From 3d5fd7b5e27d33df02ea929f73250163f2e4e007 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Fri, 17 Aug 2012 11:35:31 -0400
Subject: [PATCH 01/16] Migrate NCBI Blast+ (and blastxml) to the toolshed.

---
 lib/galaxy/datatypes/registry.py              |   3 -
 lib/galaxy/datatypes/xml.py                   | 120 ------------------
 .../tool_shed/migrate/versions/0004_tools.py  |  12 ++
 scripts/migrate_tools/0004_tools.sh           |   4 +
 scripts/migrate_tools/0004_tools.xml          |  12 ++
 5 files changed, 28 insertions(+), 123 deletions(-)
 create mode 100644 lib/galaxy/tool_shed/migrate/versions/0004_tools.py
 create mode 100644 scripts/migrate_tools/0004_tools.sh
 create mode 100644 scripts/migrate_tools/0004_tools.xml

diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
index 50315904e00..b054b423d11 100644
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -276,7 +276,6 @@ class Registry( object ):
                 'axt'         : sequence.Axt(),
                 'bam'         : binary.Bam(),
                 'bed'         : interval.Bed(), 
-                'blastxml'    : xml.BlastXml(),
                 'coverage'    : coverage.LastzCoverage(),
                 'customtrack' : interval.CustomTrack(),
                 'csfasta'     : sequence.csFasta(),
@@ -310,7 +309,6 @@ class Registry( object ):
                 'axt'         : 'text/plain',
                 'bam'         : 'application/octet-stream',
                 'bed'         : 'text/plain', 
-                'blastxml'    : 'application/xml', 
                 'customtrack' : 'text/plain',
                 'csfasta'     : 'text/plain',
                 'eland'       : 'application/octet-stream',
@@ -348,7 +346,6 @@ class Registry( object ):
             self.sniff_order = [
                 binary.Bam(),
                 binary.Sff(),
-                xml.BlastXml(),
                 xml.GenericXml(),
                 sequence.Maf(),
                 sequence.Lav(),
diff --git a/lib/galaxy/datatypes/xml.py b/lib/galaxy/datatypes/xml.py
index ef1f1623e28..37f34f55169 100644
--- a/lib/galaxy/datatypes/xml.py
+++ b/lib/galaxy/datatypes/xml.py
@@ -27,9 +27,6 @@ class GenericXml( data.Text ):
         >>> fname = get_test_fname( 'megablast_xml_parser_test1.blastxml' )
         >>> GenericXml().sniff( fname )
         True
-        >>> fname = get_test_fname( 'tblastn_four_human_vs_rhodopsin.xml' )
-        >>> BlastXml().sniff( fname )
-        True
         >>> fname = get_test_fname( 'interval.interval' )
         >>> GenericXml().sniff( fname )
         False
@@ -50,123 +47,6 @@ class GenericXml( data.Text ):
         data.Text.merge(split_files, output_file)
     merge = staticmethod(merge)
 
-class BlastXml( GenericXml ):
-    """NCBI Blast XML Output data"""
-    file_ext = "blastxml"
-
-    def set_peek( self, dataset, is_multi_byte=False ):
-        """Set the peek and blurb text"""
-        if not dataset.dataset.purged:
-            dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
-            dataset.blurb = 'NCBI Blast XML data'
-        else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
-    def sniff( self, filename ):
-        """
-        Determines whether the file is blastxml
-        
-        >>> fname = get_test_fname( 'megablast_xml_parser_test1.blastxml' )
-        >>> BlastXml().sniff( fname )
-        True
-        >>> fname = get_test_fname( 'tblastn_four_human_vs_rhodopsin.xml' )
-        >>> BlastXml().sniff( fname )
-        True
-        >>> fname = get_test_fname( 'interval.interval' )
-        >>> BlastXml().sniff( fname )
-        False
-        """
-        #TODO - Use a context manager on Python 2.5+ to close handle
-        handle = open(filename)
-        line = handle.readline()
-        if line.strip() != '<?xml version="1.0"?>':
-            handle.close()
-            return False
-        line = handle.readline()
-        if line.strip() not in ['<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">',
-                                '<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">']:
-            handle.close()
-            return False
-        line = handle.readline()
-        if line.strip() != '<BlastOutput>':
-            handle.close()
-            return False
-        handle.close()
-        return True
-    
-    def merge(split_files, output_file):
-        """Merging multiple XML files is non-trivial and must be done in subclasses."""
-        if len(split_files) == 1:
-            #For one file only, use base class method (move/copy)
-            return data.Text.merge(split_files, output_file)
-        out = open(output_file, "w")
-        h = None
-        for f in split_files:
-            h = open(f)
-            body = False
-            header = h.readline()
-            if not header:
-                out.close()
-                h.close()
-                raise ValueError("BLAST XML file %s was empty" % f)
-            if header.strip() != '<?xml version="1.0"?>':
-                out.write(header) #for diagnosis
-                out.close()
-                h.close()
-                raise ValueError("%s is not an XML file!" % f)
-            line = h.readline()
-            header += line
-            if line.strip() not in ['<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">',
-                                    '<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">']:
-                out.write(header) #for diagnosis
-                out.close()
-                h.close()
-                raise ValueError("%s is not a BLAST XML file!" % f)
-            while True:
-                line = h.readline()
-                if not line:
-                    out.write(header) #for diagnosis
-                    out.close()
-                    h.close()
-                    raise ValueError("BLAST XML file %s ended prematurely" % f)
-                header += line
-                if "<Iteration>" in line:
-                    break
-                if len(header) > 10000:
-                    #Something has gone wrong, don't load too much into memory!
-                    #Write what we have to the merged file for diagnostics
-                    out.write(header)
-                    out.close()
-                    h.close()
-                    raise ValueError("BLAST XML file %s has too long a header!" % f)
-            if "<BlastOutput>" not in header:
-                out.close()
-                h.close()
-                raise ValueError("%s is not a BLAST XML file:\n%s\n..." % (f, header))
-            if f == split_files[0]:
-                out.write(header)
-                old_header = header
-            elif old_header[:300] != header[:300]:
-                #Enough to check <BlastOutput_program> and <BlastOutput_version> match
-                out.close()
-                h.close()
-                raise ValueError("BLAST XML headers don't match for %s and %s - have:\n%s\n...\n\nAnd:\n%s\n...\n" \
-                                 % (split_files[0], f, old_header[:300], header[:300]))
-            else:
-                out.write("    <Iteration>\n")
-            for line in h:
-                if "</BlastOutput_iterations>" in line:
-                    break
-                #TODO - Increment <Iteration_iter-num> and if required automatic query names
-                #like <Iteration_query-ID>Query_3</Iteration_query-ID> to be increasing?
-                out.write(line)
-            h.close()
-        out.write("  </BlastOutput_iterations>\n")
-        out.write("</BlastOutput>\n")
-        out.close()
-    merge = staticmethod(merge)
-                                                
-
 class MEMEXml( GenericXml ):
     """MEME XML Output data"""
     file_ext = "memexml"
diff --git a/lib/galaxy/tool_shed/migrate/versions/0004_tools.py b/lib/galaxy/tool_shed/migrate/versions/0004_tools.py
new file mode 100644
index 00000000000..f20bd83b251
--- /dev/null
+++ b/lib/galaxy/tool_shed/migrate/versions/0004_tools.py
@@ -0,0 +1,12 @@
+"""
+The NCBI BLAST+ tools have been eliminated from the distribution.  The tools and datatypes are are now available in repositories named ncbi_blast_plus
+and blast_datatypes, respectively, from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu will be installed into your local Galaxy instance
+at the location discussed above by running the following command.
+"""
+
+import sys
+
+def upgrade():
+    print __doc__
+def downgrade():
+    pass
diff --git a/scripts/migrate_tools/0004_tools.sh b/scripts/migrate_tools/0004_tools.sh
new file mode 100644
index 00000000000..40b76956fa2
--- /dev/null
+++ b/scripts/migrate_tools/0004_tools.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+
+cd `dirname $0`/../..
+python ./scripts/migrate_tools/migrate_tools.py 0004_tools.xml $@
diff --git a/scripts/migrate_tools/0004_tools.xml b/scripts/migrate_tools/0004_tools.xml
new file mode 100644
index 00000000000..53664f9823c
--- /dev/null
+++ b/scripts/migrate_tools/0004_tools.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0"?>
+<toolshed name="toolshed.g2.bx.psu.edu">
+    <repository name="blast_datatypes" description="Datatypes for BLAST" changeset_revision="e1c29f302301" />
+    <repository name="ncbi_blast_plus" description="Galaxy wrappers for NCBI BLAST+" changeset_revision="d375502056f1">
+        <tool id="blastxml_to_tabular" version="0.0.8" file="blastxml_to_tabular.xml"/>
+        <tool id="ncbi_blastn_wrapper" version="0.0.11" file="ncbi_blastn_wrapper.xml"/>
+        <tool id="ncbi_blastp_wrapper" version="0.0.11" file="ncbi_blastp_wrapper.xml"/>
+        <tool id="ncbi_blastx_wrapper" version="0.0.11" file="ncbi_blastx_wrapper.xml"/>
+        <tool id="ncbi_tblastn_wrapper" version="0.0.11" file="ncbi_tblastn_wrapper.xml"/>
+        <tool id="ncbi_tblastx_wrapper" version="0.0.11" file="ncbi_tblastx_wrapper.xml"/>
+    </repository>
+</toolshed>

From 97e69fbbdfd820b3044ef3289484850bf3faa566 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Fri, 17 Aug 2012 13:55:37 -0400
Subject: [PATCH 02/16] Fix chunk-serving logic for tabular files.

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

diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py
index ce3b043b658..0939edae159 100644
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -264,10 +264,10 @@ class Tabular( data.Text ):
 
     def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, chunk=None):
         #TODO Prevent failure when displaying extremely long > 50kb lines.
-        if to_ext or not preview:
-            return self._serve_raw(trans, dataset, to_ext)
         if chunk:
             return self.get_chunk(trans, dataset, chunk)
+        if to_ext or not preview:
+            return self._serve_raw(trans, dataset, to_ext)
         else:
             column_names = 'null'
             if dataset.metadata.column_names:
@@ -644,4 +644,5 @@ class FeatureLocationIndex( Tabular ):
     """
     file_ext='fli'
     MetadataElement( name="columns", default=2, desc="Number of columns", readonly=True, visible=False )
-    MetadataElement( name="column_types", default=['str', 'str'], param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False, no_value=[] )
\ No newline at end of file
+    MetadataElement( name="column_types", default=['str', 'str'], param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False, no_value=[] )
+

From 3360fe30725e8aeb45595a44936470753d264811 Mon Sep 17 00:00:00 2001
From: Carl Eberhard <carlfeberhard@gmail.com>
Date: Fri, 17 Aug 2012 14:39:32 -0400
Subject: [PATCH 03/16] new data for bwa_wrapper/bwa_color_wrapper functional
 tests


From dbc2c27a82c11d6693b92c9dd8358879390cfca8 Mon Sep 17 00:00:00 2001
From: Scott McManus <scottmcmanus@gatech.edu>
Date: Fri, 17 Aug 2012 15:15:48 -0400
Subject: [PATCH 04/16] Minor tweak to exit code handling

---
 lib/galaxy/jobs/__init__.py | 18 ++++++------------
 1 file changed, 6 insertions(+), 12 deletions(-)

diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 5ac63f9957b..50c185834c2 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -490,7 +490,6 @@ class JobWrapper( object ):
         if stderr contains anything, then False is returned.
         Note that the job id is just for messages.
         """
-        err_msg = ""
         # By default, the tool succeeded. This covers the case where the code 
         # has a bug but the tool was ok, and it lets a workflow continue.
         success = True 
@@ -507,7 +506,7 @@ class JobWrapper( object ):
                 # Check the exit code ranges in the order in which
                 # they were specified. Each exit_code is a StdioExitCode
                 # that includes an applicable range. If the exit code was in
-                # that range, then apply the error level and add in a message.
+                # that range, then apply the error level and add a message.
                 # If we've reached a fatal error rule, then stop.
                 max_error_level = galaxy.tools.StdioErrorLevel.NO_ERROR
                 for stdio_exit_code in self.tool.stdio_exit_codes:
@@ -515,20 +514,16 @@ class JobWrapper( object ):
                          tool_exit_code <= stdio_exit_code.range_end ):
                         # Tack on a generic description of the code 
                         # plus a specific code description. For example,
-                        # this might append "Job 42: Warning: Out of Memory\n".
-                        # TODO: Find somewhere to stick the err_msg - 
-                        # possibly to the source (stderr/stdout), possibly 
-                        # in a new db column.
+                        # this might prepend "Job 42: Warning: Out of Memory\n".
                         code_desc = stdio_exit_code.desc
                         if ( None == code_desc ):
                             code_desc = ""
-                        tool_msg = ( "Job %s: %s: Exit code %d: %s" % (
-                                     job.get_id_tag(),
-                                     galaxy.tools.StdioErrorLevel.desc( tool_exit_code ),
+                        tool_msg = ( "%s: Exit code %d: %s" % (
+                                     galaxy.tools.StdioErrorLevel.desc( stdio_exit_code.error_level ),
                                      tool_exit_code,
                                      code_desc ) )
-                        log.info( tool_msg )
-                        stderr = err_msg + stderr
+                        log.info( "Job %s: %s" % (job.get_id_tag(), tool_msg) )
+                        stderr = tool_msg + "\n" + stderr
                         max_error_level = max( max_error_level, 
                                                stdio_exit_code.error_level )
                         if ( max_error_level >= 
@@ -571,7 +566,6 @@ class JobWrapper( object ):
                                                      re.IGNORECASE )
                             if ( regex_match ):
                                 rexmsg = self.regex_err_msg( regex_match, regex)
-                                # DELETEME
                                 log.info( "Job %s: %s" 
                                         % ( job.get_id_tag(), rexmsg ) )
                                 stderr = rexmsg + "\n" + stderr

From 860bb2673c6a0324a6d0dc4738fe632d2e1a458b Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Fri, 17 Aug 2012 17:49:41 -0400
Subject: [PATCH 05/16] Converters enhancements: (a) ignore track lines in
 wiggle to bigwig converter and add clip option and (b) enable visualization
 of bedgraph datasets via a bedgraph to bigwig converter.

---
 .../converters/bedgraph_to_bigwig_converter.xml    | 14 ++++++++++++++
 .../converters/wig_to_bigwig_converter.xml         |  2 +-
 lib/galaxy/datatypes/interval.py                   |  5 +++--
 3 files changed, 18 insertions(+), 3 deletions(-)
 create mode 100644 lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml

diff --git a/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
new file mode 100644
index 00000000000..77d2c2a42e6
--- /dev/null
+++ b/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
@@ -0,0 +1,14 @@
+<tool id="CONVERTER_bedgraph_to_bigwig" name="Convert BedGraph to BigWig" hidden="true">
+  <!-- Used internally to generate track indexes -->
+  <command>grep -v "^track" $input | wigToBigWig -clip stdin $chromInfo $output</command>
+  <inputs>
+    <page>
+      <param format="bedgraph" name="input" type="data" label="Choose wiggle"/>
+    </page>
+   </inputs>
+   <outputs>
+      <data format="bigwig" name="output"/>
+   </outputs>
+  <help>
+  </help>
+</tool>
\ No newline at end of file
diff --git a/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
index e85c3a7b138..d90702efe78 100644
--- a/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
@@ -1,6 +1,6 @@
 <tool id="CONVERTER_wig_to_bigwig" name="Convert Wiggle to BigWig" hidden="true">
   <!-- Used internally to generate track indexes -->
-  <command>wigToBigWig $input $chromInfo $output</command>
+  <command>grep -v "^track" $input | wigToBigWig -clip stdin $chromInfo $output</command>
   <inputs>
     <page>
       <param format="wig" name="input" type="data" label="Choose wiggle"/>
diff --git a/lib/galaxy/datatypes/interval.py b/lib/galaxy/datatypes/interval.py
index 69c77a553db..23c81cf48d2 100644
--- a/lib/galaxy/datatypes/interval.py
+++ b/lib/galaxy/datatypes/interval.py
@@ -338,7 +338,7 @@ class BedGraph( Interval ):
     file_ext = "bedgraph"
 
     def get_track_type( self ):
-        return "LineTrack", {"data": "array_tree"}
+        return "LineTrack", { "data": "bigwig", "index": "bigwig" }
         
     def as_ucsc_display_file( self, dataset, **kwd ):
         """
@@ -1141,8 +1141,9 @@ class Wiggle( Tabular, _RemoteCallMixin ):
         resolution = min( resolution, 100000 )
         resolution = max( resolution, 1 )
         return resolution
+        
     def get_track_type( self ):
-        return "LineTrack", {"data": "bigwig", "index": "bigwig"}
+        return "LineTrack", { "data": "bigwig", "index": "bigwig" }
 
 class CustomTrack ( Tabular ):
     """UCSC CustomTrack"""

From 5ab62c87460b61c29e22e9bf33bde57e93c719f8 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Sat, 18 Aug 2012 18:00:31 -0400
Subject: [PATCH 06/16] Streamline creation of stats for BBI tracks data
 provider.

---
 .../visualization/tracks/data_providers.py    | 37 ++++++++++---------
 1 file changed, 20 insertions(+), 17 deletions(-)

diff --git a/lib/galaxy/visualization/tracks/data_providers.py b/lib/galaxy/visualization/tracks/data_providers.py
index 0999f9e3932..64363b4dac6 100644
--- a/lib/galaxy/visualization/tracks/data_providers.py
+++ b/lib/galaxy/visualization/tracks/data_providers.py
@@ -968,29 +968,32 @@ class BBIDataProvider( TracksDataProvider ):
         # which we use converted_dataset
         f, bbi = self._get_dataset()
        
-        # If the stats kwarg was provide, we compute overall summary data for the 
-        # range defined by start and end but no reduced data. This is currently 
-        # used by client to determine the default range.
+        # If stats requested, compute overall summary data for the range
+        # start:endbut no reduced data. This is currently used by client 
+        # to determine the default range.
         if 'stats' in kwargs:
             summary = bbi.summarize( chrom, start, end, 1 )
             f.close()
-            if summary is None:
-                return None
-            else:
+            
+            min = 0
+            max = 0
+            mean = 0
+            sd = 0
+            if summary is not None:
                 # Does the summary contain any defined values?
                 valid_count = summary.valid_count[0]
-                if summary.valid_count < 1:
-                    return None
+                if summary.valid_count > 0:
+                    # 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 = numpy.sqrt( var )
+                    min = summary.min_val[0]
+                    max = summary.max_val[0]
 
-                # 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 = numpy.sqrt( var )
-
-                return dict( data=dict( min=summary.min_val[0], max=summary.max_val[0], mean=mean, sd=sd ) )
+            return dict( data=dict( min=min, max=max, mean=mean, sd=sd ) )
 
         # Sample from region using approximately this many samples.
         N = 1000

From 871f72c9569ff2b409a06ac341162ba8e079f689 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Sun, 19 Aug 2012 15:42:11 -0400
Subject: [PATCH 07/16] Trackster: for explicit coverage histogram mode in
 Feature Tracks, use coverage indices rather than computing on client side.

---
 lib/galaxy/web/controllers/tracks.py |  16 +++-
 static/scripts/viz/trackster.js      | 109 +++------------------------
 2 files changed, 27 insertions(+), 98 deletions(-)

diff --git a/lib/galaxy/web/controllers/tracks.py b/lib/galaxy/web/controllers/tracks.py
index d468b0dfb35..8c21cd7f8ba 100644
--- a/lib/galaxy/web/controllers/tracks.py
+++ b/lib/galaxy/web/controllers/tracks.py
@@ -387,7 +387,21 @@ class TracksController( BaseUIController, UsesVisualizationMixin, UsesHistoryDat
             return return_message
             
         extra_info = None
-        if 'index' in data_sources and data_sources['index']['name'] == "summary_tree" and kwargs.get("mode", "Auto") == "Auto":
+        mode = kwargs.get( "mode", "Auto" )
+        # Handle histogram mode uniquely for now:
+        if mode == "Coverage":
+            # Get summary using minimal cutoffs.
+            tracks_dataset_type = data_sources['index']['name']
+            converted_dataset = dataset.get_converted_dataset( trans, tracks_dataset_type )
+            indexer = get_data_provider( tracks_dataset_type )( converted_dataset, dataset )
+            summary = indexer.get_data( chrom, low, high, resolution=kwargs[ 'resolution' ], detail_cutoff=0, draw_cutoff=0 )
+            if summary == "detail":
+                # Use maximum level of detail--2--to get summary data no matter the resolution.
+                summary = indexer.get_data( chrom, low, high, resolution=kwargs[ 'resolution' ], level=2, detail_cutoff=0, draw_cutoff=0 )
+            frequencies, max_v, avg_v, delta = summary
+            return { 'dataset_type': tracks_dataset_type, 'data': frequencies, 'max': max_v, 'avg': avg_v, 'delta': delta }
+
+        if 'index' in data_sources and data_sources['index']['name'] == "summary_tree" and mode == "Auto":
             # Only check for summary_tree if it's Auto mode (which is the default)
             # 
             # Have to choose between indexer and data provider
diff --git a/static/scripts/viz/trackster.js b/static/scripts/viz/trackster.js
index 7f8acacc6d0..645b00b2be0 100644
--- a/static/scripts/viz/trackster.js
+++ b/static/scripts/viz/trackster.js
@@ -4433,7 +4433,7 @@ var FeatureTrack = function(view, container, obj_dict) {
     // initialization code.
     //
     var track = this;
-    this.display_modes = ["Auto", "Histogram", "Dense", "Squish", "Pack"];
+    this.display_modes = ["Auto", "Coverage", "Dense", "Squish", "Pack"];
     
     //
     // Initialization.
@@ -4516,8 +4516,8 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
         var track = this,
             i;
                 
-        // If mode is Histogram and tiles do not share max, redraw tiles as necessary using new max.
-        if (track.mode === "Histogram") {
+        // If mode is Coverage and tiles do not share max, redraw tiles as necessary using new max.
+        if (track.mode === "Coverage") {
             // Get global max.
             var global_max = -1;
             for (i = 0; i < tiles.length; i++) {
@@ -4534,7 +4534,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
                     track.draw_helper(true, width, tile.index, tile.resolution, tile.html_elt.parent(), w_scale, { more_tile_data: { max: global_max } } );
                 }
             }
-        }                
+        }            
         
         //
         // Update filter attributes, UI.
@@ -4649,86 +4649,6 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
 
         return slotter.slot_features( features );
     },
-    /**
-     * Given feature data, returns summary tree data. Feature data must be sorted by start 
-     * position. Return value is a dict with keys 'data', 'delta' (bin size) and 'max.' Data
-     * is a two-item list; first item is bin start, second is bin's count.
-     */
-    get_summary_tree_data: function(data, low, high, num_bins) {
-        if (num_bins > high - low) {
-            num_bins = high - low;
-        }
-        var bin_size = Math.floor((high - low)/num_bins),
-            bins = [],
-            max_count = 0;
-            
-        /*    
-        // For debugging:
-        for (var i = 0; i < data.length; i++)
-            console.log("\t", data[i][1], data[i][2], data[i][3]);
-        */
-        
-        //
-        // Loop through bins, counting data for each interval.
-        //
-        var data_index_start = 0,
-            data_index = 0,
-            data_interval,
-            bin_index = 0,
-            bin_interval = [], 
-            cur_bin;
-            
-        // Set bin interval.
-        var set_bin_interval = function(interval, low, bin_index, bin_size) {
-            interval[0] = low + bin_index * bin_size;
-            interval[1] = low + (bin_index + 1) * bin_size;
-        };
-        
-        // Loop through bins, data to compute bin counts. Only compute bin counts as long
-        // as there is data.
-        while (bin_index < num_bins && data_index_start !== data.length) {
-            // Find next bin that has data.
-            var bin_has_data = false;
-            for (; bin_index < num_bins && !bin_has_data; bin_index++) {
-                set_bin_interval(bin_interval, low, bin_index, bin_size);
-                // Loop through data and break if data found that goes in bin.
-                for (data_index = data_index_start; data_index < data.length; data_index++) {
-                    data_interval = data[data_index].slice(1, 3);
-                    if (is_overlap(data_interval, bin_interval)) {
-                        bin_has_data = true;
-                        break;
-                    }
-                }
-                // Break from bin loop if this bin has data.
-                if (bin_has_data) {
-                    break;
-                }
-            }
-            
-            // Set start index to current data, which is the first to overlap with this bin
-            // and perhaps with later bins.
-            data_start_index = data_index;
-            
-            // Count intervals that overlap with bin.
-            bins[bins.length] = cur_bin = [bin_interval[0], 0];
-            for (; data_index < data.length; data_index++) {
-                data_interval = data[data_index].slice(1, 3);
-                if (is_overlap(data_interval, bin_interval)) {
-                    cur_bin[1]++;
-                }
-                else { break; }
-            }
-            
-            // Update max count.
-            if (cur_bin[1] > max_count) {
-                max_count = cur_bin[1];
-            }
-            
-            // Go to next bin.
-            bin_index++;
-        }
-        return {max: max_count, delta: bin_size, data: bins};
-    },
     /**
      * Returns appropriate display mode based on data.
      */
@@ -4766,8 +4686,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
      * 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.
+        if (mode === "summary_tree" || mode === "Coverage") {
             return this.summary_draw_height;
         }
         else {
@@ -4796,16 +4715,8 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
             tile_high = region.get('end'),
             left_offset = this.left_offset;
         
-        // Drawing the summary tree (feature coverage histogram)
-        if (mode === "summary_tree" || mode === "Histogram") {
-            // Get summary tree data if necessary and set max if there is one.
-            if (result.dataset_type !== "summary_tree") {
-                var st_data = this.get_summary_tree_data(result.data, tile_low, tile_high, 200);
-                if (result.max) {
-                    st_data.max = result.max;
-                }
-                result = st_data;
-            }
+        // Drawing the summary tree.
+        if (mode === "summary_tree" || mode === "Coverage") {
             // Paint summary tree into canvas
             var painter = new painters.SummaryTreePainter(result, tile_low, tile_high, this.prefs);
             painter.draw(ctx, canvas.width, canvas.height, w_scale);
@@ -4872,7 +4783,11 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
         if (mode === "Auto") {
             return true;
         }
-        // All other modes--Histogram, Dense, Squish, Pack--require data + details.
+        // Histogram mode requires summary_tree data.
+        else if (mode === "Coverage") {
+            return data.dataset_type === "summary_tree";
+        }
+        // All other modes--Dense, Squish, Pack--require data + details.
         else if (data.extra_info === "no_detail" || data.dataset_type === "summary_tree") {
             return false;
         }

From 009bd6fed69a63e6b2ef3482c56ec59487ae7a07 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Mon, 20 Aug 2012 09:57:25 -0400
Subject: [PATCH 08/16] Fix URL generation bug when dictifying tools.

---
 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 b829f86f5a2..f686a9216a9 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -2631,7 +2631,7 @@ class Tool:
         if for_link:
             # Create tool link.
             if not self.tool_type.startswith( 'data_source' ):
-                link = url_for( controller='tool_runner', tool_id=self.id )
+                link = url_for( '/tool_runner', tool_id=self.id )
             else:
                 link = url_for( self.action, **self.get_static_param_values( trans ) )
             

From 8eea8de39ac593fcd1a03acba6a08c88a89fae2c Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Mon, 20 Aug 2012 10:27:44 -0400
Subject: [PATCH 09/16] Make 'add dataset to trackster' dialog compatiable with
 new modal behavior.

---
 templates/root/history.mako | 1 -
 1 file changed, 1 deletion(-)

diff --git a/templates/root/history.mako b/templates/root/history.mako
index ad9da4d6157..5dcfdc768d7 100644
--- a/templates/root/history.mako
+++ b/templates/root/history.mako
@@ -250,7 +250,6 @@ $(function() {
                         },
                         "View in saved visualization": function() {
                             // Show new modal with saved visualizations.
-                            parent.hide_modal();
                             parent.show_modal("Add Data to Saved Visualization", table_html, {
                                 "Cancel": function() {
                                     parent.hide_modal();

From 5046dac56331880a92ff36640ace51f662d7ae0c Mon Sep 17 00:00:00 2001
From: Carl Eberhard <carlfeberhard@gmail.com>
Date: Mon, 20 Aug 2012 13:50:12 -0400
Subject: [PATCH 10/16] fix to gff_to_fli.py to avoid breaking unittests

---
 lib/galaxy/datatypes/converters/gff_to_fli.py | 92 ++++++++++---------
 1 file changed, 48 insertions(+), 44 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/gff_to_fli.py b/lib/galaxy/datatypes/converters/gff_to_fli.py
index cfa056e573f..ef38576a5a3 100644
--- a/lib/galaxy/datatypes/converters/gff_to_fli.py
+++ b/lib/galaxy/datatypes/converters/gff_to_fli.py
@@ -6,48 +6,52 @@ import sys
 from galaxy import eggs
 from galaxy.datatypes.util.gff_util import read_unordered_gtf, convert_gff_coords_to_bed
 
-# Process arguments.
-in_fname = sys.argv[1]
-out_fname = sys.argv[2]
+def main():
+    # Process arguments.
+    in_fname = sys.argv[1]
+    out_fname = sys.argv[2]
+    
+    # Create dict of name-location pairings.
+    name_loc_dict = {}
+    for feature in read_unordered_gtf( open( in_fname, 'r' ) ):
+        for name in feature.attributes:
+            val = feature.attributes[ name ]
+            try:
+                float( val )
+                continue
+            except:
+                convert_gff_coords_to_bed( feature )
+                # Value is not a number, so it can be indexed.
+                if val not in name_loc_dict:
+                    # Value is not in dictionary.
+                    name_loc_dict[ val ] = {
+                        'contig': feature.chrom,
+                        'start': feature.start,
+                        'end': feature.end
+                    }
+                else:
+                    # Value already in dictionary, so update dictionary.
+                    loc = name_loc_dict[ val ]
+                    if feature.start < loc[ 'start' ]:
+                        loc[ 'start' ] = feature.start
+                    if feature.end > loc[ 'end' ]:
+                        loc[ 'end' ] = feature.end
+    
+    # Print name, loc in sorted order.
+    out = open( out_fname, 'w' )
+    max_len = 0
+    entries = []
+    for name in sorted( name_loc_dict.iterkeys() ):
+        loc = name_loc_dict[ name ]
+        entry = '%s\t%s' % ( name, '%s:%i-%i' % ( loc[ 'contig' ], loc[ 'start' ], loc[ 'end' ] ) )
+        if len( entry ) > max_len:
+            max_len = len( entry )
+        entries.append( entry )
+        
+    out.write( str( max_len + 1 ).ljust( max_len ) + '\n' )
+    for entry in entries:
+        out.write( entry.ljust( max_len ) + '\n' )
+    out.close()
 
-# Create dict of name-location pairings.
-name_loc_dict = {}
-for feature in read_unordered_gtf( open( in_fname, 'r' ) ):
-	for name in feature.attributes:
-		val = feature.attributes[ name ]
-		try:
-			float( val )
-			continue
-		except:
-			convert_gff_coords_to_bed( feature )
-			# Value is not a number, so it can be indexed.
-			if val not in name_loc_dict:
-				# Value is not in dictionary.
-				name_loc_dict[ val ] = {
-					'contig': feature.chrom,
-					'start': feature.start,
-					'end': feature.end
-				}
-			else:
-				# Value already in dictionary, so update dictionary.
-				loc = name_loc_dict[ val ]
-				if feature.start < loc[ 'start' ]:
-					loc[ 'start' ] = feature.start
-				if feature.end > loc[ 'end' ]:
-					loc[ 'end' ] = feature.end
-
-# Print name, loc in sorted order.
-out = open( out_fname, 'w' )
-max_len = 0
-entries = []
-for name in sorted( name_loc_dict.iterkeys() ):
-	loc = name_loc_dict[ name ]
-	entry = '%s\t%s' % ( name, '%s:%i-%i' % ( loc[ 'contig' ], loc[ 'start' ], loc[ 'end' ] ) )
-	if len( entry ) > max_len:
-		max_len = len( entry )
-	entries.append( entry )
-	
-out.write( str( max_len + 1 ).ljust( max_len ) + '\n' )
-for entry in entries:
-	out.write( entry.ljust( max_len ) + '\n' )
-out.close()
\ No newline at end of file
+if __name__ == '__main__':
+    main()
\ No newline at end of file

From 8faf5cc089501b2c179c64dbd8f5659420873970 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 21 Aug 2012 10:57:52 -0400
Subject: [PATCH 11/16] Rewrap text in blast tool migration script.

---
 lib/galaxy/tool_shed/migrate/versions/0004_tools.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/tool_shed/migrate/versions/0004_tools.py b/lib/galaxy/tool_shed/migrate/versions/0004_tools.py
index f20bd83b251..1a7748286af 100644
--- a/lib/galaxy/tool_shed/migrate/versions/0004_tools.py
+++ b/lib/galaxy/tool_shed/migrate/versions/0004_tools.py
@@ -1,6 +1,8 @@
 """
-The NCBI BLAST+ tools have been eliminated from the distribution.  The tools and datatypes are are now available in repositories named ncbi_blast_plus
-and blast_datatypes, respectively, from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu will be installed into your local Galaxy instance
+The NCBI BLAST+ tools have been eliminated from the distribution.  The tools and
+datatypes are are now available in repositories named ncbi_blast_plus and
+blast_datatypes, respectively, from the main Galaxy tool shed at
+http://toolshed.g2.bx.psu.edu will be installed into your local Galaxy instance
 at the location discussed above by running the following command.
 """
 

From a3d8452df5015c30fd596f3cb5121e3076ddbc37 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Tue, 21 Aug 2012 14:27:18 -0400
Subject: [PATCH 12/16] JavaScript cleanup: (a) create backbone lib in
 scripts/lib and use for backbone libraries; (b) clean up history.js; (c) pack
 scripts.

---
 .../libs/{ => backbone}/backbone-relational.js     |  0
 static/scripts/libs/{ => backbone}/backbone.js     |  0
 static/scripts/mvc/history.js                      | 14 +++++++-------
 static/scripts/packed/bootstrap.js                 |  2 +-
 .../libs/{ => backbone}/backbone-relational.js     |  0
 .../scripts/packed/libs/{ => backbone}/backbone.js |  0
 static/scripts/packed/mvc/history.js               |  1 +
 static/scripts/packed/mvc/tools.js                 |  2 +-
 .../packed/templates/compiled/panel_section.js     |  2 +-
 .../scripts/packed/templates/compiled/tool_form.js |  2 +-
 .../scripts/packed/templates/compiled/tool_link.js |  2 +-
 .../packed/templates/compiled/tool_search.js       |  2 +-
 static/scripts/packed/viz/trackster.js             |  2 +-
 templates/base.mako                                |  2 +-
 templates/base_panels.mako                         |  2 +-
 15 files changed, 17 insertions(+), 16 deletions(-)
 rename static/scripts/libs/{ => backbone}/backbone-relational.js (100%)
 rename static/scripts/libs/{ => backbone}/backbone.js (100%)
 rename static/scripts/packed/libs/{ => backbone}/backbone-relational.js (100%)
 rename static/scripts/packed/libs/{ => backbone}/backbone.js (100%)
 create mode 100644 static/scripts/packed/mvc/history.js

diff --git a/static/scripts/libs/backbone-relational.js b/static/scripts/libs/backbone/backbone-relational.js
similarity index 100%
rename from static/scripts/libs/backbone-relational.js
rename to static/scripts/libs/backbone/backbone-relational.js
diff --git a/static/scripts/libs/backbone.js b/static/scripts/libs/backbone/backbone.js
similarity index 100%
rename from static/scripts/libs/backbone.js
rename to static/scripts/libs/backbone/backbone.js
diff --git a/static/scripts/mvc/history.js b/static/scripts/mvc/history.js
index 9fe5642fe43..297847bef93 100644
--- a/static/scripts/mvc/history.js
+++ b/static/scripts/mvc/history.js
@@ -33,13 +33,13 @@ var HistoryItem = BaseModel.extend({
     
     display     : function(){},
     edit_attr   : function(){},
-    delete      : function(){},
+    remove      : function(){},
     download    : function(){},
     details     : function(){},
     rerun       : function(){},
     tags        : function(){},
     annotations : function(){},
-    peek        : function(){},
+    peek        : function(){}
 });
 
 //..............................................................................
@@ -51,17 +51,17 @@ var HistoryItemView = BaseView.extend({
     icons       : {
         display     : 'path to icon',
         edit_attr   : 'path to icon',
-        delete      : 'path to icon',
+        remove      : 'path to icon',
         download    : 'path to icon',
         details     : 'path to icon',
         rerun       : 'path to icon',
         tags        : 'path to icon',
-        annotations : 'path to icon',
+        annotations : 'path to icon'
     },
     
     render      : function(){
-        this.$el.append( 'div' )
-    },
+        this.$el.append( 'div' );
+    }
     
 });
 
@@ -139,7 +139,7 @@ var HistoryCollectionView = BaseView.extend({
     
     render      : function(){
         
-    },
+    }
     
 });
 
diff --git a/static/scripts/packed/bootstrap.js b/static/scripts/packed/bootstrap.js
index 34aabcdf6c4..7926b4540b1 100644
--- a/static/scripts/packed/bootstrap.js
+++ b/static/scripts/packed/bootstrap.js
@@ -1 +1 @@
-!function(a){a(function(){a.support.transition=(function(){var b=(function(){var e=document.createElement("bootstrap"),d={WebkitTransition:"webkitTransitionEnd",MozTransition:"transitionend",OTransition:"oTransitionEnd",msTransition:"MSTransitionEnd",transition:"transitionend"},c;for(c in d){if(e.style[c]!==undefined){return d[c]}}}());return b&&{end:b}})()})}(window.jQuery);!function(b){var a=function(c){this.element=b(c)};a.prototype={constructor:a,show:function(){var i=this.element,f=i.closest("ul:not(.dropdown-menu)"),d=i.attr("data-target"),g,c,h;if(!d){d=i.attr("href");d=d&&d.replace(/.*(?=#[^\s]*$)/,"")}if(i.parent("li").hasClass("active")){return}g=f.find(".active a").last()[0];h=b.Event("show",{relatedTarget:g});i.trigger(h);if(h.isDefaultPrevented()){return}c=b(d);this.activate(i.parent("li"),f);this.activate(c,c.parent(),function(){i.trigger({type:"shown",relatedTarget:g})})},activate:function(e,d,h){var c=d.find("> .active"),g=h&&b.support.transition&&c.hasClass("fade");function f(){c.removeClass("active").find("> .dropdown-menu > .active").removeClass("active");e.addClass("active");if(g){e[0].offsetWidth;e.addClass("in")}else{e.removeClass("fade")}if(e.parent(".dropdown-menu")){e.closest("li.dropdown").addClass("active")}h&&h()}g?c.one(b.support.transition.end,f):f();c.removeClass("in")}};b.fn.tab=function(c){return this.each(function(){var e=b(this),d=e.data("tab");if(!d){e.data("tab",(d=new a(this)))}if(typeof c=="string"){d[c]()}})};b.fn.tab.Constructor=a;b(function(){b("body").on("click.tab.data-api",'[data-toggle="tab"], [data-toggle="pill"]',function(c){c.preventDefault();b(this).tab("show")})})}(window.jQuery);!function(b){var a=function(d,c){this.init("tooltip",d,c)};a.prototype={constructor:a,init:function(f,e,d){var 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\ No newline at end of file
+!function(a){a(function(){a.support.transition=(function(){var b=(function(){var e=document.createElement("bootstrap"),d={WebkitTransition:"webkitTransitionEnd",MozTransition:"transitionend",OTransition:"oTransitionEnd",msTransition:"MSTransitionEnd",transition:"transitionend"},c;for(c in d){if(e.style[c]!==undefined){return d[c]}}}());return b&&{end:b}})()})}(window.jQuery);!function(b){var a=function(c){this.element=b(c)};a.prototype={constructor:a,show:function(){var i=this.element,f=i.closest("ul:not(.dropdown-menu)"),d=i.attr("data-target"),g,c,h;if(!d){d=i.attr("href");d=d&&d.replace(/.*(?=#[^\s]*$)/,"")}if(i.parent("li").hasClass("active")){return}g=f.find(".active a").last()[0];h=b.Event("show",{relatedTarget:g});i.trigger(h);if(h.isDefaultPrevented()){return}c=b(d);this.activate(i.parent("li"),f);this.activate(c,c.parent(),function(){i.trigger({type:"shown",relatedTarget:g})})},activate:function(e,d,h){var c=d.find("> 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\ No newline at end of file
diff --git a/static/scripts/packed/libs/backbone-relational.js b/static/scripts/packed/libs/backbone/backbone-relational.js
similarity index 100%
rename from static/scripts/packed/libs/backbone-relational.js
rename to static/scripts/packed/libs/backbone/backbone-relational.js
diff --git a/static/scripts/packed/libs/backbone.js b/static/scripts/packed/libs/backbone/backbone.js
similarity index 100%
rename from static/scripts/packed/libs/backbone.js
rename to static/scripts/packed/libs/backbone/backbone.js
diff --git a/static/scripts/packed/mvc/history.js b/static/scripts/packed/mvc/history.js
new file mode 100644
index 00000000000..a9564037790
--- /dev/null
+++ b/static/scripts/packed/mvc/history.js
@@ -0,0 +1 @@
+var HistoryItem=BaseModel.extend({display:function(){},edit_attr:function(){},remove:function(){},download:function(){},details:function(){},rerun:function(){},tags:function(){},annotations:function(){},peek:function(){}});var HistoryItemView=BaseView.extend({tagName:"div",className:"historyItemContainer",icons:{display:"path to icon",edit_attr:"path to icon",remove:"path to icon",download:"path to icon",details:"path to icon",rerun:"path to icon",tags:"path to icon",annotations:"path to icon"},render:function(){this.$el.append("div")}});var History=Backbone.Collection.extend({});var HistoryCollectionView=BaseView.extend({tagName:"body",className:"historyCollection",render:function(){}});
\ No newline at end of file
diff --git a/static/scripts/packed/mvc/tools.js b/static/scripts/packed/mvc/tools.js
index 2c0a1c55da3..70c198358ee 100644
--- a/static/scripts/packed/mvc/tools.js
+++ b/static/scripts/packed/mvc/tools.js
@@ -1 +1 @@
-var BaseModel=Backbone.RelationalModel.extend({defaults:{name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var Tool=BaseModel.extend({defaults:{description:null,target:null,inputs:[]},relations:[{type:Backbone.HasMany,key:"inputs",relatedModel:"ToolInput",reverseRelation:{key:"tool",includeInJSON:false}}],urlRoot:galaxy_paths.get("tool_url"),copy:function(b){var c=new Tool(this.toJSON());if(b){var a=new Backbone.Collection();c.get("inputs").each(function(d){if(d.get_samples()){a.push(d)}});c.set("inputs",a)}return c},apply_search_results:function(a){(_.indexOf(a,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()},set_input_value:function(a,b){this.get("inputs").find(function(c){return c.get("name")===a}).set("value",b)},set_input_values:function(b){var a=this;_.each(_.keys(b),function(c){a.set_input_value(c,b[c])})},run:function(){return this._run()},rerun:function(b,a){return this._run({action:"rerun",target_dataset_id:b.id,regions:a})},get_inputs_dict:function(){var a={};this.get("inputs").each(function(b){a[b.get("name")]=b.get("value")});return a},_run:function(c){var d=_.extend({tool_id:this.id,inputs:this.get_inputs_dict()},c);var b=$.Deferred(),a=new ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(d),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(e){return e!=="pending"}});$.when(a.go()).then(function(e){b.resolve(new DatasetCollection().reset(e))});return b}});var ToolInput=Backbone.RelationalModel.extend({defaults:{name:null,label:null,type:null,value:null,num_samples:5},initialize:function(){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new ToolInput(this.toJSON())},get_samples:function(){var b=this.get("type"),a=null;if(b==="number"){a=d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}else{if(b==="select"){a=_.map(this.get("options"),function(c){return c[0]})}}return a}});var ToolCollection=Backbone.Collection.extend({model:Tool});var ToolPanelLabel=BaseModel.extend({});var ToolPanelSection=BaseModel.extend({defaults:{elems:[],open:false},clear_search_results:function(){_.each(this.attributes.elems,function(a){a.show()});this.show();this.set("open",false)},apply_search_results:function(b){var c=true,a;_.each(this.attributes.elems,function(d){if(d instanceof ToolPanelLabel){a=d;a.hide()}else{if(d instanceof Tool){if(d.apply_search_results(b)){c=false;if(a){a.show()}}}}});if(c){this.hide()}else{this.show();this.set("open",true)}}});var ToolSearch=BaseModel.extend({defaults:{spinner_url:"",search_url:"",visible:true,query:"",results:null},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var c=this.attributes.query;if(c.length<3){this.set("results",null);return}var b=c+"*";if(this.timer){clearTimeout(this.timer)}$("#search-spinner").show();var a=this;this.timer=setTimeout(function(){$.get(a.attributes.search_url,{query:b},function(d){a.set("results",d);$("#search-spinner").hide()},"json")},200)}});var ToolPanel=Backbone.Collection.extend({url:"/tools",tools:new ToolCollection(),parse:function(a){var b=function(e){var d=e.type;if(d==="tool"){return new Tool(e)}else{if(d==="section"){var c=_.map(e.elems,b);e.elems=c;return new ToolPanelSection(e)}else{if(d==="label"){return new ToolPanelLabel(e)}}}};return _.map(a,b)},initialize:function(a){this.tool_search=a.tool_search;this.tool_search.on("change:results",this.apply_search_results,this);this.on("reset",this.populate_tools,this)},populate_tools:function(){var a=this;a.tools=new ToolCollection();this.each(function(b){if(b instanceof ToolPanelSection){_.each(b.attributes.elems,function(c){if(c instanceof Tool){a.tools.push(c)}})}else{if(b instanceof Tool){a.tools.push(b)}}})},clear_search_results:function(){this.each(function(a){if(a instanceof ToolPanelSection){a.clear_search_results()}else{a.show()}})},apply_search_results:function(){var b=this.tool_search.attributes.results;if(b===null){this.clear_search_results();return}var a=null;this.each(function(c){if(c instanceof ToolPanelLabel){a=c;a.hide()}else{if(c instanceof Tool){if(c.apply_search_results(b)){if(a){a.show()}}}else{a=null;c.apply_search_results(b)}}})}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var ToolLinkView=BaseView.extend({tagName:"div",template:Handlebars.templates.tool_link,render:function(){this.$el.append(this.template(this.model.toJSON()));return this}});var ToolPanelLabelView=BaseView.extend({tagName:"div",className:"toolPanelLabel",render:function(){this.$el.append($("<span/>").text(this.model.attributes.name));return this}});var ToolPanelSectionView=BaseView.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){BaseView.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var a=this.$el.find(".toolSectionBody");_.each(this.model.attributes.elems,function(b){if(b instanceof Tool){var c=new ToolLinkView({model:b,className:"toolTitle"});c.render();a.append(c.$el)}else{if(b instanceof ToolPanelLabel){var d=new ToolPanelLabelView({model:b});d.render();a.append(d.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var ToolSearchView=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed"},render:function(){this.$el.append(this.template(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}return this},focus_and_select:function(){this.$el.find(":input").focus().select()},query_changed:function(){this.model.set("query",this.$el.find(":input").val())}});var ToolPanelView=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.collection.tool_search.on("change:results",this.handle_search_results,this)},render:function(){var a=this;var b=new ToolSearchView({model:this.collection.tool_search});b.render();a.$el.append(b.$el);this.collection.each(function(d){if(d instanceof ToolPanelSection){var c=new ToolPanelSectionView({model:d});c.render();a.$el.append(c.$el)}else{if(d instanceof Tool){var e=new ToolLinkView({model:d,className:"toolTitleNoSection"});e.render();a.$el.append(e.$el)}else{if(d instanceof ToolPanelLabel){var f=new ToolPanelLabelView({model:d});f.render();a.$el.append(f.$el)}}}});a.$el.find("a.tool-link").click(function(f){var d=$(this).attr("class").split(/\s+/)[0],c=a.collection.tools.get(d);a.trigger("tool_link_click",f,c)});return this},handle_search_results:function(){var a=this.collection.tool_search.attributes.results;if(a&&a.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var ToolFormView=Backbone.View.extend({className:"toolForm",template:Handlebars.templates.tool_form,render:function(){this.$el.children().remove();this.$el.append(this.template(this.model.toJSON()))}});var IntegratedToolMenuAndView=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new ToolPanelView({collection:this.collection});this.tool_form_view=new ToolFormView()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.hide();this.$el.append(this.tool_form_view.$el);var a=this;this.tool_panel_view.on("tool_link_click",function(c,b){c.preventDefault();a.show_tool(b)})},show_tool:function(b){var a=this;b.fetch().done(function(){a.tool_form_view.model=b;a.tool_form_view.render();a.tool_form_view.$el.show();$("#left").width("650px")})}});
\ No newline at end of file
+var BaseModel=Backbone.RelationalModel.extend({defaults:{name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var Tool=BaseModel.extend({defaults:{description:null,target:null,inputs:[]},relations:[{type:Backbone.HasMany,key:"inputs",relatedModel:"ToolInput",reverseRelation:{key:"tool",includeInJSON:false}}],urlRoot:galaxy_paths.get("tool_url"),copy:function(b){var c=new Tool(this.toJSON());if(b){var a=new Backbone.Collection();c.get("inputs").each(function(d){if(d.get_samples()){a.push(d)}});c.set("inputs",a)}return c},apply_search_results:function(a){(_.indexOf(a,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()},set_input_value:function(a,b){this.get("inputs").find(function(c){return c.get("name")===a}).set("value",b)},set_input_values:function(b){var a=this;_.each(_.keys(b),function(c){a.set_input_value(c,b[c])})},run:function(){return this._run()},rerun:function(b,a){return this._run({action:"rerun",target_dataset_id:b.id,regions:a})},get_inputs_dict:function(){var a={};this.get("inputs").each(function(b){a[b.get("name")]=b.get("value")});return a},_run:function(c){var d=_.extend({tool_id:this.id,inputs:this.get_inputs_dict()},c);var b=$.Deferred(),a=new ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(d),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(e){return e!=="pending"}});$.when(a.go()).then(function(e){b.resolve(new DatasetCollection().reset(e))});return b}});var ToolInput=Backbone.RelationalModel.extend({defaults:{name:null,label:null,type:null,value:null,num_samples:5},initialize:function(){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new ToolInput(this.toJSON())},get_samples:function(){var b=this.get("type"),a=null;if(b==="number"){a=d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}else{if(b==="select"){a=_.map(this.get("options"),function(c){return c[0]})}}return a}});var ToolCollection=Backbone.Collection.extend({model:Tool});var ToolPanelLabel=BaseModel.extend({});var ToolPanelSection=BaseModel.extend({defaults:{elems:[],open:false},clear_search_results:function(){_.each(this.attributes.elems,function(a){a.show()});this.show();this.set("open",false)},apply_search_results:function(b){var c=true,a;_.each(this.attributes.elems,function(d){if(d instanceof ToolPanelLabel){a=d;a.hide()}else{if(d instanceof Tool){if(d.apply_search_results(b)){c=false;if(a){a.show()}}}}});if(c){this.hide()}else{this.show();this.set("open",true)}}});var ToolSearch=BaseModel.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:true,query:"",results:null,clear_key:27},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var c=this.attributes.query;if(c.length<this.attributes.min_chars_for_search){this.set("results",null);return}var b=c+"*";if(this.timer){clearTimeout(this.timer)}$("#search-clear-btn").hide();$("#search-spinner").show();var a=this;this.timer=setTimeout(function(){$.get(a.attributes.search_url,{query:b},function(d){a.set("results",d);$("#search-spinner").hide();$("#search-clear-btn").show()},"json")},200)},clear_search:function(){this.set("query","");this.set("results",null)}});var ToolPanel=Backbone.Collection.extend({url:"/tools",tools:new ToolCollection(),parse:function(a){var b=function(e){var d=e.type;if(d==="tool"){return new Tool(e)}else{if(d==="section"){var c=_.map(e.elems,b);e.elems=c;return new ToolPanelSection(e)}else{if(d==="label"){return new ToolPanelLabel(e)}}}};return _.map(a,b)},initialize:function(a){this.tool_search=a.tool_search;this.tool_search.on("change:results",this.apply_search_results,this);this.on("reset",this.populate_tools,this)},populate_tools:function(){var a=this;a.tools=new ToolCollection();this.each(function(b){if(b instanceof ToolPanelSection){_.each(b.attributes.elems,function(c){if(c instanceof Tool){a.tools.push(c)}})}else{if(b instanceof Tool){a.tools.push(b)}}})},clear_search_results:function(){this.each(function(a){if(a instanceof ToolPanelSection){a.clear_search_results()}else{a.show()}})},apply_search_results:function(){var b=this.tool_search.attributes.results;if(b===null){this.clear_search_results();return}var a=null;this.each(function(c){if(c instanceof ToolPanelLabel){a=c;a.hide()}else{if(c instanceof Tool){if(c.apply_search_results(b)){if(a){a.show()}}}else{a=null;c.apply_search_results(b)}}})}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var ToolLinkView=BaseView.extend({tagName:"div",template:Handlebars.templates.tool_link,render:function(){this.$el.append(this.template(this.model.toJSON()));return this}});var ToolPanelLabelView=BaseView.extend({tagName:"div",className:"toolPanelLabel",render:function(){this.$el.append($("<span/>").text(this.model.attributes.name));return this}});var ToolPanelSectionView=BaseView.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){BaseView.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var a=this.$el.find(".toolSectionBody");_.each(this.model.attributes.elems,function(b){if(b instanceof Tool){var c=new ToolLinkView({model:b,className:"toolTitle"});c.render();a.append(c.$el)}else{if(b instanceof ToolPanelLabel){var d=new ToolPanelLabelView({model:b});d.render();a.append(d.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var ToolSearchView=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){this.$el.append(this.template(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}return this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){this.model.clear_search();this.$el.find(":input").val(this.model.attributes.search_hint_string);this.focus_and_select();return false},query_changed:function(a){if((this.model.attributes.clear_key)&&(this.model.attributes.clear_key===a.which)){this.clear();return false}this.model.set("query",this.$el.find(":input").val())}});var ToolPanelView=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.collection.tool_search.on("change:results",this.handle_search_results,this)},render:function(){var a=this;var b=new ToolSearchView({model:this.collection.tool_search});b.render();a.$el.append(b.$el);this.collection.each(function(d){if(d instanceof ToolPanelSection){var c=new ToolPanelSectionView({model:d});c.render();a.$el.append(c.$el)}else{if(d instanceof Tool){var e=new ToolLinkView({model:d,className:"toolTitleNoSection"});e.render();a.$el.append(e.$el)}else{if(d instanceof ToolPanelLabel){var f=new ToolPanelLabelView({model:d});f.render();a.$el.append(f.$el)}}}});a.$el.find("a.tool-link").click(function(f){var d=$(this).attr("class").split(/\s+/)[0],c=a.collection.tools.get(d);a.trigger("tool_link_click",f,c)});return this},handle_search_results:function(){var a=this.collection.tool_search.attributes.results;if(a&&a.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var ToolFormView=Backbone.View.extend({className:"toolForm",template:Handlebars.templates.tool_form,render:function(){this.$el.children().remove();this.$el.append(this.template(this.model.toJSON()))}});var IntegratedToolMenuAndView=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new ToolPanelView({collection:this.collection});this.tool_form_view=new ToolFormView()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.hide();this.$el.append(this.tool_form_view.$el);var a=this;this.tool_panel_view.on("tool_link_click",function(c,b){c.preventDefault();a.show_tool(b)})},show_tool:function(b){var a=this;b.fetch().done(function(){a.tool_form_view.model=b;a.tool_form_view.render();a.tool_form_view.$el.show();$("#left").width("650px")})}});
\ No newline at end of file
diff --git a/static/scripts/packed/templates/compiled/panel_section.js b/static/scripts/packed/templates/compiled/panel_section.js
index 65e313324db..f88fe62609f 100644
--- a/static/scripts/packed/templates/compiled/panel_section.js
+++ b/static/scripts/packed/templates/compiled/panel_section.js
@@ -1 +1 @@
-(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a.panel_section=b(function(e,n,d,l,k){d=d||e.helpers;var i="",c,h,o=this,f="function",m=d.helperMissing,g=void 0,j=this.escapeExpression;i+='<div class="toolSectionTitle" id="title_';h=d.id;c=h||n.id;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"id",{hash:{}})}}i+=j(c)+'">\n    <a href="javascript:void(0)"><span>';h=d.name;c=h||n.name;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"name",{hash:{}})}}i+=j(c)+'</span></a>\n</div>\n<div id="';h=d.id;c=h||n.id;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"id",{hash:{}})}}i+=j(c)+'" class="toolSectionBody" style="display: none; ">\n    <div class="toolSectionBg"></div>\n<div>';return i})})();
\ No newline at end of file
+(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a.panel_section=b(function(e,l,d,k,j){d=d||e.helpers;var h="",c,g,f="function",i=this.escapeExpression;h+='<div class="toolSectionTitle" id="title_';g=d.id;if(g){c=g.call(l,{hash:{}})}else{c=l.id;c=typeof c===f?c():c}h+=i(c)+'">\n    <a href="javascript:void(0)"><span>';g=d.name;if(g){c=g.call(l,{hash:{}})}else{c=l.name;c=typeof c===f?c():c}h+=i(c)+'</span></a>\n</div>\n<div id="';g=d.id;if(g){c=g.call(l,{hash:{}})}else{c=l.id;c=typeof c===f?c():c}h+=i(c)+'" class="toolSectionBody" style="display: none; ">\n    <div class="toolSectionBg"></div>\n<div>';return h})})();
\ No newline at end of file
diff --git a/static/scripts/packed/templates/compiled/tool_form.js b/static/scripts/packed/templates/compiled/tool_form.js
index a9e4221e283..db3d9376eb8 100644
--- a/static/scripts/packed/templates/compiled/tool_form.js
+++ b/static/scripts/packed/templates/compiled/tool_form.js
@@ -1 +1 @@
-(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a.tool_form=b(function(f,p,e,n,m){e=e||f.helpers;var k="",c,r,j,i,q=this,g="function",o=e.helperMissing,h=void 0,l=this.escapeExpression;function d(v,u){var s="",t;s+='\n        <div class="form-row">\n            <label for="';j=e.name;t=j||v.name;if(typeof t===g){t=t.call(v,{hash:{}})}else{if(t===h){t=o.call(v,"name",{hash:{}})}}s+=l(t)+'">';j=e.label;t=j||v.label;if(typeof t===g){t=t.call(v,{hash:{}})}else{if(t===h){t=o.call(v,"label",{hash:{}})}}s+=l(t)+':</label>\n            <div class="form-row-input">\n                ';j=e.html;t=j||v.html;if(typeof t===g){t=t.call(v,{hash:{}})}else{if(t===h){t=o.call(v,"html",{hash:{}})}}if(t||t===0){s+=t}s+='\n            </div>\n            <div class="toolParamHelp" style="clear: both;">\n                ';j=e.help;t=j||v.help;if(typeof t===g){t=t.call(v,{hash:{}})}else{if(t===h){t=o.call(v,"help",{hash:{}})}}s+=l(t)+'\n            </div>\n            <div style="clear: both;"></div>\n        </div>\n        ';return s}k+='<div class="toolFormTitle">';j=e.name;c=j||p.name;if(typeof c===g){c=c.call(p,{hash:{}})}else{if(c===h){c=o.call(p,"name",{hash:{}})}}k+=l(c)+" (version ";j=e.version;c=j||p.version;if(typeof c===g){c=c.call(p,{hash:{}})}else{if(c===h){c=o.call(p,"version",{hash:{}})}}k+=l(c)+')</div>\n    <div class="toolFormBody">\n        ';j=e.inputs;c=j||p.inputs;r=e.each;i=q.program(1,d,m);i.hash={};i.fn=i;i.inverse=q.noop;c=r.call(p,c,i);if(c||c===0){k+=c}k+='\n    </div>\n    <div class="form-row form-actions">\n    <input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute">\n</div>\n<div class="toolHelp">\n    <div class="toolHelpBody">';j=e.help;c=j||p.help;if(typeof c===g){c=c.call(p,{hash:{}})}else{if(c===h){c=o.call(p,"help",{hash:{}})}}k+=l(c)+"</div>\n</div>";return k})})();
\ No newline at end of file
+(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a.tool_form=b(function(f,m,e,l,k){e=e||f.helpers;var i="",c,h,g="function",j=this.escapeExpression,n=this;function d(s,r){var p="",q,o;p+='\n        <div class="form-row">\n            <label for="';o=e.name;if(o){q=o.call(s,{hash:{}})}else{q=s.name;q=typeof q===g?q():q}p+=j(q)+'">';o=e.label;if(o){q=o.call(s,{hash:{}})}else{q=s.label;q=typeof q===g?q():q}p+=j(q)+':</label>\n            <div class="form-row-input">\n                ';o=e.html;if(o){q=o.call(s,{hash:{}})}else{q=s.html;q=typeof q===g?q():q}if(q||q===0){p+=q}p+='\n            </div>\n            <div class="toolParamHelp" style="clear: both;">\n                ';o=e.help;if(o){q=o.call(s,{hash:{}})}else{q=s.help;q=typeof q===g?q():q}p+=j(q)+'\n            </div>\n            <div style="clear: both;"></div>\n        </div>\n        ';return p}i+='<div class="toolFormTitle">';h=e.name;if(h){c=h.call(m,{hash:{}})}else{c=m.name;c=typeof c===g?c():c}i+=j(c)+" (version ";h=e.version;if(h){c=h.call(m,{hash:{}})}else{c=m.version;c=typeof c===g?c():c}i+=j(c)+')</div>\n    <div class="toolFormBody">\n        ';c=m.inputs;c=e.each.call(m,c,{hash:{},inverse:n.noop,fn:n.program(1,d,k)});if(c||c===0){i+=c}i+='\n    </div>\n    <div class="form-row form-actions">\n    <input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute">\n</div>\n<div class="toolHelp">\n    <div class="toolHelpBody">';h=e.help;if(h){c=h.call(m,{hash:{}})}else{c=m.help;c=typeof c===g?c():c}i+=j(c)+"</div>\n</div>";return i})})();
\ No newline at end of file
diff --git a/static/scripts/packed/templates/compiled/tool_link.js b/static/scripts/packed/templates/compiled/tool_link.js
index 69e5e91e842..1dba3d05bc5 100644
--- a/static/scripts/packed/templates/compiled/tool_link.js
+++ b/static/scripts/packed/templates/compiled/tool_link.js
@@ -1 +1 @@
-(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a.tool_link=b(function(e,n,d,l,k){d=d||e.helpers;var i="",c,h,o=this,f="function",m=d.helperMissing,g=void 0,j=this.escapeExpression;i+='<a class="';h=d.id;c=h||n.id;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"id",{hash:{}})}}i+=j(c)+' tool-link" href="';h=d.link;c=h||n.link;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"link",{hash:{}})}}i+=j(c)+'" target="';h=d.target;c=h||n.target;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"target",{hash:{}})}}i+=j(c)+'" minsizehint="';h=d.min_width;c=h||n.min_width;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"min_width",{hash:{}})}}i+=j(c)+'">';h=d.name;c=h||n.name;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"name",{hash:{}})}}i+=j(c)+"</a> ";h=d.description;c=h||n.description;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"description",{hash:{}})}}i+=j(c);return i})})();
\ No newline at end of file
+(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a.tool_link=b(function(e,l,d,k,j){d=d||e.helpers;var h="",c,g,f="function",i=this.escapeExpression;h+='<a class="';g=d.id;if(g){c=g.call(l,{hash:{}})}else{c=l.id;c=typeof c===f?c():c}h+=i(c)+' tool-link" href="';g=d.link;if(g){c=g.call(l,{hash:{}})}else{c=l.link;c=typeof c===f?c():c}h+=i(c)+'" target="';g=d.target;if(g){c=g.call(l,{hash:{}})}else{c=l.target;c=typeof c===f?c():c}h+=i(c)+'" minsizehint="';g=d.min_width;if(g){c=g.call(l,{hash:{}})}else{c=l.min_width;c=typeof c===f?c():c}h+=i(c)+'">';g=d.name;if(g){c=g.call(l,{hash:{}})}else{c=l.name;c=typeof c===f?c():c}h+=i(c)+"</a> ";g=d.description;if(g){c=g.call(l,{hash:{}})}else{c=l.description;c=typeof c===f?c():c}h+=i(c);return h})})();
\ No newline at end of file
diff --git a/static/scripts/packed/templates/compiled/tool_search.js b/static/scripts/packed/templates/compiled/tool_search.js
index f23b6bcfcbf..eb34e20ace6 100644
--- a/static/scripts/packed/templates/compiled/tool_search.js
+++ b/static/scripts/packed/templates/compiled/tool_search.js
@@ -1 +1 @@
-(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a.tool_search=b(function(e,n,d,l,k){d=d||e.helpers;var i="",c,h,o=this,f="function",m=d.helperMissing,g=void 0,j=this.escapeExpression;i+='<input type="text" name="query" value="search tools" id="tool-search-query" autocomplete="off" class="search-query parent-width" />\n<img src="';h=d.spinner_url;c=h||n.spinner_url;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"spinner_url",{hash:{}})}}i+=j(c)+'" id="search-spinner" class="search-spinner"/>\n';return i})})();
\ No newline at end of file
+(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a.tool_search=b(function(e,l,d,k,j){d=d||e.helpers;var h="",c,g,f="function",i=this.escapeExpression;h+='<input type="text" name="query" value="';g=d.search_hint_string;if(g){c=g.call(l,{hash:{}})}else{c=l.search_hint_string;c=typeof c===f?c():c}h+=i(c)+'" id="tool-search-query" autocomplete="off" class="search-query parent-width" />\n<a id="search-clear-btn" class="icon-button cross-circle tooltip" title="clear search (esc)"> </a>\n<img src="';g=d.spinner_url;if(g){c=g.call(l,{hash:{}})}else{c=l.spinner_url;c=typeof c===f?c():c}h+=i(c)+'" id="search-spinner" class="search-spinner"/>';return h})})();
\ No newline at end of file
diff --git a/static/scripts/packed/viz/trackster.js b/static/scripts/packed/viz/trackster.js
index 0c352c0760b..9a755b313b7 100644
--- a/static/scripts/packed/viz/trackster.js
+++ b/static/scripts/packed/viz/trackster.js
@@ -1 +1 @@
-var class_module=function(b,a){var c=function(){var g=arguments[0];for(var f=1;f<arguments.length;f++){var d=arguments[f];for(var e in d){g[e]=d[e]}}return g};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 is_deferred=function(a){return("isResolved" in a)};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 n=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(v,u,w,s,i,t){return(Math.max(v,s)-Math.min(v,s))+(Math.max(u,i)-Math.min(u,i))+(Math.max(w,t)-Math.min(w,t))};var g,o,f,k,q,h,r,c,d,b,p,m=false,l=0;do{g=Math.round(Math.random()*16777215);o=(g&16711680)>>16;f=(g&65280)>>8;k=g&255;d=n(o,f,k);m=true;for(j=0;j<a.length;j++){q=a[j];h=(q&16711680)>>16;r=(q&65280)>>8;c=q&255;b=n(h,r,c);p=e(o,f,k,h,r,c);if((Math.abs(d-b)<40)||(p<200)){m=false;break}}l++}while(!m&&l<=10);return"#"+(16777216+g).toString(16).substr(1,6)};var create_action_icon=function(c,b,a){return $("<a/>").attr("href","javascript:void(0);").attr("title",c).addClass("icon-button").addClass(b).tooltip().click(a)};var trackster_module=function(d,S){var o=d("class").extend,s=d("slotting"),I=d("painters");var m={};var k=function(Z,aa){m[Z.attr("id")]=aa};var l=function(Z,ab,ad,ac){ad=".group";var aa={};m[Z.attr("id")]=ac;Z.bind("drag",{handle:"."+ab,relative:true},function(al,am){var ak=$(this),ap=$(this).parent(),ah=ap.children(),aj=m[$(this).attr("id")],ag,af,an,ae,ai;af=$(this).parents(ad);if(af.length!==0){an=af.position().top;ae=an+af.outerHeight();if(am.offsetY<an){$(this).insertBefore(af);var ao=m[af.attr("id")];ao.remove_drawable(aj);ao.container.add_drawable_before(aj,ao);return}else{if(am.offsetY>ae){$(this).insertAfter(af);var ao=m[af.attr("id")];ao.remove_drawable(aj);ao.container.add_drawable(aj);return}}}af=null;for(ai=0;ai<ah.length;ai++){ag=$(ah.get(ai));an=ag.position().top;ae=an+ag.outerHeight();if(ag.is(ad)&&this!==ag.get(0)&&am.offsetY>=an&&am.offsetY<=ae){if(am.offsetY-an<ae-am.offsetY){ag.find(".content-div").prepend(this)}else{ag.find(".content-div").append(this)}if(aj.container){aj.container.remove_drawable(aj)}m[ag.attr("id")].add_drawable(aj);return}}for(ai=0;ai<ah.length;ai++){ag=$(ah.get(ai));if(am.offsetY<ag.position().top&&!(ag.hasClass("reference-track")||ag.hasClass("intro"))){break}}if(ai===ah.length){if(this!==ah.get(ai-1)){ap.append(this);m[ap.attr("id")].move_drawable(aj,ai)}}else{if(this!==ah.get(ai)){$(this).insertBefore(ah.get(ai));m[ap.attr("id")].move_drawable(aj,(am.deltaY>0?ai-1:ai))}}}).bind("dragstart",function(){aa["border-top"]=Z.css("border-top");aa["border-bottom"]=Z.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(aa)})};S.moveable=l;var Y=16,D=9,A=20,x=100,F=12000,P=400,H=5000,u=100,n="There was an error in indexing this dataset. ",G="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",B="No data for this chrom/contig.",t="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",v="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",N=10,E=20;function U(aa,Z){if(!Z){Z=0}var ab=Math.pow(10,Z);return Math.round(aa*ab)/ab}var p=function(aa,Z,ac){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.name=ac.name;this.view=aa;this.container=Z;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ac.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ac.drag_handle_class;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(ad){ad.stopPropagation()});var ab=this;this.container_div.hover(function(){ab.icons_div.show()},function(){ab.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(Z){if(Z.content_visible){Z.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");Z.hide_contents();Z.content_visible=false}else{Z.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");Z.content_visible=true;Z.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(aa){var ac=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},Z=function(){aa.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ab=function(ad){if((ad.keyCode||ad.which)===27){ac()}else{if((ad.keyCode||ad.which)===13){Z()}}};$(window).bind("keypress.check_enter_esc",ab);show_modal("Configure",aa.config.build_form(),{Cancel:ac,OK:Z})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(Z){$(".bs-tooltip").remove();Z.remove()}}];o(p.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(Z){this.old_name=this.name;this.name=Z;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var Z=this.view;this.container_div.hide(0,function(){$(this).remove();Z.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(aa,af,ae,ad,Z,ac){var ab=this;this.action_icons[aa]=$("<a/>").attr("href","javascript:void(0);").attr("title",af).addClass("icon-button").addClass(ae).tooltip().click(function(){ad(ab)}).appendTo(this.icons_div);if(ac){this.action_icons[aa].hide()}},build_action_icons:function(Z){var ab;for(var aa=0;aa<Z.length;aa++){ab=Z[aa];this.add_action_icon(ab.name,ab.title,ab.css_class,ab.on_click_fn,ab.prepend,ab.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){}});var w=function(aa,Z,ab){p.call(this,aa,Z,ab);this.obj_type=ab.obj_type;this.drawables=[]};o(w.prototype,p.prototype,{unpack_drawables:function(ab){this.drawables=[];var aa;for(var Z=0;Z<ab.length;Z++){aa=object_from_template(ab[Z],this.view,this);this.add_drawable(aa)}},init:function(){for(var Z=0;Z<this.drawables.length;Z++){this.drawables[Z].init()}},_draw:function(){for(var Z=0;Z<this.drawables.length;Z++){this.drawables[Z]._draw()}},to_dict:function(){var aa=[];for(var Z=0;Z<this.drawables.length;Z++){aa.push(this.drawables[Z].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:aa}},add_drawable:function(Z){this.drawables.push(Z);Z.container=this;this.changed()},add_drawable_before:function(ab,Z){this.changed();var aa=this.drawables.indexOf(Z);if(aa!==-1){this.drawables.splice(aa,0,ab);return true}return false},replace_drawable:function(ab,Z,aa){var ac=this.drawables.indexOf(ab);if(ac!==-1){this.drawables[ac]=Z;if(aa){ab.container_div.replaceWith(Z.container_div)}this.changed()}return ac},remove_drawable:function(aa){var Z=this.drawables.indexOf(aa);if(Z!==-1){this.drawables.splice(Z,1);aa.container=null;this.changed();return true}return false},move_drawable:function(aa,ab){var Z=this.drawables.indexOf(aa);if(Z!==-1){this.drawables.splice(Z,1);this.drawables.splice(ab,0,aa);this.changed();return true}return false}});var M=function(aa,Z,ac){o(ac,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});w.call(this,aa,Z,ac);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);l(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new V(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ac){this.unpack_drawables(ac.drawables)}if("filters" in ac){var ab=this.filters_manager;this.filters_manager=new V(this,ac.filters);ab.parent_div.replaceWith(this.filters_manager.parent_div);if(ac.filters.visible){this.setup_multitrack_filtering()}}};o(M.prototype,p.prototype,w.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(Z){$(".bs-tooltip").remove();Z.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(Z){if(Z.filters_manager.visible()){Z.filters_manager.clear_filters();Z._restore_filter_managers()}else{Z.setup_multitrack_filtering();Z.request_draw(true)}Z.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var Z=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(Z)}return Z},build_header_div:function(){var Z=$("<div/>").addClass("track-header");Z.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(Z);return Z},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ab=this.drawables.length;if(ab===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ab===1){if(this.drawables[0] instanceof g){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ai,ah,af,al=true,ad=this.drawables[0].get_type(),Z=0;for(ai=0;ai<ab;ai++){af=this.drawables[ai];if(af.get_type()!==ad){can_composite=false;break}if(af instanceof c){Z++}}if(al||Z===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(Z>1&&Z===this.drawables.length){var am={},aa;af=this.drawables[0];for(ah=0;ah<af.filters_manager.filters.length;ah++){aa=af.filters_manager.filters[ah];am[aa.name]=[aa]}for(ai=1;ai<this.drawables.length;ai++){af=this.drawables[ai];for(ah=0;ah<af.filters_manager.filters.length;ah++){aa=af.filters_manager.filters[ah];if(aa.name in am){am[aa.name].push(aa)}}}this.filters_manager.remove_all();var ac,ae,ag,aj;for(var ak in am){ac=am[ak];if(ac.length===Z){ae=new Q({name:ac[0].name,index:ac[0].index});this.filters_manager.add_filter(ae)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var Z=0;Z<this.drawables.length;Z++){this.drawables[Z].filters_manager=this.saved_filters_managers[Z]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var Z=0;Z<this.drawables.length;Z++){drawable=this.drawables[Z];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ad=[];for(var aa=0;aa<this.drawables.length;aa++){ad.push(this.drawables[aa].name)}var ab="Composite Track of "+this.drawables.length+" tracks ("+ad.join(", ")+")";var ac=new g(this.view,this.view,{name:ab,drawables:this.drawables});var Z=this.container.replace_drawable(this,ac,true);ac.request_draw()},add_drawable:function(Z){w.prototype.add_drawable.call(this,Z);this.update_icons()},remove_drawable:function(Z){w.prototype.remove_drawable.call(this,Z);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var Z=o(w.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return Z},request_draw:function(Z,ab){for(var aa=0;aa<this.drawables.length;aa++){this.drawables[aa].request_draw(Z,ab)}}});var X=function(Z){o(Z,{obj_type:"View"});w.call(this,"View",Z.container,Z);this.chrom=null;this.vis_id=Z.vis_id;this.dbkey=Z.dbkey;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 CanvasManager(this.container.get(0).ownerDocument);this.reset()};_.extend(X.prototype,Backbone.Events);o(X.prototype,w.prototype,{init:function(){this.requested_redraw=false;var ab=this.container,Z=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ab);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ab);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ab);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;k(this.viewport_container,Z);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ac=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_datasets(add_datasets_url,add_track_async_url,function(ad){_.each(ad,function(ae){Z.add_drawable(object_from_template(ae,Z,Z))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<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=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var aa=function(ad){if(ad.type==="focusout"||(ad.keyCode||ad.which)===13||(ad.keyCode||ad.which)===27){if((ad.keyCode||ad.which)!==27){Z.go_to($(this).val())}$(this).hide();$(this).val("");Z.location_span.show();Z.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",aa).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){Z.location_span.hide();Z.chrom_select.hide();Z.nav_input.val(Z.chrom+":"+Z.low+"-"+Z.high);Z.nav_input.css("display","inline-block");Z.nav_input.select();Z.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").tooltip({placement:"bottom"}).click(function(){Z.zoom_out();Z.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){Z.zoom_in();Z.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){Z.change_chrom(Z.chrom_select.val())});this.browser_content_div.click(function(ad){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ad){Z.zoom_in(ad.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ad,ae){this.current_x=ae.offsetX}).bind("drag",function(ad,af){var ag=af.offsetX-this.current_x;this.current_x=af.offsetX;var ae=Math.round(ag/Z.viewport_container.width()*(Z.max_high-Z.max_low));Z.move_delta(-ae)});this.overview_close.click(function(){Z.reset_overview()});this.viewport_container.bind("draginit",function(ad,ae){if(ad.clientX>Z.viewport_container.width()-16){return false}}).bind("dragstart",function(ad,ae){ae.original_low=Z.low;ae.current_height=ad.clientY;ae.current_x=ae.offsetX}).bind("drag",function(af,ah){var ad=$(this);var ai=ah.offsetX-ah.current_x;var ae=ad.scrollTop()-(af.clientY-ah.current_height);ad.scrollTop(ae);ah.current_height=af.clientY;ah.current_x=ah.offsetX;var ag=Math.round(ai/Z.viewport_container.width()*(Z.high-Z.low));Z.move_delta(ag)}).bind("mousewheel",function(af,ah,ae,ad){if(ae){ae*=50;var ag=Math.round(-ae/Z.viewport_container.width()*(Z.high-Z.low));Z.move_delta(ag)}});this.top_labeltrack.bind("dragstart",function(ad,ae){return $("<div />").css({height:Z.browser_content_div.height()+Z.top_labeltrack.height()+Z.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ah,ai){$(ai.proxy).css({left:Math.min(ah.pageX,ai.startX)-Z.container.offset().left,width:Math.abs(ah.pageX-ai.startX)});var ae=Math.min(ah.pageX,ai.startX)-Z.container.offset().left,ad=Math.max(ah.pageX,ai.startX)-Z.container.offset().left,ag=(Z.high-Z.low),af=Z.viewport_container.width();Z.update_location(Math.round(ae/af*ag)+Z.low,Math.round(ad/af*ag)+Z.low)}).bind("dragend",function(ai,aj){var ae=Math.min(ai.pageX,aj.startX),ad=Math.max(ai.pageX,aj.startX),ag=(Z.high-Z.low),af=Z.viewport_container.width(),ah=Z.low;Z.low=Math.round(ae/af*ag)+ah;Z.high=Math.round(ad/af*ag)+ah;$(aj.proxy).remove();Z.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){Z.resize_window()},500)});$(document).bind("redraw",function(){Z.redraw()});this.reset();$(window).trigger("resize")},changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(aa,ac,Z,ad){if(this.timer){clearTimeout(this.timer)}if(ad){var ab=this;this.timer=setTimeout(function(){ab.trigger("navigate",aa+":"+ac+"-"+Z)},500)}else{view.trigger("navigate",aa+":"+ac+"-"+Z)}},update_location:function(Z,ab){this.location_span.text(commatize(Z)+" - "+commatize(ab));this.nav_input.val(this.chrom+":"+commatize(Z)+"-"+commatize(ab));var aa=view.chrom_select.val();if(aa!==""){this.trigger_navigate(aa,view.low,view.high,true)}},load_chroms:function(ab){ab.num=u;ab.dbkey=this.dbkey;var Z=this,aa=$.Deferred();$.ajax({url:chrom_url,data:ab,dataType:"json",success:function(ad){if(ad.chrom_info.length===0){alert("Invalid chromosome: "+ab.chrom);return}if(ad.reference){Z.add_label_track(new y(Z))}Z.chrom_data=ad.chrom_info;var ag='<option value="">Select Chrom/Contig</option>';for(var af=0,ac=Z.chrom_data.length;af<ac;af++){var ae=Z.chrom_data[af].chrom;ag+='<option value="'+ae+'">'+ae+"</option>"}if(ad.prev_chroms){ag+='<option value="previous">Previous '+u+"</option>"}if(ad.next_chroms){ag+='<option value="next">Next '+u+"</option>"}Z.chrom_select.html(ag);Z.chrom_start_index=ad.start_index;aa.resolve(ad)},error:function(){alert("Could not load chroms for this dbkey:",Z.dbkey)}});return aa},change_chrom:function(ae,aa,ag){var ab=this;if(!ab.chrom_data){ab.load_chroms_deferred.then(function(){ab.change_chrom(ae,aa,ag)});return}if(!ae||ae==="None"){return}if(ae==="previous"){ab.load_chroms({low:this.chrom_start_index-u});return}if(ae==="next"){ab.load_chroms({low:this.chrom_start_index+u});return}var af=$.grep(ab.chrom_data,function(ah,ai){return ah.chrom===ae})[0];if(af===undefined){ab.load_chroms({chrom:ae},function(){ab.change_chrom(ae,aa,ag)});return}else{if(ae!==ab.chrom){ab.chrom=ae;ab.chrom_select.val(ab.chrom);ab.max_high=af.len-1;ab.reset();ab.request_redraw(true);for(var ad=0,Z=ab.drawables.length;ad<Z;ad++){var ac=ab.drawables[ad];if(ac.init){ac.init()}}if(ab.reference_track){ab.reference_track.init()}}if(aa!==undefined&&ag!==undefined){ab.low=Math.max(aa,0);ab.high=Math.min(ag,ab.max_high)}else{ab.low=0;ab.high=ab.max_high}ab.reset_overview();ab.request_redraw()}},go_to:function(ad){ad=ad.replace(/ |,/g,"");var ah=this,Z,ac,aa=ad.split(":"),af=aa[0],ag=aa[1];if(ag!==undefined){try{var ae=ag.split("-");Z=parseInt(ae[0],10);ac=parseInt(ae[1],10)}catch(ab){return false}}ah.change_chrom(af,Z,ac)},move_fraction:function(ab){var Z=this;var aa=Z.high-Z.low;this.move_delta(ab*aa)},move_delta:function(ac){var Z=this;var ab=Z.high-Z.low;if(Z.low-ac<Z.max_low){Z.low=Z.max_low;Z.high=Z.max_low+ab}else{if(Z.high-ac>Z.max_high){Z.high=Z.max_high;Z.low=Z.max_high-ab}else{Z.high-=ac;Z.low-=ac}}Z.request_redraw();var aa=Z.chrom_select.val();this.trigger_navigate(aa,Z.low,Z.high,true)},add_drawable:function(Z){w.prototype.add_drawable.call(this,Z);Z.init();this.changed();this.update_intro_div()},add_label_track:function(Z){Z.view=this;Z.init();this.label_tracks.push(Z)},remove_drawable:function(ab,aa){w.prototype.remove_drawable.call(this,ab);if(aa){var Z=this;ab.container_div.hide(0,function(){$(this).remove();Z.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ah,Z,ag,ai){var af=this,ae=(ai?[ai]:af.drawables),ab;var aa;for(var ad=0;ad<ae.length;ad++){aa=ae[ad];ab=-1;for(var ac=0;ac<af.tracks_to_be_redrawn.length;ac++){if(af.tracks_to_be_redrawn[ac][0]===aa){ab=ac;break}}if(ab<0){af.tracks_to_be_redrawn.push([aa,Z,ag])}else{af.tracks_to_be_redrawn[ad][1]=Z;af.tracks_to_be_redrawn[ad][2]=ag}}if(!this.requested_redraw){requestAnimationFrame(function(){af._redraw(ah)});this.requested_redraw=true}},_redraw:function(aj){this.requested_redraw=false;var ag=this.low,ac=this.high;if(ag<this.max_low){ag=this.max_low}if(ac>this.max_high){ac=this.max_high}var ai=this.high-this.low;if(this.high!==0&&ai<this.min_separation){ac=ag+this.min_separation}this.low=Math.floor(ag);this.high=Math.ceil(ac);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var Z=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var af=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ak=13;this.overview_box.css({left:Z,width:Math.max(ak,af)}).show();if(af<ak){this.overview_box.css("left",Z-(ak-af)/2)}if(this.overview_highlight){this.overview_highlight.css({left:Z,width:af})}if(!aj){var ab,aa,ah;for(var ad=0,ae=this.tracks_to_be_redrawn.length;ad<ae;ad++){ab=this.tracks_to_be_redrawn[ad][0];aa=this.tracks_to_be_redrawn[ad][1];ah=this.tracks_to_be_redrawn[ad][2];if(ab){ab._draw(aa,ah)}}this.tracks_to_be_redrawn=[];for(ad=0,ae=this.label_tracks.length;ad<ae;ad++){this.label_tracks[ad]._draw()}}},zoom_in:function(aa,ab){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ac=this.high-this.low,ad=ac/2+this.low,Z=(ac/this.zoom_factor)/2;if(aa){ad=aa/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ad-Z);this.high=Math.round(ad+Z);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var aa=this.high-this.low,ab=aa/2+this.low,Z=(aa*this.zoom_factor)/2;this.low=Math.round(ab-Z);this.high=Math.round(ab+Z);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ab){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ab.dataset_id){return}this.overview_viewport.find(".track").remove()}var aa=ab.copy({content_div:this.overview_viewport}),Z=this;aa.header_div.hide();aa.is_overview=true;Z.overview_drawable=aa;this.overview_drawable.postdraw_actions=function(){Z.overview_highlight.show().height(Z.overview_drawable.content_div.height());Z.overview_viewport.height(Z.overview_drawable.content_div.height()+Z.overview_box.outerHeight());Z.overview_close.show();Z.resize_window()};Z.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-tooltip").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 q=function(ab,ag,ac){this.track=ab;this.name=ag.name;this.params=[];var an=ag.params;for(var ad=0;ad<an.length;ad++){var ai=an[ad],aa=ai.name,am=ai.label,ae=unescape(ai.html),ao=ai.value,ak=ai.type;if(ak==="number"){this.params.push(new e(aa,am,ae,(aa in ac?ac[aa]:ao),ai.min,ai.max))}else{if(ak==="select"){this.params.push(new K(aa,am,ae,(aa in ac?ac[aa]:ao)))}else{console.log("WARNING: unrecognized tool parameter type:",aa,ak)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aq){aq.stopPropagation()}).click(function(aq){aq.stopPropagation()}).bind("dblclick",function(aq){aq.stopPropagation()});var al=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aj=this.params;var ah=this;$.each(this.params,function(ar,av){var au=$("<div>").addClass("param-row").appendTo(ah.parent_div);var aq=$("<div>").addClass("param-label").text(av.label).appendTo(au);var at=$("<div/>").addClass("param-input").html(av.html).appendTo(au);at.find(":input").val(av.value);$("<div style='clear: both;'/>").appendTo(au)});this.parent_div.find("input").click(function(){$(this).select()});var ap=$("<div>").addClass("param-row").appendTo(this.parent_div);var af=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ap);var Z=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ap);Z.click(function(){ah.run_on_region()});af.click(function(){ah.run_on_dataset()});if("visible" in ac&&ac.visible){this.parent_div.show()}};o(q.prototype,{update_params:function(){for(var Z=0;Z<this.params.length;Z++){this.params[Z].update_value()}},state_dict:function(){var aa={};for(var Z=0;Z<this.params.length;Z++){aa[this.params[Z].name]=this.params[Z].value}aa.visible=this.parent_div.is(":visible");return aa},get_param_values_dict:function(){var Z={};this.parent_div.find(":input").each(function(){var aa=$(this).attr("name"),ab=$(this).val();Z[aa]=ab});return Z},get_param_values:function(){var Z=[];this.parent_div.find(":input").each(function(){var aa=$(this).attr("name"),ab=$(this).val();if(aa){Z[Z.length]=ab}});return Z},run_on_dataset:function(){var Z=this;Z.run({target_dataset_id:this.track.original_dataset_id,tool_id:Z.name},null,function(aa){show_modal(Z.name+" is Running",Z.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var aa={target_dataset_id:this.track.original_dataset_id,action:"rerun",tool_id:this.name,regions:[{chrom:this.track.view.chrom,start:this.track.view.low,end:this.track.view.high}]},ae=this.track,ab=aa.tool_id+ae.tool_region_and_parameters_str(aa.chrom,aa.low,aa.high),Z;if(ae.container===view){var ad=new M(view,view,{name:this.name});var ac=ae.container.replace_drawable(ae,ad,false);ad.container_div.insertBefore(ae.view.content_div.children()[ac]);ad.add_drawable(ae);ae.container_div.appendTo(ad.content_div);Z=ad}else{Z=ae.container}var af=new ae.constructor(view,Z,{name:ab,hda_ldda:"hda"});af.init_for_tool_data();af.change_mode(ae.mode);af.set_filters_manager(ae.filters_manager.copy(af));af.update_icons();Z.add_drawable(af);af.tiles_div.text("Starting job.");this.update_params();this.run(aa,af,function(ag){af.set_dataset(new Dataset(ag));af.tiles_div.text("Running job.");af.init()})},run:function(Z,ab,ac){Z.inputs=this.get_param_values_dict();var aa=new ServerStateDeferred({ajax_settings:{url:galaxy_paths.get("tool_url"),data:JSON.stringify(Z),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ad){return ad!=="pending"}});$.when(aa.go()).then(function(ad){if(ad==="no converter"){ab.container_div.addClass("error");ab.content_div.text(G)}else{if(ad.error){ab.container_div.addClass("error");ab.content_div.text(v+ad.message)}else{ac(ad)}}})}});var K=function(aa,Z,ab,ac){this.name=aa;this.label=Z;this.html=$(ab);this.value=ac};o(K.prototype,{update_value:function(){this.value=$(this.html).val()}});var e=function(ab,aa,ad,ae,ac,Z){K.call(this,ab,aa,ad,ae);this.min=ac;this.max=Z};o(e.prototype,K.prototype,{update_value:function(){K.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var f=function(Z){this.manager=null;this.name=Z.name;this.index=Z.index;this.tool_id=Z.tool_id;this.tool_exp_name=Z.tool_exp_name};o(f.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var Q=function(ah){f.call(this,ah);this.low=("low" in ah?ah.low:-Number.MAX_VALUE);this.high=("high" in ah?ah.high:Number.MAX_VALUE);this.min=("min" in ah?ah.min:Number.MAX_VALUE);this.max=("max" in ah?ah.max:-Number.MAX_VALUE);this.container=null;this.slider=null;this.slider_label=null;var ad=function(ai,aj,ak){ai.click(function(){var ap=aj.text(),an=parseFloat(ak.slider("option","max")),am=(an<=1?4:an<=1000000?an.toString().length:6),ao=false,al=$(this).parents(".slider-row");al.addClass("input");if(ak.slider("option","values")){am=2*am+1;ao=true}aj.text("");$("<input type='text'/>").attr("size",am).attr("maxlength",am).attr("value",ap).appendTo(aj).focus().select().click(function(aq){aq.stopPropagation()}).blur(function(){$(this).remove();aj.text(ap);al.removeClass("input")}).keyup(function(av){if(av.keyCode===27){$(this).trigger("blur")}else{if(av.keyCode===13){var at=ak.slider("option","min"),aq=ak.slider("option","max"),au=function(aw){return(isNaN(aw)||aw>aq||aw<at)},ar=$(this).val();if(!ao){ar=parseFloat(ar);if(au(ar)){alert("Parameter value must be in the range ["+at+"-"+aq+"]");return $(this)}}else{ar=ar.split("-");ar=[parseFloat(ar[0]),parseFloat(ar[1])];if(au(ar[0])||au(ar[1])){alert("Parameter value must be in the range ["+at+"-"+aq+"]");return $(this)}}ak.slider((ao?"values":"value"),ar);al.removeClass("input")}}})})};var aa=this;aa.parent_div=$("<div/>").addClass("filter-row slider-row");var Z=$("<div/>").addClass("elt-label").appendTo(aa.parent_div),af=$("<span/>").addClass("slider-name").text(aa.name+"  ").appendTo(Z),ab=$("<span/>").text(this.low+"-"+this.high),ac=$("<span/>").addClass("slider-value").appendTo(Z).append("[").append(ab).append("]");aa.values_span=ab;var ae=$("<div/>").addClass("slider").appendTo(aa.parent_div);aa.control_element=$("<div/>").attr("id",aa.name+"-filter-control").appendTo(ae);aa.control_element.slider({range:true,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(ai,aj){aa.slide(ai,aj)},change:function(ai,aj){aa.control_element.slider("option","slide").call(aa.control_element,ai,aj)}});aa.slider=aa.control_element;aa.slider_label=ab;ad(ac,ab,aa.control_element);var ag=$("<div/>").addClass("display-controls").appendTo(aa.parent_div);this.transparency_icon=create_action_icon("Use filter for data transparency","layer-transparent",function(){if(aa.manager.alpha_filter!==aa){aa.manager.alpha_filter=aa;aa.manager.parent_div.find(".layer-transparent").removeClass("active").hide();aa.transparency_icon.addClass("active").show()}else{aa.manager.alpha_filter=null;aa.transparency_icon.removeClass("active")}aa.manager.track.request_draw(true,true)}).appendTo(ag).hide();this.height_icon=create_action_icon("Use filter for data height","arrow-resize-090",function(){if(aa.manager.height_filter!==aa){aa.manager.height_filter=aa;aa.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide();aa.height_icon.addClass("active").show()}else{aa.manager.height_filter=null;aa.height_icon.removeClass("active")}aa.manager.track.request_draw(true,true)}).appendTo(ag).hide();aa.parent_div.hover(function(){aa.transparency_icon.show();aa.height_icon.show()},function(){if(aa.manager.alpha_filter!==aa){aa.transparency_icon.hide()}if(aa.manager.height_filter!==aa){aa.height_icon.hide()}});$("<div style='clear: both;'/>").appendTo(aa.parent_div)};o(Q.prototype,{to_dict:function(){var Z=f.prototype.to_dict.call(this);return o(Z,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new Q({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(ab,Z){var aa=Z-ab;return(aa<=2?0.01:1)},slide:function(ab,ac){var aa=ac.values;this.values_span.text(aa[0]+"-"+aa[1]);this.low=aa[0];this.high=aa[1];var Z=this;setTimeout(function(){if(aa[0]===Z.low&&aa[1]===Z.high){Z.manager.track.request_draw(true,true)}},25)},applies_to:function(Z){if(Z.length>this.index){return true}return false},_keep_val:function(Z){return(isNaN(Z)||(Z>=this.low&&Z<=this.high))},keep:function(aa){if(!this.applies_to(aa)){return true}var ac=this;var ad=aa[this.index];if(ad instanceof Array){var ab=true;for(var Z=0;Z<ad.length;Z++){if(!this._keep_val(ad[Z])){ab=false;break}}return ab}else{return this._keep_val(aa[this.index])}},update_attrs:function(ac){var Z=false;if(!this.applies_to(ac)){return Z}var aa=ac[this.index];if(!(aa instanceof Array)){aa=[aa]}for(var ab=0;ab<aa.length;ab++){var ad=aa[ab];if(ad<this.min){this.min=Math.floor(ad);Z=true}if(ad>this.max){this.max=Math.ceil(ad);Z=true}}return Z},update_ui_elt:function(){if(this.min<this.max){this.parent_div.show()}else{this.parent_div.hide()}var aa=this.slider.slider("option","min"),Z=this.slider.slider("option","max");if(this.min<aa||this.max>Z){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",this.get_slider_step(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var V=function(ab,ah){this.track=ab;this.alpha_filter=null;this.height_filter=null;this.filters=[];this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aj){aj.stopPropagation()}).click(function(aj){aj.stopPropagation()}).bind("dblclick",function(aj){aj.stopPropagation()}).bind("keydown",function(aj){aj.stopPropagation()});if(ah&&"filters" in ah){var Z=("alpha_filter" in ah?ah.alpha_filter:null),ac=("height_filter" in ah?ah.height_filter:null),ae=ah.filters,aa;for(var af=0;af<ae.length;af++){if(ae[af].type==="number"){aa=new Q(ae[af]);this.add_filter(aa);if(aa.name===Z){this.alpha_filter=aa;aa.transparency_icon.addClass("active").show()}if(aa.name===ac){this.height_filter=aa;aa.height_icon.addClass("active").show()}}else{console.log("ERROR: unsupported filter: ",name,type)}}if("visible" in ah&&ah.visible){this.parent_div.show()}}if(this.filters.length!==0){var ai=$("<div/>").addClass("param-row").appendTo(this.parent_div);var ag=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ai);var ad=this;ag.click(function(){ad.run_on_dataset()})}};o(V.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){var ac={},ab=[],aa;for(var Z=0;Z<this.filters.length;Z++){aa=this.filters[Z];ab.push(aa.to_dict())}ac.filters=ab;ac.alpha_filter=(this.alpha_filter?this.alpha_filter.name:null);ac.height_filter=(this.height_filter?this.height_filter.name:null);ac.visible=this.parent_div.is(":visible");return ac},copy:function(aa){var ab=new V(aa);for(var Z=0;Z<this.filters.length;Z++){ab.add_filter(this.filters[Z].copy())}return ab},add_filter:function(Z){Z.manager=this;this.parent_div.append(Z.parent_div);this.filters.push(Z)},remove_all:function(){this.filters=[];this.parent_div.children().remove()},init_filters:function(){for(var Z=0;Z<this.filters.length;Z++){var aa=this.filters[Z];aa.update_ui_elt()}},clear_filters:function(){for(var Z=0;Z<this.filters.length;Z++){var aa=this.filters[Z];aa.slider.slider("option","values",[aa.min,aa.max])}this.alpha_filter=null;this.height_filter=null;this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){var af=function(aj,ah,ai){if(!(ah in aj)){aj[ah]=ai}return aj[ah]};var ae={},ag,Z;for(var ad=0;ad<this.filters.length;ad++){ag=this.filters[ad];if(ag.tool_id){if(ag.min!==ag.low){Z=af(ae,ag.tool_id,[]);Z[Z.length]=ag.tool_exp_name+" >= "+ag.low}if(ag.max!==ag.high){Z=af(ae,ag.tool_id,[]);Z[Z.length]=ag.tool_exp_name+" <= "+ag.high}}}var aa=[];for(var ac in ae){aa[aa.length]=[ac,ae[ac]]}(function ab(an,ak){var ai=ak[0],aj=ai[0],am=ai[1],al="("+am.join(") and (")+")",ah={cond:al,input:an,target_dataset_id:an,tool_id:aj},ak=ak.slice(1);$.getJSON(run_tool_url,ah,function(ao){if(ao.error){show_modal("Filter Dataset","Error running tool "+aj,{Close:hide_modal})}else{if(ak.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ab(ao.dataset_id,ak)}}})})(this.track.dataset_id,aa)}});var z=function(Z,aa){I.Scaler.call(this,aa);this.filter=Z};z.prototype.gen_val=function(Z){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(Z[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var C=function(Z){this.track=Z.track;this.params=Z.params;this.values={};this.restore_values((Z.saved_values?Z.saved_values:{}));this.onchange=Z.onchange};o(C.prototype,{restore_values:function(Z){var aa=this;$.each(this.params,function(ab,ac){if(Z[ac.key]!==undefined){aa.values[ac.key]=Z[ac.key]}else{aa.values[ac.key]=ac.default_value}})},build_form:function(){var ac=this;var Z=$("<div />");var ab;function aa(ah,ad){for(var al=0;al<ah.length;al++){ab=ah[al];if(ab.hidden){continue}var af="param_"+al;var ap=ac.values[ab.key];var ar=$("<div class='form-row' />").appendTo(ad);ar.append($("<label />").attr("for",af).text(ab.label+":"));if(ab.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",af).attr("name",af).attr("checked",ap))}else{if(ab.type==="text"){ar.append($('<input type="text"/>').attr("id",af).val(ap).click(function(){$(this).select()}))}else{if(ab.type==="select"){var an=$("<select />").attr("id",af);for(var aj=0;aj<ab.options.length;aj++){$("<option/>").text(ab.options[aj].label).attr("value",ab.options[aj].value).appendTo(an)}an.val(ap);ar.append(an)}else{if(ab.type==="color"){var aq=$("<div/>").appendTo(ar),am=$("<input />").attr("id",af).attr("name",af).val(ap).css("float","left").appendTo(aq).click(function(au){$(".bs-tooltip").removeClass("in");var at=$(this).siblings(".bs-tooltip").addClass("in");at.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(at).height()/2)+($(this).height()/2)}).show();at.click(function(av){av.stopPropagation()});$(document).bind("click.color-picker",function(){at.hide();$(document).unbind("click.color-picker")});au.stopPropagation()}),ak=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(aq).attr("title","Set new random color").tooltip(),ao=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(aq).hide(),ag=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(ao),ae=$("<div class='tooltip-arrow'></div>").appendTo(ao),ai=$.farbtastic(ag,{width:100,height:100,callback:am,color:ap});aq.append($("<div/>").css("clear","both"));(function(at){ak.click(function(){at.setColor(get_random_color())})})(ai)}else{ar.append($("<input />").attr("id",af).attr("name",af).val(ap))}}}}if(ab.help){ar.append($("<div class='help'/>").text(ab.help))}}}aa(this.params,Z);return Z},update_from_form:function(Z){var ab=this;var aa=false;$.each(this.params,function(ac,ae){if(!ae.hidden){var af="param_"+ac;var ad=Z.find("#"+af).val();if(ae.type==="float"){ad=parseFloat(ad)}else{if(ae.type==="int"){ad=parseInt(ad)}else{if(ae.type==="bool"){ad=Z.find("#"+af).is(":checked")}}}if(ad!==ab.values[ae.key]){ab.values[ae.key]=ad;aa=true}}});if(aa){this.onchange();this.track.changed()}}});var b=function(Z,ad,ab,aa,ac){this.track=Z;this.region=ad;this.low=ad.get("start");this.high=ad.get("end");this.resolution=ab;this.html_elt=$("<div class='track-tile'/>").append(aa).height($(aa).attr("height"));this.data=ac;this.stale=false};b.prototype.predisplay_actions=function(){};var j=function(Z,ae,ab,aa,ac,ad){b.call(this,Z,ae,ab,aa,ac);this.max_val=ad};o(j.prototype,b.prototype);var L=function(ac,ak,ad,ab,af,am,ag,an,aa,aj){b.call(this,ac,ak,ad,ab,af);this.mode=ag;this.all_slotted=aa;this.feature_mapper=aj;this.has_icons=false;if(an){this.has_icons=true;var ah=this;ab=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:A-1,width:ab.width}).prependTo(this.html_elt);var ai=new GenomeRegion({chrom:ac.view.chrom,start:this.low,end:this.high}),al=af.length,ae=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+al+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),Z=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+al+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ae.click(function(){ah.stale=true;ac.data_manager.get_more_data(ai,ac.mode,ah.resolution,{},ac.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();ac.request_draw(true)}).dblclick(function(ao){ao.stopPropagation()});Z.click(function(){ah.stale=true;ac.data_manager.get_more_data(ai,ac.mode,ah.resolution,{},ac.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();ac.request_draw(true)}).dblclick(function(ao){ao.stopPropagation()})}};o(L.prototype,b.prototype);L.prototype.predisplay_actions=function(){var aa=this,Z={};if(aa.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(al){if(!this.hovered){return}var ag=$(this).offset(),ak=al.pageX-ag.left,aj=al.pageY-ag.top,ap=aa.feature_mapper.get_feature_data(ak,aj),ah=(ap?ap[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ah||$(this).attr("id")!==ah.toString()){$(this).remove()}});if(ap){var ac=Z[ah];if(!ac){var ah=ap[0],am={name:ap[3],start:ap[1],end:ap[2],strand:ap[4]},af=aa.track.filters_manager.filters,ae;for(var ai=0;ai<af.length;ai++){ae=af[ai];am[ae.name]=ap[ae.index]}var ac=$("<div/>").attr("id",ah).addClass("feature-popup"),aq=$("<table/>"),ao,an,ar;for(ao in am){an=am[ao];ar=$("<tr/>").appendTo(aq);$("<th/>").appendTo(ar).text(ao);$("<td/>").attr("align","left").appendTo(ar).text(typeof(an)==="number"?U(an,2):an)}ac.append($("<div class='feature-popup-inner'>").append(aq));Z[ah]=ac}ac.appendTo($(this).parents(".track-content").children(".overlay"));var ad=ak+parseInt(aa.html_elt.css("left"))-ac.width()/2,ab=aj+parseInt(aa.html_elt.css("top"))+7;ac.css("left",ad+"px").css("top",ab+"px")}else{if(!al.isPropagationStopped()){al.stopPropagation();$(this).siblings().each(function(){$(this).trigger(al)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var h=function(ab,aa,ad){o(ad,{drag_handle_class:"draghandle"});p.call(this,ab,aa,ad);this.data_url=("data_url" in ad?ad.data_url:default_data_url);this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ad?ad.data_query_wait:H);this.dataset_check_url=("converted_datasets_state_url" in ad?ad.converted_datasets_state_url:converted_datasets_state_url);var Z=this,ac=new Dataset({id:ad.dataset_id,hda_ldda:ad.hda_ldda});this.data_manager=("data_manager" in ad?ad.data_manager:new GenomeDataManager({dataset:ac,data_url:Z.data_url,dataset_state_url:Z.dataset_check_url,data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ad)||ad.resize){this.add_resize_handle()}}};o(h.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(Z){Z.view.set_overview(Z)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(Z){if(Z.filters_manager.visible()){Z.filters_manager.clear_filters()}else{Z.filters_manager.init_filters()}Z.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(Z){Z.dynamic_tool_div.toggle();if(Z.dynamic_tool_div.is(":visible")){Z.set_name(Z.name+Z.tool_region_and_parameters_str())}else{Z.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(Z){var ac='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ab=_.template(ac,{track:Z});var ae=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aa=function(){var ag=$('select[name="regions"] option:selected').val(),ai,af=new GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ah=_.map($(".bookmark"),function(aj){return new GenomeRegion({from_str:$(aj).children(".position").text()})});if(ag==="cur"){ai=[af]}else{if(ag==="bookmarks"){ai=ah}else{ai=[af].concat(ah)}}hide_modal();window.location.href=galaxy_paths.get("sweepster_url")+"?"+$.param({dataset_id:Z.dataset_id,hda_ldda:Z.hda_ldda,regions:JSON.stringify(new Backbone.Collection(ai).toJSON())})},ad=function(af){if((af.keyCode||af.which)===27){ae()}else{if((af.keyCode||af.which)===13){aa()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",ab,{No:ae,Yes:aa})}},p.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&p.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var Z=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(Z)}this.name_div=$("<div/>").addClass("track-name").appendTo(Z).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return Z},on_resize:function(){},add_resize_handle:function(){var Z=this;var ac=false;var ab=false;var aa=$("<div class='track-resize'>");$(Z.container_div).hover(function(){if(Z.content_visible){ac=true;aa.show()}},function(){ac=false;if(!ab){aa.hide()}});aa.hide().bind("dragstart",function(ad,ae){ab=true;ae.original_height=$(Z.content_div).height()}).bind("drag",function(ae,af){var ad=Math.min(Math.max(af.original_height+af.deltaY,Z.min_height_px),Z.max_height_px);$(Z.tiles_div).css("height",ad);Z.visible_height_px=(Z.max_height_px===ad?0:ad);Z.on_resize()}).bind("dragend",function(ad,ae){Z.tile_cache.clear();ab=false;if(!ac){aa.hide()}Z.config.values.height=Z.visible_height_px;Z.changed()}).appendTo(Z.container_div)},set_display_modes:function(ac,af){this.display_modes=ac;this.mode=(af?af:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var aa=this,ad={};for(var ab=0,Z=aa.display_modes.length;ab<Z;ab++){var ae=aa.display_modes[ab];ad[ae]=function(ag){return function(){aa.change_mode(ag);aa.icons_div.show();aa.container_div.mouseleave(function(){aa.icons_div.hide()})}}(ae)}make_popupmenu(this.action_icons.mode_icon,ad)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof y){return"ReferenceTrack"}else{if(this instanceof i){return"LineTrack"}else{if(this instanceof R){return"ReadTrack"}else{if(this instanceof O){return"VcfTrack"}else{if(this instanceof g){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(){var aa=this;aa.enabled=false;aa.tile_cache.clear();aa.data_manager.clear();aa.content_div.css("height","auto");aa.tiles_div.children().remove();aa.container_div.removeClass("nodata error pending");if(!aa.dataset_id){return}var Z=$.Deferred();$.getJSON(this.dataset_check_url,{hda_ldda:aa.hda_ldda,dataset_id:aa.dataset_id,chrom:aa.view.chrom},function(ab){if(!ab||ab==="error"||ab.kind==="error"){aa.container_div.addClass("error");aa.tiles_div.text(n);if(ab.message){var ac=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ab.message+"</pre>",{Close:hide_modal})});aa.tiles_div.append(ac)}}else{if(ab==="no converter"){aa.container_div.addClass("error");aa.tiles_div.text(G)}else{if(ab==="no data"||(ab.data!==undefined&&(ab.data===null||ab.data.length===0))){aa.container_div.addClass("nodata");aa.tiles_div.text(B)}else{if(ab==="pending"){aa.container_div.addClass("pending");aa.tiles_div.html(t);setTimeout(function(){aa.init()},aa.data_query_wait)}else{if(ab==="data"||ab.status==="data"){if(ab.valid_chroms){aa.valid_chroms=ab.valid_chroms;aa.update_icons()}aa.tiles_div.text(T);if(aa.view.chrom){aa.tiles_div.text("");aa.tiles_div.css("height",aa.visible_height_px+"px");aa.enabled=true;$.when(aa.predraw_init()).done(function(){Z.resolve();aa.container_div.removeClass("nodata error pending");aa.request_draw()})}else{Z.resolve()}}}}}}});this.update_icons();return Z},predraw_init:function(){}});var J=function(ab,aa,ac){h.call(this,ab,aa,ac);var Z=this,ab=Z.view;l(Z.container_div,Z.drag_handle_class,".group",Z);this.filters_manager=new V(this,("filters" in ac?ac.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in ac&&ac.tool?new q(this,ac.tool,ac.tool_state):null);this.tile_cache=new Cache(N);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ac.mode){this.change_mode(ac.mode)}};o(J.prototype,p.prototype,h.prototype,{action_icons_def:h.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(Z){$(".bs-tooltip").remove();Z.slotters[Z.view.resolution_px_b].max_rows*=2;Z.request_draw(true)},hide:true}]),copy:function(Z){var aa=this.to_dict();o(aa,{data_manager:this.data_manager});var ab=new this.constructor(this.view,Z,aa);ab.change_mode(this.mode);ab.enabled=this.enabled;return ab},set_filters_manager:function(Z){this.filters_manager=Z;this.header_div.after(this.filters_manager.parent_div)},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,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(aa){var Z=this;Z.mode=aa;Z.config.values.mode=aa;Z.tile_cache.clear();Z.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+Z.mode+")");return Z},update_icons:function(){var Z=this;if(Z.filters_available){Z.action_icons.filters_icon.show()}else{Z.action_icons.filters_icon.hide()}if(Z.tool){Z.action_icons.tools_icon.show();Z.action_icons.param_space_viz_icon.show()}else{Z.action_icons.tools_icon.hide();Z.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(aa,ab,Z){return aa+"_"+ab+"_"+Z},request_draw:function(aa,Z){this.view.request_redraw(false,aa,Z,this)},before_draw:function(){},_draw:function(aa,ak){if(!this.can_draw()){return}var ai=this.view.low,ae=this.view.high,ag=ae-ai,ab=this.view.container.width(),am=this.view.resolution_px_b,ad=this.view.resolution_b_px;if(this.is_overview){ai=this.view.max_low;ae=this.view.max_high;ad=Math.pow(RESOLUTION,Math.ceil(Math.log((view.max_high-view.max_low)/P)/Math.log(RESOLUTION)));am=ab/(view.max_high-view.max_low)}this.before_draw();this.tiles_div.children().addClass("remove");var Z=Math.floor(ai/(ad*P)),ah=true,al=[],af=function(an){return(an&&"track" in an)};while((Z*P*ad)<ae){var aj=this.draw_helper(aa,ab,Z,ad,this.tiles_div,am);if(af(aj)){al.push(aj)}else{ah=false}Z+=1}if(!ak){this.tiles_div.children(".remove").removeClass("remove").remove()}var ac=this;if(ah){this.tiles_div.children(".remove").remove();ac.postdraw_actions(al,ab,am,ak)}},postdraw_actions:function(ac,ad,af,Z){var ab=this;var ae=false;for(var aa=0;aa<ac.length;aa++){if(ac[aa].has_icons){ae=true;break}}if(ae){for(var aa=0;aa<ac.length;aa++){tile=ac[aa];if(!tile.has_icons){tile.html_elt.css("padding-top",A)}}}},draw_helper:function(Z,al,aq,ao,ae,af,am){var ak=this,au=this._gen_tile_cache_key(al,af,aq),ac=this._get_tile_bounds(aq,ao);if(!am){am={}}var at=(Z?undefined:ak.tile_cache.get_elt(au));if(at){ak.show_tile(at,ae,af);return at}var ai=true;var ap=ak.data_manager.get_data(ac,ak.mode,ao,ak.data_url_extra_params);if(is_deferred(ap)){ai=false}var ag;if(view.reference_track&&af>view.canvas_manager.char_width_px){ag=view.reference_track.data_manager.get_data(ac,ak.mode,ao,view.reference_track.data_url_extra_params);if(is_deferred(ag)){ai=false}}if(ai){o(ap,am.more_tile_data);var ah=ak.mode;if(ah==="Auto"){ah=ak.get_mode(ap);ak.update_auto_mode(ah)}var ab=ak.view.canvas_manager.new_canvas(),ar=ac.get("start"),aa=ac.get("end"),al=Math.ceil((aa-ar)*af)+ak.left_offset,aj=ak.get_canvas_height(ap,ah,af,al);ab.width=al;ab.height=aj;var an=ab.getContext("2d");an.translate(this.left_offset,0);var at=ak.draw_tile(ap,an,ah,ao,ac,af,ag);if(at!==undefined){ak.tile_cache.set_elt(au,at);ak.show_tile(at,ae,af)}return at}var ad=$.Deferred();$.when(ap,ag).then(function(){view.request_redraw(false,false,false,ak);ad.resolve()});return ad},get_canvas_height:function(Z,ab,ac,aa){return this.visible_height_px},draw_tile:function(Z,aa,ae,ac,ad,af,ab){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ab,ad,ae){var aa=this,Z=ab.html_elt;ab.predisplay_actions();var ac=(ab.low-(this.is_overview?this.view.max_low:this.view.low))*ae;if(this.left_offset){ac-=this.left_offset}Z.css({position:"absolute",top:0,left:ac});if(Z.hasClass("remove")){Z.removeClass("remove")}else{ad.append(Z)}aa.after_show_tile(ab)},after_show_tile:function(Z){this.max_height_px=Math.max(this.max_height_px,Z.html_elt.height());Z.html_elt.parent().children().css("height",this.max_height_px+"px");var aa=this.max_height_px;if(this.visible_height_px!==0){aa=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",aa+"px")},_get_tile_bounds:function(Z,aa){var ac=Math.floor(Z*P*aa),ad=Math.ceil(P*aa),ab=(ac+ad<=this.view.max_high?ac+ad:this.view.max_high);return new GenomeRegion({chrom:this.view.chrom,start:ac,end:ab})},tool_region_and_parameters_str:function(ab,Z,ac){var aa=this,ad=(ab!==undefined&&Z!==undefined&&ac!==undefined?ab+":"+Z+"-"+ac:"all");return" - region=["+ad+"], parameters=["+aa.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(Z,aa){return true},can_subset:function(Z){return false},init_for_tool_data:function(){this.data_manager.set("data_url",raw_data_url);this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ab,ac,ae,Z){var aa=this;aa.normal_postdraw_actions(ab,ac,ae,Z);aa.dataset_state_url=converted_datasets_state_url;aa.data_query_wait=H;var ad=new ServerStateDeferred({url:aa.dataset_state_url,url_params:{dataset_id:aa.dataset_id,hda_ldda:aa.hda_ldda},interval:aa.data_query_wait,success_fn:function(af){return af!=="pending"}});$.when(ad.go()).then(function(){aa.data_manager.set("data_url",default_data_url)});aa.postdraw_actions=aa.normal_postdraw_actions}}});var W=function(aa,Z){var ab={resize:false};h.call(this,aa,Z,ab);this.container_div.addClass("label-track")};o(W.prototype,h.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ab=this.view,ac=ab.high-ab.low,af=Math.floor(Math.pow(10,Math.floor(Math.log(ac)/Math.log(10)))),Z=Math.floor(ab.low/af)*af,ad=this.view.container.width(),aa=$("<div style='position: relative; height: 1.3em;'></div>");while(Z<ab.high){var ae=(Z-ab.low)/ac*ad;aa.append($("<div class='label'>"+commatize(Z)+"</div>").css({position:"absolute",left:ae-1}));Z+=af}this.content_div.children(":first").remove();this.content_div.append(aa)}});var g=function(aa,Z,ad){J.call(this,aa,Z,ad);this.drawables=[];this.left_offset=0;if("drawables" in ad){var ac;for(var ab=0;ab<ad.drawables.length;ab++){ac=ad.drawables[ab];this.drawables[ab]=object_from_template(ac,aa,null);if(ac.left_offset>this.left_offset){this.left_offset=ac.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};o(g.prototype,J.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(Z){$(".bs-tooltip").remove();Z.show_group()}}].concat(J.prototype.action_icons_def),to_dict:w.prototype.to_dict,add_drawable:w.prototype.add_drawable,unpack_drawables:w.prototype.unpack_drawables,change_mode:function(Z){J.prototype.change_mode.call(this,Z);for(var aa=0;aa<this.drawables.length;aa++){this.drawables[aa].change_mode(Z)}},init:function(){var ab=[];for(var aa=0;aa<this.drawables.length;aa++){ab.push(this.drawables[aa].init())}var Z=this;$.when.apply($,ab).then(function(){Z.enabled=true;Z.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,draw_helper:function(aa,ap,aw,at,ah,aj,aq){var ao=this,aA=this._gen_tile_cache_key(ap,aj,aw),ae=this._get_tile_bounds(aw,at);if(!aq){aq={}}var az=(aa?undefined:ao.tile_cache.get_elt(aA));if(az){ao.show_tile(az,ah,aj);return az}var ai=[],ao,am=true,au,ak;for(var av=0;av<this.drawables.length;av++){ao=this.drawables[av];au=ao.data_manager.get_data(ae,ao.mode,at,ao.data_url_extra_params);if(is_deferred(au)){am=false}ai.push(au);ak=null;if(view.reference_track&&aj>view.canvas_manager.char_width_px){ak=view.reference_track.data_manager.get_data(ae,ao.mode,at,view.reference_track.data_url_extra_params);if(is_deferred(ak)){am=false}}ai.push(ak)}if(am){o(au,aq.more_tile_data);this.tile_predraw_init();var ad=ao.view.canvas_manager.new_canvas(),af=ao._get_tile_bounds(aw,at),ax=ae.get("start"),ab=ae.get("end"),ay=0,ap=Math.ceil((ab-ax)*aj)+this.left_offset,an=0,ac=[];var Z=0;for(var av=0;av<this.drawables.length;av++,ay+=2){ao=this.drawables[av];au=ai[ay];var al=ao.mode;if(al==="Auto"){al=ao.get_mode(au);ao.update_auto_mode(al)}ac.push(al);Z=ao.get_canvas_height(au,al,aj,ap);if(Z>an){an=Z}}ad.width=ap;ad.height=(aq.height?aq.height:an);ay=0;var ar=ad.getContext("2d");ar.translate(this.left_offset,0);ar.globalAlpha=0.5;ar.globalCompositeOperation="source-over";for(var av=0;av<this.drawables.length;av++,ay+=2){ao=this.drawables[av];au=ai[ay];ak=ai[ay+1];az=ao.draw_tile(au,ar,ac[av],at,ae,aj,ak)}this.tile_cache.set_elt(aA,az);this.show_tile(az,ah,aj);return az}var ag=$.Deferred(),ao=this;$.when.apply($,ai).then(function(){view.request_redraw(false,false,false,ao);ag.resolve()});return ag},show_group:function(){var ac=new M(this.view,this.container,{name:this.name}),Z;for(var ab=0;ab<this.drawables.length;ab++){Z=this.drawables[ab];ac.add_drawable(Z);Z.container=ac;ac.content_div.append(Z.container_div)}var aa=this.container.replace_drawable(this,ac,true);ac.request_draw()},tile_predraw_init:function(){var ac=Number.MAX_VALUE,Z=-ac,aa;for(var ab=0;ab<this.drawables.length;ab++){aa=this.drawables[ab];if(aa instanceof i){if(aa.prefs.min_value<ac){ac=aa.prefs.min_value}if(aa.prefs.max_value>Z){Z=aa.prefs.max_value}}}for(var ab=0;ab<this.drawables.length;ab++){aa=this.drawables[ab];aa.prefs.min_value=ac;aa.prefs.max_value=Z}},postdraw_actions:function(ab,ae,ag,aa){J.prototype.postdraw_actions.call(this,ab,ae,ag,aa);var ad=-1;for(var ac=0;ac<ab.length;ac++){var Z=ab[ac].html_elt.find("canvas").height();if(Z>ad){ad=Z}}for(var ac=0;ac<ab.length;ac++){var af=ab[ac];if(af.html_elt.find("canvas").height()!==ad){this.draw_helper(true,ae,af.index,af.resolution,af.html_elt.parent(),ag,{height:ad});af.html_elt.remove()}}}});var y=function(Z){J.call(this,Z,{content_div:Z.top_labeltrack},{resize:false});Z.reference_track=this;this.left_offset=200;this.visible_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:Z.dbkey};this.data_manager=new ReferenceTrackDataManager({data_url:reference_url});this.hide_contents()};o(y.prototype,p.prototype,J.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:p.prototype.can_draw,draw_helper:function(ad,ab,Z,aa,ae,af,ac){if(af>this.view.canvas_manager.char_width_px){return J.prototype.draw_helper.call(this,ad,ab,Z,aa,ae,af,ac)}else{this.hide_contents();return null}},draw_tile:function(ah,ai,ad,ac,af,aj){var ab=this;if(aj>this.view.canvas_manager.char_width_px){if(ah.data===null){this.hide_contents();return}var aa=ai.canvas;ai.font=ai.canvas.manager.default_font;ai.textAlign="center";ah=ah.data;for(var ae=0,ag=ah.length;ae<ag;ae++){var Z=Math.floor(ae*aj);ai.fillText(ah[ae],Z,10)}this.show_contents();return new b(ab,af,ac,aa,ah)}this.hide_contents()}});var i=function(ab,aa,ac){var Z=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";J.call(this,ab,aa,ac);this.hda_ldda=ac.hda_ldda;this.dataset_id=ac.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{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:32,hidden:true}],saved_values:ac.prefs,onchange:function(){Z.set_name(Z.prefs.name);Z.vertical_range=Z.prefs.max_value-Z.prefs.min_value;Z.set_min_value(Z.prefs.min_value);Z.set_max_value(Z.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};o(i.prototype,p.prototype,J.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(Z){this.prefs.min_value=Z;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(Z){this.prefs.max_value=Z;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var Z=this;Z.vertical_range=undefined;return $.getJSON(Z.data_url,{stats:true,chrom:Z.view.chrom,low:0,high:Z.view.max_high,hda_ldda:Z.hda_ldda,dataset_id:Z.dataset_id},function(aa){Z.container_div.addClass("line-track");var ad=aa.data;if(isNaN(parseFloat(Z.prefs.min_value))||isNaN(parseFloat(Z.prefs.max_value))){var ab=ad.min,af=ad.max;ab=Math.floor(Math.min(0,Math.max(ab,ad.mean-2*ad.sd)));af=Math.ceil(Math.max(0,Math.min(af,ad.mean+2*ad.sd)));Z.prefs.min_value=ab;Z.prefs.max_value=af;$("#track_"+Z.dataset_id+"_minval").val(Z.prefs.min_value);$("#track_"+Z.dataset_id+"_maxval").val(Z.prefs.max_value)}Z.vertical_range=Z.prefs.max_value-Z.prefs.min_value;Z.total_frequency=ad.total_frequency;Z.container_div.find(".yaxislabel").remove();var ae=$("<div/>").text(U(Z.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(ag){$(".bs-tooltip").remove();var ag=parseFloat(ag);if(!isNaN(ag)){Z.set_min_value(ag)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+Z.dataset_id+"_minval").prependTo(Z.container_div),ac=$("<div/>").text(U(Z.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(ag){$(".bs-tooltip").remove();var ag=parseFloat(ag);if(!isNaN(ag)){Z.set_max_value(ag)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+Z.dataset_id+"_maxval").prependTo(Z.container_div)})},draw_tile:function(ai,ag,ab,aa,ad,ah){var Z=ag.canvas,ac=ad.get("start"),af=ad.get("end"),ae=new I.LinePainter(ai.data,ac,af,this.prefs,ab);ae.draw(ag,Z.width,Z.height,ah);return new b(this,ad,aa,Z,ai.data)},can_subset:function(Z){return false}});var r=function(ab,aa,ac){var Z=this;this.display_modes=["Heatmap"];this.mode="Heatmap";J.call(this,ab,aa,ac);this.hda_ldda=ac.hda_ldda;this.dataset_id=ac.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"4169E1"},{key:"negative_color",label:"Negative Color",type:"color",default_value:"FF8C00"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:ac.prefs,onchange:function(){Z.set_name(Z.prefs.name);Z.vertical_range=Z.prefs.max_value-Z.prefs.min_value;Z.set_min_value(Z.prefs.min_value);Z.set_max_value(Z.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};o(r.prototype,p.prototype,J.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(Z){this.prefs.min_value=Z;this.tile_cache.clear();this.request_draw()},set_max_value:function(Z){this.prefs.max_value=Z;this.tile_cache.clear();this.request_draw()},draw_tile:function(aj,ah,ae,ac,aa,ai){var ab=ah.canvas,Z=this._get_tile_bounds(aa,ac),ad=Z[0],ag=Z[1],af=new I.DiagonalHeatmapPainter(aj.data,ad,ag,this.prefs,ae);af.draw(ah,ab.width,ab.height,ai);return new b(this,aa,ac,ab,aj.data)}});var c=function(ac,ab,ae){var aa=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];J.call(this,ac,ab,ae);var ad=get_random_color(),Z=get_random_color([ad,"#ffffff"]);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ad},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:Z},{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:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{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},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:ae.prefs,onchange:function(){aa.set_name(aa.prefs.name);aa.tile_cache.clear();aa.set_painter_from_config();aa.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=ae.hda_ldda;this.dataset_id=ae.dataset_id;this.original_dataset_id=ae.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,J.prototype,{set_dataset:function(Z){this.dataset_id=Z.get("id");this.hda_ldda=Z.get("hda_ldda");this.data_manager.set("dataset",Z)},set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=I.ArcLinkedFeaturePainter}else{this.painter=I.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},postdraw_actions:function(ao,aj,ae,ad){J.prototype.postdraw_actions.call(this,ao,ad);var ai=this;if(ai.mode==="Histogram"){var al,aa=-1;for(al=0;al<ao.length;al++){var ak=ao[al].max_val;if(ak>aa){aa=ak}}for(al=0;al<ao.length;al++){var aq=ao[al];if(aq.max_val!==aa){aq.html_elt.remove();ai.draw_helper(true,aj,aq.index,aq.resolution,aq.html_elt.parent(),ae,{more_tile_data:{max:aa}})}}}if(ai.filters_manager){var af=ai.filters_manager.filters;for(var an=0;an<af.length;an++){af[an].update_ui_elt()}var ap=false,Z,ag;for(var al=0;al<ao.length;al++){if(ao[al].data.length){Z=ao[al].data[0];for(var an=0;an<af.length;an++){ag=af[an];if(ag.applies_to(Z)&&ag.min!==ag.max){ap=true;break}}}}if(ai.filters_available!==ap){ai.filters_available=ap;if(!ai.filters_available){ai.filters_manager.hide()}ai.update_icons()}}this.container_div.find(".yaxislabel").remove();var ac=ao[0];if(ac instanceof j){var ah=(this.prefs.histogram_max?this.prefs.histogram_max:ac.max_val),ab=$("<div/>").text(ah).make_text_editable({num_cols:12,on_finish:function(ar){$(".bs-tooltip").remove();var ar=parseFloat(ar);ai.prefs.histogram_max=(!isNaN(ar)?ar:null);ai.tile_cache.clear();ai.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ab)}if(ac instanceof L){var am=true;for(var al=0;al<ao.length;al++){if(!ao[al].all_slotted){am=false;break}}if(!am){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(Z){var Z;if(this.mode==="Auto"){if(Z==="no_detail"){Z="feature spans"}else{if(Z==="summary_tree"){Z="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+Z+")")}},incremental_slots:function(ad,Z,ac){var aa=this.view.canvas_manager.dummy_context,ab=this.slotters[ad];if(!ab||(ab.mode!==ac)){ab=new (s.FeatureSlotter)(ad,ac,x,function(ae){return aa.measureText(ae)});this.slotters[ad]=ab}return ab.slot_features(Z)},get_summary_tree_data:function(ad,ag,ab,ao){if(ao>ab-ag){ao=ab-ag}var ak=Math.floor((ab-ag)/ao),an=[],ac=0;var ae=0,af=0,aj,am=0,ah=[],al,ai;var aa=function(ar,aq,at,ap){ar[0]=aq+at*ap;ar[1]=aq+(at+1)*ap};while(am<ao&&ae!==ad.length){var Z=false;for(;am<ao&&!Z;am++){aa(ah,ag,am,ak);for(af=ae;af<ad.length;af++){aj=ad[af].slice(1,3);if(is_overlap(aj,ah)){Z=true;break}}if(Z){break}}data_start_index=af;an[an.length]=al=[ah[0],0];for(;af<ad.length;af++){aj=ad[af].slice(1,3);if(is_overlap(aj,ah)){al[1]++}else{break}}if(al[1]>ac){ac=al[1]}am++}return{max:ac,delta:ak,data:an}},get_mode:function(Z){if(Z.dataset_type==="summary_tree"){mode="summary_tree"}else{if(Z.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>F){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(Z,ad,ae,aa){if(ad==="summary_tree"||ad==="Histogram"){return this.summary_draw_height}else{var ac=this.incremental_slots(ae,Z.data,ad);var ab=new (this.painter)(null,null,null,this.prefs,ad);return Math.max(Y,ab.get_required_height(ac,aa))}},draw_tile:function(ak,ao,am,ap,ac,ag,ab){var an=this,aa=ao.canvas,aw=ac.get("start"),Z=ac.get("end"),aB=25,ad=this.left_offset;if(am==="summary_tree"||am==="Histogram"){if(ak.dataset_type!=="summary_tree"){var ah=this.get_summary_tree_data(ak.data,aw,Z,200);if(ak.max){ah.max=ak.max}ak=ah}var ay=new I.SummaryTreePainter(ak,aw,Z,this.prefs);ay.draw(ao,aa.width,aa.height,ag);return new j(an,ac,ap,aa,ak.data,ak.max)}var af=[],al=this.slotters[ag].slots;all_slotted=true;if(ak.data){var ai=this.filters_manager.filters;for(var aq=0,at=ak.data.length;aq<at;aq++){var ae=ak.data[aq];var ar=false;var aj;for(var av=0,aA=ai.length;av<aA;av++){aj=ai[av];aj.update_attrs(ae);if(!aj.keep(ae)){ar=true;break}}if(!ar){af.push(ae);if(!(ae[0] in al)){all_slotted=false}}}}var az=(this.filters_manager.alpha_filter?new z(this.filters_manager.alpha_filter):null);var ax=(this.filters_manager.height_filter?new z(this.filters_manager.height_filter):null);var ay=new (this.painter)(af,aw,Z,this.prefs,am,az,ax,ab);var au=null;ao.fillStyle=this.prefs.block_color;ao.font=ao.canvas.manager.default_font;ao.textAlign="right";if(ak.data){au=ay.draw(ao,aa.width,aa.height,ag,al);au.translation=-ad}return new L(an,ac,ap,aa,ak.data,ag,am,ak.message,all_slotted,au)},data_and_mode_compatible:function(Z,aa){if(aa==="Auto"){return true}else{if(Z.extra_info==="no_detail"||Z.dataset_type==="summary_tree"){return false}else{return true}}},can_subset:function(Z){if(Z.dataset_type==="summary_tree"||Z.message||Z.extra_info==="no_detail"){return false}return true}});var O=function(aa,Z,ab){c.call(this,aa,Z,ab);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.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:ab.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=I.ReadPainter};o(O.prototype,p.prototype,J.prototype,c.prototype);var R=function(ab,aa,ad){c.call(this,ab,aa,ad);var ac=get_random_color(),Z=get_random_color([ac,"#ffffff"]);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ac},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:Z},{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:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ad.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=I.ReadPainter;this.update_icons()};o(R.prototype,p.prototype,J.prototype,c.prototype);S.View=X;S.DrawableGroup=M;S.LineTrack=i;S.FeatureTrack=c;S.DiagonalHeatmapTrack=r;S.ReadTrack=R;S.VcfTrack=O;S.CompositeTrack=g};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.mode=h;this.include_label=(h==="Pack");this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,h=this.start_end_dct,x=[],z=[],n=0,y=this.max_rows;for(var v=0,w=m.length;v<w;v++){var k=m[v],o=k[0];if(this.slots[o]!==undefined){n=Math.max(n,this.slots[o]);z.push(this.slots[o])}else{x.push(v)}}var q=function(E,F){for(var D=0;D<=y;D++){var B=false,G=h[D];if(G!==undefined){for(var A=0,C=G.length;A<C;A++){var i=G[A];if(F>i[0]&&E<i[1]){B=true;break}}}if(!B){return D}}return -1};for(var v=0,w=x.length;v<w;v++){var k=m[x[v]],o=k[0],t=k[1],f=k[2],r=k[3],g=Math.floor(t*p),l=Math.ceil(f*p),u=this.measureText(r).width,j;if(r!==undefined&&this.include_label){u+=(d+a);if(g-u>=0){g-=u;j="left"}else{l+=u;j="right"}}var s=q(g,l);if(s>=0){if(h[s]===undefined){h[s]=[]}h[s].push([g,l]);this.slots[o]=s;n=Math.max(n,s)}}return n+1}})};var painters_module=function(require,exports){var extend=require("class").extend;var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var SummaryTreePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode)};SummaryTreePainter.prototype.default_prefs={show_counts:false};SummaryTreePainter.prototype.draw=function(ctx,width,height,w_scale){var view_start=this.view_start,view_range=this.view_end-this.view_start,points=this.data.data,max=(this.prefs.histogram_max?this.prefs.histogram_max:this.data.max),base_y=height;delta_x_px=Math.ceil(this.data.delta*w_scale);ctx.save();for(var i=0,len=points.length;i<len;i++){var x=Math.floor((points[i][0]-view_start)*w_scale);var y=points[i][1];if(!y){continue}var y_px=y/max*height;if(y!==0&&y_px<1){y_px=1}ctx.fillStyle=this.prefs.block_color;ctx.fillRect(x,base_y-y_px,delta_x_px,y_px);var text_padding_req_x=4;if(this.prefs.show_counts&&(ctx.measureText(y).width+text_padding_req_x)<delta_x_px){ctx.fillStyle=this.prefs.label_color;ctx.textAlign="center";ctx.fillText(y,x+(delta_x_px/2),10)}}ctx.restore()};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);if(this.prefs.min_value===undefined){var min_value=Infinity;for(var i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][1])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(var i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][1])}this.prefs.max_value=max_value}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,view_range=this.view_end-this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var pref_color=parseInt(this.prefs.color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255;for(var i=0,len=data.length;i<len;i++){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;if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,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{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=this.prefs.color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};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})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}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}}};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_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"};extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=y_scale=this.get_row_height(),mode=this.mode;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)},get_top_padding:function(width){return 0},get_bottom_padding:function(width){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var view_range=this.view_end-this.view_start,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],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((feature_start<view_end&&feature_end>view_start)&&(this.mode==="Dense"||slot!==null)){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();feature_mapper.y_translation=this.get_top_padding(width);return feature_mapper},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){console.log("WARNING: Unimplemented function.");return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";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);this.draw_background_connector=true;this.draw_individual_connectors=false};extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2]-1,feature_name=feature[3],feature_strand=feature[4],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+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;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{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}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{var cur_y_center,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_center=y_center+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_center=y_center;cur_height=thick_height}else{cur_y_center+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{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)}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]-1-tile_low)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_center+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);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);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height)}}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}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),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)}}}ctx.globalAlpha=1;if(mode==="Pack"&&feature_start>tile_low){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+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.globalAlpha=1;return[draw_start,draw_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)};extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},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,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var draw_last=[];if((mode==="Pack"||this.mode==="Auto")&&orig_seq!==undefined&&w_scale>char_width_px){gap=Math.round(w_scale/2)}if(!cigar){cigar=[[0,orig_seq.length]]}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];if(cig_op==="H"||cig_op==="S"){base_offset-=cig_len}var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(0,(seq_start-tile_low)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":break;case"S":case"M":case"=":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=orig_seq.slice(seq_offset,seq_offset+cig_len);if(gap>0){ctx.fillStyle=block_color;ctx.fillRect(s_start-gap,y_center+1,s_end-s_start,9);ctx.fillStyle=CONNECTOR_COLOR;for(var c=0,str_len=seq.length;c<str_len;c++){if(this.prefs.show_differences){if(this.ref_seq){var ref_char=this.ref_seq[seq_start-tile_low+c];if(!ref_char||ref_char.toLowerCase()===seq[c].toLowerCase()){continue}}else{continue}}if(seq_start+c>=tile_low&&seq_start+c<=tile_high){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start,y_center+9)}}}else{ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+4,s_end-s_start,SQUISH_FEATURE_HEIGHT)}}seq_offset+=cig_len;base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start-gap,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="red";ctx.fillRect(s_start-gap,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"P":break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=orig_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&orig_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&orig_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break;case"X":seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],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))),y_center=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color,gap=0;if((mode==="Pack"||this.mode==="Auto")&&w_scale>ctx.canvas.manager.char_width_px){var gap=Math.round(w_scale/2)}if(feature[5] instanceof Array){var b1_start=Math.floor(Math.max(0,(feature[4][0]-tile_low)*w_scale)),b1_end=Math.ceil(Math.min(width,Math.max(0,(feature[4][1]-tile_low)*w_scale))),b2_start=Math.floor(Math.max(0,(feature[5][0]-tile_low)*w_scale)),b2_end=Math.ceil(Math.min(width,Math.max(0,(feature[5][1]-tile_low)*w_scale))),connector=true;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])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){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])}else{connector=false}if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end-gap,y_center+5,b2_start-gap,y_center+5)}}else{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!=="."){ctx.fillStyle=this.prefs.label_color;var tile_index=1;if(tile_index===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING-gap,y_center+8)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING-gap,y_center+8)}}return[0,0]}});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);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){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;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()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);if(this.prefs.min_value===undefined){var min_value=Infinity;for(var i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(var i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"4169E1",neg_color:"FF8C00"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,view_range=this.view_end-this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};exports.Scaler=Scaler;exports.SummaryTreePainter=SummaryTreePainter;exports.LinePainter=LinePainter;exports.LinkedFeaturePainter=LinkedFeaturePainter;exports.ReadPainter=ReadPainter;exports.ArcLinkedFeaturePainter=ArcLinkedFeaturePainter;exports.DiagonalHeatmapPainter=DiagonalHeatmapPainter};(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 g=arguments[0];for(var f=1;f<arguments.length;f++){var d=arguments[f];for(var e in d){g[e]=d[e]}}return g};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 is_deferred=function(a){return("isResolved" in a)};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 n=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(v,u,w,s,i,t){return(Math.max(v,s)-Math.min(v,s))+(Math.max(u,i)-Math.min(u,i))+(Math.max(w,t)-Math.min(w,t))};var g,o,f,k,q,h,r,c,d,b,p,m=false,l=0;do{g=Math.round(Math.random()*16777215);o=(g&16711680)>>16;f=(g&65280)>>8;k=g&255;d=n(o,f,k);m=true;for(j=0;j<a.length;j++){q=a[j];h=(q&16711680)>>16;r=(q&65280)>>8;c=q&255;b=n(h,r,c);p=e(o,f,k,h,r,c);if((Math.abs(d-b)<40)||(p<200)){m=false;break}}l++}while(!m&&l<=10);return"#"+(16777216+g).toString(16).substr(1,6)};var create_action_icon=function(c,b,a){return $("<a/>").attr("href","javascript:void(0);").attr("title",c).addClass("icon-button").addClass(b).tooltip().click(a)};var trackster_module=function(d,S){var o=d("class").extend,s=d("slotting"),I=d("painters");var m={};var k=function(Z,aa){m[Z.attr("id")]=aa};var l=function(Z,ab,ad,ac){ad=".group";var aa={};m[Z.attr("id")]=ac;Z.bind("drag",{handle:"."+ab,relative:true},function(al,am){var ak=$(this),ap=$(this).parent(),ah=ap.children(),aj=m[$(this).attr("id")],ag,af,an,ae,ai;af=$(this).parents(ad);if(af.length!==0){an=af.position().top;ae=an+af.outerHeight();if(am.offsetY<an){$(this).insertBefore(af);var ao=m[af.attr("id")];ao.remove_drawable(aj);ao.container.add_drawable_before(aj,ao);return}else{if(am.offsetY>ae){$(this).insertAfter(af);var ao=m[af.attr("id")];ao.remove_drawable(aj);ao.container.add_drawable(aj);return}}}af=null;for(ai=0;ai<ah.length;ai++){ag=$(ah.get(ai));an=ag.position().top;ae=an+ag.outerHeight();if(ag.is(ad)&&this!==ag.get(0)&&am.offsetY>=an&&am.offsetY<=ae){if(am.offsetY-an<ae-am.offsetY){ag.find(".content-div").prepend(this)}else{ag.find(".content-div").append(this)}if(aj.container){aj.container.remove_drawable(aj)}m[ag.attr("id")].add_drawable(aj);return}}for(ai=0;ai<ah.length;ai++){ag=$(ah.get(ai));if(am.offsetY<ag.position().top&&!(ag.hasClass("reference-track")||ag.hasClass("intro"))){break}}if(ai===ah.length){if(this!==ah.get(ai-1)){ap.append(this);m[ap.attr("id")].move_drawable(aj,ai)}}else{if(this!==ah.get(ai)){$(this).insertBefore(ah.get(ai));m[ap.attr("id")].move_drawable(aj,(am.deltaY>0?ai-1:ai))}}}).bind("dragstart",function(){aa["border-top"]=Z.css("border-top");aa["border-bottom"]=Z.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(aa)})};S.moveable=l;var Y=16,D=9,A=20,x=100,F=12000,P=400,H=5000,u=100,n="There was an error in indexing this dataset. ",G="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",B="No data for this chrom/contig.",t="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",v="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",N=10,E=20;function U(aa,Z){if(!Z){Z=0}var ab=Math.pow(10,Z);return Math.round(aa*ab)/ab}var p=function(aa,Z,ac){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.name=ac.name;this.view=aa;this.container=Z;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ac.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ac.drag_handle_class;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(ad){ad.stopPropagation()});var ab=this;this.container_div.hover(function(){ab.icons_div.show()},function(){ab.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(Z){if(Z.content_visible){Z.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");Z.hide_contents();Z.content_visible=false}else{Z.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");Z.content_visible=true;Z.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(aa){var ac=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},Z=function(){aa.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ab=function(ad){if((ad.keyCode||ad.which)===27){ac()}else{if((ad.keyCode||ad.which)===13){Z()}}};$(window).bind("keypress.check_enter_esc",ab);show_modal("Configure",aa.config.build_form(),{Cancel:ac,OK:Z})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(Z){$(".bs-tooltip").remove();Z.remove()}}];o(p.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(Z){this.old_name=this.name;this.name=Z;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var Z=this.view;this.container_div.hide(0,function(){$(this).remove();Z.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(aa,af,ae,ad,Z,ac){var ab=this;this.action_icons[aa]=$("<a/>").attr("href","javascript:void(0);").attr("title",af).addClass("icon-button").addClass(ae).tooltip().click(function(){ad(ab)}).appendTo(this.icons_div);if(ac){this.action_icons[aa].hide()}},build_action_icons:function(Z){var ab;for(var aa=0;aa<Z.length;aa++){ab=Z[aa];this.add_action_icon(ab.name,ab.title,ab.css_class,ab.on_click_fn,ab.prepend,ab.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){}});var w=function(aa,Z,ab){p.call(this,aa,Z,ab);this.obj_type=ab.obj_type;this.drawables=[]};o(w.prototype,p.prototype,{unpack_drawables:function(ab){this.drawables=[];var aa;for(var Z=0;Z<ab.length;Z++){aa=object_from_template(ab[Z],this.view,this);this.add_drawable(aa)}},init:function(){for(var Z=0;Z<this.drawables.length;Z++){this.drawables[Z].init()}},_draw:function(){for(var Z=0;Z<this.drawables.length;Z++){this.drawables[Z]._draw()}},to_dict:function(){var aa=[];for(var Z=0;Z<this.drawables.length;Z++){aa.push(this.drawables[Z].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:aa}},add_drawable:function(Z){this.drawables.push(Z);Z.container=this;this.changed()},add_drawable_before:function(ab,Z){this.changed();var aa=this.drawables.indexOf(Z);if(aa!==-1){this.drawables.splice(aa,0,ab);return true}return false},replace_drawable:function(ab,Z,aa){var ac=this.drawables.indexOf(ab);if(ac!==-1){this.drawables[ac]=Z;if(aa){ab.container_div.replaceWith(Z.container_div)}this.changed()}return ac},remove_drawable:function(aa){var Z=this.drawables.indexOf(aa);if(Z!==-1){this.drawables.splice(Z,1);aa.container=null;this.changed();return true}return false},move_drawable:function(aa,ab){var Z=this.drawables.indexOf(aa);if(Z!==-1){this.drawables.splice(Z,1);this.drawables.splice(ab,0,aa);this.changed();return true}return false}});var M=function(aa,Z,ac){o(ac,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});w.call(this,aa,Z,ac);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);l(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new V(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ac){this.unpack_drawables(ac.drawables)}if("filters" in ac){var ab=this.filters_manager;this.filters_manager=new V(this,ac.filters);ab.parent_div.replaceWith(this.filters_manager.parent_div);if(ac.filters.visible){this.setup_multitrack_filtering()}}};o(M.prototype,p.prototype,w.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(Z){$(".bs-tooltip").remove();Z.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(Z){if(Z.filters_manager.visible()){Z.filters_manager.clear_filters();Z._restore_filter_managers()}else{Z.setup_multitrack_filtering();Z.request_draw(true)}Z.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var Z=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(Z)}return Z},build_header_div:function(){var Z=$("<div/>").addClass("track-header");Z.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(Z);return Z},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ab=this.drawables.length;if(ab===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ab===1){if(this.drawables[0] instanceof g){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ai,ah,af,al=true,ad=this.drawables[0].get_type(),Z=0;for(ai=0;ai<ab;ai++){af=this.drawables[ai];if(af.get_type()!==ad){can_composite=false;break}if(af instanceof c){Z++}}if(al||Z===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(Z>1&&Z===this.drawables.length){var am={},aa;af=this.drawables[0];for(ah=0;ah<af.filters_manager.filters.length;ah++){aa=af.filters_manager.filters[ah];am[aa.name]=[aa]}for(ai=1;ai<this.drawables.length;ai++){af=this.drawables[ai];for(ah=0;ah<af.filters_manager.filters.length;ah++){aa=af.filters_manager.filters[ah];if(aa.name in am){am[aa.name].push(aa)}}}this.filters_manager.remove_all();var ac,ae,ag,aj;for(var ak in am){ac=am[ak];if(ac.length===Z){ae=new Q({name:ac[0].name,index:ac[0].index});this.filters_manager.add_filter(ae)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var Z=0;Z<this.drawables.length;Z++){this.drawables[Z].filters_manager=this.saved_filters_managers[Z]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var Z=0;Z<this.drawables.length;Z++){drawable=this.drawables[Z];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ad=[];for(var aa=0;aa<this.drawables.length;aa++){ad.push(this.drawables[aa].name)}var ab="Composite Track of "+this.drawables.length+" tracks ("+ad.join(", ")+")";var ac=new g(this.view,this.view,{name:ab,drawables:this.drawables});var Z=this.container.replace_drawable(this,ac,true);ac.request_draw()},add_drawable:function(Z){w.prototype.add_drawable.call(this,Z);this.update_icons()},remove_drawable:function(Z){w.prototype.remove_drawable.call(this,Z);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var Z=o(w.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return Z},request_draw:function(Z,ab){for(var aa=0;aa<this.drawables.length;aa++){this.drawables[aa].request_draw(Z,ab)}}});var X=function(Z){o(Z,{obj_type:"View"});w.call(this,"View",Z.container,Z);this.chrom=null;this.vis_id=Z.vis_id;this.dbkey=Z.dbkey;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 CanvasManager(this.container.get(0).ownerDocument);this.reset()};_.extend(X.prototype,Backbone.Events);o(X.prototype,w.prototype,{init:function(){this.requested_redraw=false;var ab=this.container,Z=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ab);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ab);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ab);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;k(this.viewport_container,Z);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ac=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_datasets(add_datasets_url,add_track_async_url,function(ad){_.each(ad,function(ae){Z.add_drawable(object_from_template(ae,Z,Z))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<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=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var aa=function(ad){if(ad.type==="focusout"||(ad.keyCode||ad.which)===13||(ad.keyCode||ad.which)===27){if((ad.keyCode||ad.which)!==27){Z.go_to($(this).val())}$(this).hide();$(this).val("");Z.location_span.show();Z.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",aa).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){Z.location_span.hide();Z.chrom_select.hide();Z.nav_input.val(Z.chrom+":"+Z.low+"-"+Z.high);Z.nav_input.css("display","inline-block");Z.nav_input.select();Z.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").tooltip({placement:"bottom"}).click(function(){Z.zoom_out();Z.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){Z.zoom_in();Z.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){Z.change_chrom(Z.chrom_select.val())});this.browser_content_div.click(function(ad){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ad){Z.zoom_in(ad.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ad,ae){this.current_x=ae.offsetX}).bind("drag",function(ad,af){var ag=af.offsetX-this.current_x;this.current_x=af.offsetX;var ae=Math.round(ag/Z.viewport_container.width()*(Z.max_high-Z.max_low));Z.move_delta(-ae)});this.overview_close.click(function(){Z.reset_overview()});this.viewport_container.bind("draginit",function(ad,ae){if(ad.clientX>Z.viewport_container.width()-16){return false}}).bind("dragstart",function(ad,ae){ae.original_low=Z.low;ae.current_height=ad.clientY;ae.current_x=ae.offsetX}).bind("drag",function(af,ah){var ad=$(this);var ai=ah.offsetX-ah.current_x;var ae=ad.scrollTop()-(af.clientY-ah.current_height);ad.scrollTop(ae);ah.current_height=af.clientY;ah.current_x=ah.offsetX;var ag=Math.round(ai/Z.viewport_container.width()*(Z.high-Z.low));Z.move_delta(ag)}).bind("mousewheel",function(af,ah,ae,ad){if(ae){ae*=50;var ag=Math.round(-ae/Z.viewport_container.width()*(Z.high-Z.low));Z.move_delta(ag)}});this.top_labeltrack.bind("dragstart",function(ad,ae){return $("<div />").css({height:Z.browser_content_div.height()+Z.top_labeltrack.height()+Z.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ah,ai){$(ai.proxy).css({left:Math.min(ah.pageX,ai.startX)-Z.container.offset().left,width:Math.abs(ah.pageX-ai.startX)});var ae=Math.min(ah.pageX,ai.startX)-Z.container.offset().left,ad=Math.max(ah.pageX,ai.startX)-Z.container.offset().left,ag=(Z.high-Z.low),af=Z.viewport_container.width();Z.update_location(Math.round(ae/af*ag)+Z.low,Math.round(ad/af*ag)+Z.low)}).bind("dragend",function(ai,aj){var ae=Math.min(ai.pageX,aj.startX),ad=Math.max(ai.pageX,aj.startX),ag=(Z.high-Z.low),af=Z.viewport_container.width(),ah=Z.low;Z.low=Math.round(ae/af*ag)+ah;Z.high=Math.round(ad/af*ag)+ah;$(aj.proxy).remove();Z.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){Z.resize_window()},500)});$(document).bind("redraw",function(){Z.redraw()});this.reset();$(window).trigger("resize")},changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(aa,ac,Z,ad){if(this.timer){clearTimeout(this.timer)}if(ad){var ab=this;this.timer=setTimeout(function(){ab.trigger("navigate",aa+":"+ac+"-"+Z)},500)}else{view.trigger("navigate",aa+":"+ac+"-"+Z)}},update_location:function(Z,ab){this.location_span.text(commatize(Z)+" - "+commatize(ab));this.nav_input.val(this.chrom+":"+commatize(Z)+"-"+commatize(ab));var aa=view.chrom_select.val();if(aa!==""){this.trigger_navigate(aa,view.low,view.high,true)}},load_chroms:function(ab){ab.num=u;ab.dbkey=this.dbkey;var Z=this,aa=$.Deferred();$.ajax({url:chrom_url,data:ab,dataType:"json",success:function(ad){if(ad.chrom_info.length===0){alert("Invalid chromosome: "+ab.chrom);return}if(ad.reference){Z.add_label_track(new y(Z))}Z.chrom_data=ad.chrom_info;var ag='<option value="">Select Chrom/Contig</option>';for(var af=0,ac=Z.chrom_data.length;af<ac;af++){var ae=Z.chrom_data[af].chrom;ag+='<option value="'+ae+'">'+ae+"</option>"}if(ad.prev_chroms){ag+='<option value="previous">Previous '+u+"</option>"}if(ad.next_chroms){ag+='<option value="next">Next '+u+"</option>"}Z.chrom_select.html(ag);Z.chrom_start_index=ad.start_index;aa.resolve(ad)},error:function(){alert("Could not load chroms for this dbkey:",Z.dbkey)}});return aa},change_chrom:function(ae,aa,ag){var ab=this;if(!ab.chrom_data){ab.load_chroms_deferred.then(function(){ab.change_chrom(ae,aa,ag)});return}if(!ae||ae==="None"){return}if(ae==="previous"){ab.load_chroms({low:this.chrom_start_index-u});return}if(ae==="next"){ab.load_chroms({low:this.chrom_start_index+u});return}var af=$.grep(ab.chrom_data,function(ah,ai){return ah.chrom===ae})[0];if(af===undefined){ab.load_chroms({chrom:ae},function(){ab.change_chrom(ae,aa,ag)});return}else{if(ae!==ab.chrom){ab.chrom=ae;ab.chrom_select.val(ab.chrom);ab.max_high=af.len-1;ab.reset();ab.request_redraw(true);for(var ad=0,Z=ab.drawables.length;ad<Z;ad++){var ac=ab.drawables[ad];if(ac.init){ac.init()}}if(ab.reference_track){ab.reference_track.init()}}if(aa!==undefined&&ag!==undefined){ab.low=Math.max(aa,0);ab.high=Math.min(ag,ab.max_high)}else{ab.low=0;ab.high=ab.max_high}ab.reset_overview();ab.request_redraw()}},go_to:function(ad){ad=ad.replace(/ |,/g,"");var ah=this,Z,ac,aa=ad.split(":"),af=aa[0],ag=aa[1];if(ag!==undefined){try{var ae=ag.split("-");Z=parseInt(ae[0],10);ac=parseInt(ae[1],10)}catch(ab){return false}}ah.change_chrom(af,Z,ac)},move_fraction:function(ab){var Z=this;var aa=Z.high-Z.low;this.move_delta(ab*aa)},move_delta:function(ac){var Z=this;var ab=Z.high-Z.low;if(Z.low-ac<Z.max_low){Z.low=Z.max_low;Z.high=Z.max_low+ab}else{if(Z.high-ac>Z.max_high){Z.high=Z.max_high;Z.low=Z.max_high-ab}else{Z.high-=ac;Z.low-=ac}}Z.request_redraw();var aa=Z.chrom_select.val();this.trigger_navigate(aa,Z.low,Z.high,true)},add_drawable:function(Z){w.prototype.add_drawable.call(this,Z);Z.init();this.changed();this.update_intro_div()},add_label_track:function(Z){Z.view=this;Z.init();this.label_tracks.push(Z)},remove_drawable:function(ab,aa){w.prototype.remove_drawable.call(this,ab);if(aa){var Z=this;ab.container_div.hide(0,function(){$(this).remove();Z.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ah,Z,ag,ai){var af=this,ae=(ai?[ai]:af.drawables),ab;var aa;for(var ad=0;ad<ae.length;ad++){aa=ae[ad];ab=-1;for(var ac=0;ac<af.tracks_to_be_redrawn.length;ac++){if(af.tracks_to_be_redrawn[ac][0]===aa){ab=ac;break}}if(ab<0){af.tracks_to_be_redrawn.push([aa,Z,ag])}else{af.tracks_to_be_redrawn[ad][1]=Z;af.tracks_to_be_redrawn[ad][2]=ag}}if(!this.requested_redraw){requestAnimationFrame(function(){af._redraw(ah)});this.requested_redraw=true}},_redraw:function(aj){this.requested_redraw=false;var ag=this.low,ac=this.high;if(ag<this.max_low){ag=this.max_low}if(ac>this.max_high){ac=this.max_high}var ai=this.high-this.low;if(this.high!==0&&ai<this.min_separation){ac=ag+this.min_separation}this.low=Math.floor(ag);this.high=Math.ceil(ac);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var Z=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var af=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ak=13;this.overview_box.css({left:Z,width:Math.max(ak,af)}).show();if(af<ak){this.overview_box.css("left",Z-(ak-af)/2)}if(this.overview_highlight){this.overview_highlight.css({left:Z,width:af})}if(!aj){var ab,aa,ah;for(var ad=0,ae=this.tracks_to_be_redrawn.length;ad<ae;ad++){ab=this.tracks_to_be_redrawn[ad][0];aa=this.tracks_to_be_redrawn[ad][1];ah=this.tracks_to_be_redrawn[ad][2];if(ab){ab._draw(aa,ah)}}this.tracks_to_be_redrawn=[];for(ad=0,ae=this.label_tracks.length;ad<ae;ad++){this.label_tracks[ad]._draw()}}},zoom_in:function(aa,ab){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ac=this.high-this.low,ad=ac/2+this.low,Z=(ac/this.zoom_factor)/2;if(aa){ad=aa/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ad-Z);this.high=Math.round(ad+Z);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var aa=this.high-this.low,ab=aa/2+this.low,Z=(aa*this.zoom_factor)/2;this.low=Math.round(ab-Z);this.high=Math.round(ab+Z);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ab){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ab.dataset_id){return}this.overview_viewport.find(".track").remove()}var aa=ab.copy({content_div:this.overview_viewport}),Z=this;aa.header_div.hide();aa.is_overview=true;Z.overview_drawable=aa;this.overview_drawable.postdraw_actions=function(){Z.overview_highlight.show().height(Z.overview_drawable.content_div.height());Z.overview_viewport.height(Z.overview_drawable.content_div.height()+Z.overview_box.outerHeight());Z.overview_close.show();Z.resize_window()};Z.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-tooltip").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 q=function(ab,ag,ac){this.track=ab;this.name=ag.name;this.params=[];var an=ag.params;for(var ad=0;ad<an.length;ad++){var ai=an[ad],aa=ai.name,am=ai.label,ae=unescape(ai.html),ao=ai.value,ak=ai.type;if(ak==="number"){this.params.push(new e(aa,am,ae,(aa in ac?ac[aa]:ao),ai.min,ai.max))}else{if(ak==="select"){this.params.push(new K(aa,am,ae,(aa in ac?ac[aa]:ao)))}else{console.log("WARNING: unrecognized tool parameter type:",aa,ak)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aq){aq.stopPropagation()}).click(function(aq){aq.stopPropagation()}).bind("dblclick",function(aq){aq.stopPropagation()});var al=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aj=this.params;var ah=this;$.each(this.params,function(ar,av){var au=$("<div>").addClass("param-row").appendTo(ah.parent_div);var aq=$("<div>").addClass("param-label").text(av.label).appendTo(au);var at=$("<div/>").addClass("param-input").html(av.html).appendTo(au);at.find(":input").val(av.value);$("<div style='clear: both;'/>").appendTo(au)});this.parent_div.find("input").click(function(){$(this).select()});var ap=$("<div>").addClass("param-row").appendTo(this.parent_div);var af=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ap);var Z=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ap);Z.click(function(){ah.run_on_region()});af.click(function(){ah.run_on_dataset()});if("visible" in ac&&ac.visible){this.parent_div.show()}};o(q.prototype,{update_params:function(){for(var Z=0;Z<this.params.length;Z++){this.params[Z].update_value()}},state_dict:function(){var aa={};for(var Z=0;Z<this.params.length;Z++){aa[this.params[Z].name]=this.params[Z].value}aa.visible=this.parent_div.is(":visible");return aa},get_param_values_dict:function(){var Z={};this.parent_div.find(":input").each(function(){var aa=$(this).attr("name"),ab=$(this).val();Z[aa]=ab});return Z},get_param_values:function(){var Z=[];this.parent_div.find(":input").each(function(){var aa=$(this).attr("name"),ab=$(this).val();if(aa){Z[Z.length]=ab}});return Z},run_on_dataset:function(){var Z=this;Z.run({target_dataset_id:this.track.original_dataset_id,tool_id:Z.name},null,function(aa){show_modal(Z.name+" is Running",Z.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var aa={target_dataset_id:this.track.original_dataset_id,action:"rerun",tool_id:this.name,regions:[{chrom:this.track.view.chrom,start:this.track.view.low,end:this.track.view.high}]},ae=this.track,ab=aa.tool_id+ae.tool_region_and_parameters_str(aa.chrom,aa.low,aa.high),Z;if(ae.container===view){var ad=new M(view,view,{name:this.name});var ac=ae.container.replace_drawable(ae,ad,false);ad.container_div.insertBefore(ae.view.content_div.children()[ac]);ad.add_drawable(ae);ae.container_div.appendTo(ad.content_div);Z=ad}else{Z=ae.container}var af=new ae.constructor(view,Z,{name:ab,hda_ldda:"hda"});af.init_for_tool_data();af.change_mode(ae.mode);af.set_filters_manager(ae.filters_manager.copy(af));af.update_icons();Z.add_drawable(af);af.tiles_div.text("Starting job.");this.update_params();this.run(aa,af,function(ag){af.set_dataset(new Dataset(ag));af.tiles_div.text("Running job.");af.init()})},run:function(Z,ab,ac){Z.inputs=this.get_param_values_dict();var aa=new ServerStateDeferred({ajax_settings:{url:galaxy_paths.get("tool_url"),data:JSON.stringify(Z),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ad){return ad!=="pending"}});$.when(aa.go()).then(function(ad){if(ad==="no converter"){ab.container_div.addClass("error");ab.content_div.text(G)}else{if(ad.error){ab.container_div.addClass("error");ab.content_div.text(v+ad.message)}else{ac(ad)}}})}});var K=function(aa,Z,ab,ac){this.name=aa;this.label=Z;this.html=$(ab);this.value=ac};o(K.prototype,{update_value:function(){this.value=$(this.html).val()}});var e=function(ab,aa,ad,ae,ac,Z){K.call(this,ab,aa,ad,ae);this.min=ac;this.max=Z};o(e.prototype,K.prototype,{update_value:function(){K.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var f=function(Z){this.manager=null;this.name=Z.name;this.index=Z.index;this.tool_id=Z.tool_id;this.tool_exp_name=Z.tool_exp_name};o(f.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var Q=function(ah){f.call(this,ah);this.low=("low" in ah?ah.low:-Number.MAX_VALUE);this.high=("high" in ah?ah.high:Number.MAX_VALUE);this.min=("min" in ah?ah.min:Number.MAX_VALUE);this.max=("max" in ah?ah.max:-Number.MAX_VALUE);this.container=null;this.slider=null;this.slider_label=null;var ad=function(ai,aj,ak){ai.click(function(){var ap=aj.text(),an=parseFloat(ak.slider("option","max")),am=(an<=1?4:an<=1000000?an.toString().length:6),ao=false,al=$(this).parents(".slider-row");al.addClass("input");if(ak.slider("option","values")){am=2*am+1;ao=true}aj.text("");$("<input type='text'/>").attr("size",am).attr("maxlength",am).attr("value",ap).appendTo(aj).focus().select().click(function(aq){aq.stopPropagation()}).blur(function(){$(this).remove();aj.text(ap);al.removeClass("input")}).keyup(function(av){if(av.keyCode===27){$(this).trigger("blur")}else{if(av.keyCode===13){var at=ak.slider("option","min"),aq=ak.slider("option","max"),au=function(aw){return(isNaN(aw)||aw>aq||aw<at)},ar=$(this).val();if(!ao){ar=parseFloat(ar);if(au(ar)){alert("Parameter value must be in the range ["+at+"-"+aq+"]");return $(this)}}else{ar=ar.split("-");ar=[parseFloat(ar[0]),parseFloat(ar[1])];if(au(ar[0])||au(ar[1])){alert("Parameter value must be in the range ["+at+"-"+aq+"]");return $(this)}}ak.slider((ao?"values":"value"),ar);al.removeClass("input")}}})})};var aa=this;aa.parent_div=$("<div/>").addClass("filter-row slider-row");var Z=$("<div/>").addClass("elt-label").appendTo(aa.parent_div),af=$("<span/>").addClass("slider-name").text(aa.name+"  ").appendTo(Z),ab=$("<span/>").text(this.low+"-"+this.high),ac=$("<span/>").addClass("slider-value").appendTo(Z).append("[").append(ab).append("]");aa.values_span=ab;var ae=$("<div/>").addClass("slider").appendTo(aa.parent_div);aa.control_element=$("<div/>").attr("id",aa.name+"-filter-control").appendTo(ae);aa.control_element.slider({range:true,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(ai,aj){aa.slide(ai,aj)},change:function(ai,aj){aa.control_element.slider("option","slide").call(aa.control_element,ai,aj)}});aa.slider=aa.control_element;aa.slider_label=ab;ad(ac,ab,aa.control_element);var ag=$("<div/>").addClass("display-controls").appendTo(aa.parent_div);this.transparency_icon=create_action_icon("Use filter for data 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style='clear: both;'/>").appendTo(aa.parent_div)};o(Q.prototype,{to_dict:function(){var Z=f.prototype.to_dict.call(this);return o(Z,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new Q({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(ab,Z){var aa=Z-ab;return(aa<=2?0.01:1)},slide:function(ab,ac){var aa=ac.values;this.values_span.text(aa[0]+"-"+aa[1]);this.low=aa[0];this.high=aa[1];var Z=this;setTimeout(function(){if(aa[0]===Z.low&&aa[1]===Z.high){Z.manager.track.request_draw(true,true)}},25)},applies_to:function(Z){if(Z.length>this.index){return true}return false},_keep_val:function(Z){return(isNaN(Z)||(Z>=this.low&&Z<=this.high))},keep:function(aa){if(!this.applies_to(aa)){return true}var ac=this;var ad=aa[this.index];if(ad instanceof Array){var ab=true;for(var Z=0;Z<ad.length;Z++){if(!this._keep_val(ad[Z])){ab=false;break}}return ab}else{return this._keep_val(aa[this.index])}},update_attrs:function(ac){var Z=false;if(!this.applies_to(ac)){return Z}var aa=ac[this.index];if(!(aa instanceof Array)){aa=[aa]}for(var ab=0;ab<aa.length;ab++){var ad=aa[ab];if(ad<this.min){this.min=Math.floor(ad);Z=true}if(ad>this.max){this.max=Math.ceil(ad);Z=true}}return Z},update_ui_elt:function(){if(this.min<this.max){this.parent_div.show()}else{this.parent_div.hide()}var aa=this.slider.slider("option","min"),Z=this.slider.slider("option","max");if(this.min<aa||this.max>Z){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",this.get_slider_step(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var V=function(ab,ah){this.track=ab;this.alpha_filter=null;this.height_filter=null;this.filters=[];this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aj){aj.stopPropagation()}).click(function(aj){aj.stopPropagation()}).bind("dblclick",function(aj){aj.stopPropagation()}).bind("keydown",function(aj){aj.stopPropagation()});if(ah&&"filters" in ah){var Z=("alpha_filter" in ah?ah.alpha_filter:null),ac=("height_filter" in ah?ah.height_filter:null),ae=ah.filters,aa;for(var af=0;af<ae.length;af++){if(ae[af].type==="number"){aa=new Q(ae[af]);this.add_filter(aa);if(aa.name===Z){this.alpha_filter=aa;aa.transparency_icon.addClass("active").show()}if(aa.name===ac){this.height_filter=aa;aa.height_icon.addClass("active").show()}}else{console.log("ERROR: unsupported filter: ",name,type)}}if("visible" in ah&&ah.visible){this.parent_div.show()}}if(this.filters.length!==0){var ai=$("<div/>").addClass("param-row").appendTo(this.parent_div);var ag=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ai);var ad=this;ag.click(function(){ad.run_on_dataset()})}};o(V.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){var ac={},ab=[],aa;for(var Z=0;Z<this.filters.length;Z++){aa=this.filters[Z];ab.push(aa.to_dict())}ac.filters=ab;ac.alpha_filter=(this.alpha_filter?this.alpha_filter.name:null);ac.height_filter=(this.height_filter?this.height_filter.name:null);ac.visible=this.parent_div.is(":visible");return ac},copy:function(aa){var ab=new V(aa);for(var Z=0;Z<this.filters.length;Z++){ab.add_filter(this.filters[Z].copy())}return ab},add_filter:function(Z){Z.manager=this;this.parent_div.append(Z.parent_div);this.filters.push(Z)},remove_all:function(){this.filters=[];this.parent_div.children().remove()},init_filters:function(){for(var Z=0;Z<this.filters.length;Z++){var aa=this.filters[Z];aa.update_ui_elt()}},clear_filters:function(){for(var Z=0;Z<this.filters.length;Z++){var aa=this.filters[Z];aa.slider.slider("option","values",[aa.min,aa.max])}this.alpha_filter=null;this.height_filter=null;this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){var af=function(aj,ah,ai){if(!(ah in aj)){aj[ah]=ai}return aj[ah]};var ae={},ag,Z;for(var ad=0;ad<this.filters.length;ad++){ag=this.filters[ad];if(ag.tool_id){if(ag.min!==ag.low){Z=af(ae,ag.tool_id,[]);Z[Z.length]=ag.tool_exp_name+" >= "+ag.low}if(ag.max!==ag.high){Z=af(ae,ag.tool_id,[]);Z[Z.length]=ag.tool_exp_name+" <= "+ag.high}}}var aa=[];for(var ac in ae){aa[aa.length]=[ac,ae[ac]]}(function ab(an,ak){var ai=ak[0],aj=ai[0],am=ai[1],al="("+am.join(") and (")+")",ah={cond:al,input:an,target_dataset_id:an,tool_id:aj},ak=ak.slice(1);$.getJSON(run_tool_url,ah,function(ao){if(ao.error){show_modal("Filter Dataset","Error running tool 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Outputs are in dataset's history.",{Close:hide_modal})}else{ab(ao.dataset_id,ak)}}})})(this.track.dataset_id,aa)}});var z=function(Z,aa){I.Scaler.call(this,aa);this.filter=Z};z.prototype.gen_val=function(Z){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(Z[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var C=function(Z){this.track=Z.track;this.params=Z.params;this.values={};this.restore_values((Z.saved_values?Z.saved_values:{}));this.onchange=Z.onchange};o(C.prototype,{restore_values:function(Z){var aa=this;$.each(this.params,function(ab,ac){if(Z[ac.key]!==undefined){aa.values[ac.key]=Z[ac.key]}else{aa.values[ac.key]=ac.default_value}})},build_form:function(){var ac=this;var Z=$("<div />");var ab;function aa(ah,ad){for(var al=0;al<ah.length;al++){ab=ah[al];if(ab.hidden){continue}var af="param_"+al;var ap=ac.values[ab.key];var ar=$("<div class='form-row' />").appendTo(ad);ar.append($("<label />").attr("for",af).text(ab.label+":"));if(ab.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",af).attr("name",af).attr("checked",ap))}else{if(ab.type==="text"){ar.append($('<input type="text"/>').attr("id",af).val(ap).click(function(){$(this).select()}))}else{if(ab.type==="select"){var an=$("<select />").attr("id",af);for(var aj=0;aj<ab.options.length;aj++){$("<option/>").text(ab.options[aj].label).attr("value",ab.options[aj].value).appendTo(an)}an.val(ap);ar.append(an)}else{if(ab.type==="color"){var aq=$("<div/>").appendTo(ar),am=$("<input />").attr("id",af).attr("name",af).val(ap).css("float","left").appendTo(aq).click(function(au){$(".bs-tooltip").removeClass("in");var at=$(this).siblings(".bs-tooltip").addClass("in");at.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(at).height()/2)+($(this).height()/2)}).show();at.click(function(av){av.stopPropagation()});$(document).bind("click.color-picker",function(){at.hide();$(document).unbind("click.color-picker")});au.stopPropagation()}),ak=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(aq).attr("title","Set new random color").tooltip(),ao=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(aq).hide(),ag=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(ao),ae=$("<div class='tooltip-arrow'></div>").appendTo(ao),ai=$.farbtastic(ag,{width:100,height:100,callback:am,color:ap});aq.append($("<div/>").css("clear","both"));(function(at){ak.click(function(){at.setColor(get_random_color())})})(ai)}else{ar.append($("<input />").attr("id",af).attr("name",af).val(ap))}}}}if(ab.help){ar.append($("<div class='help'/>").text(ab.help))}}}aa(this.params,Z);return Z},update_from_form:function(Z){var ab=this;var aa=false;$.each(this.params,function(ac,ae){if(!ae.hidden){var af="param_"+ac;var ad=Z.find("#"+af).val();if(ae.type==="float"){ad=parseFloat(ad)}else{if(ae.type==="int"){ad=parseInt(ad)}else{if(ae.type==="bool"){ad=Z.find("#"+af).is(":checked")}}}if(ad!==ab.values[ae.key]){ab.values[ae.key]=ad;aa=true}}});if(aa){this.onchange();this.track.changed()}}});var b=function(Z,ad,ab,aa,ac){this.track=Z;this.region=ad;this.low=ad.get("start");this.high=ad.get("end");this.resolution=ab;this.html_elt=$("<div class='track-tile'/>").append(aa).height($(aa).attr("height"));this.data=ac;this.stale=false};b.prototype.predisplay_actions=function(){};var j=function(Z,ae,ab,aa,ac,ad){b.call(this,Z,ae,ab,aa,ac);this.max_val=ad};o(j.prototype,b.prototype);var L=function(ac,ak,ad,ab,af,am,ag,an,aa,aj){b.call(this,ac,ak,ad,ab,af);this.mode=ag;this.all_slotted=aa;this.feature_mapper=aj;this.has_icons=false;if(an){this.has_icons=true;var ah=this;ab=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:A-1,width:ab.width}).prependTo(this.html_elt);var ai=new GenomeRegion({chrom:ac.view.chrom,start:this.low,end:this.high}),al=af.length,ae=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+al+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),Z=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+al+" features in this region were obtained from server. 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ag=$(this).offset(),ak=al.pageX-ag.left,aj=al.pageY-ag.top,ap=aa.feature_mapper.get_feature_data(ak,aj),ah=(ap?ap[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ah||$(this).attr("id")!==ah.toString()){$(this).remove()}});if(ap){var ac=Z[ah];if(!ac){var ah=ap[0],am={name:ap[3],start:ap[1],end:ap[2],strand:ap[4]},af=aa.track.filters_manager.filters,ae;for(var ai=0;ai<af.length;ai++){ae=af[ai];am[ae.name]=ap[ae.index]}var ac=$("<div/>").attr("id",ah).addClass("feature-popup"),aq=$("<table/>"),ao,an,ar;for(ao in am){an=am[ao];ar=$("<tr/>").appendTo(aq);$("<th/>").appendTo(ar).text(ao);$("<td/>").attr("align","left").appendTo(ar).text(typeof(an)==="number"?U(an,2):an)}ac.append($("<div class='feature-popup-inner'>").append(aq));Z[ah]=ac}ac.appendTo($(this).parents(".track-content").children(".overlay"));var ad=ak+parseInt(aa.html_elt.css("left"))-ac.width()/2,ab=aj+parseInt(aa.html_elt.css("top"))+7;ac.css("left",ad+"px").css("top",ab+"px")}else{if(!al.isPropagationStopped()){al.stopPropagation();$(this).siblings().each(function(){$(this).trigger(al)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var h=function(ab,aa,ad){o(ad,{drag_handle_class:"draghandle"});p.call(this,ab,aa,ad);this.data_url=("data_url" in ad?ad.data_url:default_data_url);this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ad?ad.data_query_wait:H);this.dataset_check_url=("converted_datasets_state_url" in ad?ad.converted_datasets_state_url:converted_datasets_state_url);var Z=this,ac=new Dataset({id:ad.dataset_id,hda_ldda:ad.hda_ldda});this.data_manager=("data_manager" in ad?ad.data_manager:new 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bookmarks</option></select>',ab=_.template(ac,{track:Z});var ae=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aa=function(){var ag=$('select[name="regions"] option:selected').val(),ai,af=new GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ah=_.map($(".bookmark"),function(aj){return new GenomeRegion({from_str:$(aj).children(".position").text()})});if(ag==="cur"){ai=[af]}else{if(ag==="bookmarks"){ai=ah}else{ai=[af].concat(ah)}}hide_modal();window.location.href=galaxy_paths.get("sweepster_url")+"?"+$.param({dataset_id:Z.dataset_id,hda_ldda:Z.hda_ldda,regions:JSON.stringify(new Backbone.Collection(ai).toJSON())})},ad=function(af){if((af.keyCode||af.which)===27){ae()}else{if((af.keyCode||af.which)===13){aa()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",ab,{No:ae,Yes:aa})}},p.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&p.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var Z=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(Z)}this.name_div=$("<div/>").addClass("track-name").appendTo(Z).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return Z},on_resize:function(){},add_resize_handle:function(){var Z=this;var ac=false;var ab=false;var aa=$("<div class='track-resize'>");$(Z.container_div).hover(function(){if(Z.content_visible){ac=true;aa.show()}},function(){ac=false;if(!ab){aa.hide()}});aa.hide().bind("dragstart",function(ad,ae){ab=true;ae.original_height=$(Z.content_div).height()}).bind("drag",function(ae,af){var ad=Math.min(Math.max(af.original_height+af.deltaY,Z.min_height_px),Z.max_height_px);$(Z.tiles_div).css("height",ad);Z.visible_height_px=(Z.max_height_px===ad?0:ad);Z.on_resize()}).bind("dragend",function(ad,ae){Z.tile_cache.clear();ab=false;if(!ac){aa.hide()}Z.config.values.height=Z.visible_height_px;Z.changed()}).appendTo(Z.container_div)},set_display_modes:function(ac,af){this.display_modes=ac;this.mode=(af?af:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var aa=this,ad={};for(var ab=0,Z=aa.display_modes.length;ab<Z;ab++){var ae=aa.display_modes[ab];ad[ae]=function(ag){return function(){aa.change_mode(ag);aa.icons_div.show();aa.container_div.mouseleave(function(){aa.icons_div.hide()})}}(ae)}make_popupmenu(this.action_icons.mode_icon,ad)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof y){return"ReferenceTrack"}else{if(this instanceof i){return"LineTrack"}else{if(this instanceof R){return"ReadTrack"}else{if(this instanceof O){return"VcfTrack"}else{if(this instanceof g){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(){var aa=this;aa.enabled=false;aa.tile_cache.clear();aa.data_manager.clear();aa.content_div.css("height","auto");aa.tiles_div.children().remove();aa.container_div.removeClass("nodata error pending");if(!aa.dataset_id){return}var Z=$.Deferred();$.getJSON(this.dataset_check_url,{hda_ldda:aa.hda_ldda,dataset_id:aa.dataset_id,chrom:aa.view.chrom},function(ab){if(!ab||ab==="error"||ab.kind==="error"){aa.container_div.addClass("error");aa.tiles_div.text(n);if(ab.message){var ac=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ab.message+"</pre>",{Close:hide_modal})});aa.tiles_div.append(ac)}}else{if(ab==="no converter"){aa.container_div.addClass("error");aa.tiles_div.text(G)}else{if(ab==="no data"||(ab.data!==undefined&&(ab.data===null||ab.data.length===0))){aa.container_div.addClass("nodata");aa.tiles_div.text(B)}else{if(ab==="pending"){aa.container_div.addClass("pending");aa.tiles_div.html(t);setTimeout(function(){aa.init()},aa.data_query_wait)}else{if(ab==="data"||ab.status==="data"){if(ab.valid_chroms){aa.valid_chroms=ab.valid_chroms;aa.update_icons()}aa.tiles_div.text(T);if(aa.view.chrom){aa.tiles_div.text("");aa.tiles_div.css("height",aa.visible_height_px+"px");aa.enabled=true;$.when(aa.predraw_init()).done(function(){Z.resolve();aa.container_div.removeClass("nodata error pending");aa.request_draw()})}else{Z.resolve()}}}}}}});this.update_icons();return Z},predraw_init:function(){}});var J=function(ab,aa,ac){h.call(this,ab,aa,ac);var Z=this;l(Z.container_div,Z.drag_handle_class,".group",Z);this.filters_manager=new V(this,("filters" in ac?ac.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in ac&&ac.tool?new q(this,ac.tool,ac.tool_state):null);this.tile_cache=new Cache(N);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ac.mode){this.change_mode(ac.mode)}};o(J.prototype,p.prototype,h.prototype,{action_icons_def:h.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(Z){$(".bs-tooltip").remove();Z.slotters[Z.view.resolution_px_b].max_rows*=2;Z.request_draw(true)},hide:true}]),copy:function(Z){var aa=this.to_dict();o(aa,{data_manager:this.data_manager});var ab=new this.constructor(this.view,Z,aa);ab.change_mode(this.mode);ab.enabled=this.enabled;return ab},set_filters_manager:function(Z){this.filters_manager=Z;this.header_div.after(this.filters_manager.parent_div)},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,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(aa){var Z=this;Z.mode=aa;Z.config.values.mode=aa;Z.tile_cache.clear();Z.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+Z.mode+")");return Z},update_icons:function(){var Z=this;if(Z.filters_available){Z.action_icons.filters_icon.show()}else{Z.action_icons.filters_icon.hide()}if(Z.tool){Z.action_icons.tools_icon.show();Z.action_icons.param_space_viz_icon.show()}else{Z.action_icons.tools_icon.hide();Z.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(aa,ab,Z){return aa+"_"+ab+"_"+Z},request_draw:function(aa,Z){this.view.request_redraw(false,aa,Z,this)},before_draw:function(){},_draw:function(aa,ak){if(!this.can_draw()){return}var ai=this.view.low,ae=this.view.high,ag=ae-ai,ab=this.view.container.width(),am=this.view.resolution_px_b,ad=this.view.resolution_b_px;if(this.is_overview){ai=this.view.max_low;ae=this.view.max_high;ad=(view.max_high-view.max_low)/ab;am=1/ad}this.before_draw();this.tiles_div.children().addClass("remove");var Z=Math.floor(ai/(ad*P)),ah=true,al=[],af=function(an){return(an&&"track" in an)};while((Z*P*ad)<ae){var aj=this.draw_helper(aa,ab,Z,ad,this.tiles_div,am);if(af(aj)){al.push(aj)}else{ah=false}Z+=1}if(!ak){this.tiles_div.children(".remove").removeClass("remove").remove()}var ac=this;if(ah){this.tiles_div.children(".remove").remove();ac.postdraw_actions(al,ab,am,ak)}},postdraw_actions:function(ab,ac,ae,Z){var ad=false;for(var aa=0;aa<ab.length;aa++){if(ab[aa].has_icons){ad=true;break}}if(ad){for(var aa=0;aa<ab.length;aa++){tile=ab[aa];if(!tile.has_icons){tile.html_elt.css("padding-top",A)}}}},draw_helper:function(Z,al,aq,ao,ae,af,am){var ak=this,au=this._gen_tile_cache_key(al,af,aq),ac=this._get_tile_bounds(aq,ao);if(!am){am={}}var at=(Z?undefined:ak.tile_cache.get_elt(au));if(at){ak.show_tile(at,ae,af);return at}var ai=true;var ap=ak.data_manager.get_data(ac,ak.mode,ao,ak.data_url_extra_params);if(is_deferred(ap)){ai=false}var ag;if(view.reference_track&&af>view.canvas_manager.char_width_px){ag=view.reference_track.data_manager.get_data(ac,ak.mode,ao,view.reference_track.data_url_extra_params);if(is_deferred(ag)){ai=false}}if(ai){o(ap,am.more_tile_data);var ah=ak.mode;if(ah==="Auto"){ah=ak.get_mode(ap);ak.update_auto_mode(ah)}var ab=ak.view.canvas_manager.new_canvas(),ar=ac.get("start"),aa=ac.get("end"),al=Math.ceil((aa-ar)*af)+ak.left_offset,aj=ak.get_canvas_height(ap,ah,af,al);ab.width=al;ab.height=aj;var an=ab.getContext("2d");an.translate(this.left_offset,0);var at=ak.draw_tile(ap,an,ah,ao,ac,af,ag);if(at!==undefined){ak.tile_cache.set_elt(au,at);ak.show_tile(at,ae,af)}return at}var ad=$.Deferred();$.when(ap,ag).then(function(){view.request_redraw(false,false,false,ak);ad.resolve()});return ad},get_canvas_height:function(Z,ab,ac,aa){return this.visible_height_px},draw_tile:function(Z,aa,ae,ac,ad,af,ab){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ab,ad,ae){var aa=this,Z=ab.html_elt;ab.predisplay_actions();var ac=(ab.low-(this.is_overview?this.view.max_low:this.view.low))*ae;if(this.left_offset){ac-=this.left_offset}Z.css({position:"absolute",top:0,left:ac});if(Z.hasClass("remove")){Z.removeClass("remove")}else{ad.append(Z)}aa.after_show_tile(ab)},after_show_tile:function(Z){this.max_height_px=Math.max(this.max_height_px,Z.html_elt.height());Z.html_elt.parent().children().css("height",this.max_height_px+"px");var aa=this.max_height_px;if(this.visible_height_px!==0){aa=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",aa+"px")},_get_tile_bounds:function(Z,aa){var ac=Math.floor(Z*P*aa),ad=Math.ceil(P*aa),ab=(ac+ad<=this.view.max_high?ac+ad:this.view.max_high);return new GenomeRegion({chrom:this.view.chrom,start:ac,end:ab})},tool_region_and_parameters_str:function(ab,Z,ac){var aa=this,ad=(ab!==undefined&&Z!==undefined&&ac!==undefined?ab+":"+Z+"-"+ac:"all");return" - region=["+ad+"], parameters=["+aa.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(Z,aa){return true},can_subset:function(Z){return false},init_for_tool_data:function(){this.data_manager.set("data_url",raw_data_url);this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ab,ac,ae,Z){var aa=this;aa.normal_postdraw_actions(ab,ac,ae,Z);aa.dataset_state_url=converted_datasets_state_url;aa.data_query_wait=H;var ad=new ServerStateDeferred({url:aa.dataset_state_url,url_params:{dataset_id:aa.dataset_id,hda_ldda:aa.hda_ldda},interval:aa.data_query_wait,success_fn:function(af){return af!=="pending"}});$.when(ad.go()).then(function(){aa.data_manager.set("data_url",default_data_url)});aa.postdraw_actions=aa.normal_postdraw_actions}}});var W=function(aa,Z){var ab={resize:false};h.call(this,aa,Z,ab);this.container_div.addClass("label-track")};o(W.prototype,h.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ab=this.view,ac=ab.high-ab.low,af=Math.floor(Math.pow(10,Math.floor(Math.log(ac)/Math.log(10)))),Z=Math.floor(ab.low/af)*af,ad=this.view.container.width(),aa=$("<div style='position: relative; height: 1.3em;'></div>");while(Z<ab.high){var ae=(Z-ab.low)/ac*ad;aa.append($("<div class='label'>"+commatize(Z)+"</div>").css({position:"absolute",left:ae-1}));Z+=af}this.content_div.children(":first").remove();this.content_div.append(aa)}});var g=function(aa,Z,ad){J.call(this,aa,Z,ad);this.drawables=[];this.left_offset=0;if("drawables" in ad){var ac;for(var ab=0;ab<ad.drawables.length;ab++){ac=ad.drawables[ab];this.drawables[ab]=object_from_template(ac,aa,null);if(ac.left_offset>this.left_offset){this.left_offset=ac.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};o(g.prototype,J.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(Z){$(".bs-tooltip").remove();Z.show_group()}}].concat(J.prototype.action_icons_def),to_dict:w.prototype.to_dict,add_drawable:w.prototype.add_drawable,unpack_drawables:w.prototype.unpack_drawables,change_mode:function(Z){J.prototype.change_mode.call(this,Z);for(var aa=0;aa<this.drawables.length;aa++){this.drawables[aa].change_mode(Z)}},init:function(){var ab=[];for(var aa=0;aa<this.drawables.length;aa++){ab.push(this.drawables[aa].init())}var Z=this;$.when.apply($,ab).then(function(){Z.enabled=true;Z.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,draw_helper:function(aa,ap,aw,at,ah,aj,aq){var ao=this,aA=this._gen_tile_cache_key(ap,aj,aw),ae=this._get_tile_bounds(aw,at);if(!aq){aq={}}var az=(aa?undefined:ao.tile_cache.get_elt(aA));if(az){ao.show_tile(az,ah,aj);return az}var ai=[],ao,am=true,au,ak;for(var av=0;av<this.drawables.length;av++){ao=this.drawables[av];au=ao.data_manager.get_data(ae,ao.mode,at,ao.data_url_extra_params);if(is_deferred(au)){am=false}ai.push(au);ak=null;if(view.reference_track&&aj>view.canvas_manager.char_width_px){ak=view.reference_track.data_manager.get_data(ae,ao.mode,at,view.reference_track.data_url_extra_params);if(is_deferred(ak)){am=false}}ai.push(ak)}if(am){o(au,aq.more_tile_data);this.tile_predraw_init();var ad=ao.view.canvas_manager.new_canvas(),af=ao._get_tile_bounds(aw,at),ax=ae.get("start"),ab=ae.get("end"),ay=0,ap=Math.ceil((ab-ax)*aj)+this.left_offset,an=0,ac=[],av;var Z=0;for(av=0;av<this.drawables.length;av++,ay+=2){ao=this.drawables[av];au=ai[ay];var al=ao.mode;if(al==="Auto"){al=ao.get_mode(au);ao.update_auto_mode(al)}ac.push(al);Z=ao.get_canvas_height(au,al,aj,ap);if(Z>an){an=Z}}ad.width=ap;ad.height=(aq.height?aq.height:an);ay=0;var ar=ad.getContext("2d");ar.translate(this.left_offset,0);ar.globalAlpha=0.5;ar.globalCompositeOperation="source-over";for(av=0;av<this.drawables.length;av++,ay+=2){ao=this.drawables[av];au=ai[ay];ak=ai[ay+1];az=ao.draw_tile(au,ar,ac[av],at,ae,aj,ak)}this.tile_cache.set_elt(aA,az);this.show_tile(az,ah,aj);return az}var ag=$.Deferred(),ao=this;$.when.apply($,ai).then(function(){view.request_redraw(false,false,false,ao);ag.resolve()});return ag},show_group:function(){var ac=new M(this.view,this.container,{name:this.name}),Z;for(var ab=0;ab<this.drawables.length;ab++){Z=this.drawables[ab];Z.update_icons();ac.add_drawable(Z);Z.container=ac;ac.content_div.append(Z.container_div)}var aa=this.container.replace_drawable(this,ac,true);ac.request_draw()},tile_predraw_init:function(){var ac=Number.MAX_VALUE,Z=-ac,aa;for(var ab=0;ab<this.drawables.length;ab++){aa=this.drawables[ab];if(aa instanceof i){if(aa.prefs.min_value<ac){ac=aa.prefs.min_value}if(aa.prefs.max_value>Z){Z=aa.prefs.max_value}}}for(var ab=0;ab<this.drawables.length;ab++){aa=this.drawables[ab];aa.prefs.min_value=ac;aa.prefs.max_value=Z}},postdraw_actions:function(ab,ae,ag,aa){J.prototype.postdraw_actions.call(this,ab,ae,ag,aa);var ad=-1;for(var ac=0;ac<ab.length;ac++){var Z=ab[ac].html_elt.find("canvas").height();if(Z>ad){ad=Z}}for(var ac=0;ac<ab.length;ac++){var af=ab[ac];if(af.html_elt.find("canvas").height()!==ad){this.draw_helper(true,ae,af.index,af.resolution,af.html_elt.parent(),ag,{height:ad});af.html_elt.remove()}}}});var y=function(Z){J.call(this,Z,{content_div:Z.top_labeltrack},{resize:false});Z.reference_track=this;this.left_offset=200;this.visible_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:Z.dbkey};this.data_manager=new ReferenceTrackDataManager({data_url:reference_url});this.hide_contents()};o(y.prototype,p.prototype,J.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:p.prototype.can_draw,draw_helper:function(ad,ab,Z,aa,ae,af,ac){if(af>this.view.canvas_manager.char_width_px){return J.prototype.draw_helper.call(this,ad,ab,Z,aa,ae,af,ac)}else{this.hide_contents();return null}},draw_tile:function(ah,ai,ad,ac,af,aj){var ab=this;if(aj>this.view.canvas_manager.char_width_px){if(ah.data===null){this.hide_contents();return}var aa=ai.canvas;ai.font=ai.canvas.manager.default_font;ai.textAlign="center";ah=ah.data;for(var ae=0,ag=ah.length;ae<ag;ae++){var Z=Math.floor(ae*aj);ai.fillText(ah[ae],Z,10)}this.show_contents();return new b(ab,af,ac,aa,ah)}this.hide_contents()}});var i=function(ab,aa,ac){var Z=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";J.call(this,ab,aa,ac);this.hda_ldda=ac.hda_ldda;this.dataset_id=ac.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{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:32,hidden:true}],saved_values:ac.prefs,onchange:function(){Z.set_name(Z.prefs.name);Z.vertical_range=Z.prefs.max_value-Z.prefs.min_value;Z.set_min_value(Z.prefs.min_value);Z.set_max_value(Z.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};o(i.prototype,p.prototype,J.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(Z){this.prefs.min_value=Z;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(Z){this.prefs.max_value=Z;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var Z=this;Z.vertical_range=undefined;return $.getJSON(Z.data_url,{stats:true,chrom:Z.view.chrom,low:0,high:Z.view.max_high,hda_ldda:Z.hda_ldda,dataset_id:Z.dataset_id},function(aa){Z.container_div.addClass("line-track");var ad=aa.data;if(isNaN(parseFloat(Z.prefs.min_value))||isNaN(parseFloat(Z.prefs.max_value))){var ab=ad.min,af=ad.max;ab=Math.floor(Math.min(0,Math.max(ab,ad.mean-2*ad.sd)));af=Math.ceil(Math.max(0,Math.min(af,ad.mean+2*ad.sd)));Z.prefs.min_value=ab;Z.prefs.max_value=af;$("#track_"+Z.dataset_id+"_minval").val(Z.prefs.min_value);$("#track_"+Z.dataset_id+"_maxval").val(Z.prefs.max_value)}Z.vertical_range=Z.prefs.max_value-Z.prefs.min_value;Z.total_frequency=ad.total_frequency;Z.container_div.find(".yaxislabel").remove();var ae=$("<div/>").text(U(Z.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(ag){$(".bs-tooltip").remove();var ag=parseFloat(ag);if(!isNaN(ag)){Z.set_min_value(ag)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+Z.dataset_id+"_minval").prependTo(Z.container_div),ac=$("<div/>").text(U(Z.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(ag){$(".bs-tooltip").remove();var ag=parseFloat(ag);if(!isNaN(ag)){Z.set_max_value(ag)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+Z.dataset_id+"_maxval").prependTo(Z.container_div)})},draw_tile:function(ai,ag,ab,aa,ad,ah){var Z=ag.canvas,ac=ad.get("start"),af=ad.get("end"),ae=new I.LinePainter(ai.data,ac,af,this.prefs,ab);ae.draw(ag,Z.width,Z.height,ah);return new b(this,ad,aa,Z,ai.data)},can_subset:function(Z){return false}});var r=function(ab,aa,ac){var Z=this;this.display_modes=["Heatmap"];this.mode="Heatmap";J.call(this,ab,aa,ac);this.hda_ldda=ac.hda_ldda;this.dataset_id=ac.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"4169E1"},{key:"negative_color",label:"Negative Color",type:"color",default_value:"FF8C00"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:ac.prefs,onchange:function(){Z.set_name(Z.prefs.name);Z.vertical_range=Z.prefs.max_value-Z.prefs.min_value;Z.set_min_value(Z.prefs.min_value);Z.set_max_value(Z.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};o(r.prototype,p.prototype,J.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(Z){this.prefs.min_value=Z;this.tile_cache.clear();this.request_draw()},set_max_value:function(Z){this.prefs.max_value=Z;this.tile_cache.clear();this.request_draw()},draw_tile:function(aj,ah,ae,ac,aa,ai){var ab=ah.canvas,Z=this._get_tile_bounds(aa,ac),ad=Z[0],ag=Z[1],af=new I.DiagonalHeatmapPainter(aj.data,ad,ag,this.prefs,ae);af.draw(ah,ab.width,ab.height,ai);return new b(this,aa,ac,ab,aj.data)}});var c=function(ac,ab,ae){var aa=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];J.call(this,ac,ab,ae);var ad=get_random_color(),Z=get_random_color([ad,"#ffffff"]);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ad},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:Z},{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:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{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},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:ae.prefs,onchange:function(){aa.set_name(aa.prefs.name);aa.tile_cache.clear();aa.set_painter_from_config();aa.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=ae.hda_ldda;this.dataset_id=ae.dataset_id;this.original_dataset_id=ae.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,J.prototype,{set_dataset:function(Z){this.dataset_id=Z.get("id");this.hda_ldda=Z.get("hda_ldda");this.data_manager.set("dataset",Z)},set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=I.ArcLinkedFeaturePainter}else{this.painter=I.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},postdraw_actions:function(ao,aj,ae,ad){J.prototype.postdraw_actions.call(this,ao,ad);var ai=this,al;if(ai.mode==="Coverage"){var aa=-1;for(al=0;al<ao.length;al++){var ak=ao[al].max_val;if(ak>aa){aa=ak}}for(al=0;al<ao.length;al++){var aq=ao[al];if(aq.max_val!==aa){aq.html_elt.remove();ai.draw_helper(true,aj,aq.index,aq.resolution,aq.html_elt.parent(),ae,{more_tile_data:{max:aa}})}}}if(ai.filters_manager){var af=ai.filters_manager.filters;for(var an=0;an<af.length;an++){af[an].update_ui_elt()}var ap=false,Z,ag;for(al=0;al<ao.length;al++){if(ao[al].data.length){Z=ao[al].data[0];for(var an=0;an<af.length;an++){ag=af[an];if(ag.applies_to(Z)&&ag.min!==ag.max){ap=true;break}}}}if(ai.filters_available!==ap){ai.filters_available=ap;if(!ai.filters_available){ai.filters_manager.hide()}ai.update_icons()}}this.container_div.find(".yaxislabel").remove();var ac=ao[0];if(ac instanceof j){var ah=(this.prefs.histogram_max?this.prefs.histogram_max:ac.max_val),ab=$("<div/>").text(ah).make_text_editable({num_cols:12,on_finish:function(ar){$(".bs-tooltip").remove();var ar=parseFloat(ar);ai.prefs.histogram_max=(!isNaN(ar)?ar:null);ai.tile_cache.clear();ai.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ab)}if(ac instanceof L){var am=true;for(al=0;al<ao.length;al++){if(!ao[al].all_slotted){am=false;break}}if(!am){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(Z){var Z;if(this.mode==="Auto"){if(Z==="no_detail"){Z="feature spans"}else{if(Z==="summary_tree"){Z="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+Z+")")}},incremental_slots:function(ad,Z,ac){var aa=this.view.canvas_manager.dummy_context,ab=this.slotters[ad];if(!ab||(ab.mode!==ac)){ab=new (s.FeatureSlotter)(ad,ac,x,function(ae){return aa.measureText(ae)});this.slotters[ad]=ab}return ab.slot_features(Z)},get_mode:function(Z){if(Z.dataset_type==="summary_tree"){mode="summary_tree"}else{if(Z.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>F){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(Z,ad,ae,aa){if(ad==="summary_tree"||ad==="Coverage"){return this.summary_draw_height}else{var ac=this.incremental_slots(ae,Z.data,ad);var ab=new (this.painter)(null,null,null,this.prefs,ad);return Math.max(Y,ab.get_required_height(ac,aa))}},draw_tile:function(aj,an,al,ao,ac,ag,ab){var am=this,aa=an.canvas,av=ac.get("start"),Z=ac.get("end"),ad=this.left_offset;if(al==="summary_tree"||al==="Coverage"){var ax=new I.SummaryTreePainter(aj,av,Z,this.prefs);ax.draw(an,aa.width,aa.height,ag);return new j(am,ac,ao,aa,aj.data,aj.max)}var af=[],ak=this.slotters[ag].slots;all_slotted=true;if(aj.data){var ah=this.filters_manager.filters;for(var ap=0,ar=aj.data.length;ap<ar;ap++){var ae=aj.data[ap];var aq=false;var ai;for(var au=0,az=ah.length;au<az;au++){ai=ah[au];ai.update_attrs(ae);if(!ai.keep(ae)){aq=true;break}}if(!aq){af.push(ae);if(!(ae[0] in ak)){all_slotted=false}}}}var ay=(this.filters_manager.alpha_filter?new z(this.filters_manager.alpha_filter):null);var aw=(this.filters_manager.height_filter?new z(this.filters_manager.height_filter):null);var ax=new (this.painter)(af,av,Z,this.prefs,al,ay,aw,ab);var at=null;an.fillStyle=this.prefs.block_color;an.font=an.canvas.manager.default_font;an.textAlign="right";if(aj.data){at=ax.draw(an,aa.width,aa.height,ag,ak);at.translation=-ad}return new L(am,ac,ao,aa,aj.data,ag,al,aj.message,all_slotted,at)},data_and_mode_compatible:function(Z,aa){if(aa==="Auto"){return true}else{if(aa==="Coverage"){return Z.dataset_type==="summary_tree"}else{if(Z.extra_info==="no_detail"||Z.dataset_type==="summary_tree"){return false}else{return true}}}},can_subset:function(Z){if(Z.dataset_type==="summary_tree"||Z.message||Z.extra_info==="no_detail"){return false}return true}});var O=function(aa,Z,ab){c.call(this,aa,Z,ab);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.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:ab.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=I.ReadPainter};o(O.prototype,p.prototype,J.prototype,c.prototype);var R=function(ab,aa,ad){c.call(this,ab,aa,ad);var ac=get_random_color(),Z=get_random_color([ac,"#ffffff"]);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ac},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:Z},{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:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ad.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=I.ReadPainter;this.update_icons()};o(R.prototype,p.prototype,J.prototype,c.prototype);S.View=X;S.DrawableGroup=M;S.LineTrack=i;S.FeatureTrack=c;S.DiagonalHeatmapTrack=r;S.ReadTrack=R;S.VcfTrack=O;S.CompositeTrack=g};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.mode=h;this.include_label=(h==="Pack");this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,h=this.start_end_dct,x=[],z=[],n=0,y=this.max_rows;for(var v=0,w=m.length;v<w;v++){var k=m[v],o=k[0];if(this.slots[o]!==undefined){n=Math.max(n,this.slots[o]);z.push(this.slots[o])}else{x.push(v)}}var q=function(E,F){for(var D=0;D<=y;D++){var B=false,G=h[D];if(G!==undefined){for(var A=0,C=G.length;A<C;A++){var i=G[A];if(F>i[0]&&E<i[1]){B=true;break}}}if(!B){return D}}return -1};for(var v=0,w=x.length;v<w;v++){var k=m[x[v]],o=k[0],t=k[1],f=k[2],r=k[3],g=Math.floor(t*p),l=Math.ceil(f*p),u=this.measureText(r).width,j;if(r!==undefined&&this.include_label){u+=(d+a);if(g-u>=0){g-=u;j="left"}else{l+=u;j="right"}}var s=q(g,l);if(s>=0){if(h[s]===undefined){h[s]=[]}h[s].push([g,l]);this.slots[o]=s;n=Math.max(n,s)}}return n+1}})};var painters_module=function(require,exports){var extend=require("class").extend;var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var SummaryTreePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode)};SummaryTreePainter.prototype.default_prefs={show_counts:false};SummaryTreePainter.prototype.draw=function(ctx,width,height,w_scale){var view_start=this.view_start,points=this.data.data,max=(this.prefs.histogram_max?this.prefs.histogram_max:this.data.max),base_y=height;delta_x_px=Math.ceil(this.data.delta*w_scale);ctx.save();for(var i=0,len=points.length;i<len;i++){var x=Math.floor((points[i][0]-view_start)*w_scale);var y=points[i][1];if(!y){continue}var y_px=y/max*height;if(y!==0&&y_px<1){y_px=1}ctx.fillStyle=this.prefs.block_color;ctx.fillRect(x,base_y-y_px,delta_x_px,y_px);var text_padding_req_x=4;if(this.prefs.show_counts&&(ctx.measureText(y).width+text_padding_req_x)<delta_x_px){ctx.fillStyle=this.prefs.label_color;ctx.textAlign="center";ctx.fillText(y,x+(delta_x_px/2),10)}}ctx.restore()};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][1])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][1])}this.prefs.max_value=max_value}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var pref_color=parseInt(this.prefs.color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=this.prefs.color;x_scaled=Math.round((data[i][0]-view_start-1)*w_scale);y=data[i][1];var top_overflow=false,bot_overflow=false;if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,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{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=this.prefs.color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};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})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}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}}};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_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"};extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;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)},get_top_padding:function(width){return 0},get_bottom_padding:function(width){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var 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],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((feature_start<view_end&&feature_end>view_start)&&(this.mode==="Dense"||slot!==null)){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();feature_mapper.y_translation=this.get_top_padding(width);return feature_mapper},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){console.log("WARNING: Unimplemented function.");return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";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);this.draw_background_connector=true;this.draw_individual_connectors=false};extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2]-1,feature_name=feature[3],feature_strand=feature[4],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+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;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{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}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{var cur_y_center,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_center=y_center+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_center=y_center;cur_height=thick_height}else{cur_y_center+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{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)}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]-1-tile_low)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_center+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);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);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height)}}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}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),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)}}}ctx.globalAlpha=1;if(mode==="Pack"&&feature_start>tile_low){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+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.globalAlpha=1;return[draw_start,draw_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)};extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,orig_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=0,char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var draw_last=[];if((mode==="Pack"||this.mode==="Auto")&&orig_seq!==undefined&&w_scale>char_width_px){gap=Math.round(w_scale/2)}if(!cigar){cigar=[[0,orig_seq.length]]}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];if(cig_op==="H"||cig_op==="S"){base_offset-=cig_len}var seq_start=(feature_start-1)+base_offset,s_start=Math.floor(Math.max(0,(seq_start-tile_low)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":break;case"S":case"M":case"=":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=orig_seq.slice(seq_offset,seq_offset+cig_len);if(gap>0){ctx.fillStyle=block_color;ctx.fillRect(s_start-gap,y_center+1,s_end-s_start,9);ctx.fillStyle=CONNECTOR_COLOR;for(var c=0,str_len=seq.length;c<str_len;c++){if(this.prefs.show_differences){if(this.ref_seq){var ref_char=this.ref_seq[seq_start-tile_low+c];if(!ref_char||ref_char.toLowerCase()===seq[c].toLowerCase()){continue}}else{continue}}if(seq_start+c>=tile_low&&seq_start+c<=tile_high){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start,y_center+9)}}}else{ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+4,s_end-s_start,SQUISH_FEATURE_HEIGHT)}}seq_offset+=cig_len;base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start-gap,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="red";ctx.fillRect(s_start-gap,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"P":break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=orig_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&orig_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&orig_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break;case"X":seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],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))),y_center=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color,gap=0;if((mode==="Pack"||this.mode==="Auto")&&w_scale>ctx.canvas.manager.char_width_px){var gap=Math.round(w_scale/2)}if(feature[5] instanceof Array){var b1_start=Math.floor(Math.max(0,(feature[4][0]-tile_low)*w_scale)),b1_end=Math.ceil(Math.min(width,Math.max(0,(feature[4][1]-tile_low)*w_scale))),b2_start=Math.floor(Math.max(0,(feature[5][0]-tile_low)*w_scale)),b2_end=Math.ceil(Math.min(width,Math.max(0,(feature[5][1]-tile_low)*w_scale))),connector=true;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])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){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])}else{connector=false}if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end-gap,y_center+5,b2_start-gap,y_center+5)}}else{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!=="."){ctx.fillStyle=this.prefs.label_color;var tile_index=1;if(tile_index===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING-gap,y_center+8)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING-gap,y_center+8)}}return[0,0]}});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);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){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;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()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"4169E1",neg_color:"FF8C00"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};exports.Scaler=Scaler;exports.SummaryTreePainter=SummaryTreePainter;exports.LinePainter=LinePainter;exports.LinkedFeaturePainter=LinkedFeaturePainter;exports.ReadPainter=ReadPainter;exports.ArcLinkedFeaturePainter=ArcLinkedFeaturePainter;exports.DiagonalHeatmapPainter=DiagonalHeatmapPainter};(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/templates/base.mako b/templates/base.mako
index 056ebf5585e..1b860d8ab2c 100644
--- a/templates/base.mako
+++ b/templates/base.mako
@@ -26,7 +26,7 @@
   ## <!--[if lt IE 7]>
   ## <script type='text/javascript' src="/static/scripts/IE7.js"> </script>
   ## <![endif]-->
-  ${h.js( "jquery", "bootstrap", "galaxy.base", "libs/underscore", "libs/backbone", "libs/backbone-relational", "libs/handlebars.runtime", "mvc/ui" )}
+  ${h.js( "jquery", "bootstrap", "galaxy.base", "libs/underscore", "libs/backbone/backbone", "libs/backbone/backbone-relational", "libs/handlebars.runtime", "mvc/ui" )}
   <script type="text/javascript">
       // Set up needed paths.
       var galaxy_paths = new GalaxyPaths({
diff --git a/templates/base_panels.mako b/templates/base_panels.mako
index b53bf784df6..092a5650736 100644
--- a/templates/base_panels.mako
+++ b/templates/base_panels.mako
@@ -48,7 +48,7 @@
     <!--[if lt IE 7]>
     ${h.js( 'IE7', 'ie7-recalc' )}
     <![endif]-->
-    ${h.js( 'jquery', 'bootstrap', 'libs/underscore', 'libs/backbone', 'libs/backbone-relational', 'libs/handlebars.runtime', 'mvc/ui' )}
+    ${h.js( 'jquery', 'bootstrap', 'libs/underscore', 'libs/backbone/backbone', 'libs/backbone/backbone-relational', 'libs/handlebars.runtime', 'mvc/ui' )}
     <script type="text/javascript">
         // Set up needed paths.
         var galaxy_paths = new GalaxyPaths({

From 44d37d7eee0911b824f03f1706490ced7f7efb7e Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Tue, 21 Aug 2012 15:52:50 -0400
Subject: [PATCH 13/16] Move most jQuery files into own libs directory.

---
 static/scripts/jquery.event.drag.js.patch          | 10 ----------
 static/scripts/{ => libs/jquery}/jqtouch.js        |  0
 .../{ => libs/jquery}/jquery.autocomplete.js       |  0
 static/scripts/{ => libs/jquery}/jquery.cookie.js  |  0
 .../scripts/{ => libs/jquery}/jquery.dynatree.js   |  0
 .../scripts/{ => libs/jquery}/jquery.event.drag.js |  0
 .../scripts/{ => libs/jquery}/jquery.event.drop.js |  0
 .../{ => libs/jquery}/jquery.event.hover.js        |  0
 static/scripts/{ => libs/jquery}/jquery.form.js    |  0
 static/scripts/{ => libs/jquery}/jquery.js         |  0
 .../scripts/{ => libs/jquery}/jquery.mousewheel.js |  0
 static/scripts/{ => libs/jquery}/jquery.rating.js  |  0
 static/scripts/{ => libs/jquery}/jquery.tipsy.js   |  0
 .../{ => libs/jquery}/jquery.ui.sortable.slider.js |  0
 .../scripts/{ => libs/jquery}/jquery.wymeditor.js  |  0
 static/scripts/{ => libs/jquery}/jstorage.js       |  0
 static/scripts/packed/{ => libs/jquery}/jqtouch.js |  0
 .../{ => libs/jquery}/jquery.autocomplete.js       |  0
 .../packed/{ => libs/jquery}/jquery.cookie.js      |  0
 .../packed/{ => libs/jquery}/jquery.dynatree.js    |  0
 .../packed/{ => libs/jquery}/jquery.event.drag.js  |  0
 .../packed/{ => libs/jquery}/jquery.event.drop.js  |  0
 .../packed/{ => libs/jquery}/jquery.event.hover.js |  0
 .../packed/{ => libs/jquery}/jquery.form.js        |  0
 static/scripts/packed/{ => libs/jquery}/jquery.js  |  0
 .../packed/{ => libs/jquery}/jquery.mousewheel.js  |  0
 .../packed/{ => libs/jquery}/jquery.rating.js      |  0
 .../packed/{ => libs/jquery}/jquery.tipsy.js       |  0
 .../{ => libs/jquery}/jquery.ui.sortable.slider.js |  0
 .../packed/{ => libs/jquery}/jquery.wymeditor.js   |  0
 .../scripts/packed/{ => libs/jquery}/jstorage.js   |  0
 templates/admin/data_admin/data_form.mako          |  2 +-
 templates/admin/data_admin/generic_error.mako      |  2 +-
 templates/admin/data_admin/local_data.mako         |  2 +-
 .../requests/select_datasets_to_transfer.mako      |  2 +-
 .../tool_shed_repository/browse_repository.mako    |  2 +-
 .../browse_tool_dependency.mako                    |  2 +-
 templates/base.mako                                |  2 +-
 templates/base_panels.mako                         |  4 ++--
 templates/dataset/copy_view.mako                   |  2 +-
 templates/dataset/edit_attributes.mako             |  2 +-
 templates/display_base.mako                        |  6 +++---
 templates/form.mako                                |  2 +-
 templates/grid_base.mako                           |  2 +-
 templates/history/view.mako                        |  2 +-
 templates/library/common/browse_library.mako       |  2 +-
 .../common/import_datasets_to_histories.mako       |  2 +-
 templates/library/common/ldda_edit_info.mako       |  2 +-
 .../common/library_dataset_search_results.mako     |  2 +-
 templates/library/common/move_library_item.mako    |  2 +-
 templates/library/common/upload.mako               |  2 +-
 templates/mobile/index.mako                        |  4 ++--
 templates/page/editor.mako                         |  4 ++--
 templates/requests/common/create_request.mako      |  2 +-
 templates/requests/common/find_samples.mako        |  2 +-
 templates/root/history.mako                        |  2 +-
 templates/tool_form.mako                           |  2 +-
 templates/tracks/browser.mako                      |  2 +-
 templates/visualization/sweepster.mako             |  2 +-
 templates/webapps/community/admin/index.mako       |  2 +-
 templates/webapps/community/index.mako             |  2 +-
 .../community/repository/browse_repository.mako    |  2 +-
 .../community/repository/manage_repository.mako    |  2 +-
 .../repository/preview_tools_in_changeset.mako     |  2 +-
 .../community/repository/rate_repository.mako      |  2 +-
 templates/webapps/community/repository/upload.mako |  4 ++--
 .../community/repository/view_changelog.mako       |  2 +-
 .../community/repository/view_changeset.mako       |  2 +-
 .../community/repository/view_repository.mako      |  2 +-
 templates/webapps/galaxy/admin/index.mako          |  2 +-
 templates/webapps/reports/index.mako               |  2 +-
 templates/workflow/edit_attributes.mako            |  2 +-
 templates/workflow/editor.mako                     | 14 +++++++-------
 templates/workflow/run.mako                        |  2 +-
 74 files changed, 55 insertions(+), 65 deletions(-)
 delete mode 100644 static/scripts/jquery.event.drag.js.patch
 rename static/scripts/{ => libs/jquery}/jqtouch.js (100%)
 rename static/scripts/{ => libs/jquery}/jquery.autocomplete.js (100%)
 rename static/scripts/{ => libs/jquery}/jquery.cookie.js (100%)
 rename static/scripts/{ => libs/jquery}/jquery.dynatree.js (100%)
 rename static/scripts/{ => libs/jquery}/jquery.event.drag.js (100%)
 rename static/scripts/{ => libs/jquery}/jquery.event.drop.js (100%)
 rename static/scripts/{ => libs/jquery}/jquery.event.hover.js (100%)
 rename static/scripts/{ => libs/jquery}/jquery.form.js (100%)
 rename static/scripts/{ => libs/jquery}/jquery.js (100%)
 rename static/scripts/{ => libs/jquery}/jquery.mousewheel.js (100%)
 rename static/scripts/{ => libs/jquery}/jquery.rating.js (100%)
 rename static/scripts/{ => libs/jquery}/jquery.tipsy.js (100%)
 rename static/scripts/{ => libs/jquery}/jquery.ui.sortable.slider.js (100%)
 rename static/scripts/{ => libs/jquery}/jquery.wymeditor.js (100%)
 rename static/scripts/{ => libs/jquery}/jstorage.js (100%)
 rename static/scripts/packed/{ => libs/jquery}/jqtouch.js (100%)
 rename static/scripts/packed/{ => libs/jquery}/jquery.autocomplete.js (100%)
 rename static/scripts/packed/{ => libs/jquery}/jquery.cookie.js (100%)
 rename static/scripts/packed/{ => libs/jquery}/jquery.dynatree.js (100%)
 rename static/scripts/packed/{ => libs/jquery}/jquery.event.drag.js (100%)
 rename static/scripts/packed/{ => libs/jquery}/jquery.event.drop.js (100%)
 rename static/scripts/packed/{ => libs/jquery}/jquery.event.hover.js (100%)
 rename static/scripts/packed/{ => libs/jquery}/jquery.form.js (100%)
 rename static/scripts/packed/{ => libs/jquery}/jquery.js (100%)
 rename static/scripts/packed/{ => libs/jquery}/jquery.mousewheel.js (100%)
 rename static/scripts/packed/{ => libs/jquery}/jquery.rating.js (100%)
 rename static/scripts/packed/{ => libs/jquery}/jquery.tipsy.js (100%)
 rename static/scripts/packed/{ => libs/jquery}/jquery.ui.sortable.slider.js (100%)
 rename static/scripts/packed/{ => libs/jquery}/jquery.wymeditor.js (100%)
 rename static/scripts/packed/{ => libs/jquery}/jstorage.js (100%)

diff --git a/static/scripts/jquery.event.drag.js.patch b/static/scripts/jquery.event.drag.js.patch
deleted file mode 100644
index 1c5178021e0..00000000000
--- a/static/scripts/jquery.event.drag.js.patch
+++ /dev/null
@@ -1,10 +0,0 @@
-96c96
-< 			if ( drag.dragging ){
----
-> 			if ( drag.dragging ) {
-99c99,101
-< 				}
----
-> 			} else {
-> 				hijack( event, "dragclickonly", elem );
-> 			}
diff --git a/static/scripts/jqtouch.js b/static/scripts/libs/jquery/jqtouch.js
similarity index 100%
rename from static/scripts/jqtouch.js
rename to static/scripts/libs/jquery/jqtouch.js
diff --git a/static/scripts/jquery.autocomplete.js b/static/scripts/libs/jquery/jquery.autocomplete.js
similarity index 100%
rename from static/scripts/jquery.autocomplete.js
rename to static/scripts/libs/jquery/jquery.autocomplete.js
diff --git a/static/scripts/jquery.cookie.js b/static/scripts/libs/jquery/jquery.cookie.js
similarity index 100%
rename from static/scripts/jquery.cookie.js
rename to static/scripts/libs/jquery/jquery.cookie.js
diff --git a/static/scripts/jquery.dynatree.js b/static/scripts/libs/jquery/jquery.dynatree.js
similarity index 100%
rename from static/scripts/jquery.dynatree.js
rename to static/scripts/libs/jquery/jquery.dynatree.js
diff --git a/static/scripts/jquery.event.drag.js b/static/scripts/libs/jquery/jquery.event.drag.js
similarity index 100%
rename from static/scripts/jquery.event.drag.js
rename to static/scripts/libs/jquery/jquery.event.drag.js
diff --git a/static/scripts/jquery.event.drop.js b/static/scripts/libs/jquery/jquery.event.drop.js
similarity index 100%
rename from static/scripts/jquery.event.drop.js
rename to static/scripts/libs/jquery/jquery.event.drop.js
diff --git a/static/scripts/jquery.event.hover.js b/static/scripts/libs/jquery/jquery.event.hover.js
similarity index 100%
rename from static/scripts/jquery.event.hover.js
rename to static/scripts/libs/jquery/jquery.event.hover.js
diff --git a/static/scripts/jquery.form.js b/static/scripts/libs/jquery/jquery.form.js
similarity index 100%
rename from static/scripts/jquery.form.js
rename to static/scripts/libs/jquery/jquery.form.js
diff --git a/static/scripts/jquery.js b/static/scripts/libs/jquery/jquery.js
similarity index 100%
rename from static/scripts/jquery.js
rename to static/scripts/libs/jquery/jquery.js
diff --git a/static/scripts/jquery.mousewheel.js b/static/scripts/libs/jquery/jquery.mousewheel.js
similarity index 100%
rename from static/scripts/jquery.mousewheel.js
rename to static/scripts/libs/jquery/jquery.mousewheel.js
diff --git a/static/scripts/jquery.rating.js b/static/scripts/libs/jquery/jquery.rating.js
similarity index 100%
rename from static/scripts/jquery.rating.js
rename to static/scripts/libs/jquery/jquery.rating.js
diff --git a/static/scripts/jquery.tipsy.js b/static/scripts/libs/jquery/jquery.tipsy.js
similarity index 100%
rename from static/scripts/jquery.tipsy.js
rename to static/scripts/libs/jquery/jquery.tipsy.js
diff --git a/static/scripts/jquery.ui.sortable.slider.js b/static/scripts/libs/jquery/jquery.ui.sortable.slider.js
similarity index 100%
rename from static/scripts/jquery.ui.sortable.slider.js
rename to static/scripts/libs/jquery/jquery.ui.sortable.slider.js
diff --git a/static/scripts/jquery.wymeditor.js b/static/scripts/libs/jquery/jquery.wymeditor.js
similarity index 100%
rename from static/scripts/jquery.wymeditor.js
rename to static/scripts/libs/jquery/jquery.wymeditor.js
diff --git a/static/scripts/jstorage.js b/static/scripts/libs/jquery/jstorage.js
similarity index 100%
rename from static/scripts/jstorage.js
rename to static/scripts/libs/jquery/jstorage.js
diff --git a/static/scripts/packed/jqtouch.js b/static/scripts/packed/libs/jquery/jqtouch.js
similarity index 100%
rename from static/scripts/packed/jqtouch.js
rename to static/scripts/packed/libs/jquery/jqtouch.js
diff --git a/static/scripts/packed/jquery.autocomplete.js b/static/scripts/packed/libs/jquery/jquery.autocomplete.js
similarity index 100%
rename from static/scripts/packed/jquery.autocomplete.js
rename to static/scripts/packed/libs/jquery/jquery.autocomplete.js
diff --git a/static/scripts/packed/jquery.cookie.js b/static/scripts/packed/libs/jquery/jquery.cookie.js
similarity index 100%
rename from static/scripts/packed/jquery.cookie.js
rename to static/scripts/packed/libs/jquery/jquery.cookie.js
diff --git a/static/scripts/packed/jquery.dynatree.js b/static/scripts/packed/libs/jquery/jquery.dynatree.js
similarity index 100%
rename from static/scripts/packed/jquery.dynatree.js
rename to static/scripts/packed/libs/jquery/jquery.dynatree.js
diff --git a/static/scripts/packed/jquery.event.drag.js b/static/scripts/packed/libs/jquery/jquery.event.drag.js
similarity index 100%
rename from static/scripts/packed/jquery.event.drag.js
rename to static/scripts/packed/libs/jquery/jquery.event.drag.js
diff --git a/static/scripts/packed/jquery.event.drop.js b/static/scripts/packed/libs/jquery/jquery.event.drop.js
similarity index 100%
rename from static/scripts/packed/jquery.event.drop.js
rename to static/scripts/packed/libs/jquery/jquery.event.drop.js
diff --git a/static/scripts/packed/jquery.event.hover.js b/static/scripts/packed/libs/jquery/jquery.event.hover.js
similarity index 100%
rename from static/scripts/packed/jquery.event.hover.js
rename to static/scripts/packed/libs/jquery/jquery.event.hover.js
diff --git a/static/scripts/packed/jquery.form.js b/static/scripts/packed/libs/jquery/jquery.form.js
similarity index 100%
rename from static/scripts/packed/jquery.form.js
rename to static/scripts/packed/libs/jquery/jquery.form.js
diff --git a/static/scripts/packed/jquery.js b/static/scripts/packed/libs/jquery/jquery.js
similarity index 100%
rename from static/scripts/packed/jquery.js
rename to static/scripts/packed/libs/jquery/jquery.js
diff --git a/static/scripts/packed/jquery.mousewheel.js b/static/scripts/packed/libs/jquery/jquery.mousewheel.js
similarity index 100%
rename from static/scripts/packed/jquery.mousewheel.js
rename to static/scripts/packed/libs/jquery/jquery.mousewheel.js
diff --git a/static/scripts/packed/jquery.rating.js b/static/scripts/packed/libs/jquery/jquery.rating.js
similarity index 100%
rename from static/scripts/packed/jquery.rating.js
rename to static/scripts/packed/libs/jquery/jquery.rating.js
diff --git a/static/scripts/packed/jquery.tipsy.js b/static/scripts/packed/libs/jquery/jquery.tipsy.js
similarity index 100%
rename from static/scripts/packed/jquery.tipsy.js
rename to static/scripts/packed/libs/jquery/jquery.tipsy.js
diff --git a/static/scripts/packed/jquery.ui.sortable.slider.js b/static/scripts/packed/libs/jquery/jquery.ui.sortable.slider.js
similarity index 100%
rename from static/scripts/packed/jquery.ui.sortable.slider.js
rename to static/scripts/packed/libs/jquery/jquery.ui.sortable.slider.js
diff --git a/static/scripts/packed/jquery.wymeditor.js b/static/scripts/packed/libs/jquery/jquery.wymeditor.js
similarity index 100%
rename from static/scripts/packed/jquery.wymeditor.js
rename to static/scripts/packed/libs/jquery/jquery.wymeditor.js
diff --git a/static/scripts/packed/jstorage.js b/static/scripts/packed/libs/jquery/jstorage.js
similarity index 100%
rename from static/scripts/packed/jstorage.js
rename to static/scripts/packed/libs/jquery/jstorage.js
diff --git a/templates/admin/data_admin/data_form.mako b/templates/admin/data_admin/data_form.mako
index 1ed3e25f3c3..dde487ff86d 100644
--- a/templates/admin/data_admin/data_form.mako
+++ b/templates/admin/data_admin/data_form.mako
@@ -27,7 +27,7 @@
 </%def>
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js("jquery.autocomplete", "autocomplete_tagging" )}
+    ${h.js("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
 </%def>
 ##
 ## Override methods from base.mako and base_panels.mako
diff --git a/templates/admin/data_admin/generic_error.mako b/templates/admin/data_admin/generic_error.mako
index 2c70ed051df..fd46c54c927 100644
--- a/templates/admin/data_admin/generic_error.mako
+++ b/templates/admin/data_admin/generic_error.mako
@@ -27,7 +27,7 @@
 </%def>
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js("jquery.autocomplete", "autocomplete_tagging" )}
+    ${h.js("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
 </%def>
 ##
 ## Override methods from base.mako and base_panels.mako
diff --git a/templates/admin/data_admin/local_data.mako b/templates/admin/data_admin/local_data.mako
index 84f0f9e650c..256d9e47377 100644
--- a/templates/admin/data_admin/local_data.mako
+++ b/templates/admin/data_admin/local_data.mako
@@ -27,7 +27,7 @@
 </%def>
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js("jquery.autocomplete", "autocomplete_tagging" )}
+    ${h.js("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
 </%def>
 ##
 ## Override methods from base.mako and base_panels.mako
diff --git a/templates/admin/requests/select_datasets_to_transfer.mako b/templates/admin/requests/select_datasets_to_transfer.mako
index 991d9f76c1b..011636ed718 100644
--- a/templates/admin/requests/select_datasets_to_transfer.mako
+++ b/templates/admin/requests/select_datasets_to_transfer.mako
@@ -8,7 +8,7 @@
    ${common_javascripts()}
 </%def>
 
-${h.js( "ui.core", "jquery.cookie", "jquery.dynatree" )}
+${h.js( "ui.core", "libs/jquery/jquery.cookie", "libs/jquery/jquery.dynatree" )}
 ${h.css( "dynatree_skin/ui.dynatree" )}
 
 <script type="text/javascript">
diff --git a/templates/admin/tool_shed_repository/browse_repository.mako b/templates/admin/tool_shed_repository/browse_repository.mako
index 1b9065a5077..765670d0b19 100644
--- a/templates/admin/tool_shed_repository/browse_repository.mako
+++ b/templates/admin/tool_shed_repository/browse_repository.mako
@@ -9,7 +9,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "ui.core", "jquery.dynatree" )}
+    ${h.js( "ui.core", "libs/jquery/jquery.dynatree" )}
     ${browse_files(repository.name, repository.repo_files_directory(trans.app))}
 </%def>
 
diff --git a/templates/admin/tool_shed_repository/browse_tool_dependency.mako b/templates/admin/tool_shed_repository/browse_tool_dependency.mako
index 5e50832704b..b24d031e6ca 100644
--- a/templates/admin/tool_shed_repository/browse_tool_dependency.mako
+++ b/templates/admin/tool_shed_repository/browse_tool_dependency.mako
@@ -9,7 +9,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "ui.core", "jquery.dynatree" )}
+    ${h.js( "ui.core", "libs/jquery/jquery.dynatree" )}
     ${browse_files(tool_dependency.name, tool_dependency.installation_directory( trans.app ))}
 </%def>
 
diff --git a/templates/base.mako b/templates/base.mako
index 1b860d8ab2c..c54db53162c 100644
--- a/templates/base.mako
+++ b/templates/base.mako
@@ -26,7 +26,7 @@
   ## <!--[if lt IE 7]>
   ## <script type='text/javascript' src="/static/scripts/IE7.js"> </script>
   ## <![endif]-->
-  ${h.js( "jquery", "bootstrap", "galaxy.base", "libs/underscore", "libs/backbone/backbone", "libs/backbone/backbone-relational", "libs/handlebars.runtime", "mvc/ui" )}
+  ${h.js( "libs/jquery/jquery", "bootstrap", "galaxy.base", "libs/underscore", "libs/backbone/backbone", "libs/backbone/backbone-relational", "libs/handlebars.runtime", "mvc/ui" )}
   <script type="text/javascript">
       // Set up needed paths.
       var galaxy_paths = new GalaxyPaths({
diff --git a/templates/base_panels.mako b/templates/base_panels.mako
index 092a5650736..9d9e5503758 100644
--- a/templates/base_panels.mako
+++ b/templates/base_panels.mako
@@ -48,7 +48,7 @@
     <!--[if lt IE 7]>
     ${h.js( 'IE7', 'ie7-recalc' )}
     <![endif]-->
-    ${h.js( 'jquery', 'bootstrap', 'libs/underscore', 'libs/backbone/backbone', 'libs/backbone/backbone-relational', 'libs/handlebars.runtime', 'mvc/ui' )}
+    ${h.js( 'libs/jquery/jquery', 'bootstrap', 'libs/underscore', 'libs/backbone/backbone', 'libs/backbone/backbone-relational', 'libs/handlebars.runtime', 'mvc/ui' )}
     <script type="text/javascript">
         // Set up needed paths.
         var galaxy_paths = new GalaxyPaths({
@@ -73,7 +73,7 @@
 <%def name="late_javascripts()">
     ## Scripts can be loaded later since they progressively add features to
     ## the panels, but do not change layout
-    ${h.js( 'jquery.event.drag', 'jquery.event.hover', 'jquery.form', 'jquery.rating', 'galaxy.base', 'galaxy.panels' )}
+    ${h.js( 'libs/jquery/jquery.event.drag', 'libs/jquery/jquery.event.hover', 'libs/jquery/jquery.form', 'libs/jquery/jquery.rating', 'galaxy.base', 'galaxy.panels' )}
     <script type="text/javascript">
         
     ensure_dd_helper();
diff --git a/templates/dataset/copy_view.mako b/templates/dataset/copy_view.mako
index 7b781f52a95..d908a163b5b 100644
--- a/templates/dataset/copy_view.mako
+++ b/templates/dataset/copy_view.mako
@@ -4,7 +4,7 @@
 <%def name="javascripts()">
 
     ${parent.javascripts()}
-    ${h.js( "jquery", "galaxy.base" )}
+    ${h.js( "libs/jquery/jquery", "galaxy.base" )}
     
     <script type="text/javascript">
         $(function() {
diff --git a/templates/dataset/edit_attributes.mako b/templates/dataset/edit_attributes.mako
index 33bd3363a6e..aae0f1682de 100644
--- a/templates/dataset/edit_attributes.mako
+++ b/templates/dataset/edit_attributes.mako
@@ -11,7 +11,7 @@
 <%def name="javascripts()">
     ${parent.javascripts()}
     ${message_ns.javascripts()}
-    ${h.js( "galaxy.base", "jquery.autocomplete", "autocomplete_tagging" )}
+    ${h.js( "galaxy.base", "libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
 </%def>
 
 <%def name="datatype( dataset, datatypes )">
diff --git a/templates/display_base.mako b/templates/display_base.mako
index 019ada2ad48..f21d9ba0298 100644
--- a/templates/display_base.mako
+++ b/templates/display_base.mako
@@ -32,9 +32,9 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "jquery", "bootstrap", "galaxy.base", "json2", "jstorage", "jquery.autocomplete", "jquery.rating", 
-            "autocomplete_tagging", "viz/trackster", "viz/trackster_ui", "jquery.event.drag", "jquery.mousewheel", 
-            "jquery.autocomplete", "jquery.ui.sortable.slider", "farbtastic", "mvc/data", "viz/visualization" )}
+    ${h.js( "libs/jquery/jquery", "bootstrap", "galaxy.base", "json2", "libs/jquery/jstorage", "libs/jquery/jquery.autocomplete", "libs/jquery/jquery.rating", 
+            "autocomplete_tagging", "viz/trackster", "viz/trackster_ui", "libs/jquery/jquery.event.drag", "libs/jquery/jquery.mousewheel", 
+            "libs/jquery/jquery.autocomplete", "libs/jquery/jquery.ui.sortable.slider", "farbtastic", "mvc/data", "viz/visualization" )}
 
     <script type="text/javascript">
         
diff --git a/templates/form.mako b/templates/form.mako
index 7cc2d6e3c2e..a27939be1c3 100644
--- a/templates/form.mako
+++ b/templates/form.mako
@@ -26,7 +26,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js("jquery.autocomplete")}
+    ${h.js("libs/jquery/jquery.autocomplete")}
     <script type="text/javascript">
         $(function(){
             $("input:text:first").focus();
diff --git a/templates/grid_base.mako b/templates/grid_base.mako
index 8c6c4bdcae1..74c523db946 100644
--- a/templates/grid_base.mako
+++ b/templates/grid_base.mako
@@ -52,7 +52,7 @@
 </%def>
 
 <%def name="grid_javascripts()">
-    ${h.js("jquery.autocomplete", "autocomplete_tagging", "jquery.rating" )}
+    ${h.js("libs/jquery/jquery.autocomplete", "autocomplete_tagging", "libs/jquery/jquery.rating" )}
     <script type="text/javascript">
         // This is necessary so that, when nested arrays are used in ajax/post/get methods, square brackets ('[]') are
         // not appended to the identifier of a nested array.
diff --git a/templates/history/view.mako b/templates/history/view.mako
index fdef5575a9f..56e17d8386d 100644
--- a/templates/history/view.mako
+++ b/templates/history/view.mako
@@ -13,7 +13,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "galaxy.base", "jquery", "json2", "jstorage" )}
+    ${h.js( "galaxy.base", "libs/jquery/jquery", "json2", "libs/jquery/jstorage" )}
     <script type="text/javascript">
         $(function() {
             init_history_items( $("div.historyItemWrapper"), false, "nochanges" );
diff --git a/templates/library/common/browse_library.mako b/templates/library/common/browse_library.mako
index ca9fc53d1fc..ffa3445f696 100644
--- a/templates/library/common/browse_library.mako
+++ b/templates/library/common/browse_library.mako
@@ -49,7 +49,7 @@
 <%def name="javascripts()">
     ${parent.javascripts()}
     ${h.js("json2")}
-    ${h.js("jstorage")}
+    ${h.js("libs/jquery/jstorage")}
     ${common_javascripts()}
     ${self.grid_javascripts()}
 </%def>
diff --git a/templates/library/common/import_datasets_to_histories.mako b/templates/library/common/import_datasets_to_histories.mako
index d3a5bb15d44..8b823a2f098 100644
--- a/templates/library/common/import_datasets_to_histories.mako
+++ b/templates/library/common/import_datasets_to_histories.mako
@@ -5,7 +5,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "jquery", "galaxy.base" )}
+    ${h.js( "libs/jquery/jquery", "galaxy.base" )}
     <script type="text/javascript">
         $(function() {
             $("#select-multiple").click(function() {
diff --git a/templates/library/common/ldda_edit_info.mako b/templates/library/common/ldda_edit_info.mako
index c32326af961..38311e5ea04 100644
--- a/templates/library/common/ldda_edit_info.mako
+++ b/templates/library/common/ldda_edit_info.mako
@@ -5,7 +5,7 @@
 
 <%def name="javascripts()">
    ${parent.javascripts()}
-   ${h.js("jquery.autocomplete", "autocomplete_tagging" )}
+   ${h.js("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
 </%def>
 
 <%def name="stylesheets()">
diff --git a/templates/library/common/library_dataset_search_results.mako b/templates/library/common/library_dataset_search_results.mako
index 3a8c41ffca1..85dc41bfb4b 100644
--- a/templates/library/common/library_dataset_search_results.mako
+++ b/templates/library/common/library_dataset_search_results.mako
@@ -46,7 +46,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js("jstorage")}
+    ${h.js("libs/jquery/jstorage")}
     ${common_javascripts()}
 </%def>
 
diff --git a/templates/library/common/move_library_item.mako b/templates/library/common/move_library_item.mako
index 5a53b734fe2..2f6c7483eec 100644
--- a/templates/library/common/move_library_item.mako
+++ b/templates/library/common/move_library_item.mako
@@ -3,7 +3,7 @@
 
 <%def name="javascripts()">
    ${parent.javascripts()}
-   ${h.js("jquery.autocomplete", "autocomplete_tagging" )}
+   ${h.js("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
 </%def>
 
 <%def name="stylesheets()">
diff --git a/templates/library/common/upload.mako b/templates/library/common/upload.mako
index b8dffce267e..769d2e1d74d 100644
--- a/templates/library/common/upload.mako
+++ b/templates/library/common/upload.mako
@@ -13,7 +13,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js("jquery.autocomplete", "autocomplete_tagging" )}
+    ${h.js("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
 </%def>
 
 <%def name="stylesheets()">
diff --git a/templates/mobile/index.mako b/templates/mobile/index.mako
index 16e0c5f1fdf..2879520dc67 100644
--- a/templates/mobile/index.mako
+++ b/templates/mobile/index.mako
@@ -26,8 +26,8 @@
     </style>
     
     <style type="text/css" media="screen">@import "${h.url_for('/static/jqtouch/jqtouch.css')}";</style>
-    <script type="text/javascript" src="${h.url_for('/static/scripts/jquery.js')}"></script>
-    <script type="text/javascript" src="${h.url_for('/static/scripts/jqtouch.js')}"></script>
+    <script type="text/javascript" src="${h.url_for('/static/scripts/libs/jquery/jquery.js')}"></script>
+    <script type="text/javascript" src="${h.url_for('/static/scripts/libs/jquery/jqtouch.js')}"></script>
     <script type="text/javascript" charset="utf-8">
         $(document).jQTouch( {
             icon: "${h.url_for('static/images/galaxyIcon_noText.png')}",
diff --git a/templates/page/editor.mako b/templates/page/editor.mako
index 7a9c7e4a648..ae68886515e 100644
--- a/templates/page/editor.mako
+++ b/templates/page/editor.mako
@@ -21,8 +21,8 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "jquery.event.drag", "jquery.event.drop", "jquery.event.hover", "jquery.form", "json2", "jstorage",
-            "galaxy.base", "jquery.wymeditor", "jquery.autocomplete", "autocomplete_tagging")}    
+    ${h.js( "libs/jquery/jquery.event.drag", "libs/jquery/jquery.event.drop", "libs/jquery/jquery.event.hover", "libs/jquery/jquery.form", "json2", "libs/jquery/jstorage",
+            "galaxy.base", "libs/jquery/jquery.wymeditor", "libs/jquery/jquery.autocomplete", "autocomplete_tagging")}    
     <script type="text/javascript">
             
     // Useful Galaxy stuff.
diff --git a/templates/requests/common/create_request.mako b/templates/requests/common/create_request.mako
index ac0b5e70b73..550500857f8 100644
--- a/templates/requests/common/create_request.mako
+++ b/templates/requests/common/create_request.mako
@@ -3,7 +3,7 @@
 
 <%def name="javascripts()">
    ${parent.javascripts()}
-   ${h.js("jquery.autocomplete", "autocomplete_tagging" )}
+   ${h.js("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
 </%def>
 
 <%def name="stylesheets()">
diff --git a/templates/requests/common/find_samples.mako b/templates/requests/common/find_samples.mako
index 29512adef24..83f52ba0d22 100644
--- a/templates/requests/common/find_samples.mako
+++ b/templates/requests/common/find_samples.mako
@@ -3,7 +3,7 @@
 
 <%def name="javascripts()">
    ${parent.javascripts()}
-   ${h.js("jquery.autocomplete", "autocomplete_tagging" )}
+   ${h.js("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
 </%def>
 
 <%def name="stylesheets()">
diff --git a/templates/root/history.mako b/templates/root/history.mako
index 5dcfdc768d7..4eb4b8dff63 100644
--- a/templates/root/history.mako
+++ b/templates/root/history.mako
@@ -17,7 +17,7 @@
 <meta http-equiv="Pragma" content="no-cache">
 
 ${h.css( "base", "history", "autocomplete_tagging" )}
-${h.js( "jquery", "bootstrap", "galaxy.base", "json2", "jstorage", "jquery.autocomplete", "autocomplete_tagging" )}
+${h.js( "libs/jquery/jquery", "bootstrap", "galaxy.base", "json2", "libs/jquery/jstorage", "libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
 
 <script type="text/javascript">
 
diff --git a/templates/tool_form.mako b/templates/tool_form.mako
index 25068f511d5..84562cbc719 100644
--- a/templates/tool_form.mako
+++ b/templates/tool_form.mako
@@ -12,7 +12,7 @@
 </%def>
 
 <%def name="javascripts()">
-    ${h.js( "jquery", "galaxy.panels", "galaxy.base", "jquery.autocomplete", "jstorage" )}
+    ${h.js( "libs/jquery/jquery", "galaxy.panels", "galaxy.base", "libs/jquery/jquery.autocomplete", "libs/jquery/jstorage" )}
     <script type="text/javascript">
     $(function() {
         $(window).bind("refresh_on_change", function() {
diff --git a/templates/tracks/browser.mako b/templates/tracks/browser.mako
index dffc5eaa8f9..59a5e3e3b16 100644
--- a/templates/tracks/browser.mako
+++ b/templates/tracks/browser.mako
@@ -21,7 +21,7 @@ ${parent.javascripts()}
   <script type='text/javascript' src="${h.url_for('/static/scripts/excanvas.js')}"></script>
 <![endif]-->
 
-${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "bootstrap", "jstorage", "jquery.event.drag", "jquery.event.hover","jquery.mousewheel", "jquery.autocomplete", "mvc/data", "viz/visualization", "viz/trackster", "viz/trackster_ui", "jquery.ui.sortable.slider", "farbtastic" )}
+${h.js( "galaxy.base", "galaxy.panels", "json2", "libs/jquery/jquery", "bootstrap", "libs/jquery/jstorage", "libs/jquery/jquery.event.drag", "libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel", "libs/jquery/jquery.autocomplete", "mvc/data", "viz/visualization", "viz/trackster", "viz/trackster_ui", "libs/jquery/jquery.ui.sortable.slider", "farbtastic" )}
 
 <script type="text/javascript">
     //
diff --git a/templates/visualization/sweepster.mako b/templates/visualization/sweepster.mako
index e9d0ba176f6..65ee81ddce0 100644
--- a/templates/visualization/sweepster.mako
+++ b/templates/visualization/sweepster.mako
@@ -108,7 +108,7 @@
 
     ${h.templates( "tool_link", "panel_section", "tool_search", "tool_form" )}
     ${h.js( "libs/d3", "mvc/data", "mvc/tools", "viz/visualization", "viz/sweepster", 
-            "viz/trackster", "viz/trackster_ui", "jquery.ui.sortable.slider" )}
+            "viz/trackster", "viz/trackster_ui", "libs/jquery/jquery.ui.sortable.slider" )}
 
     <script type="text/javascript">
         var viz;
diff --git a/templates/webapps/community/admin/index.mako b/templates/webapps/community/admin/index.mako
index 50085558edc..66b7949b3ee 100644
--- a/templates/webapps/community/admin/index.mako
+++ b/templates/webapps/community/admin/index.mako
@@ -18,7 +18,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "jquery", "galaxy.base" )}
+    ${h.js( "libs/jquery/jquery", "galaxy.base" )}
 </%def>
 
 <%def name="init()">
diff --git a/templates/webapps/community/index.mako b/templates/webapps/community/index.mako
index 16c40dc44c6..6e8c293e660 100644
--- a/templates/webapps/community/index.mako
+++ b/templates/webapps/community/index.mako
@@ -19,7 +19,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "jquery", "galaxy.base" )}
+    ${h.js( "libs/jquery/jquery", "galaxy.base" )}
 </%def>
 
 <%def name="init()">
diff --git a/templates/webapps/community/repository/browse_repository.mako b/templates/webapps/community/repository/browse_repository.mako
index 1d3c5ab2761..931eb9f97e5 100644
--- a/templates/webapps/community/repository/browse_repository.mako
+++ b/templates/webapps/community/repository/browse_repository.mako
@@ -57,7 +57,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "jquery.rating", "ui.core", "jquery.cookie", "jquery.dynatree" )}
+    ${h.js( "libs/jquery/jquery.rating", "ui.core", "libs/jquery/jquery.cookie", "libs/jquery/jquery.dynatree" )}
     ${common_javascripts(repository)}
 </%def>
 
diff --git a/templates/webapps/community/repository/manage_repository.mako b/templates/webapps/community/repository/manage_repository.mako
index 4156af5710a..e8128247ca5 100644
--- a/templates/webapps/community/repository/manage_repository.mako
+++ b/templates/webapps/community/repository/manage_repository.mako
@@ -63,7 +63,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "jquery.rating" )}
+    ${h.js( "libs/jquery/jquery.rating" )}
     ${common_javascripts(repository)}
 </%def>
 
diff --git a/templates/webapps/community/repository/preview_tools_in_changeset.mako b/templates/webapps/community/repository/preview_tools_in_changeset.mako
index 494077e599e..84cc5c778ed 100644
--- a/templates/webapps/community/repository/preview_tools_in_changeset.mako
+++ b/templates/webapps/community/repository/preview_tools_in_changeset.mako
@@ -58,7 +58,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "jquery.rating" )}
+    ${h.js( "libs/jquery/jquery.rating" )}
     ${common_javascripts(repository)}
 </%def>
 
diff --git a/templates/webapps/community/repository/rate_repository.mako b/templates/webapps/community/repository/rate_repository.mako
index 37b13346e32..189fbb13a84 100644
--- a/templates/webapps/community/repository/rate_repository.mako
+++ b/templates/webapps/community/repository/rate_repository.mako
@@ -61,7 +61,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "jquery.rating" )}
+    ${h.js( "libs/jquery/jquery.rating" )}
 </%def>
 
 %if message:
diff --git a/templates/webapps/community/repository/upload.mako b/templates/webapps/community/repository/upload.mako
index 2b71e897ab7..45602e5e939 100644
--- a/templates/webapps/community/repository/upload.mako
+++ b/templates/webapps/community/repository/upload.mako
@@ -23,12 +23,12 @@
 
 <%def name="stylesheets()">
     ${parent.stylesheets()}
-    ${h.css( "jquery.rating", "dynatree_skin/ui.dynatree" )}
+    ${h.css( "libs/jquery/jquery.rating", "dynatree_skin/ui.dynatree" )}
 </%def>
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "ui.core", "jquery.cookie", "jquery.dynatree" )}
+    ${h.js( "ui.core", "libs/jquery/jquery.cookie", "libs/jquery/jquery.dynatree" )}
     ${common_javascripts(repository)}
     <script type="text/javascript">
     $( function() {
diff --git a/templates/webapps/community/repository/view_changelog.mako b/templates/webapps/community/repository/view_changelog.mako
index 6a6d8bcbf5b..1f02b737c4d 100644
--- a/templates/webapps/community/repository/view_changelog.mako
+++ b/templates/webapps/community/repository/view_changelog.mako
@@ -36,7 +36,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "jquery.rating" )}
+    ${h.js( "libs/jquery/jquery.rating" )}
 </%def>
 
 <br/><br/>
diff --git a/templates/webapps/community/repository/view_changeset.mako b/templates/webapps/community/repository/view_changeset.mako
index 00a65ec1dd0..16fa2bda032 100644
--- a/templates/webapps/community/repository/view_changeset.mako
+++ b/templates/webapps/community/repository/view_changeset.mako
@@ -37,7 +37,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "jquery.rating" )}
+    ${h.js( "libs/jquery/jquery.rating" )}
 </%def>
 
 <br/><br/>
diff --git a/templates/webapps/community/repository/view_repository.mako b/templates/webapps/community/repository/view_repository.mako
index f53d46bf4a1..12c2e531ec4 100644
--- a/templates/webapps/community/repository/view_repository.mako
+++ b/templates/webapps/community/repository/view_repository.mako
@@ -59,7 +59,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "jquery.rating" )}
+    ${h.js( "libs/jquery/jquery.rating" )}
     ${common_javascripts(repository)}
 </%def>
 
diff --git a/templates/webapps/galaxy/admin/index.mako b/templates/webapps/galaxy/admin/index.mako
index a4dd17ff776..778825be64b 100644
--- a/templates/webapps/galaxy/admin/index.mako
+++ b/templates/webapps/galaxy/admin/index.mako
@@ -22,7 +22,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "jquery", "galaxy.base" )}
+    ${h.js( "libs/jquery/jquery", "galaxy.base" )}
 </%def>
 
 <%def name="init()">
diff --git a/templates/webapps/reports/index.mako b/templates/webapps/reports/index.mako
index 29273bb10bf..ce571f7b18a 100644
--- a/templates/webapps/reports/index.mako
+++ b/templates/webapps/reports/index.mako
@@ -26,7 +26,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "jquery", "galaxy.base" )}
+    ${h.js( "libs/jquery/jquery", "galaxy.base" )}
 </%def>
 
 <%def name="left_panel()">
diff --git a/templates/workflow/edit_attributes.mako b/templates/workflow/edit_attributes.mako
index 5a63cad4eb1..09f396a97cb 100644
--- a/templates/workflow/edit_attributes.mako
+++ b/templates/workflow/edit_attributes.mako
@@ -9,7 +9,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "galaxy.base", "jquery.autocomplete", "autocomplete_tagging" )}
+    ${h.js( "galaxy.base", "libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
 </%def>
 
 %if msg:
diff --git a/templates/workflow/editor.mako b/templates/workflow/editor.mako
index b589cba239b..b6ef46d6425 100644
--- a/templates/workflow/editor.mako
+++ b/templates/workflow/editor.mako
@@ -25,17 +25,17 @@
       <script type='text/javascript' src="${h.url_for('/static/scripts/excanvas.js')}"></script>
     <![endif]-->
 
-    ${h.js( "jquery",
+    ${h.js( "libs/jquery/jquery",
             "bootstrap",
-            "jquery.event.drag",
-            "jquery.event.drop",
-            "jquery.event.hover",
-            "jquery.form",
+            "libs/jquery/jquery.event.drag",
+            "libs/jquery/jquery.event.drop",
+            "libs/jquery/jquery.event.hover",
+            "libs/jquery/jquery.form",
             "json2",
-            "jstorage",
+            "libs/jquery/jstorage",
             "galaxy.base",
             "galaxy.workflow_editor.canvas",
-            "jquery.autocomplete",
+            "libs/jquery/jquery.autocomplete",
             "autocomplete_tagging")}
 
     <!--[if lt IE 7]>
diff --git a/templates/workflow/run.mako b/templates/workflow/run.mako
index 3c85da423c2..b12790f05f1 100644
--- a/templates/workflow/run.mako
+++ b/templates/workflow/run.mako
@@ -2,7 +2,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "jquery.autocomplete", "bootstrap" )}
+    ${h.js( "libs/jquery/jquery.autocomplete", "bootstrap" )}
     <script type="text/javascript">
         $( function() {
             function show_tool_body(title){

From 85c985db828e092ce4cb3d20d7f52d756df8d24f Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Tue, 21 Aug 2012 16:05:55 -0400
Subject: [PATCH 14/16] Remove blastxml from datatypes_conf.xml.sample.

---
 datatypes_conf.xml.sample | 2 --
 1 file changed, 2 deletions(-)

diff --git a/datatypes_conf.xml.sample b/datatypes_conf.xml.sample
index 099addfa73a..7d27266dc53 100644
--- a/datatypes_conf.xml.sample
+++ b/datatypes_conf.xml.sample
@@ -169,7 +169,6 @@
     <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="xml" type="galaxy.datatypes.xml:GenericXml" 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"/>
@@ -246,7 +245,6 @@
     <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.xml:GenericXml"/>
     <sniffer type="galaxy.datatypes.sequence:Maf"/>
     <sniffer type="galaxy.datatypes.sequence:Lav"/>

From 66d189236418fba4601ee27e84897ea3a1b38ecf Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Tue, 21 Aug 2012 16:54:19 -0400
Subject: [PATCH 15/16] More JS file reorganization: (a) move IE and rgenetics
 into their own directories; (b) move additional external libraries to libs.

---
 ...terval_to_interval_index_converter.py.orig |  79 ------------------
 static/scripts/{ => libs/IE}/IE7.js           |   0
 static/scripts/{ => libs/IE}/IE8.js           |   0
 static/scripts/{ => libs/IE}/blank.gif        | Bin
 static/scripts/{ => libs/IE}/excanvas.js      |   0
 static/scripts/{ => libs/IE}/ie7-recalc.js    |   0
 static/scripts/{ => libs}/bootstrap.js        |   0
 static/scripts/{ => libs}/farbtastic.js       |   0
 static/scripts/{ => libs}/json2.js            |   0
 static/scripts/packed/blank.gif               | Bin 48 -> 0 bytes
 static/scripts/packed/{ => libs/IE}/IE7.js    |   0
 static/scripts/packed/{ => libs/IE}/IE8.js    |   0
 .../scripts/packed/{ => libs/IE}/excanvas.js  |   0
 .../packed/{ => libs/IE}/ie7-recalc.js        |   0
 static/scripts/packed/{ => libs}/bootstrap.js |   0
 .../scripts/packed/{ => libs}/farbtastic.js   |   0
 static/scripts/packed/{ => libs}/json2.js     |   0
 .../checkbox_and_radiobutton.js               |   0
 .../{ => rgenetics}/helper_functions.js       |   0
 .../scripts/packed/{ => rgenetics}/timer.js   |   0
 .../checkbox_and_radiobutton.js               |   0
 .../{ => rgenetics}/helper_functions.js       |   0
 static/scripts/{ => rgenetics}/timer.js       |   0
 templates/base.mako                           |   4 +-
 templates/base_panels.mako                    |   4 +-
 templates/display_base.mako                   |   4 +-
 templates/history/view.mako                   |   2 +-
 templates/library/common/browse_library.mako  |   2 +-
 templates/page/editor.mako                    |   2 +-
 templates/root/history.mako                   |   2 +-
 templates/root/tool_menu.mako                 |   2 +-
 templates/tracks/browser.mako                 |   4 +-
 templates/visualization/display.mako          |   2 +-
 templates/workflow/editor.mako                |   6 +-
 templates/workflow/run.mako                   |   2 +-
 tools/rgenetics/rgGRR.py                      |   6 +-
 36 files changed, 21 insertions(+), 100 deletions(-)
 delete mode 100644 lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py.orig
 rename static/scripts/{ => libs/IE}/IE7.js (100%)
 rename static/scripts/{ => libs/IE}/IE8.js (100%)
 rename static/scripts/{ => libs/IE}/blank.gif (100%)
 rename static/scripts/{ => libs/IE}/excanvas.js (100%)
 rename static/scripts/{ => libs/IE}/ie7-recalc.js (100%)
 rename static/scripts/{ => libs}/bootstrap.js (100%)
 rename static/scripts/{ => libs}/farbtastic.js (100%)
 rename static/scripts/{ => libs}/json2.js (100%)
 delete mode 100644 static/scripts/packed/blank.gif
 rename static/scripts/packed/{ => libs/IE}/IE7.js (100%)
 rename static/scripts/packed/{ => libs/IE}/IE8.js (100%)
 rename static/scripts/packed/{ => libs/IE}/excanvas.js (100%)
 rename static/scripts/packed/{ => libs/IE}/ie7-recalc.js (100%)
 rename static/scripts/packed/{ => libs}/bootstrap.js (100%)
 rename static/scripts/packed/{ => libs}/farbtastic.js (100%)
 rename static/scripts/packed/{ => libs}/json2.js (100%)
 rename static/scripts/packed/{ => rgenetics}/checkbox_and_radiobutton.js (100%)
 rename static/scripts/packed/{ => rgenetics}/helper_functions.js (100%)
 rename static/scripts/packed/{ => rgenetics}/timer.js (100%)
 rename static/scripts/{ => rgenetics}/checkbox_and_radiobutton.js (100%)
 rename static/scripts/{ => rgenetics}/helper_functions.js (100%)
 rename static/scripts/{ => rgenetics}/timer.js (100%)

diff --git a/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py.orig b/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py.orig
deleted file mode 100644
index 15d84bd4141..00000000000
--- a/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py.orig
+++ /dev/null
@@ -1,79 +0,0 @@
-#!/usr/bin/env python
-
-"""
-Convert from interval file to interval index file. Default input file format is BED (0-based, half-open intervals).
-
-usage: %prog in_file out_file
-    -G, --gff: input is GFF format, meaning start and end coordinates are 1-based, closed interval
-"""
-
-from __future__ import division
-
-import sys, fileinput
-from galaxy import eggs
-import pkg_resources; pkg_resources.require( "bx-python" )
-from galaxy.visualization.tracks.summary import *
-from bx.cookbook import doc_optparse
-from galaxy.tools.util.gff_util import convert_gff_coords_to_bed
-from bx.interval_index_file import Indexes
-from galaxy.tools.util.gff_util import parse_gff_attributes
-
-def main():
-    
-    # Read options, args.
-    options, args = doc_optparse.parse( __doc__ )
-    try:
-        gff_format = bool( options.gff )
-        input_fname, out_fname = args
-    except:
-        doc_optparse.exception()
-    
-    # Do conversion.
-    # TODO: take column numbers from command line.
-    if gff_format:
-        chr_col, start_col, end_col = ( 0, 3, 4 )
-    else:
-        chr_col, start_col, end_col = ( 0, 1, 2 )
-    index = Indexes()
-    offset = 0
-    # Need to keep track of last gene, transcript id for indexing GTF files.
-    last_gene_id = None
-    last_transcript_id = None
-    for line in open(input_fname, "r"):
-        feature = line.strip().split('\t')
-        if not feature or feature[0].startswith("track") or feature[0].startswith("#"):
-            offset += len(line)
-            continue
-        chrom = feature[ chr_col ]
-        chrom_start = int( feature[ start_col ] )
-        chrom_end = int( feature[ end_col ] )
-        if gff_format:
-            chrom_start, chrom_end = convert_gff_coords_to_bed( [chrom_start, chrom_end ] )
-            
-            # Only add feature if gene_id, transcript_id are different from last 
-            # values.
-            if len( feature ) == 9:
-                attributes = parse_gff_attributes( feature[8] )
-                gene_id = attributes.get( 'gene_id', None )
-                transcript_id = attributes.get( 'transcript_id', None )
-                if gene_id and transcript_id and gene_id == last_gene_id and \
-                   transcript_id == last_transcript_id:
-                    # Feature has same gene_id, transcript as last feature, so 
-                    # do not add.
-                    offset += len(line)
-                    continue
-                else:
-                    # gene_id, transcript_id set and are different from last 
-                    # values.
-                    last_gene_id = gene_id
-                    last_transcript_id = transcript_id
-
-        #print "%s %s %s %s %i %i %i" % (feature[2], last_gene_id, last_transcript_id, chrom, chrom_start, chrom_end, offset)
-        index.add( chrom, chrom_start, chrom_end, offset )
-        offset += len(line)
-            
-    index.write( open(out_fname, "w") )
-
-if __name__ == "__main__": 
-    main()
-    
\ No newline at end of file
diff --git a/static/scripts/IE7.js b/static/scripts/libs/IE/IE7.js
similarity index 100%
rename from static/scripts/IE7.js
rename to static/scripts/libs/IE/IE7.js
diff --git a/static/scripts/IE8.js b/static/scripts/libs/IE/IE8.js
similarity index 100%
rename from static/scripts/IE8.js
rename to static/scripts/libs/IE/IE8.js
diff --git a/static/scripts/blank.gif b/static/scripts/libs/IE/blank.gif
similarity index 100%
rename from static/scripts/blank.gif
rename to static/scripts/libs/IE/blank.gif
diff --git a/static/scripts/excanvas.js b/static/scripts/libs/IE/excanvas.js
similarity index 100%
rename from static/scripts/excanvas.js
rename to static/scripts/libs/IE/excanvas.js
diff --git a/static/scripts/ie7-recalc.js b/static/scripts/libs/IE/ie7-recalc.js
similarity index 100%
rename from static/scripts/ie7-recalc.js
rename to static/scripts/libs/IE/ie7-recalc.js
diff --git a/static/scripts/bootstrap.js b/static/scripts/libs/bootstrap.js
similarity index 100%
rename from static/scripts/bootstrap.js
rename to static/scripts/libs/bootstrap.js
diff --git a/static/scripts/farbtastic.js b/static/scripts/libs/farbtastic.js
similarity index 100%
rename from static/scripts/farbtastic.js
rename to static/scripts/libs/farbtastic.js
diff --git a/static/scripts/json2.js b/static/scripts/libs/json2.js
similarity index 100%
rename from static/scripts/json2.js
rename to static/scripts/libs/json2.js
diff --git a/static/scripts/packed/blank.gif b/static/scripts/packed/blank.gif
deleted file mode 100644
index a4fe2e6297c7a013637b0e15f842dca1ef3128c4..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 48
wcmZ?wbhEHbWMp7un83&Y1poj4SNzEWWHK`7fcPL81|}vSMh3-y@(c{t0P2MZQ2+n{

diff --git a/static/scripts/packed/IE7.js b/static/scripts/packed/libs/IE/IE7.js
similarity index 100%
rename from static/scripts/packed/IE7.js
rename to static/scripts/packed/libs/IE/IE7.js
diff --git a/static/scripts/packed/IE8.js b/static/scripts/packed/libs/IE/IE8.js
similarity index 100%
rename from static/scripts/packed/IE8.js
rename to static/scripts/packed/libs/IE/IE8.js
diff --git a/static/scripts/packed/excanvas.js b/static/scripts/packed/libs/IE/excanvas.js
similarity index 100%
rename from static/scripts/packed/excanvas.js
rename to static/scripts/packed/libs/IE/excanvas.js
diff --git a/static/scripts/packed/ie7-recalc.js b/static/scripts/packed/libs/IE/ie7-recalc.js
similarity index 100%
rename from static/scripts/packed/ie7-recalc.js
rename to static/scripts/packed/libs/IE/ie7-recalc.js
diff --git a/static/scripts/packed/bootstrap.js b/static/scripts/packed/libs/bootstrap.js
similarity index 100%
rename from static/scripts/packed/bootstrap.js
rename to static/scripts/packed/libs/bootstrap.js
diff --git a/static/scripts/packed/farbtastic.js b/static/scripts/packed/libs/farbtastic.js
similarity index 100%
rename from static/scripts/packed/farbtastic.js
rename to static/scripts/packed/libs/farbtastic.js
diff --git a/static/scripts/packed/json2.js b/static/scripts/packed/libs/json2.js
similarity index 100%
rename from static/scripts/packed/json2.js
rename to static/scripts/packed/libs/json2.js
diff --git a/static/scripts/packed/checkbox_and_radiobutton.js b/static/scripts/packed/rgenetics/checkbox_and_radiobutton.js
similarity index 100%
rename from static/scripts/packed/checkbox_and_radiobutton.js
rename to static/scripts/packed/rgenetics/checkbox_and_radiobutton.js
diff --git a/static/scripts/packed/helper_functions.js b/static/scripts/packed/rgenetics/helper_functions.js
similarity index 100%
rename from static/scripts/packed/helper_functions.js
rename to static/scripts/packed/rgenetics/helper_functions.js
diff --git a/static/scripts/packed/timer.js b/static/scripts/packed/rgenetics/timer.js
similarity index 100%
rename from static/scripts/packed/timer.js
rename to static/scripts/packed/rgenetics/timer.js
diff --git a/static/scripts/checkbox_and_radiobutton.js b/static/scripts/rgenetics/checkbox_and_radiobutton.js
similarity index 100%
rename from static/scripts/checkbox_and_radiobutton.js
rename to static/scripts/rgenetics/checkbox_and_radiobutton.js
diff --git a/static/scripts/helper_functions.js b/static/scripts/rgenetics/helper_functions.js
similarity index 100%
rename from static/scripts/helper_functions.js
rename to static/scripts/rgenetics/helper_functions.js
diff --git a/static/scripts/timer.js b/static/scripts/rgenetics/timer.js
similarity index 100%
rename from static/scripts/timer.js
rename to static/scripts/rgenetics/timer.js
diff --git a/templates/base.mako b/templates/base.mako
index c54db53162c..9507075c2ec 100644
--- a/templates/base.mako
+++ b/templates/base.mako
@@ -24,9 +24,9 @@
 ## Default javascripts
 <%def name="javascripts()">
   ## <!--[if lt IE 7]>
-  ## <script type='text/javascript' src="/static/scripts/IE7.js"> </script>
+  ## <script type='text/javascript' src="/static/scripts/libs/IE/IE7.js"> </script>
   ## <![endif]-->
-  ${h.js( "libs/jquery/jquery", "bootstrap", "galaxy.base", "libs/underscore", "libs/backbone/backbone", "libs/backbone/backbone-relational", "libs/handlebars.runtime", "mvc/ui" )}
+  ${h.js( "libs/jquery/jquery", "libs/bootstrap", "galaxy.base", "libs/underscore", "libs/backbone/backbone", "libs/backbone/backbone-relational", "libs/handlebars.runtime", "mvc/ui" )}
   <script type="text/javascript">
       // Set up needed paths.
       var galaxy_paths = new GalaxyPaths({
diff --git a/templates/base_panels.mako b/templates/base_panels.mako
index 9d9e5503758..eda98eaa201 100644
--- a/templates/base_panels.mako
+++ b/templates/base_panels.mako
@@ -46,9 +46,9 @@
 ## Default javascripts
 <%def name="javascripts()">
     <!--[if lt IE 7]>
-    ${h.js( 'IE7', 'ie7-recalc' )}
+    ${h.js( 'libs/IE/IE7', 'libs/IE/ie7-recalc' )}
     <![endif]-->
-    ${h.js( 'libs/jquery/jquery', 'bootstrap', 'libs/underscore', 'libs/backbone/backbone', 'libs/backbone/backbone-relational', 'libs/handlebars.runtime', 'mvc/ui' )}
+    ${h.js( 'libs/jquery/jquery', 'libs/bootstrap', 'libs/underscore', 'libs/backbone/backbone', 'libs/backbone/backbone-relational', 'libs/handlebars.runtime', 'mvc/ui' )}
     <script type="text/javascript">
         // Set up needed paths.
         var galaxy_paths = new GalaxyPaths({
diff --git a/templates/display_base.mako b/templates/display_base.mako
index f21d9ba0298..bd9305d1dd0 100644
--- a/templates/display_base.mako
+++ b/templates/display_base.mako
@@ -32,9 +32,9 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "libs/jquery/jquery", "bootstrap", "galaxy.base", "json2", "libs/jquery/jstorage", "libs/jquery/jquery.autocomplete", "libs/jquery/jquery.rating", 
+    ${h.js( "libs/jquery/jquery", "libs/bootstrap", "galaxy.base", "libs/json2", "libs/jquery/jstorage", "libs/jquery/jquery.autocomplete", "libs/jquery/jquery.rating", 
             "autocomplete_tagging", "viz/trackster", "viz/trackster_ui", "libs/jquery/jquery.event.drag", "libs/jquery/jquery.mousewheel", 
-            "libs/jquery/jquery.autocomplete", "libs/jquery/jquery.ui.sortable.slider", "farbtastic", "mvc/data", "viz/visualization" )}
+            "libs/jquery/jquery.autocomplete", "libs/jquery/jquery.ui.sortable.slider", "libs/farbtastic", "mvc/data", "viz/visualization" )}
 
     <script type="text/javascript">
         
diff --git a/templates/history/view.mako b/templates/history/view.mako
index 56e17d8386d..57a94cb3fe2 100644
--- a/templates/history/view.mako
+++ b/templates/history/view.mako
@@ -13,7 +13,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "galaxy.base", "libs/jquery/jquery", "json2", "libs/jquery/jstorage" )}
+    ${h.js( "galaxy.base", "libs/jquery/jquery", "libs/json2", "libs/jquery/jstorage" )}
     <script type="text/javascript">
         $(function() {
             init_history_items( $("div.historyItemWrapper"), false, "nochanges" );
diff --git a/templates/library/common/browse_library.mako b/templates/library/common/browse_library.mako
index ffa3445f696..68029124c20 100644
--- a/templates/library/common/browse_library.mako
+++ b/templates/library/common/browse_library.mako
@@ -48,7 +48,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js("json2")}
+    ${h.js("libs/json2")}
     ${h.js("libs/jquery/jstorage")}
     ${common_javascripts()}
     ${self.grid_javascripts()}
diff --git a/templates/page/editor.mako b/templates/page/editor.mako
index ae68886515e..f82c9d920e5 100644
--- a/templates/page/editor.mako
+++ b/templates/page/editor.mako
@@ -21,7 +21,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "libs/jquery/jquery.event.drag", "libs/jquery/jquery.event.drop", "libs/jquery/jquery.event.hover", "libs/jquery/jquery.form", "json2", "libs/jquery/jstorage",
+    ${h.js( "libs/jquery/jquery.event.drag", "libs/jquery/jquery.event.drop", "libs/jquery/jquery.event.hover", "libs/jquery/jquery.form", "libs/json2", "libs/jquery/jstorage",
             "galaxy.base", "libs/jquery/jquery.wymeditor", "libs/jquery/jquery.autocomplete", "autocomplete_tagging")}    
     <script type="text/javascript">
             
diff --git a/templates/root/history.mako b/templates/root/history.mako
index 4eb4b8dff63..6d4cf9f7b64 100644
--- a/templates/root/history.mako
+++ b/templates/root/history.mako
@@ -17,7 +17,7 @@
 <meta http-equiv="Pragma" content="no-cache">
 
 ${h.css( "base", "history", "autocomplete_tagging" )}
-${h.js( "libs/jquery/jquery", "bootstrap", "galaxy.base", "json2", "libs/jquery/jstorage", "libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
+${h.js( "libs/jquery/jquery", "libs/bootstrap", "galaxy.base", "libs/json2", "libs/jquery/jstorage", "libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
 
 <script type="text/javascript">
 
diff --git a/templates/root/tool_menu.mako b/templates/root/tool_menu.mako
index 26b68d6d38d..958b11adbd7 100644
--- a/templates/root/tool_menu.mako
+++ b/templates/root/tool_menu.mako
@@ -17,7 +17,7 @@
 <%def name="javascripts()">
     ${parent.javascripts()}
     ${h.templates( "tool_link", "panel_section", "tool_search" )}
-    ${h.js( "galaxy.base", "json2", "autocomplete_tagging", "mvc/tools", "bootstrap" )}
+    ${h.js( "galaxy.base", "libs/json2", "autocomplete_tagging", "mvc/tools", "libs/bootstrap" )}
     
     <%
         # Set up for creating tool panel.
diff --git a/templates/tracks/browser.mako b/templates/tracks/browser.mako
index 59a5e3e3b16..8fb392eed76 100644
--- a/templates/tracks/browser.mako
+++ b/templates/tracks/browser.mako
@@ -18,10 +18,10 @@
 ${parent.javascripts()}
 
 <!--[if lt IE 9]>
-  <script type='text/javascript' src="${h.url_for('/static/scripts/excanvas.js')}"></script>
+  <script type='text/javascript' src="${h.url_for('/static/scripts/libs/IE/excanvas.js')}"></script>
 <![endif]-->
 
-${h.js( "galaxy.base", "galaxy.panels", "json2", "libs/jquery/jquery", "bootstrap", "libs/jquery/jstorage", "libs/jquery/jquery.event.drag", "libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel", "libs/jquery/jquery.autocomplete", "mvc/data", "viz/visualization", "viz/trackster", "viz/trackster_ui", "libs/jquery/jquery.ui.sortable.slider", "farbtastic" )}
+${h.js( "galaxy.base", "galaxy.panels", "libs/json2", "libs/jquery/jquery", "libs/bootstrap", "libs/jquery/jstorage", "libs/jquery/jquery.event.drag", "libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel", "libs/jquery/jquery.autocomplete", "mvc/data", "viz/visualization", "viz/trackster", "viz/trackster_ui", "libs/jquery/jquery.ui.sortable.slider", "libs/farbtastic" )}
 
 <script type="text/javascript">
     //
diff --git a/templates/visualization/display.mako b/templates/visualization/display.mako
index bd6b250ad92..9d92afc2494 100644
--- a/templates/visualization/display.mako
+++ b/templates/visualization/display.mako
@@ -15,7 +15,7 @@
     </script>
     
     <!--[if lt IE 9]>
-      <script type='text/javascript' src="${h.url_for('/static/scripts/excanvas.js')}"></script>
+      <script type='text/javascript' src="${h.url_for('/static/scripts/libs/IE/excanvas.js')}"></script>
     <![endif]-->
 </%def>
 
diff --git a/templates/workflow/editor.mako b/templates/workflow/editor.mako
index b6ef46d6425..1d8e7b75f45 100644
--- a/templates/workflow/editor.mako
+++ b/templates/workflow/editor.mako
@@ -22,16 +22,16 @@
     ${parent.javascripts()}
 
     <!--[if lt IE 9]>
-      <script type='text/javascript' src="${h.url_for('/static/scripts/excanvas.js')}"></script>
+      <script type='text/javascript' src="${h.url_for('/static/scripts/libs/IE/excanvas.js')}"></script>
     <![endif]-->
 
     ${h.js( "libs/jquery/jquery",
-            "bootstrap",
+            "libs/bootstrap",
             "libs/jquery/jquery.event.drag",
             "libs/jquery/jquery.event.drop",
             "libs/jquery/jquery.event.hover",
             "libs/jquery/jquery.form",
-            "json2",
+            "libs/json2",
             "libs/jquery/jstorage",
             "galaxy.base",
             "galaxy.workflow_editor.canvas",
diff --git a/templates/workflow/run.mako b/templates/workflow/run.mako
index b12790f05f1..1a62ab50ce2 100644
--- a/templates/workflow/run.mako
+++ b/templates/workflow/run.mako
@@ -2,7 +2,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "libs/jquery/jquery.autocomplete", "bootstrap" )}
+    ${h.js( "libs/jquery/jquery.autocomplete", "libs/bootstrap" )}
     <script type="text/javascript">
         $( function() {
             function show_tool_body(title){
diff --git a/tools/rgenetics/rgGRR.py b/tools/rgenetics/rgGRR.py
index 07da056b375..f6f5becb6de 100644
--- a/tools/rgenetics/rgGRR.py
+++ b/tools/rgenetics/rgGRR.py
@@ -187,9 +187,9 @@ SVG_HEADER = '''<?xml version="1.0" standalone="no"?>
      xmlns="http://www.w3.org/2000/svg" version="1.2"
      xmlns:xlink="http://www.w3.org/1999/xlink" viewBox="0 0 1280 800" onload="init()">
 
-  <script type="text/ecmascript" xlink:href="/static/scripts/checkbox_and_radiobutton.js"/>
-  <script type="text/ecmascript" xlink:href="/static/scripts/helper_functions.js"/>
-  <script type="text/ecmascript" xlink:href="/static/scripts/timer.js"/>
+  <script type="text/ecmascript" xlink:href="/static/scripts/rgenetics/checkbox_and_radiobutton.js"/>
+  <script type="text/ecmascript" xlink:href="/static/scripts/rgenetics/helper_functions.js"/>
+  <script type="text/ecmascript" xlink:href="/static/scripts/rgenetics/timer.js"/>
   <script type="text/ecmascript">
     <![CDATA[
       var checkBoxes = new Array();

From 2a4012e03deadcf430b8e6f83bbe3de40abde062 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Tue, 21 Aug 2012 17:08:35 -0400
Subject: [PATCH 16/16] Final JS reorg to rename and move files so that all
 files follow standard conventions.

---
 .../{autocomplete_tagging.js => galaxy.autocom_tagging.js}      | 0
 static/scripts/{ui.core.js => libs/jquery/jquery.ui.core.js}    | 0
 .../{autocomplete_tagging.js => galaxy.autocom_tagging.js}      | 0
 .../packed/{ui.core.js => libs/jquery/jquery.ui.core.js}        | 0
 templates/admin/data_admin/data_form.mako                       | 2 +-
 templates/admin/data_admin/generic_error.mako                   | 2 +-
 templates/admin/data_admin/local_data.mako                      | 2 +-
 templates/admin/requests/select_datasets_to_transfer.mako       | 2 +-
 templates/admin/tool_shed_repository/browse_repository.mako     | 2 +-
 .../admin/tool_shed_repository/browse_tool_dependency.mako      | 2 +-
 templates/dataset/edit_attributes.mako                          | 2 +-
 templates/display_base.mako                                     | 2 +-
 templates/grid_base.mako                                        | 2 +-
 templates/library/common/ldda_edit_info.mako                    | 2 +-
 templates/library/common/move_library_item.mako                 | 2 +-
 templates/library/common/upload.mako                            | 2 +-
 templates/page/editor.mako                                      | 2 +-
 templates/requests/common/create_request.mako                   | 2 +-
 templates/requests/common/find_samples.mako                     | 2 +-
 templates/root/history.mako                                     | 2 +-
 templates/root/tool_menu.mako                                   | 2 +-
 templates/webapps/community/repository/browse_repository.mako   | 2 +-
 templates/webapps/community/repository/upload.mako              | 2 +-
 templates/workflow/edit_attributes.mako                         | 2 +-
 templates/workflow/editor.mako                                  | 2 +-
 25 files changed, 21 insertions(+), 21 deletions(-)
 rename static/scripts/{autocomplete_tagging.js => galaxy.autocom_tagging.js} (100%)
 rename static/scripts/{ui.core.js => libs/jquery/jquery.ui.core.js} (100%)
 rename static/scripts/packed/{autocomplete_tagging.js => galaxy.autocom_tagging.js} (100%)
 rename static/scripts/packed/{ui.core.js => libs/jquery/jquery.ui.core.js} (100%)

diff --git a/static/scripts/autocomplete_tagging.js b/static/scripts/galaxy.autocom_tagging.js
similarity index 100%
rename from static/scripts/autocomplete_tagging.js
rename to static/scripts/galaxy.autocom_tagging.js
diff --git a/static/scripts/ui.core.js b/static/scripts/libs/jquery/jquery.ui.core.js
similarity index 100%
rename from static/scripts/ui.core.js
rename to static/scripts/libs/jquery/jquery.ui.core.js
diff --git a/static/scripts/packed/autocomplete_tagging.js b/static/scripts/packed/galaxy.autocom_tagging.js
similarity index 100%
rename from static/scripts/packed/autocomplete_tagging.js
rename to static/scripts/packed/galaxy.autocom_tagging.js
diff --git a/static/scripts/packed/ui.core.js b/static/scripts/packed/libs/jquery/jquery.ui.core.js
similarity index 100%
rename from static/scripts/packed/ui.core.js
rename to static/scripts/packed/libs/jquery/jquery.ui.core.js
diff --git a/templates/admin/data_admin/data_form.mako b/templates/admin/data_admin/data_form.mako
index dde487ff86d..000652ebd63 100644
--- a/templates/admin/data_admin/data_form.mako
+++ b/templates/admin/data_admin/data_form.mako
@@ -27,7 +27,7 @@
 </%def>
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
+    ${h.js("libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )}
 </%def>
 ##
 ## Override methods from base.mako and base_panels.mako
diff --git a/templates/admin/data_admin/generic_error.mako b/templates/admin/data_admin/generic_error.mako
index fd46c54c927..c0debdb4fd1 100644
--- a/templates/admin/data_admin/generic_error.mako
+++ b/templates/admin/data_admin/generic_error.mako
@@ -27,7 +27,7 @@
 </%def>
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
+    ${h.js("libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )}
 </%def>
 ##
 ## Override methods from base.mako and base_panels.mako
diff --git a/templates/admin/data_admin/local_data.mako b/templates/admin/data_admin/local_data.mako
index 256d9e47377..cba4f802deb 100644
--- a/templates/admin/data_admin/local_data.mako
+++ b/templates/admin/data_admin/local_data.mako
@@ -27,7 +27,7 @@
 </%def>
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
+    ${h.js("libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )}
 </%def>
 ##
 ## Override methods from base.mako and base_panels.mako
diff --git a/templates/admin/requests/select_datasets_to_transfer.mako b/templates/admin/requests/select_datasets_to_transfer.mako
index 011636ed718..44a43f9399f 100644
--- a/templates/admin/requests/select_datasets_to_transfer.mako
+++ b/templates/admin/requests/select_datasets_to_transfer.mako
@@ -8,7 +8,7 @@
    ${common_javascripts()}
 </%def>
 
-${h.js( "ui.core", "libs/jquery/jquery.cookie", "libs/jquery/jquery.dynatree" )}
+${h.js( "libs/jquery/jquery.ui.core", "libs/jquery/jquery.cookie", "libs/jquery/jquery.dynatree" )}
 ${h.css( "dynatree_skin/ui.dynatree" )}
 
 <script type="text/javascript">
diff --git a/templates/admin/tool_shed_repository/browse_repository.mako b/templates/admin/tool_shed_repository/browse_repository.mako
index 765670d0b19..f5420813256 100644
--- a/templates/admin/tool_shed_repository/browse_repository.mako
+++ b/templates/admin/tool_shed_repository/browse_repository.mako
@@ -9,7 +9,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "ui.core", "libs/jquery/jquery.dynatree" )}
+    ${h.js( "libs/jquery/jquery.ui.core", "libs/jquery/jquery.dynatree" )}
     ${browse_files(repository.name, repository.repo_files_directory(trans.app))}
 </%def>
 
diff --git a/templates/admin/tool_shed_repository/browse_tool_dependency.mako b/templates/admin/tool_shed_repository/browse_tool_dependency.mako
index b24d031e6ca..7a80d7e976d 100644
--- a/templates/admin/tool_shed_repository/browse_tool_dependency.mako
+++ b/templates/admin/tool_shed_repository/browse_tool_dependency.mako
@@ -9,7 +9,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "ui.core", "libs/jquery/jquery.dynatree" )}
+    ${h.js( "libs/jquery/jquery.ui.core", "libs/jquery/jquery.dynatree" )}
     ${browse_files(tool_dependency.name, tool_dependency.installation_directory( trans.app ))}
 </%def>
 
diff --git a/templates/dataset/edit_attributes.mako b/templates/dataset/edit_attributes.mako
index aae0f1682de..bf56e9bee31 100644
--- a/templates/dataset/edit_attributes.mako
+++ b/templates/dataset/edit_attributes.mako
@@ -11,7 +11,7 @@
 <%def name="javascripts()">
     ${parent.javascripts()}
     ${message_ns.javascripts()}
-    ${h.js( "galaxy.base", "libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
+    ${h.js( "galaxy.base", "libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )}
 </%def>
 
 <%def name="datatype( dataset, datatypes )">
diff --git a/templates/display_base.mako b/templates/display_base.mako
index bd9305d1dd0..a556138b756 100644
--- a/templates/display_base.mako
+++ b/templates/display_base.mako
@@ -33,7 +33,7 @@
 <%def name="javascripts()">
     ${parent.javascripts()}
     ${h.js( "libs/jquery/jquery", "libs/bootstrap", "galaxy.base", "libs/json2", "libs/jquery/jstorage", "libs/jquery/jquery.autocomplete", "libs/jquery/jquery.rating", 
-            "autocomplete_tagging", "viz/trackster", "viz/trackster_ui", "libs/jquery/jquery.event.drag", "libs/jquery/jquery.mousewheel", 
+            "galaxy.autocom_tagging", "viz/trackster", "viz/trackster_ui", "libs/jquery/jquery.event.drag", "libs/jquery/jquery.mousewheel", 
             "libs/jquery/jquery.autocomplete", "libs/jquery/jquery.ui.sortable.slider", "libs/farbtastic", "mvc/data", "viz/visualization" )}
 
     <script type="text/javascript">
diff --git a/templates/grid_base.mako b/templates/grid_base.mako
index 74c523db946..8c4f522d6f4 100644
--- a/templates/grid_base.mako
+++ b/templates/grid_base.mako
@@ -52,7 +52,7 @@
 </%def>
 
 <%def name="grid_javascripts()">
-    ${h.js("libs/jquery/jquery.autocomplete", "autocomplete_tagging", "libs/jquery/jquery.rating" )}
+    ${h.js("libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging", "libs/jquery/jquery.rating" )}
     <script type="text/javascript">
         // This is necessary so that, when nested arrays are used in ajax/post/get methods, square brackets ('[]') are
         // not appended to the identifier of a nested array.
diff --git a/templates/library/common/ldda_edit_info.mako b/templates/library/common/ldda_edit_info.mako
index 38311e5ea04..e28156bcecc 100644
--- a/templates/library/common/ldda_edit_info.mako
+++ b/templates/library/common/ldda_edit_info.mako
@@ -5,7 +5,7 @@
 
 <%def name="javascripts()">
    ${parent.javascripts()}
-   ${h.js("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
+   ${h.js("libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )}
 </%def>
 
 <%def name="stylesheets()">
diff --git a/templates/library/common/move_library_item.mako b/templates/library/common/move_library_item.mako
index 2f6c7483eec..43284dd2e60 100644
--- a/templates/library/common/move_library_item.mako
+++ b/templates/library/common/move_library_item.mako
@@ -3,7 +3,7 @@
 
 <%def name="javascripts()">
    ${parent.javascripts()}
-   ${h.js("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
+   ${h.js("libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )}
 </%def>
 
 <%def name="stylesheets()">
diff --git a/templates/library/common/upload.mako b/templates/library/common/upload.mako
index 769d2e1d74d..1f1b33bf981 100644
--- a/templates/library/common/upload.mako
+++ b/templates/library/common/upload.mako
@@ -13,7 +13,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
+    ${h.js("libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )}
 </%def>
 
 <%def name="stylesheets()">
diff --git a/templates/page/editor.mako b/templates/page/editor.mako
index f82c9d920e5..0a4c53f11da 100644
--- a/templates/page/editor.mako
+++ b/templates/page/editor.mako
@@ -22,7 +22,7 @@
 <%def name="javascripts()">
     ${parent.javascripts()}
     ${h.js( "libs/jquery/jquery.event.drag", "libs/jquery/jquery.event.drop", "libs/jquery/jquery.event.hover", "libs/jquery/jquery.form", "libs/json2", "libs/jquery/jstorage",
-            "galaxy.base", "libs/jquery/jquery.wymeditor", "libs/jquery/jquery.autocomplete", "autocomplete_tagging")}    
+            "galaxy.base", "libs/jquery/jquery.wymeditor", "libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging")}
     <script type="text/javascript">
             
     // Useful Galaxy stuff.
diff --git a/templates/requests/common/create_request.mako b/templates/requests/common/create_request.mako
index 550500857f8..e841a6f5630 100644
--- a/templates/requests/common/create_request.mako
+++ b/templates/requests/common/create_request.mako
@@ -3,7 +3,7 @@
 
 <%def name="javascripts()">
    ${parent.javascripts()}
-   ${h.js("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
+   ${h.js("libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )}
 </%def>
 
 <%def name="stylesheets()">
diff --git a/templates/requests/common/find_samples.mako b/templates/requests/common/find_samples.mako
index 83f52ba0d22..0617428fc49 100644
--- a/templates/requests/common/find_samples.mako
+++ b/templates/requests/common/find_samples.mako
@@ -3,7 +3,7 @@
 
 <%def name="javascripts()">
    ${parent.javascripts()}
-   ${h.js("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
+   ${h.js("libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )}
 </%def>
 
 <%def name="stylesheets()">
diff --git a/templates/root/history.mako b/templates/root/history.mako
index 6d4cf9f7b64..83ef56d4184 100644
--- a/templates/root/history.mako
+++ b/templates/root/history.mako
@@ -17,7 +17,7 @@
 <meta http-equiv="Pragma" content="no-cache">
 
 ${h.css( "base", "history", "autocomplete_tagging" )}
-${h.js( "libs/jquery/jquery", "libs/bootstrap", "galaxy.base", "libs/json2", "libs/jquery/jstorage", "libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
+${h.js( "libs/jquery/jquery", "libs/bootstrap", "galaxy.base", "libs/json2", "libs/jquery/jstorage", "libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )}
 
 <script type="text/javascript">
 
diff --git a/templates/root/tool_menu.mako b/templates/root/tool_menu.mako
index 958b11adbd7..0aa28c2199e 100644
--- a/templates/root/tool_menu.mako
+++ b/templates/root/tool_menu.mako
@@ -17,7 +17,7 @@
 <%def name="javascripts()">
     ${parent.javascripts()}
     ${h.templates( "tool_link", "panel_section", "tool_search" )}
-    ${h.js( "galaxy.base", "libs/json2", "autocomplete_tagging", "mvc/tools", "libs/bootstrap" )}
+    ${h.js( "galaxy.base", "libs/json2", "galaxy.autocom_tagging", "mvc/tools", "libs/bootstrap" )}
     
     <%
         # Set up for creating tool panel.
diff --git a/templates/webapps/community/repository/browse_repository.mako b/templates/webapps/community/repository/browse_repository.mako
index 931eb9f97e5..25804b16cad 100644
--- a/templates/webapps/community/repository/browse_repository.mako
+++ b/templates/webapps/community/repository/browse_repository.mako
@@ -57,7 +57,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "libs/jquery/jquery.rating", "ui.core", "libs/jquery/jquery.cookie", "libs/jquery/jquery.dynatree" )}
+    ${h.js( "libs/jquery/jquery.rating", "libs/jquery/jquery.ui.core", "libs/jquery/jquery.cookie", "libs/jquery/jquery.dynatree" )}
     ${common_javascripts(repository)}
 </%def>
 
diff --git a/templates/webapps/community/repository/upload.mako b/templates/webapps/community/repository/upload.mako
index 45602e5e939..3cf779c465a 100644
--- a/templates/webapps/community/repository/upload.mako
+++ b/templates/webapps/community/repository/upload.mako
@@ -28,7 +28,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "ui.core", "libs/jquery/jquery.cookie", "libs/jquery/jquery.dynatree" )}
+    ${h.js( "libs/jquery/jquery.ui.core", "libs/jquery/jquery.cookie", "libs/jquery/jquery.dynatree" )}
     ${common_javascripts(repository)}
     <script type="text/javascript">
     $( function() {
diff --git a/templates/workflow/edit_attributes.mako b/templates/workflow/edit_attributes.mako
index 09f396a97cb..b707f4abe68 100644
--- a/templates/workflow/edit_attributes.mako
+++ b/templates/workflow/edit_attributes.mako
@@ -9,7 +9,7 @@
 
 <%def name="javascripts()">
     ${parent.javascripts()}
-    ${h.js( "galaxy.base", "libs/jquery/jquery.autocomplete", "autocomplete_tagging" )}
+    ${h.js( "galaxy.base", "libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )}
 </%def>
 
 %if msg:
diff --git a/templates/workflow/editor.mako b/templates/workflow/editor.mako
index 1d8e7b75f45..d3735a9c46c 100644
--- a/templates/workflow/editor.mako
+++ b/templates/workflow/editor.mako
@@ -36,7 +36,7 @@
             "galaxy.base",
             "galaxy.workflow_editor.canvas",
             "libs/jquery/jquery.autocomplete",
-            "autocomplete_tagging")}
+            "galaxy.autocom_tagging")}
 
     <!--[if lt IE 7]>
     <script type='text/javascript'>