From faafc762bf92e753af85d09913df2e6b29e8a172 Mon Sep 17 00:00:00 2001 From: Jeremy Goecks Date: Wed, 4 May 2011 10:20:54 -0400 Subject: [PATCH] Trackster: enable a tool to be run on complete dataset or a visible region. --- lib/galaxy/web/controllers/tracks.py | 111 +++++++++++++-------------- static/scripts/packed/trackster.js | 2 +- static/scripts/trackster.js | 86 +++++++++++++++------ 3 files changed, 118 insertions(+), 81 deletions(-) diff --git a/lib/galaxy/web/controllers/tracks.py b/lib/galaxy/web/controllers/tracks.py index ddefb749f68..a0839f94cbc 100644 --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -645,16 +645,17 @@ class TracksController( BaseController, UsesVisualization, UsesHistoryDatasetAss return self.tracks_grid( trans, **kwargs ) @web.expose - def run_tool( self, trans, dataset_id, chrom, low, high, tool_id, **kwargs ): + def run_tool( self, trans, dataset_id, tool_id, chrom=None, low=None, high=None, **kwargs ): """ Run a tool on a subset of input data to produce a new output dataset that corresponds to a dataset that a user is currently viewing. """ - # Parameter checks. - if not chrom or not low or not high: - return messages.NO_DATA - low, high = int( low ), int( high ) + # Run tool on region if region is specificied. + run_on_region = False + if chrom and low and high: + run_on_region = True + low, high = int( low ), int( high ) # Dataset check. original_dataset = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) @@ -678,27 +679,23 @@ class TracksController( BaseController, UsesVisualization, UsesHistoryDatasetAss tool_params = tool.params_from_strings( tool_params, self.app ) # - # Convert input datasets so that region of dataset can be quickly - # extracted. - # TODO: Is it useful/necessary to create data subsets for all input - # datasets or only the original dataset (aka the dataset that the user - # is viewing)? Currently we create data subsets for all input datasets - # because this provides the best performance as the tool runs on small - # datasets. + # If running tool on region, convert input datasets (create indices) so + # that can regions of data can be quickly extracted. # messages_list = [] - for jida in original_job.input_datasets: - input_dataset = jida.dataset - # TODO: put together more robust way to determine if a dataset can be indexed. - if hasattr( input_dataset, 'get_track_type' ): - # Can index dataset. - track_type, data_sources = input_dataset.datatype.get_track_type() - # Convert to datasource that provides 'data' because we need to - # extract the original data. - data_source = data_sources[ 'data' ] - msg = self._convert_dataset( trans, input_dataset, data_source ) - if msg is not None: - messages_list.append( msg ) + if run_on_region: + for jida in original_job.input_datasets: + input_dataset = jida.dataset + # TODO: put together more robust way to determine if a dataset can be indexed. + if hasattr( input_dataset, 'get_track_type' ): + # Can index dataset. + track_type, data_sources = input_dataset.datatype.get_track_type() + # Convert to datasource that provides 'data' because we need to + # extract the original data. + data_source = data_sources[ 'data' ] + msg = self._convert_dataset( trans, input_dataset, data_source ) + if msg is not None: + messages_list.append( msg ) # Return any messages generated during conversions. return_message = _get_highest_priority_msg( messages_list ) @@ -706,41 +703,40 @@ class TracksController( BaseController, UsesVisualization, UsesHistoryDatasetAss return return_message # - # Set input datasets for tool. Input datasets are subsets of full - # datasets and are based on chrom, low, high. + # Set target history (the history that tool will use for inputs/outputs). + # If user owns dataset, put new data in original dataset's history; if + # user does not own dataset (and hence is accessing dataset via sharing), + # put new data in user's current history. # - - # If user is rerunning own tool, put new data in original dataset's - # history. If another user is running tool, put new data in current - # history. if original_dataset.history.user == trans.user: - working_history = original_dataset.history + target_history = original_dataset.history else: - working_history = trans.get_history( create=True ) - hda_permissions = trans.app.security_agent.history_get_default_permissions( working_history ) - messages_list = [] + target_history = trans.get_history( create=True ) + hda_permissions = trans.app.security_agent.history_get_default_permissions( target_history ) + + # + # Set input datasets for tool. If running on region, extract and use subset + # when possible. + # for jida in original_job.input_datasets: input_dataset = jida.dataset - if hasattr( input_dataset.datatype, 'get_track_type' ): - # - # Dataset can be indexed and hence a subset can be extracted. - # + if run_on_region and hasattr( input_dataset.datatype, 'get_track_type' ): + # Dataset is indexed and hence a subset can be extracted and used + # as input. track_type, data_sources = input_dataset.datatype.get_track_type() data_source = data_sources[ 'data' ] converted_dataset = input_dataset.get_converted_dataset( trans, data_source ) deps = input_dataset.get_converted_dataset_deps( trans, data_source ) - # # Create new HDA for input dataset's subset. - # new_dataset = trans.app.model.HistoryDatasetAssociation( extension=input_dataset.ext, \ - dbkey=input_dataset.dbkey, \ - create_dataset=True, \ - sa_session=trans.sa_session, - name="Subset [%s:%i-%i] of data %i" % \ - ( chrom, low, high, input_dataset.hid ), - visible=False ) - working_history.add_dataset( new_dataset ) + dbkey=input_dataset.dbkey, \ + create_dataset=True, \ + sa_session=trans.sa_session, + name="Subset [%s:%i-%i] of data %i" % \ + ( chrom, low, high, input_dataset.hid ), + visible=False ) + target_history.add_dataset( new_dataset ) trans.sa_session.add( new_dataset ) trans.app.security_agent.set_all_dataset_permissions( new_dataset.dataset, hda_permissions ) @@ -751,7 +747,7 @@ class TracksController( BaseController, UsesVisualization, UsesHistoryDatasetAss dependencies=deps ) data_provider.write_data_to_file( chrom, low, high, new_dataset.file_name ) - # TODO: size not working. + # TODO: (a) size not working; (b) need to set peek. new_dataset.set_size() new_dataset.info = "Data subset for trackster" new_dataset.set_dataset_state( trans.app.model.Dataset.states.OK ) @@ -761,18 +757,21 @@ class TracksController( BaseController, UsesVisualization, UsesHistoryDatasetAss tool_params[ jida.name ] = new_dataset # - # Start tool and handle outputs. + # Execute tool and handle outputs. # try: - subset_job, subset_job_outputs = tool.execute( trans, incoming=tool_params, history=working_history ) + subset_job, subset_job_outputs = tool.execute( trans, incoming=tool_params, history=target_history ) except Exception, e: # Lots of things can go wrong when trying to execute tool. return to_json_string( { "error" : True, "message" : e.__class__.__name__ + ": " + str(e) } ) - for output in subset_job_outputs.values(): - output.visible = False - trans.sa_session.flush() - + if run_on_region: + for output in subset_job_outputs.values(): + output.visible = False + trans.sa_session.flush() + + # # Return new track that corresponds to the original dataset. + # output_name = None for joda in original_job.output_datasets: if joda.dataset == original_dataset: @@ -784,9 +783,9 @@ class TracksController( BaseController, UsesVisualization, UsesHistoryDatasetAss return self.add_track_async( trans, output_dataset.id ) - # + # ----------------- # Helper methods. - # + # ----------------- def _check_dataset_state( self, trans, dataset ): """ diff --git a/static/scripts/packed/trackster.js b/static/scripts/packed/trackster.js index 68ea939176f..8dd61ce467e 100644 --- a/static/scripts/packed/trackster.js +++ b/static/scripts/packed/trackster.js @@ -1 +1 @@ -var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;ec){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var trackster_module=function(f,T){var o=f("class").extend,q=f("slotting"),I=f("painters");var Z=function(aa,ab){this.document=aa;this.default_font=ab!==undefined?ab:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};o(Z.prototype,{load_pattern:function(aa,ae){var ab=this.patterns,ac=this.dummy_context,ad=new Image();ad.src=image_path+ae;ad.onload=function(){ab[aa]=ac.createPattern(ad,"repeat")}},get_pattern:function(aa){return this.patterns[aa]},new_canvas:function(){var aa=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(aa)}aa.manager=this;return aa}});var C=function(aa,ab){aa.bind("drag",{handle:ab,relative:true},function(af,ag){var ae=$(this).parent();var ad=ae.children();var ac;for(ac=0;ac=this.num_elements){var aa=this.key_ary.shift();delete this.obj_cache[aa]}this.key_ary.push(ab)}this.obj_cache[ab]=ac;return ac},move_key_to_end:function(ab,aa){this.key_ary.splice(aa,1);this.key_ary.push(ab)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var N=function(ab,aa,ac){c.call(this,ab);this.track=aa;this.subset=(ac!==undefined?ac:true)};o(N.prototype,c.prototype,{load_data:function(ai,aj,ae,ah,ab,ag){var ad={chrom:ai,low:aj,high:ae,mode:ah,resolution:ab,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ad,ag);if(this.track.filters_manager){var ak=[];var aa=this.track.filters_manager.filters;for(var af=0;af1){return}return N.prototype.load_data.call(this,ac,aa,ae,af,ab,ad)}});var Y=function(aa,ad,ac,ab,ae){this.container=aa;this.chrom=null;this.vis_id=ac;this.dbkey=ab;this.title=ad;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(ae);this.canvas_manager=new Z(aa.get(0).ownerDocument);this.reset()};o(Y.prototype,{init:function(ad){var ac=this.container,aa=this;this.top_container=$("
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").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("
").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("
").appendTo(this.header_div)}this.name_div=$("
").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("
").appendTo(this.container_div);this.parent_element.append(this.container_div)};o(k.prototype,{init:function(){var aa=this;aa.enabled=false;aa.tile_cache.clear();aa.data_cache.clear();aa.initial_canvas=undefined;aa.content_div.css("height","auto");aa.container_div.removeClass("nodata error pending");if(!aa.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:aa.hda_ldda,dataset_id:aa.dataset_id,chrom:aa.view.chrom},function(ab){if(!ab||ab==="error"||ab.kind==="error"){aa.container_div.addClass("error");aa.content_div.text(n);if(ab.message){var ad=aa.view.tracks.indexOf(aa);var ac=$(" ").text("View error").bind("click",function(){show_modal("Trackster Error","
"+ab.message+"
",{Close:hide_modal})});aa.content_div.append(ac)}}else{if(ab==="no converter"){aa.container_div.addClass("error");aa.content_div.text(G)}else{if(ab==="no data"||(ab.data!==undefined&&(ab.data===null||ab.data.length===0))){aa.container_div.addClass("nodata");aa.content_div.text(B)}else{if(ab==="pending"){aa.container_div.addClass("pending");aa.content_div.text(r);setTimeout(function(){aa.init()},aa.data_query_wait)}else{if(ab.status==="data"){if(ab.valid_chroms){aa.valid_chroms=ab.valid_chroms;aa.make_name_popup_menu()}aa.content_div.text(U);if(aa.view.chrom){aa.content_div.text("");aa.content_div.css("height",aa.height_px+"px");aa.enabled=true;$.when(aa.predraw_init()).done(function(){aa.container_div.removeClass("nodata error pending");aa.draw()})}}}}}}})},predraw_init:function(){},update_name:function(aa){this.old_name=this.name;this.name=aa;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var J=function(ai,ag,aj){var ab=this,ak=ab.view;this.filters_manager=(ai!==undefined?new W(this,ai):undefined);this.filters_available=false;this.filters_visible=false;this.tool=(ag!==undefined&&obj_length(ag)>0?new p(this,ag):undefined);this.parent_track=aj;this.child_tracks=[];if(ab.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}ab.child_tracks_container=$("
").addClass("child-tracks-container").hide();ab.container_div.append(ab.child_tracks_container);if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(ab.display_modes!==undefined){if(ab.mode_div===undefined){ab.mode_div=$("
").appendTo(ab.header_div);var ad=(ab.track_config&&ab.track_config.values.mode?ab.track_config.values.mode:ab.display_modes[0]);ab.mode=ad;ab.mode_div.text(ad);var ac=function(al){ab.mode_div.text(al);ab.mode=al;ab.track_config.values.mode=al;ab.tile_cache.clear();ab.draw()};var aa={};for(var ae=0,ah=ab.display_modes.length;ae0){var ae=(ab.filters_div.is(":visible")?"Hide filters":"Show filters");aa[ae]=function(){ab.filters_visible=(ab.filters_div.is(":visible"));ab.filters_div.toggle();ab.make_name_popup_menu()}}if(ab.tool){var ae=(ab.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");aa[ae]=function(){if(!ab.dynamic_tool_div.is(":visible")){ab.update_name(ab.name+ab.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ab.revert_name()}ab.dynamic_tool_div.toggle();ab.make_name_popup_menu()}}if(ab.valid_chroms){aa["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","

"+ab.valid_chroms.join("
")+"

",{Close:function(){hide_modal()}})}}var ac=view;var ad=function(){$("#no-tracks").show()};if(this.parent_track){ac=this.parent_track;ad=function(){}}aa.Remove=function(){ac.remove_track(ab);if(ac.num_tracks===0){ad()}};make_popupmenu(ab.name_div,aa)},draw:function(aa,ac){var au=this.view.low,ag=this.view.high,ai=ag-au,ak=this.view.container.width(),ae=ak/ai,al=this.view.resolution,ad=$("
"),am=function(aw,ax,av){return aw+"_"+ax+"_"+av};if(!ac){this.content_div.children().remove()}this.content_div.append(ad);this.max_height=0;var ao=Math.floor(au/al/M);var af=[];var ap=0;while((ao*M*al)=aD;ax--){var aw=$(ay[ax]);if(az){aw.remove()}else{if(aw.children().length!==0){az=true}}}}if(aj.track_type=="FeatureTrack"&&aj.mode=="Histogram"){var aC=-1;for(var ax=0;axaC){aC=aF}}for(var ax=0;ax=ad.view.low){var an=(ab?undefined:ad.tile_cache.get(ai));if(an){ad.show_tile(an,aj,ag,am);ak[ak.length]=an}else{$.when(ad.data_cache.get_data(view.chrom,ag,al,ad.mode,ae,ad.data_url_extra_params)).then(function(ao){o(ao,af);if(view.reference_track&&am>view.canvas_manager.char_width_px){$.when(view.reference_track.data_cache.get_data(view.chrom,ag,al,ad.mode,ae,view.reference_track.data_url_extra_params)).then(function(ap){ah(aa,ao,ae,ac,aj,am,ap)})}else{ah(aa,ao,ae,ac,aj,am)}})}}},50)},show_tile:function(ad,ag,ae,ah){var ab=this;var ac=this.view.high-this.view.low,af=(ae-this.view.low)*ah;if(this.left_offset){af-=this.left_offset}var aa=ad.canvas;aa.css({position:"absolute",top:0,left:af,height:""});ag.append(aa);ab.max_height=Math.max(ab.max_height,aa.height());ab.content_div.css("height",ab.max_height+"px");ag.children().css("height",ab.max_height+"px")},set_overview:function(){var aa=this.view;if(this.initial_canvas&&this.is_overview){aa.overview_close.show();aa.overview_viewport.append(this.initial_canvas);aa.overview_highlight.show().height(this.initial_canvas.height());aa.overview_viewport.height(this.initial_canvas.height()+aa.overview_box.height())}$(window).trigger("resize")},tool_region_and_parameters_str:function(ac,aa,ad){var ab=this,ae=(ac!==undefined&&aa!==undefined&&ad!==undefined?ac+":"+aa+"-"+ad:"all");return" - region=["+ae+"], parameters=["+ab.tool.get_param_values().join(", ")+"]"},add_track:function(aa){aa.track_id=this.track_id+"_"+this.child_tracks.length;aa.container_div.attr("id","track_"+aa.track_id);this.child_tracks_container.append(aa.container_div);C(aa.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(aa);this.view.has_changes=true},remove_track:function(aa){aa.container_div.fadeOut("slow",function(){$(this).remove()})}});var X=function(aa,ab){this.track_type="LabelTrack";this.hidden=true;k.call(this,null,aa,ab);this.container_div.addClass("label-track")};o(X.prototype,k.prototype,{draw:function(){var ac=this.view,ad=ac.high-ac.low,ag=Math.floor(Math.pow(10,Math.floor(Math.log(ad)/Math.log(10)))),aa=Math.floor(ac.low/ag)*ag,ae=this.view.container.width(),ab=$("
");while(aa"+commatize(aa)+"
").css({position:"absolute",left:af-1}));aa+=ag}this.content_div.children(":first").remove();this.content_div.append(ab)}});var y=function(aa){this.track_type="ReferenceTrack";this.hidden=true;k.call(this,null,aa,aa.top_labeltrack);J.call(this);aa.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:aa.dbkey};this.data_cache=new E(z,this,false);this.tile_cache=new c(s)};o(y.prototype,J.prototype,{draw_tile:function(ai,af,ab,ak){var ae=this,ac=M*af;if(ak>this.view.canvas_manager.char_width_px){if(ai===null){ae.content_div.css("height","0px");return}var ad=this.view.canvas_manager.new_canvas();var aj=ad.getContext("2d");ad.width=Math.ceil(ac*ak+ae.left_offset);ad.height=ae.height_px;aj.font=aj.canvas.manager.default_font;aj.textAlign="center";for(var ag=0,ah=ai.length;ag");$(aa.container_div).hover(function(){ad=true;ab.show()},function(){ad=false;if(!ac){ab.hide()}});ab.hide().bind("dragstart",function(ae,af){ac=true;af.original_height=$(aa.content_div).height()}).bind("drag",function(af,ag){var ae=Math.min(Math.max(ag.original_height+ag.deltaY,aa.min_height_px),aa.max_height_px);$(aa.content_div).css("height",ae);aa.height_px=ae;aa.draw(true)}).bind("dragend",function(ae,af){aa.tile_cache.clear();ac=false;if(!ad){ab.hide()}aa.track_config.values.height=aa.height_px}).appendTo(aa.container_div)},predraw_init:function(){var aa=this,ab=aa.view.tracks.indexOf(aa);aa.vertical_range=undefined;return $.getJSON(aa.data_url,{stats:true,chrom:aa.view.chrom,low:null,high:null,hda_ldda:aa.hda_ldda,dataset_id:aa.dataset_id},function(ac){aa.container_div.addClass("line-track");var ae=ac.data;if(isNaN(parseFloat(aa.prefs.min_value))||isNaN(parseFloat(aa.prefs.max_value))){aa.prefs.min_value=ae.min;aa.prefs.max_value=ae.max;$("#track_"+ab+"_minval").val(aa.prefs.min_value);$("#track_"+ab+"_maxval").val(aa.prefs.max_value)}aa.vertical_range=aa.prefs.max_value-aa.prefs.min_value;aa.total_frequency=ae.total_frequency;aa.container_div.find(".yaxislabel").remove();var af=$("
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").addClass("yaxislabel");aa.text(an.max);aa.css({position:"absolute",top:"22px",left:"10px"});aa.prependTo(this.container_div);var ac=this.view.canvas_manager.new_canvas();ac.width=au+ae;ac.height=af+O;if(an.dataset_type!="summary_tree"){var ak=this.get_summary_tree_data(an.data,aC,ab,200);if(an.max){ak.max=an.max}an=ak}var aD=new I.SummaryTreePainter(an,aC,ab,this.prefs);var av=ac.getContext("2d");av.translate(ae,O);aD.draw(av,au,af);return new m(aA,aw,ac,an.max)}var ao,ah=1;if(ar==="no_detail"||ar==="Squish"||ar==="Pack"){ah=this.incremental_slots(aj,an.data,ar);ao=this.inc_slots[aj].slots}var ai=[];if(an.data){var al=this.filters_manager.filters;for(var ax=0,az=an.data.length;axB[0]&&G=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(j,w){var t=j("class").extend;var o=function(H,z,F,y,E,C){if(C===undefined){C=4}var B=y-z;var A=E-F;var D=Math.floor(Math.sqrt(B*B+A*A)/C);var I=B/D;var G=A/D;var x;for(x=0;x1){C=Math.ceil((S[1][0]-S[0][0])*B)}else{C=10}for(var P=0,Q=S.length;PD){E=D}}if(I==="Histogram"){E=Math.round(E/K*z);O.fillRect(R,T,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/K*255);O.fillStyle="rgb("+E+","+E+","+E+")";O.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/K*z);if(F){O.lineTo(R,E)}else{F=true;if(I==="Filled"){O.moveTo(R,z);O.lineTo(R,E)}else{O.moveTo(R,E)}}}}}if(I==="Filled"){if(F){O.lineTo(R,T);O.lineTo(0,T)}O.fill()}else{O.stroke()}var x=-1,J=-1;O.fillStyle=this.prefs.overflow_color;var G;for(var P=0,Q=S.length;P=0&&(E===null||E=0&&(E===null||E>H)){O.fillRect(x,L-2,G+C-x,2);x=-1}}if(E!==null&&E>D&&J<0){J=R}else{if(E!==null&&EG)&&(this.mode=="Dense"||H!==null)){this.draw_element(J,this.mode,L,H,G,K,M,z,A)}}J.restore()}});var d=10,h=3,l=5,v=10,f=1,r=3,e=3,a=9,k=2,g="#ccc";var q=function(z,B,x,y,A){n.call(this,z,B,x,y,A)};t(q.prototype,n.prototype,{get_row_height:function(){var y=this.mode,x;if(y==="Dense"){x=d}else{if(y==="no_detail"){x=h}else{if(y==="Squish"){x=l}else{x=v}}}return x},draw_element:function(J,C,R,E,L,ab,af,ag,x){var O=R[0],ad=R[1],V=R[2],M=R[3],W=Math.floor(Math.max(0,(ad-L)*af)),K=Math.ceil(Math.min(x,Math.max(0,(V-L)*af))),U=(C==="Dense"?0:(0+E))*ag,I,Z,N=null,ah=null,A=this.prefs.block_color,Y=this.prefs.label_color;if(C=="Dense"){E=1}if(C==="no_detail"){J.fillStyle=A;J.fillRect(W,U+5,K-W,f)}else{var H=R[4],T=R[5],X=R[6],B=R[7];if(T&&X){N=Math.floor(Math.max(0,(T-L)*af));ah=Math.ceil(Math.min(x,Math.max(0,(X-L)*af)))}var ae,P;if(C==="Squish"||C==="Dense"){ae=1;P=e}else{ae=5;P=a}if(!B){if(R.strand){if(R.strand==="+"){J.fillStyle=J.canvas.manager.get_pattern("right_strand_inv")}else{if(R.strand==="-"){J.fillStyle=J.canvas.manager.get_pattern("left_strand_inv")}}}else{J.fillStyle=A}J.fillRect(W,U,K-W,P)}else{var G,Q;if(C==="Squish"||C==="Dense"){J.fillStyle=g;G=U+Math.floor(e/2)+1;Q=1}else{if(H){var G=U;var Q=P;if(H==="+"){J.fillStyle=J.canvas.manager.get_pattern("right_strand")}else{if(H==="-"){J.fillStyle=J.canvas.manager.get_pattern("left_strand")}}}else{J.fillStyle=g;G+=(e/2)+1;Q=1}}J.fillRect(W,G,K-W,Q);for(var ac=0,z=B.length;acS){continue}J.fillStyle=A;J.fillRect(y,U+(P-ae)/2+1,S-y,ae);if(N!==undefined&&X>T&&!(y>ah||SL){J.fillStyle=Y;if(L===0&&W-J.measureText(M).width<0){J.textAlign="left";J.fillText(M,K+k,U+8)}else{J.textAlign="right";J.fillText(M,W-k,U+8)}J.fillStyle=A}}}});var b=function(z,B,x,y,A){n.call(this,z,B,x,y,A)};t(b.prototype,n.prototype,{draw_element:function(Q,L,F,B,T,z,I,R,O){var F=data[i],H=F[0],P=F[1],A=F[2],K=F[3],D=Math.floor(Math.max(0,(P-T)*I)),G=Math.ceil(Math.min(O,Math.max(0,(A-T)*I))),C=(L==="Dense"?0:(0+B))*R,x,U,y=null,J=null;if(no_label){Q.fillStyle=block_color;Q.fillRect(D+left_offset,C+5,G-D,1)}else{var S=F[4],N=F[5],E=F[6];x=9;U=1;Q.fillRect(D+left_offset,C,G-D,x);if(L!=="Dense"&&K!==undefined&&P>T){Q.fillStyle=label_color;if(T===0&&D-Q.measureText(K).width<0){Q.textAlign="left";Q.fillText(K,G+2+left_offset,C+8)}else{Q.textAlign="right";Q.fillText(K,D-2+left_offset,C+8)}Q.fillStyle=block_color}var M=S+" / "+N;if(P>T&&Q.measureText(M).width<(G-D)){Q.fillStyle="white";Q.textAlign="center";Q.fillText(M,left_offset+D+(G-D)/2,C+8);Q.fillStyle=block_color}}}});var s=function(A,C,x,z,B,y){n.call(this,A,C,x,z,B);this.ref_seq=y};s.prototype.default_prefs=t({},n.prototype.default_prefs,{show_insertions:false});t(s.prototype,n.prototype,{get_row_height:function(){var x,y=this.mode;if(y==="Dense"){x=d}else{if(y==="Squish"){x=l}else{x=v;if(this.prefs.show_insertions){x*=2}}}return x},draw_read:function(T,O,K,Y,z,S,H,E,D){T.textAlign="center";var R=this,y=[Y,z],N=0,U=0,Q=0;ref_seq=this.ref_seq,char_width_px=T.canvas.manager.char_width_px;var ad=[];if((O==="Pack"||this.mode==="Auto")&&E!==undefined&&K>char_width_px){Q=Math.round(K/2)}if(!H){H=[[0,E.length]]}for(var L=0,W=H.length;L0){T.fillStyle=this.prefs.block_color;T.fillRect(ac-Q,D+1,G-ac,9);T.fillStyle=g;for(var aa=0,x=P.length;aa=Y&&F+aa<=z){var ab=Math.floor(Math.max(0,(F+aa-Y)*K));T.fillText(P[aa],ab,D+9)}}}else{T.fillStyle=this.prefs.block_color;T.fillRect(ac,D+4,G-ac,e)}}U+=M;N+=M;break;case"N":T.fillStyle=g;T.fillRect(ac-Q,D+5,G-ac,1);N+=M;break;case"D":T.fillStyle="red";T.fillRect(ac-Q,D+4,G-ac,3);N+=M;break;case"P":break;case"I":var X=ac-Q;if(is_overlap([F,F+M],y)){var P=E.slice(U,U+M);if(this.prefs.show_insertions){var C=ac-(G-ac)/2;if((O==="Pack"||this.mode==="Auto")&&E!==undefined&&K>char_width_px){T.fillStyle="yellow";T.fillRect(C-Q,D-9,G-ac,9);ad[ad.length]={type:"triangle",data:[X,D+4,5]};T.fillStyle=g;switch(seq_tile_overlap){case (OVERLAP_START):P=P.slice(Y-F);break;case (OVERLAP_END):P=P.slice(0,F-z);break;case (CONTAINED_BY):break;case 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S=1;if(S===0&&C-Q.measureText(I).width<0){Q.textAlign="left";Q.fillText(I,E+k-N,B+8)}else{Q.textAlign="right";Q.fillText(I,C-k-N,B+8)}Q.fillStyle=U}}});w.SummaryTreePainter=u;w.LinePainter=c;w.LinkedFeaturePainter=q;w.ReadPainter=s;w.VariantPainter=b};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file +var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;ec){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var trackster_module=function(f,S){var n=f("class").extend,p=f("slotting"),H=f("painters");var Y=function(Z,aa){this.document=Z;this.default_font=aa!==undefined?aa:"9px Monaco, Lucida Console, 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ac=ad.children();var ab;for(ab=0;ab=this.num_elements){var Z=this.key_ary.shift();delete this.obj_cache[Z]}this.key_ary.push(aa)}this.obj_cache[aa]=ab;return ab},move_key_to_end:function(aa,Z){this.key_ary.splice(Z,1);this.key_ary.push(aa)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var M=function(aa,Z,ab){c.call(this,aa);this.track=Z;this.subset=(ab!==undefined?ab:true)};n(M.prototype,c.prototype,{load_data:function(ah,ai,ad,ag,aa,af){var ac={chrom:ah,low:ai,high:ad,mode:ag,resolution:aa,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ac,af);if(this.track.filters_manager){var aj=[];var Z=this.track.filters_manager.filters;for(var ae=0;ae1){return}return M.prototype.load_data.call(this,ab,Z,ad,ae,aa,ac)}});var X=function(Z,ac,ab,aa,ad){this.container=Z;this.chrom=null;this.vis_id=ab;this.dbkey=aa;this.title=ac;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(ad);this.canvas_manager=new Y(Z.get(0).ownerDocument);this.reset()};n(X.prototype,{init:function(ac){var ab=this.container,Z=this;this.top_container=$("
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").addClass("bottom-container").appendTo(ab);this.top_labeltrack=$("
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").css({height:Z.content_div.height()+Z.top_labeltrack.height()+Z.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ah,ai){$(ai.proxy).css({left:Math.min(ah.pageX,ai.startX),width:Math.abs(ah.pageX-ai.startX)});var ae=Math.min(ah.pageX,ai.startX)-Z.container.offset().left,ad=Math.max(ah.pageX,ai.startX)-Z.container.offset().left,ag=(Z.high-Z.low),af=Z.viewport_container.width();Z.update_location(Math.round(ae/af*ag)+Z.low,Math.round(ad/af*ag)+Z.low)}).bind("dragend",function(ai,aj){var ae=Math.min(ai.pageX,aj.startX),ad=Math.max(ai.pageX,aj.startX),ag=(Z.high-Z.low),af=Z.viewport_container.width(),ah=Z.low;Z.low=Math.round(ae/af*ag)+ah;Z.high=Math.round(ad/af*ag)+ah;$(aj.proxy).remove();Z.redraw()});this.add_label_track(new W(this,this.top_labeltrack));this.add_label_track(new W(this,this.nav_labeltrack));$(window).bind("resize",function(){Z.resize_window()});$(document).bind("redraw",function(){Z.redraw()});this.reset();$(window).trigger("resize")},update_location:function(Z,aa){this.location_span.text(commatize(Z)+" - "+commatize(aa));this.nav_input.val(this.chrom+":"+commatize(Z)+"-"+commatize(aa))},load_chroms:function(aa,ab){aa.num=t;$.extend(aa,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var Z=this;$.ajax({url:chrom_url,data:aa,dataType:"json",success:function(ad){if(ad.chrom_info.length===0){alert("Invalid chromosome: "+aa.chrom);return}if(ad.reference){Z.add_label_track(new x(Z))}Z.chrom_data=ad.chrom_info;var ag='';for(var af=0,ac=Z.chrom_data.length;af'+ae+""}if(ad.prev_chroms){ag+='"}if(ad.next_chroms){ag+='"}Z.chrom_select.html(ag);if(ab){ab()}Z.chrom_start_index=ad.start_index},error:function(){alert("Could not load chroms for this dbkey:",Z.dbkey)}})},change_chrom:function(ad,aa,af){if(!ad||ad==="None"){return}var ac=this;if(ad==="previous"){ac.load_chroms({low:this.chrom_start_index-t});return}if(ad==="next"){ac.load_chroms({low:this.chrom_start_index+t});return}var ae=$.grep(ac.chrom_data,function(ah,ai){return ah.chrom===ad})[0];if(ae===undefined){ac.load_chroms({chrom:ad},function(){ac.change_chrom(ad,aa,af)});return}else{if(ad!==ac.chrom){ac.chrom=ad;if(!ac.chrom){ac.intro_div.show()}else{ac.intro_div.hide()}ac.chrom_select.val(ac.chrom);ac.max_high=ae.len-1;ac.reset();ac.redraw(true);for(var ag=0,Z=ac.tracks.length;agZ.max_high){Z.high=Z.max_high;Z.low=Z.max_high-aa}else{Z.high-=ab;Z.low-=ab}}Z.redraw()},add_track:function(Z){Z.view=this;Z.track_id=this.track_id_counter;this.tracks.push(Z);if(Z.init){Z.init()}Z.container_div.attr("id","track_"+Z.track_id);B(Z.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(Z){Z.view=this;this.label_tracks.push(Z)},remove_track:function(Z){this.has_changes=true;Z.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(Z)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(ag){var af=this.high-this.low,ae=this.low,aa=this.high;if(aethis.max_high){aa=this.max_high}if(this.high!==0&&af").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ap){ap.stopPropagation()}).bind("click",function(ap){ap.stopPropagation()}).bind("dblclick",function(ap){ap.stopPropagation()});var ak=$("
").appendTo(this.parent_div).text(this.name);var ai=this.params;var ag=this;$.each(this.params,function(aq,au){var at=$("
").addClass("param-row").appendTo(ag.parent_div);var ap=$("
").addClass("param-label").text(au.label).appendTo(at);var ar=$("
").addClass("slider").html(au.html).appendTo(at);ar.find(":input").val(au.value);$("
").appendTo(at)});this.parent_div.find("input").click(function(){$(this).select()});var ao=$("
").addClass("param-row").appendTo(this.parent_div);var ae=$("").attr("value","Run on complete dataset").appendTo(ao);var Z=$("").attr("value","Run on visible region").css("margin-left","3em").appendTo(ao);var ag=this;Z.click(function(){ag.run_on_region()});ae.click(function(){ag.run_on_dataset()})};n(o.prototype,{get_param_values_dict:function(){var Z={};this.parent_div.find(":input").each(function(){var aa=$(this).attr("name"),ab=$(this).val();Z[aa]=JSON.stringify(ab)});return Z},get_param_values:function(){var aa=[];var Z={};this.parent_div.find(":input").each(function(){var ab=$(this).attr("name"),ac=$(this).val();if(ab){aa[aa.length]=ac}});return aa},run_on_dataset:function(){var Z=this;Z.run({dataset_id:this.track.original_dataset_id,tool_id:Z.name},function(aa){show_modal(Z.name+" is Running",Z.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var Z={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},ab=this.track,aa=Z.tool_id+ab.tool_region_and_parameters_str(Z.chrom,Z.low,Z.high),ac;if(ab.track_type==="FeatureTrack"){ac=new P(aa,view,ab.hda_ldda,undefined,{},{},ab)}this.track.add_track(ac);ac.content_div.text("Starting job.");this.run(Z,function(ad){ac.dataset_id=ad.dataset_id;ac.content_div.text("Running job.");ac.init()})},run:function(aa,ab){$.extend(aa,this.get_param_values_dict());var Z=function(){$.getJSON(run_tool_url,aa,function(ac){if(ac==="no converter"){new_track.container_div.addClass("error");new_track.content_div.text(F)}else{if(ac.error){new_track.container_div.addClass("error");new_track.content_div.text(v+ac.message)}else{if(ac==="pending"){new_track.container_div.addClass("pending");new_track.content_div.text("Converting input data so that it can be easily reused.");setTimeout(Z,2000)}else{ab(ac)}}}})};Z()}});var J=function(aa,Z,ab,ac){this.name=aa;this.label=Z;this.html=ab;this.value=ac};var g=function(ab,aa,ad,ae,ac,Z){J.call(this,ab,aa,ad,ae);this.min=ac;this.max=Z};var h=function(aa,Z,ab){this.name=aa;this.index=Z;this.value=ab};var Q=function(aa,Z){this.name=aa;this.index=Z;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};n(Q.prototype,{applies_to:function(Z){if(Z.length>this.index){return true}return false},keep:function(Z){if(!this.applies_to(Z)){return true}var aa=parseInt(Z[this.index]);return(isNaN(aa)||(aa>=this.low&&aa<=this.high))},update_attrs:function(aa){var Z=false;if(!this.applies_to(aa)){return Z}if(aa[this.index]this.max){this.max=Math.ceil(aa[this.index]);Z=true}return Z},update_ui_elt:function(){var ab=function(ae,ac){var ad=ac-ae;return(ad<=2?0.01:1)};var aa=this.slider.slider("option","min"),Z=this.slider.slider("option","max");if(this.minZ){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ab(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var V=function(ab,ah){this.track=ab;this.filters=[];for(var ad=0;ad").attr("size",input_size).attr("maxlength",input_size).attr("value",al).appendTo(aj).focus().select().click(function(am){am.stopPropagation()}).blur(function(){$(this).remove();aj.text(al)}).keyup(function(aq){if(aq.keyCode===27){$(this).trigger("blur")}else{if(aq.keyCode===13){var ao=ak.slider("option","min"),am=ak.slider("option","max"),ap=function(ar){return(isNaN(ar)||ar>am||ar").addClass("filters").hide();this.parent_div.bind("drag",function(ai){ai.stopPropagation()}).bind("click",function(ai){ai.stopPropagation()}).bind("dblclick",function(ai){ai.stopPropagation()}).bind("keydown",function(ai){ai.stopPropagation()});var ac=this;$.each(this.filters,function(ao,aj){var al=$("
").addClass("slider-row").appendTo(ac.parent_div);var ai=$("
").addClass("slider-label").appendTo(al);var aq=$("").addClass("slider-name").text(aj.name+" ").appendTo(ai);var ak=$("");var am=$("").addClass("slider-value").appendTo(ai).append("[").append(ak).append("]");var ap=$("
").addClass("slider").appendTo(al);aj.control_element=$("
").attr("id",aj.name+"-filter-control").appendTo(ap);var an=[0,0];aj.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(ar,at){an=at.values;ak.text(at.values[0]+"-"+at.values[1]);setTimeout(function(){if(at.values[0]==an[0]&&at.values[1]==an[1]){var au=at.values;ak.text(au[0]+"-"+au[1]);aj.low=au[0];aj.high=au[1];ac.track.draw(true,true)}},50)},change:function(ar,at){aj.control_element.slider("option","slide").call(aj.control_element,ar,at)}});aj.slider=aj.control_element;aj.slider_label=ak;af(am,ak,aj.control_element);$("
").appendTo(al)})};var U=function(Z){this.track=Z.track;this.params=Z.params;this.values={};if(Z.saved_values){this.restore_values(Z.saved_values)}this.onchange=Z.onchange};n(U.prototype,{restore_values:function(Z){var aa=this;$.each(this.params,function(ab,ac){if(Z[ac.key]!==undefined){aa.values[ac.key]=Z[ac.key]}else{aa.values[ac.key]=ac.default_value}})},build_form:function(){var aa=this;var Z=$("
");$.each(this.params,function(ae,ac){if(!ac.hidden){var ab="param_"+ae;var aj=$("
").appendTo(Z);aj.append($("