10px;
         }
         %endif
+        div.def_tab {
+            float: left;
+            padding: 0.2em 0.5em;
+            background-color: white;
+        }
+        div.def_tab.active {
+            background-color: #CCF;
+            border: solid 1px #66A;
+        }
     </style>
 </%def>
 
@@ -60,6 +69,43 @@
         $("#show_installed_builds").click(function() {
             $("#installed_builds").show();
         });
+        
+        // Set up behavior for build definition tab controls.
+        $("div.def_tab > a").each(function() {
+            $(this).click(function() {
+                var tab_id = $(this).attr("id");
+
+                // Hide all build inputs, help.
+                $("div.build_definition").children(":input").hide();
+                $(".infomessagesmall > div").hide();
+                
+                // Show input item, help corresponding to tab id.
+                $("#" + tab_id + "_input").show();
+                $("." + tab_id + "_help").show();
+                
+                // Update tabs.
+                $("div.def_tab").removeClass("active");
+                $(this).parent().addClass("active");
+            });
+        });
+        
+        ## If there are fasta HDAs available, show fasta tab; otherwise show len file tab.
+        // Set starting tab.
+        % if fasta_hdas.first():
+            $("#fasta").click();
+        % else:
+            $("#len_file").click();
+        % endif
+        
+        // Before submit, remove inputs not associated with the active tab.
+        $("#submit").click(function() {
+            var id = $(".active > a").attr("id");
+            $("div.build_definition").children(":input").each(function() {
+                if ( $(this).attr("id") !== (id + "_input")  ) {
+                    $(this).remove();
+                }
+            });
+        });
     });
 
     </script>
@@ -70,7 +116,6 @@
 </%def>
 
 <%def name="body()">
-
     % if message:
         <div class="errormessagelarge">${message}</div>
     % elif lines_skipped > 0:
@@ -123,50 +168,82 @@
     <hr />
     <h3>Add a Custom Build</h3>
     <form action="dbkeys" method="post" enctype="multipart/form-data">
+        ## Custom build via fasta in history.
         <div class="toolForm" style="float: left;">
             <div class="toolFormTitle">New Build</div>
             <div class="toolFormBody">
                 <div class="form-row">
-                    <label for="name">Build Name (eg: Mouse):</label>
+                    <label for="name">Name (eg: Hamster):</label>
                     <input type="text" id="name" name="name" />
                 </div>
                 <div class="form-row">
-                    <label for="key">Build Key (eg: mm9):</label>
+                    <label for="key">Key (eg: hamster_v1):</label>
                     <input type="text" id="key" name="key" />
                 </div>
-                <div class="form-row">
-                    <label for="len_file">Build Genome:</label>
-                    <select name="dataset_id">
+                <div class="form-row build_definition">
+                    <label>Definition:</label>
+                    <div class="def_tab">
+                        <a id="fasta" href="javascript:void(0)">FASTA</a>
+                    </div>
+                    <div class="def_tab">
+                        <a id="len_file" href="javascript:void(0)">Len File</a>
+                    </div>
+                    <div class="def_tab">
+                        <a id="len_entry" href="javascript:void(0)">Len Entry</a>
+                    </div>
+                    <div style="clear: both; padding-bottom: 0.5em"></div>
+                    <select id="fasta_input" name="dataset_id">
                     %for dataset in fasta_hdas:
                         <option value="${trans.security.encode_id( dataset.id )}">${dataset.hid}: ${dataset.name}</option>
                     %endfor
                     </select>
-                </div>
-            
-                <div class="form-row"><input type="submit" name="add" value="Submit"/></div>
+                    <input type="file" id="len_file_input" name="len_file" /></input>
+                    <textarea id="len_entry_input" name="len_text" cols="30" rows="8"></textarea>
+                </div>            
+                <div class="form-row"><input id="submit" type="submit" name="add" value="Submit"/></div>
             </div>
         </div>
     </form>
     <div class="infomessagesmall" style="float: left; margin-left: 10px; width: 40%;">
-        <h3>Length Format</h3>
-        <p>
-            The length format is two-column, separated by whitespace, of the form:
-            <pre>chrom/contig   length of chrom/contig</pre>
-        </p>
-        <p>
-            For example, the first few entries of <em>mm9.len</em> are as follows:
-            <pre>
-chr1    197195432
-chr2    181748087
-chr3    159599783
-chr4    155630120
-chr5    152537259
-            </pre>
-        </p>
-        
-        <p>Trackster uses this information to populate the select box for chrom/contig, and
-        to set the maximum basepair of the track browser. You may either upload a .len file
-        of this format, or directly enter the information into the box.</p>
+        <div class="fasta_help">
+            <h3>FASTA format</h3>
+            <p>
+                This is a multi-fasta file from your current history that provides the genome 
+                sequences for each chromosome/contig in your build.
+            </p>
+            
+            <p>
+                Here is a snippet from an example multi-fasta file:
+                <pre>
+    >chr1
+    ATTATATATAAGACCACAGAGAGAATATTTTGCCCGG...
+    >chr2
+    GGCGGCCGCGGCGATATAGAACTACTCATTATATATA...
+    ...
+                </pre>
+            </p>
+        </div>
+        <div class="len_file_help len_entry_help">
+            <h3>Length Format</h3>
+            <p>
+                The length format is two-column, separated by whitespace, of the form:
+                <pre>chrom/contig   length of chrom/contig</pre>
+            </p>
+            <p>
+                For example, the first few entries of <em>mm9.len</em> are as follows:
+                <pre>
+    chr1    197195432
+    chr2    181748087
+    chr3    159599783
+    chr4    155630120
+    chr5    152537259
+                </pre>
+            </p>
         
+            <p>Trackster uses this information to populate the select box for chrom/contig, and
+            to set the maximum basepair of the track browser. You may either upload a .len file
+            of this format (Len File option), or directly enter the information into the box 
+            (Len Entry option).</p>
+        </div>
     </div>
 </%def>
\ No newline at end of file

From 2666421bd75291170b923562363a895eff77fff1 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Fri, 16 Dec 2011 11:19:29 -0500
Subject: [PATCH 344/362] Enhance the datatypes registry to: (a) enable use of
 config files that do not include a "sniffers" tag set section, (b) not load a
 datatypes if the registry already includes a datatype with that extension.

---
 lib/galaxy/datatypes/registry.py | 40 ++++++++++++++++++--------------
 1 file changed, 22 insertions(+), 18 deletions(-)

diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
index e341d649702..717816c5c95 100644
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -62,7 +62,10 @@ class Registry( object ):
                     mimetype = elem.get( 'mimetype', None )
                     display_in_upload = elem.get( 'display_in_upload', False )
                     make_subclass = galaxy.util.string_as_bool( elem.get( 'subclass', False ) )
-                    if extension and ( dtype or type_extension ):
+                    if extension and extension in self.datatypes_by_extension:
+                        self.log.debug( "Ignoring datatype with extension '%s' from '%s' because the registry already includes a datatype with that extension." \
+                                        % ( extension, config ) )
+                    elif extension and ( dtype or type_extension ):
                         if dtype:
                             fields = dtype.split( ':' )
                             datatype_module = fields[0]
@@ -142,23 +145,24 @@ class Registry( object ):
                         d_type1.add_display_application( display_app )
             # Load datatype sniffers from the config
             sniffers = root.find( 'sniffers' )
-            for elem in sniffers.findall( 'sniffer' ):
-                dtype = elem.get( 'type', None )
-                if dtype:
-                    try:
-                        fields = dtype.split( ":" )
-                        datatype_module = fields[0]
-                        datatype_class = fields[1]
-                        module = __import__( datatype_module )
-                        for comp in datatype_module.split('.')[1:]:
-                            module = getattr(module, comp)
-                        aclass = getattr( module, datatype_class )() 
-                        self.sniff_order.append( aclass )
-                        self.log.debug( 'Loaded sniffer for datatype: %s' % dtype )
-                    except Exception, exc:
-                        self.log.warning( 'Error appending datatype %s to sniff_order, problem: %s' % ( dtype, str( exc ) ) )
-        #default values
-        if len(self.datatypes_by_extension) < 1:
+            if sniffers:
+                for elem in sniffers.findall( 'sniffer' ):
+                    dtype = elem.get( 'type', None )
+                    if dtype:
+                        try:
+                            fields = dtype.split( ":" )
+                            datatype_module = fields[0]
+                            datatype_class = fields[1]
+                            module = __import__( datatype_module )
+                            for comp in datatype_module.split('.')[1:]:
+                                module = getattr(module, comp)
+                            aclass = getattr( module, datatype_class )() 
+                            self.sniff_order.append( aclass )
+                            self.log.debug( 'Loaded sniffer for datatype: %s' % dtype )
+                        except Exception, exc:
+                            self.log.warning( 'Error appending datatype %s to sniff_order, problem: %s' % ( dtype, str( exc ) ) )
+        # Default values.
+        if not self.datatypes_by_extension:
             self.datatypes_by_extension = { 
                 'ab1'         : binary.Ab1(),
                 'axt'         : sequence.Axt(),

From 695aa191ef2f859972b3929c37044a66e4b60d07 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Fri, 16 Dec 2011 11:34:35 -0500
Subject: [PATCH 345/362] 1) Add a new InstalledRepositoryManager class which
 currently enables loading datatypes from previously installed tool shed
 repositories into the datatypes registry.  This component will enable
 additional features in the future.

2) Enhance the Iinstall_repository method in the admin_toolshed controller to skip displaying the page for selecting a tool panel section if no tools exist in any of the repositories being installed.

3) Eliminate duplicate generate_datatypes_metadata generate_tool_metadata generate_workflow_metadata methods and use those now contained in shed_util.py.

4) Fixes for handling tool shed repository metadata for repositories that do not include any tools.
---
 lib/galaxy/app.py                             |   6 +-
 lib/galaxy/tool_shed/__init__.py              |  23 +++-
 lib/galaxy/tool_shed/install_manager.py       |   9 ++
 lib/galaxy/util/shed_util.py                  | 105 +++++++++------
 lib/galaxy/web/controllers/admin_toolshed.py  |  14 +-
 .../webapps/community/controllers/common.py   | 124 ++++--------------
 .../community/controllers/repository.py       |  25 ++--
 .../admin/tool_shed_repository/common.mako    |  21 ++-
 .../select_tool_panel_section.mako            |   2 +-
 .../webapps/community/repository/common.mako  |  21 ++-
 10 files changed, 168 insertions(+), 182 deletions(-)

diff --git a/lib/galaxy/app.py b/lib/galaxy/app.py
index 408de19658d..516a91f53af 100644
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -22,7 +22,7 @@ class UniverseApplication( object ):
         self.config = config.Configuration( **kwargs )
         self.config.check()
         config.configure_logging( self.config )
-        # Set up datatypes registry
+        # Initialize the datatypes registry to the default data types included in self.config.datatypes_config.
         self.datatypes_registry = galaxy.datatypes.registry.Registry()
         self.datatypes_registry.load_datatypes( self.config.root, self.config.datatypes_config )
         galaxy.model.set_datatypes_registry( self.datatypes_registry )
@@ -68,6 +68,10 @@ class UniverseApplication( object ):
         if self.config.get_bool( 'enable_tool_shed_check', False ):
             from tool_shed import update_manager
             self.update_manager = update_manager.UpdateManager( self )
+        # Manage installed tool shed repositories
+        self.installed_repository_manager = galaxy.tool_shed.InstalledRepositoryManager( self )
+        # Add additional datatypes from installed tool shed repositories to the datatypes registry.
+        self.installed_repository_manager.load_datatypes()
         # Load datatype converters
         self.datatypes_registry.load_datatype_converters( self.toolbox )
         # Load history import/export tools
diff --git a/lib/galaxy/tool_shed/__init__.py b/lib/galaxy/tool_shed/__init__.py
index 422c3577184..b37d90de34f 100644
--- a/lib/galaxy/tool_shed/__init__.py
+++ b/lib/galaxy/tool_shed/__init__.py
@@ -1,3 +1,22 @@
 """
-Classes encapsulating the relationships between Galaxy and Galaxy tool sheds.
-"""
\ No newline at end of file
+Classes encapsulating the management of repositories installed from Galaxy tool sheds.
+"""
+import os, logging
+from galaxy.model.orm import *
+
+log = logging.getLogger(__name__)
+
+class InstalledRepositoryManager( object ):
+    def __init__( self, app ):
+        self.app = app
+        self.model = self.app.model
+        self.sa_session = self.model.context.current
+    def load_datatypes( self ):
+        for tool_shed_repository in self.sa_session.query( self.model.ToolShedRepository ) \
+                                                   .filter( and_( self.model.ToolShedRepository.table.c.includes_datatypes==True,
+                                                                  self.model.ToolShedRepository.table.c.deleted==False ) ):
+            metadata = tool_shed_repository.metadata
+            datatypes_config = metadata[ 'datatypes_config' ]
+            full_path = os.path.abspath( datatypes_config )
+            self.app.datatypes_registry.load_datatypes( self.app.config.root, full_path )
+        
\ No newline at end of file
diff --git a/lib/galaxy/tool_shed/install_manager.py b/lib/galaxy/tool_shed/install_manager.py
index 1f182f98c7c..e114a7d71d9 100644
--- a/lib/galaxy/tool_shed/install_manager.py
+++ b/lib/galaxy/tool_shed/install_manager.py
@@ -158,4 +158,13 @@ class InstallManager( object ):
                 if os.path.exists( clone_dir ):
                     installed = True
                     break
+        if not installed:
+            full_path = os.path.abspath( clone_dir )
+            # We may have a repository that contains no tools.
+            if os.path.exists( full_path ):
+                for root, dirs, files in os.walk( full_path ):
+                    if '.hg' in dirs:
+                        # Assume that the repository has been installed if we find a .hg directory.
+                        installed = True
+                        break
         return installed
diff --git a/lib/galaxy/util/shed_util.py b/lib/galaxy/util/shed_util.py
index 1ac108ab04c..2e7ee898a24 100644
--- a/lib/galaxy/util/shed_util.py
+++ b/lib/galaxy/util/shed_util.py
@@ -109,6 +109,7 @@ def generate_datatypes_metadata( datatypes_config, metadata_dict ):
     Update the received metadata_dict with changes that have been applied
     to the received datatypes_config.  This method is used by the InstallManager,
     which does not have access to trans.
+    TODO: Handle converters, indexers, sniffers, etc...
     """
     # Parse datatypes_config.
     tree = ElementTree.parse( datatypes_config )
@@ -125,13 +126,29 @@ def generate_datatypes_metadata( datatypes_config, metadata_dict ):
     registration = root.find( 'registration' )
     if registration:
         for elem in registration.findall( 'datatype' ):
-            extension = elem.get( 'extension', None ) 
+            datatypes_dict = {}
+            display_in_upload = elem.get( 'display_in_upload', None )
+            if display_in_upload:
+                datatypes_dict[ 'display_in_upload' ] = display_in_upload
             dtype = elem.get( 'type', None )
+            if dtype:
+                datatypes_dict[ 'dtype' ] = dtype
+            extension = elem.get( 'extension', None )
+            if extension:
+                datatypes_dict[ 'extension' ] = extension
+            max_optional_metadata_filesize = elem.get( 'max_optional_metadata_filesize', None )
+            if max_optional_metadata_filesize:
+                datatypes_dict[ 'max_optional_metadata_filesize' ] = max_optional_metadata_filesize
             mimetype = elem.get( 'mimetype', None )
-            datatypes.append( dict( extension=extension,
-                                    dtype=dtype,
-                                    mimetype=mimetype ) )
-        metadata_dict[ 'datatypes' ] = datatypes
+            if mimetype:
+                datatypes_dict[ 'mimetype' ] = mimetype
+            subclass = elem.get( 'subclass', None )
+            if subclass:
+                datatypes_dict[ 'subclass' ] = subclass
+            if datatypes_dict:
+                datatypes.append( datatypes_dict )
+        if datatypes:
+            metadata_dict[ 'datatypes' ] = datatypes
     return metadata_dict
 def generate_metadata( toolbox, relative_install_dir, repository_clone_url ):
     """
@@ -426,46 +443,52 @@ def load_datatypes( app, datatypes_config, relative_intall_dir ):
     # This method is used by the InstallManager, which does not have access to trans.
     imported_module = None
     # Parse datatypes_config.
-    tree = parse_xml( datatypes_config )
+    tree = util.parse_xml( datatypes_config )
     datatypes_config_root = tree.getroot()
     relative_path_to_datatype_file_name = None
     datatype_files = datatypes_config_root.find( 'datatype_files' )
-    # Currently only a single datatype_file is supported.  For example:
-    # <datatype_files>
-    #    <datatype_file name="gmap.py"/>
-    # </datatype_files>
-    for elem in datatype_files.findall( 'datatype_file' ):
-        datatype_file_name = elem.get( 'name', None )
-        if datatype_file_name:
-            # Find the file in the installed repository.
-            for root, dirs, files in os.walk( relative_intall_dir ):
-                if root.find( '.hg' ) < 0:
-                    for name in files:
-                        if name == datatype_file_name:
-                            relative_path_to_datatype_file_name = os.path.join( root, name )
-                            break
-            break
-    if relative_path_to_datatype_file_name:
-        relative_head, relative_tail = os.path.split( relative_path_to_datatype_file_name )
-        registration = datatypes_config_root.find( 'registration' )
-        # Get the module by parsing the <datatype> tag.
-        for elem in registration.findall( 'datatype' ):
-            # A 'type' attribute is currently required.  The attribute
-            # should be something like: type="gmap:GmapDB".
-            dtype = elem.get( 'type', None )
-            if dtype:
-                fields = dtype.split( ':' )
-                datatype_module = fields[0]
-                datatype_class_name = fields[1]
-                # Since we currently support only a single datatype_file,
-                #  we have what we need.
+    if datatype_files:
+        # Currently only a single datatype_file is supported.  For example:
+        # <datatype_files>
+        #    <datatype_file name="gmap.py"/>
+        # </datatype_files>
+        for elem in datatype_files.findall( 'datatype_file' ):
+            datatype_file_name = elem.get( 'name', None )
+            if datatype_file_name:
+                # Find the file in the installed repository.
+                for root, dirs, files in os.walk( relative_intall_dir ):
+                    if root.find( '.hg' ) < 0:
+                        for name in files:
+                            if name == datatype_file_name:
+                                relative_path_to_datatype_file_name = os.path.join( root, name )
+                                break
                 break
-        try:
-            sys.path.insert( 0, relative_head )
-            imported_module = __import__( datatype_module )
-            sys.path.pop( 0 )
-        except Exception, e:
-            log.debug( "Exception importing datatypes code file included in installed repository: %s" % str( e ) )
+        if relative_path_to_datatype_file_name:
+            relative_head, relative_tail = os.path.split( relative_path_to_datatype_file_name )
+            registration = datatypes_config_root.find( 'registration' )
+            # Get the module by parsing the <datatype> tag.
+            for elem in registration.findall( 'datatype' ):
+                # A 'type' attribute is currently required.  The attribute
+                # should be something like: type="gmap:GmapDB".
+                dtype = elem.get( 'type', None )
+                if dtype:
+                    fields = dtype.split( ':' )
+                    datatype_module = fields[0]
+                    datatype_class_name = fields[1]
+                    # Since we currently support only a single datatype_file,
+                    #  we have what we need.
+                    break
+            try:
+                sys.path.insert( 0, relative_head )
+                imported_module = __import__( datatype_module )
+                sys.path.pop( 0 )
+            except Exception, e:
+                log.debug( "Exception importing datatypes code file included in installed repository: %s" % str( e ) )
+    else:
+        # The repository includes a datayptes_conf.xml file, but no code file that
+        # contains data type classes.  This implies that the data types in datayptes_conf.xml
+        # are all subclasses of data types that are in the distribution.
+        imported_module = None
     app.datatypes_registry.load_datatypes( root_dir=app.config.root, config=datatypes_config, imported_module=imported_module )
 def load_repository_contents( app, name, description, owner, changeset_revision, tool_path, repository_clone_url, relative_install_dir,
                               current_working_dir, tmp_name, tool_section=None, shed_tool_conf=None, new_install=True ):
diff --git a/lib/galaxy/web/controllers/admin_toolshed.py b/lib/galaxy/web/controllers/admin_toolshed.py
index a5dc6b2bcda..9aa4426d6c3 100644
--- a/lib/galaxy/web/controllers/admin_toolshed.py
+++ b/lib/galaxy/web/controllers/admin_toolshed.py
@@ -191,13 +191,20 @@ class AdminToolshed( AdminGalaxy ):
         repo_info_dict = kwd[ 'repo_info_dict' ]
         new_tool_panel_section = kwd.get( 'new_tool_panel_section', '' )
         tool_panel_section = kwd.get( 'tool_panel_section', '' )
-        if kwd.get( 'select_tool_panel_section_button', False ):
-            shed_tool_conf = kwd[ 'shed_tool_conf' ]
+        includes_tools = util.string_as_bool( kwd.get( 'includes_tools', False ) )
+        if not includes_tools or ( includes_tools and kwd.get( 'select_tool_panel_section_button', False ) ):
+            if includes_tools:
+                shed_tool_conf = kwd[ 'shed_tool_conf' ]
+            else:
+                # If installing a repository that includes no tools, get the relative
+                # tool_path from the file to which the install_tool_config_file config
+                # setting points.
+                shed_tool_conf = trans.app.config.install_tool_config
             # Get the tool path.
             for k, tool_path in trans.app.toolbox.shed_tool_confs.items():
                 if k == shed_tool_conf:
                     break
-            if new_tool_panel_section or tool_panel_section:
+            if includes_tools and ( new_tool_panel_section or tool_panel_section ):
                 if new_tool_panel_section:
                     section_id = new_tool_panel_section.lower().replace( ' ', '_' )
                     new_section_key = 'section_%s' % str( section_id )
@@ -290,6 +297,7 @@ class AdminToolshed( AdminGalaxy ):
                                     tool_shed_url=tool_shed_url,
                                     repo_info_dict=repo_info_dict,
                                     shed_tool_conf=shed_tool_conf,
+                                    includes_tools=includes_tools,
                                     shed_tool_conf_select_field=shed_tool_conf_select_field,
                                     tool_panel_section_select_field=tool_panel_section_select_field,
                                     new_tool_panel_section=new_tool_panel_section,
diff --git a/lib/galaxy/webapps/community/controllers/common.py b/lib/galaxy/webapps/community/controllers/common.py
index fec93f73879..9be25a0325e 100644
--- a/lib/galaxy/webapps/community/controllers/common.py
+++ b/lib/galaxy/webapps/community/controllers/common.py
@@ -4,6 +4,7 @@ from datetime import *
 from galaxy.tools import *
 from galaxy.util.json import from_json_string, to_json_string
 from galaxy.util.hash_util import *
+from galaxy.util.shed_util import generate_datatypes_metadata, generate_tool_metadata, generate_workflow_metadata
 from galaxy.web.base.controller import *
 from galaxy.webapps.community import model
 from galaxy.model.orm import *
@@ -149,6 +150,7 @@ def get_latest_repository_metadata( trans, id ):
                            .order_by( trans.model.RepositoryMetadata.table.c.id.desc() ) \
                            .first()
 def generate_clone_url( trans, repository_id ):
+    """Generate the URL for cloning a repository."""
     repository = get_repository( trans, repository_id )
     protocol, base = trans.request.base.split( '://' )
     if trans.user:
@@ -220,54 +222,6 @@ def check_tool_input_params( trans, name, tool, sample_files, invalid_files ):
                         correction_msg += "Upload a file named <b>%s.sample</b> to the repository to correct this error." % str( index_tail )
                         invalid_files.append( ( name, correction_msg ) )
     return can_set_metadata, invalid_files
-def generate_tool_metadata( trans, id, changeset_revision, tool_config, tool, metadata_dict ):
-    """
-    Update the received metadata_dict with changes that have been
-    applied to the received tool.
-    """
-    repository = get_repository( trans, id )
-    # Handle tool.requirements.
-    tool_requirements = []
-    for tr in tool.requirements:
-        name=tr.name
-        type=tr.type
-        if type == 'fabfile':
-            version = None
-            fabfile = tr.fabfile
-            method = tr.method
-        else:
-            version = tr.version
-            fabfile = None
-            method = None
-        requirement_dict = dict( name=name,
-                                 type=type,
-                                 version=version,
-                                 fabfile=fabfile,
-                                 method=method )
-        tool_requirements.append( requirement_dict )
-    # Handle tool.tests.
-    tool_tests = []
-    if tool.tests:
-        for ttb in tool.tests:
-            test_dict = dict( name=ttb.name,
-                              required_files=ttb.required_files,
-                              inputs=ttb.inputs,
-                              outputs=ttb.outputs )
-            tool_tests.append( test_dict )
-    tool_dict = dict( id=tool.id,
-                      guid = generate_tool_guid( trans, repository, tool ),
-                      name=tool.name,
-                      version=tool.version,
-                      description=tool.description,
-                      version_string_cmd = tool.version_string_cmd,
-                      tool_config=tool_config,
-                      requirements=tool_requirements,
-                      tests=tool_tests )
-    if 'tools' in metadata_dict:
-        metadata_dict[ 'tools' ].append( tool_dict )
-    else:
-        metadata_dict[ 'tools' ] = [ tool_dict ]
-    return metadata_dict
 def new_tool_metadata_required( trans, id, metadata_dict ):
     """
     Compare the last saved metadata for each tool in the repository with the new metadata
@@ -309,16 +263,6 @@ def new_tool_metadata_required( trans, id, metadata_dict ):
     # The received metadata_dict includes no metadata for tools, so a new repository_metadata table
     # record is not needed.
     return False
-def generate_workflow_metadata( trans, id, changeset_revision, exported_workflow_dict, metadata_dict ):
-    """
-    Update the received metadata_dict with changes that have been applied
-    to the received exported_workflow_dict.  Store everything in the database.
-    """
-    if 'workflows' in metadata_dict:
-        metadata_dict[ 'workflows' ].append( exported_workflow_dict )
-    else:
-        metadata_dict[ 'workflows' ] = [ exported_workflow_dict ]
-    return metadata_dict
 def new_workflow_metadata_required( trans, id, metadata_dict ):
     """
     Currently everything about an exported workflow except the name is hard-coded, so there's
@@ -337,34 +281,6 @@ def new_workflow_metadata_required( trans, id, metadata_dict ):
     # The received metadata_dict includes no metadata for workflows, so a new repository_metadata table
     # record is not needed.
     return False
-def generate_datatypes_metadata( trans, id, changeset_revision, datatypes_config, metadata_dict ):
-    """
-    Update the received metadata_dict with changes that have been applied
-    to the received datatypes_config.
-    """
-    # Parse datatypes_config.
-    tree = ElementTree.parse( datatypes_config )
-    root = tree.getroot()
-    ElementInclude.include( root )
-    repository_datatype_code_files = []
-    datatype_files = root.find( 'datatype_files' )
-    if datatype_files:
-        for elem in datatype_files.findall( 'datatype_file' ):
-            name = elem.get( 'name', None )
-            repository_datatype_code_files.append( name )
-        metadata_dict[ 'datatype_files' ] = repository_datatype_code_files
-    datatypes = []
-    registration = root.find( 'registration' )
-    if registration:
-        for elem in registration.findall( 'datatype' ):
-            extension = elem.get( 'extension', None ) 
-            dtype = elem.get( 'type', None )
-            mimetype = elem.get( 'mimetype', None )
-            datatypes.append( dict( extension=extension,
-                                    dtype=dtype,
-                                    mimetype=mimetype ) )
-        metadata_dict[ 'datatypes' ] = datatypes
-    return metadata_dict
 def generate_metadata_for_repository_tip( trans, id, ctx, changeset_revision, repo_dir ):
     # Browse the repository tip files on disk to generate metadata.  This is faster than
     # the generate_metadata_for_changeset_revision() method below because fctx.data() does
@@ -382,7 +298,7 @@ def generate_metadata_for_repository_tip( trans, id, ctx, changeset_revision, re
                     datatypes_config = os.path.abspath( os.path.join( root, name ) )
                     break
     if datatypes_config:
-        metadata_dict = generate_datatypes_metadata( trans, id, changeset_revision, datatypes_config, metadata_dict )
+        metadata_dict = generate_datatypes_metadata( datatypes_config, metadata_dict )
     # Find all special .sample files.
     for root, dirs, files in os.walk( repo_dir ):
         if root.find( '.hg' ) < 0:
@@ -409,19 +325,19 @@ def generate_metadata_for_repository_tip( trans, id, ctx, changeset_revision, re
                         if can_set_metadata:
                             # Update the list of metadata dictionaries for tools in metadata_dict.
                             tool_config = os.path.join( root, name )
-                            metadata_dict = generate_tool_metadata( trans, id, changeset_revision, tool_config, tool, metadata_dict )
+                            repository_clone_url = generate_clone_url( trans, id )
+                            metadata_dict = generate_tool_metadata( tool_config, tool, repository_clone_url, metadata_dict )
                 # Find all exported workflows
                 elif name.endswith( '.ga' ):
                     try:
-                        full_path = os.path.abspath( os.path.join( root, name ) )
+                        relative_path = os.path.join( root, name )
                         # Convert workflow data from json
-                        fp = open( full_path, 'rb' )
+                        fp = open( relative_path, 'rb' )
                         workflow_text = fp.read()
                         fp.close()
                         exported_workflow_dict = from_json_string( workflow_text )
                         if 'a_galaxy_workflow' in exported_workflow_dict and exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true':
-                            # Update the list of metadata dictionaries for workflows in metadata_dict.
-                            metadata_dict = generate_workflow_metadata( trans, id, changeset_revision, exported_workflow_dict, metadata_dict )
+                            metadata_dict = generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict )
                     except Exception, e:
                         invalid_files.append( ( name, str( e ) ) )
     return metadata_dict, invalid_files
@@ -438,7 +354,7 @@ def generate_metadata_for_changeset_revision( trans, id, ctx, changeset_revision
             datatypes_config = fctx.data()
             break
     if datatypes_config:
-        metadata_dict = generate_datatypes_metadata( trans, id, changeset_revision, datatypes_config, metadata_dict )
+        metadata_dict = generate_datatypes_metadata( datatypes_config, metadata_dict )
     # Get all tool config file names from the hgweb url, something like:
     # /repos/test/convert_chars1/file/e58dcf0026c7/convert_characters.xml
     for filename in ctx:
@@ -469,7 +385,8 @@ def generate_metadata_for_changeset_revision( trans, id, ctx, changeset_revision
                 # anything, but may result in a bit of confusion when maintaining the code / data over time.
                 # IMPORTANT NOTE:  Here we are assuming that since the current change set is not the repository
                 # tip, we do not have to handle any .loc.sample files since they would have been handled previously.
-                metadata_dict = generate_tool_metadata( trans, id, changeset_revision, filename, tool, metadata_dict )
+                repository_clone_url = generate_clone_url( trans, id )
+                metadata_dict = generate_tool_metadata( filename, tool, repository_clone_url, metadata_dict )
             try:
                 os.unlink( tmp_filename )
             except:
@@ -481,8 +398,7 @@ def generate_metadata_for_changeset_revision( trans, id, ctx, changeset_revision
                 workflow_text = fctx.data()
                 exported_workflow_dict = from_json_string( workflow_text )
                 if 'a_galaxy_workflow' in exported_workflow_dict and exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true':
-                    # Update the list of metadata dictionaries for workflows in metadata_dict.
-                    metadata_dict = generate_workflow_metadata( trans, id, changeset_revision, exported_workflow_dict, metadata_dict )
+                    metadata_dict = generate_workflow_metadata( '', exported_workflow_dict, metadata_dict )
             except Exception, e:
                 invalid_files.append( ( name, str( e ) ) )
     return metadata_dict, invalid_files
@@ -510,12 +426,18 @@ def set_repository_metadata( trans, id, changeset_revision, content_alert_str=''
                     if len( repository.downloadable_revisions ) == 1:
                         handle_email_alerts( trans, repository, content_alert_str='', new_repo_alert=True, admin_only=False )
                 else:
-                    # Update the last saved repository_metadata table row.
                     repository_metadata = get_latest_repository_metadata( trans, id )
-                    repository_metadata.changeset_revision = changeset_revision
-                    repository_metadata.metadata = metadata_dict
-                    trans.sa_session.add( repository_metadata )
-                    trans.sa_session.flush()
+                    if repository_metadata:
+                        # Update the last saved repository_metadata table row.
+                        repository_metadata.changeset_revision = changeset_revision
+                        repository_metadata.metadata = metadata_dict
+                        trans.sa_session.add( repository_metadata )
+                        trans.sa_session.flush()
+                    else:
+                        # There are no tools in the repository, and we're setting metadat on the repository tip.
+                        repository_metadata = trans.model.RepositoryMetadata( repository.id, changeset_revision, metadata_dict )
+                        trans.sa_session.add( repository_metadata )
+                        trans.sa_session.flush()
             else:
                 # We're re-generating metadata for an old repository revision.
                 repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision )
diff --git a/lib/galaxy/webapps/community/controllers/repository.py b/lib/galaxy/webapps/community/controllers/repository.py
index 43712752bda..53147bb7853 100644
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -436,9 +436,9 @@ class RepositoryController( BaseUIController, ItemRatings ):
                                                                       **kwd ) )
                 if operation == "install":
                     galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' )
-                    encoded_repo_info_dict = self.__encode_repo_info_dict( trans, webapp, util.listify( item_id ) )
-                    url = '%s/admin_toolshed/install_repository?tool_shed_url=%s&webapp=%s&repo_info_dict=%s' % \
-                        ( galaxy_url, url_for( '', qualified=True ), webapp, encoded_repo_info_dict )
+                    encoded_repo_info_dict, includes_tools = self.__encode_repo_info_dict( trans, webapp, util.listify( item_id ) )
+                    url = '%s/admin_toolshed/install_repository?tool_shed_url=%s&webapp=%s&repo_info_dict=%s&includes_tools=%s' % \
+                        ( galaxy_url, url_for( '', qualified=True ), webapp, encoded_repo_info_dict, str( includes_tools ) )
                     return trans.response.send_redirect( url )
             else:
                 # This can only occur when there is a multi-select grid with check boxes and an operation,
@@ -512,9 +512,9 @@ class RepositoryController( BaseUIController, ItemRatings ):
                                                                       **kwd ) )
                 if operation == "install":
                     galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' )
-                    encoded_repo_info_dict = self.__encode_repo_info_dict( trans, webapp, util.listify( item_id ) )
-                    url = '%s/admin_toolshed/install_repository?tool_shed_url=%s&webapp=%s&repo_info_dict=%s' % \
-                        ( galaxy_url, url_for( '', qualified=True ), webapp, encoded_repo_info_dict )
+                    encoded_repo_info_dict, includes_tools = self.__encode_repo_info_dict( trans, webapp, util.listify( item_id ) )
+                    url = '%s/admin_toolshed/install_repository?tool_shed_url=%s&webapp=%s&repo_info_dict=%s&includes_tools=%s' % \
+                        ( galaxy_url, url_for( '', qualified=True ), webapp, encoded_repo_info_dict, str( includes_tools ) )
                     return trans.response.send_redirect( url )
             else:
                 # This can only occur when there is a multi-select grid with check boxes and an operation,
@@ -707,14 +707,17 @@ class RepositoryController( BaseUIController, ItemRatings ):
         return match_tuples
     def __encode_repo_info_dict( self, trans, webapp, repository_metadata_ids ):
         repo_info_dict = {}
+        includes_tools = False
         for repository_metadata_id in repository_metadata_ids:
             repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id )
+            if not includes_tools and 'tools' in repository_metadata.metadata:
+                includes_tools = True
             repository = get_repository( trans, trans.security.encode_id( repository_metadata.repository_id ) )
             repository_id = trans.security.encode_id( repository.id )
             changeset_revision = repository_metadata.changeset_revision
             repository_clone_url = generate_clone_url( trans, repository_id )
             repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, changeset_revision )
-        return encode( repo_info_dict )
+        return encode( repo_info_dict ), includes_tools
     @web.expose
     def preview_tools_in_changeset( self, trans, repository_id, **kwd ):
         params = util.Params( kwd )
@@ -755,12 +758,16 @@ class RepositoryController( BaseUIController, ItemRatings ):
         repository_clone_url = generate_clone_url( trans, repository_id )        
         repository = get_repository( trans, repository_id )
         changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) )
+        repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision )
+        # Tell the caller if the repository includes Galaxy tools so the page
+        # enabling selection of the tool panel section can be displayed.
+        includes_tools = 'tools' in repository_metadata.metadata
         repo_info_dict = {}
         repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, changeset_revision )
         encoded_repo_info_dict = encode( repo_info_dict )
         # Redirect back to local Galaxy to perform install.
-        url = '%s/admin_toolshed/install_repository?tool_shed_url=%s&repo_info_dict=%s' % \
-            ( galaxy_url, url_for( '', qualified=True ), encoded_repo_info_dict )
+        url = '%s/admin_toolshed/install_repository?tool_shed_url=%s&repo_info_dict=%s&includes_tools=%s' % \
+            ( galaxy_url, url_for( '', qualified=True ), encoded_repo_info_dict, str( includes_tools ) )
         return trans.response.send_redirect( url )
     @web.expose
     def check_for_updates( self, trans, **kwd ):
diff --git a/templates/admin/tool_shed_repository/common.mako b/templates/admin/tool_shed_repository/common.mako
index d4455358c91..48f69195818 100644
--- a/templates/admin/tool_shed_repository/common.mako
+++ b/templates/admin/tool_shed_repository/common.mako
@@ -128,25 +128,22 @@
                         <table class="grid">
                             <tr>
                                 <td><b>extension</b></td>
-                                <td><b>dtype</b></td>
+                                <td><b>type</b></td>
                                 <td><b>mimetype</b></td>
+                                <td><b>subclass</b></td>
                             </tr>
                             %for datatypes_dict in datatypes_dicts:
-                                <% 
-                                    extension = datatypes_dict[ 'extension' ]
-                                    dtype = datatypes_dict[ 'dtype' ]
-                                    mimetype = datatypes_dict[ 'mimetype' ]
+                                <%
+                                    extension = datatypes_dict.get( 'extension', '&nbsp;' )
+                                    dtype = datatypes_dict.get( 'dtype', '&nbsp;' )
+                                    mimetype = datatypes_dict.get( 'mimetype', '&nbsp;' )
+                                    subclass = datatypes_dict.get( 'subclass', '&nbsp;' )
                                 %>
                                 <tr>
                                     <td>${extension}</td>
                                     <td>${dtype}</td>
-                                    <td>
-                                        %if mimetype:
-                                            ${mimetype}
-                                        %else:
-                                            &nbsp;
-                                        %endif
-                                    </td>
+                                    <td>${mimetype}</td>
+                                    <td>${subclass}</td>
                                 </tr>
                             %endfor
                         </table>
diff --git a/templates/admin/tool_shed_repository/select_tool_panel_section.mako b/templates/admin/tool_shed_repository/select_tool_panel_section.mako
index bf8665af822..5200e7c7f29 100644
--- a/templates/admin/tool_shed_repository/select_tool_panel_section.mako
+++ b/templates/admin/tool_shed_repository/select_tool_panel_section.mako
@@ -25,7 +25,7 @@
 <div class="toolForm">
     <div class="toolFormTitle">Choose tool panel section to contain installed tools (optional)</div>
     <div class="toolFormBody">
-        <form name="select_tool_panel_section" id="select_tool_panel_section" action="${h.url_for( controller='admin_toolshed', action='install_repository', tool_shed_url=tool_shed_url, repo_info_dict=repo_info_dict )}" method="post" >
+        <form name="select_tool_panel_section" id="select_tool_panel_section" action="${h.url_for( controller='admin_toolshed', action='install_repository', tool_shed_url=tool_shed_url, repo_info_dict=repo_info_dict, includes_tools=includes_tools )}" method="post" >
             %if shed_tool_conf_select_field:
                 <div class="form-row">
                     <label>Shed tool configuration file:</label>
diff --git a/templates/webapps/community/repository/common.mako b/templates/webapps/community/repository/common.mako
index efd69ebaa80..6eb6516cc2b 100644
--- a/templates/webapps/community/repository/common.mako
+++ b/templates/webapps/community/repository/common.mako
@@ -209,25 +209,22 @@
                             <table class="grid">
                                 <tr>
                                     <td><b>extension</b></td>
-                                    <td><b>dtype</b></td>
+                                    <td><b>type</b></td>
                                     <td><b>mimetype</b></td>
+                                    <td><b>subclass</b></td>
                                 </tr>
                                 %for datatypes_dict in datatypes_dicts:
-                                    <% 
-                                        extension = datatypes_dict[ 'extension' ]
-                                        dtype = datatypes_dict[ 'dtype' ]
-                                        mimetype = datatypes_dict[ 'mimetype' ]
+                                    <%
+                                        extension = datatypes_dict.get( 'extension', '&nbsp;' )
+                                        dtype = datatypes_dict.get( 'dtype', '&nbsp;' )
+                                        mimetype = datatypes_dict.get( 'mimetype', '&nbsp;' )
+                                        subclass = datatypes_dict.get( 'subclass', '&nbsp;' )
                                     %>
                                     <tr>
                                         <td>${extension}</td>
                                         <td>${dtype}</td>
-                                        <td>
-                                            %if mimetype:
-                                                ${mimetype}
-                                            %else:
-                                                &nbsp;
-                                            %endif
-                                        </td>
+                                        <td>${mimetype}</td>
+                                        <td>${subclass}</td>
                                     </tr>
                                 %endfor
                             </table>

From d59b7ec5913a00ee83c7d3461e105d7f6b221502 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Fri, 16 Dec 2011 12:54:21 -0500
Subject: [PATCH 346/362] Add Maximal Information-based Nonparametric
 Exploration (MINE) tool.

---
 tool_conf.xml.sample        |  1 +
 tools/stats/MINE.xml        | 82 +++++++++++++++++++++++++++++++++++
 tools/stats/mine_wrapper.py | 85 +++++++++++++++++++++++++++++++++++++
 3 files changed, 168 insertions(+)
 create mode 100644 tools/stats/MINE.xml
 create mode 100644 tools/stats/mine_wrapper.py

diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index 5405c591cb7..2e038351e73 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -149,6 +149,7 @@
     <tool file="stats/plot_from_lda.xml" />
     <tool file="regVariation/t_test_two_samples.xml" />
     <tool file="regVariation/compute_q_values.xml" />
+    <tool file="stats/MINE.xml" />
     
     <label text="GFF" id="gff" />
     <tool file="stats/count_gff_features.xml" />
diff --git a/tools/stats/MINE.xml b/tools/stats/MINE.xml
new file mode 100644
index 00000000000..7f8666b28ec
--- /dev/null
+++ b/tools/stats/MINE.xml
@@ -0,0 +1,82 @@
+<tool id="maximal_information_based_nonparametric_exploration" name="MINE" version="0.0.1">
+  <description>- Maximal Information-based Nonparametric Exploration</description>
+  <requirements>
+      <requirement type="package" version="1.0">MINE</requirement>
+  </requirements>
+  <command interpreter="python">mine_wrapper.py
+    --jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/mine/MINE.jar" 
+    
+    --infile "${input_file}"
+    
+    #if str( $master_variable_type.master_variable_type_selector ) in [ 'allPairs', 'adjacentPairs' ]:
+      --master_variable "${master_variable_type.master_variable_type_selector}"
+    #else:
+        --master_variable "${master_variable_type.master_variable}"
+    #end if
+    
+    --cv "${cv}"
+    
+    --exp "${exp}"
+    
+    --c "${c}"
+    
+    ##--gc ##skip
+    
+    
+    #if str( $master_variable_type.master_variable_type_selector ) != 'allPairs' and $master_variable_type.permute:
+      --permute
+    #end if
+    
+    --output_results "${output_results}"
+    
+    --output_log "${output_log}"
+  </command>
+  <inputs>
+    <param name="input_file" type="data" format="csv" label="CSV file" />
+    
+    <conditional name="master_variable_type">
+      <param name="master_variable_type_selector" type="select" label="Choose the master variable type">
+        <option value="allPairs">allPairs</option>
+        <option value="adjacentPairs">adjacentPairs</option>
+        <option value="compare_against_ith" selected="True">compare against i-th</option>
+      </param>
+      <when value="compare_against_ith">
+        <param type="integer" value="0" name="master_variable" />
+        <param type="boolean" truevalue="--permute" false_value="" name="permute" checked="False" />
+      </when>
+      <when value="adjacentPairs">
+        <param type="boolean" truevalue="--permute" false_value="" name="permute" checked="False" />
+      </when>
+    </conditional>
+    
+    <param type="float" value="0" name="cv" />
+    
+    <param type="float" value="0.6" name="exp" />
+    
+    <param type="float" value="15" name="c" />
+    
+  </inputs>
+  <outputs>
+    <data format="csv" name="output_results" label="${tool.name} on ${on_string} (Results)" />
+    <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
+  </outputs>
+  <tests>
+      <!-- TODO -->
+  </tests>
+  <help>
+**What it does**
+
+Applies the Maximal Information-based Nonparametric Exploration strategy to an input dataset.
+
+See http://www.exploredata.net/ for more information.
+
+------
+
+**Citation**
+
+For the underlying tool, please cite `David N. Reshef, Yakir A. Reshef, Hilary K. Finucane5, Sharon R. Grossman, Gilean McVean, Peter J. Turnbaugh, Eric S. Lander, Michael Mitzenmacher, Pardis C. Sabeti Detecting Novel Associations in Large Data Sets. Science. 2011 Dec. &lt;http://www.sciencemag.org/content/334/6062/1518&gt;`_
+
+If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
+
+  </help>
+</tool>
diff --git a/tools/stats/mine_wrapper.py b/tools/stats/mine_wrapper.py
new file mode 100644
index 00000000000..4e8b30b0dd3
--- /dev/null
+++ b/tools/stats/mine_wrapper.py
@@ -0,0 +1,85 @@
+#!/usr/bin/env python
+#Dan Blankenberg
+
+"""
+A wrapper script for running the MINE.jar commands.
+"""
+
+import sys, optparse, os, tempfile, subprocess, shutil
+
+CHUNK_SIZE = 2**20 #1mb
+
+BASE_NAME = "galaxy_mime_file.txt"
+JOB_ID = "galaxy_mine"
+
+def cleanup_before_exit( tmp_dir ):
+    if tmp_dir and os.path.exists( tmp_dir ):
+        print os.listdir( tmp_dir )
+        shutil.rmtree( tmp_dir )
+
+def open_file_from_option( filename, mode = 'rb' ):
+    if filename:
+        return open( filename, mode = mode )
+    return None
+
+
+def __main__():
+    #Parse Command Line
+    parser = optparse.OptionParser()
+    parser.add_option( '-j', '--jar', dest='jar', action='store', type="string", help='Location of JAR file' )
+    parser.add_option( '-i', '--infile', dest='infile', action='store', type="string", help='infile' )
+    parser.add_option( '-m', '--master_variable', dest='master_variable', action='store', type="string", help='master_variable' )
+    parser.add_option( '-v', '--cv', dest='cv', action='store', type="string", help='cv' )
+    parser.add_option( '-e', '--exp', dest='exp', action='store', type="string", help='exp' )
+    parser.add_option( '-c', '--c', dest='c', action='store', type="string", help='c' )
+    parser.add_option( '-p', '--permute', dest='permute', action='store_true', default=False, help='permute' )
+    parser.add_option( '-o', '--output_results', dest='output_results', action='store', type="string", help='output_results' )
+    parser.add_option( '-l', '--output_log', dest='output_log', action='store', type="string", help='output_log' )
+    parser.add_option( '', '--stdout', dest='stdout', action='store', type="string", default=None, help='If specified, the output of stdout will be written to this file.' )
+    parser.add_option( '', '--stderr', dest='stderr', action='store', type="string", default=None, help='If specified, the output of stderr will be written to this file.' )
+    (options, args) = parser.parse_args()
+    
+    tmp_dir = tempfile.mkdtemp( prefix='tmp-MINE-' )
+    tmp_input_name = os.path.join( tmp_dir, BASE_NAME )
+    if options.permute:
+        permute = "-permute"
+    else:
+        permute = ""
+    
+    os.symlink( options.infile, tmp_input_name )
+    
+    cmd = 'java -jar "%s" "%s" %s -cv%s -exp%s -c%s %s "%s"' % ( options.jar, tmp_input_name, options.master_variable, options.cv, options.exp, options.c, permute, JOB_ID )
+    print cmd
+    
+    #set up stdout and stderr output options
+    stdout = open_file_from_option( options.stdout, mode = 'wb' )
+    stderr = open_file_from_option( options.stderr, mode = 'wb' )
+    #if no stderr file is specified, we'll use our own
+    if stderr is None:
+        stderr = tempfile.NamedTemporaryFile( prefix="MINE-stderr-", dir=tmp_dir )
+    
+    proc = subprocess.Popen( args=cmd, stdout=stdout, stderr=stderr, shell=True, cwd=tmp_dir )
+    return_code = proc.wait()
+    
+    if return_code:
+        stderr_target = sys.stderr
+    else:
+        stderr_target = sys.stdout
+    stderr.flush()
+    stderr.seek(0)
+    while True:
+        chunk = stderr.read( CHUNK_SIZE )
+        if chunk:
+            stderr_target.write( chunk )
+        else:
+            break
+    stderr.close()
+    
+    print os.listdir( tmp_dir )
+    
+    shutil.move( '%s,%s,Results.csv' % ( tmp_input_name, JOB_ID ), options.output_results )
+    shutil.move( '%s,%s,Status.csv' % ( tmp_input_name, JOB_ID ), options.output_log )
+    
+    cleanup_before_exit( tmp_dir )
+
+if __name__=="__main__": __main__()

From cc38aae783d04c6d4809599005938ba975fa452a Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Fri, 16 Dec 2011 14:39:40 -0500
Subject: [PATCH 347/362] Add Picard Interval List to BED6 converter.

---
 datatypes_conf.xml.sample                     |  4 +-
 .../picard_interval_list_to_bed6_converter.py | 44 +++++++++++++++++++
 ...picard_interval_list_to_bed6_converter.xml | 12 +++++
 3 files changed, 59 insertions(+), 1 deletion(-)
 create mode 100644 lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py
 create mode 100644 lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml

diff --git a/datatypes_conf.xml.sample b/datatypes_conf.xml.sample
index 11c43eedb72..0597212ef76 100644
--- a/datatypes_conf.xml.sample
+++ b/datatypes_conf.xml.sample
@@ -101,7 +101,9 @@
       <display file="ensembl/ensembl_interval_as_bed.xml" inherit="True"/>
       <display file="gbrowse/gbrowse_interval_as_bed.xml" inherit="True"/>
     </datatype>
-    <datatype extension="picard_interval_list" type="galaxy.datatypes.data:Text" subclass="True" display_in_upload="True"/>
+    <datatype extension="picard_interval_list" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True">
+      <converter file="picard_interval_list_to_bed6_converter.xml" target_datatype="bed6"/>
+    </datatype>
     <datatype extension="gatk_interval" type="galaxy.datatypes.data:Text" subclass="True" display_in_upload="True"/>
     <datatype extension="gatk_dbsnp" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"/>
     <datatype extension="gatk_tranche" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"/>
diff --git a/lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py b/lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py
new file mode 100644
index 00000000000..63e7c5ce5a4
--- /dev/null
+++ b/lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py
@@ -0,0 +1,44 @@
+#!/usr/bin/env python
+#Dan Blankenberg
+
+import sys
+
+assert sys.version_info[:2] >= ( 2, 5 )
+HEADER_STARTS_WITH = ( '@' )
+
+def __main__():
+    input_name = sys.argv[1]
+    output_name = sys.argv[2]
+    skipped_lines = 0
+    first_skipped_line = 0
+    header_lines = 0
+    out = open( output_name, 'w' )
+    i = 0
+    for i, line in enumerate( open( input_name ) ):
+        complete_interval = False
+        line = line.rstrip( '\r\n' )
+        if line: 
+            if line.startswith( HEADER_STARTS_WITH ):
+                header_lines += 1
+            else:
+                try:
+                    elems = line.split( '\t' )
+                    if len( elems ) >= 5:
+                        complete_interval = True
+                    out.write( '%s\t%s\t%s\t%s\t0\t%s\n' % ( elems[0], int(elems[1])-1, elems[2], elems[4], elems[3] ) )
+                except Exception, e:
+                    print e
+                    skipped_lines += 1
+                    if not first_skipped_line:
+                        first_skipped_line = i + 1
+        else:
+            skipped_lines += 1
+            if not first_skipped_line:
+                first_skipped_line = i + 1
+    out.close()
+    info_msg = "%i lines converted to BED.  " % ( i + 1 - skipped_lines )
+    if skipped_lines > 0:
+        info_msg += "Skipped %d blank/comment/invalid lines starting with line #%d." % ( skipped_lines, first_skipped_line )
+    print info_msg
+
+if __name__ == "__main__": __main__()
diff --git a/lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml b/lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml
new file mode 100644
index 00000000000..120eb641624
--- /dev/null
+++ b/lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml
@@ -0,0 +1,12 @@
+<tool id="CONVERTER_picard_interval_list_to_bed6" name="Convert Picard Interval List to BED6" version="1.0.0">
+    <description>converter</description>
+    <command interpreter="python">picard_interval_list_to_bed6_converter.py "$input" "$output"</command>
+    <inputs>
+        <param name="input" type="data" format="picard_interval_list" label="Picard Interval List file"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="bed6"/>
+    </outputs>
+    <help>
+    </help>
+</tool>

From 529b559490896f0fcde88df3c85346a19341dbc4 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Fri, 16 Dec 2011 16:10:06 -0500
Subject: [PATCH 348/362] Enhance the datatypes registry so that it can be
 persisted as an xml file, which is then used for all tools instead of the
 datatypes config file.

---
 lib/galaxy/app.py                   |  9 +++++-
 lib/galaxy/datatypes/metadata.py    |  1 +
 lib/galaxy/datatypes/registry.py    | 47 +++++++++++++++++++++++++++--
 lib/galaxy/jobs/__init__.py         |  2 +-
 lib/galaxy/tool_shed/__init__.py    |  3 +-
 lib/galaxy/tools/__init__.py        |  3 +-
 lib/galaxy/util/__init__.py         | 26 +++++++++++++---
 lib/galaxy/util/none_like.py        |  1 +
 lib/galaxy/util/shed_util.py        | 20 ++----------
 lib/galaxy/web/base/controller.py   |  4 ---
 lib/galaxy/webapps/community/app.py |  1 +
 11 files changed, 84 insertions(+), 33 deletions(-)

diff --git a/lib/galaxy/app.py b/lib/galaxy/app.py
index 516a91f53af..76579324023 100644
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -118,9 +118,16 @@ class UniverseApplication( object ):
         self.job_stop_queue = self.job_manager.job_stop_queue
         # Initialize the external service types
         self.external_service_types = external_service_types.ExternalServiceTypesCollection( self.config.external_service_type_config_file, self.config.external_service_type_path, self )
-        
     def shutdown( self ):
         self.job_manager.shutdown()
         self.object_store.shutdown()
         if self.heartbeat:
             self.heartbeat.shutdown()
+        try:
+            # If the datatypes registry was persisted, attempt to
+            # remove the temporary file in which it was written.
+            tmp_filename = self.datatypes_registry.xml_filename
+            if tmp_filename:
+                os.unlink( tmp_filename )
+        except:
+            pass
diff --git a/lib/galaxy/datatypes/metadata.py b/lib/galaxy/datatypes/metadata.py
index fc87870511a..48a036d1a37 100644
--- a/lib/galaxy/datatypes/metadata.py
+++ b/lib/galaxy/datatypes/metadata.py
@@ -544,6 +544,7 @@ class JobExternalOutputMetadataWrapper( object ):
         if config_root is None:
             config_root = os.path.abspath( os.getcwd() )
         if datatypes_config is None:
+            raise Exception( 'In setup_external_metadata, the received datatypes_config is None.' )
             datatypes_config = 'datatypes_conf.xml'
         metadata_files_list = []
         for dataset in datasets:
diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
index 717816c5c95..9d18c8fd2c8 100644
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -27,9 +27,15 @@ class Registry( object ):
         self.sniff_order = []
         self.upload_file_formats = []
         self.display_applications = odict() #map a display application id to a display application
+        self.converters_path_attr = None
         self.datatype_converters_path = None
+        self.indexers_path_attr = None
         self.datatype_indexers_path = None
+        self.display_path_attr = None
         self.display_applications_path = None
+        self.datatype_elems = []
+        self.sniffer_elems = []
+        self.xml_filename = None
     def load_datatypes( self, root_dir=None, config=None, imported_module=None ):
         if root_dir and config:
             inherit_display_application_by_class = []
@@ -45,16 +51,21 @@ class Registry( object ):
             # files installed with repositories from tool sheds must use the same paths.  However, we
             # may discover at some future time that allowing for multiple paths is more optimal.
             if not self.datatype_converters_path:
-                self.datatype_converters_path = os.path.join( root_dir, registration.get( 'converters_path', 'lib/galaxy/datatypes/converters' ) )
+                self.converters_path_attr = registration.get( 'converters_path', 'lib/galaxy/datatypes/converters' )
+                self.datatype_converters_path = os.path.join( root_dir, self.converters_path_attr )
                 if not os.path.isdir( self.datatype_converters_path ):
                     raise ConfigurationError( "Directory does not exist: %s" % self.datatype_converters_path )
             if not self.datatype_indexers_path:
-                self.datatype_indexers_path = os.path.join( root_dir, registration.get( 'indexers_path', 'lib/galaxy/datatypes/indexers' ) )
+                self.indexers_path_attr = registration.get( 'indexers_path', 'lib/galaxy/datatypes/indexers' )
+                self.datatype_indexers_path = os.path.join( root_dir, self.indexers_path_attr )
                 if not os.path.isdir( self.datatype_indexers_path ):
                     raise ConfigurationError( "Directory does not exist: %s" % self.datatype_indexers_path )
             if not self.display_applications_path:
-                self.display_applications_path = os.path.join( root_dir, registration.get( 'display_path', 'display_applications' ) )
+                self.display_path_attr = registration.get( 'display_path', 'display_applications' )
+                self.display_applications_path = os.path.join( root_dir, self.display_path_attr )
             for elem in registration.findall( 'datatype' ):
+                # Keep an in-memory list of datatype elems to enable persistence.
+                self.datatype_elems.append( elem )
                 try:
                     extension = elem.get( 'extension', None ) 
                     dtype = elem.get( 'type', None )
@@ -147,6 +158,8 @@ class Registry( object ):
             sniffers = root.find( 'sniffers' )
             if sniffers:
                 for elem in sniffers.findall( 'sniffer' ):
+                    # Keep an in-memory list of sniffer elems to enable persistence.
+                    self.sniffer_elems.append( elem )
                     dtype = elem.get( 'type', None )
                     if dtype:
                         try:
@@ -418,3 +431,31 @@ class Registry( object ):
         if 'auto' not in rval and 'txt' in rval: #need to manually add 'auto' datatype
             rval[ 'auto' ] = rval[ 'txt' ]
         return rval
+    def to_xml_file( self ):
+        fd, filename = tempfile.mkstemp()
+        self.xml_filename = filename
+        if self.converters_path_attr:
+            converters_path_str = ' converters_path="%s"' % self.converters_path_attr
+        else:
+            converters_path_str = ''
+        if self.indexers_path_attr:
+            indexers_path_str = ' indexers_path="%s"' % self.indexers_path_attr
+        else:
+            indexers_path_str = ''
+        if self.display_path_attr:
+            display_path_str = ' display_path="%s"' % self.display_path_attr
+        else:
+            display_path_str = ''
+        os.write( fd, '<?xml version="1.0"?>\n' )
+        os.write( fd, '<datatypes>\n' )
+        os.write( fd, '<registration%s%s%s>\n' % ( converters_path_str, indexers_path_str, display_path_str ) )
+        for elem in self.datatype_elems:
+            os.write( fd, '%s' % galaxy.util.xml_to_string( elem ) )
+        os.write( fd, '</registration>\n' )
+        os.write( fd, '<sniffers>\n' )
+        for elem in self.sniffer_elems:
+            os.write( fd, '%s' % galaxy.util.xml_to_string( elem ) )
+        os.write( fd, '</sniffers>\n' )
+        os.write( fd, '</datatypes>\n' )
+        os.close( fd )
+        return filename
diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index a4b49678dc6..ce5ceaca601 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -868,7 +868,7 @@ class JobWrapper( object ):
         if config_root is None:
             config_root = self.app.config.root
         if datatypes_config is None:
-            datatypes_config = self.app.config.datatypes_config
+            datatypes_config = self.app.datatypes_registry.to_xml_file()
         return self.external_output_metadata.setup_external_metadata( [ output_dataset_assoc.dataset for output_dataset_assoc in job.output_datasets ],
                                                                       self.sa_session,
                                                                       exec_dir = exec_dir,
diff --git a/lib/galaxy/tool_shed/__init__.py b/lib/galaxy/tool_shed/__init__.py
index b37d90de34f..4428ccc22ff 100644
--- a/lib/galaxy/tool_shed/__init__.py
+++ b/lib/galaxy/tool_shed/__init__.py
@@ -14,7 +14,8 @@ class InstalledRepositoryManager( object ):
     def load_datatypes( self ):
         for tool_shed_repository in self.sa_session.query( self.model.ToolShedRepository ) \
                                                    .filter( and_( self.model.ToolShedRepository.table.c.includes_datatypes==True,
-                                                                  self.model.ToolShedRepository.table.c.deleted==False ) ):
+                                                                  self.model.ToolShedRepository.table.c.deleted==False ) ) \
+                                                   .order_by( self.model.ToolShedRepository.table.c.id ):
             metadata = tool_shed_repository.metadata
             datatypes_config = metadata[ 'datatypes_config' ]
             full_path = os.path.abspath( datatypes_config )
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index c74290718be..d3d5a8ae849 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1672,7 +1672,8 @@ class Tool:
         # For the upload tool, we need to know the root directory and the 
         # datatypes conf path, so we can load the datatypes registry
         param_dict['__root_dir__'] = param_dict['GALAXY_ROOT_DIR'] = os.path.abspath( self.app.config.root )
-        param_dict['__datatypes_config__'] = param_dict['GALAXY_DATATYPES_CONF_FILE'] = os.path.abspath( self.app.config.datatypes_config )
+        datatypes_config = self.app.datatypes_registry.to_xml_file()
+        param_dict['__datatypes_config__'] = param_dict['GALAXY_DATATYPES_CONF_FILE'] = os.path.abspath( datatypes_config )
         # Return the dictionary of parameters
         return param_dict
     
diff --git a/lib/galaxy/util/__init__.py b/lib/galaxy/util/__init__.py
index 5910f6a3d1b..708f473cbc6 100644
--- a/lib/galaxy/util/__init__.py
+++ b/lib/galaxy/util/__init__.py
@@ -107,10 +107,28 @@ def parse_xml(fname):
     ElementInclude.include(root)
     return tree
 
-def xml_to_string(elem):
-    """Returns an string from and xml tree"""
-    text = ElementTree.tostring(elem)
-    return text
+def xml_to_string( elem, pretty=False ):
+    """Returns a string from an xml tree"""
+    if pretty:
+        return ElementTree.tostring( pretty_print_xml( elem ) )
+    return ElementTree.tostring( elem )
+
+def pretty_print_xml( elem, level=0 ):
+    pad = '    '
+    i = "\n" + level * pad
+    if len( elem ):
+        if not elem.text or not elem.text.strip():
+            elem.text = i + pad + pad
+        if not elem.tail or not elem.tail.strip():
+            elem.tail = i
+        for e in elem:
+            pretty_print_xml( e, level + 1 )
+        if not elem.tail or not elem.tail.strip():
+            elem.tail = i
+    else:
+        if level and ( not elem.tail or not elem.tail.strip() ):
+            elem.tail = i + pad
+    return elem
 
 # characters that are valid
 valid_chars  = set(string.letters + string.digits + " -=_.()/+*^,:?!")
diff --git a/lib/galaxy/util/none_like.py b/lib/galaxy/util/none_like.py
index 9ba4e1f8df1..349926ad4bf 100644
--- a/lib/galaxy/util/none_like.py
+++ b/lib/galaxy/util/none_like.py
@@ -21,6 +21,7 @@ class NoneDataset( RecursiveNone ):
         self.ext = self.extension = ext
         self.dbkey = dbkey
         if datatypes_registry is None:
+            # Default Value Required for unit tests
             datatypes_registry = Registry()
             datatypes_registry.load_datatypes()
         self.datatype = datatypes_registry.get_datatype_by_extension( ext )
diff --git a/lib/galaxy/util/shed_util.py b/lib/galaxy/util/shed_util.py
index 2e7ee898a24..5cc1ede63fb 100644
--- a/lib/galaxy/util/shed_util.py
+++ b/lib/galaxy/util/shed_util.py
@@ -9,7 +9,7 @@ from galaxy.model.orm import *
 
 pkg_resources.require( 'elementtree' )
 from elementtree import ElementTree, ElementInclude
-from elementtree.ElementTree import Element, SubElement, tostring
+from elementtree.ElementTree import Element, SubElement
 
 log = logging.getLogger( __name__ )
 
@@ -39,7 +39,7 @@ def add_shed_tool_conf_entry( app, shed_tool_conf, tool_panel_entry ):
         if line.startswith( '</toolbox>' ):
             # We're at the end of the original config file, so add our entry.
             new_shed_tool_conf.write( '    ' )
-            new_shed_tool_conf.write( tostring( pretty_print_xml( tool_panel_entry ) ) )
+            new_shed_tool_conf.write( util.xml_to_string( tool_panel_entry, pretty=True ) )
             new_shed_tool_conf.write( line )
         else:
             new_shed_tool_conf.write( line )
@@ -554,22 +554,6 @@ def load_repository_contents( app, name, description, owner, changeset_revision,
     log.debug( "Adding new row (or updating an existing row) for repository '%s' in the tool_shed_repository table." % name )
     create_or_update_tool_shed_repository( app, name, description, changeset_revision, repository_clone_url, metadata_dict )
     return metadata_dict
-def pretty_print_xml( elem, level=0 ):
-    pad = '    '
-    i = "\n" + level * pad
-    if len( elem ):
-        if not elem.text or not elem.text.strip():
-            elem.text = i + pad + pad
-        if not elem.tail or not elem.tail.strip():
-            elem.tail = i
-        for e in elem:
-            pretty_print_xml( e, level + 1 )
-        if not elem.tail or not elem.tail.strip():
-            elem.tail = i
-    else:
-        if level and ( not elem.tail or not elem.tail.strip() ):
-            elem.tail = i + pad
-    return elem
 def pull_repository( current_working_dir, repo_files_dir, name ):
     # Pull the latest possible contents to the repository.
     log.debug( "Pulling latest updates to the repository named '%s'" % name )
diff --git a/lib/galaxy/web/base/controller.py b/lib/galaxy/web/base/controller.py
index 96674e9c96e..8dbeb927b3d 100644
--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -22,10 +22,6 @@ from galaxy.exceptions import *
 
 from Cheetah.Template import Template
 
-pkg_resources.require( 'elementtree' )
-from elementtree import ElementTree, ElementInclude
-from elementtree.ElementTree import Element, SubElement, tostring
-
 log = logging.getLogger( __name__ )
 
 # States for passing messages
diff --git a/lib/galaxy/webapps/community/app.py b/lib/galaxy/webapps/community/app.py
index 2eb4d0cc9f4..f01576d8475 100644
--- a/lib/galaxy/webapps/community/app.py
+++ b/lib/galaxy/webapps/community/app.py
@@ -16,6 +16,7 @@ class UniverseApplication( object ):
         config.configure_logging( self.config )
         # Set up datatypes registry
         self.datatypes_registry = galaxy.datatypes.registry.Registry()
+        # TODO: Handle datatypes included in repositories - the following will only load datatypes_conf.xml.
         self.datatypes_registry.load_datatypes( self.config.root, self.config.datatypes_config )
         # Determine the database url
         if self.config.database_connection:

From 95b740f5df3954b56762b36355dc0266b0cdf4ff Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Fri, 16 Dec 2011 17:08:35 -0500
Subject: [PATCH 349/362] Always attempt to remove previously written temporary
 xml files when persisting the current datatypes registry.

---
 lib/galaxy/app.py                | 5 ++---
 lib/galaxy/datatypes/registry.py | 8 ++++++++
 2 files changed, 10 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/app.py b/lib/galaxy/app.py
index 76579324023..8f96dab2f7b 100644
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -126,8 +126,7 @@ class UniverseApplication( object ):
         try:
             # If the datatypes registry was persisted, attempt to
             # remove the temporary file in which it was written.
-            tmp_filename = self.datatypes_registry.xml_filename
-            if tmp_filename:
-                os.unlink( tmp_filename )
+            if self.datatypes_registry.xml_filename is not None:
+                os.unlink( self.datatypes_registry.xml_filename )
         except:
             pass
diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
index 9d18c8fd2c8..8a826558b60 100644
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -432,6 +432,14 @@ class Registry( object ):
             rval[ 'auto' ] = rval[ 'txt' ]
         return rval
     def to_xml_file( self ):
+        if self.xml_filename is not None:
+            # If persisted previously, attempt to remove
+            # the temporary file in which we were written.
+            try:
+                os.unlink( self.xml_filename )
+            except:
+                pass
+            self.xml_filename = None
         fd, filename = tempfile.mkstemp()
         self.xml_filename = filename
         if self.converters_path_attr:

From 63523e1dcb368f2070e8866eeece944010afca6c Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Sat, 17 Dec 2011 14:29:23 -0500
Subject: [PATCH 350/362] Trackster: fix bug in 13ba6909faae that prevented
 display in Dense mode.

---
 static/scripts/trackster.js | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index e49f9ff25f7..5c3b76ba6f5 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -3966,10 +3966,8 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
             return this.summary_draw_height + SUMMARY_TREE_TOP_PADDING;
         }
         else {
-            var rows_required = 1;
-            if (mode === "no_detail" || mode === "Squish" || mode === "Pack") {
-                var rows_required = this.incremental_slots(w_scale, result.data, mode);
-            }
+            // All other modes require slotting.
+            var rows_required = this.incremental_slots(w_scale, result.data, mode);
             // HACK: use dummy painter to get required height. Painter should be extended so that get_required_height
             // works as a static function.
             var dummy_painter = new (this.painter)(null, null, null, this.prefs, mode);

From c2c3e8c005077633b287a9ab43014dff577fc113 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Sun, 18 Dec 2011 09:16:52 -0500
Subject: [PATCH 351/362] Send the persisted data types registry instead of
 None as the value of the datatypes_config parameter to the
 setup_external_metadata method when creating the cmd_line in the
 SetMetadataToolAction.execute() method.  This eliminates the use of the
 hard-coded 'datatypes_conf.xml' file name when setting metadata externally.

---
 lib/galaxy/tools/actions/metadata.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/tools/actions/metadata.py b/lib/galaxy/tools/actions/metadata.py
index 18849849d25..b7b34ddd334 100644
--- a/lib/galaxy/tools/actions/metadata.py
+++ b/lib/galaxy/tools/actions/metadata.py
@@ -51,7 +51,7 @@ class SetMetadataToolAction( ToolAction ):
                                                                       dataset_files_path = trans.app.model.Dataset.file_path,
                                                                       output_fnames = None,
                                                                       config_root = None,
-                                                                      datatypes_config = None,
+                                                                      datatypes_config = trans.app.datatypes_registry.to_xml_file(),
                                                                       job_metadata = None,
                                                                       kwds = { 'overwrite' : overwrite } )
         incoming[ '__SET_EXTERNAL_METADATA_COMMAND_LINE__' ] = cmd_line

From 67f285a8c69484dd4f57bdc72e1653bc26aa6eb3 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Sun, 18 Dec 2011 10:52:02 -0500
Subject: [PATCH 352/362] Always set / return the absolute path of the file to
 which the datatypes registry is persisted.

---
 lib/galaxy/datatypes/registry.py | 4 ++--
 lib/galaxy/tools/__init__.py     | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
index 8a826558b60..1efa85b8607 100644
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -441,7 +441,7 @@ class Registry( object ):
                 pass
             self.xml_filename = None
         fd, filename = tempfile.mkstemp()
-        self.xml_filename = filename
+        self.xml_filename = os.path.abspath( filename )
         if self.converters_path_attr:
             converters_path_str = ' converters_path="%s"' % self.converters_path_attr
         else:
@@ -466,4 +466,4 @@ class Registry( object ):
         os.write( fd, '</sniffers>\n' )
         os.write( fd, '</datatypes>\n' )
         os.close( fd )
-        return filename
+        return os.path.abspath( filename )
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index d3d5a8ae849..a3bee301a7a 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1673,7 +1673,7 @@ class Tool:
         # datatypes conf path, so we can load the datatypes registry
         param_dict['__root_dir__'] = param_dict['GALAXY_ROOT_DIR'] = os.path.abspath( self.app.config.root )
         datatypes_config = self.app.datatypes_registry.to_xml_file()
-        param_dict['__datatypes_config__'] = param_dict['GALAXY_DATATYPES_CONF_FILE'] = os.path.abspath( datatypes_config )
+        param_dict['__datatypes_config__'] = param_dict['GALAXY_DATATYPES_CONF_FILE'] = datatypes_config
         # Return the dictionary of parameters
         return param_dict
     

From 0d1d9582e7b2ef5e0382d780e3baf8abe9188cff Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Sun, 18 Dec 2011 13:49:26 -0500
Subject: [PATCH 353/362] Only persist the datatypes registry when the
 load_datatypes() method is called.  Tools and metadata setting processes that
 create their own datatypes registry will use the existing temporary file
 rather than persisting the registry themselves.

---
 lib/galaxy/datatypes/registry.py     | 4 +++-
 lib/galaxy/jobs/__init__.py          | 2 +-
 lib/galaxy/tools/__init__.py         | 3 +--
 lib/galaxy/tools/actions/metadata.py | 2 +-
 4 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
index 1efa85b8607..1eab74e61d8 100644
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -174,6 +174,9 @@ class Registry( object ):
                             self.log.debug( 'Loaded sniffer for datatype: %s' % dtype )
                         except Exception, exc:
                             self.log.warning( 'Error appending datatype %s to sniff_order, problem: %s' % ( dtype, str( exc ) ) )
+            # Persist the xml form of the registry into a temporary file so that it
+            # can be loaded from the command line by tools and set_metadata processing.
+            self.to_xml_file()
         # Default values.
         if not self.datatypes_by_extension:
             self.datatypes_by_extension = { 
@@ -466,4 +469,3 @@ class Registry( object ):
         os.write( fd, '</sniffers>\n' )
         os.write( fd, '</datatypes>\n' )
         os.close( fd )
-        return os.path.abspath( filename )
diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index ce5ceaca601..bffefc54df1 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -868,7 +868,7 @@ class JobWrapper( object ):
         if config_root is None:
             config_root = self.app.config.root
         if datatypes_config is None:
-            datatypes_config = self.app.datatypes_registry.to_xml_file()
+            datatypes_config = self.app.datatypes_registry.xml_filename
         return self.external_output_metadata.setup_external_metadata( [ output_dataset_assoc.dataset for output_dataset_assoc in job.output_datasets ],
                                                                       self.sa_session,
                                                                       exec_dir = exec_dir,
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index a3bee301a7a..7959ddcb301 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1672,8 +1672,7 @@ class Tool:
         # For the upload tool, we need to know the root directory and the 
         # datatypes conf path, so we can load the datatypes registry
         param_dict['__root_dir__'] = param_dict['GALAXY_ROOT_DIR'] = os.path.abspath( self.app.config.root )
-        datatypes_config = self.app.datatypes_registry.to_xml_file()
-        param_dict['__datatypes_config__'] = param_dict['GALAXY_DATATYPES_CONF_FILE'] = datatypes_config
+        param_dict['__datatypes_config__'] = param_dict['GALAXY_DATATYPES_CONF_FILE'] = self.app.datatypes_registry.xml_filename
         # Return the dictionary of parameters
         return param_dict
     
diff --git a/lib/galaxy/tools/actions/metadata.py b/lib/galaxy/tools/actions/metadata.py
index b7b34ddd334..f5b6151d6a8 100644
--- a/lib/galaxy/tools/actions/metadata.py
+++ b/lib/galaxy/tools/actions/metadata.py
@@ -51,7 +51,7 @@ class SetMetadataToolAction( ToolAction ):
                                                                       dataset_files_path = trans.app.model.Dataset.file_path,
                                                                       output_fnames = None,
                                                                       config_root = None,
-                                                                      datatypes_config = trans.app.datatypes_registry.to_xml_file(),
+                                                                      datatypes_config = trans.app.datatypes_registry.xml_filename,
                                                                       job_metadata = None,
                                                                       kwds = { 'overwrite' : overwrite } )
         incoming[ '__SET_EXTERNAL_METADATA_COMMAND_LINE__' ] = cmd_line

From 7ed16efcf9b3e816520baa90be9ea76ab825ab17 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Mon, 19 Dec 2011 13:40:18 -0500
Subject: [PATCH 354/362] Add hidden attribute to tool outputs so that an
 output can be hidden by default.

---
 lib/galaxy/tools/__init__.py         | 4 +++-
 lib/galaxy/tools/actions/__init__.py | 2 ++
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 7959ddcb301..61bcd7edb36 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -316,7 +316,7 @@ class ToolOutput( object ):
     """
 
     def __init__( self, name, format=None, format_source=None, metadata_source=None, 
-                  parent=None, label=None, filters = None, actions = None ):
+                  parent=None, label=None, filters = None, actions = None, hidden=False ):
         self.name = name
         self.format = format
         self.format_source = format_source
@@ -325,6 +325,7 @@ class ToolOutput( object ):
         self.label = label
         self.filters = filters or []
         self.actions = actions
+        self.hidden = hidden
 
     # Tuple emulation
 
@@ -677,6 +678,7 @@ class Tool:
             output.count = int( data_elem.get("count", 1) )
             output.filters = data_elem.findall( 'filter' )
             output.from_work_dir = data_elem.get("from_work_dir", None)
+            output.hidden = data_elem.get("hidden", None) in [ 'true', 'True' ]
             output.tool = self
             output.actions = ToolOutputActionGroup( output, data_elem.find( 'actions' ) )
             self.outputs[ output.name ] = output
diff --git a/lib/galaxy/tools/actions/__init__.py b/lib/galaxy/tools/actions/__init__.py
index 4b702e4d722..67f83f5ebed 100644
--- a/lib/galaxy/tools/actions/__init__.py
+++ b/lib/galaxy/tools/actions/__init__.py
@@ -286,6 +286,8 @@ class DefaultToolAction( object ):
                                             if str( getattr( check, when_elem.get( 'attribute' ) ) ) == when_elem.get( 'value', None ):
                                                 ext = when_elem.get( 'format', ext )
                     data = trans.app.model.HistoryDatasetAssociation( extension=ext, create_dataset=True, sa_session=trans.sa_session )
+                    if output.hidden:
+                        data.visible = False
                     # Commit the dataset immediately so it gets database assigned unique id
                     trans.sa_session.add( data )
                     trans.sa_session.flush()

From 1db16e413bfd780cc35760e5252c7b6dfd792082 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Mon, 19 Dec 2011 15:00:53 -0500
Subject: [PATCH 355/362] Clean up implementation in 303741fda0ec

---
 lib/galaxy/tools/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 61bcd7edb36..5d0303ab377 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -678,7 +678,7 @@ class Tool:
             output.count = int( data_elem.get("count", 1) )
             output.filters = data_elem.findall( 'filter' )
             output.from_work_dir = data_elem.get("from_work_dir", None)
-            output.hidden = data_elem.get("hidden", None) in [ 'true', 'True' ]
+            output.hidden = util.string_as_bool( data_elem.get("hidden", "") )
             output.tool = self
             output.actions = ToolOutputActionGroup( output, data_elem.find( 'actions' ) )
             self.outputs[ output.name ] = output

From b61113f65c38dd554ed396b8d6c9b268fbecc2b4 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Tue, 20 Dec 2011 09:38:15 -0500
Subject: [PATCH 356/362] Ensure that the integrated datatypes registry configs
 exist when needed.

---
 lib/galaxy/app.py                    | 4 ++--
 lib/galaxy/datatypes/registry.py     | 6 ++++++
 lib/galaxy/jobs/__init__.py          | 2 +-
 lib/galaxy/tools/__init__.py         | 2 +-
 lib/galaxy/tools/actions/metadata.py | 2 +-
 5 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/app.py b/lib/galaxy/app.py
index 8f96dab2f7b..088f9cc31ed 100644
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -126,7 +126,7 @@ class UniverseApplication( object ):
         try:
             # If the datatypes registry was persisted, attempt to
             # remove the temporary file in which it was written.
-            if self.datatypes_registry.xml_filename is not None:
-                os.unlink( self.datatypes_registry.xml_filename )
+            if self.datatypes_registry.integrated_datatypes_configs is not None:
+                os.unlink( self.datatypes_registry.integrated_datatypes_configs )
         except:
             pass
diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
index 1eab74e61d8..188c9968901 100644
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -434,6 +434,12 @@ class Registry( object ):
         if 'auto' not in rval and 'txt' in rval: #need to manually add 'auto' datatype
             rval[ 'auto' ] = rval[ 'txt' ]
         return rval
+    @property
+    def integrated_datatypes_configs( self ):
+        if self.xml_filename and os.path.isfile( self.xml_filename ):
+            return self.xml_filename
+        self.to_xml_file()
+        return self.xml_filename
     def to_xml_file( self ):
         if self.xml_filename is not None:
             # If persisted previously, attempt to remove
diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index bffefc54df1..737d2e6f185 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -868,7 +868,7 @@ class JobWrapper( object ):
         if config_root is None:
             config_root = self.app.config.root
         if datatypes_config is None:
-            datatypes_config = self.app.datatypes_registry.xml_filename
+            datatypes_config = self.app.datatypes_registry.integrated_datatypes_configs
         return self.external_output_metadata.setup_external_metadata( [ output_dataset_assoc.dataset for output_dataset_assoc in job.output_datasets ],
                                                                       self.sa_session,
                                                                       exec_dir = exec_dir,
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 5d0303ab377..25034b7f5fb 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1674,7 +1674,7 @@ class Tool:
         # For the upload tool, we need to know the root directory and the 
         # datatypes conf path, so we can load the datatypes registry
         param_dict['__root_dir__'] = param_dict['GALAXY_ROOT_DIR'] = os.path.abspath( self.app.config.root )
-        param_dict['__datatypes_config__'] = param_dict['GALAXY_DATATYPES_CONF_FILE'] = self.app.datatypes_registry.xml_filename
+        param_dict['__datatypes_config__'] = param_dict['GALAXY_DATATYPES_CONF_FILE'] = self.app.datatypes_registry.integrated_datatypes_configs
         # Return the dictionary of parameters
         return param_dict
     
diff --git a/lib/galaxy/tools/actions/metadata.py b/lib/galaxy/tools/actions/metadata.py
index f5b6151d6a8..ce7ca540395 100644
--- a/lib/galaxy/tools/actions/metadata.py
+++ b/lib/galaxy/tools/actions/metadata.py
@@ -51,7 +51,7 @@ class SetMetadataToolAction( ToolAction ):
                                                                       dataset_files_path = trans.app.model.Dataset.file_path,
                                                                       output_fnames = None,
                                                                       config_root = None,
-                                                                      datatypes_config = trans.app.datatypes_registry.xml_filename,
+                                                                      datatypes_config = trans.app.datatypes_registry.integrated_datatypes_configs,
                                                                       job_metadata = None,
                                                                       kwds = { 'overwrite' : overwrite } )
         incoming[ '__SET_EXTERNAL_METADATA_COMMAND_LINE__' ] = cmd_line

From 726dc8df9fe9e413cf60140bee062fb35f81482d Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Tue, 20 Dec 2011 14:15:39 -0500
Subject: [PATCH 357/362] Make the tool_shed_install.xml.sample file ready for
 installing the correct versions of the emboss_5 and emboss_datatypes
 repositories from the main Galaxy tool shed.

---
 tool_shed_install.xml.sample | 218 ++++++++++++++++++-----------------
 1 file changed, 110 insertions(+), 108 deletions(-)

diff --git a/tool_shed_install.xml.sample b/tool_shed_install.xml.sample
index d5eb434ca7f..01e117f7e4f 100644
--- a/tool_shed_install.xml.sample
+++ b/tool_shed_install.xml.sample
@@ -1,114 +1,116 @@
 <?xml version="1.0"?>
 <toolshed name="toolshed.g2.bx.psu.edu">
+    <!-- The following repository includes no tools, so nothing will be loaded into the tool panel. -->
+    <repository name="emboss_datatypes" description="Datatypes for Emboss tools" changeset_revision="a89163f31369" />
     <section name="EMBOSS" id="EMBOSSLite">
-        <repository name="emboss_5" description="Galaxy wrappers for EMBOSS version 5 tools" changeset_revision="PlaceHereWhenKnown">
-            <tool file="emboss_5/emboss_antigenic.xml" id="EMBOSS: antigenic1" version="5.0.0" />
-            <tool file="emboss_5/emboss_backtranseq.xml" id="EMBOSS: backtranseq2" version="5.0.0" />
-            <tool file="emboss_5/emboss_banana.xml" id="EMBOSS: banana3" version="5.0.0" />
-            <tool file="emboss_5/emboss_biosed.xml" id="EMBOSS: biosed4" version="5.0.0" />
-            <tool file="emboss_5/emboss_btwisted.xml" id="EMBOSS: btwisted5" version="5.0.0" />
-            <tool file="emboss_5/emboss_cai_custom.xml" id="EMBOSS: cai_custom6" version="5.0.0" />
-            <tool file="emboss_5/emboss_cai.xml" id="EMBOSS: cai6" version="5.0.0" />
-            <tool file="emboss_5/emboss_chaos.xml" id="EMBOSS: chaos7" version="5.0.0" />
-            <tool file="emboss_5/emboss_charge.xml" id="EMBOSS: charge8" version="5.0.0" />
-            <tool file="emboss_5/emboss_checktrans.xml" id="EMBOSS: checktrans9" version="5.0.0" />
-            <tool file="emboss_5/emboss_chips.xml" id="EMBOSS: chips10" version="5.0.0" />
-            <tool file="emboss_5/emboss_cirdna.xml" id="EMBOSS: cirdna11" version="5.0.0" />
-            <tool file="emboss_5/emboss_codcmp.xml" id="EMBOSS: codcmp12" version="5.0.0" />
-            <tool file="emboss_5/emboss_coderet.xml" id="EMBOSS: coderet13" version="5.0.0" />
-            <tool file="emboss_5/emboss_compseq.xml" id="EMBOSS: compseq14" version="5.0.0" />
-            <tool file="emboss_5/emboss_cpgplot.xml" id="EMBOSS: cpgplot15" version="5.0.0" />
-            <tool file="emboss_5/emboss_cpgreport.xml" id="EMBOSS: cpgreport16" version="5.0.0" />
-            <tool file="emboss_5/emboss_cusp.xml" id="EMBOSS: cusp17" version="5.0.0" />
-            <tool file="emboss_5/emboss_cutseq.xml" id="EMBOSS: cutseq18" version="5.0.0" />
-            <tool file="emboss_5/emboss_dan.xml" id="EMBOSS: dan19" version="5.0.0" />
-            <tool file="emboss_5/emboss_degapseq.xml" id="EMBOSS: degapseq20" version="5.0.0" />
-            <tool file="emboss_5/emboss_descseq.xml" id="EMBOSS: descseq21" version="5.0.0" />
-            <tool file="emboss_5/emboss_diffseq.xml" id="EMBOSS: diffseq22" version="5.0.0" />
-            <tool file="emboss_5/emboss_digest.xml" id="EMBOSS: digest23" version="5.0.0" />
-            <tool file="emboss_5/emboss_dotmatcher.xml" id="EMBOSS: dotmatcher24" version="5.0.0" />
-            <tool file="emboss_5/emboss_dotpath.xml" id="EMBOSS: dotpath25" version="5.0.0" />
-            <tool file="emboss_5/emboss_dottup.xml" id="EMBOSS: dottup26" version="5.0.0" />
-            <tool file="emboss_5/emboss_dreg.xml" id="EMBOSS: dreg27" version="5.0.0" />
-            <tool file="emboss_5/emboss_einverted.xml" id="EMBOSS: einverted28" version="5.0.0" />
-            <tool file="emboss_5/emboss_epestfind.xml" id="EMBOSS: epestfind29" version="5.0.0" />
-            <tool file="emboss_5/emboss_equicktandem.xml" id="EMBOSS: equicktandem31" version="5.0.0" />
-            <tool file="emboss_5/emboss_est2genome.xml" id="EMBOSS: est2genome32" version="5.0.0" />
-            <tool file="emboss_5/emboss_etandem.xml" id="EMBOSS: etandem33" version="5.0.0" />
-            <tool file="emboss_5/emboss_extractfeat.xml" id="EMBOSS: extractfeat34" version="5.0.0" />
-            <tool file="emboss_5/emboss_extractseq.xml" id="EMBOSS: extractseq35" version="5.0.0" />
-            <tool file="emboss_5/emboss_freak.xml" id="EMBOSS: freak36" version="5.0.0" />
-            <tool file="emboss_5/emboss_fuzznuc.xml" id="EMBOSS: fuzznuc37" version="5.0.0" />
-            <tool file="emboss_5/emboss_fuzzpro.xml" id="EMBOSS: fuzzpro38" version="5.0.0" />
-            <tool file="emboss_5/emboss_fuzztran.xml" id="EMBOSS: fuzztran39" version="5.0.0" />
-            <tool file="emboss_5/emboss_garnier.xml" id="EMBOSS: garnier40" version="5.0.0" />
-            <tool file="emboss_5/emboss_geecee.xml" id="EMBOSS: geecee41" version="5.0.0" />
-            <tool file="emboss_5/emboss_getorf.xml" id="EMBOSS: getorf42" version="5.0.0" />
-            <tool file="emboss_5/emboss_helixturnhelix.xml" id="EMBOSS: helixturnhelix43" version="5.0.0" />
-            <tool file="emboss_5/emboss_hmoment.xml" id="EMBOSS: hmoment44" version="5.0.0" />
-            <tool file="emboss_5/emboss_iep.xml" id="EMBOSS: iep45" version="5.0.0" />
-            <tool file="emboss_5/emboss_infoseq.xml" id="EMBOSS: infoseq46" version="5.0.0" />
-            <tool file="emboss_5/emboss_isochore.xml" id="EMBOSS: isochore47" version="5.0.0" />
-            <tool file="emboss_5/emboss_lindna.xml" id="EMBOSS: lindna48" version="5.0.0" />
-            <tool file="emboss_5/emboss_marscan.xml" id="EMBOSS: marscan49" version="5.0.0" />
-            <tool file="emboss_5/emboss_maskfeat.xml" id="EMBOSS: maskfeat50" version="5.0.0" />
-            <tool file="emboss_5/emboss_maskseq.xml" id="EMBOSS: maskseq51" version="5.0.0" />
-            <tool file="emboss_5/emboss_matcher.xml" id="EMBOSS: matcher52" version="5.0.0" />
-            <tool file="emboss_5/emboss_megamerger.xml" id="EMBOSS: megamerger53" version="5.0.0" />
-            <tool file="emboss_5/emboss_merger.xml" id="EMBOSS: merger54" version="5.0.0" />
-            <tool file="emboss_5/emboss_msbar.xml" id="EMBOSS: msbar55" version="5.0.0" />
-            <tool file="emboss_5/emboss_needle.xml" id="EMBOSS: needle56" version="5.0.0" />
-            <tool file="emboss_5/emboss_newcpgreport.xml" id="EMBOSS: newcpgreport57" version="5.0.0" />
-            <tool file="emboss_5/emboss_newcpgseek.xml" id="EMBOSS: newcpgseek58" version="5.0.0" />
-            <tool file="emboss_5/emboss_newseq.xml" id="EMBOSS: newseq59" version="5.0.0" />
-            <tool file="emboss_5/emboss_noreturn.xml" id="EMBOSS: noreturn60" version="5.0.0" />
-            <tool file="emboss_5/emboss_notseq.xml" id="EMBOSS: notseq61" version="5.0.0" />
-            <tool file="emboss_5/emboss_nthseq.xml" id="EMBOSS: nthseq62" version="5.0.0" />
-            <tool file="emboss_5/emboss_octanol.xml" id="EMBOSS: octanol63" version="5.0.0" />
-            <tool file="emboss_5/emboss_oddcomp.xml" id="EMBOSS: oddcomp64" version="5.0.0" />
-            <tool file="emboss_5/emboss_palindrome.xml" id="EMBOSS: palindrome65" version="5.0.0" />
-            <tool file="emboss_5/emboss_pasteseq.xml" id="EMBOSS: pasteseq66" version="5.0.0" />
-            <tool file="emboss_5/emboss_patmatdb.xml" id="EMBOSS: patmatdb67" version="5.0.0" />
-            <tool file="emboss_5/emboss_pepcoil.xml" id="EMBOSS: pepcoil68" version="5.0.0" />
-            <tool file="emboss_5/emboss_pepinfo.xml" id="EMBOSS: pepinfo69" version="5.0.0" />
-            <tool file="emboss_5/emboss_pepnet.xml" id="EMBOSS: pepnet70" version="5.0.0" />
-            <tool file="emboss_5/emboss_pepstats.xml" id="EMBOSS: pepstats71" version="5.0.0" />
-            <tool file="emboss_5/emboss_pepwheel.xml" id="EMBOSS: pepwheel72" version="5.0.0" />
-            <tool file="emboss_5/emboss_pepwindow.xml" id="EMBOSS: pepwindow73" version="5.0.0" />
-            <tool file="emboss_5/emboss_pepwindowall.xml" id="EMBOSS: pepwindowall74" version="5.0.0" />
-            <tool file="emboss_5/emboss_plotcon.xml" id="EMBOSS: plotcon75" version="5.0.0" />
-            <tool file="emboss_5/emboss_plotorf.xml" id="EMBOSS: plotorf76" version="5.0.0" />
-            <tool file="emboss_5/emboss_polydot.xml" id="EMBOSS: polydot77" version="5.0.0" />
-            <tool file="emboss_5/emboss_preg.xml" id="EMBOSS: preg78" version="5.0.0" />
-            <tool file="emboss_5/emboss_prettyplot.xml" id="EMBOSS: prettyplot79" version="5.0.0" />
-            <tool file="emboss_5/emboss_prettyseq.xml" id="EMBOSS: prettyseq80" version="5.0.0" />
-            <tool file="emboss_5/emboss_primersearch.xml" id="EMBOSS: primersearch81" version="5.0.0" />
-            <tool file="emboss_5/emboss_revseq.xml" id="EMBOSS: revseq82" version="5.0.0" />
-            <tool file="emboss_5/emboss_seqmatchall.xml" id="EMBOSS: seqmatchall83" version="5.0.0" />
-            <tool file="emboss_5/emboss_seqret.xml" id="EMBOSS: seqret84" version="5.0.0" />
-            <tool file="emboss_5/emboss_showfeat.xml" id="EMBOSS: showfeat85" version="5.0.0" />
-            <tool file="emboss_5/emboss_shuffleseq.xml" id="EMBOSS: shuffleseq87" version="5.0.0" />
-            <tool file="emboss_5/emboss_sigcleave.xml" id="EMBOSS: sigcleave88" version="5.0.0" />
-            <tool file="emboss_5/emboss_sirna.xml" id="EMBOSS: sirna89" version="5.0.0" />
-            <tool file="emboss_5/emboss_sixpack.xml" id="EMBOSS: sixpack90" version="5.0.0" />
-            <tool file="emboss_5/emboss_skipseq.xml" id="EMBOSS: skipseq91" version="5.0.0" />
-            <tool file="emboss_5/emboss_splitter.xml" id="EMBOSS: splitter92" version="5.0.0" />
-            <tool file="emboss_5/emboss_supermatcher.xml" id="EMBOSS: supermatcher95" version="5.0.0" />
-            <tool file="emboss_5/emboss_syco.xml" id="EMBOSS: syco96" version="5.0.0" />
-            <tool file="emboss_5/emboss_tcode.xml" id="EMBOSS: tcode97" version="5.0.0" />
-            <tool file="emboss_5/emboss_textsearch.xml" id="EMBOSS: textsearch98" version="5.0.0" />
-            <tool file="emboss_5/emboss_tmap.xml" id="EMBOSS: tmap99" version="5.0.0" />
-            <tool file="emboss_5/emboss_tranalign.xml" id="EMBOSS: tranalign100" version="5.0.0" />
-            <tool file="emboss_5/emboss_transeq.xml" id="EMBOSS: transeq101" version="5.0.0" />
-            <tool file="emboss_5/emboss_trimest.xml" id="EMBOSS: trimest102" version="5.0.0" />
-            <tool file="emboss_5/emboss_trimseq.xml" id="EMBOSS: trimseq103" version="5.0.0" />
-            <tool file="emboss_5/emboss_twofeat.xml" id="EMBOSS: twofeat104" version="5.0.0" />
-            <tool file="emboss_5/emboss_union.xml" id="EMBOSS: union105" version="5.0.0" />
-            <tool file="emboss_5/emboss_vectorstrip.xml" id="EMBOSS: vectorstrip106" version="5.0.0" />
-            <tool file="emboss_5/emboss_water.xml" id="EMBOSS: water107" version="5.0.0" />
-            <tool file="emboss_5/emboss_wobble.xml" id="EMBOSS: wobble108" version="5.0.0" />
-            <tool file="emboss_5/emboss_wordcount.xml" id="EMBOSS: wordcount109" version="5.0.0" />
-            <tool file="emboss_5/emboss_wordmatch.xml" id="EMBOSS: wordmatch110" version="5.0.0" />
+        <repository name="emboss_5" description="Galaxy wrappers for EMBOSS version 5.0.0 tools" changeset_revision="b94ca591877b">
+            <tool id="EMBOSS: antigenic1" version="5.0.0" />
+            <tool id="EMBOSS: backtranseq2" version="5.0.0" />
+            <tool id="EMBOSS: banana3" version="5.0.0" />
+            <tool id="EMBOSS: biosed4" version="5.0.0" />
+            <tool id="EMBOSS: btwisted5" version="5.0.0" />
+            <tool id="EMBOSS: cai_custom6" version="5.0.0" />
+            <tool id="EMBOSS: cai6" version="5.0.0" />
+            <tool id="EMBOSS: chaos7" version="5.0.0" />
+            <tool id="EMBOSS: charge8" version="5.0.0" />
+            <tool id="EMBOSS: checktrans9" version="5.0.0" />
+            <tool id="EMBOSS: chips10" version="5.0.0" />
+            <tool id="EMBOSS: cirdna11" version="5.0.0" />
+            <tool id="EMBOSS: codcmp12" version="5.0.0" />
+            <tool id="EMBOSS: coderet13" version="5.0.0" />
+            <tool id="EMBOSS: compseq14" version="5.0.0" />
+            <tool id="EMBOSS: cpgplot15" version="5.0.0" />
+            <tool id="EMBOSS: cpgreport16" version="5.0.0" />
+            <tool id="EMBOSS: cusp17" version="5.0.0" />
+            <tool id="EMBOSS: cutseq18" version="5.0.0" />
+            <tool id="EMBOSS: dan19" version="5.0.0" />
+            <tool id="EMBOSS: degapseq20" version="5.0.0" />
+            <tool id="EMBOSS: descseq21" version="5.0.0" />
+            <tool id="EMBOSS: diffseq22" version="5.0.0" />
+            <tool id="EMBOSS: digest23" version="5.0.0" />
+            <tool id="EMBOSS: dotmatcher24" version="5.0.0" />
+            <tool id="EMBOSS: dotpath25" version="5.0.0" />
+            <tool id="EMBOSS: dottup26" version="5.0.0" />
+            <tool id="EMBOSS: dreg27" version="5.0.0" />
+            <tool id="EMBOSS: einverted28" version="5.0.0" />
+            <tool id="EMBOSS: epestfind29" version="5.0.0" />
+            <tool id="EMBOSS: equicktandem31" version="5.0.0" />
+            <tool id="EMBOSS: est2genome32" version="5.0.0" />
+            <tool id="EMBOSS: etandem33" version="5.0.0" />
+            <tool id="EMBOSS: extractfeat34" version="5.0.0" />
+            <tool id="EMBOSS: extractseq35" version="5.0.0" />
+            <tool id="EMBOSS: freak36" version="5.0.0" />
+            <tool id="EMBOSS: fuzznuc37" version="5.0.0" />
+            <tool id="EMBOSS: fuzzpro38" version="5.0.0" />
+            <tool id="EMBOSS: fuzztran39" version="5.0.0" />
+            <tool id="EMBOSS: garnier40" version="5.0.0" />
+            <tool id="EMBOSS: geecee41" version="5.0.0" />
+            <tool id="EMBOSS: getorf42" version="5.0.0" />
+            <tool id="EMBOSS: helixturnhelix43" version="5.0.0" />
+            <tool id="EMBOSS: hmoment44" version="5.0.0" />
+            <tool id="EMBOSS: iep45" version="5.0.0" />
+            <tool id="EMBOSS: infoseq46" version="5.0.0" />
+            <tool id="EMBOSS: isochore47" version="5.0.0" />
+            <tool id="EMBOSS: lindna48" version="5.0.0" />
+            <tool id="EMBOSS: marscan49" version="5.0.0" />
+            <tool id="EMBOSS: maskfeat50" version="5.0.0" />
+            <tool id="EMBOSS: maskseq51" version="5.0.0" />
+            <tool id="EMBOSS: matcher52" version="5.0.0" />
+            <tool id="EMBOSS: megamerger53" version="5.0.0" />
+            <tool id="EMBOSS: merger54" version="5.0.0" />
+            <tool id="EMBOSS: msbar55" version="5.0.0" />
+            <tool id="EMBOSS: needle56" version="5.0.0" />
+            <tool id="EMBOSS: newcpgreport57" version="5.0.0" />
+            <tool id="EMBOSS: newcpgseek58" version="5.0.0" />
+            <tool id="EMBOSS: newseq59" version="5.0.0" />
+            <tool id="EMBOSS: noreturn60" version="5.0.0" />
+            <tool id="EMBOSS: notseq61" version="5.0.0" />
+            <tool id="EMBOSS: nthseq62" version="5.0.0" />
+            <tool id="EMBOSS: octanol63" version="5.0.0" />
+            <tool id="EMBOSS: oddcomp64" version="5.0.0" />
+            <tool id="EMBOSS: palindrome65" version="5.0.0" />
+            <tool id="EMBOSS: pasteseq66" version="5.0.0" />
+            <tool id="EMBOSS: patmatdb67" version="5.0.0" />
+            <tool id="EMBOSS: pepcoil68" version="5.0.0" />
+            <tool id="EMBOSS: pepinfo69" version="5.0.0" />
+            <tool id="EMBOSS: pepnet70" version="5.0.0" />
+            <tool id="EMBOSS: pepstats71" version="5.0.0" />
+            <tool id="EMBOSS: pepwheel72" version="5.0.0" />
+            <tool id="EMBOSS: pepwindow73" version="5.0.0" />
+            <tool id="EMBOSS: pepwindowall74" version="5.0.0" />
+            <tool id="EMBOSS: plotcon75" version="5.0.0" />
+            <tool id="EMBOSS: plotorf76" version="5.0.0" />
+            <tool id="EMBOSS: polydot77" version="5.0.0" />
+            <tool id="EMBOSS: preg78" version="5.0.0" />
+            <tool id="EMBOSS: prettyplot79" version="5.0.0" />
+            <tool id="EMBOSS: prettyseq80" version="5.0.0" />
+            <tool id="EMBOSS: primersearch81" version="5.0.0" />
+            <tool id="EMBOSS: revseq82" version="5.0.0" />
+            <tool id="EMBOSS: seqmatchall83" version="5.0.0" />
+            <tool id="EMBOSS: seqret84" version="5.0.0" />
+            <tool id="EMBOSS: showfeat85" version="5.0.0" />
+            <tool id="EMBOSS: shuffleseq87" version="5.0.0" />
+            <tool id="EMBOSS: sigcleave88" version="5.0.0" />
+            <tool id="EMBOSS: sirna89" version="5.0.0" />
+            <tool id="EMBOSS: sixpack90" version="5.0.0" />
+            <tool id="EMBOSS: skipseq91" version="5.0.0" />
+            <tool id="EMBOSS: splitter92" version="5.0.0" />
+            <tool id="EMBOSS: supermatcher95" version="5.0.0" />
+            <tool id="EMBOSS: syco96" version="5.0.0" />
+            <tool id="EMBOSS: tcode97" version="5.0.0" />
+            <tool id="EMBOSS: textsearch98" version="5.0.0" />
+            <tool id="EMBOSS: tmap99" version="5.0.0" />
+            <tool id="EMBOSS: tranalign100" version="5.0.0" />
+            <tool id="EMBOSS: transeq101" version="5.0.0" />
+            <tool id="EMBOSS: trimest102" version="5.0.0" />
+            <tool id="EMBOSS: trimseq103" version="5.0.0" />
+            <tool id="EMBOSS: twofeat104" version="5.0.0" />
+            <tool id="EMBOSS: union105" version="5.0.0" />
+            <tool id="EMBOSS: vectorstrip106" version="5.0.0" />
+            <tool id="EMBOSS: water107" version="5.0.0" />
+            <tool id="EMBOSS: wobble108" version="5.0.0" />
+            <tool id="EMBOSS: wordcount109" version="5.0.0" />
+            <tool id="EMBOSS: wordmatch110" version="5.0.0" />
         </repository>
     </section>
 </toolshed>

From 98264b48275410f43547b4ffb1702a9a94207fd1 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Tue, 20 Dec 2011 14:31:13 -0500
Subject: [PATCH 358/362] Don't allow repository names to be changed if the
 repository has been cloned at least 1 time.

---
 .../webapps/community/repository/manage_repository.mako  | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/templates/webapps/community/repository/manage_repository.mako b/templates/webapps/community/repository/manage_repository.mako
index 5adea847aaa..a4c1195ab13 100644
--- a/templates/webapps/community/repository/manage_repository.mako
+++ b/templates/webapps/community/repository/manage_repository.mako
@@ -139,7 +139,14 @@
             %endif
             <div class="form-row">
                 <label>Name:</label>
-                <input name="repo_name" type="textfield" value="${repo_name}" size="40"/>
+                %if repository.times_downloaded > 0:
+                    ${repo_name}
+                %else:
+                    <input name="repo_name" type="textfield" value="${repo_name}" size="40"/>
+                %endif
+                <div class="toolParamHelp" style="clear: both;">
+                    Repository names cannot be changed if the repository has been cloned.
+                </div>
                 <div style="clear: both"></div>
             </div>
             <div class="form-row">

From 08013f4ef1934fd160a236da72fe819d3e79cd14 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Tue, 20 Dec 2011 15:40:07 -0500
Subject: [PATCH 359/362] Add UCSC VCF external display application.

---
 datatypes_conf.xml.sample         |  1 +
 display_applications/ucsc/vcf.xml | 17 +++++++++++++++++
 2 files changed, 18 insertions(+)
 create mode 100644 display_applications/ucsc/vcf.xml

diff --git a/datatypes_conf.xml.sample b/datatypes_conf.xml.sample
index 0597212ef76..73e147ee71f 100644
--- a/datatypes_conf.xml.sample
+++ b/datatypes_conf.xml.sample
@@ -162,6 +162,7 @@
       <converter file="vcf_to_vcf_bgzip_converter.xml" target_datatype="vcf_bgzip"/>
       <converter file="vcf_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
       <converter file="vcf_to_summary_tree_converter.xml" target_datatype="summary_tree"/>
+      <display file="ucsc/vcf.xml" />
       <display file="igv/vcf.xml" />
     </datatype>
     <datatype extension="bcf" type="galaxy.datatypes.binary:Binary" subclass="True"/>
diff --git a/display_applications/ucsc/vcf.xml b/display_applications/ucsc/vcf.xml
new file mode 100644
index 00000000000..1791199d06e
--- /dev/null
+++ b/display_applications/ucsc/vcf.xml
@@ -0,0 +1,17 @@
+<display id="ucsc_vcf" version="1.0.0" name="display at UCSC">
+    <!-- Load links from file: one line to one link -->
+    <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0">
+        <!-- Define parameters by column from file, allow splitting on builds -->
+        <dynamic_param name="site_id" value="0"/>
+        <dynamic_param name="ucsc_link" value="1"/>
+        <dynamic_param name="builds" value="2" split="True" separator="," />
+        <!-- Filter out some of the links based upon matching site_id to a Galaxy application configuration parameter and by dataset dbkey -->
+        <filter>${site_id in $APP.config.ucsc_display_sites}</filter>
+        <filter>${dataset.dbkey in $builds}</filter>
+        <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
+        <url>${ucsc_link}db=${qp($bgzip_file.dbkey)}&amp;hgt.customText=${qp($track.url)}</url>
+        <param type="data" name="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz" format="vcf_bgzip" />
+        <param type="data" name="tabix_file" dataset="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz.tbi" format="tabix" />
+        <param type="template" name="track" viewable="True">track type="vcfTabix" name="${bgzip_file.name.replace( '\\', '\\\\' ).replace( '"', '\\"' )}" bigDataUrl="${bgzip_file.url}" db="${bgzip_file.dbkey}"</param>
+    </dynamic_links>
+</display>

From 9d0e6312038386d0db024aa7fa085ecd9ccc997c Mon Sep 17 00:00:00 2001
From: Dave Clements <clements@galaxyproject.org>
Date: Mon, 19 Dec 2011 02:44:31 -0800
Subject: [PATCH 360/362] Updated "Example" images shown at the bottom of many
 "Operate on Genomic Invervals" tool pages.  Old onew were looking dated. New
 ones look, well, newer, and cover more cases.

---
 static/operation_icons/gops_baseCoverage.gif  | Bin 0 -> 11961 bytes
 static/operation_icons/gops_clusterFind.gif   | Bin 0 -> 8995 bytes
 static/operation_icons/gops_clusterMerge.gif  | Bin 0 -> 8259 bytes
 static/operation_icons/gops_complement.gif    | Bin 1328 -> 10054 bytes
 static/operation_icons/gops_concatenate.gif   | Bin 1716 -> 13189 bytes
 .../gops_intersectOverlappingIntervals.gif    | Bin 0 -> 9518 bytes
 .../gops_intersectOverlappingPieces.gif       | Bin 0 -> 7353 bytes
 static/operation_icons/gops_joinFullOuter.gif | Bin 0 -> 15322 bytes
 static/operation_icons/gops_joinInner.gif     | Bin 0 -> 9648 bytes
 static/operation_icons/gops_joinLeftOuter.gif | Bin 0 -> 13683 bytes
 .../operation_icons/gops_joinRecordsList.gif  | Bin 0 -> 70212 bytes
 .../operation_icons/gops_joinRightOuter.gif   | Bin 0 -> 14250 bytes
 static/operation_icons/gops_merge.gif         | Bin 1473 -> 9138 bytes
 .../gops_subtractOverlappingIntervals.gif     | Bin 0 -> 9416 bytes
 .../gops_subtractOverlappingPieces.gif        | Bin 0 -> 9373 bytes
 tools/new_operations/basecoverage.xml         |   6 ++-
 tools/new_operations/cluster.xml              |  12 +++--
 tools/new_operations/intersect.xml            |  12 +++--
 tools/new_operations/join.xml                 |  44 +++++-------------
 tools/new_operations/subtract.xml             |  10 +++-
 20 files changed, 42 insertions(+), 42 deletions(-)
 create mode 100644 static/operation_icons/gops_baseCoverage.gif
 create mode 100644 static/operation_icons/gops_clusterFind.gif
 create mode 100644 static/operation_icons/gops_clusterMerge.gif
 create mode 100644 static/operation_icons/gops_intersectOverlappingIntervals.gif
 create mode 100644 static/operation_icons/gops_intersectOverlappingPieces.gif
 create mode 100644 static/operation_icons/gops_joinFullOuter.gif
 create mode 100644 static/operation_icons/gops_joinInner.gif
 create mode 100644 static/operation_icons/gops_joinLeftOuter.gif
 create mode 100644 static/operation_icons/gops_joinRecordsList.gif
 create mode 100644 static/operation_icons/gops_joinRightOuter.gif
 create mode 100644 static/operation_icons/gops_subtractOverlappingIntervals.gif
 create mode 100644 static/operation_icons/gops_subtractOverlappingPieces.gif

diff --git a/static/operation_icons/gops_baseCoverage.gif b/static/operation_icons/gops_baseCoverage.gif
new file mode 100644
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new file mode 100644
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diff --git a/tools/new_operations/basecoverage.xml b/tools/new_operations/basecoverage.xml
index 5daf4aff402..9bbdd50d3b7 100644
--- a/tools/new_operations/basecoverage.xml
+++ b/tools/new_operations/basecoverage.xml
@@ -36,6 +36,10 @@ See Galaxy Interval Operation Screencasts_ (right click to open this link in ano
 
 .. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
 
+**Example**
+
+.. image:: ./static/operation_icons/gops_baseCoverage.gif
+
 
 </help>
-</tool>
\ No newline at end of file
+</tool>
diff --git a/tools/new_operations/cluster.xml b/tools/new_operations/cluster.xml
index 14029e8e814..06a88987d36 100644
--- a/tools/new_operations/cluster.xml
+++ b/tools/new_operations/cluster.xml
@@ -82,9 +82,15 @@ See Galaxy Interval Operation Screencasts_ (right click to open this link in ano
 
 -----
 
-**Example**
+**Examples**
 
-.. image:: ./static/operation_icons/gops_cluster.gif
+Find Clusters:
+
+.. image:: ./static/operation_icons/gops_clusterFind.gif
+
+Merge Clusters:
+
+.. image:: ./static/operation_icons/gops_clusterMerge.gif
 
 </help>
-</tool>
\ No newline at end of file
+</tool>
diff --git a/tools/new_operations/intersect.xml b/tools/new_operations/intersect.xml
index c5ed66d00ad..75e3750f9f9 100644
--- a/tools/new_operations/intersect.xml
+++ b/tools/new_operations/intersect.xml
@@ -129,9 +129,15 @@ See Galaxy Interval Operation Screencasts_ (right click to open this link in ano
 
 -----
 
-**Example**
+**Examples**
 
-.. image:: ./static/operation_icons/gops_intersect.gif
+Overlapping Intervals:
+
+.. image:: ./static/operation_icons/gops_intersectOverlappingIntervals.gif
+
+Overlapping Pieces of Intervals:
+
+.. image:: ./static/operation_icons/gops_intersectOverlappingPieces.gif
 
 </help>
-</tool>
\ No newline at end of file
+</tool>
diff --git a/tools/new_operations/join.xml b/tools/new_operations/join.xml
index c329378f613..257887342de 100644
--- a/tools/new_operations/join.xml
+++ b/tools/new_operations/join.xml
@@ -92,48 +92,26 @@ See Galaxy Interval Operation Screencasts_ (right click to open this link in ano
 
 -----
 
-**Example**
+**Examples**
 
-If **First dataset** is::
+.. image:: ./static/operation_icons/gops_joinRecordsList.gif
 
-   chr1 10   100  Query1.1
-   chr1 500  1000 Query1.2
-   chr1 1100 1250 Query1.3
+Only records that are joined (inner join):
 
-and **Second dataset** is::
+.. image:: ./static/operation_icons/gops_joinInner.gif
 
-   chr1 20   80   Query2.1
-   chr1 2000 2204 Query2.2
-   chr1 2500 3000 Query2.3
+All records of first dataset:
 
+.. image:: ./static/operation_icons/gops_joinLeftOuter.gif
 
-The four return options will generate:
+All records of second dataset:
 
+.. image:: ./static/operation_icons/gops_joinRightOuter.gif
 
-- **Return only records that are joined**::
+All records of both datasets:
 
-   chr1 10 100 Query1.1 chr1 20 80 Query2.1
+.. image:: ./static/operation_icons/gops_joinFullOuter.gif
 
-- **Return all records of first dataset**::
-
-   chr1 10   100  Query1.1 chr1 20 80 Query2.1
-   chr1 500  1000 Query1.2 .    .  .  .
-   chr1 1100 1250 Query1.3 .    .  .  .
-
-- **Return all records of second dataset**::
-
-   chr1 10 100 Query1.1 chr1 20   80   Query2.1
-   .    .  .   .        chr1 2000 2204 Query2.2
-   .    .  .   .        chr1 2500 3000 Query2.3
-
-- **Return all records of both datasets**::
-
-   chr1 10   100  Query1.1 chr1 20   80   Query2.1
-   chr1 500  1000 Query1.2 .    .    .    .
-   chr1 1100 1250 Query1.3 .    .    .    .
-   .    .    .    .        chr1 2000 2204 Query2.2
-   .    .    .    .        chr1 2500 3000 Query2.3
-   
 
 </help>
-</tool>
\ No newline at end of file
+</tool>
diff --git a/tools/new_operations/subtract.xml b/tools/new_operations/subtract.xml
index 709eb91737b..2aca5de5010 100644
--- a/tools/new_operations/subtract.xml
+++ b/tools/new_operations/subtract.xml
@@ -112,7 +112,13 @@ See Galaxy Interval Operation Screencasts_ (right click to open this link in ano
 
 **Example**
 
-.. image:: ./static/operation_icons/gops_subtract.gif
+Intervals with no overlap:
+
+.. image:: ./static/operation_icons/gops_subtractOverlappingIntervals.gif
+
+Non-overlapping pieces of intervals:
+
+.. image:: ./static/operation_icons/gops_subtractOverlappingPieces.gif
 
 </help>
-</tool>
\ No newline at end of file
+</tool>

From cdab8a780460974f2c91477610a9750be5fdae6d Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Wed, 21 Dec 2011 17:04:23 -0500
Subject: [PATCH 361/362] Trackster: add support for including a global model
 when running tools in Trackster. This is done by using a new
 HiddenDataToolParameter and implementing 'set parameter' actions in a tool's
 trackster configuration. Cufflinks now uses a global model to produce correct
 output when run in Trackster.

---
 lib/galaxy/tools/__init__.py                  |  7 +-
 lib/galaxy/tools/parameters/basic.py          | 17 +++++
 .../visualization/tracks/visual_analytics.py  | 25 +++++++
 lib/galaxy/web/controllers/tracks.py          | 33 ++++++---
 tools/ngs_rna/cufflinks_wrapper.py            | 69 ++++++++++++++++---
 tools/ngs_rna/cufflinks_wrapper.xml           | 12 +++-
 6 files changed, 145 insertions(+), 18 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 25034b7f5fb..1794fbefff9 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -29,6 +29,7 @@ from galaxy.datatypes import sniff
 from cgi import FieldStorage
 from galaxy.util.hash_util import *
 from galaxy.util import listify
+from galaxy.visualization.tracks.visual_analytics import TracksterConfig
 
 log = logging.getLogger( __name__ )
 
@@ -567,7 +568,11 @@ class Tool:
         # Determine if this tool can be used in workflows
         self.is_workflow_compatible = self.check_workflow_compatible()
         # Trackster configuration.
-        self.trackster_conf = ( root.find( "trackster_conf" ) is not None )
+        trackster_conf = root.find( "trackster_conf" )
+        if trackster_conf:
+            self.trackster_conf = TracksterConfig.parse( trackster_conf )
+        else:
+            self.trackster_conf = None
             
     def parse_inputs( self, root ):
         """
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index 8d98e2cc832..0e0301e7310 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -1549,6 +1549,22 @@ class DataToolParameter( ToolParameter ):
         if call_attribute:
             ref = ref()
         return ref
+        
+class HiddenDataToolParameter( HiddenToolParameter, DataToolParameter ):
+    """
+    Hidden parameter that behaves as a DataToolParameter. As with all hidden 
+    parameters, this is a HACK.
+    """
+    def __init__( self, tool, elem ):
+        DataToolParameter.__init__( self, tool, elem )
+        self.value = "None"
+        
+    def get_initial_value( self, trans, context ):
+        return None
+        
+    def get_html_field( self, trans=None, value=None, other_values={} ):
+        return form_builder.HiddenField( self.name, self.value )
+        
 
 class LibraryDatasetToolParameter( ToolParameter ):
     """
@@ -1644,6 +1660,7 @@ parameter_types = dict( text            = TextToolParameter,
                         select          = SelectToolParameter,
                         data_column     = ColumnListParameter,
                         hidden          = HiddenToolParameter,
+                        hidden_data     = HiddenDataToolParameter,
                         baseurl         = BaseURLToolParameter,
                         file            = FileToolParameter,
                         ftpfile         = FTPFileToolParameter,
diff --git a/lib/galaxy/visualization/tracks/visual_analytics.py b/lib/galaxy/visualization/tracks/visual_analytics.py
index 63849e4ae5d..e0f3903b05e 100644
--- a/lib/galaxy/visualization/tracks/visual_analytics.py
+++ b/lib/galaxy/visualization/tracks/visual_analytics.py
@@ -3,6 +3,31 @@ import urllib
 from galaxy.tools.parameters.basic import IntegerToolParameter, FloatToolParameter, SelectToolParameter
 from galaxy.tools.parameters.dynamic_options import DynamicOptions
 
+class TracksterConfig:
+    """ Trackster configuration encapsulation. """
+    
+    def __init__( self, actions ):
+        self.actions = actions
+    
+    @staticmethod
+    def parse( root ):
+        actions = []
+        for action_elt in root.findall( "action" ):
+            actions.append( SetParamAction.parse( action_elt ) )
+        return TracksterConfig( actions )
+        
+class SetParamAction:
+    """ Set parameter action. """
+    
+    def __init__( self, name, output_name ):
+        self.name = name
+        self.output_name = output_name
+        
+    @staticmethod
+    def parse( elt ):
+        """ Parse action from element. """
+        return SetParamAction( elt.get( "name" ), elt.get( "output_name" ) )    
+
 def get_dataset_job( hda ):
     # Get dataset's job.
     job = None
diff --git a/lib/galaxy/web/controllers/tracks.py b/lib/galaxy/web/controllers/tracks.py
index d130c6b67d1..33354f6c737 100644
--- a/lib/galaxy/web/controllers/tracks.py
+++ b/lib/galaxy/web/controllers/tracks.py
@@ -824,7 +824,7 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
             return to_json_string( msg )
             
         #
-        # Set tool parameters--except dataset parameters--using combination of
+        # Set tool parameters--except non-hidden dataset parameters--using combination of
         # job's previous parameters and incoming parameters. Incoming parameters
         # have priority.
         #
@@ -872,15 +872,10 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
         else:
             target_history = trans.get_history( create=True )
         hda_permissions = trans.app.security_agent.history_get_default_permissions( target_history )
-            
-        #
-        # Set input datasets for tool. If running on region, extract and use subset
-        # when possible.
-        #
         
         def set_param_value( param_dict, param_name, param_value ):
             """
-            Set new parameter value in a parameter dictionary.
+            Set new parameter value in a tool's parameter dictionary.
             """
             
             # Recursive function to set param value.
@@ -913,8 +908,30 @@ class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetA
                 group_index = int( group[ index + 1: ] )
             
             return set_value( param_dict, group_name, group_index, param_name, param_value )
-            
+        
+        # Set parameters based tool's trackster config.
+        params_set = {}
+        for action in tool.trackster_conf.actions:
+            success = False
+            for joda in original_job.output_datasets:
+                if joda.name == action.output_name:
+                    set_param_value( tool_params, action.name, joda.dataset )
+                    params_set[ action.name ] = True
+                    success = True
+                    break
+                    
+            if not success:
+                return messages.ERROR
+                
+        #
+        # Set input datasets for tool. If running on region, extract and use subset
+        # when possible.
+        #
         for jida in original_job.input_datasets:
+            # If param set previously by config actions, do nothing.
+            if jida.name in params_set:
+                continue
+                
             input_dataset = jida.dataset
             if input_dataset is None: #optional dataset and dataset wasn't selected
                 tool_params[ jida.name ] = None
diff --git a/tools/ngs_rna/cufflinks_wrapper.py b/tools/ngs_rna/cufflinks_wrapper.py
index 975c7a07d9f..962c24708a8 100644
--- a/tools/ngs_rna/cufflinks_wrapper.py
+++ b/tools/ngs_rna/cufflinks_wrapper.py
@@ -1,6 +1,8 @@
 #!/usr/bin/env python
 
 import optparse, os, shutil, subprocess, sys, tempfile
+from galaxy import eggs
+from galaxy.datatypes.util.gff_util import parse_gff_attributes, gff_attributes_to_str
 
 def stop_err( msg ):
     sys.stderr.write( "%s\n" % msg )
@@ -51,6 +53,9 @@ def __main__():
     parser.add_option( '', '--index_dir', dest='index_dir', help='GALAXY_DATA_INDEX_DIR' )
     parser.add_option( '', '--ref_file', dest='ref_file', help='The reference dataset from the history' )
     
+    # Global model.
+    parser.add_option( '', '--global_model', dest='global_model_file', help='Global model used for computing on local data' )
+    
     (options, args) = parser.parse_args()
     
     # output version # of tool
@@ -122,7 +127,9 @@ def __main__():
     # Add input files.
     cmd += " " + options.input
     
+    #
     # Run command.
+    #
     try:
         tmp_name = tempfile.NamedTemporaryFile( dir="." ).name
         tmp_stderr = open( tmp_name, 'wb' )
@@ -130,7 +137,60 @@ def __main__():
         returncode = proc.wait()
         tmp_stderr.close()
         
-        # Get stderr, allowing for case where it's very large.
+        # Read standard error to get total map mass.
+        total_map_mass = -1
+        tmp_stderr = open( tmp_name, 'r' )
+        for line in tmp_stderr:
+            if line.lower().find( "total map mass") >= 0:
+                total_map_mass = float( line.split(":")[1].strip() )
+                break
+        tmp_stderr.close()
+        
+        #
+        # If there's a global model provided, use model's total map mass
+        # to adjust FPKM + confidence intervals.
+        #
+        if options.global_model_file:        
+            # Global model is simply total map mass from original run.
+            global_model_file = open( options.global_model_file, 'r' )
+            global_model_total_map_mass = float( global_model_file.readline() )
+            global_model_file.close()
+        
+            # Ratio of global model's total map mass to original run's map mass is
+            # factor used to adjust FPKM.
+            fpkm_map_mass_ratio = total_map_mass / global_model_total_map_mass
+        
+            # Update FPKM values in transcripts.gtf file.
+            transcripts_file = open( "transcripts.gtf", 'r' )
+            tmp_transcripts = tempfile.NamedTemporaryFile( dir="." ).name
+            new_transcripts_file = open( tmp_transcripts, 'w' )
+            for line in transcripts_file:
+                fields = line.split( '\t' )
+                attrs = parse_gff_attributes( fields[8] )
+                attrs[ "FPKM" ] = str( float( attrs[ "FPKM" ] ) * fpkm_map_mass_ratio )
+                attrs[ "conf_lo" ] = str( float( attrs[ "conf_lo" ] ) * fpkm_map_mass_ratio )
+                attrs[ "conf_hi" ] = str( float( attrs[ "conf_hi" ] ) * fpkm_map_mass_ratio )
+                fields[8] = gff_attributes_to_str( attrs, "GTF" )
+                new_transcripts_file.write( "%s\n" % '\t'.join( fields ) )
+            transcripts_file.close()
+            new_transcripts_file.close()
+            shutil.copyfile( tmp_transcripts, "transcripts.gtf" )
+            
+        # TODO: update expression files as well.
+            
+        # Set outputs. Transcript and gene expression handled by wrapper directives.
+        shutil.copyfile( "transcripts.gtf" , options.assembled_isoforms_output_file )
+        if total_map_mass > -1:
+            f = open( "global_model.txt", 'w' )
+            f.write( "%f\n" % total_map_mass )
+            f.close()
+
+        # Error checking.
+        if returncode != 0:
+            raise Exception, stderr
+    except Exception, e:
+        raise e
+        # Read stderr so that it can be reported:
         tmp_stderr = open( tmp_name, 'rb' )
         stderr = ''
         buffsize = 1048576
@@ -142,14 +202,7 @@ def __main__():
         except OverflowError:
             pass
         tmp_stderr.close()
-
-        # Copy outputs.
-        shutil.copyfile( "transcripts.gtf" , options.assembled_isoforms_output_file )
         
-        # Error checking.
-        if returncode != 0:
-            raise Exception, stderr            
-    except Exception, e:
         stop_err( 'Error running cufflinks. ' + str( e ) )
 
 if __name__=="__main__": __main__()
diff --git a/tools/ngs_rna/cufflinks_wrapper.xml b/tools/ngs_rna/cufflinks_wrapper.xml
index 34caf3681b7..5551ff18ec5 100644
--- a/tools/ngs_rna/cufflinks_wrapper.xml
+++ b/tools/ngs_rna/cufflinks_wrapper.xml
@@ -43,6 +43,11 @@
                 --dbkey=${input.metadata.dbkey} 
                 --index_dir=${GALAXY_DATA_INDEX_DIR}
             #end if
+
+            ## Include global model if available.
+            #if $global_model:
+                --global_model=$global_model
+            #end if
     </command>
     <inputs>
         <param format="sam,bam" name="input" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""/>
@@ -97,15 +102,20 @@
                 <param name="inner_distance_std_dev" type="integer" value="20" label="Standard Deviation for Inner Distance between Mate Pairs"/>
             </when>
         </conditional>
+        <param name="global_model" type="hidden_data" label="Global model (for use in Trackster)" optional="True"/>
     </inputs>
 
     <outputs>
         <data format="tabular" name="genes_expression" label="${tool.name} on ${on_string}: gene expression" from_work_dir="genes.fpkm_tracking"/>
         <data format="tabular" name="transcripts_expression" label="${tool.name} on ${on_string}: transcript expression" from_work_dir="isoforms.fpkm_tracking"/>
         <data format="gtf" name="assembled_isoforms" label="${tool.name} on ${on_string}: assembled transcripts"/>
+        <data format="txt" name="total_map_mass" label="${tool.name} on ${on_string}: total map mass" hidden="true" from_work_dir="global_model.txt"/>
     </outputs>
 
-    <trackster_conf/>
+    <trackster_conf>
+        <action type="set_param" name="global_model" output_name="total_map_mass"/>
+    </trackster_conf>
+    
     <tests>
         <!--
             Simple test that uses test data included with cufflinks.

From c404729689bbc099f4232a1b0de1ea1814e9310f Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Thu, 22 Dec 2011 10:43:17 -0500
Subject: [PATCH 362/362] Trackster: use integer for dummy filter value rather
 than string because it is easier for client to decode.

---
 lib/galaxy/visualization/tracks/data_providers.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/visualization/tracks/data_providers.py b/lib/galaxy/visualization/tracks/data_providers.py
index a54d9c369b4..d632b98c981 100644
--- a/lib/galaxy/visualization/tracks/data_providers.py
+++ b/lib/galaxy/visualization/tracks/data_providers.py
@@ -1053,5 +1053,5 @@ def package_gff_feature( feature, no_detail=False, filter_cols=[] ):
                 payload.append( feature.attributes[col] )
         else:
             # Dummy value.
-            payload.append( "na" )
+            payload.append( 0 )
     return payload