diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py index 336317fa9fb..7d48aa6a577 100644 --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1508,7 +1508,7 @@ class DatasetInstance( object ): return msg -class HistoryDatasetAssociation( DatasetInstance, UsesAnnotations ): +class HistoryDatasetAssociation( DatasetInstance, DictifiableMixin, UsesAnnotations ): """ Resource class that creates a relation between a dataset and a user history. """ diff --git a/lib/galaxy/model/item_attrs.py b/lib/galaxy/model/item_attrs.py index dc197f06fce..d374fa40946 100644 --- a/lib/galaxy/model/item_attrs.py +++ b/lib/galaxy/model/item_attrs.py @@ -193,7 +193,7 @@ class DictifiableMixin: try: visible_keys = self.__getattribute__( 'dict_' + view + '_visible_keys' ) except AttributeError: - raise Exception( 'Unknown API view: %s' % view ) + raise Exception( 'Unknown DictifiableMixin view: %s' % view ) for key in visible_keys: try: item = self.__getattribute__( key ) diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py index 002fa6888e6..8184eee5e4a 100755 --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -59,6 +59,7 @@ from galaxy.util.odict import odict from galaxy.util.template import fill_template from galaxy.web import url_for from galaxy.web.form_builder import SelectField +from galaxy.model.item_attrs import DictifiableMixin from tool_shed.util import shed_util_common from .loader import load_tool, template_macro_params @@ -92,7 +93,7 @@ class StdioErrorLevel( object ): class ToolNotFoundException( Exception ): pass -class ToolBox( object ): +class ToolBox( object, DictifiableMixin ): """Container for a collection of tools""" def __init__( self, config_filenames, tool_root_dir, app ): @@ -701,7 +702,7 @@ class ToolBox( object ): """ return self.app.model.context - def to_dict( self, trans, in_panel=True, **kwds ): + def dictify( self, trans, in_panel=True, **kwds ): """ Dictify toolbox. """ @@ -722,11 +723,11 @@ class ToolBox( object ): # Produce panel. rval = [] for elt in panel_elts: - rval.append( elt.to_dict( trans, for_link=True ) ) + rval.append( elt.dictify( trans, link_details=True ) ) else: tools = [] for id, tool in self.tools_by_id.items(): - tools.append( tool.to_dict( trans, for_link=True ) ) + tools.append( tool.dictify( trans, link_details=True ) ) rval = tools return rval @@ -787,11 +788,14 @@ def _filter_for_panel( item, filters, context ): -class ToolSection( object ): +class ToolSection( object, DictifiableMixin ): """ A group of tools with similar type/purpose that will be displayed as a group in the user interface. """ + + dict_collection_visible_keys = ( 'id', 'name', 'version' ) + def __init__( self, elem=None ): f = lambda elem, val: elem is not None and elem.get( val ) or '' self.name = f( elem, 'name' ) @@ -807,27 +811,33 @@ class ToolSection( object ): copy.elems = self.elems.copy() return copy - def to_dict( self, trans, for_link=False ): + def dictify( self, trans, link_details=False ): """ Return a dict that includes section's attributes. """ + + section_dict = super( ToolSection, self ).dictify() section_elts = [] for key, val in self.elems.items(): - section_elts.append( val.to_dict( trans, for_link=for_link ) ) - return { 'type': 'section', 'id': self.id, 'name': self.name, 'version': self.version, 'elems': section_elts } + if isinstance( val, ToolSectionLabel ): + section_elts.append( val.dictify() ) + else: + section_elts.append( val.dictify( trans, link_details=link_details ) ) + section_dict[ 'elems' ] = section_elts -class ToolSectionLabel( object ): + return section_dict + +class ToolSectionLabel( object, DictifiableMixin ): """ A label for a set of tools that can be displayed above groups of tools and sections in the user interface """ + + dict_collection_visible_keys = ( 'id', 'text', 'version' ) + def __init__( self, elem ): self.text = elem.get( "text" ) self.id = elem.get( "id" ) self.version = elem.get( "version" ) or '' - def to_dict( self, trans, **kwargs ): - """ Return a dict that includes label's attributes. """ - return { 'type': 'label', 'id': self.id, 'name': self.text, 'version': self.version } - class DefaultToolState( object ): """ Keeps track of the state of a users interaction with a tool between @@ -874,7 +884,7 @@ class DefaultToolState( object ): self.rerun_remap_job_id = None self.inputs = params_from_strings( tool.inputs, values, app, ignore_errors=True ) -class ToolOutput( object ): +class ToolOutput( object, DictifiableMixin ): """ Represents an output datasets produced by a tool. For backward compatibility this behaves as if it were the tuple:: @@ -882,6 +892,8 @@ class ToolOutput( object ): (format, metadata_source, parent) """ + dict_collection_visible_keys = ( 'name', 'format', 'label', 'hidden' ) + def __init__( self, name, format=None, format_source=None, metadata_source=None, parent=None, label=None, filters = None, actions = None, hidden=False ): self.name = name @@ -912,14 +924,6 @@ class ToolOutput( object ): def __iter__( self ): return iter( ( self.format, self.metadata_source, self.parent ) ) - def to_dict( self ): - return { - 'name': self.name, - 'format': self.format, - 'label': self.label, - 'hidden': self.hidden - } - class ToolRequirement( object ): """ Represents an external requirement that must be available for the tool to run (for example, a program, package, or library). @@ -930,13 +934,14 @@ class ToolRequirement( object ): self.type = type self.version = version -class Tool( object ): +class Tool( object, DictifiableMixin ): """ Represents a computational tool that can be executed through Galaxy. """ tool_type = 'default' default_tool_action = DefaultToolAction + dict_collection_visible_keys = ( 'id', 'name', 'version', 'description' ) def __init__( self, config_file, root, app, guid=None, repository_id=None ): """Load a tool from the config named by `config_file`""" @@ -1225,7 +1230,6 @@ class Tool( object ): # Trackster configuration. trackster_conf = root.find( "trackster_conf" ) if trackster_conf is not None: - from galaxy.visualization.genome.visual_analytics import TracksterConfig self.trackster_conf = TracksterConfig.parse( trackster_conf ) else: self.trackster_conf = None @@ -2944,66 +2948,29 @@ class Tool( object ): self.sa_session.flush() return primary_datasets - def to_dict( self, trans, for_link=False, for_display=False ): + def dictify( self, trans, link_details=False, io_details=False ): """ Returns dict of tool. """ # Basic information - tool_dict = { 'id': self.id, 'name': self.name, - 'version': self.version, 'description': self.description } - - if for_link: - # Create tool link. + tool_dict = super( Tool, self ).dictify() + + # Add link details. + if link_details: + # Add details for creating a hyperlink to the tool. if not self.tool_type.startswith( 'data_source' ): link = url_for( '/tool_runner', tool_id=self.id ) else: link = url_for( self.action, **self.get_static_param_values( trans ) ) # Basic information - tool_dict.update( { 'type': 'tool', 'link': link, + tool_dict.update( { 'link': link, 'min_width': self.uihints.get( 'minwidth', -1 ), 'target': self.target } ) - if for_display: - # Dictify inputs. - inputs = [] - for name, input in self.inputs.items(): - param_dict = { 'name' : name, 'label' : input.label } - if isinstance( input, DataToolParameter ): - param_dict.update( { 'type' : 'data', 'html' : urllib.quote( input.get_html( trans ) ) } ) - elif isinstance( input, SelectToolParameter ): - # Get options, value. - options = input.get_options( trans, [] ) - value = options[0][1] - for option in options: - if option[2]: - # Found selected option. - value = option[1] - - # Pack input. - param_dict.update( { 'type' : 'select', - 'html' : urllib.quote( input.get_html( trans ) ), - 'options': options, - 'value': value - } ) - elif isinstance( input, Conditional ): - # TODO. - pass - elif isinstance( input, ( IntegerToolParameter, FloatToolParameter ) ): - param_dict.update( { 'type' : 'number', 'init_value' : input.value, - 'html' : urllib.quote( input.get_html( trans ) ), - 'min': input.min, - 'max': input.max, - 'value': input.value - } ) - else: - param_dict.update( { 'type' : '??', 'init_value' : input.value, \ - 'html' : urllib.quote( input.get_html( trans ) ) } ) - inputs.append( param_dict ) - - tool_dict[ 'inputs' ] = inputs - - # Dictify outputs. - pass + # Add input and output details. + if io_details: + tool_dict[ 'inputs' ] = [ input.dictify( trans ) for input in self.inputs.values() ] + tool_dict[ 'outputs' ] = [ output.dictify() for output in self.outputs.values() ] return tool_dict @@ -3240,6 +3207,31 @@ for tool_class in [ Tool, DataDestinationTool, SetMetadataTool, DataSourceTool, # ---- Utility classes to be factored out ----------------------------------- +class TracksterConfig: + """ Trackster configuration encapsulation. """ + + def __init__( self, actions ): + self.actions = actions + + @staticmethod + def parse( root ): + actions = [] + for action_elt in root.findall( "action" ): + actions.append( SetParamAction.parse( action_elt ) ) + return TracksterConfig( actions ) + +class SetParamAction: + """ Set parameter action. """ + + def __init__( self, name, output_name ): + self.name = name + self.output_name = output_name + + @staticmethod + def parse( elt ): + """ Parse action from element. """ + return SetParamAction( elt.get( "name" ), elt.get( "output_name" ) ) + class BadValue( object ): def __init__( self, value ): self.value = value diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py index 317876ce3d7..9fdd824f3d9 100644 --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -2,7 +2,7 @@ Basic tool parameters. """ -import logging, string, sys, os, os.path +import logging, string, sys, os, os.path, urllib from elementtree.ElementTree import XML, Element from galaxy import config, datatypes, util from galaxy.web import form_builder @@ -12,16 +12,19 @@ from sanitize import ToolParameterSanitizer import validation, dynamic_options # For BaseURLToolParameter from galaxy.web import url_for +from galaxy.model.item_attrs import DictifiableMixin import galaxy.model log = logging.getLogger(__name__) -class ToolParameter( object ): +class ToolParameter( object, DictifiableMixin ): """ Describes a parameter accepted by a tool. This is just a simple stub at the moment but in the future should encapsulate more complex parameters (lists of valid choices, validation logic, ...) """ + dict_collection_visible_keys = ( 'name', 'type', 'label', 'help' ) + def __init__( self, tool, param, context=None ): self.tool = tool self.refresh_on_change = False @@ -167,6 +170,15 @@ class ToolParameter( object ): for validator in self.validators: validator.validate( value, history ) + def dictify( self, trans, view='collection', value_mapper=None ): + """ Dictify tool parameter. This can be overridden by subclasses. """ + + tool_dict = super( ToolParameter, self ).dictify() + tool_dict[ 'html' ] = urllib.quote( self.get_html( trans ) ) + if hasattr( self, 'value' ): + tool_dict[ 'value' ] = self.value + return tool_dict + @classmethod def build( cls, tool, param ): """Factory method to create parameter of correct type""" @@ -223,6 +235,9 @@ class IntegerToolParameter( TextToolParameter ): ... ValueError: An integer is required """ + + dict_colletion_visible_keys = ToolParameter.dict_collection_visible_keys + ( 'min', 'max' ) + def __init__( self, tool, elem ): TextToolParameter.__init__( self, tool, elem ) if self.value: @@ -276,7 +291,7 @@ class IntegerToolParameter( TextToolParameter ): return int( self.value ) else: return None - + class FloatToolParameter( TextToolParameter ): """ Parameter that takes a real number value. @@ -293,6 +308,9 @@ class FloatToolParameter( TextToolParameter ): ... ValueError: A real number is required """ + + dict_collection_visible_keys = ToolParameter.dict_collection_visible_keys + ( 'min', 'max' ) + def __init__( self, tool, elem ): TextToolParameter.__init__( self, tool, elem ) self.min = elem.get( 'min' ) @@ -854,6 +872,24 @@ class SelectToolParameter( ToolParameter ): else: return [] + def dictify( self, trans, view='collection', value_mapper=None ): + d = super( SelectToolParameter, self ).dictify( trans ) + + # Get options, value. + options = self.get_options( trans, [] ) + value = options[0][1] + for option in options: + if option[2]: + # Found selected option. + value = option[1] + + d.update( { + 'options': options, + 'value': value + } ) + return d + + class GenomeBuildParameter( SelectToolParameter ): """ Select list that sets the last used genome build for the current history @@ -1680,7 +1716,7 @@ class DataToolParameter( ToolParameter ): if call_attribute: ref = ref() return ref - + class HiddenDataToolParameter( HiddenToolParameter, DataToolParameter ): """ Hidden parameter that behaves as a DataToolParameter. As with all hidden @@ -1689,6 +1725,7 @@ class HiddenDataToolParameter( HiddenToolParameter, DataToolParameter ): def __init__( self, tool, elem ): DataToolParameter.__init__( self, tool, elem ) self.value = "None" + self.type = "hidden_data" def get_initial_value( self, trans, context ): return None diff --git a/lib/galaxy/tools/parameters/grouping.py b/lib/galaxy/tools/parameters/grouping.py index aaaf5fc1c9a..8eaace4e1da 100644 --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -15,30 +15,44 @@ from galaxy.util import relpath from galaxy.util import sanitize_for_filename from galaxy.util.bunch import Bunch from galaxy.util.expressions import ExpressionContext +from galaxy.model.item_attrs import DictifiableMixin + +class Group( object, DictifiableMixin ): + + dict_collection_visible_keys = ( 'name', 'type' ) -class Group( object ): def __init__( self ): self.name = None + self.type = 'group' + @property def visible( self ): return True + def value_to_basic( self, value, app ): """ Convert value to a (possibly nested) representation using only basic types (dict, list, tuple, str, unicode, int, long, float, bool, None) """ return value + def value_from_basic( self, value, app, ignore_errors=False ): """ Convert a basic representation as produced by `value_to_basic` back into the preferred value form. """ return value + def get_initial_value( self, trans, context ): """ Return the initial state/value for this group """ raise TypeError( "Not implemented" ) + + def dictify( self, trans, view='collection', value_mapper=None ): + # TODO: need to dictify conditions. + group_dict = super( Group, self ).dictify( view=view, value_mapper=value_mapper ) + return group_dict class Repeat( Group ): type = "repeat" diff --git a/lib/galaxy/visualization/genome/visual_analytics.py b/lib/galaxy/visualization/genome/visual_analytics.py deleted file mode 100644 index de95e88d396..00000000000 --- a/lib/galaxy/visualization/genome/visual_analytics.py +++ /dev/null @@ -1,82 +0,0 @@ -import urllib - -from galaxy.tools.parameters.basic import IntegerToolParameter, FloatToolParameter, SelectToolParameter -from galaxy.tools.parameters.dynamic_options import DynamicOptions - -class TracksterConfig: - """ Trackster configuration encapsulation. """ - - def __init__( self, actions ): - self.actions = actions - - @staticmethod - def parse( root ): - actions = [] - for action_elt in root.findall( "action" ): - actions.append( SetParamAction.parse( action_elt ) ) - return TracksterConfig( actions ) - -class SetParamAction: - """ Set parameter action. """ - - def __init__( self, name, output_name ): - self.name = name - self.output_name = output_name - - @staticmethod - def parse( elt ): - """ Parse action from element. """ - return SetParamAction( elt.get( "name" ), elt.get( "output_name" ) ) - -def get_dataset_job( hda ): - # Get dataset's job. - job = None - for job_output_assoc in hda.creating_job_associations: - job = job_output_assoc.job - break - return job - -def get_tool_def( trans, hda ): - """ Returns definition of an interactive tool for an HDA. """ - - #FIXME: use tools.to_dict rather than custom code here. - - job = get_dataset_job( hda ) - # TODO: could use this assertion to provide more information. - # assert job is not None, 'Requested job has not been loaded.' - if not job: - return None - tool = trans.app.toolbox.get_tool( job.tool_id ) - # TODO: could use this assertion to provide more information. - # assert tool is not None, 'Requested tool has not been loaded.' - if not tool: - return None - - # Tool must have a Trackster configuration. - if not tool.trackster_conf: - return None - - # Get list of tool parameters that can be interactively modified. - tool_params = [] - tool_param_values = dict( [ ( p.name, p.value ) for p in job.parameters ] ) - tool_param_values = tool.params_from_strings( tool_param_values, trans.app, ignore_errors=True ) - for name, input in tool.inputs.items(): - if type( input ) == IntegerToolParameter or type( input ) == FloatToolParameter: - param_dict = { 'name' : name, 'label' : input.label, \ - 'value' : tool_param_values.get( name, input.value ), \ - 'type' : 'number', 'init_value' : input.value, - 'html' : urllib.quote( input.get_html() ) } - if input.min: - param_dict['min'] = input.min - if input.max: - param_dict['max'] = input.max - tool_params.append( param_dict ) - elif type( input ) == SelectToolParameter and type( input.options ) != DynamicOptions: - tool_params.append( { 'name' : name, 'label' : input.label, 'type' : 'select', \ - 'value' : tool_param_values.get( name, '' ), \ - 'html' : urllib.quote( input.get_html() ) } ) - - # If tool has parameters that can be interactively modified, return tool. - if len( tool_params ) != 0: - return { 'id': tool.id, 'name' : tool.name, 'inputs' : tool_params } - return None \ No newline at end of file diff --git a/lib/galaxy/visualization/genomes.py b/lib/galaxy/visualization/genomes.py index 003bf5fedb3..4ce035ba273 100644 --- a/lib/galaxy/visualization/genomes.py +++ b/lib/galaxy/visualization/genomes.py @@ -73,7 +73,7 @@ class Genome( object ): self.len_file = len_file self.twobit_file = twobit_file - def to_dict( self, num=None, chrom=None, low=None ): + def dictify( self, num=None, chrom=None, low=None ): """ Returns representation of self as a dictionary. """ @@ -289,7 +289,7 @@ class Genomes( object ): # Set up return value or log exception if genome not found for key. rval = None if genome: - rval = genome.to_dict( num=num, chrom=chrom, low=low ) + rval = genome.dictify( num=num, chrom=chrom, low=low ) else: log.exception( 'genome not found for key %s' % dbkey ) diff --git a/lib/galaxy/web/base/controller.py b/lib/galaxy/web/base/controller.py index ae87805e048..1dec55d6550 100644 --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -32,12 +32,12 @@ from galaxy.workflow.modules import module_factory from galaxy.model.orm import eagerload, eagerload_all from galaxy.security.validate_user_input import validate_publicname from galaxy.util.sanitize_html import sanitize_html +from galaxy.model.item_attrs import DictifiableMixin from galaxy.datatypes.interval import ChromatinInteractions from galaxy.datatypes.data import Text -from galaxy.model import ExtendedMetadata, ExtendedMetadataIndex, LibraryDatasetDatasetAssociation -from galaxy.visualization.genome.visual_analytics import get_tool_def +from galaxy.model import ExtendedMetadata, ExtendedMetadataIndex, LibraryDatasetDatasetAssociation,HistoryDatasetAssociation from galaxy.datatypes.display_applications import util as da_util from galaxy.datatypes.metadata import FileParameter @@ -704,6 +704,15 @@ class UsesHistoryDatasetAssociationMixin: return changed + def get_hda_job( self, hda ): + # Get dataset's job. + job = None + for job_output_assoc in hda.creating_job_associations: + job = job_output_assoc.job + break + return job + + class UsesLibraryMixin: @@ -1105,6 +1114,37 @@ class UsesVisualizationMixin( UsesHistoryDatasetAssociationMixin, UsesLibraryMix encoded_id = trans.security.encode_id( vis.id ) return { "vis_id": encoded_id, "url": url_for( controller='visualization', action=vis.type, id=encoded_id ) } + def get_tool_def( self, trans, hda ): + """ Returns definition of an interactive tool for an HDA. """ + + job = self.get_hda_job( hda ) + if not job: + return None + tool = trans.app.toolbox.get_tool( job.tool_id ) + if not tool: + return None + + # Tool must have a Trackster configuration. + if not tool.trackster_conf: + return None + + # Get tool definition and add input values from job. + tool_dict = tool.dictify( trans, io_details=True ) + inputs_dict = tool_dict[ 'inputs' ] + tool_param_values = dict( [ ( p.name, p.value ) for p in job.parameters ] ) + tool_param_values = tool.params_from_strings( tool_param_values, trans.app, ignore_errors=True ) + for t_input in inputs_dict: + # Add value to tool. + if 'name' in t_input: + name = t_input[ 'name' ] + if name in tool_param_values: + value = tool_param_values[ name ] + if isinstance( value, DictifiableMixin ): + value = value.dictify() + t_input[ 'value' ] = value + + return tool_dict + def get_visualization_config( self, trans, visualization ): """ Returns a visualization's configuration. Only works for trackster visualizations right now. """ config = None @@ -1137,7 +1177,7 @@ class UsesVisualizationMixin( UsesHistoryDatasetAssociationMixin, UsesLibraryMix "prefs": prefs, "mode": track_dict.get( 'mode', 'Auto' ), "filters": track_dict.get( 'filters', { 'filters' : track_data_provider.get_filters() } ), - "tool": get_tool_def( trans, dataset ), + "tool": self.get_tool_def( trans, dataset ), "tool_state": track_dict.get( 'tool_state', {} ) } @@ -1215,7 +1255,7 @@ class UsesVisualizationMixin( UsesHistoryDatasetAssociationMixin, UsesLibraryMix "dataset": trans.security.encode_dict_ids( dataset.dictify() ), "prefs": {}, "filters": { 'filters' : track_data_provider.get_filters() }, - "tool": get_tool_def( trans, dataset ), + "tool": self.get_tool_def( trans, dataset ), "tool_state": {} } diff --git a/lib/galaxy/webapps/galaxy/api/datasets.py b/lib/galaxy/webapps/galaxy/api/datasets.py index 6a60c065f11..e7457b55450 100644 --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -199,7 +199,7 @@ class DatasetsController( BaseAPIController, UsesVisualizationMixin, UsesHistory data_dict = self.app.genomes.reference( trans, dbkey=dataset.dbkey, chrom=chrom, low=low, high=high ) if data_dict: ref_seq = data_dict[ 'data' ] - + # Get and return data from data_provider. result = data_provider.get_data( chrom, int( low ), int( high ), int( start_val ), int( max_vals ), ref_seq=ref_seq, **kwargs ) diff --git a/lib/galaxy/webapps/galaxy/api/tools.py b/lib/galaxy/webapps/galaxy/api/tools.py index f8cd9ef5ac5..99aef8c68aa 100644 --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -1,6 +1,5 @@ from galaxy import web, util from galaxy.web.base.controller import BaseAPIController, UsesHistoryDatasetAssociationMixin, UsesVisualizationMixin -from galaxy.visualization.genome.visual_analytics import get_dataset_job from galaxy.visualization.genomes import GenomeRegion from galaxy.util.json import to_json_string, from_json_string from galaxy.visualization.data_providers.genome import * @@ -33,7 +32,7 @@ class ToolsController( BaseAPIController, UsesVisualizationMixin ): # Create return value. try: - return self.app.toolbox.to_dict( trans, in_panel=in_panel, trackster=trackster ) + return self.app.toolbox.dictify( trans, in_panel=in_panel, trackster=trackster ) except Exception, exc: log.error( 'could not convert toolbox to dictionary: %s', str( exc ), exc_info=True ) trans.response.status = 500 @@ -46,7 +45,7 @@ class ToolsController( BaseAPIController, UsesVisualizationMixin ): Returns tool information, including parameters and inputs. """ try: - return self.app.toolbox.tools_by_id[ id ].to_dict( trans, for_display=True ) + return self.app.toolbox.tools_by_id[ id ].dictify( trans, for_display=True ) except Exception, exc: log.error( 'could not convert tool (%s) to dictionary: %s', id, str( exc ), exc_info=True ) trans.response.status = 500 @@ -217,7 +216,7 @@ class ToolsController( BaseAPIController, UsesVisualizationMixin ): # job's previous parameters and incoming parameters. Incoming parameters # have priority. # - original_job = get_dataset_job( original_dataset ) + original_job = self.get_hda_job( original_dataset ) tool = trans.app.toolbox.get_tool( original_job.tool_id ) if not tool: return trans.app.model.Dataset.conversion_messages.NO_TOOL diff --git a/lib/galaxy/webapps/galaxy/controllers/visualization.py b/lib/galaxy/webapps/galaxy/controllers/visualization.py index 32d99173ea7..7a1c0a36fbc 100644 --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -14,7 +14,6 @@ from galaxy.datatypes.interval import Bed from galaxy.util.json import from_json_string from galaxy.util.sanitize_html import sanitize_html from galaxy.visualization.genomes import decode_dbkey -from galaxy.visualization.genome.visual_analytics import get_dataset_job from galaxy.visualization.data_providers.phyloviz import PhylovizDataProvider from galaxy.visualization.genomes import GenomeRegion @@ -865,7 +864,7 @@ class VisualizationController( BaseUIController, SharableMixin, UsesAnnotations, else: # Loading new visualization. dataset = self.get_hda_or_ldda( trans, hda_ldda, dataset_id ) - job = get_dataset_job( dataset ) + job = self.get_hda_job( dataset ) viz_config = { 'dataset_id': dataset_id, 'tool_id': job.tool_id, @@ -874,7 +873,7 @@ class VisualizationController( BaseUIController, SharableMixin, UsesAnnotations, # Add tool, dataset attributes to config based on id. tool = trans.app.toolbox.get_tool( viz_config[ 'tool_id' ] ) - viz_config[ 'tool' ] = tool.to_dict( trans, for_display=True ) + viz_config[ 'tool' ] = tool.dictify( trans, for_display=True ) viz_config[ 'dataset' ] = dataset.dictify() return trans.fill_template_mako( "visualization/sweepster.mako", config=viz_config ) diff --git a/static/scripts/mvc/tools.js b/static/scripts/mvc/tools.js index 5597100ef24..340921dd07e 100644 --- a/static/scripts/mvc/tools.js +++ b/static/scripts/mvc/tools.js @@ -268,12 +268,12 @@ var ToolCollection = Backbone.Collection.extend({ /** * Label or section header in tool panel. */ -var ToolPanelLabel = Backbone.Model.extend(VisibilityMixin); +var ToolSectionLabel = Backbone.Model.extend(VisibilityMixin); /** * Section of tool panel with elements (labels and tools). */ -var ToolPanelSection = Backbone.Model.extend({ +var ToolSection = Backbone.Model.extend({ defaults: { elems: [], open: false @@ -292,7 +292,7 @@ var ToolPanelSection = Backbone.Model.extend({ var all_hidden = true, cur_label; _.each(this.attributes.elems, function(elt) { - if (elt instanceof ToolPanelLabel) { + if (elt instanceof ToolSectionLabel) { cur_label = elt; cur_label.hide(); } @@ -315,7 +315,7 @@ var ToolPanelSection = Backbone.Model.extend({ } } }); -_.extend(ToolPanelSection.prototype, VisibilityMixin); +_.extend(ToolSection.prototype, VisibilityMixin); /** * Tool search that updates results when query is changed. Result value of null @@ -399,18 +399,20 @@ var ToolPanel = Backbone.Model.extend({ var self = this, // Helper to recursively parse tool panel. parse_elt = function(elt_dict) { - var type = elt_dict.type; - if (type === 'tool') { + var type = elt_dict.model_class; + // There are many types of tools; for now, anything that ends in 'Tool' + // is treated as a generic tool. + if ( type.indexOf('Tool') === type.length - 4 ) { return self.attributes.tools.get(elt_dict.id); } - else if (type === 'section') { + else if (type === 'ToolSection') { // Parse elements. var elems = _.map(elt_dict.elems, parse_elt); elt_dict.elems = elems; - return new ToolPanelSection(elt_dict); + return new ToolSection(elt_dict); } - else if (type === 'label') { - return new ToolPanelLabel(elt_dict); + else if (type === 'ToolSectionLabel') { + return new ToolSectionLabel(elt_dict); } }; @@ -419,7 +421,7 @@ var ToolPanel = Backbone.Model.extend({ clear_search_results: function() { this.get('layout').each(function(panel_elt) { - if (panel_elt instanceof ToolPanelSection) { + if (panel_elt instanceof ToolSection) { panel_elt.clear_search_results(); } else { @@ -438,7 +440,7 @@ var ToolPanel = Backbone.Model.extend({ var cur_label = null; this.get('layout').each(function(panel_elt) { - if (panel_elt instanceof ToolPanelLabel) { + if (panel_elt instanceof ToolSectionLabel) { cur_label = panel_elt; cur_label.hide(); } @@ -495,12 +497,12 @@ var ToolLinkView = BaseView.extend({ /** * Panel label/section header. */ -var ToolPanelLabelView = BaseView.extend({ +var ToolSectionLabelView = BaseView.extend({ tagName: 'div', - className: 'toolPanelLabel', + className: 'ToolSectionLabel', render: function() { - this.$el.append( $("").text(this.model.attributes.name) ); + this.$el.append( $("").text(this.model.attributes.text) ); return this; } }); @@ -508,7 +510,7 @@ var ToolPanelLabelView = BaseView.extend({ /** * Panel section. */ -var ToolPanelSectionView = BaseView.extend({ +var ToolSectionView = BaseView.extend({ tagName: 'div', className: 'toolSectionWrapper', template: Handlebars.templates.panel_section, @@ -528,8 +530,8 @@ var ToolPanelSectionView = BaseView.extend({ tool_view.render(); section_body.append(tool_view.$el); } - else if (elt instanceof ToolPanelLabel) { - var label_view = new ToolPanelLabelView({model: elt}); + else if (elt instanceof ToolSectionLabel) { + var label_view = new ToolSectionLabelView({model: elt}); label_view.render(); section_body.append(label_view.$el); } @@ -630,8 +632,8 @@ var ToolPanelView = Backbone.View.extend({ // Render panel. this.model.get('layout').each(function(panel_elt) { - if (panel_elt instanceof ToolPanelSection) { - var section_title_view = new ToolPanelSectionView({model: panel_elt}); + if (panel_elt instanceof ToolSection) { + var section_title_view = new ToolSectionView({model: panel_elt}); section_title_view.render(); self.$el.append(section_title_view.$el); } @@ -640,8 +642,8 @@ var ToolPanelView = Backbone.View.extend({ tool_view.render(); self.$el.append(tool_view.$el); } - else if (panel_elt instanceof ToolPanelLabel) { - var label_view = new ToolPanelLabelView({model: panel_elt}); + else if (panel_elt instanceof ToolSectionLabel) { + var label_view = new ToolSectionLabelView({model: panel_elt}); label_view.render(); self.$el.append(label_view.$el); } diff --git a/static/scripts/packed/libs/jquery/jstorage.js b/static/scripts/packed/libs/jquery/jstorage.js index 1e7c03881fd..87c2f5facff 100644 --- a/static/scripts/packed/libs/jquery/jstorage.js +++ b/static/scripts/packed/libs/jquery/jstorage.js @@ -1 +1 @@ -(function(f){if(!f||!(f.toJSON||Object.toJSON||window.JSON)){throw new Error("jQuery, MooTools or Prototype needs to be loaded before jStorage!")}var g={},d={jStorage:"{}"},h=null,j=0,l=f.toJSON||Object.toJSON||(window.JSON&&(JSON.encode||JSON.stringify)),e=f.evalJSON||(window.JSON&&(JSON.decode||JSON.parse))||function(m){return 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pkgName,pkgConfig,mapValue,nameParts,i,j,nameSegment,foundMap,foundI,foundStarMap,starI,baseParts=baseName&&baseName.split("/"),normalizedBaseParts=baseParts,map=config.map,starMap=map&&map["*"];if(name&&name.charAt(0)==="."){if(baseName){if(config.pkgs[baseName]){normalizedBaseParts=baseParts=[baseName]}else{normalizedBaseParts=baseParts.slice(0,baseParts.length-1)}name=normalizedBaseParts.concat(name.split("/"));trimDots(name);pkgConfig=config.pkgs[(pkgName=name[0])];name=name.join("/");if(pkgConfig&&name===pkgName+"/"+pkgConfig.main){name=pkgName}}else{if(name.indexOf("./")===0){name=name.substring(2)}}}if(applyMap&&(baseParts||starMap)&&map){nameParts=name.split("/");for(i=nameParts.length;i>0;i-=1){nameSegment=nameParts.slice(0,i).join("/");if(baseParts){for(j=baseParts.length;j>0;j-=1){mapValue=map[baseParts.slice(0,j).join("/")];if(mapValue){mapValue=mapValue[nameSegment];if(mapValue){foundMap=mapValue;foundI=i;break}}}}if(foundMap){break}if(!foundStarMap&&starMap&&starMap[nameSegment]){foundStarMap=starMap[nameSegment];starI=i}}if(!foundMap&&foundStarMap){foundMap=foundStarMap;foundI=starI}if(foundMap){nameParts.splice(0,foundI,foundMap);name=nameParts.join("/")}}return name}function removeScript(name){if(isBrowser){each(scripts(),function(scriptNode){if(scriptNode.getAttribute("data-requiremodule")===name&&scriptNode.getAttribute("data-requirecontext")===context.contextName){scriptNode.parentNode.removeChild(scriptNode);return true}})}}function hasPathFallback(id){var pathConfig=config.paths[id];if(pathConfig&&isArray(pathConfig)&&pathConfig.length>1){removeScript(id);pathConfig.shift();context.undef(id);context.require([id]);return true}}function makeModuleMap(name,parentModuleMap,isNormalized,applyMap){var url,pluginModule,suffix,index=name?name.indexOf("!"):-1,prefix=null,parentName=parentModuleMap?parentModuleMap.name:null,originalName=name,isDefine=true,normalizedName="";if(!name){isDefine=false;name="_@r"+(requireCounter+=1)}if(index!==-1){prefix=name.substring(0,index);name=name.substring(index+1,name.length)}if(prefix){prefix=normalize(prefix,parentName,applyMap);pluginModule=defined[prefix]}if(name){if(prefix){if(pluginModule&&pluginModule.normalize){normalizedName=pluginModule.normalize(name,function(name){return normalize(name,parentName,applyMap)})}else{normalizedName=normalize(name,parentName,applyMap)}}else{normalizedName=normalize(name,parentName,applyMap);url=context.nameToUrl(normalizedName)}}suffix=prefix&&!pluginModule&&!isNormalized?"_unnormalized"+(unnormalizedCounter+=1):"";return{prefix:prefix,name:normalizedName,parentMap:parentModuleMap,unnormalized:!!suffix,url:url,originalName:originalName,isDefine:isDefine,id:(prefix?prefix+"!"+normalizedName:normalizedName)+suffix}}function getModule(depMap){var id=depMap.id,mod=registry[id];if(!mod){mod=registry[id]=new context.Module(depMap)}return mod}function on(depMap,name,fn){var id=depMap.id,mod=registry[id];if(hasProp(defined,id)&&(!mod||mod.defineEmitComplete)){if(name==="defined"){fn(defined[id])}}else{getModule(depMap).on(name,fn)}}function onError(err,errback){var ids=err.requireModules,notified=false;if(errback){errback(err)}else{each(ids,function(id){var mod=registry[id];if(mod){mod.error=err;if(mod.events.error){notified=true;mod.emit("error",err)}}});if(!notified){req.onError(err)}}}function takeGlobalQueue(){if(globalDefQueue.length){apsp.apply(defQueue,[defQueue.length-1,0].concat(globalDefQueue));globalDefQueue=[]}}function makeRequire(mod,enableBuildCallback,altRequire){var relMap=mod&&mod.map,modRequire=makeContextModuleFunc(altRequire||context.require,relMap,enableBuildCallback);addRequireMethods(modRequire,context,relMap);modRequire.isBrowser=isBrowser;return modRequire}handlers={require:function(mod){return makeRequire(mod)},exports:function(mod){mod.usingExports=true;if(mod.map.isDefine){return(mod.exports=defined[mod.map.id]={})}},module:function(mod){return(mod.module={id:mod.map.id,uri:mod.map.url,config:function(){return(config.config&&config.config[mod.map.id])||{}},exports:defined[mod.map.id]})}};function removeWaiting(id){delete 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defined[id]}function modCheck(mod){mod.check()}function checkLoaded(){var map,modId,err,usingPathFallback,waitInterval=config.waitSeconds*1000,expired=waitInterval&&(context.startTime+waitInterval)0;i-=1){parentModule=syms.slice(0,i).join("/");pkg=pkgs[parentModule];parentPath=paths[parentModule];if(parentPath){if(isArray(parentPath)){parentPath=parentPath[0]}syms.splice(0,i,parentPath);break}else{if(pkg){if(moduleName===pkg.name){pkgPath=pkg.location+"/"+pkg.main}else{pkgPath=pkg.location}syms.splice(0,i,pkgPath);break}}}url=syms.join("/");url+=(ext||(/\?/.test(url)?"":".js"));url=(url.charAt(0)==="/"||url.match(/^[\w\+\.\-]+:/)?"":config.baseUrl)+url}return config.urlArgs?url+((url.indexOf("?")===-1?"?":"&")+config.urlArgs):url},load:function(id,url){req.load(context,id,url)},execCb:function(name,callback,args,exports){return callback.apply(exports,args)},onScriptLoad:function(evt){if(evt.type==="load"||(readyRegExp.test((evt.currentTarget||evt.srcElement).readyState))){interactiveScript=null;var data=getScriptData(evt);context.completeLoad(data.id)}},onScriptError:function(evt){var data=getScriptData(evt);if(!hasPathFallback(data.id)){return onError(makeError("scripterror","Script error",evt,[data.id]))}}})}req=requirejs=function(deps,callback,errback,optional){var context,config,contextName=defContextName;if(!isArray(deps)&&typeof deps!=="string"){config=deps;if(isArray(callback)){deps=callback;callback=errback;errback=optional}else{deps=[]}}if(config&&config.context){contextName=config.context}context=contexts[contextName];if(!context){context=contexts[contextName]=req.s.newContext(contextName)}if(config){context.configure(config)}return context.require(deps,callback,errback)};req.config=function(config){return req(config)};if(!require){require=req}req.version=version;req.jsExtRegExp=/^\/|:|\?|\.js$/;req.isBrowser=isBrowser;s=req.s={contexts:contexts,newContext:newContext};req({});addRequireMethods(req);if(isBrowser){head=s.head=document.getElementsByTagName("head")[0];baseElement=document.getElementsByTagName("base")[0];if(baseElement){head=s.head=baseElement.parentNode}}req.onError=function(err){throw err};req.load=function(context,moduleName,url){var config=(context&&context.config)||{},node;if(isBrowser){node=config.xhtml?document.createElementNS("http://www.w3.org/1999/xhtml","html:script"):document.createElement("script");node.type=config.scriptType||"text/javascript";node.charset="utf-8";node.async=true;node.setAttribute("data-requirecontext",context.contextName);node.setAttribute("data-requiremodule",moduleName);if(node.attachEvent&&!(node.attachEvent.toString&&node.attachEvent.toString().indexOf("[native 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interactiveScript}if(isBrowser){eachReverse(scripts(),function(script){if(!head){head=script.parentNode}dataMain=script.getAttribute("data-main");if(dataMain){if(!cfg.baseUrl){src=dataMain.split("/");mainScript=src.pop();subPath=src.length?src.join("/")+"/":"./";cfg.baseUrl=subPath;dataMain=mainScript}dataMain=dataMain.replace(jsSuffixRegExp,"");cfg.deps=cfg.deps?cfg.deps.concat(dataMain):[dataMain];return true}})}define=function(name,deps,callback){var node,context;if(typeof 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Error(msg+"\nhttp://requirejs.org/docs/errors.html#"+id);e.requireType=id;e.requireModules=requireModules;if(err){e.originalError=err}return e}if(typeof define!=="undefined"){return}if(typeof requirejs!=="undefined"){if(isFunction(requirejs)){return}cfg=requirejs;requirejs=undefined}if(typeof require!=="undefined"&&!isFunction(require)){cfg=require;require=undefined}function newContext(contextName){var inCheckLoaded,Module,context,handlers,checkLoadedTimeoutId,config={waitSeconds:7,baseUrl:"./",paths:{},pkgs:{},shim:{},config:{}},registry={},enabledRegistry={},undefEvents={},defQueue=[],defined={},urlFetched={},requireCounter=1,unnormalizedCounter=1;function trimDots(ary){var i,part;for(i=0;ary[i];i+=1){part=ary[i];if(part==="."){ary.splice(i,1);i-=1}else{if(part===".."){if(i===1&&(ary[2]===".."||ary[0]==="..")){break}else{if(i>0){ary.splice(i-1,2);i-=2}}}}}}function normalize(name,baseName,applyMap){var pkgName,pkgConfig,mapValue,nameParts,i,j,nameSegment,foundMap,foundI,foundStarMap,starI,baseParts=baseName&&baseName.split("/"),normalizedBaseParts=baseParts,map=config.map,starMap=map&&map["*"];if(name&&name.charAt(0)==="."){if(baseName){if(getOwn(config.pkgs,baseName)){normalizedBaseParts=baseParts=[baseName]}else{normalizedBaseParts=baseParts.slice(0,baseParts.length-1)}name=normalizedBaseParts.concat(name.split("/"));trimDots(name);pkgConfig=getOwn(config.pkgs,(pkgName=name[0]));name=name.join("/");if(pkgConfig&&name===pkgName+"/"+pkgConfig.main){name=pkgName}}else{if(name.indexOf("./")===0){name=name.substring(2)}}}if(applyMap&&map&&(baseParts||starMap)){nameParts=name.split("/");for(i=nameParts.length;i>0;i-=1){nameSegment=nameParts.slice(0,i).join("/");if(baseParts){for(j=baseParts.length;j>0;j-=1){mapValue=getOwn(map,baseParts.slice(0,j).join("/"));if(mapValue){mapValue=getOwn(mapValue,nameSegment);if(mapValue){foundMap=mapValue;foundI=i;break}}}}if(foundMap){break}if(!foundStarMap&&starMap&&getOwn(starMap,nameSegment)){foundStarMap=getOwn(starMap,nameSegment);starI=i}}if(!foundMap&&foundStarMap){foundMap=foundStarMap;foundI=starI}if(foundMap){nameParts.splice(0,foundI,foundMap);name=nameParts.join("/")}}return name}function removeScript(name){if(isBrowser){each(scripts(),function(scriptNode){if(scriptNode.getAttribute("data-requiremodule")===name&&scriptNode.getAttribute("data-requirecontext")===context.contextName){scriptNode.parentNode.removeChild(scriptNode);return true}})}}function hasPathFallback(id){var pathConfig=getOwn(config.paths,id);if(pathConfig&&isArray(pathConfig)&&pathConfig.length>1){removeScript(id);pathConfig.shift();context.require.undef(id);context.require([id]);return true}}function splitPrefix(name){var prefix,index=name?name.indexOf("!"):-1;if(index>-1){prefix=name.substring(0,index);name=name.substring(index+1,name.length)}return[prefix,name]}function makeModuleMap(name,parentModuleMap,isNormalized,applyMap){var url,pluginModule,suffix,nameParts,prefix=null,parentName=parentModuleMap?parentModuleMap.name:null,originalName=name,isDefine=true,normalizedName="";if(!name){isDefine=false;name="_@r"+(requireCounter+=1)}nameParts=splitPrefix(name);prefix=nameParts[0];name=nameParts[1];if(prefix){prefix=normalize(prefix,parentName,applyMap);pluginModule=getOwn(defined,prefix)}if(name){if(prefix){if(pluginModule&&pluginModule.normalize){normalizedName=pluginModule.normalize(name,function(name){return 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onError(err,errback){var ids=err.requireModules,notified=false;if(errback){errback(err)}else{each(ids,function(id){var mod=getOwn(registry,id);if(mod){mod.error=err;if(mod.events.error){notified=true;mod.emit("error",err)}}});if(!notified){req.onError(err)}}}function takeGlobalQueue(){if(globalDefQueue.length){apsp.apply(defQueue,[defQueue.length-1,0].concat(globalDefQueue));globalDefQueue=[]}}handlers={require:function(mod){if(mod.require){return mod.require}else{return(mod.require=context.makeRequire(mod.map))}},exports:function(mod){mod.usingExports=true;if(mod.map.isDefine){if(mod.exports){return mod.exports}else{return(mod.exports=defined[mod.map.id]={})}}},module:function(mod){if(mod.module){return mod.module}else{return(mod.module={id:mod.map.id,uri:mod.map.url,config:function(){var c,pkg=getOwn(config.pkgs,mod.map.id);c=pkg?getOwn(config.config,mod.map.id+"/"+pkg.main):getOwn(config.config,mod.map.id);return c||{}},exports:defined[mod.map.id]})}}};function cleanRegistry(id){delete registry[id];delete enabledRegistry[id]}function breakCycle(mod,traced,processed){var id=mod.map.id;if(mod.error){mod.emit("error",mod.error)}else{traced[id]=true;each(mod.depMaps,function(depMap,i){var depId=depMap.id,dep=getOwn(registry,depId);if(dep&&!mod.depMatched[i]&&!processed[depId]){if(getOwn(traced,depId)){mod.defineDep(i,defined[depId]);mod.check()}else{breakCycle(dep,traced,processed)}}});processed[id]=true}}function checkLoaded(){var map,modId,err,usingPathFallback,waitInterval=config.waitSeconds*1000,expired=waitInterval&&(context.startTime+waitInterval)1)){ext=moduleNamePlusExt.substring(index,moduleNamePlusExt.length);moduleNamePlusExt=moduleNamePlusExt.substring(0,index)}return context.nameToUrl(normalize(moduleNamePlusExt,relMap&&relMap.id,true),ext,true)},defined:function(id){return hasProp(defined,makeModuleMap(id,relMap,false,true).id)},specified:function(id){id=makeModuleMap(id,relMap,false,true).id;return hasProp(defined,id)||hasProp(registry,id)}});if(!relMap){localRequire.undef=function(id){takeGlobalQueue();var map=makeModuleMap(id,relMap,true),mod=getOwn(registry,id);delete defined[id];delete urlFetched[map.url];delete undefEvents[id];if(mod){if(mod.events.defined){undefEvents[id]=mod.events}cleanRegistry(id)}}}return localRequire},enable:function(depMap){var mod=getOwn(registry,depMap.id);if(mod){getModule(depMap).enable()}},completeLoad:function(moduleName){var found,args,mod,shim=getOwn(config.shim,moduleName)||{},shExports=shim.exports;takeGlobalQueue();while(defQueue.length){args=defQueue.shift();if(args[0]===null){args[0]=moduleName;if(found){break}found=true}else{if(args[0]===moduleName){found=true}}callGetModule(args)}mod=getOwn(registry,moduleName);if(!found&&!hasProp(defined,moduleName)&&mod&&!mod.inited){if(config.enforceDefine&&(!shExports||!getGlobal(shExports))){if(hasPathFallback(moduleName)){return}else{return onError(makeError("nodefine","No define call for 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config.urlArgs?url+((url.indexOf("?")===-1?"?":"&")+config.urlArgs):url},load:function(id,url){req.load(context,id,url)},execCb:function(name,callback,args,exports){return callback.apply(exports,args)},onScriptLoad:function(evt){if(evt.type==="load"||(readyRegExp.test((evt.currentTarget||evt.srcElement).readyState))){interactiveScript=null;var data=getScriptData(evt);context.completeLoad(data.id)}},onScriptError:function(evt){var data=getScriptData(evt);if(!hasPathFallback(data.id)){return onError(makeError("scripterror","Script error for: "+data.id,evt,[data.id]))}}};context.require=context.makeRequire();return context}req=requirejs=function(deps,callback,errback,optional){var context,config,contextName=defContextName;if(!isArray(deps)&&typeof deps!=="string"){config=deps;if(isArray(callback)){deps=callback;callback=errback;errback=optional}else{deps=[]}}if(config&&config.context){contextName=config.context}context=getOwn(contexts,contextName);if(!context){context=contexts[contextName]=req.s.newContext(contextName)}if(config){context.configure(config)}return context.require(deps,callback,errback)};req.config=function(config){return req(config)};req.nextTick=typeof setTimeout!=="undefined"?function(fn){setTimeout(fn,4)}:function(fn){fn()};if(!require){require=req}req.version=version;req.jsExtRegExp=/^\/|:|\?|\.js$/;req.isBrowser=isBrowser;s=req.s={contexts:contexts,newContext:newContext};req({});each(["toUrl","undef","defined","specified"],function(prop){req[prop]=function(){var ctx=contexts[defContextName];return ctx.require[prop].apply(ctx,arguments)}});if(isBrowser){head=s.head=document.getElementsByTagName("head")[0];baseElement=document.getElementsByTagName("base")[0];if(baseElement){head=s.head=baseElement.parentNode}}req.onError=defaultOnError;req.createNode=function(config,moduleName,url){var node=config.xhtml?document.createElementNS("http://www.w3.org/1999/xhtml","html:script"):document.createElement("script");node.type=config.scriptType||"text/javascript";node.charset="utf-8";node.async=true;return node};req.load=function(context,moduleName,url){var config=(context&&context.config)||{},node;if(isBrowser){node=req.createNode(config,moduleName,url);node.setAttribute("data-requirecontext",context.contextName);node.setAttribute("data-requiremodule",moduleName);if(node.attachEvent&&!(node.attachEvent.toString&&node.attachEvent.toString().indexOf("[native code")<0)&&!isOpera){useInteractive=true;node.attachEvent("onreadystatechange",context.onScriptLoad)}else{node.addEventListener("load",context.onScriptLoad,false);node.addEventListener("error",context.onScriptError,false)}node.src=url;currentlyAddingScript=node;if(baseElement){head.insertBefore(node,baseElement)}else{head.appendChild(node)}currentlyAddingScript=null;return node}else{if(isWebWorker){try{importScripts(url);context.completeLoad(moduleName)}catch(e){context.onError(makeError("importscripts","importScripts failed for "+moduleName+" at "+url,e,[moduleName]))}}}};function getInteractiveScript(){if(interactiveScript&&interactiveScript.readyState==="interactive"){return interactiveScript}eachReverse(scripts(),function(script){if(script.readyState==="interactive"){return(interactiveScript=script)}});return interactiveScript}if(isBrowser){eachReverse(scripts(),function(script){if(!head){head=script.parentNode}dataMain=script.getAttribute("data-main");if(dataMain){mainScript=dataMain;if(!cfg.baseUrl){src=mainScript.split("/");mainScript=src.pop();subPath=src.length?src.join("/")+"/":"./";cfg.baseUrl=subPath}mainScript=mainScript.replace(jsSuffixRegExp,"");if(req.jsExtRegExp.test(mainScript)){mainScript=dataMain}cfg.deps=cfg.deps?cfg.deps.concat(mainScript):[mainScript];return true}})}define=function(name,deps,callback){var node,context;if(typeof name!=="string"){callback=deps;deps=name;name=null}if(!isArray(deps)){callback=deps;deps=null}if(!deps&&isFunction(callback)){deps=[];if(callback.length){callback.toString().replace(commentRegExp,"").replace(cjsRequireRegExp,function(match,dep){deps.push(dep)});deps=(callback.length===1?["require"]:["require","exports","module"]).concat(deps)}}if(useInteractive){node=currentlyAddingScript||getInteractiveScript();if(node){if(!name){name=node.getAttribute("data-requiremodule")}context=contexts[node.getAttribute("data-requirecontext")]}}(context?context.defQueue:globalDefQueue).push([name,deps,callback])};define.amd={jQuery:true};req.exec=function(text){return eval(text)};req(cfg)}(this)); \ No newline at end of file diff --git a/static/scripts/packed/mvc/tools.js b/static/scripts/packed/mvc/tools.js index 77fc89477b5..733efab4e2b 100644 --- a/static/scripts/packed/mvc/tools.js +++ b/static/scripts/packed/mvc/tools.js @@ -1 +1 @@ -define(["libs/underscore","viz/trackster/util","mvc/data","libs/backbone/backbone-relational"],function(t,a,u){var e={hidden:false,show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}};var d=Backbone.RelationalModel.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new d(this.toJSON())},get_samples:function(){var w=this.get("type"),v=null;if(w==="number"){v=d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}else{if(w==="select"){v=t.map(this.get("options"),function(x){return x[0]})}}return v},set_value:function(v){this.set("value",v||"")}},{TYPE_DICT:{number:c},create:function(v){var w=d.TYPE_DICT[v.type]||d;return new w(v)}});var c=d.extend({defaults:t.extend({},d.prototype.defaults,{min:null,max:null}),initialize:function(){d.prototype.initialize.call(this);if(this.attributes.min){this.attributes.min=parseInt(this.attributes.min,10)}if(this.attributes.max){this.attributes.max=parseInt(this.attributes.max,10)}},set_value:function(v){this.set("value",parseInt(v,10))}});var h=Backbone.RelationalModel.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[]},initialize:function(v){this.attributes.inputs=new Backbone.Collection(t.map(v.inputs,function(w){return d.create(w)}))},urlRoot:galaxy_config.root+"api/tools",copy:function(w){var x=new h(this.toJSON());if(w){var v=new Backbone.Collection();x.get("inputs").each(function(y){if(y.get_samples()){v.push(y)}});x.set("inputs",v)}return x},apply_search_results:function(v){(t.indexOf(v,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()},set_input_value:function(v,w){this.get("inputs").find(function(x){return x.get("name")===v}).set("value",w)},set_input_values:function(w){var v=this;t.each(t.keys(w),function(x){v.set_input_value(x,w[x])})},run:function(){return this._run()},rerun:function(w,v){return this._run({action:"rerun",target_dataset_id:w.id,regions:v})},get_inputs_dict:function(){var v={};this.get("inputs").each(function(w){v[w.get("name")]=w.get("value")});return v},_run:function(x){var y=t.extend({tool_id:this.id,inputs:this.get_inputs_dict()},x);var w=$.Deferred(),v=new a.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(y),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(z){return z!=="pending"}});$.when(v.go()).then(function(z){w.resolve(new u.DatasetCollection().reset(z))});return w}});t.extend(h.prototype,e);var n=Backbone.View.extend({});var k=Backbone.Collection.extend({model:h});var o=Backbone.Model.extend(e);var r=Backbone.Model.extend({defaults:{elems:[],open:false},clear_search_results:function(){t.each(this.attributes.elems,function(v){v.show()});this.show();this.set("open",false)},apply_search_results:function(w){var x=true,v;t.each(this.attributes.elems,function(y){if(y instanceof o){v=y;v.hide()}else{if(y instanceof h){if(y.apply_search_results(w)){x=false;if(v){v.show()}}}}});if(x){this.hide()}else{this.show();this.set("open",true)}}});t.extend(r.prototype,e);var b=Backbone.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:true,query:"",results:null,clear_key:27},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var x=this.attributes.query;if(x.length").text(this.model.attributes.name));return this}});var i=p.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){p.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var v=this.$el.find(".toolSectionBody");t.each(this.model.attributes.elems,function(w){if(w instanceof h){var x=new j({model:w,className:"toolTitle"});x.render();v.append(x.$el)}else{if(w instanceof o){var y=new f({model:w});y.render();v.append(y.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var m=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){this.$el.append(this.template(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}this.$el.find(".tooltip").tooltip();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(v){if((this.model.attributes.clear_key)&&(this.model.attributes.clear_key===v.which)){this.clear();return false}this.model.set("query",this.$el.find(":input").val())}});var s=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var v=this;var w=new m({model:this.model.get("tool_search")});w.render();v.$el.append(w.$el);this.model.get("layout").each(function(y){if(y instanceof r){var x=new i({model:y});x.render();v.$el.append(x.$el)}else{if(y instanceof h){var z=new j({model:y,className:"toolTitleNoSection"});z.render();v.$el.append(z.$el)}else{if(y instanceof o){var A=new f({model:y});A.render();v.$el.append(A.$el)}}}});v.$el.find("a.tool-link").click(function(z){var y=$(this).attr("class").split(/\s+/)[0],x=v.model.get("tools").get(y);v.trigger("tool_link_click",z,x)});return this},handle_search_results:function(){var v=this.model.get("tool_search").get("results");if(v&&v.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var q=Backbone.View.extend({className:"toolForm",template:Handlebars.templates.tool_form,render:function(){this.$el.children().remove();this.$el.append(this.template(this.model.toJSON()))}});var g=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new s({collection:this.collection});this.tool_form_view=new q()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$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.$el);var v=this;this.tool_panel_view.on("tool_link_click",function(x,w){x.preventDefault();v.show_tool(w)})},show_tool:function(w){var v=this;w.fetch().done(function(){v.tool_form_view.model=w;v.tool_form_view.render();v.tool_form_view.$el.show();$("#left").width("650px")})}});return{ToolParameter:d,IntegerToolParameter:c,Tool:h,ToolCollection:k,ToolSearch:b,ToolPanel:l,ToolPanelView:s,ToolFormView:q}}); \ No newline at end of file +define(["libs/underscore","viz/trackster/util","mvc/data","libs/backbone/backbone-relational"],function(t,a,u){var f={hidden:false,show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}};var e=Backbone.RelationalModel.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new e(this.toJSON())},get_samples:function(){var w=this.get("type"),v=null;if(w==="number"){v=d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}else{if(w==="select"){v=t.map(this.get("options"),function(x){return x[0]})}}return v},set_value:function(v){this.set("value",v||"")}},{TYPE_DICT:{number:d},create:function(v){var w=e.TYPE_DICT[v.type]||e;return new w(v)}});var d=e.extend({defaults:t.extend({},e.prototype.defaults,{min:null,max:null}),initialize:function(){e.prototype.initialize.call(this);if(this.attributes.min){this.attributes.min=parseInt(this.attributes.min,10)}if(this.attributes.max){this.attributes.max=parseInt(this.attributes.max,10)}},set_value:function(v){this.set("value",parseInt(v,10))}});var h=Backbone.RelationalModel.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[]},initialize:function(v){this.attributes.inputs=new Backbone.Collection(t.map(v.inputs,function(w){return e.create(w)}))},urlRoot:galaxy_config.root+"api/tools",copy:function(w){var x=new h(this.toJSON());if(w){var v=new Backbone.Collection();x.get("inputs").each(function(y){if(y.get_samples()){v.push(y)}});x.set("inputs",v)}return x},apply_search_results:function(v){(t.indexOf(v,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()},set_input_value:function(v,w){this.get("inputs").find(function(x){return x.get("name")===v}).set("value",w)},set_input_values:function(w){var v=this;t.each(t.keys(w),function(x){v.set_input_value(x,w[x])})},run:function(){return this._run()},rerun:function(w,v){return this._run({action:"rerun",target_dataset_id:w.id,regions:v})},get_inputs_dict:function(){var v={};this.get("inputs").each(function(w){v[w.get("name")]=w.get("value")});return v},_run:function(x){var y=t.extend({tool_id:this.id,inputs:this.get_inputs_dict()},x);var w=$.Deferred(),v=new a.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(y),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(z){return z!=="pending"}});$.when(v.go()).then(function(z){w.resolve(new u.DatasetCollection().reset(z))});return w}});t.extend(h.prototype,f);var n=Backbone.View.extend({});var k=Backbone.Collection.extend({model:h});var r=Backbone.Model.extend(f);var i=Backbone.Model.extend({defaults:{elems:[],open:false},clear_search_results:function(){t.each(this.attributes.elems,function(v){v.show()});this.show();this.set("open",false)},apply_search_results:function(w){var x=true,v;t.each(this.attributes.elems,function(y){if(y instanceof r){v=y;v.hide()}else{if(y instanceof h){if(y.apply_search_results(w)){x=false;if(v){v.show()}}}}});if(x){this.hide()}else{this.show();this.set("open",true)}}});t.extend(i.prototype,f);var c=Backbone.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:true,query:"",results:null,clear_key:27},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var x=this.attributes.query;if(x.length").text(this.model.attributes.text));return this}});var o=p.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){p.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var v=this.$el.find(".toolSectionBody");t.each(this.model.attributes.elems,function(w){if(w instanceof h){var x=new j({model:w,className:"toolTitle"});x.render();v.append(x.$el)}else{if(w instanceof r){var y=new b({model:w});y.render();v.append(y.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var m=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){this.$el.append(this.template(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}this.$el.find(".tooltip").tooltip();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(v){if((this.model.attributes.clear_key)&&(this.model.attributes.clear_key===v.which)){this.clear();return false}this.model.set("query",this.$el.find(":input").val())}});var s=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var v=this;var w=new m({model:this.model.get("tool_search")});w.render();v.$el.append(w.$el);this.model.get("layout").each(function(y){if(y instanceof i){var x=new o({model:y});x.render();v.$el.append(x.$el)}else{if(y instanceof h){var z=new j({model:y,className:"toolTitleNoSection"});z.render();v.$el.append(z.$el)}else{if(y instanceof r){var A=new b({model:y});A.render();v.$el.append(A.$el)}}}});v.$el.find("a.tool-link").click(function(z){var y=$(this).attr("class").split(/\s+/)[0],x=v.model.get("tools").get(y);v.trigger("tool_link_click",z,x)});return this},handle_search_results:function(){var v=this.model.get("tool_search").get("results");if(v&&v.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var q=Backbone.View.extend({className:"toolForm",template:Handlebars.templates.tool_form,render:function(){this.$el.children().remove();this.$el.append(this.template(this.model.toJSON()))}});var g=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new s({collection:this.collection});this.tool_form_view=new q()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$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.$el);var v=this;this.tool_panel_view.on("tool_link_click",function(x,w){x.preventDefault();v.show_tool(w)})},show_tool:function(w){var v=this;w.fetch().done(function(){v.tool_form_view.model=w;v.tool_form_view.render();v.tool_form_view.$el.show();$("#left").width("650px")})}});return{ToolParameter:e,IntegerToolParameter:d,Tool:h,ToolCollection:k,ToolSearch:c,ToolPanel:l,ToolPanelView:s,ToolFormView:q}}); \ No newline at end of file diff --git a/static/scripts/packed/viz/trackster/tracks.js b/static/scripts/packed/viz/trackster/tracks.js index f9f24c9dee6..c7fc4644388 100644 --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1 +1 @@ -define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools"],function(ac,w,j,s,L,h,X,R){var o=ac.extend;var l={};var i=function(ad,ae){l[ad.attr("id")]=ae};var k=function(ad,af,ah,ag){ah=".group";var ae={};l[ad.attr("id")]=ag;ad.bind("drag",{handle:"."+af,relative:true},function(ap,aq){var ao=$(this),au=$(this).parent(),al=au.children(),an=l[$(this).attr("id")],ak,aj,ar,ai,am;aj=$(this).parents(ah);if(aj.length!==0){ar=aj.position().top;ai=ar+aj.outerHeight();if(aq.offsetYai){$(this).insertAfter(aj);var at=l[aj.attr("id")];at.remove_drawable(an);at.container.add_drawable(an);return}}}aj=null;for(am=0;am=ar&&aq.offsetY<=ai){if(aq.offsetY-ar0?am-1:am))}}}).bind("dragstart",function(){ae["border-top"]=ad.css("border-top");ae["border-bottom"]=ad.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ae)})};var aa=16,G=9,D=20,z=100,I=12000,S=400,K=5000,v=100,m="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",Q=10,H=20,A=["Histogram","Line","Filled","Intensity"];function V(ae,ad){if(!ad){ad=0}var af=Math.pow(10,ad);return Math.round(ae*af)/af}var p=function(ae,ad,ag){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.name=ag.name;this.view=ae;this.container=ad;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ag.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=$("
").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("
"));this.header_div.dblclick(function(ah){ah.stopPropagation()});var af=this;this.container_div.hover(function(){af.icons_div.show()},function(){af.icons_div.hide()});$("
").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ad){if(ad.content_visible){ad.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ad.hide_contents();ad.content_visible=false}else{ad.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ad.content_visible=true;ad.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ae){var ag=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ad=function(){ae.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ad()}}};$(window).bind("keypress.check_enter_esc",af);show_modal("Configure",ae.config.build_form(),{Cancel:ag,OK:ad})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.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(ad){},to_dict:function(){},set_name:function(ad){this.old_name=this.name;this.name=ad;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 ad=this.view;this.container_div.hide(0,function(){$(this).remove();ad.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ae,aj,ai,ah,ad,ag){var af=this;this.action_icons[ae]=$("").attr("href","javascript:void(0);").attr("title",aj).addClass("icon-button").addClass(ai).tooltip().click(function(){ah(af)}).appendTo(this.icons_div);if(ag){this.action_icons[ae].hide()}},build_action_icons:function(ad){var af;for(var ae=0;ae").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ag){this.unpack_drawables(ag.drawables)}if("filters" in ag){var af=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ag.filters);af.parent_div.replaceWith(this.filters_manager.parent_div);if(ag.filters.visible){this.setup_multitrack_filtering()}}};o(P.prototype,p.prototype,y.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(ad){$(".bs-tooltip").remove();ad.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ad){if(ad.filters_manager.visible()){ad.filters_manager.clear_filters();ad._restore_filter_managers()}else{ad.setup_multitrack_filtering();ad.request_draw({clear_tile_cache:true})}ad.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ad=$("
").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ad)}return ad},build_header_div:function(){var ad=$("
").addClass("track-header");ad.append($("
").addClass(this.drag_handle_class));this.name_div=$("
").addClass("track-name").text(this.name).appendTo(ad);return ad},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var af=this.drawables.length;if(af===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(af===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var am,al,aj,ap=true,ah=this.drawables[0].get_type(),ad=0;for(am=0;am1&&ad===this.drawables.length){var aq={},ae;aj=this.drawables[0];for(al=0;al0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ad=0;ad0){this.saved_filters_managers=[];for(var ad=0;ad").addClass("top-container").appendTo(af);this.browser_content_div=$("
").addClass("content").css("position","relative").appendTo(af);this.bottom_container=$("
").addClass("bottom-container").appendTo(af);this.top_labeltrack=$("
").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("
").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ad);this.intro_div=$("
").addClass("intro").appendTo(this.viewport_container).hide();var ag=$("
").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ad.dbkey},function(ah){ac.each(ah,function(ai){ad.add_drawable(n(ai,ad,ad))})})});this.nav_labeltrack=$("
").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("
").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("
").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("
").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("
").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("
").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("
").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("
").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("
").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("").addClass("nav-input").hide().bind("keyup focusout",ae).appendTo(this.nav_controls);this.location_span=$("").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ad.location_span.hide();ad.chrom_select.hide();ad.nav_input.val(ad.chrom+":"+ad.low+"-"+ad.high);ad.nav_input.css("display","inline-block");ad.nav_input.select();ad.nav_input.focus();ad.nav_input.autocomplete({source:function(aj,ah){var ak=[],ai=$.map(ad.get_tracks(c),function(al){return al.data_manager.search_features(aj.term).success(function(am){ak=ak.concat(am)})});$.when.apply($,ai).done(function(){ah($.map(ak,function(al){return{label:al[0],value:al[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ad.zoom_out();ad.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ad.zoom_in();ad.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ad.change_chrom(ad.chrom_select.val())});this.browser_content_div.click(function(ah){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ah){ad.zoom_in(ah.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ah,ai){this.current_x=ai.offsetX}).bind("drag",function(ah,aj){var ak=aj.offsetX-this.current_x;this.current_x=aj.offsetX;var ai=Math.round(ak/ad.viewport_container.width()*(ad.max_high-ad.max_low));ad.move_delta(-ai)});this.overview_close.click(function(){ad.reset_overview()});this.viewport_container.bind("draginit",function(ah,ai){if(ah.clientX>ad.viewport_container.width()-16){return false}}).bind("dragstart",function(ah,ai){ai.original_low=ad.low;ai.current_height=ah.clientY;ai.current_x=ai.offsetX}).bind("drag",function(aj,al){var ah=$(this);var am=al.offsetX-al.current_x;var ai=ah.scrollTop()-(aj.clientY-al.current_height);ah.scrollTop(ai);al.current_height=aj.clientY;al.current_x=al.offsetX;var ak=Math.round(am/ad.viewport_container.width()*(ad.high-ad.low));ad.move_delta(ak)}).bind("mousewheel",function(aj,al,ai,ah){if(ai){ai*=50;var ak=Math.round(-ai/ad.viewport_container.width()*(ad.high-ad.low));ad.move_delta(ak)}});this.top_labeltrack.bind("dragstart",function(ah,ai){return $("
").css({height:ad.browser_content_div.height()+ad.top_labeltrack.height()+ad.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(al,am){$(am.proxy).css({left:Math.min(al.pageX,am.startX)-ad.container.offset().left,width:Math.abs(al.pageX-am.startX)});var ai=Math.min(al.pageX,am.startX)-ad.container.offset().left,ah=Math.max(al.pageX,am.startX)-ad.container.offset().left,ak=(ad.high-ad.low),aj=ad.viewport_container.width();ad.update_location(Math.round(ai/aj*ak)+ad.low,Math.round(ah/aj*ak)+ad.low)}).bind("dragend",function(am,an){var ai=Math.min(am.pageX,an.startX),ah=Math.max(am.pageX,an.startX),ak=(ad.high-ad.low),aj=ad.viewport_container.width(),al=ad.low;ad.low=Math.round(ai/aj*ak)+al;ad.high=Math.round(ah/aj*ak)+al;$(an.proxy).remove();ad.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}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ad.resize_window()},500)});$(document).bind("redraw",function(){ad.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ad){return this.config.values[ad.toLowerCase()+"_color"]||this.config.values.n_color}});o(Y.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ae,ag,ad,ah){if(this.timer){clearTimeout(this.timer)}if(ah){var af=this;this.timer=setTimeout(function(){af.trigger("navigate",ae+":"+ag+"-"+ad)},500)}else{view.trigger("navigate",ae+":"+ag+"-"+ad)}},update_location:function(ad,af){this.location_span.text(commatize(ad)+" - "+commatize(af));this.nav_input.val(this.chrom+":"+commatize(ad)+"-"+commatize(af));var ae=view.chrom_select.val();if(ae!==""){this.trigger_navigate(ae,view.low,view.high,true)}},load_chroms:function(af){af.num=v;var ad=this,ae=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:af,dataType:"json",success:function(ah){if(ah.chrom_info.length===0){return}if(ah.reference){ad.add_label_track(new B(ad))}ad.chrom_data=ah.chrom_info;var ak='';for(var aj=0,ag=ad.chrom_data.length;aj'+ai+""}if(ah.prev_chroms){ak+='"}if(ah.next_chroms){ak+='"}ad.chrom_select.html(ak);ad.chrom_start_index=ah.start_index;ae.resolve(ah.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ad.dbkey)}});return ae},change_chrom:function(ai,ae,ak){var af=this;if(!af.chrom_data){af.load_chroms_deferred.then(function(){af.change_chrom(ai,ae,ak)});return}if(!ai||ai==="None"){return}if(ai==="previous"){af.load_chroms({low:this.chrom_start_index-v});return}if(ai==="next"){af.load_chroms({low:this.chrom_start_index+v});return}var aj=$.grep(af.chrom_data,function(al,am){return al.chrom===ai})[0];if(aj===undefined){af.load_chroms({chrom:ai},function(){af.change_chrom(ai,ae,ak)});return}else{if(ai!==af.chrom){af.chrom=ai;af.chrom_select.val(af.chrom);af.max_high=aj.len-1;af.reset();for(var ah=0,ad=af.drawables.length;ahad.max_high){ad.high=ad.max_high;ad.low=ad.max_high-af}else{ad.high-=ag;ad.low-=ag}}ad.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ad.request_redraw()},200);var ae=ad.chrom_select.val();this.trigger_navigate(ae,ad.low,ad.high,true)},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);ad.init();this.changed();this.update_intro_div()},add_label_track:function(ad){ad.view=this;ad.init();this.label_tracks.push(ad)},remove_drawable:function(af,ae){y.prototype.remove_drawable.call(this,af);if(ae){var ad=this;af.container_div.hide(0,function(){$(this).remove();ad.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ae,af){var ad=this,ag=(af?[af]:ad.drawables);ac.each(ag,function(ah){var ai=ac.find(ad.tracks_to_be_redrawn,function(aj){return aj[0]===ah});if(ai){ai[1]=ae}else{ad.tracks_to_be_redrawn.push([ah,ae])}});if(!this.requested_redraw){requestAnimationFrame(function(){ad._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ad=this.low,ah=this.high;if(adthis.max_high){ah=this.max_high}var ae=this.high-this.low;if(this.high!==0&&ae").addClass("param-label").text(ag.get("label")).appendTo(af);var ae=$("
").addClass("param-input").html(ag.get("html")).appendTo(af);ae.find(":input").val(ag.get("value"));$("
").appendTo(af)},update_value:function(ad){this.model.set_value($(ad.target).val())}});var ab=Backbone.View.extend({render:function(){var ae=this;tool=this.model.get("tool"),parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ai){ai.stopPropagation()}).click(function(ai){ai.stopPropagation()}).bind("dblclick",function(ai){ai.stopPropagation()}).keydown(function(ai){ai.stopPropagation()});var af=$("
").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(aj){var ai=new t({model:aj});ai.render();parent_div.append(ai.$el)});parent_div.find("input").click(function(){$(this).select()});var ag=$("
").addClass("param-row").appendTo(parent_div);var ah=$("").attr("value","Run on complete dataset").appendTo(ag);var ad=$("").attr("value","Run on visible region").css("margin-left","3em").appendTo(ag);ad.click(function(){ae.run_on_region()});ah.click(function(){ae.run_on_dataset()})},update_params:function(){for(var ad=0;ad");var af;function ae(al,ah){for(var ap=0;ap").appendTo(ah);aw.append($("").addClass("icon-button arrow-circle").appendTo(av).attr("title","Set new random color").tooltip(),at=$("
").appendTo(av).hide(),ak=$("
").appendTo(at),ai=$("
").appendTo(at),am=$.farbtastic(ak,{width:100,height:100,callback:aq,color:au});av.append($("
").css("clear","both"));(function(ax){ao.click(function(){ax.setColor(j.get_random_color())})})(am)}else{aw.append($("").attr("id",aj).attr("name",aj).val(au))}}}}if(af.help){aw.append($("
").text(af.help))}}}ae(this.params,ad);return ad},update_from_form:function(ad){var af=this;var ae=false;$.each(this.params,function(ag,ai){if(!ai.hidden){var aj="param_"+ag;var ah=ad.find("#"+aj).val();if(ai.type==="bool"){ah=ad.find("#"+aj).is(":checked")}ae=af.set_param_value(ai.key,ah)||ae}});if(ae){this.onchange();this.track.changed()}}});var b=function(ad,ah,af,ae,ag){this.track=ad;this.region=ah;this.low=ah.get("start");this.high=ah.get("end");this.resolution=af;this.html_elt=$("
").append(ae).height($(ae).attr("height"));this.data=ag;this.stale=false};b.prototype.predisplay_actions=function(){};var M=function(ad,ah,af,ae,ag){b.call(this,ad,ah,af,ae,ag)};M.prototype.predisplay_actions=function(){};var O=function(ag,ao,ah,af,aj,aq,ak,ar,ae,an){b.call(this,ag,ao,ah,af,aj);this.mode=ak;this.all_slotted=ae;this.feature_mapper=an;this.has_icons=false;if(ar){this.has_icons=true;var al=this;af=this.html_elt.children()[0],message_div=$("
").addClass("tile-message").css({height:D-1,width:af.width}).prependTo(this.html_elt);var am=new w.GenomeRegion({chrom:ag.view.chrom,start:this.low,end:this.high}),ap=aj.length,ai=$("").addClass("icon more-down").attr("title","For speed, only the first "+ap+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ad=$("").addClass("icon more-across").attr("title","For speed, only the first "+ap+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ai.click(function(){al.stale=true;ag.data_manager.get_more_data(am,ag.mode,al.resolution,{},ag.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();ag.request_draw()}).dblclick(function(at){at.stopPropagation()});ad.click(function(){al.stale=true;ag.data_manager.get_more_data(am,ag.mode,al.resolution,{},ag.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();ag.request_draw()}).dblclick(function(at){at.stopPropagation()})}};o(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var ae=this,ad={};if(ae.mode!=="Pack"){return}$(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(ap){if(!this.hovered){return}var ak=$(this).offset(),ao=ap.pageX-ak.left,an=ap.pageY-ak.top,au=ae.feature_mapper.get_feature_data(ao,an),al=(au?au[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!al||$(this).attr("id")!==al.toString()){$(this).remove()}});if(au){var ag=ad[al];if(!ag){var al=au[0],aq={name:au[3],start:au[1],end:au[2],strand:au[4]},aj=ae.track.filters_manager.filters,ai;for(var am=0;am").attr("id",al).addClass("feature-popup"),av=$(""),at,ar,aw;for(at in aq){ar=aq[at];aw=$("").appendTo(av);$("
").appendTo(aw).text(at);$("").attr("align","left").appendTo(aw).text(typeof(ar)==="number"?V(ar,2):ar)}ag.append($("
").append(av));ad[al]=ag}ag.appendTo($(this).parents(".track-content").children(".overlay"));var ah=ao+parseInt(ae.html_elt.css("left"))-ag.width()/2,af=an+parseInt(ae.html_elt.css("top"))+7;ag.css("left",ah+"px").css("top",af+"px")}else{if(!ap.isPropagationStopped()){ap.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ap)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ae,ad,af){o(af,{drag_handle_class:"draghandle"});p.call(this,ae,ad,af);this.dataset=(af.dataset?new X.Dataset(af.dataset):null);this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in af?af.data_query_wait:K);this.data_manager=("data_manager" in af?af.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ae.dbkey,chroms_info:{chrom_info:ae.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("
").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in af)||af.resize){this.add_resize_handle()}}};o(f.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(ad){ad.view.set_overview(ad)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ad){if(ad.filters_manager.visible()){ad.filters_manager.clear_filters()}else{ad.filters_manager.init_filters()}ad.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ad){ad.dynamic_tool_div.toggle();if(ad.dynamic_tool_div.is(":visible")){ad.set_name(ad.name+ad.tool_region_and_parameters_str())}else{ad.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ad){var ag='Tool: <%= track.tool.name %>
Dataset: <%= track.name %>
Region(s): ',af=ac.template(ag,{track:ad});var ai=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(){var ak=$('select[name="regions"] option:selected').val(),am,aj=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),al=ac.map($(".bookmark"),function(an){return new w.GenomeRegion({from_str:$(an).children(".position").text()})});if(ak==="cur"){am=[aj]}else{if(ak==="bookmarks"){am=al}else{am=[aj].concat(al)}}hide_modal();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ad.dataset.id,hda_ldda:ad.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(am).toJSON())})},ah=function(aj){if((aj.keyCode||aj.which)===27){ai()}else{if((aj.keyCode||aj.which)===13){ae()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",af,{No:ai,Yes:ae})}},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 $("
").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ad=$("
");if(this.view.editor){this.drag_div=$("
").addClass(this.drag_handle_class).appendTo(ad)}this.name_div=$("
").addClass("track-name").appendTo(ad).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ad},set_dataset:function(ad){this.dataset=ad;this.data_manager.set("dataset",ad)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ad=this;var ag=false;var af=false;var ae=$("
");$(ad.container_div).hover(function(){if(ad.content_visible){ag=true;ae.show()}},function(){ag=false;if(!af){ae.hide()}});ae.hide().bind("dragstart",function(ah,ai){af=true;ai.original_height=$(ad.content_div).height()}).bind("drag",function(ai,aj){var ah=Math.min(Math.max(aj.original_height+aj.deltaY,ad.min_height_px),ad.max_height_px);$(ad.tiles_div).css("height",ah);ad.visible_height_px=(ad.max_height_px===ah?0:ah);ad.on_resize()}).bind("dragend",function(ah,ai){ad.tile_cache.clear();af=false;if(!ag){ae.hide()}ad.config.values.height=ad.visible_height_px;ad.changed()}).appendTo(ad.container_div)},set_display_modes:function(ag,aj){this.display_modes=ag;this.mode=(aj?aj:(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 ae=this,ah={};for(var af=0,ad=ae.display_modes.length;af").text("View error").click(function(){show_modal("Trackster Error","
"+ah.message+"
",{Close:hide_modal})}));ae.tiles_div.append($("").text(" "));ae.tiles_div.append($("").text("Try again").click(function(){ae.init(true)}))}}else{if(ah==="no converter"){ae.container_div.addClass("error");ae.tiles_div.text(J)}else{if(ah==="no data"||(ah.data!==undefined&&(ah.data===null||ah.data.length===0))){ae.container_div.addClass("nodata");ae.tiles_div.text(E)}else{if(ah==="pending"){ae.container_div.addClass("pending");ae.tiles_div.html(u);setTimeout(function(){ae.init()},ae.data_query_wait)}else{if(ah==="data"||ah.status==="data"){if(ah.valid_chroms){ae.valid_chroms=ah.valid_chroms;ae.update_icons()}ae.tiles_div.text(U);if(ae.view.chrom){ae.tiles_div.text("");ae.tiles_div.css("height",ae.visible_height_px+"px");ae.enabled=true;$.when.apply($,ae.predraw_init()).done(function(){ad.resolve();ae.container_div.removeClass("nodata error pending");ae.request_draw()})}else{ad.resolve()}}}}}}});this.update_icons();return ad},predraw_init:function(){var ad=this;return $.getJSON(ad.dataset.url(),{data_type:"data",stats:true,chrom:ad.view.chrom,low:0,high:ad.view.max_high,hda_ldda:ad.dataset.get("hda_ldda")},function(ae){ad.container_div.addClass("line-track");var ag=ae.data;if(ag&&ag.min&&ag.max){var af=ag.min,ah=ag.max;af=Math.floor(Math.min(0,Math.max(af,ag.mean-2*ag.sd)));ah=Math.ceil(Math.max(0,Math.min(ah,ag.mean+2*ag.sd)));ad.config.set_param_default_value("min_value",af);ad.config.set_param_default_value("max_value",ah);ad.prefs.min_value=af;ad.prefs.max_value=ah}})},get_drawables:function(){return this}});var N=function(af,ae,ah){f.call(this,af,ae,ah);var ad=this;k(ad.container_div,ad.drag_handle_class,".group",ad);this.filters_manager=new h.FiltersManager(this,("filters" in ah?ah.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ah.tool?new q({track:this,tool:ah.tool,tool_state:ah.tool_state}):null);this.tile_cache=new w.Cache(Q);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ag=new ab({model:this.tool});ag.render();this.dynamic_tool_div=ag.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("
").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("
").addClass("overlay").appendTo(this.content_div);if(ah.mode){this.change_mode(ah.mode)}};o(N.prototype,p.prototype,f.prototype,{action_icons_def:f.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(ad){$(".bs-tooltip").remove();ad.slotters[ad.view.resolution_px_b].max_rows*=2;ad.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ad){var ae=this.to_dict();o(ae,{data_manager:this.data_manager});var af=new this.constructor(this.view,ad,ae);af.change_mode(this.mode);af.enabled=this.enabled;return af},set_filters_manager:function(ad){this.filters_manager=ad;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ad=this;return $.getJSON(ad.dataset.url(),{data_type:"data",stats:true,chrom:ad.view.chrom,low:0,high:ad.view.max_high,hda_ldda:ad.dataset.get("hda_ldda")},function(ae){var ag=ae.data;if(isNaN(parseFloat(ad.prefs.min_value))||isNaN(parseFloat(ad.prefs.max_value))){var af=ag.min,ah=ag.max;af=Math.floor(Math.min(0,Math.max(af,ag.mean-2*ag.sd)));ah=Math.ceil(Math.max(0,Math.min(ah,ag.mean+2*ag.sd)));ad.prefs.min_value=af;ad.prefs.max_value=ah}})},change_mode:function(ae){var ad=this;ad.mode=ae;ad.config.values.mode=ae;if(ae==="Auto"){this.data_manager.clear()}ad.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ad.mode+")");return ad},update_icons:function(){var ad=this;if(ad.filters_available){ad.action_icons.filters_icon.show()}else{ad.action_icons.filters_icon.hide()}if(ad.tool){ad.action_icons.tools_icon.show();ad.action_icons.param_space_viz_icon.show()}else{ad.action_icons.tools_icon.hide();ad.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ae,ad){return ae+"_"+ad},request_draw:function(ad){if(ad&&ad.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ad,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ah=this.view.high,ak=ah-al,ae=this.view.container.width(),ap=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=(view.max_high-view.max_low)/ae;ap=1/ag}this.before_draw();this.tiles_div.children().addClass("remove");var ad=Math.floor(al/(ag*S)),am,ai,aj=[],ao=[];while((ad*S*ag)").text(ae.prefs[ad]).make_text_editable({num_cols:12,on_finish:function(ak){$(".bs-tooltip").remove();ae.config.set_param_value(ad,ak);ai()},help_text:"Set "+aj+" value"}).addClass("yaxislabel "+ah).css("color",this.prefs.label_color);this.container_div.prepend(af)}},postdraw_actions:function(ag,ah,aj,ad){var af=ac.filter(ag,function(ak){return(ak instanceof M)});if(af.length>0){this.max_height_px=0;var ae=this;ac.each(ag,function(ak){if(!(ak instanceof M)){ak.html_elt.remove();ae.draw_helper(ak.region,ak.resolution,aj,{force:true,mode:"Coverage"})}});ae._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ai=ac.find(ag,function(ak){return ak.has_icons});if(ai){ac.each(ag,function(ak){if(!ak.has_icons){ak.html_elt.css("padding-top",D)}})}}},get_mode:function(ad){return this.mode},update_auto_mode:function(ad){},_get_drawables:function(){return[this]},draw_helper:function(am,ag,ap,aq){if(!aq){aq={}}var ae=aq.force,ao=!(aq.data_fetch===false),aj=aq.mode||this.mode,af=this,ah=this._get_drawables(),an=this._gen_tile_cache_key(ap,am),ai=function(ar){return(ar&&"track" in ar)};var ak=(ae?undefined:af.tile_cache.get_elt(an));if(ak){if(ai(ak)){af.show_tile(ak,ap)}return ak}if(!ao){return null}var al=function(){var ar=(ac.find(A,function(au){return au===aj})?"Coverage":aj);var at=ac.map(ah,function(au){return au.data_manager.get_data(am,ar,ag,af.data_url_extra_params)});if(view.reference_track){at.push(view.reference_track.data_manager.get_data(am,aj,ag,view.reference_track.data_url_extra_params))}return at};var ad=$.Deferred();af.tile_cache.set_elt(an,ad);$.when.apply($,al()).then(function(){var ar=al(),ax=ar,aD;if(view.reference_track){aD=view.reference_track.data_manager.subset_entry(ar.pop(),am)}var ay=[],av=[];ac.each(ah,function(aI,aF){var aH=aI.mode,aG=ax[aF];if(aH==="Auto"){aH=aI.get_mode(aG);aI.update_auto_mode(aH)}ay.push(aH);av.push(aI.get_canvas_height(aG,aH,ap,at))});var aw=af.view.canvas_manager.new_canvas(),az=am.get("start"),aE=am.get("end"),au=0,at=Math.ceil((aE-az)*ap)+af.left_offset,aB=ac.max(av),aA;aw.width=at;aw.height=(aq.height||aB);var aC=aw.getContext("2d");aC.translate(af.left_offset,0);if(ah.length>1){aC.globalAlpha=0.5;aC.globalCompositeOperation="source-over"}ac.each(ah,function(aG,aF){aA=aG.draw_tile(ax[aF],aC,ay[aF],ag,am,ap,aD)});if(aA!==undefined){af.tile_cache.set_elt(an,aA);af.show_tile(aA,ap)}ad.resolve(aA)});return ad},get_canvas_height:function(ad,af,ag,ae){return this.visible_height_px},_draw_line_track_tile:function(ad,af,aj,ah,ai,ak){var ag=af.canvas,ae=new L.LinePainter(ad.data,ai.get("start"),ai.get("end"),this.prefs,aj);ae.draw(af,ag.width,ag.height,ak);return new M(this,ai,ah,ag,ad.data)},draw_tile:function(ad,ae,ai,ag,ah,aj,af){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(af,ai){var ae=this,ad=af.html_elt;af.predisplay_actions();var ah=(af.low-(this.is_overview?this.view.max_low:this.view.low))*ai;if(this.left_offset){ah-=this.left_offset}ad.css({position:"absolute",top:0,left:ah});if(ad.hasClass("remove")){ad.removeClass("remove")}else{this.tiles_div.append(ad)}af.html_elt.height("auto");this.max_height_px=Math.max(this.max_height_px,af.html_elt.height());af.html_elt.parent().children().css("height",this.max_height_px+"px");var ag=this.max_height_px;if(this.visible_height_px!==0){ag=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ag+"px")},_get_tile_bounds:function(ad,ae){var ag=Math.floor(ad*S*ae),ah=Math.ceil(S*ae),af=(ag+ah<=this.view.max_high?ag+ah:this.view.max_high);return new w.GenomeRegion({chrom:this.view.chrom,start:ag,end:af})},tool_region_and_parameters_str:function(ag){var ad=this,af=(ag!==undefined?ag.toString():"all"),ae=ac.values(ad.tool.get("tool").get_inputs_dict()).join(", ");return" - region=["+af+"], parameters=["+ae+"]"},data_and_mode_compatible:function(ad,ae){if(ae==="Auto"){return true}else{if(ae==="Coverage"){return ad.dataset_type==="bigwig"}else{if(ad.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ad){if(ad.dataset_type==="bigwig"||ad.message||ad.extra_info==="no_detail"){return false}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(af,ag,ai,ad){var ae=this;ae.normal_postdraw_actions(af,ag,ai,ad);ae.dataset_check_type="converted_datasets_state";ae.data_query_wait=K;var ah=new j.ServerStateDeferred({url:ae.dataset_state_url,url_params:{dataset_id:ae.dataset.id,hda_ldda:ae.dataset.get("hda_ldda")},interval:ae.data_query_wait,success_fn:function(aj){return aj!=="pending"}});$.when(ah.go()).then(function(){ae.data_manager.set("data_type","data")});ae.postdraw_actions=ae.normal_postdraw_actions}}});var W=function(ae,ad){var af={resize:false};f.call(this,ae,ad,af);this.container_div.addClass("label-track")};o(W.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ah){var af=this.view,ag=af.high-af.low,ak=Math.floor(Math.pow(10,Math.floor(Math.log(ag)/Math.log(10)))),ad=Math.floor(af.low/ak)*ak,ai=this.view.container.width(),ae=$("
");while(ad"+commatize(ad)+"
").css({position:"absolute",left:aj-1}));ad+=ak}this.content_div.children(":first").remove();this.content_div.append(ae)}});var e=function(ae,ad,ah){this.display_modes=A;N.call(this,ae,ad,ah);this.drawables=[];if("drawables" in ah){var ag;for(var af=0;afthis.left_offset){this.left_offset=ag.left_offset}}this.enabled=true}ac.each(this.drawables,function(ai){if(ai instanceof c||ai instanceof T){ai.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,N.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.show_group()}}].concat(N.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,change_mode:function(ad){N.prototype.change_mode.call(this,ad);for(var ae=0;aeah){ah=ak}}for(var af=0;afthis.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,af,ae,ag,ad)}else{this.tiles_div.hide();return null}},can_subset:function(ad){return true},draw_tile:function(ag,am,ah,ae,aj,an){var af=this.data_manager.subset_entry(ag,aj),al=af.data;var ad=am.canvas;am.font=am.canvas.manager.default_font;am.textAlign="center";for(var ai=0,ak=al.length;aiI){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ad,ah,ai,ae){if(ah==="Coverage"||ad.dataset_type==="bigwig"){return this.summary_draw_height}else{var ag=this.incremental_slots(ai,ad.data,ah);var af=new (this.painter)(null,null,null,this.prefs,ah);return Math.max(aa,af.get_required_height(ag,ae))}},draw_tile:function(an,ar,ap,at,ag,ak,af){var aq=this,ae=ar.canvas,az=ag.get("start"),ad=ag.get("end"),ah=this.left_offset;if(an.dataset_type==="bigwig"){return this._draw_line_track_tile(an,ar,ap,at,ag,ak)}var aj=[],ao=this.slotters[ak].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var au=0,aw=an.data.length;au").text("Summary").addClass("yaxislabel variant top").css({"font-size":ad+"px",top:(this.prefs.summary_height-ad)/2+"px"}));if(this.prefs.show_sample_data){var ai=this.dataset.get("metadata").get("sample_names").join("
");this.tiles_div.prepend($("
").html(ai).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height+2,}))}}ad=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ad,"line-height":ad});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(af,ae,ah){c.call(this,af,ae,ah);var ag=j.get_random_color(),ad=j.get_random_color([ag,"#ffffff"]);this.config=new F({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:ag},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ad},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"}],saved_values:ah.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=(af.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};o(T.prototype,p.prototype,N.prototype,c.prototype);var d={CompositeTrack:e,DrawableGroup:P,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var n=function(af,ae,ad){if("copy" in af){return af.copy(ad)}else{var ag=af.obj_type;if(!ag){ag=af.track_type}return new d[ag](ae,ad,af)}};return{TracksterView:Y,DrawableGroup:P,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:T,VariantTrack:Z,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools"],function(ac,w,j,s,L,h,X,R){var o=ac.extend;var l={};var i=function(ad,ae){l[ad.attr("id")]=ae};var k=function(ad,af,ah,ag){ah=".group";var ae={};l[ad.attr("id")]=ag;ad.bind("drag",{handle:"."+af,relative:true},function(ap,aq){var ao=$(this),au=$(this).parent(),al=au.children(),an=l[$(this).attr("id")],ak,aj,ar,ai,am;aj=$(this).parents(ah);if(aj.length!==0){ar=aj.position().top;ai=ar+aj.outerHeight();if(aq.offsetYai){$(this).insertAfter(aj);var at=l[aj.attr("id")];at.remove_drawable(an);at.container.add_drawable(an);return}}}aj=null;for(am=0;am=ar&&aq.offsetY<=ai){if(aq.offsetY-ar0?am-1:am))}}}).bind("dragstart",function(){ae["border-top"]=ad.css("border-top");ae["border-bottom"]=ad.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ae)})};var aa=16,G=9,D=20,z=100,I=12000,S=400,K=5000,v=100,m="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",Q=10,H=20,A=["Histogram","Line","Filled","Intensity"];function V(ae,ad){if(!ad){ad=0}var af=Math.pow(10,ad);return Math.round(ae*af)/af}var p=function(ae,ad,ag){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.name=ag.name;this.view=ae;this.container=ad;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ag.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=$("
").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("
"));this.header_div.dblclick(function(ah){ah.stopPropagation()});var af=this;this.container_div.hover(function(){af.icons_div.show()},function(){af.icons_div.hide()});$("
").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ad){if(ad.content_visible){ad.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ad.hide_contents();ad.content_visible=false}else{ad.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ad.content_visible=true;ad.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ae){var ag=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ad=function(){ae.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ad()}}};$(window).bind("keypress.check_enter_esc",af);show_modal("Configure",ae.config.build_form(),{Cancel:ag,OK:ad})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.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(ad){},to_dict:function(){},set_name:function(ad){this.old_name=this.name;this.name=ad;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 ad=this.view;this.container_div.hide(0,function(){$(this).remove();ad.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ae,aj,ai,ah,ad,ag){var af=this;this.action_icons[ae]=$("").attr("href","javascript:void(0);").attr("title",aj).addClass("icon-button").addClass(ai).tooltip().click(function(){ah(af)}).appendTo(this.icons_div);if(ag){this.action_icons[ae].hide()}},build_action_icons:function(ad){var af;for(var ae=0;ae").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ag){this.unpack_drawables(ag.drawables)}if("filters" in ag){var af=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ag.filters);af.parent_div.replaceWith(this.filters_manager.parent_div);if(ag.filters.visible){this.setup_multitrack_filtering()}}};o(P.prototype,p.prototype,y.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(ad){$(".bs-tooltip").remove();ad.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ad){if(ad.filters_manager.visible()){ad.filters_manager.clear_filters();ad._restore_filter_managers()}else{ad.setup_multitrack_filtering();ad.request_draw({clear_tile_cache:true})}ad.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ad=$("
").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ad)}return ad},build_header_div:function(){var ad=$("
").addClass("track-header");ad.append($("
").addClass(this.drag_handle_class));this.name_div=$("
").addClass("track-name").text(this.name).appendTo(ad);return ad},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var af=this.drawables.length;if(af===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(af===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var am,al,aj,ap=true,ah=this.drawables[0].get_type(),ad=0;for(am=0;am1&&ad===this.drawables.length){var aq={},ae;aj=this.drawables[0];for(al=0;al0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ad=0;ad0){this.saved_filters_managers=[];for(var ad=0;ad").addClass("top-container").appendTo(af);this.browser_content_div=$("
").addClass("content").css("position","relative").appendTo(af);this.bottom_container=$("
").addClass("bottom-container").appendTo(af);this.top_labeltrack=$("
").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("
").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ad);this.intro_div=$("
").addClass("intro").appendTo(this.viewport_container).hide();var ag=$("
").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ad.dbkey},function(ah){ac.each(ah,function(ai){ad.add_drawable(n(ai,ad,ad))})})});this.nav_labeltrack=$("
").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("
").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("
").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("
").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("
").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("
").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("
").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("
").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("
").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("").addClass("nav-input").hide().bind("keyup focusout",ae).appendTo(this.nav_controls);this.location_span=$("").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ad.location_span.hide();ad.chrom_select.hide();ad.nav_input.val(ad.chrom+":"+ad.low+"-"+ad.high);ad.nav_input.css("display","inline-block");ad.nav_input.select();ad.nav_input.focus();ad.nav_input.autocomplete({source:function(aj,ah){var ak=[],ai=$.map(ad.get_tracks(c),function(al){return al.data_manager.search_features(aj.term).success(function(am){ak=ak.concat(am)})});$.when.apply($,ai).done(function(){ah($.map(ak,function(al){return{label:al[0],value:al[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ad.zoom_out();ad.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ad.zoom_in();ad.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ad.change_chrom(ad.chrom_select.val())});this.browser_content_div.click(function(ah){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ah){ad.zoom_in(ah.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ah,ai){this.current_x=ai.offsetX}).bind("drag",function(ah,aj){var ak=aj.offsetX-this.current_x;this.current_x=aj.offsetX;var ai=Math.round(ak/ad.viewport_container.width()*(ad.max_high-ad.max_low));ad.move_delta(-ai)});this.overview_close.click(function(){ad.reset_overview()});this.viewport_container.bind("draginit",function(ah,ai){if(ah.clientX>ad.viewport_container.width()-16){return false}}).bind("dragstart",function(ah,ai){ai.original_low=ad.low;ai.current_height=ah.clientY;ai.current_x=ai.offsetX}).bind("drag",function(aj,al){var ah=$(this);var am=al.offsetX-al.current_x;var ai=ah.scrollTop()-(aj.clientY-al.current_height);ah.scrollTop(ai);al.current_height=aj.clientY;al.current_x=al.offsetX;var ak=Math.round(am/ad.viewport_container.width()*(ad.high-ad.low));ad.move_delta(ak)}).bind("mousewheel",function(aj,al,ai,ah){if(ai){ai*=50;var ak=Math.round(-ai/ad.viewport_container.width()*(ad.high-ad.low));ad.move_delta(ak)}});this.top_labeltrack.bind("dragstart",function(ah,ai){return $("
").css({height:ad.browser_content_div.height()+ad.top_labeltrack.height()+ad.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(al,am){$(am.proxy).css({left:Math.min(al.pageX,am.startX)-ad.container.offset().left,width:Math.abs(al.pageX-am.startX)});var ai=Math.min(al.pageX,am.startX)-ad.container.offset().left,ah=Math.max(al.pageX,am.startX)-ad.container.offset().left,ak=(ad.high-ad.low),aj=ad.viewport_container.width();ad.update_location(Math.round(ai/aj*ak)+ad.low,Math.round(ah/aj*ak)+ad.low)}).bind("dragend",function(am,an){var ai=Math.min(am.pageX,an.startX),ah=Math.max(am.pageX,an.startX),ak=(ad.high-ad.low),aj=ad.viewport_container.width(),al=ad.low;ad.low=Math.round(ai/aj*ak)+al;ad.high=Math.round(ah/aj*ak)+al;$(an.proxy).remove();ad.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}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ad.resize_window()},500)});$(document).bind("redraw",function(){ad.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ad){return this.config.values[ad.toLowerCase()+"_color"]||this.config.values.n_color}});o(Y.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ae,ag,ad,ah){if(this.timer){clearTimeout(this.timer)}if(ah){var af=this;this.timer=setTimeout(function(){af.trigger("navigate",ae+":"+ag+"-"+ad)},500)}else{view.trigger("navigate",ae+":"+ag+"-"+ad)}},update_location:function(ad,af){this.location_span.text(commatize(ad)+" - "+commatize(af));this.nav_input.val(this.chrom+":"+commatize(ad)+"-"+commatize(af));var ae=view.chrom_select.val();if(ae!==""){this.trigger_navigate(ae,view.low,view.high,true)}},load_chroms:function(af){af.num=v;var ad=this,ae=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:af,dataType:"json",success:function(ah){if(ah.chrom_info.length===0){return}if(ah.reference){ad.add_label_track(new B(ad))}ad.chrom_data=ah.chrom_info;var ak='';for(var aj=0,ag=ad.chrom_data.length;aj'+ai+""}if(ah.prev_chroms){ak+='"}if(ah.next_chroms){ak+='"}ad.chrom_select.html(ak);ad.chrom_start_index=ah.start_index;ae.resolve(ah.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ad.dbkey)}});return ae},change_chrom:function(ai,ae,ak){var af=this;if(!af.chrom_data){af.load_chroms_deferred.then(function(){af.change_chrom(ai,ae,ak)});return}if(!ai||ai==="None"){return}if(ai==="previous"){af.load_chroms({low:this.chrom_start_index-v});return}if(ai==="next"){af.load_chroms({low:this.chrom_start_index+v});return}var aj=$.grep(af.chrom_data,function(al,am){return al.chrom===ai})[0];if(aj===undefined){af.load_chroms({chrom:ai},function(){af.change_chrom(ai,ae,ak)});return}else{if(ai!==af.chrom){af.chrom=ai;af.chrom_select.val(af.chrom);af.max_high=aj.len-1;af.reset();for(var ah=0,ad=af.drawables.length;ahad.max_high){ad.high=ad.max_high;ad.low=ad.max_high-af}else{ad.high-=ag;ad.low-=ag}}ad.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ad.request_redraw()},200);var ae=ad.chrom_select.val();this.trigger_navigate(ae,ad.low,ad.high,true)},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);ad.init();this.changed();this.update_intro_div()},add_label_track:function(ad){ad.view=this;ad.init();this.label_tracks.push(ad)},remove_drawable:function(af,ae){y.prototype.remove_drawable.call(this,af);if(ae){var ad=this;af.container_div.hide(0,function(){$(this).remove();ad.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ae,af){var ad=this,ag=(af?[af]:ad.drawables);ac.each(ag,function(ah){var ai=ac.find(ad.tracks_to_be_redrawn,function(aj){return aj[0]===ah});if(ai){ai[1]=ae}else{ad.tracks_to_be_redrawn.push([ah,ae])}});if(!this.requested_redraw){requestAnimationFrame(function(){ad._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ad=this.low,ah=this.high;if(adthis.max_high){ah=this.max_high}var ae=this.high-this.low;if(this.high!==0&&ae").addClass("param-label").text(ag.get("label")).appendTo(af);var ae=$("
").addClass("param-input").html(ag.get("html")).appendTo(af);ae.find(":input").val(ag.get("value"));$("
").appendTo(af)},update_value:function(ad){this.model.set_value($(ad.target).val())}});var ab=Backbone.View.extend({render:function(){var ae=this;tool=this.model.get("tool"),parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ai){ai.stopPropagation()}).click(function(ai){ai.stopPropagation()}).bind("dblclick",function(ai){ai.stopPropagation()}).keydown(function(ai){ai.stopPropagation()});var af=$("
").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(aj){var ai=new t({model:aj});ai.render();parent_div.append(ai.$el)});parent_div.find("input").click(function(){$(this).select()});var ag=$("
").addClass("param-row").appendTo(parent_div);var ah=$("").attr("value","Run on complete dataset").appendTo(ag);var ad=$("").attr("value","Run on visible region").css("margin-left","3em").appendTo(ag);ad.click(function(){ae.run_on_region()});ah.click(function(){ae.run_on_dataset()})},update_params:function(){for(var ad=0;ad");var af;function ae(al,ah){for(var ap=0;ap").appendTo(ah);aw.append($("").addClass("icon-button arrow-circle").appendTo(av).attr("title","Set new random color").tooltip(),at=$("
").appendTo(av).hide(),ak=$("
").appendTo(at),ai=$("
").appendTo(at),am=$.farbtastic(ak,{width:100,height:100,callback:aq,color:au});av.append($("
").css("clear","both"));(function(ax){ao.click(function(){ax.setColor(j.get_random_color())})})(am)}else{aw.append($("").attr("id",aj).attr("name",aj).val(au))}}}}if(af.help){aw.append($("
").text(af.help))}}}ae(this.params,ad);return ad},update_from_form:function(ad){var af=this;var ae=false;$.each(this.params,function(ag,ai){if(!ai.hidden){var aj="param_"+ag;var ah=ad.find("#"+aj).val();if(ai.type==="bool"){ah=ad.find("#"+aj).is(":checked")}ae=af.set_param_value(ai.key,ah)||ae}});if(ae){this.onchange();this.track.changed()}}});var b=function(ad,ah,af,ae,ag){this.track=ad;this.region=ah;this.low=ah.get("start");this.high=ah.get("end");this.resolution=af;this.html_elt=$("
").append(ae).height($(ae).attr("height"));this.data=ag;this.stale=false};b.prototype.predisplay_actions=function(){};var M=function(ad,ah,af,ae,ag){b.call(this,ad,ah,af,ae,ag)};M.prototype.predisplay_actions=function(){};var O=function(ag,ao,ah,af,aj,aq,ak,ar,ae,an){b.call(this,ag,ao,ah,af,aj);this.mode=ak;this.all_slotted=ae;this.feature_mapper=an;this.has_icons=false;if(ar){this.has_icons=true;var al=this;af=this.html_elt.children()[0],message_div=$("
").addClass("tile-message").css({height:D-1,width:af.width}).prependTo(this.html_elt);var am=new w.GenomeRegion({chrom:ag.view.chrom,start:this.low,end:this.high}),ap=aj.length,ai=$("").addClass("icon more-down").attr("title","For speed, only the first "+ap+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ad=$("").addClass("icon more-across").attr("title","For speed, only the first "+ap+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ai.click(function(){al.stale=true;ag.data_manager.get_more_data(am,ag.mode,al.resolution,{},ag.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();ag.request_draw()}).dblclick(function(at){at.stopPropagation()});ad.click(function(){al.stale=true;ag.data_manager.get_more_data(am,ag.mode,al.resolution,{},ag.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();ag.request_draw()}).dblclick(function(at){at.stopPropagation()})}};o(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var ae=this,ad={};if(ae.mode!=="Pack"){return}$(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(ap){if(!this.hovered){return}var ak=$(this).offset(),ao=ap.pageX-ak.left,an=ap.pageY-ak.top,au=ae.feature_mapper.get_feature_data(ao,an),al=(au?au[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!al||$(this).attr("id")!==al.toString()){$(this).remove()}});if(au){var ag=ad[al];if(!ag){var al=au[0],aq={name:au[3],start:au[1],end:au[2],strand:au[4]},aj=ae.track.filters_manager.filters,ai;for(var am=0;am").attr("id",al).addClass("feature-popup"),av=$(""),at,ar,aw;for(at in aq){ar=aq[at];aw=$("").appendTo(av);$("
").appendTo(aw).text(at);$("").attr("align","left").appendTo(aw).text(typeof(ar)==="number"?V(ar,2):ar)}ag.append($("
").append(av));ad[al]=ag}ag.appendTo($(this).parents(".track-content").children(".overlay"));var ah=ao+parseInt(ae.html_elt.css("left"))-ag.width()/2,af=an+parseInt(ae.html_elt.css("top"))+7;ag.css("left",ah+"px").css("top",af+"px")}else{if(!ap.isPropagationStopped()){ap.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ap)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ae,ad,af){o(af,{drag_handle_class:"draghandle"});p.call(this,ae,ad,af);this.dataset=(af.dataset?new X.Dataset(af.dataset):null);this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in af?af.data_query_wait:K);this.data_manager=("data_manager" in af?af.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ae.dbkey,chroms_info:{chrom_info:ae.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("
").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in af)||af.resize){this.add_resize_handle()}}};o(f.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(ad){ad.view.set_overview(ad)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ad){if(ad.filters_manager.visible()){ad.filters_manager.clear_filters()}else{ad.filters_manager.init_filters()}ad.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ad){ad.dynamic_tool_div.toggle();if(ad.dynamic_tool_div.is(":visible")){ad.set_name(ad.name+ad.tool_region_and_parameters_str())}else{ad.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ad){var ag='Tool: <%= track.tool.name %>
Dataset: <%= track.name %>
Region(s): ',af=ac.template(ag,{track:ad});var ai=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(){var ak=$('select[name="regions"] option:selected').val(),am,aj=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),al=ac.map($(".bookmark"),function(an){return new w.GenomeRegion({from_str:$(an).children(".position").text()})});if(ak==="cur"){am=[aj]}else{if(ak==="bookmarks"){am=al}else{am=[aj].concat(al)}}hide_modal();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ad.dataset.id,hda_ldda:ad.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(am).toJSON())})},ah=function(aj){if((aj.keyCode||aj.which)===27){ai()}else{if((aj.keyCode||aj.which)===13){ae()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",af,{No:ai,Yes:ae})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("
").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ad=$("
");if(this.view.editor){this.drag_div=$("
").addClass(this.drag_handle_class).appendTo(ad)}this.name_div=$("
").addClass("track-name").appendTo(ad).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ad},set_dataset:function(ad){this.dataset=ad;this.data_manager.set("dataset",ad)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ad=this;var ag=false;var af=false;var ae=$("
");$(ad.container_div).hover(function(){if(ad.content_visible){ag=true;ae.show()}},function(){ag=false;if(!af){ae.hide()}});ae.hide().bind("dragstart",function(ah,ai){af=true;ai.original_height=$(ad.content_div).height()}).bind("drag",function(ai,aj){var ah=Math.min(Math.max(aj.original_height+aj.deltaY,ad.min_height_px),ad.max_height_px);$(ad.tiles_div).css("height",ah);ad.visible_height_px=(ad.max_height_px===ah?0:ah);ad.on_resize()}).bind("dragend",function(ah,ai){ad.tile_cache.clear();af=false;if(!ag){ae.hide()}ad.config.values.height=ad.visible_height_px;ad.changed()}).appendTo(ad.container_div)},set_display_modes:function(ag,aj){this.display_modes=ag;this.mode=(aj?aj:(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 ae=this,ah={};for(var af=0,ad=ae.display_modes.length;af").text("View error").click(function(){show_modal("Trackster Error","
"+ah.message+"
",{Close:hide_modal})}));ae.tiles_div.append($("").text(" "));ae.tiles_div.append($("").text("Try again").click(function(){ae.init(true)}))}}else{if(ah==="no converter"){ae.container_div.addClass("error");ae.tiles_div.text(J)}else{if(ah==="no data"||(ah.data!==undefined&&(ah.data===null||ah.data.length===0))){ae.container_div.addClass("nodata");ae.tiles_div.text(E)}else{if(ah==="pending"){ae.container_div.addClass("pending");ae.tiles_div.html(u);setTimeout(function(){ae.init()},ae.data_query_wait)}else{if(ah==="data"||ah.status==="data"){if(ah.valid_chroms){ae.valid_chroms=ah.valid_chroms;ae.update_icons()}ae.tiles_div.text(U);if(ae.view.chrom){ae.tiles_div.text("");ae.tiles_div.css("height",ae.visible_height_px+"px");ae.enabled=true;$.when.apply($,ae.predraw_init()).done(function(){ad.resolve();ae.container_div.removeClass("nodata error pending");ae.request_draw()})}else{ad.resolve()}}}}}}});this.update_icons();return ad},predraw_init:function(){var ad=this;return $.getJSON(ad.dataset.url(),{data_type:"data",stats:true,chrom:ad.view.chrom,low:0,high:ad.view.max_high,hda_ldda:ad.dataset.get("hda_ldda")},function(ae){ad.container_div.addClass("line-track");var ag=ae.data;if(ag&&ag.min&&ag.max){var af=ag.min,ah=ag.max;af=Math.floor(Math.min(0,Math.max(af,ag.mean-2*ag.sd)));ah=Math.ceil(Math.max(0,Math.min(ah,ag.mean+2*ag.sd)));ad.config.set_param_default_value("min_value",af);ad.config.set_param_default_value("max_value",ah);ad.prefs.min_value=af;ad.prefs.max_value=ah}})},get_drawables:function(){return this}});var N=function(af,ae,ah){f.call(this,af,ae,ah);var ad=this;k(ad.container_div,ad.drag_handle_class,".group",ad);this.filters_manager=new h.FiltersManager(this,("filters" in ah?ah.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ah.tool?new q({track:this,tool:ah.tool,tool_state:ah.tool_state}):null);this.tile_cache=new w.Cache(Q);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ag=new ab({model:this.tool});ag.render();this.dynamic_tool_div=ag.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("
").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("
").addClass("overlay").appendTo(this.content_div);if(ah.mode){this.change_mode(ah.mode)}};o(N.prototype,p.prototype,f.prototype,{action_icons_def:f.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(ad){$(".bs-tooltip").remove();ad.slotters[ad.view.resolution_px_b].max_rows*=2;ad.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ad){var ae=this.to_dict();o(ae,{data_manager:this.data_manager});var af=new this.constructor(this.view,ad,ae);af.change_mode(this.mode);af.enabled=this.enabled;return af},set_filters_manager:function(ad){this.filters_manager=ad;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ad=this;return $.getJSON(ad.dataset.url(),{data_type:"data",stats:true,chrom:ad.view.chrom,low:0,high:ad.view.max_high,hda_ldda:ad.dataset.get("hda_ldda")},function(ae){var ag=ae.data;if(isNaN(parseFloat(ad.prefs.min_value))||isNaN(parseFloat(ad.prefs.max_value))){var af=ag.min,ah=ag.max;af=Math.floor(Math.min(0,Math.max(af,ag.mean-2*ag.sd)));ah=Math.ceil(Math.max(0,Math.min(ah,ag.mean+2*ag.sd)));ad.prefs.min_value=af;ad.prefs.max_value=ah}})},change_mode:function(ae){var ad=this;ad.mode=ae;ad.config.values.mode=ae;if(ae==="Auto"){this.data_manager.clear()}ad.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ad.mode+")");return ad},update_icons:function(){var ad=this;if(ad.filters_available){ad.action_icons.filters_icon.show()}else{ad.action_icons.filters_icon.hide()}if(ad.tool){ad.action_icons.tools_icon.show();ad.action_icons.param_space_viz_icon.show()}else{ad.action_icons.tools_icon.hide();ad.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ae,ad){return ae+"_"+ad},request_draw:function(ad){if(ad&&ad.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ad,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ah=this.view.high,ak=ah-al,ae=this.view.container.width(),ap=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=(view.max_high-view.max_low)/ae;ap=1/ag}this.before_draw();this.tiles_div.children().addClass("remove");var ad=Math.floor(al/(ag*S)),am,ai,aj=[],ao=[];while((ad*S*ag)").text(ae.prefs[ad]).make_text_editable({num_cols:12,on_finish:function(ak){$(".bs-tooltip").remove();ae.config.set_param_value(ad,ak);ai()},help_text:"Set "+aj+" value"}).addClass("yaxislabel "+ah).css("color",this.prefs.label_color);this.container_div.prepend(af)}},postdraw_actions:function(ag,ah,aj,ad){var af=ac.filter(ag,function(ak){return(ak instanceof M)});if(af.length>0){this.max_height_px=0;var ae=this;ac.each(ag,function(ak){if(!(ak instanceof M)){ak.html_elt.remove();ae.draw_helper(ak.region,ak.resolution,aj,{force:true,mode:"Coverage"})}});ae._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ai=ac.find(ag,function(ak){return ak.has_icons});if(ai){ac.each(ag,function(ak){if(!ak.has_icons){ak.html_elt.css("padding-top",D)}})}}},get_mode:function(ad){return this.mode},update_auto_mode:function(ad){},_get_drawables:function(){return[this]},draw_helper:function(am,ag,ap,aq){if(!aq){aq={}}var ae=aq.force,ao=!(aq.data_fetch===false),aj=aq.mode||this.mode,af=this,ah=this._get_drawables(),an=this._gen_tile_cache_key(ap,am),ai=function(ar){return(ar&&"track" in ar)};var ak=(ae?undefined:af.tile_cache.get_elt(an));if(ak){if(ai(ak)){af.show_tile(ak,ap)}return ak}if(!ao){return null}var al=function(){var ar=(ac.find(A,function(au){return au===aj})?"Coverage":aj);var at=ac.map(ah,function(au){return au.data_manager.get_data(am,ar,ag,af.data_url_extra_params)});if(view.reference_track){at.push(view.reference_track.data_manager.get_data(am,aj,ag,view.reference_track.data_url_extra_params))}return at};var ad=$.Deferred();af.tile_cache.set_elt(an,ad);$.when.apply($,al()).then(function(){var ar=al(),ax=ar,aD;if(view.reference_track){aD=view.reference_track.data_manager.subset_entry(ar.pop(),am)}var ay=[],av=[];ac.each(ah,function(aI,aF){var aH=aI.mode,aG=ax[aF];if(aH==="Auto"){aH=aI.get_mode(aG);aI.update_auto_mode(aH)}ay.push(aH);av.push(aI.get_canvas_height(aG,aH,ap,at))});var aw=af.view.canvas_manager.new_canvas(),az=am.get("start"),aE=am.get("end"),au=0,at=Math.ceil((aE-az)*ap)+af.left_offset,aB=ac.max(av),aA;aw.width=at;aw.height=(aq.height||aB);var aC=aw.getContext("2d");aC.translate(af.left_offset,0);if(ah.length>1){aC.globalAlpha=0.5;aC.globalCompositeOperation="source-over"}ac.each(ah,function(aG,aF){aA=aG.draw_tile(ax[aF],aC,ay[aF],ag,am,ap,aD)});if(aA!==undefined){af.tile_cache.set_elt(an,aA);af.show_tile(aA,ap)}ad.resolve(aA)});return ad},get_canvas_height:function(ad,af,ag,ae){return this.visible_height_px},_draw_line_track_tile:function(ad,af,aj,ah,ai,ak){var ag=af.canvas,ae=new L.LinePainter(ad.data,ai.get("start"),ai.get("end"),this.prefs,aj);ae.draw(af,ag.width,ag.height,ak);return new M(this,ai,ah,ag,ad.data)},draw_tile:function(ad,ae,ai,ag,ah,aj,af){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(af,ai){var ae=this,ad=af.html_elt;af.predisplay_actions();var ah=(af.low-(this.is_overview?this.view.max_low:this.view.low))*ai;if(this.left_offset){ah-=this.left_offset}ad.css({position:"absolute",top:0,left:ah});if(ad.hasClass("remove")){ad.removeClass("remove")}else{this.tiles_div.append(ad)}af.html_elt.height("auto");this.max_height_px=Math.max(this.max_height_px,af.html_elt.height());af.html_elt.parent().children().css("height",this.max_height_px+"px");var ag=this.max_height_px;if(this.visible_height_px!==0){ag=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ag+"px")},_get_tile_bounds:function(ad,ae){var ag=Math.floor(ad*S*ae),ah=Math.ceil(S*ae),af=(ag+ah<=this.view.max_high?ag+ah:this.view.max_high);return new w.GenomeRegion({chrom:this.view.chrom,start:ag,end:af})},tool_region_and_parameters_str:function(ag){var ad=this,af=(ag!==undefined?ag.toString():"all"),ae=ac.values(ad.tool.get("tool").get_inputs_dict()).join(", ");return" - region=["+af+"], parameters=["+ae+"]"},data_and_mode_compatible:function(ad,ae){if(ae==="Auto"){return true}else{if(ae==="Coverage"){return ad.dataset_type==="bigwig"}else{if(ad.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ad){if(ad.dataset_type==="bigwig"||ad.message||ad.extra_info==="no_detail"){return false}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(af,ag,ai,ad){var ae=this;ae.normal_postdraw_actions(af,ag,ai,ad);ae.dataset_check_type="converted_datasets_state";ae.data_query_wait=K;var ah=new j.ServerStateDeferred({url:ae.dataset_state_url,url_params:{dataset_id:ae.dataset.id,hda_ldda:ae.dataset.get("hda_ldda")},interval:ae.data_query_wait,success_fn:function(aj){return aj!=="pending"}});$.when(ah.go()).then(function(){ae.data_manager.set("data_type","data")});ae.postdraw_actions=ae.normal_postdraw_actions}}});var W=function(ae,ad){var af={resize:false};f.call(this,ae,ad,af);this.container_div.addClass("label-track")};o(W.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ah){var af=this.view,ag=af.high-af.low,ak=Math.floor(Math.pow(10,Math.floor(Math.log(ag)/Math.log(10)))),ad=Math.floor(af.low/ak)*ak,ai=this.view.container.width(),ae=$("
");while(ad"+commatize(ad)+"
").css({position:"absolute",left:aj-1}));ad+=ak}this.content_div.children(":first").remove();this.content_div.append(ae)}});var e=function(ae,ad,ah){this.display_modes=A;N.call(this,ae,ad,ah);this.drawables=[];if("drawables" in ah){var ag;for(var af=0;afthis.left_offset){this.left_offset=ag.left_offset}}this.enabled=true}ac.each(this.drawables,function(ai){if(ai instanceof c||ai instanceof T){ai.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,N.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ad){$(".bs-tooltip").remove();ad.show_group()}}].concat(N.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,change_mode:function(ad){N.prototype.change_mode.call(this,ad);for(var ae=0;aeah){ah=ak}}for(var af=0;afthis.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,af,ae,ag,ad)}else{this.tiles_div.hide();return null}},can_subset:function(ad){return true},draw_tile:function(ag,am,ah,ae,aj,an){var af=this.data_manager.subset_entry(ag,aj),al=af.data;var ad=am.canvas;am.font=am.canvas.manager.default_font;am.textAlign="center";for(var ai=0,ak=al.length;aiI){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ad,ah,ai,ae){if(ah==="Coverage"||ad.dataset_type==="bigwig"){return this.summary_draw_height}else{var ag=this.incremental_slots(ai,ad.data,ah);var af=new (this.painter)(null,null,null,this.prefs,ah);return Math.max(aa,af.get_required_height(ag,ae))}},draw_tile:function(an,ar,ap,at,ag,ak,af){var aq=this,ae=ar.canvas,az=ag.get("start"),ad=ag.get("end"),ah=this.left_offset;if(an.dataset_type==="bigwig"){return this._draw_line_track_tile(an,ar,ap,at,ag,ak)}var aj=[],ao=this.slotters[ak].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var au=0,aw=an.data.length;au").text("Summary").addClass("yaxislabel variant top").css({"font-size":ad+"px",top:(this.prefs.summary_height-ad)/2+"px"}));if(this.prefs.show_sample_data){var ai=this.dataset.get("metadata").get("sample_names").join("
");this.tiles_div.prepend($("
").html(ai).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height+2,}))}}ad=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ad,"line-height":ad});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(af,ae,ah){c.call(this,af,ae,ah);var ag=j.get_random_color(),ad=j.get_random_color([ag,"#ffffff"]);this.config=new F({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:ag},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ad},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"}],saved_values:ah.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=(af.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};o(T.prototype,p.prototype,N.prototype,c.prototype);var d={CompositeTrack:e,DrawableGroup:P,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var n=function(af,ae,ad){if("copy" in af){return af.copy(ad)}else{var ag=af.obj_type;if(!ag){ag=af.track_type}return new d[ag](ae,ad,af)}};return{TracksterView:Y,DrawableGroup:P,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:T,VariantTrack:Z,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file diff --git a/static/scripts/viz/trackster/tracks.js b/static/scripts/viz/trackster/tracks.js index e9f1b81ee67..e3798e6f8e8 100644 --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1634,7 +1634,17 @@ var TracksterTool = Backbone.RelationalModel.extend({ key: 'tool', relatedModel: tools_mod.Tool } - ] + ], + + initialize: function(options) { + // HACK: remove data and group tool inputs because Trackster + // does not work with them right now. + var tool = this.get('tool'), + incompatible_inputs = tool.get('inputs').filter( function(input) { + return ( [ 'data', 'hidden_data', 'group'].indexOf( input.get('type') ) !== -1); + }); + tool.get('inputs').remove(incompatible_inputs); + } }); @@ -1692,6 +1702,7 @@ var TracksterToolView = Backbone.View.extend({ // Add name, inputs. var name_div = $("
").appendTo(parent_div).text(tool.get('name')); tool.get('inputs').each(function(param) { + // Render parameter. var param_view = new ToolParameterView({ model: param }); param_view.render(); parent_div.append(param_view.$el); @@ -2479,11 +2490,8 @@ extend(Track.prototype, Drawable.prototype, { Drawable.prototype.action_icons_def[2] ], - can_draw: function() { - if ( this.dataset.id && Drawable.prototype.can_draw.call(this) ) { - return true; - } - return false; + can_draw: function() { + return this.dataset && Drawable.prototype.can_draw.call(this); }, build_container_div: function () { diff --git a/templates/webapps/galaxy/root/tool_menu.mako b/templates/webapps/galaxy/root/tool_menu.mako index 4dfe51a74a8..08aa7057d89 100644 --- a/templates/webapps/galaxy/root/tool_menu.mako +++ b/templates/webapps/galaxy/root/tool_menu.mako @@ -25,12 +25,12 @@ hidden: false }), tools = new tools_mod.ToolCollection( - ${ h.to_json_string( trans.app.toolbox.to_dict( trans, in_panel=False ) ) } + ${ h.to_json_string( trans.app.toolbox.dictify( trans, in_panel=False ) ) } ), tool_panel = new tools_mod.ToolPanel({ tool_search: tool_search, tools: tools, - layout: ${h.to_json_string( trans.app.toolbox.to_dict( trans ) )} + layout: ${h.to_json_string( trans.app.toolbox.dictify( trans ) )} }), tool_panel_view = new tools_mod.ToolPanelView({ model: tool_panel });