From 75ab206ca57da42582c0ac04dc903eb68c4824ab Mon Sep 17 00:00:00 2001 From: Jeremy Goecks Date: Thu, 9 Jul 2015 12:47:15 +0200 Subject: [PATCH] Trackster fixes: (a) close data provider files after reading from them (but there are some data providers that currently lack close functions so those files will remain open); (b) fix running tools by correcting HDA manager function call; (c) remove use of underscore template because uglify does not handle it well. --- client/galaxy/scripts/viz/trackster/tracks.js | 9 +- .../visualization/data_providers/genome.py | 129 ++++++++++-------- lib/galaxy/webapps/galaxy/api/tools.py | 2 +- static/maps/viz/trackster/tracks.js.map | 2 +- static/scripts/viz/trackster/tracks.js | 5 +- 5 files changed, 79 insertions(+), 68 deletions(-) diff --git a/client/galaxy/scripts/viz/trackster/tracks.js b/client/galaxy/scripts/viz/trackster/tracks.js index 5509e20740d..f3719d6c2ef 100644 --- a/client/galaxy/scripts/viz/trackster/tracks.js +++ b/client/galaxy/scripts/viz/trackster/tracks.js @@ -2209,15 +2209,14 @@ extend(Track.prototype, Drawable.prototype, { title: "Tool parameter space visualization", css_class: "arrow-split", on_click_fn: function(track) { - var template = - 'Tool: <%= track.tool.get("name") %>
' + - 'Dataset: <%= track.config.get_value("name") %>
' + + var html = + 'Tool:' + track.tool.get("name") + '
' + + 'Dataset:' + track.config.get_value("name") + '
' + 'Region(s): ', - html = _.template(template, { track: track }); + ''; var cancel_fn = function() { Galaxy.modal.hide(); $(window).unbind("keypress.check_enter_esc"); }, ok_fn = function() { var regions_to_use = $('select[name="regions"] option:selected').val(), diff --git a/lib/galaxy/visualization/data_providers/genome.py b/lib/galaxy/visualization/data_providers/genome.py index 4a36d3f26f3..e58836d7334 100644 --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -143,11 +143,6 @@ class GenomeDataProvider( BaseDataProvider ): dependencies=dependencies, error_max_vals=error_max_vals ) - # File/pointer where data is obtained from. It is useful to set this for repeated - # queries, such as is necessary for genome-wide data. - # TODO: add functions to (a) create data_file and (b) clean up data_file. - self.data_file = None - def write_data_to_file( self, regions, filename ): """ Write data in region defined by chrom, start, and end to a file. @@ -167,7 +162,13 @@ class GenomeDataProvider( BaseDataProvider ): """ raise Exception( "Unimplemented Function" ) - def get_iterator( self, chrom, start, end, **kwargs ): + def open_data_file( self ): + """ + Open data file for reading data. + """ + raise Exception( "Unimplemented Function" ) + + def get_iterator( self, data_file, chrom, start, end, **kwargs ): """ Returns an iterator that provides data in the region chrom:start-end """ @@ -189,8 +190,19 @@ class GenomeDataProvider( BaseDataProvider ): dataset_type, data """ start, end = int( low ), int( high ) - iterator = self.get_iterator( chrom, start, end, **kwargs ) - return self.process_data( iterator, start_val, max_vals, start=start, end=end, **kwargs ) + data_file = self.open_data_file() + iterator = self.get_iterator( data_file, chrom, start, end, **kwargs ) + data = self.process_data( iterator, start_val, max_vals, start=start, end=end, **kwargs ) + try: + data_file.close() + except AttributeError: + # FIXME: some data providers do not have a close function implemented. + # Providers without a close function include: + # pysam Tabixfile + # bx IntervalIndex + pass + + return data def get_genome_data( self, chroms_info, **kwargs ): """ @@ -335,40 +347,40 @@ class TabixDataProvider( FilterableMixin, GenomeDataProvider ): col_name_data_attr_mapping = { 4 : { 'index': 4 , 'name' : 'Score' } } - def get_iterator( self, chrom, start, end, **kwargs ): + def open_data_file( self ): + return ctabix.Tabixfile(self.dependencies['bgzip'].file_name, + index_filename=self.converted_dataset.file_name) + + def get_iterator( self, data_file, chrom, start, end, **kwargs ): start, end = int(start), int(end) if end >= (2 << 29): end = (2 << 29 - 1) # Tabix-enforced maximum - bgzip_fname = self.dependencies['bgzip'].file_name - - if not self.data_file: - self.data_file = ctabix.Tabixfile(bgzip_fname, index_filename=self.converted_dataset.file_name) - # Get iterator using either naming scheme. iterator = iter( [] ) - if chrom in self.data_file.contigs: - iterator = self.data_file.fetch(reference=chrom, start=start, end=end) + if chrom in data_file.contigs: + iterator = data_file.fetch(reference=chrom, start=start, end=end) else: # Try alternative naming scheme. chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) - if chrom in self.data_file.contigs: - iterator = self.data_file.fetch(reference=chrom, start=start, end=end) + if chrom in data_file.contigs: + iterator = data_file.fetch(reference=chrom, start=start, end=end) return iterator def write_data_to_file( self, regions, filename ): out = open( filename, "w" ) + data_file = self.open_data_file() for region in regions: # Write data in region. - chrom = region.chrom - start = region.start - end = region.end - iterator = self.get_iterator( chrom, start, end ) + iterator = self.get_iterator( data_file, region.chrom, region.start, region.end ) for line in iterator: out.write( "%s\n" % line ) + # TODO: once Pysam is updated and Tabixfile has a close() method, + # data_file.close() + out.close() # @@ -385,7 +397,7 @@ class IntervalDataProvider( GenomeDataProvider ): Payload format: [ uid (offset), start, end, name, strand, thick_start, thick_end, blocks ] """ - def get_iterator( self, chrom, start, end, **kwargs ): + def get_iterator( self, data_file, chrom, start, end, **kwargs ): raise Exception( "Unimplemented Function" ) def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): @@ -470,7 +482,7 @@ class BedDataProvider( GenomeDataProvider ): dataset_type = 'interval_index' - def get_iterator( self, chrom, start, end, **kwargs ): + def get_iterator( self, data_file, chrom, start, end, **kwargs ): raise Exception( "Unimplemented Method" ) def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): @@ -545,9 +557,11 @@ class BedDataProvider( GenomeDataProvider ): chrom = region.chrom start = region.start end = region.end - iterator = self.get_iterator( chrom, start, end ) + data_file = self.open_data_file() + iterator = self.get_iterator( data_file, chrom, start, end ) for line in iterator: out.write( "%s\n" % line ) + data_file.close() out.close() @@ -567,14 +581,14 @@ class RawBedDataProvider( BedDataProvider ): for large datasets. """ - def get_iterator( self, source, chrom=None, start=None, end=None, **kwargs ): + def get_iterator( self, data_file, chrom=None, start=None, end=None, **kwargs ): # Read first line in order to match chrom naming format. - line = source.readline() + line = data_file.readline() dataset_chrom = line.split()[0] if not _chrom_naming_matches( chrom, dataset_chrom ): chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) # Undo read. - source.seek( 0 ) + data_file.seek( 0 ) def line_filter_iter(): for line in open( self.original_dataset.file_name ): @@ -741,13 +755,11 @@ class VcfDataProvider( GenomeDataProvider ): def write_data_to_file( self, regions, filename ): out = open( filename, "w" ) + data_file = self.open_data_file() for region in regions: # Write data in region. - chrom = region.chrom - start = region.start - end = region.end - iterator = self.get_iterator( chrom, start, end ) + iterator = self.get_iterator( data_file, region.chrom, region.start, region.end ) for line in iterator: out.write( "%s\n" % line ) out.close() @@ -769,12 +781,13 @@ class RawVcfDataProvider( VcfDataProvider ): for large datasets. """ - def get_iterator( self, chrom, start, end, **kwargs ): - source = open( self.original_dataset.file_name ) + def open_data_file( self ): + return open( self.original_dataset.file_name ) + def get_iterator( self, data_file, chrom, start, end, **kwargs ): # Skip comments. line = None - for line in source: + for line in data_file: if not line.startswith("#"): break @@ -796,13 +809,13 @@ class RawVcfDataProvider( VcfDataProvider ): return variant_chrom == chrom and variant_start >= start and variant_start <= end def line_filter_iter(): - """ Yields lines in source that are in region chrom:start-end """ + """ Yields lines in data that are in region chrom:start-end """ # Yield data line read above. if line_in_region( line, chrom, start, end ): yield line # Search for and yield other data lines. - for data_line in source: + for data_line in data_file: if line_in_region( data_line, chrom, start, end ): yield data_line @@ -866,23 +879,24 @@ class BamDataProvider( GenomeDataProvider, FilterableMixin ): new_bamfile.close() bamfile.close() - def get_iterator( self, chrom, start, end, **kwargs ): + def open_data_file( self ): + # Attempt to open the BAM file with index + return csamtools.Samfile( filename=self.original_dataset.file_name, mode='rb', + index_filename=self.converted_dataset.file_name ) + + def get_iterator( self, data_file, chrom, start, end, **kwargs ): """ Returns an iterator that provides data in the region chrom:start-end """ - start, end = int( start ), int( end ) - orig_data_filename = self.original_dataset.file_name - index_filename = self.converted_dataset.file_name - # Attempt to open the BAM file with index - bamfile = csamtools.Samfile( filename=orig_data_filename, mode='rb', index_filename=index_filename ) + # Fetch and return data. try: - data = bamfile.fetch( start=start, end=end, reference=chrom ) + data = data_file.fetch( start=start, end=end, reference=chrom ) except ValueError: # Try alternative chrom naming. chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) try: - data = bamfile.fetch( start=start, end=end, reference=chrom ) + data = data_file.fetch( start=start, end=end, reference=chrom ) except ValueError: return None return data @@ -1299,19 +1313,18 @@ class IntervalIndexDataProvider( FilterableMixin, GenomeDataProvider ): source.close() out.close() - def get_iterator( self, chrom, start, end, **kwargs ): - """ - Returns an array with values: (a) source file and (b) an iterator that - provides data in the region chrom:start-end - """ - start, end = int(start), int(end) - index = Indexes( self.converted_dataset.file_name ) + def open_data_file( self ): + return Indexes( self.converted_dataset.file_name ) - if chrom not in index.indexes: + def get_iterator( self, data_file, chrom, start, end, **kwargs ): + """ + Returns an iterator for data in data_file in chrom:start-end + """ + if chrom not in data_file.indexes: # Try alternative naming. chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) - return index.find(chrom, start, end) + return data_file.find(chrom, start, end) def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): results = [] @@ -1358,7 +1371,7 @@ class RawGFFDataProvider( GenomeDataProvider ): dataset_type = 'interval_index' - def get_iterator( self, chrom, start, end, **kwargs ): + def get_iterator( self, data_file, chrom, start, end, **kwargs ): """ Returns an iterator that provides data in the region chrom:start-end as well as a file offset. @@ -1467,7 +1480,7 @@ class ENCODEPeakDataProvider( GenomeDataProvider ): Payload format: [ uid (offset), start, end, name, strand, thick_start, thick_end, blocks ] """ - def get_iterator( self, chrom, start, end, **kwargs ): + def get_iterator( self, data_file, chrom, start, end, **kwargs ): raise "Unimplemented Method" def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): @@ -1615,7 +1628,7 @@ class ChromatinInteractionsDataProvider( GenomeDataProvider ): class ChromatinInteractionsTabixDataProvider( TabixDataProvider, ChromatinInteractionsDataProvider ): - def get_iterator( self, chrom, start=0, end=sys.maxint, interchromosomal=False, **kwargs ): + def get_iterator( self, data_file, chrom, start=0, end=sys.maxint, interchromosomal=False, **kwargs ): """ """ # Modify start as needed to get earlier interactions with start region. @@ -1636,7 +1649,7 @@ class ChromatinInteractionsTabixDataProvider( TabixDataProvider, ChromatinIntera # Check for interchromosal interactions. if interchromosomal and c != chrom: yield line - return filter( TabixDataProvider.get_iterator( self, chrom, filter_start, end ) ) + return filter( TabixDataProvider.get_iterator( self, data_file, chrom, filter_start, end ) ) # # -- Helper methods. -- diff --git a/lib/galaxy/webapps/galaxy/api/tools.py b/lib/galaxy/webapps/galaxy/api/tools.py index ce3346c2fff..191e21b6073 100644 --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -387,7 +387,7 @@ class ToolsController( BaseAPIController, UsesVisualizationMixin ): # job's previous parameters and incoming parameters. Incoming parameters # have priority. # - original_job = self.hda_manager.creating_job( trans, original_dataset ) + original_job = self.hda_manager.creating_job( original_dataset ) tool = trans.app.toolbox.get_tool( original_job.tool_id ) if not tool or not tool.allow_user_access( trans.user ): return trans.app.model.Dataset.conversion_messages.NO_TOOL diff --git a/static/maps/viz/trackster/tracks.js.map b/static/maps/viz/trackster/tracks.js.map index 2cfddac75de..cb677c4141f 100644 --- a/static/maps/viz/trackster/tracks.js.map +++ b/static/maps/viz/trackster/tracks.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/static/scripts/viz/trackster/tracks.js b/static/scripts/viz/trackster/tracks.js index bf72669f91d..5c1978f7195 100644 --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1,4 +1,3 @@ -define(["libs/underscore","viz/visualization","viz/viz_views","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools","utils/config"],function(a,b,c,d,e,f,g,h,i,j){var k=a.extend,l={},m=function(a,b){l[a.attr("id")]=b},n=function(a,b,c,d){c=".group",l[a.attr("id")]=d,a.bind("drag",{handle:"."+b,relative:!0},function(a,b){var d,e,f,g,h,i=($(this),$(this).parent()),j=i.children(".track,.group"),k=l[$(this).attr("id")];if(e=$(this).parents(c),0!==e.length){f=e.position().top,g=f+e.outerHeight();var m=l[e.attr("id")];if(b.offsetYg)return $(this).insertAfter(e),m.remove_drawable(k),void m.container.add_drawable(k)}for(e=null,h=0;h=f&&b.offsetY<=g)return b.offsetY-f0?h-1:h))}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})},o=20,p=100,q=12e3,r=400,s=5e3,t=100,u="Cannot display dataset due to an error. ",v="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",w="No data for this chrom/contig.",x="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",y="Tool cannot be rerun: ",z="Ready for display",A=10,B=["Histogram","Line","Filled","Intensity"],C=function(a,b,d){if(C.id_counter||(C.id_counter=0),this.id=C.id_counter++,this.view=a,this.container=b,this.drag_handle_class=d.drag_handle_class,this.is_overview=!1,this.action_icons={},this.config=j.ConfigSettingCollection.from_models_and_saved_values(this.config_params,d.prefs),this.config.get_value("name")||this.config.set_value("name",d.name),this.config_onchange&&this.config.on("change",this.config_onchange,this),this.container_div=this.build_container_div(),this.header_div=null,d.header!==!1){var e=new c.TrackHeaderView({model:this,id:this.id});this.header_div=e.$el,this.container_div.append(this.header_div);var f=e.icons_div;this.action_icons=e.action_icons,this.container_div.hover(function(){f.show()},function(){f.hide()})}};C.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(a){a.config.get_value("content_visible")?(a.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle"),a.hide_contents(),a.config.set_value("content_visible",!1)):(a.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand"),a.config.set_value("content_visible",!0),a.show_contents())}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(a){var b=new j.ConfigSettingCollectionView({collection:a.config});b.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(a){$(".tooltip").remove(),a.remove()}}],k(C.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:!0,hidden:!0}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){return this.enabled&&this.config.get_value("content_visible")?!0:!1},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(a){this.old_name=this.config.get_value("name"),this.config.set_value("name",a)},revert_name:function(){this.old_name&&this.config.set_value("name",this.old_name)},remove:function(){this.changed(),this.container.remove_drawable(this);var a=this.view;this.container_div.hide(0,function(){$(this).remove(),a.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var D=function(a,b,c){C.call(this,a,b,c),this.obj_type=c.obj_type,this.drawables=[]};k(D.prototype,C.prototype,{unpack_drawables:function(a){this.drawables=[];for(var b,c=0;c").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div),m(this.container_div,this),m(this.content_div,this),n(this.container_div,this.drag_handle_class,".group",this),this.filters_manager=new g.FiltersManager(this),this.header_div.after(this.filters_manager.parent_div),this.filters_manager.parent_div.after($("
")),this.saved_filters_managers=[],"drawables"in c&&this.unpack_drawables(c.drawables),"filters"in c){var d=this.filters_manager;this.filters_manager=new g.FiltersManager(this,c.filters),d.parent_div.replaceWith(this.filters_manager.parent_div),c.filters.visible&&this.setup_multitrack_filtering()}};k(E.prototype,C.prototype,D.prototype,{action_icons_def:[C.prototype.action_icons_def[0],C.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(a){$(".tooltip").remove(),a.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(a){a.filters_manager.visible()?(a.filters_manager.clear_filters(),a._restore_filter_managers()):(a.setup_multitrack_filtering(),a.request_draw({clear_tile_cache:!0})),a.filters_manager.toggle()}},C.prototype.action_icons_def[2]],build_container_div:function(){var a=$("
").addClass("group").attr("id","group_"+this.id);return this.container&&this.container.content_div.append(a),a},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show(),this.request_draw()},update_icons:function(){var a=this.drawables.length;if(0===a)this.action_icons.composite_icon.hide(),this.action_icons.filters_icon.hide();else if(1===a)this.action_icons.composite_icon.toggle(this.drawables[0]instanceof Q),this.action_icons.filters_icon.hide();else{var b,c,d,e=!0,f=this.drawables[0].get_type(),h=0;for(b=0;a>b;b++){if(d=this.drawables[b],d.get_type()!==f){can_composite=!1;break}d instanceof U&&h++}if(e&&this.drawables[0]instanceof S?this.action_icons.composite_icon.show():(this.action_icons.composite_icon.hide(),$(".tooltip").remove()),h>1&&h===this.drawables.length){var i,j={};for(d=this.drawables[0],c=0;c0)}else this.action_icons.filters_icon.hide()}},_restore_filter_managers:function(){for(var a=0;a0){this.saved_filters_managers=[];for(var a=0;a").addClass("top-container").appendTo(c),this.browser_content_div=$("
").addClass("content").appendTo(c),this.bottom_container=$("
").addClass("bottom-container").appendTo(c),this.top_labeltrack=$("
").addClass("top-labeltrack").appendTo(this.top_container),this.viewport_container=$("
").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div),this.content_div=this.viewport_container,m(this.viewport_container,d),this.intro_div=$("
").addClass("intro").appendTo(this.viewport_container);$("
").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){b.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":d.dbkey},function(b){a.each(b,function(a){d.add_drawable(Y(a,d,d))})})});this.nav_container=$("
").addClass("trackster-nav-container").prependTo(this.top_container),this.nav=$("
").addClass("trackster-nav").appendTo(this.nav_container),this.stand_alone&&(this.nav_container.addClass("stand-alone"),this.nav.addClass("stand-alone")),this.overview=$("
").addClass("overview").appendTo(this.bottom_container),this.overview_viewport=$("
").addClass("overview-viewport").appendTo(this.overview),this.overview_close=$("").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport),this.overview_highlight=$("
").addClass("overview-highlight").hide().appendTo(this.overview_viewport),this.overview_box_background=$("
").addClass("overview-boxback").appendTo(this.overview_viewport),this.overview_box=$("
").addClass("overview-box").appendTo(this.overview_viewport),this.default_overview_height=this.overview_box.height(),this.nav_controls=$("
").addClass("nav-controls").appendTo(this.nav),this.chrom_select=$("").addClass("nav-input").hide().bind("keyup focusout",e).appendTo(this.nav_controls),this.location_span=$("").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls),this.location_span.click(function(){d.location_span.hide(),d.chrom_select.hide(),d.nav_input.val(d.chrom+":"+d.low+"-"+d.high),d.nav_input.css("display","inline-block"),d.nav_input.select(),d.nav_input.focus(),d.nav_input.autocomplete({source:function(a,b){var c=[],e=$.map(d.get_tracks(U),function(b){return b.data_manager.search_features(a.term).success(function(a){c=c.concat(a)})});$.when.apply($,e).done(function(){b($.map(c,function(a){return{label:a[0],value:a[1]}}))})},minLength:2})}),void 0!==this.vis_id&&(this.hidden_input=$("").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)),this.zo_link=$("").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){d.zoom_out()}).appendTo(this.nav_controls),this.zi_link=$("").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){d.zoom_in()}).appendTo(this.nav_controls),this.load_chroms_deferred=this.load_chroms({low:0}),this.chrom_select.bind("change",function(){d.change_chrom(d.chrom_select.val())}),this.browser_content_div.click(function(){$(this).find("input").trigger("blur")}),this.browser_content_div.bind("dblclick",function(a){d.zoom_in(a.pageX,this.viewport_container)}),this.overview_box.bind("dragstart",function(a,b){this.current_x=b.offsetX}).bind("drag",function(a,b){var c=b.offsetX-this.current_x;this.current_x=b.offsetX;var e=Math.round(c/d.viewport_container.width()*(d.max_high-d.max_low));d.move_delta(-e)}),this.overview_close.click(function(){d.reset_overview()}),this.viewport_container.bind("draginit",function(a){return a.clientX>d.viewport_container.width()-16?!1:void 0}).bind("dragstart",function(a,b){b.original_low=d.low,b.current_height=a.clientY,b.current_x=b.offsetX}).bind("drag",function(a,b){var c=$(this),e=b.offsetX-b.current_x,f=c.scrollTop()-(a.clientY-b.current_height);c.scrollTop(f),b.current_height=a.clientY,b.current_x=b.offsetX;var g=Math.round(e/d.viewport_container.width()*(d.high-d.low));d.move_delta(g)}),this.top_labeltrack.bind("dragstart",function(){return $("
").addClass("zoom-area").css("height",d.browser_content_div.height()+d.top_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(a,b){$(b.proxy).css({left:Math.min(a.pageX,b.startX)-d.container.offset().left,width:Math.abs(a.pageX-b.startX)});var c=Math.min(a.pageX,b.startX)-d.container.offset().left,e=Math.max(a.pageX,b.startX)-d.container.offset().left,f=d.high-d.low,g=d.viewport_container.width();d.update_location(Math.round(c/g*f)+d.low,Math.round(e/g*f)+d.low)}).bind("dragend",function(a,b){var c=Math.min(a.pageX,b.startX),e=Math.max(a.pageX,b.startX),f=d.high-d.low,g=d.viewport_container.width(),h=d.low;d.low=Math.round(c/g*f)+h,d.high=Math.round(e/g*f)+h,$(b.proxy).remove(),d.request_redraw()}),this.add_label_track(new P(this,{content_div:this.top_labeltrack})),$(window).bind("resize",function(){this.resize_timer&&clearTimeout(this.resize_timer),this.resize_timer=setTimeout(function(){d.resize_window()},500)}),$(document).bind("redraw",function(){d.redraw()}),this.reset(),$(window).trigger("resize")},get_base_color:function(a){return this.config.get_value(a.toLowerCase()+"_color")||this.config.get_value("n_color")}});k(F.prototype,D.prototype,{changed:function(){this.has_changes=!0},update_intro_div:function(){this.intro_div.toggle(0===this.drawables.length)},trigger_navigate:function(a,b,c,d){if(this.timer&&clearTimeout(this.timer),d){var e=this;this.timer=setTimeout(function(){e.trigger("navigate",a+":"+b+"-"+c)},500)}else view.trigger("navigate",a+":"+b+"-"+c)},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b)),this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b));var c=this.chrom_select.val();""!==c&&this.trigger_navigate(c,this.low,this.high,!0)},load_chroms:function(a){a.num=t;var b=this,c=$.Deferred();return $.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:a,dataType:"json",success:function(a){if(0!==a.chrom_info.length){if(a.reference){var d=new R(b);b.add_label_track(d),b.reference_track=d}b.chrom_data=a.chrom_info;for(var e='',f=0,g=b.chrom_data.length;g>f;f++){var h=b.chrom_data[f].chrom;e+='"}a.prev_chroms&&(e+='"),a.next_chroms&&(e+='"),b.chrom_select.html(e),b.chrom_start_index=a.start_index,c.resolve(a.chrom_info)}},error:function(){alert("Could not load chroms for this dbkey: "+b.dbkey)}}),c},change_chrom:function(a,b,c){var d=this;if(!d.chrom_data)return void d.load_chroms_deferred.then(function(){d.change_chrom(a,b,c)});if(a&&"None"!==a){if("previous"===a)return void d.load_chroms({low:this.chrom_start_index-t});if("next"===a)return void d.load_chroms({low:this.chrom_start_index+t});var e=$.grep(d.chrom_data,function(b){return b.chrom===a})[0];if(void 0===e)return void d.load_chroms({chrom:a},function(){d.change_chrom(a,b,c)});if(a!==d.chrom){d.chrom=a,d.chrom_select.val(d.chrom),d.max_high=e.len-1,d.reset();for(var f=0,g=d.drawables.length;g>f;f++){var h=d.drawables[f];h.init&&h.init()}d.reference_track&&d.reference_track.init()}void 0===b&&void 0===c?(d.low=0,d.high=d.max_high):(d.low=void 0!==b?Math.max(b,0):0,void 0===c?(d.low=Math.max(d.low-15,0),d.high=d.low+30):d.high=Math.min(c,d.max_high)),d.request_redraw()}},go_to:function(a){a=a.replace(/,/g,""),a=a.replace(/:|\-/g," ");var b=a.split(/\s+/),c=b[0],d=b[1]?parseInt(b[1],10):void 0,e=b[2]?parseInt(b[2],10):void 0;this.change_chrom(c,d,e)},move_fraction:function(a){var b=this,c=b.high-b.low;this.move_delta(a*c)},move_delta:function(a){var b=this,c=b.high-b.low;b.low-ab.max_high?(b.high=b.max_high,b.low=b.max_high-c):(b.high-=a,b.low-=a),b.request_redraw({data_fetch:!1}),this.redraw_on_move_fn&&clearTimeout(this.redraw_on_move_fn),this.redraw_on_move_fn=setTimeout(function(){b.request_redraw()},200);var d=b.chrom_select.val();this.trigger_navigate(d,b.low,b.high,!0)},add_drawable:function(a){D.prototype.add_drawable.call(this,a),a.init(),this.changed(),this.update_intro_div();var b=this;a.config.on("change",function(){b.changed()})},add_label_track:function(a){a.view=this,a.init(),this.label_tracks.push(a)},remove_drawable:function(a,b){if(D.prototype.remove_drawable.call(this,a),b){var c=this;a.container_div.hide(0,function(){$(this).remove(),c.update_intro_div()})}},reset:function(){this.low=this.max_low,this.high=this.max_high,this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(b,c){var d=this,e=c?[c]:d.drawables;a.each(e,function(c){var e=a.find(d.tracks_to_be_redrawn,function(a){return a[0]===c});e?e[1]=b:d.tracks_to_be_redrawn.push([c,b])}),this.requested_redraw||(requestAnimationFrame(function(){d._redraw()}),this.requested_redraw=!0)},_redraw:function(){this.requested_redraw=!1;var b=this.low,c=this.high;bthis.max_high&&(c=this.max_high);var d=this.high-this.low;0!==this.high&&df&&this.overview_box.css("left",e-(g-f)/2),this.overview_highlight&&this.overview_highlight.css({left:e,width:f}),a.each(this.tracks_to_be_redrawn,function(a){var b=a[0],c=a[1];b&&b._draw(c)}),this.tracks_to_be_redrawn=[],a.each(this.label_tracks,function(a){a._draw()})},zoom_in:function(a){if(!(0===this.max_high||this.high-this.low<=this.min_separation)){var b=this.high-this.low,c=b/2+this.low,d=b/this.zoom_factor/2;a&&(c=a/this.viewport_container.width()*(this.high-this.low)+this.low),this.low=Math.round(c-d),this.high=Math.round(c+d),this.changed(),this.request_redraw()}},zoom_out:function(){if(0!==this.max_high){var a=this.high-this.low,b=a/2+this.low,c=a*this.zoom_factor/2;this.low=Math.round(b-c),this.high=Math.round(b+c),this.changed(),this.request_redraw()}},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport(),this.request_redraw()},set_overview:function(a){if(this.overview_drawable){if(this.overview_drawable.dataset.id===a.dataset.id)return;this.overview_viewport.find(".track").remove()}var b=a.copy({content_div:this.overview_viewport}),c=this;b.header_div.hide(),b.is_overview=!0,c.overview_drawable=b,this.overview_drawable.postdraw_actions=function(){c.overview_highlight.show().height(c.overview_drawable.content_div.height()),c.overview_viewport.height(c.overview_drawable.content_div.height()+c.overview_box.outerHeight()),c.overview_close.show(),c.resize_window()},c.overview_drawable.request_draw(),this.changed()},reset_overview:function(){$(".tooltip").remove(),this.overview_viewport.find(".track-tile").remove(),this.overview_viewport.height(this.default_overview_height),this.overview_box.height(this.default_overview_height),this.overview_close.hide(),this.overview_highlight.hide(),view.resize_window(),view.overview_drawable=null}});var G=i.Tool.extend({defaults:{track:null},initialize:function(a){i.Tool.prototype.initialize.call(this,a);var b=!0;void 0!==a.tool_state&&void 0!==a.tool_state.hidden&&(b=a.tool_state.hidden),this.set("hidden",b),this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(){return a.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}}),H=Backbone.View.extend({events:{"change :input":"update_value"},render:function(){var a=this.$el.addClass("param-row"),b=this.model,c=($("
").addClass("param-label").text(b.get("label")).appendTo(a),$("
").addClass("param-input").html(b.get("html")).appendTo(a));c.find(":input").val(b.get("value")),$("
").appendTo(a)},update_value:function(a){this.model.set_value($(a.target).val())}}),I=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.set_visible,this)},render:function(){var a=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide(),parent_div.bind("drag",function(a){a.stopPropagation()}).click(function(a){a.stopPropagation()}).bind("dblclick",function(a){a.stopPropagation()}).keydown(function(a){a.stopPropagation()});$("
").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(a){var b=new H({model:a});b.render(),parent_div.append(b.$el)}),parent_div.find("input").click(function(){$(this).select()});var b=$("
").addClass("param-row").appendTo(parent_div),c=$("").attr("value","Run on complete dataset").appendTo(b),d=$("").attr("value","Run on visible region").appendTo(b);d.click(function(){a.run_on_region()}),c.click(function(){a.run_on_dataset()}),tool.is_visible()&&this.$el.show()},set_visible:function(){this.$el.toggle(this.model.is_visible())},update_params:function(){for(var a=0;a").append(d),this.data=e,this.stale=!1};K.prototype.predisplay_actions=function(){};var L=function(a,b,c,d,e){K.call(this,a,b,c,d,e)};L.prototype.predisplay_actions=function(){};var M=function(a,b,c,d,e,f,g,h,i,j,k){K.call(this,a,b,c,d,e),this.mode=f,this.all_slotted=h,this.feature_mapper=i,this.has_icons=!1,this.incomplete_features=j,this.other_tiles_features_drawn={},this.seq_data=k};k(M.prototype,K.prototype),M.prototype.predisplay_actions=function(){};var N=function(a,c,d){k(d,{drag_handle_class:"draghandle"}),C.call(this,a,c,d),this.dataset=null,d.dataset&&(this.dataset=d.dataset instanceof Backbone.Model?d.dataset:new h.Dataset(d.dataset)),this.dataset_check_type="converted_datasets_state",this.data_url_extra_params={},this.data_query_wait="data_query_wait"in d?d.data_query_wait:s,this.data_manager="data_manager"in d?d.data_manager:new b.GenomeDataManager({dataset:this.dataset,genome:new b.Genome({key:a.dbkey,chroms_info:{chrom_info:a.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}),this.min_height_px=16,this.max_height_px=800,this.visible_height_px=this.config.get_value("height"),this.content_div=$("
").appendTo(this.container_div),this.container&&(this.container.content_div.append(this.container_div),"resize"in d&&!d.resize||this.add_resize_handle())};k(N.prototype,C.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},C.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(a){a.view.set_overview(a)}},C.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(a){a.filters_manager.visible()?a.filters_manager.clear_filters():a.filters_manager.init_filters(),a.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(a){a.tool.toggle(),a.tool.is_visible()?a.set_name(a.config.get_value("name")+a.tool_region_and_parameters_str()):a.revert_name(),$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(c){var d='Tool: <%= track.tool.get("name") %>
Dataset: <%= track.config.get_value("name") %>
Region(s): ',e=a.template(d,{track:c}),f=function(){Galaxy.modal.hide(),$(window).unbind("keypress.check_enter_esc")},g=function(){var d,e=$('select[name="regions"] option:selected').val(),f=new b.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),g=a.map($(".bookmark"),function(a){return new b.GenomeRegion({from_str:$(a).children(".position").text()})});d="cur"===e?[f]:"bookmarks"===e?g:[f].concat(g),Galaxy.modal.hide(),window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:c.dataset.id,hda_ldda:c.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(d).toJSON())})};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:e,buttons:{No:f,Yes:g}})}},C.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&C.prototype.can_draw.call(this)},build_container_div:function(){return $("
").addClass("track").attr("id","track_"+this.id)},set_dataset:function(a){this.dataset=a,this.data_manager.set("dataset",a)},on_resize:function(){this.request_draw({clear_tile_cache:!0})},add_resize_handle:function(){var a=this,b=!1,c=!1,d=$("
");$(a.container_div).hover(function(){a.config.get_value("content_visible")&&(b=!0,d.show())},function(){b=!1,c||d.hide()}),d.hide().bind("dragstart",function(b,d){c=!0,d.original_height=$(a.content_div).height()}).bind("drag",function(b,c){var d=Math.min(Math.max(c.original_height+c.deltaY,a.min_height_px),a.max_height_px);$(a.tiles_div).css("height",d),a.visible_height_px=a.max_height_px===d?0:d,a.on_resize()}).bind("dragend",function(){a.tile_cache.clear(),c=!1,b||d.hide(),a.config.set_value("height",a.visible_height_px),a.changed()}).appendTo(a.container_div)},hide_contents:function(){this.tiles_div.hide(),this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show(),this.container_div.find(".yaxislabel, .track-resize").show(),this.request_draw()},get_type:function(){return this instanceof P?"LabelTrack":this instanceof R?"ReferenceTrack":this instanceof S?"LineTrack":this instanceof W?"ReadTrack":this instanceof V?"VariantTrack":this instanceof Q?"CompositeTrack":this instanceof U?"FeatureTrack":""},show_message:function(a){return this.tiles_div.remove(),$("").addClass("message").html(a).appendTo(this.content_div)},init:function(a){var b=this; - -if(b.enabled=!1,b.tile_cache.clear(),b.data_manager.clear(),b.content_div.children().remove(),b.container_div.removeClass("nodata error pending"),b.tiles_div=$("
").addClass("tiles").appendTo(b.content_div),b.dataset.id){var c=$.Deferred(),d={hda_ldda:b.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:b.view.chrom,retry:a};return $.getJSON(this.dataset.url(),d,function(a){if(a&&"error"!==a&&"error"!==a.kind)"no converter"===a?(b.container_div.addClass("error"),b.show_message(v)):"no data"===a||void 0!==a.data&&(null===a.data||0===a.data.length)?(b.container_div.addClass("nodata"),b.show_message(w)):"pending"===a?(b.container_div.addClass("pending"),b.show_message(x),setTimeout(function(){b.init()},b.data_query_wait)):("data"===a||"data"===a.status)&&(a.valid_chroms&&(b.valid_chroms=a.valid_chroms,b.update_icons()),b.tiles_div.text(z),b.view.chrom?(b.tiles_div.text(""),b.tiles_div.css("height",b.visible_height_px+"px"),b.enabled=!0,$.when.apply($,b.predraw_init()).done(function(){c.resolve(),b.container_div.removeClass("nodata error pending"),b.request_draw()})):c.resolve());else{b.container_div.addClass("error");var d=b.show_message(u);a.message&&(d.append($("").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"
"+a.message+"
",buttons:{Close:function(){Galaxy.modal.hide()}}})})),d.append($("").text(" ")),d.append($("").text("Try again").click(function(){b.init(!0)})))}}),this.update_icons(),c}},predraw_init:function(){var a=this;return $.getJSON(a.dataset.url(),{data_type:"data",stats:!0,chrom:a.view.chrom,low:0,high:a.view.max_high,hda_ldda:a.dataset.get("hda_ldda")},function(b){var c=b.data;if(void 0!==c&&void 0!==c.min&&void 0!==c.max){var d=c.min,e=c.max;d=Math.floor(Math.min(0,Math.max(d,c.mean-2*c.sd))),e=Math.ceil(Math.max(0,Math.min(e,c.mean+2*c.sd))),a.config.set_default_value("min_value",d),a.config.set_default_value("max_value",e),a.config.set_value("min_value",d),a.config.set_value("max_value",e)}})},get_drawables:function(){return this}});var O=function(c,d,e){N.call(this,c,d,e);var f=this;if(n(f.container_div,f.drag_handle_class,".group",f),this.filters_manager=new g.FiltersManager(this,"filters"in e?e.filters:null),this.data_manager.set("filters_manager",this.filters_manager),this.filters_available=!1,this.tool=e.tool?new G(a.extend(e.tool,{track:this,tool_state:e.tool_state})):null,this.tile_cache=new b.Cache(A),this.left_offset=0,this.header_div&&(this.set_filters_manager(this.filters_manager),this.tool)){var h=new I({model:this.tool});h.render(),this.dynamic_tool_div=h.$el,this.header_div.after(this.dynamic_tool_div)}this.tiles_div=$("
").addClass("tiles").appendTo(this.content_div),this.config.get_value("content_visible")||this.tiles_div.hide(),this.overlay_div=$("
").addClass("overlay").appendTo(this.content_div),e.mode&&this.change_mode(e.mode)};k(O.prototype,C.prototype,N.prototype,{action_icons_def:N.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(a){$(".tooltip").remove(),a.slotters[a.view.resolution_px_b].max_rows*=2,a.request_draw({clear_tile_cache:!0})},hide:!0}]),copy:function(a){var b=this.to_dict();k(b,{data_manager:this.data_manager});var c=new this.constructor(this.view,a,b);return c.change_mode(this.mode),c.enabled=this.enabled,c},set_filters_manager:function(a){this.filters_manager=a,this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:this.tool?this.tool.state_dict():{}}},set_min_max:function(){var a=this;return $.getJSON(a.dataset.url(),{data_type:"data",stats:!0,chrom:a.view.chrom,low:0,high:a.view.max_high,hda_ldda:a.dataset.get("hda_ldda")},function(b){var c=b.data;if(isNaN(parseFloat(a.config.get_value("min_value")))||isNaN(parseFloat(a.config.get_value("max_value")))){var d=c.min,e=c.max;d=Math.floor(Math.min(0,Math.max(d,c.mean-2*c.sd))),e=Math.ceil(Math.max(0,Math.min(e,c.mean+2*c.sd))),a.config.set_value("min_value",d),a.config.set_value("max_value",e)}})},change_mode:function(a){var b=this;return b.mode=a,b.config.set_value("mode",a),"Auto"===a&&this.data_manager.clear(),b.request_draw({clear_tile_cache:!0}),this.action_icons.mode_icon.attr("title","Set display mode (now: "+b.mode+")"),b},update_icons:function(){var a=this;a.action_icons.filters_icon.toggle(a.filters_available),a.action_icons.tools_icon.toggle(null!==a.tool),a.action_icons.param_space_viz_icon.toggle(null!==a.tool)},_gen_tile_cache_key:function(a,b){return a+"_"+b},request_draw:function(a){a&&a.clear_tile_cache&&this.tile_cache.clear(),this.view.request_redraw(a,this)},before_draw:function(){this.max_height_px=0},_draw:function(c){if(this.can_draw()){var d=c&&c.clear_after,e=this.view.low,f=this.view.high,g=this.view.container.width(),h=this.view.resolution_px_b,i=1/h;this.is_overview&&(e=this.view.max_low,f=this.view.max_high,h=g/(view.max_high-view.max_low),i=1/h),this.before_draw(),this.tiles_div.children().addClass("remove");for(var j,k,l=Math.floor(r*i),m=Math.floor(e/l),n=[],o=[];f>m*l;)j=new b.GenomeRegion({chrom:this.view.chrom,start:m*l,end:Math.min((m+1)*l,this.view.max_high)}),k=this.draw_helper(j,h,c),n.push(k),$.when(k).then(function(a){o.push(a)}),m+=1;d||this.tiles_div.children(".remove").removeClass("remove").remove();var p=this;$.when.apply($,n).then(function(){p.tiles_div.children(".remove").remove(),o=a.filter(o,function(a){return null!==a}),0!==o.length&&p.postdraw_actions(o,g,h,d)})}},_add_yaxis_label:function(a,b){var c=this,d="max"===a?"top":"bottom",e="max"===a?"max":"min",f="max"===a?"max_value":"min_value",g=this.container_div.find(".yaxislabel."+d);b=b||function(){c.request_draw({clear_tile_cache:!0})},0!==g.length?g.text(c.config.get_value(f)):(g=$("
").text(c.config.get_value(f)).make_text_editable({num_cols:12,on_finish:function(a){$(".tooltip").remove(),c.config.set_value(f,a),b()},help_text:"Set "+e+" value"}).addClass("yaxislabel "+d).css("color",this.config.get_value("label_color")),this.container_div.prepend(g))},postdraw_actions:function(b,c,d){var e=a.filter(b,function(a){return a instanceof L});if(e.length>0){this.max_height_px=0;var f=this;a.each(b,function(a){a instanceof L||(a.html_elt.remove(),f.draw_helper(a.region,d,{force:!0,mode:"Coverage"}))}),f._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var g=a.find(b,function(a){return a.has_icons});g&&a.each(b,function(a){a.has_icons||a.html_elt.css("padding-top",o)})}},get_mode:function(){return this.mode},update_auto_mode:function(){},_get_drawables:function(){return[this]},draw_helper:function(b,c,e){e||(e={});var f=e.force,g=e.mode||this.mode,h=1/c,i=this,j=this._get_drawables(),k=this._gen_tile_cache_key(c,b),l=function(a){return a&&"track"in a},m=f?void 0:i.tile_cache.get_elt(k);if(m)return l(m)&&i.show_tile(m,c),m;if(e.data_fetch===!1)return null;var n=function(){var c=a.find(B,function(a){return a===g})?"Coverage":g,d=a.map(j,function(a){return a.data_manager.get_data(b,c,h,i.data_url_extra_params)});return view.reference_track&&d.push(view.reference_track.data_manager.get_data(b,g,h,view.reference_track.data_url_extra_params)),d},o=$.Deferred();return i.tile_cache.set_elt(k,o),$.when.apply($,n()).then(function(){var f,g=n(),h=g;if(a.find(g,function(a){return d.is_deferred(a)}))return i.tile_cache.set_elt(k,void 0),void $.when(i.draw_helper(b,c,e)).then(function(a){o.resolve(a)});view.reference_track&&(f=view.reference_track.data_manager.subset_entry(g.pop(),b));var l=[],m=[];a.each(j,function(a,b){var d=a.mode,e=h[b];"Auto"===d&&(d=a.get_mode(e),a.update_auto_mode(d)),l.push(d),m.push(a.get_canvas_height(e,d,c,t))});var p,q=i.view.canvas_manager.new_canvas(),r=b.get("start"),s=b.get("end"),t=Math.ceil((s-r)*c)+i.left_offset,u=a.max(m);q.width=t,q.height=e.height||u;var v=q.getContext("2d");v.translate(i.left_offset,0),j.length>1&&(v.globalAlpha=.5,v.globalCompositeOperation="source-over"),a.each(j,function(a,d){p=a.draw_tile(h[d],v,l[d],b,c,f)}),void 0!==p&&(i.tile_cache.set_elt(k,p),i.show_tile(p,c)),o.resolve(p)}),o},get_canvas_height:function(){return this.visible_height_px},_draw_line_track_tile:function(a,b,c,d,e){var g=b.canvas,h=new f.LinePainter(a.data,d.get("start"),d.get("end"),this.config.to_key_value_dict(),c);return h.draw(b,g.width,g.height,e),new L(this,d,e,g,a.data)},draw_tile:function(){},show_tile:function(a,b){var c=a.html_elt;a.predisplay_actions();var d=Math.round((a.low-(this.is_overview?this.view.max_low:this.view.low))*b);this.left_offset&&(d-=this.left_offset),c.css("left",d),c.hasClass("remove")?c.removeClass("remove"):this.tiles_div.append(c),c.css("height","auto"),this.max_height_px=Math.max(this.max_height_px,c.height()-2),c.parent().children().css("height",this.max_height_px+"px");var e=this.max_height_px;0!==this.visible_height_px&&(e=Math.min(this.max_height_px,this.visible_height_px)),this.tiles_div.css("height",e+"px")},tool_region_and_parameters_str:function(b){var c=this,d=void 0!==b?b.toString():"all",e=a.values(c.tool.get_inputs_dict()).join(", ");return" - region=["+d+"], parameters=["+e+"]"},data_and_mode_compatible:function(a,b){return"Auto"===b?!0:"Coverage"===b?"bigwig"===a.dataset_type:"bigwig"===a.dataset_type||"no_detail"===a.extra_info?!1:!0},can_subset:function(a){return a.message||"no_detail"===a.extra_info?!1:"bigwig"===a.dataset_type?a.data[1][0]-a.data[0][0]===1:!0},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data"),this.data_query_wait=1e3,this.dataset_check_type="state"}});var P=function(a,b){N.call(this,a,b,{resize:!1,header:!1}),this.container_div.addClass("label-track")};k(P.prototype,N.prototype,{init:function(){this.enabled=!0},predraw_init:function(){},_draw:function(){for(var a=this.view,b=a.high-a.low,c=Math.floor(Math.pow(10,Math.floor(Math.log(b)/Math.log(10)))),d=Math.floor(a.low/c)*c,e=this.view.container.width(),f=$("
").addClass("label-container");d").addClass("label").text(commatize(d)).css({left:g})),d+=c}this.content_div.children(":first").remove(),this.content_div.append(f)}});var Q=function(b,c,d){if(O.call(this,b,c,d),this.drawables=[],"drawables"in d){for(var e,f=0;fthis.left_offset&&(this.left_offset=e.left_offset);this.enabled=!0}a.each(this.drawables,function(a){(a instanceof U||a instanceof W)&&a.change_mode("Coverage")}),this.update_icons(),this.obj_type="CompositeTrack"};k(Q.prototype,O.prototype,{display_modes:B,config_params:a.union(C.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}]),action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(a){$(".tooltip").remove(),a.show_group()}}].concat(O.prototype.action_icons_def),to_dict:D.prototype.to_dict,add_drawable:D.prototype.add_drawable,unpack_drawables:D.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},on_resize:function(){var b=this.visible_height_px;a.each(this.drawables,function(a){a.visible_height_px=b}),N.prototype.on_resize.call(this)},change_mode:function(a){O.prototype.change_mode.call(this,a);for(var b=0;be&&(e=f)}for(d=0;dthis.view.canvas_manager.char_width_px?(this.tiles_div.show(),d=!0,f=O.prototype.draw_helper.call(this,a,b,c)):(d=!1,this.tiles_div.hide()),e!==d&&this.view.resize_viewport(),f},can_subset:function(){return!0},draw_tile:function(a,b,c,d,e){var f=this.data_manager.subset_entry(a,d),g=f.data,h=b.canvas;b.font=b.canvas.manager.default_font,b.textAlign="center";for(var i=0,j=g.length;j>i;i++)b.fillStyle=this.view.get_base_color(g[i]),b.fillText(g[i],Math.floor(i*e),10);return new K(this,d,e,h,f)}});var S=function(a,b,c){this.mode="Histogram",O.call(this,a,b,c)};k(S.prototype,C.prototype,O.prototype,{display_modes:B,config_params:a.union(C.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}]),config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},before_draw:function(){},draw_tile:function(a,b,c,d,e){return this._draw_line_track_tile(a,b,c,d,e)},can_subset:function(a){return a.data[1][0]-a.data[0][0]===1},postdraw_actions:function(){this._add_yaxis_label("max"),this._add_yaxis_label("min")}});var T=function(a,b,c){this.mode="Heatmap",O.call(this,a,b,c)};k(T.prototype,C.prototype,O.prototype,{display_modes:["Heatmap"],config_params:a.union(C.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:500,hidden:!0}]),config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},draw_tile:function(a,b,c,d,e){var g=b.canvas,h=new f.DiagonalHeatmapPainter(a.data,d.get("start"),d.get("end"),this.config.to_key_value_dict(),c);return h.draw(b,g.width,g.height,e),new K(this,d,e,g,a.data)}});var U=function(a,b,c){O.call(this,a,b,c),this.container_div.addClass("feature-track"),this.summary_draw_height=30,this.slotters={},this.start_end_dct={},this.left_offset=200,this.set_painter_from_config()};k(U.prototype,C.prototype,O.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:a.union(C.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}]),config_onchange:function(){this.set_name(this.config.get_value("name")),this.set_painter_from_config(),this.request_draw({clear_tile_cache:!0})},set_painter_from_config:function(){this.painter="arcs"===this.config.get_value("connector_style")?f.ArcLinkedFeaturePainter:f.LinkedFeaturePainter},postdraw_actions:function(b,c,d,e){O.prototype.postdraw_actions.call(this,b,c,d,e);var f,g=this,h=a.filter(b,function(a){return a instanceof L});if(0===h.length){var i={};a.each(a.pluck(b,"incomplete_features"),function(b){a.each(b,function(a){i[a[0]]=a})});var j=this;a.each(b,function(b){var c=a.omit(i,a.map(b.incomplete_features,function(a){return a[0]}));if(c=a.omit(c,a.keys(b.other_tiles_features_drawn)),0!==a.size(c)){var d={data:a.values(c)},e=j.view.canvas_manager.new_canvas(),f=e.getContext("2d");e.height=Math.max(b.canvas.height,j.get_canvas_height(d,b.mode,b.w_scale,100)),e.width=b.canvas.width,f.drawImage(b.canvas,0,0),f.translate(g.left_offset,0);var h=j.draw_tile(d,f,b.mode,b.region,b.w_scale,b.seq_data);$(b.canvas).replaceWith($(h.canvas)),b.canvas=e,a.extend(b.other_tiles_features_drawn,i)}})}if(g.filters_manager){var k,l=g.filters_manager.filters;for(k=0;kq?"Squish":"Pack",mode},get_canvas_height:function(a,b,c,d){if("Coverage"===b||"bigwig"===a.dataset_type)return this.summary_draw_height;var e=this.incremental_slots(c,a.data,b),f=new this.painter(null,null,null,this.config.to_key_value_dict(),b);return Math.max(this.min_height_px,f.get_required_height(e,d))},draw_tile:function(a,b,c,d,e,f,g){var h=this,i=b.canvas,j=d.get("start"),k=d.get("end"),l=this.left_offset;if("bigwig"===a.dataset_type)return this._draw_line_track_tile(a,b,c,d,e);var m=[],n=this.slotters[e].slots;if(all_slotted=!0,a.data)for(var o=this.filters_manager.filters,p=0,q=a.data.length;q>p;p++){for(var r,s=a.data[p],t=!1,u=0,v=o.length;v>u;u++)if(r=o[u],r.update_attrs(s),!r.keep(s)){t=!0;break}t||(m.push(s),s[0]in n||(all_slotted=!1))}var w=this.filters_manager.alpha_filter?new J(this.filters_manager.alpha_filter):null,x=this.filters_manager.height_filter?new J(this.filters_manager.height_filter):null,y=new this.painter(m,j,k,this.config.to_key_value_dict(),c,w,x,f,function(a){return h.view.get_base_color(a)}),z=null;if(b.fillStyle=this.config.get_value("block_color"),b.font=b.canvas.manager.default_font,b.textAlign="right",a.data){var A=y.draw(b,i.width,i.height,e,n);z=A.feature_mapper,incomplete_features=A.incomplete_features,z.translation=-l}return g?void 0:new M(h,d,e,i,a.data,c,a.message,all_slotted,z,incomplete_features,f)}});var V=function(a,b,c){O.call(this,a,b,c),this.painter=f.VariantPainter,this.summary_draw_height=30,this.left_offset=30};k(V.prototype,C.prototype,O.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:a.union(C.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:!0},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:!0},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}]),config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},draw_tile:function(a,b,c,d,e){if("bigwig"===a.dataset_type)return this._draw_line_track_tile(a,b,"Histogram",d,e);var f=this.view,g=new this.painter(a.data,d.get("start"),d.get("end"),this.config.to_key_value_dict(),c,function(a){return f.get_base_color(a)});return g.draw(b,b.canvas.width,b.canvas.height,e),new K(this,d,e,b.canvas,a.data)},get_canvas_height:function(a,b){if("bigwig"===a.dataset_type)return this.summary_draw_height;var c=this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0;0===c&&0!==a.data.length&&(c=a.data[0][7].match(/,/g),c=null===c?1:c.length+1);var d=new this.painter(null,null,null,this.config.to_key_value_dict(),b);return d.get_required_height(c)},predraw_init:function(){var a=[N.prototype.predraw_init.call(this)];return this.dataset.get_metadata("sample_names")||a.push(this.dataset.fetch()),a},postdraw_actions:function(b,c,d,e){O.prototype.postdraw_actions.call(this,b,c,d,e);var f=a.filter(b,function(a){return a instanceof L}),g=this.dataset.get_metadata("sample_names");if(0===f.length&&this.config.get_value("show_labels")&&g&&g.length>1){var h;if(0===this.container_div.find(".yaxislabel.variant").length&&(h=this.config.get_value("summary_height")/2,this.tiles_div.prepend($("
").text("Summary").addClass("yaxislabel variant top").css({"font-size":h+"px",top:(this.config.get_value("summary_height")-h)/2+"px"})),this.config.get_value("show_sample_data"))){var i=g.join("
");this.tiles_div.prepend($("
").html(i).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}h=("Squish"===this.mode?5:10)+"px",$(this.tiles_div).find(".sample").css({"font-size":h,"line-height":h}),$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else this.container_div.find(".yaxislabel.variant").remove()}});var W=function(a,b,c){U.call(this,a,b,c),this.painter=f.ReadPainter,this.update_icons()};k(W.prototype,C.prototype,O.prototype,U.prototype,{config_params:a.union(C.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:!1},{key:"show_differences",label:"Show differences only",type:"bool",default_value:!0},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:!0}]),config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})}});var X={CompositeTrack:Q,DrawableGroup:E,DiagonalHeatmapTrack:T,FeatureTrack:U,LineTrack:S,ReadTrack:W,VariantTrack:V,VcfTrack:V},Y=function(a,b,c){if("copy"in a)return a.copy(c);var d=a.obj_type;return d||(d=a.track_type),new X[d](b,c,a)};return{TracksterView:F,DrawableGroup:E,LineTrack:S,FeatureTrack:U,DiagonalHeatmapTrack:T,ReadTrack:W,VariantTrack:V,CompositeTrack:Q,object_from_template:Y}}); +define(["libs/underscore","viz/visualization","viz/viz_views","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools","utils/config"],function(a,b,c,d,e,f,g,h,i,j){var k=a.extend,l={},m=function(a,b){l[a.attr("id")]=b},n=function(a,b,c,d){c=".group",l[a.attr("id")]=d,a.bind("drag",{handle:"."+b,relative:!0},function(a,b){var d,e,f,g,h,i=($(this),$(this).parent()),j=i.children(".track,.group"),k=l[$(this).attr("id")];if(e=$(this).parents(c),0!==e.length){f=e.position().top,g=f+e.outerHeight();var m=l[e.attr("id")];if(b.offsetYg)return $(this).insertAfter(e),m.remove_drawable(k),void m.container.add_drawable(k)}for(e=null,h=0;h=f&&b.offsetY<=g)return b.offsetY-f0?h-1:h))}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})},o=20,p=100,q=12e3,r=400,s=5e3,t=100,u="Cannot display dataset due to an error. ",v="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",w="No data for this chrom/contig.",x="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",y="Tool cannot be rerun: ",z="Ready for display",A=10,B=["Histogram","Line","Filled","Intensity"],C=function(a,b,d){if(C.id_counter||(C.id_counter=0),this.id=C.id_counter++,this.view=a,this.container=b,this.drag_handle_class=d.drag_handle_class,this.is_overview=!1,this.action_icons={},this.config=j.ConfigSettingCollection.from_models_and_saved_values(this.config_params,d.prefs),this.config.get_value("name")||this.config.set_value("name",d.name),this.config_onchange&&this.config.on("change",this.config_onchange,this),this.container_div=this.build_container_div(),this.header_div=null,d.header!==!1){var e=new c.TrackHeaderView({model:this,id:this.id});this.header_div=e.$el,this.container_div.append(this.header_div);var f=e.icons_div;this.action_icons=e.action_icons,this.container_div.hover(function(){f.show()},function(){f.hide()})}};C.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(a){a.config.get_value("content_visible")?(a.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle"),a.hide_contents(),a.config.set_value("content_visible",!1)):(a.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand"),a.config.set_value("content_visible",!0),a.show_contents())}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(a){var b=new j.ConfigSettingCollectionView({collection:a.config});b.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(a){$(".tooltip").remove(),a.remove()}}],k(C.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:!0,hidden:!0}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){return this.enabled&&this.config.get_value("content_visible")?!0:!1},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(a){this.old_name=this.config.get_value("name"),this.config.set_value("name",a)},revert_name:function(){this.old_name&&this.config.set_value("name",this.old_name)},remove:function(){this.changed(),this.container.remove_drawable(this);var a=this.view;this.container_div.hide(0,function(){$(this).remove(),a.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var D=function(a,b,c){C.call(this,a,b,c),this.obj_type=c.obj_type,this.drawables=[]};k(D.prototype,C.prototype,{unpack_drawables:function(a){this.drawables=[];for(var b,c=0;c").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div),m(this.container_div,this),m(this.content_div,this),n(this.container_div,this.drag_handle_class,".group",this),this.filters_manager=new g.FiltersManager(this),this.header_div.after(this.filters_manager.parent_div),this.filters_manager.parent_div.after($("
")),this.saved_filters_managers=[],"drawables"in c&&this.unpack_drawables(c.drawables),"filters"in c){var d=this.filters_manager;this.filters_manager=new g.FiltersManager(this,c.filters),d.parent_div.replaceWith(this.filters_manager.parent_div),c.filters.visible&&this.setup_multitrack_filtering()}};k(E.prototype,C.prototype,D.prototype,{action_icons_def:[C.prototype.action_icons_def[0],C.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(a){$(".tooltip").remove(),a.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(a){a.filters_manager.visible()?(a.filters_manager.clear_filters(),a._restore_filter_managers()):(a.setup_multitrack_filtering(),a.request_draw({clear_tile_cache:!0})),a.filters_manager.toggle()}},C.prototype.action_icons_def[2]],build_container_div:function(){var a=$("
").addClass("group").attr("id","group_"+this.id);return this.container&&this.container.content_div.append(a),a},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show(),this.request_draw()},update_icons:function(){var a=this.drawables.length;if(0===a)this.action_icons.composite_icon.hide(),this.action_icons.filters_icon.hide();else if(1===a)this.action_icons.composite_icon.toggle(this.drawables[0]instanceof Q),this.action_icons.filters_icon.hide();else{var b,c,d,e=!0,f=this.drawables[0].get_type(),h=0;for(b=0;a>b;b++){if(d=this.drawables[b],d.get_type()!==f){can_composite=!1;break}d instanceof U&&h++}if(e&&this.drawables[0]instanceof S?this.action_icons.composite_icon.show():(this.action_icons.composite_icon.hide(),$(".tooltip").remove()),h>1&&h===this.drawables.length){var i,j={};for(d=this.drawables[0],c=0;c0)}else this.action_icons.filters_icon.hide()}},_restore_filter_managers:function(){for(var a=0;a0){this.saved_filters_managers=[];for(var a=0;a").addClass("top-container").appendTo(c),this.browser_content_div=$("
").addClass("content").appendTo(c),this.bottom_container=$("
").addClass("bottom-container").appendTo(c),this.top_labeltrack=$("
").addClass("top-labeltrack").appendTo(this.top_container),this.viewport_container=$("
").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div),this.content_div=this.viewport_container,m(this.viewport_container,d),this.intro_div=$("
").addClass("intro").appendTo(this.viewport_container);$("
").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){b.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":d.dbkey},function(b){a.each(b,function(a){d.add_drawable(Y(a,d,d))})})});this.nav_container=$("
").addClass("trackster-nav-container").prependTo(this.top_container),this.nav=$("
").addClass("trackster-nav").appendTo(this.nav_container),this.stand_alone&&(this.nav_container.addClass("stand-alone"),this.nav.addClass("stand-alone")),this.overview=$("
").addClass("overview").appendTo(this.bottom_container),this.overview_viewport=$("
").addClass("overview-viewport").appendTo(this.overview),this.overview_close=$("").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport),this.overview_highlight=$("
").addClass("overview-highlight").hide().appendTo(this.overview_viewport),this.overview_box_background=$("
").addClass("overview-boxback").appendTo(this.overview_viewport),this.overview_box=$("
").addClass("overview-box").appendTo(this.overview_viewport),this.default_overview_height=this.overview_box.height(),this.nav_controls=$("
").addClass("nav-controls").appendTo(this.nav),this.chrom_select=$("").addClass("nav-input").hide().bind("keyup focusout",e).appendTo(this.nav_controls),this.location_span=$("").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls),this.location_span.click(function(){d.location_span.hide(),d.chrom_select.hide(),d.nav_input.val(d.chrom+":"+d.low+"-"+d.high),d.nav_input.css("display","inline-block"),d.nav_input.select(),d.nav_input.focus(),d.nav_input.autocomplete({source:function(a,b){var c=[],e=$.map(d.get_tracks(U),function(b){return b.data_manager.search_features(a.term).success(function(a){c=c.concat(a)})});$.when.apply($,e).done(function(){b($.map(c,function(a){return{label:a[0],value:a[1]}}))})},minLength:2})}),void 0!==this.vis_id&&(this.hidden_input=$("").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)),this.zo_link=$("").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){d.zoom_out()}).appendTo(this.nav_controls),this.zi_link=$("").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){d.zoom_in()}).appendTo(this.nav_controls),this.load_chroms_deferred=this.load_chroms({low:0}),this.chrom_select.bind("change",function(){d.change_chrom(d.chrom_select.val())}),this.browser_content_div.click(function(){$(this).find("input").trigger("blur")}),this.browser_content_div.bind("dblclick",function(a){d.zoom_in(a.pageX,this.viewport_container)}),this.overview_box.bind("dragstart",function(a,b){this.current_x=b.offsetX}).bind("drag",function(a,b){var c=b.offsetX-this.current_x;this.current_x=b.offsetX;var e=Math.round(c/d.viewport_container.width()*(d.max_high-d.max_low));d.move_delta(-e)}),this.overview_close.click(function(){d.reset_overview()}),this.viewport_container.bind("draginit",function(a){return a.clientX>d.viewport_container.width()-16?!1:void 0}).bind("dragstart",function(a,b){b.original_low=d.low,b.current_height=a.clientY,b.current_x=b.offsetX}).bind("drag",function(a,b){var c=$(this),e=b.offsetX-b.current_x,f=c.scrollTop()-(a.clientY-b.current_height);c.scrollTop(f),b.current_height=a.clientY,b.current_x=b.offsetX;var g=Math.round(e/d.viewport_container.width()*(d.high-d.low));d.move_delta(g)}),this.top_labeltrack.bind("dragstart",function(){return $("
").addClass("zoom-area").css("height",d.browser_content_div.height()+d.top_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(a,b){$(b.proxy).css({left:Math.min(a.pageX,b.startX)-d.container.offset().left,width:Math.abs(a.pageX-b.startX)});var c=Math.min(a.pageX,b.startX)-d.container.offset().left,e=Math.max(a.pageX,b.startX)-d.container.offset().left,f=d.high-d.low,g=d.viewport_container.width();d.update_location(Math.round(c/g*f)+d.low,Math.round(e/g*f)+d.low)}).bind("dragend",function(a,b){var c=Math.min(a.pageX,b.startX),e=Math.max(a.pageX,b.startX),f=d.high-d.low,g=d.viewport_container.width(),h=d.low;d.low=Math.round(c/g*f)+h,d.high=Math.round(e/g*f)+h,$(b.proxy).remove(),d.request_redraw()}),this.add_label_track(new P(this,{content_div:this.top_labeltrack})),$(window).bind("resize",function(){this.resize_timer&&clearTimeout(this.resize_timer),this.resize_timer=setTimeout(function(){d.resize_window()},500)}),$(document).bind("redraw",function(){d.redraw()}),this.reset(),$(window).trigger("resize")},get_base_color:function(a){return this.config.get_value(a.toLowerCase()+"_color")||this.config.get_value("n_color")}});k(F.prototype,D.prototype,{changed:function(){this.has_changes=!0},update_intro_div:function(){this.intro_div.toggle(0===this.drawables.length)},trigger_navigate:function(a,b,c,d){if(this.timer&&clearTimeout(this.timer),d){var e=this;this.timer=setTimeout(function(){e.trigger("navigate",a+":"+b+"-"+c)},500)}else view.trigger("navigate",a+":"+b+"-"+c)},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b)),this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b));var c=this.chrom_select.val();""!==c&&this.trigger_navigate(c,this.low,this.high,!0)},load_chroms:function(a){a.num=t;var b=this,c=$.Deferred();return $.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:a,dataType:"json",success:function(a){if(0!==a.chrom_info.length){if(a.reference){var d=new R(b);b.add_label_track(d),b.reference_track=d}b.chrom_data=a.chrom_info;for(var e='',f=0,g=b.chrom_data.length;g>f;f++){var h=b.chrom_data[f].chrom;e+='"}a.prev_chroms&&(e+='"),a.next_chroms&&(e+='"),b.chrom_select.html(e),b.chrom_start_index=a.start_index,c.resolve(a.chrom_info)}},error:function(){alert("Could not load chroms for this dbkey: "+b.dbkey)}}),c},change_chrom:function(a,b,c){var d=this;if(!d.chrom_data)return void d.load_chroms_deferred.then(function(){d.change_chrom(a,b,c)});if(a&&"None"!==a){if("previous"===a)return void d.load_chroms({low:this.chrom_start_index-t});if("next"===a)return void d.load_chroms({low:this.chrom_start_index+t});var e=$.grep(d.chrom_data,function(b){return b.chrom===a})[0];if(void 0===e)return void d.load_chroms({chrom:a},function(){d.change_chrom(a,b,c)});if(a!==d.chrom){d.chrom=a,d.chrom_select.val(d.chrom),d.max_high=e.len-1,d.reset();for(var f=0,g=d.drawables.length;g>f;f++){var h=d.drawables[f];h.init&&h.init()}d.reference_track&&d.reference_track.init()}void 0===b&&void 0===c?(d.low=0,d.high=d.max_high):(d.low=void 0!==b?Math.max(b,0):0,void 0===c?(d.low=Math.max(d.low-15,0),d.high=d.low+30):d.high=Math.min(c,d.max_high)),d.request_redraw()}},go_to:function(a){a=a.replace(/,/g,""),a=a.replace(/:|\-/g," ");var b=a.split(/\s+/),c=b[0],d=b[1]?parseInt(b[1],10):void 0,e=b[2]?parseInt(b[2],10):void 0;this.change_chrom(c,d,e)},move_fraction:function(a){var b=this,c=b.high-b.low;this.move_delta(a*c)},move_delta:function(a){var b=this,c=b.high-b.low;b.low-ab.max_high?(b.high=b.max_high,b.low=b.max_high-c):(b.high-=a,b.low-=a),b.request_redraw({data_fetch:!1}),this.redraw_on_move_fn&&clearTimeout(this.redraw_on_move_fn),this.redraw_on_move_fn=setTimeout(function(){b.request_redraw()},200);var d=b.chrom_select.val();this.trigger_navigate(d,b.low,b.high,!0)},add_drawable:function(a){D.prototype.add_drawable.call(this,a),a.init(),this.changed(),this.update_intro_div();var b=this;a.config.on("change",function(){b.changed()})},add_label_track:function(a){a.view=this,a.init(),this.label_tracks.push(a)},remove_drawable:function(a,b){if(D.prototype.remove_drawable.call(this,a),b){var c=this;a.container_div.hide(0,function(){$(this).remove(),c.update_intro_div()})}},reset:function(){this.low=this.max_low,this.high=this.max_high,this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(b,c){var d=this,e=c?[c]:d.drawables;a.each(e,function(c){var e=a.find(d.tracks_to_be_redrawn,function(a){return a[0]===c});e?e[1]=b:d.tracks_to_be_redrawn.push([c,b])}),this.requested_redraw||(requestAnimationFrame(function(){d._redraw()}),this.requested_redraw=!0)},_redraw:function(){this.requested_redraw=!1;var b=this.low,c=this.high;bthis.max_high&&(c=this.max_high);var d=this.high-this.low;0!==this.high&&df&&this.overview_box.css("left",e-(g-f)/2),this.overview_highlight&&this.overview_highlight.css({left:e,width:f}),a.each(this.tracks_to_be_redrawn,function(a){var b=a[0],c=a[1];b&&b._draw(c)}),this.tracks_to_be_redrawn=[],a.each(this.label_tracks,function(a){a._draw()})},zoom_in:function(a){if(!(0===this.max_high||this.high-this.low<=this.min_separation)){var b=this.high-this.low,c=b/2+this.low,d=b/this.zoom_factor/2;a&&(c=a/this.viewport_container.width()*(this.high-this.low)+this.low),this.low=Math.round(c-d),this.high=Math.round(c+d),this.changed(),this.request_redraw()}},zoom_out:function(){if(0!==this.max_high){var a=this.high-this.low,b=a/2+this.low,c=a*this.zoom_factor/2;this.low=Math.round(b-c),this.high=Math.round(b+c),this.changed(),this.request_redraw()}},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport(),this.request_redraw()},set_overview:function(a){if(this.overview_drawable){if(this.overview_drawable.dataset.id===a.dataset.id)return;this.overview_viewport.find(".track").remove()}var b=a.copy({content_div:this.overview_viewport}),c=this;b.header_div.hide(),b.is_overview=!0,c.overview_drawable=b,this.overview_drawable.postdraw_actions=function(){c.overview_highlight.show().height(c.overview_drawable.content_div.height()),c.overview_viewport.height(c.overview_drawable.content_div.height()+c.overview_box.outerHeight()),c.overview_close.show(),c.resize_window()},c.overview_drawable.request_draw(),this.changed()},reset_overview:function(){$(".tooltip").remove(),this.overview_viewport.find(".track-tile").remove(),this.overview_viewport.height(this.default_overview_height),this.overview_box.height(this.default_overview_height),this.overview_close.hide(),this.overview_highlight.hide(),view.resize_window(),view.overview_drawable=null}});var G=i.Tool.extend({defaults:{track:null},initialize:function(a){i.Tool.prototype.initialize.call(this,a);var b=!0;void 0!==a.tool_state&&void 0!==a.tool_state.hidden&&(b=a.tool_state.hidden),this.set("hidden",b),this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(){return a.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}}),H=Backbone.View.extend({events:{"change :input":"update_value"},render:function(){var a=this.$el.addClass("param-row"),b=this.model,c=($("
").addClass("param-label").text(b.get("label")).appendTo(a),$("
").addClass("param-input").html(b.get("html")).appendTo(a));c.find(":input").val(b.get("value")),$("
").appendTo(a)},update_value:function(a){this.model.set_value($(a.target).val())}}),I=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.set_visible,this)},render:function(){var a=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide(),parent_div.bind("drag",function(a){a.stopPropagation()}).click(function(a){a.stopPropagation()}).bind("dblclick",function(a){a.stopPropagation()}).keydown(function(a){a.stopPropagation()});$("
").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(a){var b=new H({model:a});b.render(),parent_div.append(b.$el)}),parent_div.find("input").click(function(){$(this).select()});var b=$("
").addClass("param-row").appendTo(parent_div),c=$("").attr("value","Run on complete dataset").appendTo(b),d=$("").attr("value","Run on visible region").appendTo(b);d.click(function(){a.run_on_region()}),c.click(function(){a.run_on_dataset()}),tool.is_visible()&&this.$el.show()},set_visible:function(){this.$el.toggle(this.model.is_visible())},update_params:function(){for(var a=0;a").append(d),this.data=e,this.stale=!1};K.prototype.predisplay_actions=function(){};var L=function(a,b,c,d,e){K.call(this,a,b,c,d,e)};L.prototype.predisplay_actions=function(){};var M=function(a,b,c,d,e,f,g,h,i,j,k){K.call(this,a,b,c,d,e),this.mode=f,this.all_slotted=h,this.feature_mapper=i,this.has_icons=!1,this.incomplete_features=j,this.other_tiles_features_drawn={},this.seq_data=k};k(M.prototype,K.prototype),M.prototype.predisplay_actions=function(){};var N=function(a,c,d){k(d,{drag_handle_class:"draghandle"}),C.call(this,a,c,d),this.dataset=null,d.dataset&&(this.dataset=d.dataset instanceof Backbone.Model?d.dataset:new h.Dataset(d.dataset)),this.dataset_check_type="converted_datasets_state",this.data_url_extra_params={},this.data_query_wait="data_query_wait"in d?d.data_query_wait:s,this.data_manager="data_manager"in d?d.data_manager:new b.GenomeDataManager({dataset:this.dataset,genome:new b.Genome({key:a.dbkey,chroms_info:{chrom_info:a.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}),this.min_height_px=16,this.max_height_px=800,this.visible_height_px=this.config.get_value("height"),this.content_div=$("
").appendTo(this.container_div),this.container&&(this.container.content_div.append(this.container_div),"resize"in d&&!d.resize||this.add_resize_handle())};k(N.prototype,C.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},C.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(a){a.view.set_overview(a)}},C.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(a){a.filters_manager.visible()?a.filters_manager.clear_filters():a.filters_manager.init_filters(),a.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(a){a.tool.toggle(),a.tool.is_visible()?a.set_name(a.config.get_value("name")+a.tool_region_and_parameters_str()):a.revert_name(),$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(c){var d="Tool:"+c.tool.get("name")+"
Dataset:"+c.config.get_value("name")+'
Region(s): ',e=function(){Galaxy.modal.hide(),$(window).unbind("keypress.check_enter_esc")},f=function(){var d,e=$('select[name="regions"] option:selected').val(),f=new b.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),g=a.map($(".bookmark"),function(a){return new b.GenomeRegion({from_str:$(a).children(".position").text()})});d="cur"===e?[f]:"bookmarks"===e?g:[f].concat(g),Galaxy.modal.hide(),window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:c.dataset.id,hda_ldda:c.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(d).toJSON())})};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:d,buttons:{No:e,Yes:f}})}},C.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&C.prototype.can_draw.call(this)},build_container_div:function(){return $("
").addClass("track").attr("id","track_"+this.id)},set_dataset:function(a){this.dataset=a,this.data_manager.set("dataset",a)},on_resize:function(){this.request_draw({clear_tile_cache:!0})},add_resize_handle:function(){var a=this,b=!1,c=!1,d=$("
");$(a.container_div).hover(function(){a.config.get_value("content_visible")&&(b=!0,d.show())},function(){b=!1,c||d.hide()}),d.hide().bind("dragstart",function(b,d){c=!0,d.original_height=$(a.content_div).height()}).bind("drag",function(b,c){var d=Math.min(Math.max(c.original_height+c.deltaY,a.min_height_px),a.max_height_px);$(a.tiles_div).css("height",d),a.visible_height_px=a.max_height_px===d?0:d,a.on_resize()}).bind("dragend",function(){a.tile_cache.clear(),c=!1,b||d.hide(),a.config.set_value("height",a.visible_height_px),a.changed()}).appendTo(a.container_div)},hide_contents:function(){this.tiles_div.hide(),this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show(),this.container_div.find(".yaxislabel, .track-resize").show(),this.request_draw()},get_type:function(){return this instanceof P?"LabelTrack":this instanceof R?"ReferenceTrack":this instanceof S?"LineTrack":this instanceof W?"ReadTrack":this instanceof V?"VariantTrack":this instanceof Q?"CompositeTrack":this instanceof U?"FeatureTrack":""},show_message:function(a){return this.tiles_div.remove(),$("").addClass("message").html(a).appendTo(this.content_div)},init:function(a){var b=this;if(b.enabled=!1,b.tile_cache.clear(),b.data_manager.clear(), +b.content_div.children().remove(),b.container_div.removeClass("nodata error pending"),b.tiles_div=$("
").addClass("tiles").appendTo(b.content_div),b.dataset.id){var c=$.Deferred(),d={hda_ldda:b.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:b.view.chrom,retry:a};return $.getJSON(this.dataset.url(),d,function(a){if(a&&"error"!==a&&"error"!==a.kind)"no converter"===a?(b.container_div.addClass("error"),b.show_message(v)):"no data"===a||void 0!==a.data&&(null===a.data||0===a.data.length)?(b.container_div.addClass("nodata"),b.show_message(w)):"pending"===a?(b.container_div.addClass("pending"),b.show_message(x),setTimeout(function(){b.init()},b.data_query_wait)):("data"===a||"data"===a.status)&&(a.valid_chroms&&(b.valid_chroms=a.valid_chroms,b.update_icons()),b.tiles_div.text(z),b.view.chrom?(b.tiles_div.text(""),b.tiles_div.css("height",b.visible_height_px+"px"),b.enabled=!0,$.when.apply($,b.predraw_init()).done(function(){c.resolve(),b.container_div.removeClass("nodata error pending"),b.request_draw()})):c.resolve());else{b.container_div.addClass("error");var d=b.show_message(u);a.message&&(d.append($("").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"
"+a.message+"
",buttons:{Close:function(){Galaxy.modal.hide()}}})})),d.append($("").text(" ")),d.append($("").text("Try again").click(function(){b.init(!0)})))}}),this.update_icons(),c}},predraw_init:function(){var a=this;return $.getJSON(a.dataset.url(),{data_type:"data",stats:!0,chrom:a.view.chrom,low:0,high:a.view.max_high,hda_ldda:a.dataset.get("hda_ldda")},function(b){var c=b.data;if(void 0!==c&&void 0!==c.min&&void 0!==c.max){var d=c.min,e=c.max;d=Math.floor(Math.min(0,Math.max(d,c.mean-2*c.sd))),e=Math.ceil(Math.max(0,Math.min(e,c.mean+2*c.sd))),a.config.set_default_value("min_value",d),a.config.set_default_value("max_value",e),a.config.set_value("min_value",d),a.config.set_value("max_value",e)}})},get_drawables:function(){return this}});var O=function(c,d,e){N.call(this,c,d,e);var f=this;if(n(f.container_div,f.drag_handle_class,".group",f),this.filters_manager=new g.FiltersManager(this,"filters"in e?e.filters:null),this.data_manager.set("filters_manager",this.filters_manager),this.filters_available=!1,this.tool=e.tool?new G(a.extend(e.tool,{track:this,tool_state:e.tool_state})):null,this.tile_cache=new b.Cache(A),this.left_offset=0,this.header_div&&(this.set_filters_manager(this.filters_manager),this.tool)){var h=new I({model:this.tool});h.render(),this.dynamic_tool_div=h.$el,this.header_div.after(this.dynamic_tool_div)}this.tiles_div=$("
").addClass("tiles").appendTo(this.content_div),this.config.get_value("content_visible")||this.tiles_div.hide(),this.overlay_div=$("
").addClass("overlay").appendTo(this.content_div),e.mode&&this.change_mode(e.mode)};k(O.prototype,C.prototype,N.prototype,{action_icons_def:N.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(a){$(".tooltip").remove(),a.slotters[a.view.resolution_px_b].max_rows*=2,a.request_draw({clear_tile_cache:!0})},hide:!0}]),copy:function(a){var b=this.to_dict();k(b,{data_manager:this.data_manager});var c=new this.constructor(this.view,a,b);return c.change_mode(this.mode),c.enabled=this.enabled,c},set_filters_manager:function(a){this.filters_manager=a,this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:this.tool?this.tool.state_dict():{}}},set_min_max:function(){var a=this;return $.getJSON(a.dataset.url(),{data_type:"data",stats:!0,chrom:a.view.chrom,low:0,high:a.view.max_high,hda_ldda:a.dataset.get("hda_ldda")},function(b){var c=b.data;if(isNaN(parseFloat(a.config.get_value("min_value")))||isNaN(parseFloat(a.config.get_value("max_value")))){var d=c.min,e=c.max;d=Math.floor(Math.min(0,Math.max(d,c.mean-2*c.sd))),e=Math.ceil(Math.max(0,Math.min(e,c.mean+2*c.sd))),a.config.set_value("min_value",d),a.config.set_value("max_value",e)}})},change_mode:function(a){var b=this;return b.mode=a,b.config.set_value("mode",a),"Auto"===a&&this.data_manager.clear(),b.request_draw({clear_tile_cache:!0}),this.action_icons.mode_icon.attr("title","Set display mode (now: "+b.mode+")"),b},update_icons:function(){var a=this;a.action_icons.filters_icon.toggle(a.filters_available),a.action_icons.tools_icon.toggle(null!==a.tool),a.action_icons.param_space_viz_icon.toggle(null!==a.tool)},_gen_tile_cache_key:function(a,b){return a+"_"+b},request_draw:function(a){a&&a.clear_tile_cache&&this.tile_cache.clear(),this.view.request_redraw(a,this)},before_draw:function(){this.max_height_px=0},_draw:function(c){if(this.can_draw()){var d=c&&c.clear_after,e=this.view.low,f=this.view.high,g=this.view.container.width(),h=this.view.resolution_px_b,i=1/h;this.is_overview&&(e=this.view.max_low,f=this.view.max_high,h=g/(view.max_high-view.max_low),i=1/h),this.before_draw(),this.tiles_div.children().addClass("remove");for(var j,k,l=Math.floor(r*i),m=Math.floor(e/l),n=[],o=[];f>m*l;)j=new b.GenomeRegion({chrom:this.view.chrom,start:m*l,end:Math.min((m+1)*l,this.view.max_high)}),k=this.draw_helper(j,h,c),n.push(k),$.when(k).then(function(a){o.push(a)}),m+=1;d||this.tiles_div.children(".remove").removeClass("remove").remove();var p=this;$.when.apply($,n).then(function(){p.tiles_div.children(".remove").remove(),o=a.filter(o,function(a){return null!==a}),0!==o.length&&p.postdraw_actions(o,g,h,d)})}},_add_yaxis_label:function(a,b){var c=this,d="max"===a?"top":"bottom",e="max"===a?"max":"min",f="max"===a?"max_value":"min_value",g=this.container_div.find(".yaxislabel."+d);b=b||function(){c.request_draw({clear_tile_cache:!0})},0!==g.length?g.text(c.config.get_value(f)):(g=$("
").text(c.config.get_value(f)).make_text_editable({num_cols:12,on_finish:function(a){$(".tooltip").remove(),c.config.set_value(f,a),b()},help_text:"Set "+e+" value"}).addClass("yaxislabel "+d).css("color",this.config.get_value("label_color")),this.container_div.prepend(g))},postdraw_actions:function(b,c,d){var e=a.filter(b,function(a){return a instanceof L});if(e.length>0){this.max_height_px=0;var f=this;a.each(b,function(a){a instanceof L||(a.html_elt.remove(),f.draw_helper(a.region,d,{force:!0,mode:"Coverage"}))}),f._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var g=a.find(b,function(a){return a.has_icons});g&&a.each(b,function(a){a.has_icons||a.html_elt.css("padding-top",o)})}},get_mode:function(){return this.mode},update_auto_mode:function(){},_get_drawables:function(){return[this]},draw_helper:function(b,c,e){e||(e={});var f=e.force,g=e.mode||this.mode,h=1/c,i=this,j=this._get_drawables(),k=this._gen_tile_cache_key(c,b),l=function(a){return a&&"track"in a},m=f?void 0:i.tile_cache.get_elt(k);if(m)return l(m)&&i.show_tile(m,c),m;if(e.data_fetch===!1)return null;var n=function(){var c=a.find(B,function(a){return a===g})?"Coverage":g,d=a.map(j,function(a){return a.data_manager.get_data(b,c,h,i.data_url_extra_params)});return view.reference_track&&d.push(view.reference_track.data_manager.get_data(b,g,h,view.reference_track.data_url_extra_params)),d},o=$.Deferred();return i.tile_cache.set_elt(k,o),$.when.apply($,n()).then(function(){var f,g=n(),h=g;if(a.find(g,function(a){return d.is_deferred(a)}))return i.tile_cache.set_elt(k,void 0),void $.when(i.draw_helper(b,c,e)).then(function(a){o.resolve(a)});view.reference_track&&(f=view.reference_track.data_manager.subset_entry(g.pop(),b));var l=[],m=[];a.each(j,function(a,b){var d=a.mode,e=h[b];"Auto"===d&&(d=a.get_mode(e),a.update_auto_mode(d)),l.push(d),m.push(a.get_canvas_height(e,d,c,t))});var p,q=i.view.canvas_manager.new_canvas(),r=b.get("start"),s=b.get("end"),t=Math.ceil((s-r)*c)+i.left_offset,u=a.max(m);q.width=t,q.height=e.height||u;var v=q.getContext("2d");v.translate(i.left_offset,0),j.length>1&&(v.globalAlpha=.5,v.globalCompositeOperation="source-over"),a.each(j,function(a,d){p=a.draw_tile(h[d],v,l[d],b,c,f)}),void 0!==p&&(i.tile_cache.set_elt(k,p),i.show_tile(p,c)),o.resolve(p)}),o},get_canvas_height:function(){return this.visible_height_px},_draw_line_track_tile:function(a,b,c,d,e){var g=b.canvas,h=new f.LinePainter(a.data,d.get("start"),d.get("end"),this.config.to_key_value_dict(),c);return h.draw(b,g.width,g.height,e),new L(this,d,e,g,a.data)},draw_tile:function(){},show_tile:function(a,b){var c=a.html_elt;a.predisplay_actions();var d=Math.round((a.low-(this.is_overview?this.view.max_low:this.view.low))*b);this.left_offset&&(d-=this.left_offset),c.css("left",d),c.hasClass("remove")?c.removeClass("remove"):this.tiles_div.append(c),c.css("height","auto"),this.max_height_px=Math.max(this.max_height_px,c.height()-2),c.parent().children().css("height",this.max_height_px+"px");var e=this.max_height_px;0!==this.visible_height_px&&(e=Math.min(this.max_height_px,this.visible_height_px)),this.tiles_div.css("height",e+"px")},tool_region_and_parameters_str:function(b){var c=this,d=void 0!==b?b.toString():"all",e=a.values(c.tool.get_inputs_dict()).join(", ");return" - region=["+d+"], parameters=["+e+"]"},data_and_mode_compatible:function(a,b){return"Auto"===b?!0:"Coverage"===b?"bigwig"===a.dataset_type:"bigwig"===a.dataset_type||"no_detail"===a.extra_info?!1:!0},can_subset:function(a){return a.message||"no_detail"===a.extra_info?!1:"bigwig"===a.dataset_type?a.data[1][0]-a.data[0][0]===1:!0},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data"),this.data_query_wait=1e3,this.dataset_check_type="state"}});var P=function(a,b){N.call(this,a,b,{resize:!1,header:!1}),this.container_div.addClass("label-track")};k(P.prototype,N.prototype,{init:function(){this.enabled=!0},predraw_init:function(){},_draw:function(){for(var a=this.view,b=a.high-a.low,c=Math.floor(Math.pow(10,Math.floor(Math.log(b)/Math.log(10)))),d=Math.floor(a.low/c)*c,e=this.view.container.width(),f=$("
").addClass("label-container");d").addClass("label").text(commatize(d)).css({left:g})),d+=c}this.content_div.children(":first").remove(),this.content_div.append(f)}});var Q=function(b,c,d){if(O.call(this,b,c,d),this.drawables=[],"drawables"in d){for(var e,f=0;fthis.left_offset&&(this.left_offset=e.left_offset);this.enabled=!0}a.each(this.drawables,function(a){(a instanceof U||a instanceof W)&&a.change_mode("Coverage")}),this.update_icons(),this.obj_type="CompositeTrack"};k(Q.prototype,O.prototype,{display_modes:B,config_params:a.union(C.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}]),action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(a){$(".tooltip").remove(),a.show_group()}}].concat(O.prototype.action_icons_def),to_dict:D.prototype.to_dict,add_drawable:D.prototype.add_drawable,unpack_drawables:D.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},on_resize:function(){var b=this.visible_height_px;a.each(this.drawables,function(a){a.visible_height_px=b}),N.prototype.on_resize.call(this)},change_mode:function(a){O.prototype.change_mode.call(this,a);for(var b=0;be&&(e=f)}for(d=0;dthis.view.canvas_manager.char_width_px?(this.tiles_div.show(),d=!0,f=O.prototype.draw_helper.call(this,a,b,c)):(d=!1,this.tiles_div.hide()),e!==d&&this.view.resize_viewport(),f},can_subset:function(){return!0},draw_tile:function(a,b,c,d,e){var f=this.data_manager.subset_entry(a,d),g=f.data,h=b.canvas;b.font=b.canvas.manager.default_font,b.textAlign="center";for(var i=0,j=g.length;j>i;i++)b.fillStyle=this.view.get_base_color(g[i]),b.fillText(g[i],Math.floor(i*e),10);return new K(this,d,e,h,f)}});var S=function(a,b,c){this.mode="Histogram",O.call(this,a,b,c)};k(S.prototype,C.prototype,O.prototype,{display_modes:B,config_params:a.union(C.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:void 0},{key:"max_value",label:"Max Value",type:"float",default_value:void 0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:30,hidden:!0}]),config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},before_draw:function(){},draw_tile:function(a,b,c,d,e){return this._draw_line_track_tile(a,b,c,d,e)},can_subset:function(a){return a.data[1][0]-a.data[0][0]===1},postdraw_actions:function(){this._add_yaxis_label("max"),this._add_yaxis_label("min")}});var T=function(a,b,c){this.mode="Heatmap",O.call(this,a,b,c)};k(T.prototype,C.prototype,O.prototype,{display_modes:["Heatmap"],config_params:a.union(C.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:500,hidden:!0}]),config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},draw_tile:function(a,b,c,d,e){var g=b.canvas,h=new f.DiagonalHeatmapPainter(a.data,d.get("start"),d.get("end"),this.config.to_key_value_dict(),c);return h.draw(b,g.width,g.height,e),new K(this,d,e,g,a.data)}});var U=function(a,b,c){O.call(this,a,b,c),this.container_div.addClass("feature-track"),this.summary_draw_height=30,this.slotters={},this.start_end_dct={},this.left_offset=200,this.set_painter_from_config()};k(U.prototype,C.prototype,O.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:a.union(C.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}]),config_onchange:function(){this.set_name(this.config.get_value("name")),this.set_painter_from_config(),this.request_draw({clear_tile_cache:!0})},set_painter_from_config:function(){this.painter="arcs"===this.config.get_value("connector_style")?f.ArcLinkedFeaturePainter:f.LinkedFeaturePainter},postdraw_actions:function(b,c,d,e){O.prototype.postdraw_actions.call(this,b,c,d,e);var f,g=this,h=a.filter(b,function(a){return a instanceof L});if(0===h.length){var i={};a.each(a.pluck(b,"incomplete_features"),function(b){a.each(b,function(a){i[a[0]]=a})});var j=this;a.each(b,function(b){var c=a.omit(i,a.map(b.incomplete_features,function(a){return a[0]}));if(c=a.omit(c,a.keys(b.other_tiles_features_drawn)),0!==a.size(c)){var d={data:a.values(c)},e=j.view.canvas_manager.new_canvas(),f=e.getContext("2d");e.height=Math.max(b.canvas.height,j.get_canvas_height(d,b.mode,b.w_scale,100)),e.width=b.canvas.width,f.drawImage(b.canvas,0,0),f.translate(g.left_offset,0);var h=j.draw_tile(d,f,b.mode,b.region,b.w_scale,b.seq_data);$(b.canvas).replaceWith($(h.canvas)),b.canvas=e,a.extend(b.other_tiles_features_drawn,i)}})}if(g.filters_manager){var k,l=g.filters_manager.filters;for(k=0;kq?"Squish":"Pack",mode},get_canvas_height:function(a,b,c,d){if("Coverage"===b||"bigwig"===a.dataset_type)return this.summary_draw_height;var e=this.incremental_slots(c,a.data,b),f=new this.painter(null,null,null,this.config.to_key_value_dict(),b);return Math.max(this.min_height_px,f.get_required_height(e,d))},draw_tile:function(a,b,c,d,e,f,g){var h=this,i=b.canvas,j=d.get("start"),k=d.get("end"),l=this.left_offset;if("bigwig"===a.dataset_type)return this._draw_line_track_tile(a,b,c,d,e);var m=[],n=this.slotters[e].slots;if(all_slotted=!0,a.data)for(var o=this.filters_manager.filters,p=0,q=a.data.length;q>p;p++){for(var r,s=a.data[p],t=!1,u=0,v=o.length;v>u;u++)if(r=o[u],r.update_attrs(s),!r.keep(s)){t=!0;break}t||(m.push(s),s[0]in n||(all_slotted=!1))}var w=this.filters_manager.alpha_filter?new J(this.filters_manager.alpha_filter):null,x=this.filters_manager.height_filter?new J(this.filters_manager.height_filter):null,y=new this.painter(m,j,k,this.config.to_key_value_dict(),c,w,x,f,function(a){return h.view.get_base_color(a)}),z=null;if(b.fillStyle=this.config.get_value("block_color"),b.font=b.canvas.manager.default_font,b.textAlign="right",a.data){var A=y.draw(b,i.width,i.height,e,n);z=A.feature_mapper,incomplete_features=A.incomplete_features,z.translation=-l}return g?void 0:new M(h,d,e,i,a.data,c,a.message,all_slotted,z,incomplete_features,f)}});var V=function(a,b,c){O.call(this,a,b,c),this.painter=f.VariantPainter,this.summary_draw_height=30,this.left_offset=30};k(V.prototype,C.prototype,O.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:a.union(C.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:!0},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:!0},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"height",type:"int",default_value:0,hidden:!0}]),config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})},draw_tile:function(a,b,c,d,e){if("bigwig"===a.dataset_type)return this._draw_line_track_tile(a,b,"Histogram",d,e);var f=this.view,g=new this.painter(a.data,d.get("start"),d.get("end"),this.config.to_key_value_dict(),c,function(a){return f.get_base_color(a)});return g.draw(b,b.canvas.width,b.canvas.height,e),new K(this,d,e,b.canvas,a.data)},get_canvas_height:function(a,b){if("bigwig"===a.dataset_type)return this.summary_draw_height;var c=this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0;0===c&&0!==a.data.length&&(c=a.data[0][7].match(/,/g),c=null===c?1:c.length+1);var d=new this.painter(null,null,null,this.config.to_key_value_dict(),b);return d.get_required_height(c)},predraw_init:function(){var a=[N.prototype.predraw_init.call(this)];return this.dataset.get_metadata("sample_names")||a.push(this.dataset.fetch()),a},postdraw_actions:function(b,c,d,e){O.prototype.postdraw_actions.call(this,b,c,d,e);var f=a.filter(b,function(a){return a instanceof L}),g=this.dataset.get_metadata("sample_names");if(0===f.length&&this.config.get_value("show_labels")&&g&&g.length>1){var h;if(0===this.container_div.find(".yaxislabel.variant").length&&(h=this.config.get_value("summary_height")/2,this.tiles_div.prepend($("
").text("Summary").addClass("yaxislabel variant top").css({"font-size":h+"px",top:(this.config.get_value("summary_height")-h)/2+"px"})),this.config.get_value("show_sample_data"))){var i=g.join("
");this.tiles_div.prepend($("
").html(i).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}h=("Squish"===this.mode?5:10)+"px",$(this.tiles_div).find(".sample").css({"font-size":h,"line-height":h}),$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else this.container_div.find(".yaxislabel.variant").remove()}});var W=function(a,b,c){U.call(this,a,b,c),this.painter=f.ReadPainter,this.update_icons()};k(W.prototype,C.prototype,O.prototype,U.prototype,{config_params:a.union(C.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:!1},{key:"show_differences",label:"Show differences only",type:"bool",default_value:!0},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:!0},{key:"mode",type:"string",default_value:this.mode,hidden:!0},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:!0}]),config_onchange:function(){this.set_name(this.config.get_value("name")),this.request_draw({clear_tile_cache:!0})}});var X={CompositeTrack:Q,DrawableGroup:E,DiagonalHeatmapTrack:T,FeatureTrack:U,LineTrack:S,ReadTrack:W,VariantTrack:V,VcfTrack:V},Y=function(a,b,c){if("copy"in a)return a.copy(c);var d=a.obj_type;return d||(d=a.track_type),new X[d](b,c,a)};return{TracksterView:F,DrawableGroup:E,LineTrack:S,FeatureTrack:U,DiagonalHeatmapTrack:T,ReadTrack:W,VariantTrack:V,CompositeTrack:Q,object_from_template:Y}}); //# sourceMappingURL=../../../maps/viz/trackster/tracks.js.map \ No newline at end of file