[galaxy-commits] commit/galaxy-central: kanwei: Backend changes to implicitly converted datasets:

1 new changeset in galaxy-central:

http://bitbucket.org/galaxy/galaxy-central/changeset/0c1407634eb8/ changeset: r4976:0c1407634eb8 user: kanwei date: 2011-02-02 02:07:17 summary: Backend changes to implicitly converted datasets: - Library dataset LDDAs can now be implicitly converted to another format. For this to happen, an HDA is created by copying the LDDA info, and the HDA is then used as the tool input parameter. The implicitly converted dataset table will map the LDDA to the resulting converted output HDA. - Added set_output_history optional param to tool.execute to specify whether output dataset is added to the current (or specified) history. Defaults to true but is set to false for implicitly converted datasets so that it does not show up as a hidden history item, which show up in features like "extract workflow from history".

Initial pass at UI for adding data library datasets to trackster using the "Select Library, then Select Datasets" paradigm currently also used for adding history datasets. Currently uses browse_library.mako code but this will need to be enhanced for trackster's purposes. affected #: 12 files (4.1 KB)

--- a/lib/galaxy/datatypes/data.py Tue Feb 01 19:56:05 2011 -0500 +++ b/lib/galaxy/datatypes/data.py Tue Feb 01 20:07:17 2011 -0500 @@ -266,7 +266,7 @@ def find_conversion_destination( self, dataset, accepted_formats, datatypes_registry, **kwd ): """Returns ( target_ext, existing converted dataset )""" return datatypes_registry.find_conversion_destination_for_dataset_by_extensions( dataset, accepted_formats, **kwd ) - def convert_dataset(self, trans, original_dataset, target_type, return_output = False, visible = True, deps=None): + def convert_dataset(self, trans, original_dataset, target_type, return_output=False, visible=True, deps=None, set_output_history=True): """This function adds a job to the queue to convert a dataset to another type. Returns a message about success/failure.""" converter = trans.app.datatypes_registry.get_converter_by_target_type( original_dataset.ext, target_type )

@@ -277,14 +277,14 @@ #determine input parameter name and add to params input_name = 'input1' for key, value in converter.inputs.items(): - if (deps) and (value.name in deps): + if deps and value.name in deps: params[value.name] = deps[value.name] elif value.type == 'data': input_name = key

params[input_name] = original_dataset #Run converter, job is dispatched through Queue - converted_dataset = converter.execute( trans, incoming = params, set_output_hid = visible )[1] + converted_dataset = converter.execute( trans, incoming=params, set_output_hid=visible, set_output_history=set_output_history)[1] if len(params) > 0: trans.log_event( "Converter params: %s" % (str(params)), tool_id=converter.id ) if not visible:

--- a/lib/galaxy/model/__init__.py Tue Feb 01 19:56:05 2011 -0500 +++ b/lib/galaxy/model/__init__.py Tue Feb 01 20:07:17 2011 -0500 @@ -742,8 +742,7 @@ pass # No deps

assoc = ImplicitlyConvertedDatasetAssociation( parent=self, file_type=target_ext, metadata_safe=False ) - new_dataset = self.datatype.convert_dataset( trans, self, target_ext, return_output=True, visible=False, deps=deps ).values()[0] - new_dataset.hid = self.hid + new_dataset = self.datatype.convert_dataset( trans, self, target_ext, return_output=True, visible=False, deps=deps, set_output_history=False ).values()[0] new_dataset.name = self.name session = trans.sa_session session.add( new_dataset ) @@ -1326,7 +1325,12 @@ def __init__( self, id = None, parent = None, dataset = None, file_type = None, deleted = False, purged = False, metadata_safe = True ): self.id = id self.dataset = dataset - self.parent = parent + if isinstance(parent, HistoryDatasetAssociation): + self.parent_hda = parent + elif isinstance(parent, LibraryDatasetDatasetAssociation): + self.parent_ldda = parent + else: + raise AttributeError self.type = file_type self.deleted = deleted self.purged = purged

--- a/lib/galaxy/model/mapping.py Tue Feb 01 19:56:05 2011 -0500 +++ b/lib/galaxy/model/mapping.py Tue Feb 01 20:07:17 2011 -0500 @@ -145,6 +145,7 @@ Column( "update_time", DateTime, default=now, onupdate=now ), Column( "hda_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True, nullable=True ), Column( "hda_parent_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ), + Column( "ldda_parent_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), index=True ), Column( "deleted", Boolean, index=True, default=False ), Column( "metadata_safe", Boolean, index=True, default=True ), Column( "type", TrimmedString( 255 ) ) ) @@ -1135,13 +1136,17 @@ user = relation( User ) ) )

assign_mapper( context, ImplicitlyConvertedDatasetAssociation, ImplicitlyConvertedDatasetAssociation.table, - properties=dict( parent=relation( - HistoryDatasetAssociation, - primaryjoin=( ImplicitlyConvertedDatasetAssociation.table.c.hda_parent_id == HistoryDatasetAssociation.table.c.id ) ), + properties=dict( parent_hda=relation( + HistoryDatasetAssociation, + primaryjoin=( ImplicitlyConvertedDatasetAssociation.table.c.hda_parent_id == HistoryDatasetAssociation.table.c.id ) ), + + parent_ldda=relation( + LibraryDatasetDatasetAssociation, + primaryjoin=( ImplicitlyConvertedDatasetAssociation.table.c.ldda_parent_id == LibraryDatasetDatasetAssociation.table.c.id ) ),

dataset=relation( - HistoryDatasetAssociation, - primaryjoin=( ImplicitlyConvertedDatasetAssociation.table.c.hda_id == HistoryDatasetAssociation.table.c.id ) ) ) ) + HistoryDatasetAssociation, + primaryjoin=( ImplicitlyConvertedDatasetAssociation.table.c.hda_id == HistoryDatasetAssociation.table.c.id ) ) ) )

assign_mapper( context, History, History.table, properties=dict( galaxy_sessions=relation( GalaxySessionToHistoryAssociation ), @@ -1322,6 +1327,9 @@ HistoryDatasetAssociation, primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ), backref=backref( "copied_from_library_dataset_dataset_association", primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ), remote_side=[LibraryDatasetDatasetAssociation.table.c.id], uselist=False ) ), + implicitly_converted_datasets=relation( + ImplicitlyConvertedDatasetAssociation, + primaryjoin=( ImplicitlyConvertedDatasetAssociation.table.c.ldda_parent_id == LibraryDatasetDatasetAssociation.table.c.id ) ), children=relation( LibraryDatasetDatasetAssociation, primaryjoin=( LibraryDatasetDatasetAssociation.table.c.parent_id == LibraryDatasetDatasetAssociation.table.c.id ),

--- a/lib/galaxy/tools/__init__.py Tue Feb 01 19:56:05 2011 -0500 +++ b/lib/galaxy/tools/__init__.py Tue Feb 01 20:07:17 2011 -0500 @@ -1215,14 +1215,14 @@ raise Exception( "Unexpected parameter type" ) return args

- def execute( self, trans, incoming={}, set_output_hid=True, history=None ): + def execute( self, trans, incoming={}, set_output_hid=True, set_output_history=True, history=None ): """ Execute the tool using parameter values in `incoming`. This just dispatches to the `ToolAction` instance specified by `self.tool_action`. In general this will create a `Job` that when run will build the tool's outputs, e.g. `DefaultToolAction`. """ - return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history ) + return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, set_output_history=set_output_history, history=history )

def params_to_strings( self, params, app ): return params_to_strings( self.inputs, params, app )

--- a/lib/galaxy/tools/actions/__init__.py Tue Feb 01 19:56:05 2011 -0500 +++ b/lib/galaxy/tools/actions/__init__.py Tue Feb 01 20:07:17 2011 -0500 @@ -1,3 +1,4 @@ +from galaxy.model import LibraryDatasetDatasetAssociation from galaxy.util.bunch import Bunch from galaxy.util.odict import odict from galaxy.tools.parameters import * @@ -100,7 +101,7 @@ tool.visit_inputs( param_values, visitor ) return input_datasets

- def execute(self, tool, trans, incoming={}, return_job=False, set_output_hid=True, history=None ): + def execute(self, tool, trans, incoming={}, return_job=False, set_output_hid=True, set_output_history=True, history=None ): """ Executes a tool, creating job and tool outputs, associating them, and submitting the job to the job queue. If history is not specified, use @@ -166,11 +167,20 @@ input_ext = 'data' input_dbkey = incoming.get( "dbkey", "?" ) for name, data in inp_data.items(): - if data: - input_names.append( 'data %s' % data.hid ) - input_ext = data.ext - else: + if not data: data = NoneDataset( datatypes_registry = trans.app.datatypes_registry ) + continue + + # Convert LDDA to an HDA. + if isinstance(data, LibraryDatasetDatasetAssociation): + data = data.to_history_dataset_association( None ) + inp_data[name] = data + + else: # HDA + if data.hid: + input_names.append( 'data %s' % data.hid ) + input_ext = data.ext + if data.dbkey not in [None, '?']: input_dbkey = data.dbkey

@@ -306,11 +316,12 @@ output.actions.apply_action( data, output_action_params ) # Store all changes to database trans.sa_session.flush() - # Add all the top-level (non-child) datasets to the history + # Add all the top-level (non-child) datasets to the history unless otherwise specified for name in out_data.keys(): if name not in child_dataset_names and name not in incoming: #don't add children; or already existing datasets, i.e. async created data = out_data[ name ] - history.add_dataset( data, set_hid = set_output_hid ) + if set_output_history: + history.add_dataset( data, set_hid = set_output_hid ) trans.sa_session.add( data ) trans.sa_session.flush() # Add all the children to their parents

--- a/lib/galaxy/web/base/controller.py Tue Feb 01 19:56:05 2011 -0500 +++ b/lib/galaxy/web/base/controller.py Tue Feb 01 20:07:17 2011 -0500 @@ -164,14 +164,19 @@

# Set tracks. if 'tracks' in latest_revision.config: - hda_query = trans.sa_session.query( trans.model.HistoryDatasetAssociation ) for t in visualization.latest_revision.config['tracks']: dataset_id = t['dataset_id'] + hda_ldda = t.get('hda_ldda', 'hda') + if hda_ldda == "hda": + dataset = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) + else: + dataset = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id(dataset_id) ) + try: prefs = t['prefs'] except KeyError: prefs = {} - dataset = hda_query.get( dataset_id ) + track_type, _ = dataset.datatype.get_track_type() track_data_provider_class = get_data_provider( original_dataset=dataset ) track_data_provider = track_data_provider_class( original_dataset=dataset ) @@ -179,6 +184,7 @@ tracks.append( { "track_type": track_type, "name": t['name'], + "hda_ldda": t.get("hda_ldda", "hda"), "dataset_id": trans.security.encode_id( dataset.id ), "prefs": prefs, "filters": track_data_provider.get_filters(),

--- a/lib/galaxy/web/controllers/tracks.py Tue Feb 01 19:56:05 2011 -0500 +++ b/lib/galaxy/web/controllers/tracks.py Tue Feb 01 20:07:17 2011 -0500 @@ -9,6 +9,7 @@ from galaxy import model from galaxy.util.json import to_json_string, from_json_string from galaxy.web.base.controller import * +from galaxy.web.controllers.library import LibraryListGrid from galaxy.web.framework import simplejson from galaxy.web.framework.helpers import time_ago, grids from galaxy.util.bunch import Bunch @@ -36,8 +37,8 @@ # Provide link to list all datasets in history that have a given dbkey. # Right now, only dbkey needs to be passed through, but pass through # all for now since it's cleaner. - d = dict( action='list_history_datasets', show_item_checkboxes=True ) - d[ "f-history" ] = history.id + d = dict( action=grid.datasets_action, show_item_checkboxes=True ) + d[ grid.datasets_param ] = trans.security.encode_id( history.id ) for filter, value in grid.cur_filter_dict.iteritems(): d[ "f-" + filter ] = value return d @@ -56,6 +57,8 @@ model_class = model.History template='/tracks/history_select_grid.mako' default_sort_key = "-update_time" + datasets_action = 'list_history_datasets' + datasets_param = "f-history" columns = [ NameColumn( "History Name", key="name", filterable="standard" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), @@ -67,6 +70,24 @@ def apply_query_filter( self, trans, query, **kwargs ): return query.filter_by( user=trans.user, purged=False, deleted=False, importing=False )

+class LibrarySelectionGrid( LibraryListGrid ): + """ + Grid enables user to select a Library, which is then used to display + datasets from the history. + """ + title = "Add Track: Select Library" + template='/tracks/history_select_grid.mako' + model_class = model.Library + datasets_action = 'list_library_datasets' + datasets_param = "f-library" + columns = [ + NameColumn( "Library Name", key="name", filterable="standard" ), + grids.GridColumn( "Description", key="description" ) + ] + num_rows_per_page = 10 + use_async = True + use_paging = True + class DbKeyColumn( grids.GridColumn ): """ Column for filtering by and displaying dataset dbkey. """ def filter( self, trans, user, query, dbkey ): @@ -78,7 +99,7 @@ class HistoryColumn( grids.GridColumn ): """ Column for filtering by history id. """ def filter( self, trans, user, query, history_id ): - return query.filter( model.History.id==history_id ) + return query.filter( model.History.id==trans.security.decode_id(history_id) )

class HistoryDatasetsSelectionGrid( grids.Grid ): # Grid definition. @@ -95,7 +116,7 @@ grids.TextColumn( "Name", key="name", model_class=model.HistoryDatasetAssociation ), grids.TextColumn( "Filetype", key="extension", model_class=model.HistoryDatasetAssociation ), HistoryColumn( "History", key="history", visible=False ), - DbKeyColumn( "Dbkey", key="dbkey", model_class=model.HistoryDatasetAssociation, visible=False ) + DbKeyColumn( "Dbkey", key="dbkey", model_class=model.HistoryDatasetAssociation, visible=True, sortable=False ) ] columns.append( grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[0], columns[1] ], @@ -103,7 +124,7 @@ )

def build_initial_query( self, trans, **kwargs ): - return trans.sa_session.query( self.model_class ).join( model.History.table).join( model.Dataset.table ) + return trans.sa_session.query( self.model_class ).join( model.History.table ).join( model.Dataset.table ) def apply_query_filter( self, trans, query, **kwargs ): if self.available_tracks is None: self.available_tracks = trans.app.datatypes_registry.get_available_tracks() @@ -111,42 +132,6 @@ .filter( model.Dataset.state == model.Dataset.states.OK ) \ .filter( model.HistoryDatasetAssociation.deleted == False ) \ .filter( model.HistoryDatasetAssociation.visible == True ) - -# TODO: not currently used. Do we want to keep this? -class DatasetSelectionGrid( grids.Grid ): - """ Lists all user datasets that can be added to a visualization. """ - - # Grid definition. - available_tracks = None - title = "Add Tracks" - template = "/tracks/add_tracks.mako" - async_template = "/page/select_items_grid_async.mako" - model_class = model.HistoryDatasetAssociation - default_filter = { "deleted" : "False" , "shared" : "All" } - default_sort_key = "name" - use_async = True - use_paging = False - columns = [ - grids.TextColumn( "Name", key="name", model_class=model.HistoryDatasetAssociation ), - grids.TextColumn( "Filetype", key="extension", model_class=model.HistoryDatasetAssociation ), - DbKeyColumn( "Dbkey", key="dbkey", model_class=model.HistoryDatasetAssociation, visible=False ) - ] - columns.append( - grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[0], columns[1] ], - key="free-text-search", visible=False, filterable="standard" ) - ) - - def build_initial_query( self, trans, **kwargs ): - return trans.sa_session.query( self.model_class ).join( model.History.table).join( model.Dataset.table ) - def apply_query_filter( self, trans, query, **kwargs ): - if self.available_tracks is None: - self.available_tracks = trans.app.datatypes_registry.get_available_tracks() - return query.filter( model.History.user == trans.user ) \ - .filter( model.HistoryDatasetAssociation.extension.in_(self.available_tracks) ) \ - .filter( model.Dataset.state == model.Dataset.states.OK ) \ - .filter( model.History.deleted == False ) \ - .filter( model.HistoryDatasetAssociation.deleted == False ) \ - .filter( model.HistoryDatasetAssociation.visible == True )

class TracksterSelectionGrid( grids.Grid ): # Grid definition. @@ -178,9 +163,9 @@ datasets in the current history, and display of the resulting browser. """

+ libraries_grid = LibrarySelectionGrid() histories_grid = HistorySelectionGrid() history_datasets_grid = HistoryDatasetsSelectionGrid() - data_grid = DatasetSelectionGrid() tracks_grid = TracksterSelectionGrid()

# @@ -216,8 +201,13 @@

@web.json @web.require_login() - def add_track_async(self, trans, id): - dataset = self.get_dataset( trans, id, check_ownership=False, check_accessible=True ) + def add_track_async(self, trans, hda_id=None, ldda_id=None): + if hda_id: + hda_ldda = "hda" + dataset = self.get_dataset( trans, hda_id, check_ownership=False, check_accessible=True ) + elif ldda_id: + hda_ldda = "ldda" + dataset = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( ldda_id ) ) track_type, _ = dataset.datatype.get_track_type() track_data_provider_class = get_data_provider( original_dataset=dataset ) track_data_provider = track_data_provider_class( original_dataset=dataset ) @@ -225,6 +215,7 @@ track = { "track_type": track_type, "name": dataset.name, + "hda_ldda": hda_ldda, "dataset_id": trans.security.encode_id( dataset.id ), "prefs": {}, "filters": track_data_provider.get_filters(), @@ -371,7 +362,7 @@ return msg

@web.json - def converted_datasets_state( self, trans, dataset_id, chrom=None, low=None, high=None ): + def converted_datasets_state( self, trans, hda_ldda, dataset_id, chrom=None, low=None, high=None ): """ Returns state of dataset's converted datasets. If a genome window is specified, method checks whether dataset has data in the window. @@ -379,7 +370,10 @@ # TODO: this code is copied from data() -- should refactor.

# Dataset check. - dataset = self.get_dataset( trans, dataset_id ) + if hda_ldda == "hda": + dataset = self.get_dataset( trans, dataset_id ) + else: + dataset = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) msg = self._check_dataset_state( trans, dataset ) if msg: return msg @@ -402,7 +396,7 @@ return messages.DATA

@web.json - def data( self, trans, dataset_id, chrom, low, high, **kwargs ): + def data( self, trans, hda_ldda, dataset_id, chrom, low, high, **kwargs ): """ Called by the browser to request a block of data """ @@ -412,7 +406,10 @@ return messages.NO_DATA

# Dataset check. - dataset = self.get_dataset( trans, dataset_id ) + if hda_ldda == "hda": + dataset = self.get_dataset( trans, dataset_id ) + else: + dataset = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) msg = self._check_dataset_state( trans, dataset ) if msg: return msg @@ -491,11 +488,12 @@ # Tracks from payload tracks = [] for track in decoded_payload['tracks']: - tracks.append( { "dataset_id": str( trans.security.decode_id( track['dataset_id']) ), + tracks.append( { "dataset_id": track['dataset_id'], + "hda_ldda": track.get('hda_ldda', "hda"), "name": track['name'], "track_type": track['track_type'], "prefs": track['prefs'], - "is_child": track['is_child'] + "is_child": track.get('is_child', False) } ) # Viewport from payload if 'viewport' in decoded_payload: @@ -511,6 +509,32 @@ return trans.security.encode_id(vis.id)

@web.expose + @web.require_login( "see all available libraries" ) + def list_libraries( self, trans, **kwargs ): + """List all libraries that can be used for selecting datasets.""" + + # Render the list view + return self.libraries_grid( trans, **kwargs ) + + @web.expose + @web.require_login( "see a library's datasets that can added to this visualization" ) + def list_library_datasets( self, trans, **kwargs ): + """List a library's datasets that can be added to a visualization.""" + + library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( kwargs.get('f-library') ) ) + return trans.fill_template( '/library/common/browse_library.mako', + cntrller="library", + use_panels=False, + library=library, + created_ldda_ids='', + hidden_folder_ids='', + show_deleted=False, + comptypes=[], + current_user_roles=trans.get_current_user_roles(), + message='', + status="done" ) + + @web.expose @web.require_login( "see all available histories" ) def list_histories( self, trans, **kwargs ): """List all histories that can be used for selecting datasets.""" @@ -654,6 +678,12 @@ output_dataset = joda.dataset

return self.add_track_async( trans, output_dataset.id ) + + @web.expose + def woot( self, trans, ldda_id, target_type ): + ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( ldda_id ) ) + converted_dataset = ldda.get_converted_dataset( trans, target_type ) + raise converted_dataset

# # Helper methods.

--- a/static/scripts/packed/trackster.js Tue Feb 01 19:56:05 2011 -0500 +++ b/static/scripts/packed/trackster.js Tue Feb 01 20:07:17 2011 -0500 @@ -1,1 +1,1 @@ -CanvasRenderingContext2D.prototype.dashedLine=function(c,i,b,h,f){if(f==undefined){f=4}var e=b-c;var d=h-i;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var k=e/g;var j=d/g;for(var a=0;a<g;a++,c+=k,i+=j){if(a%2!=0){continue}this.fillRect(c,i,f,1)}};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();for(var c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c==f.length){if(this!=f.get(c-1)){g.append(this)}}else{if(this!=f.get(c)){$(this).insertBefore(f.get(c))}}})}var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_CANNOT_RUN_TOOL="Tool cannot be rerun: ",DATA_LOADING="Loading data...",DATA_OK="Ready for display",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}CONTEXT=DUMMY_CANVAS.getContext("2d");PX_PER_CHAR=CONTEXT.measureText("A").width;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.move_key_to_end(b,a)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},move_key_to_end:function(b,a){this.key_ary.splice(a,1);this.key_ary.push(b)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var DataCache=function(a){Cache.call(this,a)};$.extend(DataCache.prototype,Cache.prototype,{get_data:function(g,b,e){var h=this.get(this.gen_key(g,b,e));if(h){return h}var j,f,a,d,e,h;for(var c=0;c<this.key_ary.length;c++){j=this.key_ary[c];f=this.split_key(j);a=f[0];d=f[1];if(g>=a&&b<=d){h=this.obj_cache[j];if(h.dataset_type!=="summary_tree"&&h.extra_info!=="no_detail"){this.move_key_to_end(j,c);return h}}}return undefined},set_data:function(b,c,d,a){return this.set(this.gen_key(b,c,d),a)},gen_key:function(a,c,d){var b=a+"_"+c;return b},split_key:function(a){return a.split("_")}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.chrom_form);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.chrom_form);$.ajax({url:chrom_url,data:(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}),dataType:"json",success:function(f){if(f.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=f.chrom_info;var j='<option value="">Select Chrom/Contig</option>';for(var h=0,e=a.chrom_data.length;h<e;h++){var g=a.chrom_data[h].chrom;j+='<option value="'+g+'">'+g+"</option>"}a.chrom_select.html(j);a.intro_div.show();a.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});if(d){d()}},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var i=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(i/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX;g.enable_pan=(f.clientX<a.viewport_container.width()-16)?true:false}).bind("drag",function(h,j){if(!j.enable_pan){return}var f=$(this);var k=j.offsetX-j.current_x;var g=f.scrollTop()-(h.clientY-j.current_height);console.log(g);f.scrollTop(g);j.current_height=h.clientY;j.current_x=j.offsetX;var i=Math.round(k/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height(),top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j,k){$(k.proxy).css({left:Math.min(j.pageX,k.startX),width:Math.abs(j.pageX-k.startX)});var g=Math.min(j.pageX,k.startX)-a.container.offset().left,f=Math.max(j.pageX,k.startX)-a.container.offset().left,i=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*i)+a.low,Math.round(f/h*i)+a.low)}).bind("dragend",function(k,l){var g=Math.min(k.pageX,l.startX),f=Math.max(k.pageX,l.startX),i=(a.high-a.low),h=a.viewport_container.width(),j=a.low;a.low=Math.round(g/h*i)+j;a.high=Math.round(f/h*i)+j;$(l.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},change_chrom:function(e,b,g){var d=this;var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){return}if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()},go_to:function(f){var j=this,a,d,b=f.split(":"),h=b[0],i=b[1];if(i!==undefined){try{var g=i.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}j.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);sortable(a.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)==0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}$.getJSON(this.dataset_check_url,{dataset_id:a.dataset_id,chrom:a.view.chrom,low:a.view.max_low,high:a.view.max_high},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").attr("id",d+"_error");c.text("View error");$("#"+d+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b==="data"){a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;a.predraw_init();a.draw()}}}}}}})},predraw_init:function(){},restore_prefs:function(a){var b=this;$.each(a,function(c,d){if(d!==undefined){b.prefs[c]=d}})},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(g,d,s){var o=this,j=o.view;this.filters=(g!==undefined?get_filters_from_dict(g):[]);this.tool=(d!==undefined?get_tool_from_dict(d):undefined);this.parent_track=s;this.child_tracks=[];if(o.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filtering_div=$("<div/>").addClass("track-filters").hide();this.header_div.after(this.filtering_div);this.filtering_div.bind("drag",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var t=$("<table class='filters'>").appendTo(this.filtering_div);$.each(this.filters,function(w,z){var v=$("<tr>").appendTo(t);var y=$("<th class='filter-info'>").appendTo(v);var u=$("<span class='name'>").appendTo(y);u.text(z.name+" ");var i=$("<span class='values'>").appendTo(y);var x=$("<td>").appendTo(v);z.control_element=$("<div id='"+z.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(x);z.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(B,C){var A=C.values;i.text("["+A[0]+"-"+A[1]+"]");z.low=A[0];z.high=A[1];o.draw(true)},change:function(A,B){z.control_element.slider("option","slide").call(z.control_element,A,B)}});z.slider=z.control_element;z.slider_label=i});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(i){i.stopPropagation()}).bind("click",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var l=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var e=this.tool.params;var o=this;$.each(this.tool.params,function(A,v){var y=$("<div>").addClass("param-row").appendTo(o.dynamic_tool_div);var x=$("<div>").addClass("slider-label").appendTo(y);var C=$("<span class='param-name'>").text(v.label+" ").appendTo(x);var w=$("<span/>").text(v.value);var z=$("<span class='param-value'>").appendTo(x).append("[").append(w).append("]");var B=$("<div/>").addClass("slider").appendTo(y);var i=$("<div id='"+v.name+"-param-control'>").appendTo(B);var u=(v.max<=1?0.01:(v.max<=1000?1:5));i.slider({min:v.min,max:v.max,step:u,value:v.value,slide:function(D,F){var E=F.value;v.value=E;if(0<E&&E<1){E=parseFloat(E).toFixed(2)}w.text(E)},change:function(D,E){v.value=E.value}});z.click(function(){var F=w,E=F.text(),D=(v.max<=1?4:v.max.length);F.text("");$("<input type='text'/>").attr("size",D).attr("maxlength",D).attr("value",E).appendTo(F).focus().select().click(function(G){G.stopPropagation()}).blur(function(){$(this).remove();F.text(E)}).keyup(function(I){if(I.keyCode===27){$(this).trigger("blur")}else{if(I.keyCode===13){var G=$(this),H=parseFloat(G.val());if(isNaN(H)||H>v.max||H<v.min){alert("Parameter value must be in the range ["+v.min+"-"+v.max+"]");return $(this)}F.text(H);i.slider("value",H);v.value=H}}})});$("<div style='clear: both;'/>").appendTo(y)});var b=$("<div>").addClass("param-row").appendTo(this.dynamic_tool_div);var n=$("<input type='submit'>").attr("value","Run").appendTo(b);var o=this;n.click(function(){o.run_tool()})}o.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();o.container_div.append(o.child_tracks_container);if(o.display_modes!==undefined){if(o.mode_div===undefined){o.mode_div=$("<div class='right-float menubutton popup' />").appendTo(o.header_div);var m=o.display_modes[0];o.mode=m;o.mode_div.text(m);var a=function(i){o.mode_div.text(i);o.mode=i;o.tile_cache.clear();o.draw()};var f={};for(var q=0,r=o.display_modes.length;q<r;q++){var k=o.display_modes[q];f[k]=function(i){return function(){a(i)}}(k)}make_popupmenu(o.mode_div,f)}else{o.mode_div.hide()}}var h={};h["Edit configuration"]=function(){var v=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},i=function(){o.update_options(o.track_id);hide_modal();$(window).unbind("keypress.check_enter_esc")},u=function(w){if((w.keyCode||w.which)===27){v()}else{if((w.keyCode||w.which)===13){i()}}};$(window).bind("keypress.check_enter_esc",u);show_modal("Configure Track",o.gen_options(o.track_id),{Cancel:v,OK:i})};h["Set as overview"]=function(){j.overview_viewport.find("canvas").remove();o.is_overview=true;o.set_overview();for(var i in j.tracks){if(j.tracks[i]!==o){j.tracks[i].is_overview=false}}};if(o.filters.length>0){h["Show filters"]=function(){var i;if(!o.filtering_div.is(":visible")){i="Hide filters";o.filters_visible=true}else{i="Show filters";o.filters_visible=false}o.filtering_div.toggle()}}if(o.tool){h["Toggle Tool"]=function(){var i;if(!o.dynamic_tool_div.is(":visible")){i="Hide dynamic tool";o.update_name(o.name+o.tool_region_and_parameters_str())}else{i="Show dynamic tool";o.revert_name()}o.dynamic_tool_div.toggle()}}var c=j;var p=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;p=function(){}}h.Remove=function(){c.remove_track(o);if(c.num_tracks===0){p()}};o.popup_menu=make_popupmenu(o.name_div,h)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(a){var m=this.view.low,g=this.view.high,j=g-m,f=this.view.resolution;var p=$("<div style='position: relative;'></div>"),q=this.content_div.width()/j;this.content_div.append(p);this.max_height=0;var b=Math.floor(m/f/DENSITY);var l={};while((b*DENSITY*f)<g){var n=this.content_div.width()+"_"+q+"_"+b;var e=this.tile_cache.get(n);if(!a&&e){var k=b*DENSITY*f;var d=(k-m)*q;if(this.left_offset){d-=this.left_offset}e.css({left:d});this.show_tile(e,p)}else{this.delayed_draw(this,n,m,g,b,f,p,q,l)}b+=1}var c=this;var o=setInterval(function(){if(obj_length(l)===0){if(c.content_div.children().length>1){c.content_div.children(":first").remove()}for(var i=0;i<c.filters.length;i++){c.filters[i].update_ui_elt()}clearInterval(o)}},50);for(var h=0;h<this.child_tracks.length;h++){this.child_tracks[h].draw(a)}},delayed_draw:function(c,h,g,e,b,d,i,j,f){var a=setTimeout(function(){if(g<=c.view.high&&e>=c.view.low){var k=c.draw_tile(d,b,i,j);if(k){if(!c.initial_canvas&&!window.G_vmlCanvasManager){c.initial_canvas=$(k).clone();var n=k.get(0).getContext("2d");var l=c.initial_canvas.get(0).getContext("2d");var m=n.getImageData(0,0,n.canvas.width,n.canvas.height);l.putImageData(m,0,0);c.set_overview()}c.tile_cache.set(h,k);c.show_tile(k,i)}}delete f[a]},50);f[a]=true},show_tile:function(a,c){var b=this;c.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");if(b.hidden){return}if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type=="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f=="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f=="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.data_queue={};this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,j=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var n=e.get(0).getContext("2d");if(o>PX_PER_CHAR){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;e.css({position:"absolute",top:0,left:(g-this.view.low)*o-this.left_offset});for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o),i=Math.round(o/2);n.fillText(m[h],a+this.left_offset+i,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(d,b,a,c){this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.min_height_px=12;this.max_height_px=400;this.height_px=80;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={color:"black",min_value:undefined,max_value:undefined,mode:this.mode};this.restore_prefs(c);(function(e){var h=false;var g=false;var f=$("<div class='track-resize'>");$(e.container_div).hover(function(){h=true;f.show()},function(){h=false;if(!g){f.hide()}});f.hide().bind("dragstart",function(i,j){g=true;j.original_height=$(e.content_div).height()}).bind("drag",function(j,k){var i=Math.min(Math.max(k.original_height+k.deltaY,e.min_height_px),e.max_height_px);$(e.content_div).css("height",i);e.height_px=i;e.draw(true)}).bind("dragend",function(i,j){e.tile_cache.clear();g=false;if(!h){f.hide()}}).appendTo(e.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;$.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:this.data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,x=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(x)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(x);if(!v){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;var w=Math.round(d+k/m*d);n.beginPath();n.moveTo(0,w);n.lineTo(a*e,w);n.fillStyle="#aaa";n.stroke();n.beginPath();n.fillStyle=this.prefs.color;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(h/m*d);n.fillRect(u,w,f,-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,w);n.lineTo(0,w)}n.fill()}else{n.stroke()}c.append(b);return b},gen_options:function(m){var a=$("<div />").addClass("form-row");var e="track_"+m+"_color",b=$("<label />").attr("for",e).text("Color:"),c=$("<input />").attr("id",e).attr("name",e).val(this.prefs.color),h="track_"+m+"_minval",l=$("<label></label>").attr("for",h).text("Min value:"),d=(this.prefs.min_value===undefined?"":this.prefs.min_value),k=$("<input></input>").attr("id",h).val(d),j="track_"+m+"_maxval",g=$("<label></label>").attr("for",j).text("Max value:"),i=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",j).val(i);return a.append(l).append(k).append(g).append(f).append(b).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_color").val();if(a!==this.prefs.min_value||c!==this.prefs.max_value||b!==this.prefs.color){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.color=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(f,c,a,e,g,d,b){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,f,c,c.viewport_container);TiledTrack.call(this,g,d,b);this.height_px=0;this.container_div.addClass("feature-track");this.dataset_id=a;this.original_dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataCache(20);this.left_offset=200;this.prefs={block_color:"#444",label_color:"black",show_counts:true};this.restore_prefs(e)};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(b.data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set_data(a,d,b.mode,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,b,p){var r=this.inc_slots[a];if(!r||(r.mode!==p)){r={};r.w_scale=a;r.mode=p;this.inc_slots[a]=r;this.s_e_by_tile[a]={}}var l=r.w_scale,x=[],y=[],j=0,n=this.view.max_low;for(var v=0,w=h.length;v<w;v++){var g=h[v],k=g[0];if(r[k]!==undefined){j=Math.max(j,r[k]);y.push(r[k])}else{x.push(v)}}var q=this.s_e_by_tile[a];var m=function(D,E){var C;for(var B=0,F;B<=MAX_FEATURE_DEPTH;B++){C=true;F=q[B];if(F!==undefined){for(var z=0,A=F.length;z<A;z++){var i=F[z];if(E>i[0]&&D<i[1]){C=false;break}}}if(C){break}}if(C){return B}else{return -1}};for(var v=0,w=x.length;v<w;v++){var g=h[x[v]],k=g[0],t=g[1],c=g[2],o=g[3],d=Math.floor((t-n)*l),f=Math.ceil((c-n)*l),u=CONTEXT.measureText(o).width,e;if(o!==undefined&&!b){if(d-u<0){f+=u;e="left"}else{d-=u;e="right"}}var s=m(d,f);if(s<0){}if(s>=0){slot=q[s];if(slot===undefined){slot=q[s]=[]}slot.push([d,f]);r[k]=s;j=Math.max(j,s)}else{console.log("WARNING: not displaying feature")}}return j},rect_or_text:function(r,l,u,b,q,j,g,f){r.textAlign="center";var d=0,s=0,p=Math.round(l/2);for(var m=0,t=j.length;m<t;m++){var k=j[m],e="MIDNSHP=X"[k[0]],n=k[1];if(e==="H"||e==="S"){d-=n}var h=q+d,x=Math.floor(Math.max(0,(h-u)*l)),i=Math.floor(Math.max(0,(h+n-u)*l));switch(e){case"H":break;case"S":case"M":case"=":var o=g.slice(s,s+n);if((this.mode==="Pack"||this.mode==="Auto")&&g!==undefined&&l>PX_PER_CHAR){r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+1,i-x,9);r.fillStyle=CONNECTOR_COLOR;for(var v=0,a=o.length;v<a;v++){if(h+v>=u&&h+v<=b){var w=Math.floor(Math.max(0,(h+v-u)*l));r.fillText(o[v],w+this.left_offset+p,f+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+(this.mode!="Dense"?4:5),i-x,(this.mode!="Dense"?3:1))}s+=n;break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(x+this.left_offset,f+5,i-x,1);break;case"D":r.fillStyle="red";r.fillRect(x+this.left_offset,f+4,i-x,3);break;case"P":break;case"I":s+=n;break;case"X":s+=n;break}d+=n}},draw_tile:function(ad,n,r,ar){var L=n*DENSITY*ad,ai=(n+1)*DENSITY*ad,K=ai-L;var G=this.data_cache.get_data(L,ai,this.mode);if(G===undefined||G==="pending"||(this.mode!=="Auto"&&G.dataset_type==="summary_tree")){this.data_queue[[L,ai]]=true;this.get_data(L,ai);return}var a=Math.ceil(K*ar),af=this.prefs.label_color,h=this.prefs.block_color,q=this.mode,v=25,ab=(q==="Squish")||(q==="Dense")&&(q!=="Pack")||(q==="Auto"&&(G.extra_info==="no_detail")),U=this.left_offset,aq,B,at;var p=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(p)}p=$(p);if(G.dataset_type==="summary_tree"){B=this.summary_draw_height}else{if(q==="Dense"){B=v;at=10}else{at=(ab?this.vertical_nodetail_px:this.vertical_detail_px);var w=(ar<0.0001?1/this.view.zoom_res:ar);B=this.incremental_slots(w,G.data,ab,q)*at+v;aq=this.inc_slots[w]}}p.css({position:"absolute",top:0,left:(L-this.view.low)*ar-U});p.get(0).width=a+U;p.get(0).height=B;r.parent().css("height",Math.max(this.height_px,B)+"px");var H=p.get(0).getContext("2d");H.fillStyle=h;H.font=this.default_font;H.textAlign="right";this.container_div.find(".yaxislabel").remove();if(G.dataset_type=="summary_tree"){var W=G.data,J=G.max,b=Math.ceil(G.delta*ar);var o=$("<div />").addClass("yaxislabel");o.text(J);o.css({position:"absolute",top:"22px",left:"10px"});o.prependTo(this.container_div);for(var am=0,F=W.length;am<F;am++){var Y=Math.floor((W[am][0]-L)*ar);var X=W[am][1];if(!X){continue}var aj=X/J*this.summary_draw_height;H.fillStyle="black";H.fillRect(Y+U,this.summary_draw_height-aj,b,aj);if(this.prefs.show_counts&&H.measureText(X).width<b){H.fillStyle="#bbb";H.textAlign="center";H.fillText(X,Y+U+(b/2),this.summary_draw_height-5)}}r.append(p);return p}if(G.message){p.css({border:"solid red","border-width":"2px 2px 2px 0px"});H.fillStyle="red";H.textAlign="left";H.fillText(G.message,100+U,at);return p}for(var ao=0;ao<this.filters.length;ao++){if(this.filters[ao].applies_to(G.data[0])){p.addClass(FILTERABLE_CLASS);break}}var ap=G.data;var al=0;for(var am=0,F=ap.length;am<F;am++){var Q=ap[am],P=Q[0],an=Q[1],aa=Q[2],M=Q[3];if(this.mode!="Dense"&&aq[P]===undefined){continue}var Z=false;var S;for(var ao=0;ao<this.filters.length;ao++){S=this.filters[ao];S.update_attrs(Q);if(!S.keep(Q)){Z=true;break}}if(Z){continue}if(an<=ai&&aa>=L){var ac=Math.floor(Math.max(0,(an-L)*ar)),I=Math.ceil(Math.min(a,Math.max(0,(aa-L)*ar))),V=(q==="Dense"?1:(1+aq[P]))*at;var E,ag,N=null,au=null;if(G.dataset_type==="bai"){H.fillStyle=h;if(Q[5] instanceof Array){var C=Math.floor(Math.max(0,(Q[4][0]-L)*ar)),O=Math.ceil(Math.min(a,Math.max(0,(Q[4][1]-L)*ar))),A=Math.floor(Math.max(0,(Q[5][0]-L)*ar)),u=Math.ceil(Math.min(a,Math.max(0,(Q[5][1]-L)*ar)));if(Q[4][1]>=L&&Q[4][0]<=ai&&Q[4][2]){this.rect_or_text(H,ar,L,ai,Q[4][0],Q[4][2],Q[4][3],V)}if(Q[5][1]>=L&&Q[5][0]<=ai&&Q[5][2]){this.rect_or_text(H,ar,L,ai,Q[5][0],Q[5][2],Q[5][3],V)}if(A>O){H.fillStyle=CONNECTOR_COLOR;H.dashedLine(O+U,V+5,U+A,V+5)}}else{H.fillStyle=h;this.rect_or_text(H,ar,L,ai,an,Q[4],Q[5],V)}if(q!=="Dense"&&!ab&&an>L){H.fillStyle=this.prefs.label_color;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}}else{if(G.dataset_type==="interval_index"){if(ab){H.fillStyle=h;H.fillRect(ac+U,V+5,I-ac,1)}else{var D=Q[5],T=Q[6],ae=Q[7],g=Q[8];if(T&&ae){N=Math.floor(Math.max(0,(T-L)*ar));au=Math.ceil(Math.min(a,Math.max(0,(ae-L)*ar)))}if(q!=="Dense"&&M!==undefined&&an>L){H.fillStyle=af;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}if(g){if(D){if(D=="+"){H.fillStyle=RIGHT_STRAND}else{if(D=="-"){H.fillStyle=LEFT_STRAND}}H.fillRect(ac+U,V,I-ac,10);H.fillStyle=h}for(var ak=0,e=g.length;ak<e;ak++){var t=g[ak],d=Math.floor(Math.max(0,(t[0]-L)*ar)),R=Math.ceil(Math.min(a,Math.max((t[1]-L)*ar)));if(d>R){continue}E=5;ag=3;H.fillRect(d+U,V+ag,R-d,E);if(N!==undefined&&!(d>au||R<N)){E=9;ag=1;var ah=Math.max(d,N),z=Math.min(R,au);H.fillRect(ah+U,V+ag,z-ah,E)}}}else{E=9;ag=1;H.fillRect(ac+U,V+ag,I-ac,E);if(Q.strand){if(Q.strand=="+"){H.fillStyle=RIGHT_STRAND_INV}else{if(Q.strand=="-"){H.fillStyle=LEFT_STRAND_INV}}H.fillRect(ac+U,V,I-ac,10);H.fillStyle=h}}}}else{if(G.dataset_type==="vcf"){if(ab){H.fillStyle=h;H.fillRect(ac+U,V+5,I-ac,1)}else{var s=Q[4],m=Q[5],c=Q[6];E=9;ag=1;H.fillRect(ac+U,V,I-ac,E);if(q!=="Dense"&&M!==undefined&&an>L){H.fillStyle=af;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}var l=s+" / "+m;if(an>L&&H.measureText(l).width<(I-ac)){H.fillStyle="white";H.textAlign="center";H.fillText(l,U+ac+(I-ac)/2,V+8);H.fillStyle=h}}}}}al++}}return p},gen_options:function(i){var a=$("<div />").addClass("form-row");var e="track_"+i+"_block_color",k=$("<label />").attr("for",e).text("Block color:"),l=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),j="track_"+i+"_label_color",g=$("<label />").attr("for",j).text("Text color:"),h=$("<input />").attr("id",j).attr("name",j).val(this.prefs.label_color),f="track_"+i+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(k).append(l).append(g).append(h).append(d)},update_options:function(d){var b=$("#track_"+d+"_block_color").val(),c=$("#track_"+d+"_label_color").val(),a=$("#track_"+d+"_show_count").attr("checked");if(b!==this.prefs.block_color||c!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=c;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,a,c,e){FeatureTrack.call(this,d,b,a,c,e);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});var ToolDataFeatureTrack=function(e,c,a,d,f,b){FeatureTrack.call(this,e,c,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()==0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id},function(c){})}};a()}}); \ No newline at end of file +CanvasRenderingContext2D.prototype.dashedLine=function(c,i,b,h,f){if(f==undefined){f=4}var e=b-c;var d=h-i;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var k=e/g;var j=d/g;for(var a=0;a<g;a++,c+=k,i+=j){if(a%2!=0){continue}this.fillRect(c,i,f,1)}};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();for(var c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c==f.length){if(this!=f.get(c-1)){g.append(this)}}else{if(this!=f.get(c)){$(this).insertBefore(f.get(c))}}})}var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_CANNOT_RUN_TOOL="Tool cannot be rerun: ",DATA_LOADING="Loading data...",DATA_OK="Ready for display",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}CONTEXT=DUMMY_CANVAS.getContext("2d");PX_PER_CHAR=CONTEXT.measureText("A").width;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.move_key_to_end(b,a)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},move_key_to_end:function(b,a){this.key_ary.splice(a,1);this.key_ary.push(b)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var DataCache=function(a){Cache.call(this,a)};$.extend(DataCache.prototype,Cache.prototype,{get_data:function(g,b,e){var h=this.get(this.gen_key(g,b,e));if(h){return h}var j,f,a,d,e,h;for(var c=0;c<this.key_ary.length;c++){j=this.key_ary[c];f=this.split_key(j);a=f[0];d=f[1];if(g>=a&&b<=d){h=this.obj_cache[j];if(h.dataset_type!=="summary_tree"&&h.extra_info!=="no_detail"){this.move_key_to_end(j,c);return h}}}return undefined},set_data:function(b,c,d,a){return this.set(this.gen_key(b,c,d),a)},gen_key:function(a,c,d){var b=a+"_"+c;return b},split_key:function(a){return a.split("_")}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.chrom_form);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.chrom_form);$.ajax({url:chrom_url,data:(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}),dataType:"json",success:function(f){if(f.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=f.chrom_info;var j='<option value="">Select Chrom/Contig</option>';for(var h=0,e=a.chrom_data.length;h<e;h++){var g=a.chrom_data[h].chrom;j+='<option value="'+g+'">'+g+"</option>"}a.chrom_select.html(j);a.intro_div.show();a.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});if(d){d()}},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var i=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(i/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX;g.enable_pan=(f.clientX<a.viewport_container.width()-16)?true:false}).bind("drag",function(h,j){if(!j.enable_pan){return}var f=$(this);var k=j.offsetX-j.current_x;var g=f.scrollTop()-(h.clientY-j.current_height);f.scrollTop(g);j.current_height=h.clientY;j.current_x=j.offsetX;var i=Math.round(k/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height(),top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j,k){$(k.proxy).css({left:Math.min(j.pageX,k.startX),width:Math.abs(j.pageX-k.startX)});var g=Math.min(j.pageX,k.startX)-a.container.offset().left,f=Math.max(j.pageX,k.startX)-a.container.offset().left,i=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*i)+a.low,Math.round(f/h*i)+a.low)}).bind("dragend",function(k,l){var g=Math.min(k.pageX,l.startX),f=Math.max(k.pageX,l.startX),i=(a.high-a.low),h=a.viewport_container.width(),j=a.low;a.low=Math.round(g/h*i)+j;a.high=Math.round(f/h*i)+j;$(l.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},change_chrom:function(e,b,g){var d=this;var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){return}if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()},go_to:function(f){var j=this,a,d,b=f.split(":"),h=b[0],i=b[1];if(i!==undefined){try{var g=i.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}j.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);sortable(a.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)==0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}$.getJSON(this.dataset_check_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom,low:a.view.max_low,high:a.view.max_high},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").attr("id",d+"_error");c.text("View error");$("#"+d+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b==="data"){a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;a.predraw_init();a.draw()}}}}}}})},predraw_init:function(){},restore_prefs:function(a){var b=this;$.each(a,function(c,d){if(d!==undefined){b.prefs[c]=d}})},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(g,d,s){var o=this,j=o.view;this.filters=(g!==undefined?get_filters_from_dict(g):[]);this.tool=(d!==undefined?get_tool_from_dict(d):undefined);this.parent_track=s;this.child_tracks=[];if(o.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filtering_div=$("<div/>").addClass("track-filters").hide();this.header_div.after(this.filtering_div);this.filtering_div.bind("drag",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var t=$("<table class='filters'>").appendTo(this.filtering_div);$.each(this.filters,function(w,z){var v=$("<tr>").appendTo(t);var y=$("<th class='filter-info'>").appendTo(v);var u=$("<span class='name'>").appendTo(y);u.text(z.name+" ");var i=$("<span class='values'>").appendTo(y);var x=$("<td>").appendTo(v);z.control_element=$("<div id='"+z.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(x);z.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(B,C){var A=C.values;i.text("["+A[0]+"-"+A[1]+"]");z.low=A[0];z.high=A[1];o.draw(true)},change:function(A,B){z.control_element.slider("option","slide").call(z.control_element,A,B)}});z.slider=z.control_element;z.slider_label=i});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(i){i.stopPropagation()}).bind("click",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var l=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var e=this.tool.params;var o=this;$.each(this.tool.params,function(A,v){var y=$("<div>").addClass("param-row").appendTo(o.dynamic_tool_div);var x=$("<div>").addClass("slider-label").appendTo(y);var C=$("<span class='param-name'>").text(v.label+" ").appendTo(x);var w=$("<span/>").text(v.value);var z=$("<span class='param-value'>").appendTo(x).append("[").append(w).append("]");var B=$("<div/>").addClass("slider").appendTo(y);var i=$("<div id='"+v.name+"-param-control'>").appendTo(B);var u=(v.max<=1?0.01:(v.max<=1000?1:5));i.slider({min:v.min,max:v.max,step:u,value:v.value,slide:function(D,F){var E=F.value;v.value=E;if(0<E&&E<1){E=parseFloat(E).toFixed(2)}w.text(E)},change:function(D,E){v.value=E.value}});z.click(function(){var F=w,E=F.text(),D=(v.max<=1?4:v.max.length);F.text("");$("<input type='text'/>").attr("size",D).attr("maxlength",D).attr("value",E).appendTo(F).focus().select().click(function(G){G.stopPropagation()}).blur(function(){$(this).remove();F.text(E)}).keyup(function(I){if(I.keyCode===27){$(this).trigger("blur")}else{if(I.keyCode===13){var G=$(this),H=parseFloat(G.val());if(isNaN(H)||H>v.max||H<v.min){alert("Parameter value must be in the range ["+v.min+"-"+v.max+"]");return $(this)}F.text(H);i.slider("value",H);v.value=H}}})});$("<div style='clear: both;'/>").appendTo(y)});var b=$("<div>").addClass("param-row").appendTo(this.dynamic_tool_div);var n=$("<input type='submit'>").attr("value","Run").appendTo(b);var o=this;n.click(function(){o.run_tool()})}o.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();o.container_div.append(o.child_tracks_container);if(o.display_modes!==undefined){if(o.mode_div===undefined){o.mode_div=$("<div class='right-float menubutton popup' />").appendTo(o.header_div);var m=o.display_modes[0];o.mode=m;o.mode_div.text(m);var a=function(i){o.mode_div.text(i);o.mode=i;o.tile_cache.clear();o.draw()};var f={};for(var q=0,r=o.display_modes.length;q<r;q++){var k=o.display_modes[q];f[k]=function(i){return function(){a(i)}}(k)}make_popupmenu(o.mode_div,f)}else{o.mode_div.hide()}}var h={};h["Edit configuration"]=function(){var v=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},i=function(){o.update_options(o.track_id);hide_modal();$(window).unbind("keypress.check_enter_esc")},u=function(w){if((w.keyCode||w.which)===27){v()}else{if((w.keyCode||w.which)===13){i()}}};$(window).bind("keypress.check_enter_esc",u);show_modal("Configure Track",o.gen_options(o.track_id),{Cancel:v,OK:i})};h["Set as overview"]=function(){j.overview_viewport.find("canvas").remove();o.is_overview=true;o.set_overview();for(var i in j.tracks){if(j.tracks[i]!==o){j.tracks[i].is_overview=false}}};if(o.filters.length>0){h["Show filters"]=function(){var i;if(!o.filtering_div.is(":visible")){i="Hide filters";o.filters_visible=true}else{i="Show filters";o.filters_visible=false}o.filtering_div.toggle()}}if(o.tool){h["Toggle Tool"]=function(){var i;if(!o.dynamic_tool_div.is(":visible")){i="Hide dynamic tool";o.update_name(o.name+o.tool_region_and_parameters_str())}else{i="Show dynamic tool";o.revert_name()}o.dynamic_tool_div.toggle()}}var c=j;var p=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;p=function(){}}h.Remove=function(){c.remove_track(o);if(c.num_tracks===0){p()}};o.popup_menu=make_popupmenu(o.name_div,h)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(a){var m=this.view.low,g=this.view.high,j=g-m,f=this.view.resolution;var p=$("<div style='position: relative;'></div>"),q=this.content_div.width()/j;this.content_div.append(p);this.max_height=0;var b=Math.floor(m/f/DENSITY);var l={};while((b*DENSITY*f)<g){var n=this.content_div.width()+"_"+q+"_"+b;var e=this.tile_cache.get(n);if(!a&&e){var k=b*DENSITY*f;var d=(k-m)*q;if(this.left_offset){d-=this.left_offset}e.css({left:d});this.show_tile(e,p)}else{this.delayed_draw(this,n,m,g,b,f,p,q,l)}b+=1}var c=this;var o=setInterval(function(){if(obj_length(l)===0){if(c.content_div.children().length>1){c.content_div.children(":first").remove()}for(var i=0;i<c.filters.length;i++){c.filters[i].update_ui_elt()}clearInterval(o)}},50);for(var h=0;h<this.child_tracks.length;h++){this.child_tracks[h].draw(a)}},delayed_draw:function(c,h,g,e,b,d,i,j,f){var a=setTimeout(function(){if(g<=c.view.high&&e>=c.view.low){var k=c.draw_tile(d,b,i,j);if(k){if(!c.initial_canvas&&!window.G_vmlCanvasManager){c.initial_canvas=$(k).clone();var n=k.get(0).getContext("2d");var l=c.initial_canvas.get(0).getContext("2d");var m=n.getImageData(0,0,n.canvas.width,n.canvas.height);l.putImageData(m,0,0);c.set_overview()}c.tile_cache.set(h,k);c.show_tile(k,i)}}delete f[a]},50);f[a]=true},show_tile:function(a,c){var b=this;c.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");if(b.hidden){return}if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type=="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f=="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f=="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.data_queue={};this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,j=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var n=e.get(0).getContext("2d");if(o>PX_PER_CHAR){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;e.css({position:"absolute",top:0,left:(g-this.view.low)*o-this.left_offset});for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o),i=Math.round(o/2);n.fillText(m[h],a+this.left_offset+i,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(d,b,e,a,c){this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.min_height_px=12;this.max_height_px=400;this.height_px=80;this.hda_ldda=e;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={color:"black",min_value:undefined,max_value:undefined,mode:this.mode};this.restore_prefs(c);(function(f){var i=false;var h=false;var g=$("<div class='track-resize'>");$(f.container_div).hover(function(){i=true;g.show()},function(){i=false;if(!h){g.hide()}});g.hide().bind("dragstart",function(j,k){h=true;k.original_height=$(f.content_div).height()}).bind("drag",function(k,l){var j=Math.min(Math.max(l.original_height+l.deltaY,f.min_height_px),f.max_height_px);$(f.content_div).css("height",j);f.height_px=j;f.draw(true)}).bind("dragend",function(j,k){f.tile_cache.clear();h=false;if(!i){g.hide()}}).appendTo(f.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;$.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:this.data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,x=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(x)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(x);if(!v){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;var w=Math.round(d+k/m*d);n.beginPath();n.moveTo(0,w);n.lineTo(a*e,w);n.fillStyle="#aaa";n.stroke();n.beginPath();n.fillStyle=this.prefs.color;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(h/m*d);n.fillRect(u,w,f,-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,w);n.lineTo(0,w)}n.fill()}else{n.stroke()}c.append(b);return b},gen_options:function(m){var a=$("<div />").addClass("form-row");var e="track_"+m+"_color",b=$("<label />").attr("for",e).text("Color:"),c=$("<input />").attr("id",e).attr("name",e).val(this.prefs.color),h="track_"+m+"_minval",l=$("<label></label>").attr("for",h).text("Min value:"),d=(this.prefs.min_value===undefined?"":this.prefs.min_value),k=$("<input></input>").attr("id",h).val(d),j="track_"+m+"_maxval",g=$("<label></label>").attr("for",j).text("Max value:"),i=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",j).val(i);return a.append(l).append(k).append(g).append(f).append(b).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_color").val();if(a!==this.prefs.min_value||c!==this.prefs.max_value||b!==this.prefs.color){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.color=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(f,c,h,a,e,g,d,b){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,f,c,c.viewport_container);TiledTrack.call(this,g,d,b);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=h;this.dataset_id=a;this.original_dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataCache(20);this.left_offset=200;this.prefs={block_color:"#444",label_color:"black",show_counts:true};this.restore_prefs(e)};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(b.data_url,{chrom:b.view.chrom,low:a,high:d,hda_ldda:b.hda_ldda,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set_data(a,d,b.mode,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,b,p){var r=this.inc_slots[a];if(!r||(r.mode!==p)){r={};r.w_scale=a;r.mode=p;this.inc_slots[a]=r;this.s_e_by_tile[a]={}}var l=r.w_scale,x=[],y=[],j=0,n=this.view.max_low;for(var v=0,w=h.length;v<w;v++){var g=h[v],k=g[0];if(r[k]!==undefined){j=Math.max(j,r[k]);y.push(r[k])}else{x.push(v)}}var q=this.s_e_by_tile[a];var m=function(D,E){var C;for(var B=0,F;B<=MAX_FEATURE_DEPTH;B++){C=true;F=q[B];if(F!==undefined){for(var z=0,A=F.length;z<A;z++){var i=F[z];if(E>i[0]&&D<i[1]){C=false;break}}}if(C){break}}if(C){return B}else{return -1}};for(var v=0,w=x.length;v<w;v++){var g=h[x[v]],k=g[0],t=g[1],c=g[2],o=g[3],d=Math.floor((t-n)*l),f=Math.ceil((c-n)*l),u=CONTEXT.measureText(o).width,e;if(o!==undefined&&!b){if(d-u<0){f+=u;e="left"}else{d-=u;e="right"}}var s=m(d,f);if(s<0){}if(s>=0){slot=q[s];if(slot===undefined){slot=q[s]=[]}slot.push([d,f]);r[k]=s;j=Math.max(j,s)}else{}}return j},rect_or_text:function(r,l,u,b,q,j,g,f){r.textAlign="center";var d=0,s=0,p=Math.round(l/2);for(var m=0,t=j.length;m<t;m++){var k=j[m],e="MIDNSHP=X"[k[0]],n=k[1];if(e==="H"||e==="S"){d-=n}var h=q+d,x=Math.floor(Math.max(0,(h-u)*l)),i=Math.floor(Math.max(0,(h+n-u)*l));switch(e){case"H":break;case"S":case"M":case"=":var o=g.slice(s,s+n);if((this.mode==="Pack"||this.mode==="Auto")&&g!==undefined&&l>PX_PER_CHAR){r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+1,i-x,9);r.fillStyle=CONNECTOR_COLOR;for(var v=0,a=o.length;v<a;v++){if(h+v>=u&&h+v<=b){var w=Math.floor(Math.max(0,(h+v-u)*l));r.fillText(o[v],w+this.left_offset+p,f+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+(this.mode!="Dense"?4:5),i-x,(this.mode!="Dense"?3:1))}s+=n;break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(x+this.left_offset,f+5,i-x,1);break;case"D":r.fillStyle="red";r.fillRect(x+this.left_offset,f+4,i-x,3);break;case"P":break;case"I":s+=n;break;case"X":s+=n;break}d+=n}},draw_tile:function(ad,n,r,ar){var L=n*DENSITY*ad,ai=(n+1)*DENSITY*ad,K=ai-L;var G=this.data_cache.get_data(L,ai,this.mode);if(G===undefined||G==="pending"||(this.mode!=="Auto"&&G.dataset_type==="summary_tree")){this.data_queue[[L,ai]]=true;this.get_data(L,ai);return}var a=Math.ceil(K*ar),af=this.prefs.label_color,h=this.prefs.block_color,q=this.mode,v=25,ab=(q==="Squish")||(q==="Dense")&&(q!=="Pack")||(q==="Auto"&&(G.extra_info==="no_detail")),U=this.left_offset,aq,B,at;var p=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(p)}p=$(p);if(G.dataset_type==="summary_tree"){B=this.summary_draw_height}else{if(q==="Dense"){B=v;at=10}else{at=(ab?this.vertical_nodetail_px:this.vertical_detail_px);var w=(ar<0.0001?1/this.view.zoom_res:ar);B=this.incremental_slots(w,G.data,ab,q)*at+v;aq=this.inc_slots[w]}}p.css({position:"absolute",top:0,left:(L-this.view.low)*ar-U});p.get(0).width=a+U;p.get(0).height=B;r.parent().css("height",Math.max(this.height_px,B)+"px");var H=p.get(0).getContext("2d");H.fillStyle=h;H.font=this.default_font;H.textAlign="right";this.container_div.find(".yaxislabel").remove();if(G.dataset_type=="summary_tree"){var W=G.data,J=G.max,b=Math.ceil(G.delta*ar);var o=$("<div />").addClass("yaxislabel");o.text(J);o.css({position:"absolute",top:"22px",left:"10px"});o.prependTo(this.container_div);for(var am=0,F=W.length;am<F;am++){var Y=Math.floor((W[am][0]-L)*ar);var X=W[am][1];if(!X){continue}var aj=X/J*this.summary_draw_height;H.fillStyle="black";H.fillRect(Y+U,this.summary_draw_height-aj,b,aj);if(this.prefs.show_counts&&H.measureText(X).width<b){H.fillStyle="#bbb";H.textAlign="center";H.fillText(X,Y+U+(b/2),this.summary_draw_height-5)}}r.append(p);return p}if(G.message){p.css({border:"solid red","border-width":"2px 2px 2px 0px"});H.fillStyle="red";H.textAlign="left";H.fillText(G.message,100+U,at);return p}for(var ao=0;ao<this.filters.length;ao++){if(this.filters[ao].applies_to(G.data[0])){p.addClass(FILTERABLE_CLASS);break}}var ap=G.data;var al=0;for(var am=0,F=ap.length;am<F;am++){var Q=ap[am],P=Q[0],an=Q[1],aa=Q[2],M=Q[3];if(this.mode!="Dense"&&aq[P]===undefined){continue}var Z=false;var S;for(var ao=0;ao<this.filters.length;ao++){S=this.filters[ao];S.update_attrs(Q);if(!S.keep(Q)){Z=true;break}}if(Z){continue}if(an<=ai&&aa>=L){var ac=Math.floor(Math.max(0,(an-L)*ar)),I=Math.ceil(Math.min(a,Math.max(0,(aa-L)*ar))),V=(q==="Dense"?1:(1+aq[P]))*at;var E,ag,N=null,au=null;if(G.dataset_type==="bai"){H.fillStyle=h;if(Q[5] instanceof Array){var C=Math.floor(Math.max(0,(Q[4][0]-L)*ar)),O=Math.ceil(Math.min(a,Math.max(0,(Q[4][1]-L)*ar))),A=Math.floor(Math.max(0,(Q[5][0]-L)*ar)),u=Math.ceil(Math.min(a,Math.max(0,(Q[5][1]-L)*ar)));if(Q[4][1]>=L&&Q[4][0]<=ai&&Q[4][2]){this.rect_or_text(H,ar,L,ai,Q[4][0],Q[4][2],Q[4][3],V)}if(Q[5][1]>=L&&Q[5][0]<=ai&&Q[5][2]){this.rect_or_text(H,ar,L,ai,Q[5][0],Q[5][2],Q[5][3],V)}if(A>O){H.fillStyle=CONNECTOR_COLOR;H.dashedLine(O+U,V+5,U+A,V+5)}}else{H.fillStyle=h;this.rect_or_text(H,ar,L,ai,an,Q[4],Q[5],V)}if(q!=="Dense"&&!ab&&an>L){H.fillStyle=this.prefs.label_color;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}}else{if(G.dataset_type==="interval_index"){if(ab){H.fillStyle=h;H.fillRect(ac+U,V+5,I-ac,1)}else{var D=Q[5],T=Q[6],ae=Q[7],g=Q[8];if(T&&ae){N=Math.floor(Math.max(0,(T-L)*ar));au=Math.ceil(Math.min(a,Math.max(0,(ae-L)*ar)))}if(q!=="Dense"&&M!==undefined&&an>L){H.fillStyle=af;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}if(g){if(D){if(D=="+"){H.fillStyle=RIGHT_STRAND}else{if(D=="-"){H.fillStyle=LEFT_STRAND}}H.fillRect(ac+U,V,I-ac,10);H.fillStyle=h}for(var ak=0,e=g.length;ak<e;ak++){var t=g[ak],d=Math.floor(Math.max(0,(t[0]-L)*ar)),R=Math.ceil(Math.min(a,Math.max((t[1]-L)*ar)));if(d>R){continue}E=5;ag=3;H.fillRect(d+U,V+ag,R-d,E);if(N!==undefined&&!(d>au||R<N)){E=9;ag=1;var ah=Math.max(d,N),z=Math.min(R,au);H.fillRect(ah+U,V+ag,z-ah,E)}}}else{E=9;ag=1;H.fillRect(ac+U,V+ag,I-ac,E);if(Q.strand){if(Q.strand=="+"){H.fillStyle=RIGHT_STRAND_INV}else{if(Q.strand=="-"){H.fillStyle=LEFT_STRAND_INV}}H.fillRect(ac+U,V,I-ac,10);H.fillStyle=h}}}}else{if(G.dataset_type==="vcf"){if(ab){H.fillStyle=h;H.fillRect(ac+U,V+5,I-ac,1)}else{var s=Q[4],m=Q[5],c=Q[6];E=9;ag=1;H.fillRect(ac+U,V,I-ac,E);if(q!=="Dense"&&M!==undefined&&an>L){H.fillStyle=af;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}var l=s+" / "+m;if(an>L&&H.measureText(l).width<(I-ac)){H.fillStyle="white";H.textAlign="center";H.fillText(l,U+ac+(I-ac)/2,V+8);H.fillStyle=h}}}}}al++}}return p},gen_options:function(i){var a=$("<div />").addClass("form-row");var e="track_"+i+"_block_color",k=$("<label />").attr("for",e).text("Block color:"),l=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),j="track_"+i+"_label_color",g=$("<label />").attr("for",j).text("Text color:"),h=$("<input />").attr("id",j).attr("name",j).val(this.prefs.label_color),f="track_"+i+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(k).append(l).append(g).append(h).append(d)},update_options:function(d){var b=$("#track_"+d+"_block_color").val(),c=$("#track_"+d+"_label_color").val(),a=$("#track_"+d+"_show_count").attr("checked");if(b!==this.prefs.block_color||c!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=c;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()==0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id},function(c){})}};a()}}); \ No newline at end of file

--- a/static/scripts/trackster.js Tue Feb 01 19:56:05 2011 -0500 +++ b/static/scripts/trackster.js Tue Feb 01 20:07:17 2011 -0500 @@ -385,7 +385,6 @@ var container = $(this); var delta = d.offsetX - d.current_x; var new_scroll = container.scrollTop() - (e.clientY - d.current_height); - console.log( new_scroll ); container.scrollTop(new_scroll); d.current_height = e.clientY; d.current_x = d.offsetX; @@ -843,8 +842,8 @@

// Get dataset state; if state is fine, enable and draw track. Otherwise, show message // about track status. - $.getJSON(this.dataset_check_url, - {dataset_id : track.dataset_id, chrom: track.view.chrom, low: track.view.max_low, high: track.view.max_high}, + $.getJSON(this.dataset_check_url, { hda_ldda: track.hda_ldda, dataset_id: track.dataset_id, + chrom: track.view.chrom, low: track.view.max_low, high: track.view.max_high}, function (result) { if (!result || result === "error" || result.kind === "error") { track.container_div.addClass("error"); @@ -1548,7 +1547,7 @@ } });

-var LineTrack = function ( name, view, dataset_id, prefs ) { +var LineTrack = function ( name, view, hda_ldda, dataset_id, prefs ) { this.track_type = "LineTrack"; this.display_modes = ["Histogram", "Line", "Filled", "Intensity"]; this.mode = "Histogram"; @@ -1558,6 +1557,7 @@ this.min_height_px = 12; this.max_height_px = 400; this.height_px = 80; + this.hda_ldda = hda_ldda; this.dataset_id = dataset_id; this.original_dataset_id = dataset_id; this.data_cache = new DataCache(CACHED_DATA); @@ -1604,7 +1604,7 @@

track.vertical_range = undefined; $.getJSON( track.data_url, { stats: true, chrom: track.view.chrom, low: null, high: null, - dataset_id: track.dataset_id }, function(result) { + hda_ldda: track.hda_ldda, dataset_id: track.dataset_id }, function(result) { track.container_div.addClass( "line-track" ); var data = result.data; if ( isNaN(parseFloat(track.prefs.min_value)) || isNaN(parseFloat(track.prefs.max_value)) ) { @@ -1646,9 +1646,8 @@ track.draw(); });*/ $.ajax({ 'url': this.data_url, 'dataType': 'json', - 'data': { "chrom": this.view.chrom, - "low": low, "high": high, "dataset_id": this.dataset_id, - "resolution": this.view.resolution }, + 'data': { chrom: this.view.chrom, low: low, high: high, + hda_ldda: this.hda_ldda, dataset_id: this.dataset_id, resolution: this.view.resolution }, success: function (result) { var data = result.data; track.data_cache.set(key, data); @@ -1804,7 +1803,7 @@ } });

-var FeatureTrack = function (name, view, dataset_id, prefs, filters, tool, parent_track) { +var FeatureTrack = function (name, view, hda_ldda, dataset_id, prefs, filters, tool, parent_track) { this.track_type = "FeatureTrack"; this.display_modes = ["Auto", "Dense", "Squish", "Pack"]; Track.call(this, name, view, view.viewport_container); @@ -1812,6 +1811,7 @@

this.height_px = 0; this.container_div.addClass( "feature-track" ); + this.hda_ldda = hda_ldda; this.dataset_id = dataset_id; this.original_dataset_id = dataset_id; this.zo_slots = {}; @@ -1839,7 +1839,7 @@ if (!track.data_queue[key]) { track.data_queue[key] = true; $.getJSON( track.data_url, { chrom: track.view.chrom, - low: low, high: high, dataset_id: track.dataset_id, + low: low, high: high, hda_ldda: track.hda_ldda, dataset_id: track.dataset_id, resolution: this.view.resolution, mode: this.mode }, function (result) { track.data_cache.set_data(low, high, track.mode, result); // console.log("datacache", track.data_cache.get(key)); @@ -1987,7 +1987,7 @@ else { // TODO: remove this warning when skipped features are handled. // Show warning for skipped feature. - console.log("WARNING: not displaying feature"); // , feature_uid, f_start, f_end); + // console.log("WARNING: not displaying feature"); // , feature_uid, f_start, f_end); } }

@@ -2425,8 +2425,8 @@ } });

-var ReadTrack = function (name, view, dataset_id, prefs, filters) { - FeatureTrack.call(this, name, view, dataset_id, prefs, filters); +var ReadTrack = function (name, view, hda_ldda, dataset_id, prefs, filters) { + FeatureTrack.call(this, name, view, hda_ldda, dataset_id, prefs, filters); this.track_type = "ReadTrack"; this.vertical_detail_px = 10; this.vertical_nodetail_px = 5; @@ -2436,8 +2436,8 @@ /** * Feature track that displays data generated from tool. */ -var ToolDataFeatureTrack = function(name, view, dataset_id, prefs, filters, parent_track) { - FeatureTrack.call(this, name, view, dataset_id, prefs, filters, {}, parent_track); +var ToolDataFeatureTrack = function(name, view, hda_ldda, dataset_id, prefs, filters, parent_track) { + FeatureTrack.call(this, name, view, hda_ldda, dataset_id, prefs, filters, {}, parent_track); this.track_type = "ToolDataFeatureTrack";

// Set up track to fetch initial data from raw data URL when the dataset--not the converted datasets--

--- a/templates/tracks/browser.mako Tue Feb 01 19:56:05 2011 -0500 +++ b/templates/tracks/browser.mako Tue Feb 01 20:07:17 2011 -0500 @@ -156,7 +156,8 @@ track_config = tracks_config[i]; track = new addable_track_types[track_config["track_type"]]( track_config['name'], - view, + view, + track_config['hda_ldda'], track_config['dataset_id'], track_config['prefs'], track_config['filters'], @@ -211,10 +212,10 @@ var add_async_success = function(track_data) { var td = track_data, new_track = new addable_track_types[track_data.track_type]( - track_data.name, view, track_data.dataset_id, track_data.prefs, - track_data.filters, track_data.tool ); + track_data.name, view, track_data.hda_ldda, track_data.dataset_id, + track_data.prefs, track_data.filters, track_data.tool ); view.add_track(new_track); - // Should replace with live event but can't get working + ## Should replace with live event but can't get working sortable( new_track.container_div, ".draghandle" ); view.has_changes = true; $("#no-tracks").hide(); @@ -229,7 +230,7 @@ });

%endif - + // Use a popup grid to add more tracks $("#add-track").bind("click", function(e) { $.ajax({ @@ -238,18 +239,24 @@ error: function() { alert( "Grid failed" ); }, success: function(table_html) { show_modal( - "Add Track &mdash; Select History, then Dataset(s)", + "Add Track &mdash; Select history/library, then datasets", table_html, { "Cancel": function() { hide_modal(); }, "Insert": function() { - $('input[name=id]:checked').each(function() { - var item_id = $(this).val(); + $('input[name=id]:checked,input[name=ldda_ids]:checked').each(function() { + var data, + id = $(this).val(); + if ($(this).attr("name") === "id") { + data = { hda_id: id }; + } else { + data = { ldda_id: id}; + } $.ajax( { url: "${h.url_for( action='add_track_async' )}", - data: { id: item_id }, + data: data, dataType: "json", success: add_async_success }); @@ -286,6 +293,7 @@ tracks.push( { "track_type": track.track_type, "name": track.name, + "hda_ldda": track.hda_ldda, "dataset_id": track.dataset_id, "prefs": track.prefs, "is_child": (child_id ? true : false )

--- a/templates/tracks/history_datasets_select_grid.mako Tue Feb 01 19:56:05 2011 -0500 +++ b/templates/tracks/history_datasets_select_grid.mako Tue Feb 01 20:07:17 2011 -0500 @@ -10,6 +10,7 @@ url_dict[ "f-" + filter ] = value %> ## Use class 'label' to piggyback on URL functionality in parent template. - <a class="label" href="${h.url_for( **url_dict )}">Back to histories</a><br/> + <a class="label" href="${h.url_for( **url_dict )}">Back to histories</a> + <br /><br /> ${parent.title()} </%def> \ No newline at end of file

--- a/templates/tracks/history_select_grid.mako Tue Feb 01 19:56:05 2011 -0500 +++ b/templates/tracks/history_select_grid.mako Tue Feb 01 20:07:17 2011 -0500 @@ -6,7 +6,7 @@ <%namespace file="../grid_base.mako" import="*" />

## Need to define title so that it can be overridden by child templates. -<%def name="title()"><h2>${grid.title}</h2></%def> +<%def name="title()"></%def>

${self.title()} ${stylesheets()} @@ -19,11 +19,11 @@ var f = function() { $("a.label,.page-link>a").click(function() { var parent_body = $(this).parents("div.body"); - if (parent_body.length != 0) { + if (parent_body.length !== 0) { parent_body.load($(this).attr("href")); return false; } - }); + }); }; // Need to process label URLs when document loaded and when grid changes. $(document).ready(function() { @@ -31,5 +31,15 @@ $('#grid-table-body').bind('update', f); }); </script> + +%if getattr(grid, "datasets_param", None): + %if grid.datasets_param == "f-history": + <a class="label" href="${h.url_for( action='list_libraries' )}">Show Data Libraries</a> + %else: + <a class="label" href="${h.url_for( action='list_histories' )}">Show Histories</a> + %endif + <br /><br /> +%endif + ${render_grid_header( grid, False )} ${render_grid_table( grid, show_item_checkboxes=show_item_checkboxes )} \ No newline at end of file

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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