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commit/galaxy-central: dannon: Workflow Parameter bugfix for the case when a parameter isn't used in
by Bitbucket 14 Apr '11

14 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/6cacf178a129/ changeset: r5400:6cacf178a129 user: dannon date: 2011-04-15 05:40:19 summary: Workflow Parameter bugfix for the case when a parameter isn't used in any workflow step, but should still be available for PJAs. affected #: 1 file (62 bytes) --- a/templates/workflow/run.mako Thu Apr 14 20:25:54 2011 -0400 +++ b/templates/workflow/run.mako Thu Apr 14 23:40:19 2011 -0400 @@ -165,7 +165,7 @@ wf_parms = {} for step in steps: - for v in step.state.inputs.itervalues(): + for v in [ActionBox.get_short_str(pja) for pja in step.post_job_actions] + step.state.inputs.values(): if isinstance(v, basestring): for rematch in re.findall('\$\{.+?\}', v): if rematch[2:-1] not in wf_parms: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: kanwei: trackster:
by Bitbucket 14 Apr '11

14 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/92ac18adbdc5/ changeset: r5399:92ac18adbdc5 user: kanwei date: 2011-04-15 02:25:54 summary: trackster: - UI support for adding datasets from Data Libraries - Cleaner, more consistent "Add Tracks" dialog that implements above Sync .css changes with their corresponding .css.tmpl template affected #: 12 files (3.1 KB) --- a/lib/galaxy/web/controllers/tracks.py Thu Apr 14 16:51:40 2011 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Thu Apr 14 20:25:54 2011 -0400 @@ -60,7 +60,6 @@ datasets_param = "f-history" columns = [ NameColumn( "History Name", key="name", filterable="standard" ), - grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), DbKeyPlaceholderColumn( "Dbkey", key="dbkey", model_class=model.HistoryDatasetAssociation, visible=False ) ] num_rows_per_page = 10 @@ -80,8 +79,7 @@ datasets_action = 'list_library_datasets' datasets_param = "f-library" columns = [ - NameColumn( "Library Name", key="name", filterable="standard" ), - grids.GridColumn( "Description", key="description" ) + NameColumn( "Library Name", key="name", filterable="standard" ) ] num_rows_per_page = 10 use_async = True @@ -601,7 +599,7 @@ """List a library's datasets that can be added to a visualization.""" library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( kwargs.get('f-library') ) ) - return trans.fill_template( '/library/common/browse_library.mako', + return trans.fill_template( '/tracks/library_datasets_select_grid.mako', cntrller="library", use_panels=False, library=library, --- a/static/june_2007_style/base.css.tmpl Thu Apr 14 16:51:40 2011 -0400 +++ b/static/june_2007_style/base.css.tmpl Thu Apr 14 20:25:54 2011 -0400 @@ -947,4 +947,21 @@ -sprite-image: fugue/control-270.png; -sprite-horiz-position: right; } +.icon-button.multiinput{ + background:url(../images/documents-stack.png) no-repeat; + cursor:pointer; + float:none; + display:inline-block; + margin-left:10px; +} +.icon-button.multiinput.disabled{ + background:url(../images/documents-stack-faded.png) no-repeat; + cursor:auto; +} +.workflow-invocation-complete{ + border:solid 1px #6A6; + border-left-width:5px; + margin:10px 0; + padding-left:5px; +} --- a/static/june_2007_style/blue/panel_layout.css Thu Apr 14 16:51:40 2011 -0400 +++ b/static/june_2007_style/blue/panel_layout.css Thu Apr 14 20:25:54 2011 -0400 @@ -27,7 +27,7 @@ .dialog-box-container{position:relative;margin-top:80px;margin-right:auto;margin-left:auto;} .dialog-box-wrapper{position:relative;padding:1em;background-color:rgba(0,0,0,0.5);-moz-border-radius:1em;-webkit-border-radius:1em;} .dialog-box{border:solid #999 1px;background:white;z-index:80000;} -.dialog-box .body{padding:5px;overflow:auto;max-height:500px;} +.dialog-box .body{padding:5px;overflow:auto;max-height:500px;min-width:300px;} .dialog-box .buttons{padding:5px;} .panel-error-message,.panel-warning-message,.panel-done-message,.panel-info-message{height:24px;line-height:24px;color:#303030;padding:0px;padding-left:26px;background-color:#FFCCCC;background-image:url(error_small.png);background-repeat:no-repeat;background-position:6px 50%;} .panel-warning-message{background-image:url(warn_small.png);background-color:#FFFFCC;} --- a/static/june_2007_style/panel_layout.css.tmpl Thu Apr 14 16:51:40 2011 -0400 +++ b/static/june_2007_style/panel_layout.css.tmpl Thu Apr 14 20:25:54 2011 -0400 @@ -194,6 +194,7 @@ padding: 5px; overflow: auto; max-height: 500px; + min-width: 300px; } .dialog-box .buttons { --- a/static/june_2007_style/trackster.css.tmpl Thu Apr 14 16:51:40 2011 -0400 +++ b/static/june_2007_style/trackster.css.tmpl Thu Apr 14 20:25:54 2011 -0400 @@ -170,17 +170,14 @@ .track.error .track-content { background-color: #ECB4AF; background-image: none; - padding: 2px 0; } .track.nodata .track-content { background-color: #eee; background-image: none; - padding: 2px 0; } .track.pending .track-content { background-color: white; background-image: none; - padding: 2px 0; } .loading { @@ -237,7 +234,7 @@ margin-top: 0.4em; margin-left: 1em; } -.param-label, .slider-label { +.slider-label { float: left; font-weight: bold; } --- a/static/scripts/packed/trackster.js Thu Apr 14 16:51:40 2011 -0400 +++ b/static/scripts/packed/trackster.js Thu Apr 14 20:25:54 2011 -0400 @@ -1,1 +1,1 @@ -var extend=function(){var c=arguments[0];for(var b=1;b<arguments.length;b++){var a=arguments[b];for(key in a){c[key]=a[key]}}return c};var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var trackster_module=function(f,R){var p=f("slotting"),G=f("painters");var X=function(Y,Z){this.document=Y;this.default_font=Z!==undefined?Z:"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")};extend(X.prototype,{load_pattern:function(Y,ac){var Z=this.patterns,aa=this.dummy_context,ab=new Image();ab.src=image_path+ac;ab.onload=function(){Z[Y]=aa.createPattern(ab,"repeat")}},get_pattern:function(Y){return this.patterns[Y]},new_canvas:function(){var Y=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(Y)}Y.manager=this;return Y}});var B=function(Y,Z){Y.bind("drag",{handle:Z,relative:true},function(ad,ae){var ac=$(this).parent();var ab=ac.children();var aa;for(aa=0;aa<ab.length;aa++){if(ae.offsetY<$(ab.get(aa)).position().top){break}}if(aa===ab.length){if(this!==ab.get(aa-1)){ac.append(this)}}else{if(this!==ab.get(aa)){$(this).insertBefore(ab.get(aa))}}})};var h=function(aa,Y){var Z=Y-aa;return(Z<=2?0.01:(Z<=100?1:(Z<=1000?5:10)))};var C=9,z=10,M=C+2,w=100,D=12000,K=200,s=10,F=5000,t=100,n="There was an error in indexing this dataset. ",E="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",A="No data for this chrom/contig.",q="Currently indexing... please wait",v="Tool cannot be rerun: ",a="Loading data...",S="Ready for display",d=10,r=5,y=5;function u(Y){return Math.round(Y*1000)/1000}var c=function(Y){this.num_elements=Y;this.clear()};extend(c.prototype,{get:function(Z){var Y=this.key_ary.indexOf(Z);if(Y!==-1){this.move_key_to_end(Z,Y)}return this.obj_cache[Z]},set:function(Z,aa){if(!this.obj_cache[Z]){if(this.key_ary.length>=this.num_elements){var Y=this.key_ary.shift();delete this.obj_cache[Y]}this.key_ary.push(Z)}this.obj_cache[Z]=aa;return aa},move_key_to_end:function(Z,Y){this.key_ary.splice(Y,1);this.key_ary.push(Z)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var L=function(Z,Y,aa){c.call(this,Z);this.track=Y;this.subset=(aa!==undefined?aa:true)};extend(L.prototype,c.prototype,{load_data:function(ag,ah,ac,af,Z,ae){if(this.track.track_type=="ReferenceTrack"&&Z>1){return}var ab={chrom:ag,low:ah,high:ac,mode:af,resolution:Z,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ab,ae);if(this.track.filters_manager){var ai=[];var Y=this.track.filters_manager.filters;for(var ad=0;ad<Y.length;ad++){ai[ai.length]=Y[ad].name}ab.filter_cols=JSON.stringify(ai)}var aa=this;return $.getJSON(this.track.data_url,ab,function(aj){aa.set_data(ah,ac,af,aj)})},get_data:function(aa,Y,ad,ae,Z,ac){var ab=this.get(this.gen_key(Y,ad,ae));if(ab){return ab}ab=this.load_data(aa,Y,ad,ae,Z,ac);this.set_data(Y,ad,ae,ab);return ab},set_data:function(Z,aa,ab,Y){return this.set(this.gen_key(Z,aa,ab),Y)},gen_key:function(Y,aa,ab){var Z=Y+"_"+aa+"_"+ab;return Z},split_key:function(Y){return Y.split("_")}});var W=function(Y,ab,aa,Z,ac){this.container=Y;this.chrom=null;this.vis_id=aa;this.dbkey=Z;this.title=ab;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(ac);this.canvas_manager=new X(Y.get(0).ownerDocument);this.reset()};extend(W.prototype,{init:function(ab){var aa=this.container,Y=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aa);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aa);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aa);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var Z=function(ac){if(ac.type==="focusout"||(ac.keyCode||ac.which)===13||(ac.keyCode||ac.which)===27){if((ac.keyCode||ac.which)!==27){Y.go_to($(this).val())}$(this).hide();$(this).val("");Y.location_span.show();Y.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",Z).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.bind("click",function(){Y.location_span.hide();Y.chrom_select.hide();Y.nav_input.val(Y.chrom+":"+Y.low+"-"+Y.high);Y.nav_input.css("display","inline-block");Y.nav_input.select();Y.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){Y.zoom_out();Y.redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){Y.zoom_in();Y.redraw()}).appendTo(this.nav_controls);this.load_chroms({low:0},ab);this.chrom_select.bind("change",function(){Y.change_chrom(Y.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(ac){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(ac){Y.zoom_in(ac.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ac,ad){this.current_x=ad.offsetX}).bind("drag",function(ac,ae){var af=ae.offsetX-this.current_x;this.current_x=ae.offsetX;var ad=Math.round(af/Y.viewport_container.width()*(Y.max_high-Y.max_low));Y.move_delta(-ad)});this.overview_close.bind("click",function(){for(var ad=0,ac=Y.tracks.length;ad<ac;ad++){Y.tracks[ad].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",Y.overview_box.height());Y.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(ac,ad){if(ac.clientX>Y.viewport_container.width()-16){return false}}).bind("dragstart",function(ac,ad){ad.original_low=Y.low;ad.current_height=ac.clientY;ad.current_x=ad.offsetX}).bind("drag",function(ae,ag){var ac=$(this);var ah=ag.offsetX-ag.current_x;var ad=ac.scrollTop()-(ae.clientY-ag.current_height);ac.scrollTop(ad);ag.current_height=ae.clientY;ag.current_x=ag.offsetX;var af=Math.round(ah/Y.viewport_container.width()*(Y.high-Y.low));Y.move_delta(af)}).bind("mousewheel",function(ae,ag,ad,ac){if(ad){var af=Math.round(-ad/Y.viewport_container.width()*(Y.high-Y.low));Y.move_delta(af)}});this.top_labeltrack.bind("dragstart",function(ac,ad){return $("<div />").css({height:Y.content_div.height()+Y.top_labeltrack.height()+Y.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ag,ah){$(ah.proxy).css({left:Math.min(ag.pageX,ah.startX),width:Math.abs(ag.pageX-ah.startX)});var ad=Math.min(ag.pageX,ah.startX)-Y.container.offset().left,ac=Math.max(ag.pageX,ah.startX)-Y.container.offset().left,af=(Y.high-Y.low),ae=Y.viewport_container.width();Y.update_location(Math.round(ad/ae*af)+Y.low,Math.round(ac/ae*af)+Y.low)}).bind("dragend",function(ah,ai){var ad=Math.min(ah.pageX,ai.startX),ac=Math.max(ah.pageX,ai.startX),af=(Y.high-Y.low),ae=Y.viewport_container.width(),ag=Y.low;Y.low=Math.round(ad/ae*af)+ag;Y.high=Math.round(ac/ae*af)+ag;$(ai.proxy).remove();Y.redraw()});this.add_label_track(new V(this,this.top_labeltrack));this.add_label_track(new V(this,this.nav_labeltrack));$(window).bind("resize",function(){Y.resize_window()});$(document).bind("redraw",function(){Y.redraw()});this.reset();$(window).trigger("resize")},update_location:function(Y,Z){this.location_span.text(commatize(Y)+" - "+commatize(Z));this.nav_input.val(this.chrom+":"+commatize(Y)+"-"+commatize(Z))},load_chroms:function(Z,aa){Z.num=t;$.extend(Z,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var Y=this;$.ajax({url:chrom_url,data:Z,dataType:"json",success:function(ac){if(ac.chrom_info.length===0){alert("Invalid chromosome: "+Z.chrom);return}if(ac.reference){Y.add_label_track(new x(Y))}Y.chrom_data=ac.chrom_info;var af='<option value="">Select Chrom/Contig</option>';for(var ae=0,ab=Y.chrom_data.length;ae<ab;ae++){var ad=Y.chrom_data[ae].chrom;af+='<option value="'+ad+'">'+ad+"</option>"}if(ac.prev_chroms){af+='<option value="previous">Previous '+t+"</option>"}if(ac.next_chroms){af+='<option value="next">Next '+t+"</option>"}Y.chrom_select.html(af);if(aa){aa()}Y.chrom_start_index=ac.start_index},error:function(){alert("Could not load chroms for this dbkey:",Y.dbkey)}})},change_chrom:function(ac,Z,ae){if(!ac||ac==="None"){return}var ab=this;if(ac==="previous"){ab.load_chroms({low:this.chrom_start_index-t});return}if(ac==="next"){ab.load_chroms({low:this.chrom_start_index+t});return}var ad=$.grep(ab.chrom_data,function(ag,ah){return ag.chrom===ac})[0];if(ad===undefined){ab.load_chroms({chrom:ac},function(){ab.change_chrom(ac,Z,ae)});return}else{if(ac!==ab.chrom){ab.chrom=ac;if(!ab.chrom){ab.intro_div.show()}else{ab.intro_div.hide()}ab.chrom_select.val(ab.chrom);ab.max_high=ad.len-1;ab.reset();ab.redraw(true);for(var af=0,Y=ab.tracks.length;af<Y;af++){var aa=ab.tracks[af];if(aa.init){aa.init()}}}if(Z!==undefined&&ae!==undefined){ab.low=Math.max(Z,0);ab.high=Math.min(ae,ab.max_high)}ab.reset_overview();ab.redraw()}},go_to:function(ac){var ag=this,Y,ab,Z=ac.split(":"),ae=Z[0],af=Z[1];if(af!==undefined){try{var ad=af.split("-");Y=parseInt(ad[0].replace(/,/g,""),10);ab=parseInt(ad[1].replace(/,/g,""),10)}catch(aa){return false}}ag.change_chrom(ae,Y,ab)},move_fraction:function(aa){var Y=this;var Z=Y.high-Y.low;this.move_delta(aa*Z)},move_delta:function(aa){var Y=this;var Z=Y.high-Y.low;if(Y.low-aa<Y.max_low){Y.low=Y.max_low;Y.high=Y.max_low+Z}else{if(Y.high-aa>Y.max_high){Y.high=Y.max_high;Y.low=Y.max_high-Z}else{Y.high-=aa;Y.low-=aa}}Y.redraw()},add_track:function(Y){Y.view=this;Y.track_id=this.track_id_counter;this.tracks.push(Y);if(Y.init){Y.init()}Y.container_div.attr("id","track_"+Y.track_id);B(Y.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(Y){Y.view=this;this.label_tracks.push(Y)},remove_track:function(Y){this.has_changes=true;Y.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(Y)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(af){var ae=this.high-this.low,ad=this.low,Z=this.high;if(ad<this.max_low){ad=this.max_low}if(Z>this.max_high){Z=this.max_high}if(this.high!==0&&ae<this.min_separation){Z=ad+this.min_separation}this.low=Math.floor(ad);this.high=Math.ceil(Z);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/K)/Math.LN10));this.zoom_res=Math.pow(s,Math.max(0,Math.ceil(Math.log(this.resolution,s)/Math.log(s))));var Y=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ac=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ag=13;this.overview_box.css({left:Y,width:Math.max(ag,ac)}).show();if(ac<ag){this.overview_box.css("left",Y-(ag-ac)/2)}if(this.overview_highlight){this.overview_highlight.css({left:Y,width:ac})}this.update_location(this.low,this.high);if(!af){for(var aa=0,ab=this.tracks.length;aa<ab;aa++){if(this.tracks[aa]&&this.tracks[aa].enabled){this.tracks[aa].draw()}}for(aa=0,ab=this.label_tracks.length;aa<ab;aa++){this.label_tracks[aa].draw()}}},zoom_in:function(Z,aa){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ab=this.high-this.low,ac=ab/2+this.low,Y=(ab/this.zoom_factor)/2;if(Z){ac=Z/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ac-Y);this.high=Math.round(ac+Y);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var Z=this.high-this.low,aa=Z/2+this.low,Y=(Z*this.zoom_factor)/2;this.low=Math.round(aa-Y);this.high=Math.round(aa+Y);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var o=function(Z,ac){this.track=Z;this.name=ac.name;this.params=[];var ak=ac.params;for(var aa=0;aa<ak.length;aa++){var af=ak[aa],Y=af.name,aj=af.label,ab=unescape(af.html),ah=af.type;if(ah==="number"){this.params[this.params.length]=new g(Y,aj,ab,af.min,af.max)}else{if(ah=="select"){this.params[this.params.length]=new I(Y,aj,ab)}else{console.log("WARNING: unrecognized tool parameter type:",Y,ah)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(am){am.stopPropagation()}).bind("click",function(am){am.stopPropagation()}).bind("dblclick",function(am){am.stopPropagation()});var ai=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ag=this.params;var ad=this;$.each(this.params,function(an,aq){var ap=$("<div>").addClass("param-row").appendTo(ad.parent_div);var am=$("<div>").addClass("param-label").text(aq.label).appendTo(ap);var ao=$("<div/>").addClass("slider").html(aq.html).appendTo(ap);$("<div style='clear: both;'/>").appendTo(ap)});this.parent_div.find("input").click(function(){$(this).select()});var al=$("<div>").addClass("slider-row").appendTo(this.parent_div);var ae=$("<input type='submit'>").attr("value","Run").appendTo(al);var ad=this;ae.click(function(){ad.run()})};extend(o.prototype,{get_param_values_dict:function(){var Y={};this.parent_div.find(":input").each(function(){var Z=$(this).attr("name"),aa=$(this).val();Y[Z]=JSON.stringify(aa)});return Y},get_param_values:function(){var Z=[];var Y={};this.parent_div.find(":input").each(function(){var aa=$(this).attr("name"),ab=$(this).val();if(aa){Z[Z.length]=ab}});return Z},run:function(){var Z={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name};$.extend(Z,this.get_param_values_dict());var 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 O(aa,view,ab.hda_ldda,undefined,{},{},ab)}this.track.add_track(ac);ac.content_div.text("Starting job.");var Y=function(){$.getJSON(run_tool_url,Z,function(ad){if(ad==="no converter"){ac.container_div.addClass("error");ac.content_div.text(E)}else{if(ad.error){ac.container_div.addClass("error");ac.content_div.text(v+ad.message)}else{if(ad==="pending"){ac.container_div.addClass("pending");ac.content_div.text("Converting input data so that it can be easily reused.");setTimeout(Y,2000)}else{ac.dataset_id=ad.dataset_id;ac.content_div.text("Running job.");ac.init()}}}})};Y()}});var I=function(Z,Y,aa){this.name=Z;this.label=Y;this.html=aa};var g=function(aa,Z,ac,ab,Y){I.call(this,aa,Z,ac);this.min=ab;this.max=Y};var j=function(Z,Y,aa){this.name=Z;this.index=Y;this.value=aa};var P=function(Z,Y){this.name=Z;this.index=Y;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};extend(P.prototype,{applies_to:function(Y){if(Y.length>this.index){return true}return false},keep:function(Y){if(!this.applies_to(Y)){return true}var Z=parseInt(Y[this.index]);return(isNaN(Z)||(Z>=this.low&&Z<=this.high))},update_attrs:function(Z){var Y=false;if(!this.applies_to(Z)){return Y}if(Z[this.index]<this.min){this.min=Math.floor(Z[this.index]);Y=true}if(Z[this.index]>this.max){this.max=Math.ceil(Z[this.index]);Y=true}return Y},update_ui_elt:function(){var Z=this.slider.slider("option","min"),Y=this.slider.slider("option","max");if(this.min<Z||this.max>Y){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",h(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var U=function(aa,ag){this.track=aa;this.filters=[];for(var ac=0;ac<ag.length;ac++){var Y=ag[ac];var Z=Y.name,af=Y.type,ad=Y.index;if(af==="int"||af==="float"){this.filters[ac]=new P(Z,ad)}else{this.filters[ac]=new j(Z,ad,af)}}var ae=function(ah,ai,aj){ah.click(function(){var ak=ai.text();max=parseFloat(aj.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aj.slider("option","values")){input_size=2*input_size+1;multi_value=true}ai.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",ak).appendTo(ai).focus().select().click(function(al){al.stopPropagation()}).blur(function(){$(this).remove();ai.text(ak)}).keyup(function(ap){if(ap.keyCode===27){$(this).trigger("blur")}else{if(ap.keyCode===13){var an=aj.slider("option","min"),al=aj.slider("option","max"),ao=function(aq){return(isNaN(aq)||aq>al||aq<an)},am=$(this).val();if(!multi_value){am=parseFloat(am);if(ao(am)){alert("Parameter value must be in the range ["+an+"-"+al+"]");return $(this)}}else{am=am.split("-");am=[parseFloat(am[0]),parseFloat(am[1])];if(ao(am[0])||ao(am[1])){alert("Parameter value must be in the range ["+an+"-"+al+"]");return $(this)}}aj.slider((multi_value?"values":"value"),am)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(ah){ah.stopPropagation()}).bind("click",function(ah){ah.stopPropagation()}).bind("dblclick",function(ah){ah.stopPropagation()});var ab=this;$.each(this.filters,function(an,ai){var ak=$("<div/>").addClass("slider-row").appendTo(ab.parent_div);var ah=$("<div/>").addClass("slider-label").appendTo(ak);var ap=$("<span/>").addClass("slider-name").text(ai.name+" ").appendTo(ah);var aj=$("<span/>");var al=$("<span/>").addClass("slider-value").appendTo(ah).append("[").append(aj).append("]");var ao=$("<div/>").addClass("slider").appendTo(ak);ai.control_element=$("<div/>").attr("id",ai.name+"-filter-control").appendTo(ao);var am=[0,0];ai.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aq,ar){am=ar.values;aj.text(ar.values[0]+"-"+ar.values[1]);setTimeout(function(){if(ar.values[0]==am[0]&&ar.values[1]==am[1]){var at=ar.values;aj.text(at[0]+"-"+at[1]);ai.low=at[0];ai.high=at[1];ab.track.draw(true,true)}},50)},change:function(aq,ar){ai.control_element.slider("option","slide").call(ai.control_element,aq,ar)}});ai.slider=ai.control_element;ai.slider_label=aj;ae(al,aj,ai.control_element);$("<div style='clear: both;'/>").appendTo(ak)})};var T=function(Y){this.track=Y.track;this.params=Y.params;this.values={};if(Y.saved_values){this.restore_values(Y.saved_values)}this.onchange=Y.onchange};extend(T.prototype,{restore_values:function(Y){var Z=this;$.each(this.params,function(aa,ab){if(Y[ab.key]!==undefined){Z.values[ab.key]=Y[ab.key]}else{Z.values[ab.key]=ab.default_value}})},build_form:function(){var Z=this;var Y=$("<div />");$.each(this.params,function(ad,ab){if(!ab.hidden){var aa="param_"+ad;var ai=$("<div class='form-row' />").appendTo(Y);ai.append($("<label />").attr("for",aa).text(ab.label+":"));if(ab.type==="bool"){ai.append($('<input type="checkbox" />').attr("id",aa).attr("name",aa).attr("checked",Z.values[ab.key]))}else{if(ab.type==="color"){var af=Z.values[ab.key];var ae=$("<input />").attr("id",aa).attr("name",aa).val(af);var ag=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var ac=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ag);var ah=$("<div/>").appendTo(ac).farbtastic({width:100,height:100,callback:ae,color:af});$("<div />").append(ae).append(ag).appendTo(ai).bind("click",function(aj){ag.css({left:$(this).position().left+($(ae).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ag.hide();$(document).unbind("click.color-picker")});aj.stopPropagation()})}else{ai.append($("<input />").attr("id",aa).attr("name",aa).val(Z.values[ab.key]))}}}});return Y},update_from_form:function(Y){var aa=this;var Z=false;$.each(this.params,function(ab,ad){if(!ad.hidden){var ae="param_"+ab;var ac=Y.find("#"+ae).val();if(ad.type==="float"){ac=parseFloat(ac)}else{if(ad.type==="int"){ac=parseInt(ac)}else{if(ad.type==="bool"){ac=Y.find("#"+ae).is(":checked")}}}if(ac!==aa.values[ad.key]){aa.values[ad.key]=ac;Z=true}}});if(Z){this.onchange()}}});var b=function(aa,Z,Y){this.index=aa;this.resolution=Z;this.canvas=$("<div class='track-tile'/>").append(Y)};var m=function(aa,Z,Y,ab){b.call(this,aa,Z,Y);this.max_val=ab};var J=function(aa,Z,Y){b.call(this,aa,Z,Y)};var k=function(Z,Y,ac,aa,ab){this.name=Z;this.view=Y;this.parent_element=ac;this.data_url=(aa?aa:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ab?ab:F);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};extend(k.prototype,{init:function(){var Y=this;Y.enabled=false;Y.tile_cache.clear();Y.data_cache.clear();Y.initial_canvas=undefined;Y.content_div.css("height","auto");Y.container_div.removeClass("nodata error pending");if(!Y.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:Y.hda_ldda,dataset_id:Y.dataset_id,chrom:Y.view.chrom},function(Z){if(!Z||Z==="error"||Z.kind==="error"){Y.container_div.addClass("error");Y.content_div.text(n);if(Z.message){var ab=Y.view.tracks.indexOf(Y);var aa=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+Z.message+"</pre>",{Close:hide_modal})});Y.content_div.append(aa)}}else{if(Z==="no converter"){Y.container_div.addClass("error");Y.content_div.text(E)}else{if(Z==="no data"||(Z.data!==undefined&&(Z.data===null||Z.data.length===0))){Y.container_div.addClass("nodata");Y.content_div.text(A)}else{if(Z==="pending"){Y.container_div.addClass("pending");Y.content_div.text(q);setTimeout(function(){Y.init()},Y.data_query_wait)}else{if(Z.status==="data"){if(Z.valid_chroms){Y.valid_chroms=Z.valid_chroms;Y.make_name_popup_menu()}Y.content_div.text(S);if(Y.view.chrom){Y.content_div.text("");Y.content_div.css("height",Y.height_px+"px");Y.enabled=true;$.when(Y.predraw_init()).done(function(){Y.container_div.removeClass("nodata error pending");Y.draw()})}}}}}}})},predraw_init:function(){},update_name:function(Y){this.old_name=this.name;this.name=Y;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var H=function(ag,ae,ah){var Z=this,ai=Z.view;this.filters_manager=(ag!==undefined?new U(this,ag):undefined);this.filters_available=false;this.filters_visible=false;this.tool=(ae!==undefined&&obj_length(ae)>0?new o(this,ae):undefined);this.parent_track=ah;this.child_tracks=[];if(Z.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}Z.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();Z.container_div.append(Z.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(Z.display_modes!==undefined){if(Z.mode_div===undefined){Z.mode_div=$("<div class='right-float menubutton popup' />").appendTo(Z.header_div);var ab=(Z.track_config&&Z.track_config.values.mode?Z.track_config.values.mode:Z.display_modes[0]);Z.mode=ab;Z.mode_div.text(ab);var aa=function(aj){Z.mode_div.text(aj);Z.mode=aj;Z.track_config.values.mode=aj;Z.tile_cache.clear();Z.draw()};var Y={};for(var ac=0,af=Z.display_modes.length;ac<af;ac++){var ad=Z.display_modes[ac];Y[ad]=function(aj){return function(){aa(aj)}}(ad)}make_popupmenu(Z.mode_div,Y)}else{Z.mode_div.hide()}}this.make_name_popup_menu()};extend(H.prototype,k.prototype,{make_name_popup_menu:function(){var Z=this;var Y={};Y["Edit configuration"]=function(){var af=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ad=function(){Z.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(ag){if((ag.keyCode||ag.which)===27){af()}else{if((ag.keyCode||ag.which)===13){ad()}}};$(window).bind("keypress.check_enter_esc",ae);show_modal("Configure Track",Z.track_config.build_form(),{Cancel:af,OK:ad})};if(Z.filters_available>0){var ac=(Z.filters_div.is(":visible")?"Hide filters":"Show filters");Y[ac]=function(){Z.filters_visible=(Z.filters_div.is(":visible"));Z.filters_div.toggle();Z.make_name_popup_menu()}}if(Z.tool){var ac=(Z.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");Y[ac]=function(){if(!Z.dynamic_tool_div.is(":visible")){Z.update_name(Z.name+Z.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";Z.revert_name()}Z.dynamic_tool_div.toggle();Z.make_name_popup_menu()}}if(Z.valid_chroms){Y["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+Z.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var aa=view;var ab=function(){$("#no-tracks").show()};if(this.parent_track){aa=this.parent_track;ab=function(){}}Y.Remove=function(){aa.remove_track(Z);if(aa.num_tracks===0){ab()}};make_popupmenu(Z.name_div,Y)},draw:function(Y,aa){var ar=this.view.low,ae=this.view.high,ag=ae-ar,ai=this.view.container.width(),ac=ai/ag,aj=this.view.resolution,ab=$("<div style='position: relative;'></div>"),ak=function(au,av,at){return au+"_"+av+"_"+at};if(!aa){this.content_div.children().remove()}this.content_div.append(ab);this.max_height=0;var am=Math.floor(ar/aj/K);var ad=[];var an=0;while((am*K*aj)<ae){var aq=ak(ai,ac,am);var af=this.tile_cache.get(aq);var ao=am*K*this.view.resolution;var Z=ao+K*this.view.resolution;if(!Y&&af){ad[ad.length]=af;this.show_tile(af,ab,ao,ac)}else{this.delayed_draw(Y,aq,am,aj,ab,ac,ad)}am+=1;an++}var ah=this;var ap=setInterval(function(){if(ad.length===an){clearInterval(ap);if(aa){var aw=ah.content_div.children();var ax=false;for(var av=aw.length-1,aB=0;av>=aB;av--){var au=$(aw[av]);if(ax){au.remove()}else{if(au.children().length!==0){ax=true}}}}if(ah.track_type=="FeatureTrack"&&ah.mode=="Histogram"){var aA=-1;for(var av=0;av<ad.length;av++){var aD=ad[av].max_val;if(aD>aA){aA=aD}}for(var av=0;av<ad.length;av++){if(ad[av].max_val!==aA){var aC=ad[av];aC.canvas.remove();ah.delayed_draw(true,ak(ai,ac,aC.index),aC.index,aC.resolution,ab,ac,[],{max:aA})}}}if(ah.filters_manager){var at=ah.filters_manager.filters;for(var az=0;az<at.length;az++){at[az].update_ui_elt()}var ay=false;if(ah.example_feature){for(var az=0;az<at.length;az++){if(at[az].applies_to(ah.example_feature)){ay=true;break}}}if(ah.filters_available!==ay){ah.filters_available=ay;if(!ah.filters_available){ah.filters_div.hide()}ah.make_name_popup_menu()}}}},50);for(var al=0;al<this.child_tracks.length;al++){this.child_tracks[al].draw(Y,aa)}},delayed_draw:function(Z,ag,aa,ac,ah,ak,ai,ad){var ab=this,ae=aa*K*ac,aj=ae+K*ac;var af=function(at,al,an,am,aq,ar,ao){var ap=ab.draw_tile(al,an,am,ar,ao);ab.tile_cache.set(ag,ap);ab.show_tile(ap,aq,ae,ar);ai[ai.length]=ap};var Y=setTimeout(function(){if(ae<=ab.view.high&&aj>=ab.view.low){var al=(Z?undefined:ab.tile_cache.get(ag));if(al){ab.show_tile(al,ah,ae,ak);ai[ai.length]=al}else{$.when(ab.data_cache.get_data(view.chrom,ae,aj,ab.mode,ac,ab.data_url_extra_params)).then(function(am){extend(am,ad);if(view.reference_track&&ak>view.canvas_manager.char_width_px){$.when(view.reference_track.data_cache.get_data(view.chrom,ae,aj,ab.mode,ac,view.reference_track.data_url_extra_params)).then(function(an){af(Y,am,ac,aa,ah,ak,an)})}else{af(Y,am,ac,aa,ah,ak)}})}}},50)},show_tile:function(ab,ae,ac,af){var Z=this;var aa=this.view.high-this.view.low,ad=(ac-this.view.low)*af;if(this.left_offset){ad-=this.left_offset}var Y=ab.canvas;Y.css({position:"absolute",top:0,left:ad,height:""});ae.append(Y);Z.max_height=Math.max(Z.max_height,Y.height());Z.content_div.css("height",Z.max_height+"px");ae.children().css("height",Z.max_height+"px")},set_overview:function(){var Y=this.view;if(this.initial_canvas&&this.is_overview){Y.overview_close.show();Y.overview_viewport.append(this.initial_canvas);Y.overview_highlight.show().height(this.initial_canvas.height());Y.overview_viewport.height(this.initial_canvas.height()+Y.overview_box.height())}$(window).trigger("resize")},tool_region_and_parameters_str:function(aa,Y,ab){var Z=this,ac=(aa!==undefined&&Y!==undefined&&ab!==undefined?aa+":"+Y+"-"+ab:"all");return" - region=["+ac+"], parameters=["+Z.tool.get_param_values().join(", ")+"]"},add_track:function(Y){Y.track_id=this.track_id+"_"+this.child_tracks.length;Y.container_div.attr("id","track_"+Y.track_id);this.child_tracks_container.append(Y.container_div);B(Y.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(Y);this.view.has_changes=true},remove_track:function(Y){Y.container_div.fadeOut("slow",function(){$(this).remove()})}});var V=function(Y,Z){this.track_type="LabelTrack";this.hidden=true;k.call(this,null,Y,Z);this.container_div.addClass("label-track")};extend(V.prototype,k.prototype,{draw:function(){var aa=this.view,ab=aa.high-aa.low,ae=Math.floor(Math.pow(10,Math.floor(Math.log(ab)/Math.log(10)))),Y=Math.floor(aa.low/ae)*ae,ac=this.view.container.width(),Z=$("<div style='position: relative; height: 1.3em;'></div>");while(Y<aa.high){var ad=(Y-aa.low)/ab*ac;Z.append($("<div class='label'>"+commatize(Y)+"</div>").css({position:"absolute",left:ad-1}));Y+=ae}this.content_div.children(":first").remove();this.content_div.append(Z)}});var x=function(Y){this.track_type="ReferenceTrack";this.hidden=true;k.call(this,null,Y,Y.top_labeltrack);H.call(this);Y.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:Y.dbkey};this.data_cache=new L(y,this,false);this.tile_cache=new c(r)};extend(x.prototype,H.prototype,{draw_tile:function(ag,ad,Z,ai){var ac=this,aa=K*ad;if(ai>this.view.canvas_manager.char_width_px){if(ag===null){ac.content_div.css("height","0px");return}var ab=this.view.canvas_manager.new_canvas();var ah=ab.getContext("2d");ab.width=Math.ceil(aa*ai+ac.left_offset);ab.height=ac.height_px;ah.font=ah.canvas.manager.default_font;ah.textAlign="center";for(var ae=0,af=ag.length;ae<af;ae++){var Y=Math.round(ae*ai);ah.fillText(ag[ae],Y+ac.left_offset,10)}return new b(Z,ad,ab)}this.content_div.css("height","0px")}});var l=function(ac,aa,ad,Y,ab){var Z=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";k.call(this,ac,aa,aa.viewport_container);H.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=ad;this.dataset_id=Y;this.original_dataset_id=Y;this.data_cache=new L(y,this);this.tile_cache=new c(r);this.track_config=new T({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:ab,onchange:function(){Z.vertical_range=Z.prefs.max_value-Z.prefs.min_value;$("#linetrack_"+Z.track_id+"_minval").text(Z.prefs.min_value);$("#linetrack_"+Z.track_id+"_maxval").text(Z.prefs.max_value);Z.tile_cache.clear();Z.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;this.add_resize_handle()};extend(l.prototype,H.prototype,{add_resize_handle:function(){var Y=this;var ab=false;var aa=false;var Z=$("<div class='track-resize'>");$(Y.container_div).hover(function(){ab=true;Z.show()},function(){ab=false;if(!aa){Z.hide()}});Z.hide().bind("dragstart",function(ac,ad){aa=true;ad.original_height=$(Y.content_div).height()}).bind("drag",function(ad,ae){var ac=Math.min(Math.max(ae.original_height+ae.deltaY,Y.min_height_px),Y.max_height_px);$(Y.content_div).css("height",ac);Y.height_px=ac;Y.draw(true)}).bind("dragend",function(ac,ad){Y.tile_cache.clear();aa=false;if(!ab){Z.hide()}Y.track_config.values.height=Y.height_px}).appendTo(Y.container_div)},predraw_init:function(){var Y=this,Z=Y.view.tracks.indexOf(Y);Y.vertical_range=undefined;return $.getJSON(Y.data_url,{stats:true,chrom:Y.view.chrom,low:null,high:null,hda_ldda:Y.hda_ldda,dataset_id:Y.dataset_id},function(aa){Y.container_div.addClass("line-track");var ac=aa.data;if(isNaN(parseFloat(Y.prefs.min_value))||isNaN(parseFloat(Y.prefs.max_value))){Y.prefs.min_value=ac.min;Y.prefs.max_value=ac.max;$("#track_"+Z+"_minval").val(Y.prefs.min_value);$("#track_"+Z+"_maxval").val(Y.prefs.max_value)}Y.vertical_range=Y.prefs.max_value-Y.prefs.min_value;Y.total_frequency=ac.total_frequency;Y.container_div.find(".yaxislabel").remove();var ad=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+Z+"_minval").text(u(Y.prefs.min_value));var ab=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+Z+"_maxval").text(u(Y.prefs.max_value));ab.css({position:"absolute",top:"24px",left:"10px"});ab.prependTo(Y.container_div);ad.css({position:"absolute",bottom:"2px",left:"10px"});ad.prependTo(Y.container_div)})},draw_tile:function(ai,ac,Z,ah){if(this.vertical_range===undefined){return}var ad=Z*K*ac,ab=K*ac,Y=Math.ceil(ab*ah),af=this.height_px;var aa=this.view.canvas_manager.new_canvas();aa.width=Y,aa.height=af;var ag=aa.getContext("2d");var ae=new G.LinePainter(ai.data,ad,ad+ab,this.prefs,this.mode);ae.draw(ag,Y,af);return new b(ab,ac,aa)}});var e=function(Y,ad,ac,ag,af,aa,ab,ae){var Z=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];this.track_config=new T({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:af,onchange:function(){Z.tile_cache.clear();Z.draw()}});this.prefs=this.track_config.values;k.call(this,Y,ad,ad.viewport_container);H.call(this,aa,ab,ae);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=ac;this.dataset_id=ag;this.original_dataset_id=ag;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_cache=new L(20,this);this.left_offset=200;this.painter=G.LinkedFeaturePainter};extend(e.prototype,H.prototype,{update_auto_mode:function(Y){if(this.mode=="Auto"){if(Y=="no_detail"){Y="feature spans"}else{if(Y=="summary_tree"){Y="coverage histogram"}}this.mode_div.text("Auto ("+Y+")")}},incremental_slots:function(ac,Z,ab){var aa=this.view.canvas_manager.dummy_context,Y=this.inc_slots[ac];if(!Y||(Y.mode!==ab)){Y=new (p.FeatureSlotter)(ac,ab==="Pack",w,function(ad){return aa.measureText(ad)});Y.mode=ab;this.inc_slots[ac]=Y}return Y.slot_features(Z)},get_summary_tree_data:function(ac,af,aa,an){if(an>aa-af){an=aa-af}var aj=Math.floor((aa-af)/an),am=[],ab=0;var ad=0,ae=0,ai,al=0,ag=[],ak,ah;var Z=function(aq,ap,ar,ao){aq[0]=ap+ar*ao;aq[1]=ap+(ar+1)*ao};while(al<an&&ad!==ac.length){var Y=false;for(;al<an&&!Y;al++){Z(ag,af,al,aj);for(ae=ad;ae<ac.length;ae++){ai=ac[ae].slice(1,3);if(is_overlap(ai,ag)){Y=true;break}}if(Y){break}}data_start_index=ae;am[am.length]=ak=[ag[0],0];for(;ae<ac.length;ae++){ai=ac[ae].slice(1,3);if(is_overlap(ai,ag)){ak[1]++}else{break}}if(ak[1]>ab){ab=ak[1]}al++}return{max:ab,delta:aj,data:am}},draw_tile:function(al,au,ay,ah,ab){var aq=this,aA=ay*K*au,Z=(ay+1)*K*au,an=Z-aA,ar=Math.ceil(an*ah),ap=this.mode,aE=25,ac=this.left_offset,am,ad;if(ap==="Auto"){if(al.dataset_type==="summary_tree"){ap=al.dataset_type}else{if(al.extra_info==="no_detail"){ap="no_detail"}else{var aD=al.data;if(this.view.high-this.view.low>D){ap="Squish"}else{ap="Pack"}}}this.update_auto_mode(ap)}if(ap==="summary_tree"||ap==="Histogram"){ad=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var Y=$("<div />").addClass("yaxislabel");Y.text(al.max);Y.css({position:"absolute",top:"22px",left:"10px"});Y.prependTo(this.container_div);var aa=this.view.canvas_manager.new_canvas();aa.width=ar+ac;aa.height=ad+M;if(al.dataset_type!="summary_tree"){var ai=this.get_summary_tree_data(al.data,aA,Z,200);if(al.max){ai.max=al.max}al=ai}var aB=new G.SummaryTreePainter(al,aA,Z,this.prefs);var at=aa.getContext("2d");at.translate(ac,M);aB.draw(at,ar,ad);return new m(ay,au,aa,al.max)}var am,af=1;if(ap==="no_detail"||ap==="Squish"||ap==="Pack"){af=this.incremental_slots(ah,al.data,ap);am=this.inc_slots[ah].slots}var ag=[];if(al.data){var aj=this.filters_manager.filters;for(var av=0,ax=al.data.length;av<ax;av++){var ae=al.data[av];var aw=false;var ak;for(var az=0,aC=aj.length;az<aC;az++){ak=aj[az];ak.update_attrs(ae);if(!ak.keep(ae)){aw=true;break}}if(!aw){ag.push(ae)}}}var aB=new (this.painter)(ag,aA,Z,this.prefs,ap,ab);var ad=aB.get_required_height(af)+z;var aa=this.view.canvas_manager.new_canvas();aa.width=ar+ac;aa.height=ad;var at=aa.getContext("2d");at.fillStyle=this.prefs.block_color;at.font=at.canvas.manager.default_font;at.textAlign="right";this.container_div.find(".yaxislabel").remove();if(al.message){$(aa).css({"border-top":"1px solid red"});at.fillStyle="red";at.textAlign="left";var ao=at.textBaseline;at.textBaseline="top";at.fillText(al.message,ac,0);at.textBaseline=ao;if(!al.data){return new b(ay,au,aa,ad)}}this.example_feature=(al.data.length?al.data[0]:undefined);at.translate(ac,z);aB.draw(at,ar,ad,am);return new J(ay,au,aa)}});var N=function(ab,Z,ad,Y,aa,ac){e.call(this,ab,Z,ad,Y,aa,ac);this.track_type="VcfTrack";this.painter=G.VariantPainter};extend(N.prototype,H.prototype,e.prototype);var Q=function(ab,Z,ad,Y,aa,ac){e.call(this,ab,Z,ad,Y,aa,ac);this.track_config=new T({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:aa,onchange:function(){this.track.tile_cache.clear();this.track.draw()}});this.prefs=this.track_config.values;this.track_type="ReadTrack";this.painter=G.ReadPainter;this.make_name_popup_menu()};extend(Q.prototype,H.prototype,e.prototype);var O=function(ac,aa,ae,Y,ab,ad,Z){e.call(this,ac,aa,ae,Y,ab,ad,{},Z);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};extend(O.prototype,H.prototype,e.prototype,{predraw_init:function(){var Z=this;var Y=function(){if(Z.data_cache.size()===0){setTimeout(Y,300)}else{Z.data_url=default_data_url;Z.data_query_wait=F;Z.dataset_state_url=converted_datasets_state_url;$.getJSON(Z.dataset_state_url,{dataset_id:Z.dataset_id,hda_ldda:Z.hda_ldda},function(aa){})}};Y()}});R.View=W;R.LineTrack=l;R.FeatureTrack=e;R.ReadTrack=Q};var slotting_module=function(c,b){var d=2,a=5;b.FeatureSlotter=function(h,g,e,f){this.slots={};this.start_end_dct={};this.w_scale=h;this.include_label=g;this.max_rows=e;this.measureText=f};extend(b.FeatureSlotter.prototype,{slot_features:function(l){var o=this.w_scale,r=this.slots,g=this.start_end_dct,x=[],z=[],m=0,y=this.max_rows;for(var v=0,w=l.length;v<w;v++){var k=l[v],n=k[0];if(r[n]!==undefined){m=Math.max(m,r[n]);z.push(r[n])}else{x.push(v)}}var p=function(F,G){for(var E=0;E<=y;E++){var C=false,H=g[E];if(H!==undefined){for(var B=0,D=H.length;B<D;B++){var A=H[B];if(G>A[0]&&F<A[1]){C=true;break}}}if(!C){return E}}return -1};for(var v=0,w=x.length;v<w;v++){var k=l[x[v]],n=k[0],t=k[1],e=k[2],q=k[3],f=Math.floor(t*o),j=Math.ceil(e*o),u=this.measureText(q).width,h;if(q!==undefined&&this.include_label){u+=(d+a);if(f-u>=0){f-=u;h="left"}else{j+=u;h="right"}}var s=p(f,j);if(s>=0){if(g[s]===undefined){g[s]=[]}g[s].push([f,j]);r[n]=s;m=Math.max(m,s)}else{}}return m+1}})};var painters_module=function(j,v){var o=function(G,y,E,x,D,B){if(B===undefined){B=4}var A=x-y;var z=D-E;var C=Math.floor(Math.sqrt(A*A+z*z)/B);var H=A/C;var F=z/C;var w;for(w=0;w<C;w++,y+=H,E+=F){if(w%2!==0){continue}G.fillRect(y,E,B,1)}};var p=function(z,x,w,C){var B=x-C/2,A=x+C/2,D=w-Math.sqrt(C*3/2);z.beginPath();z.moveTo(B,D);z.lineTo(A,D);z.lineTo(x,w);z.lineTo(B,D);z.strokeStyle=this.fillStyle;z.fill();z.stroke();z.closePath()};var l=function(y,A,w,x,z){this.data=y;this.view_start=A;this.view_end=w;this.prefs=extend({},this.default_prefs,x);this.mode=z};l.prototype.default_prefs={};var t=function(y,A,w,x,z){l.call(this,y,A,w,x,z)};t.prototype.default_prefs={show_counts:false};t.prototype.draw=function(L,w,K){var D=this.view_start,N=this.view_end-this.view_start,M=w/N;var I=this.data.data,H=this.data.delta,F=this.data.max,A=K;delta_x_px=Math.ceil(H*M);L.save();for(var B=0,C=I.length;B<C;B++){var G=Math.floor((I[B][0]-D)*M);var E=I[B][1];if(!E){continue}var J=E/F*K;if(E!==0&&J<1){J=1}L.fillStyle="black";L.fillRect(G,A-J,delta_x_px,J);var z=4;if(this.prefs.show_counts&&(L.measureText(E).width+z)<delta_x_px){L.fillStyle="#666";L.textAlign="center";L.fillText(E,G+(delta_x_px/2),10)}}L.restore()};var c=function(y,A,w,x,z){l.call(this,y,A,w,x,z)};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(M,L,J){var E=false,F=this.prefs.min_value,C=this.prefs.max_value,I=C-F,x=J,z=this.view_start,K=this.view_end-this.view_start,A=L/K,G=this.mode,Q=this.data;M.save();var R=Math.round(J+F/I*J);if(G!=="Intensity"){M.fillStyle="#aaa";M.fillRect(0,R,L,1)}M.beginPath();M.fillStyle=this.prefs.color;var P,D,B;if(Q.length>1){B=Math.ceil((Q[1][0]-Q[0][0])*A)}else{B=10}for(var N=0,O=Q.length;N<O;N++){P=Math.round((Q[N][0]-z)*A);D=Q[N][1];if(D===null){if(E&&G==="Filled"){M.lineTo(P,x)}E=false;continue}if(D<F){D=F}else{if(D>C){D=C}}if(G==="Histogram"){D=Math.round(D/I*x);M.fillRect(P,R,B,-D)}else{if(G==="Intensity"){D=255-Math.floor((D-F)/I*255);M.fillStyle="rgb("+D+","+D+","+D+")";M.fillRect(P,0,B,x)}else{D=Math.round(x-(D-F)/I*x);if(E){M.lineTo(P,D)}else{E=true;if(G==="Filled"){M.moveTo(P,x);M.lineTo(P,D)}else{M.moveTo(P,D)}}}}}if(G==="Filled"){if(E){M.lineTo(P,R);M.lineTo(0,R)}M.fill()}else{M.stroke()}var w=-1,H=-1;M.fillStyle=this.prefs.overflow_color;for(var N=0,O=Q.length;N<O;N++){D=Q[N][1];P=Math.round((Q[N][0]-z)*A);x_minus_scaled=Math.round((Q[N][0]-1-z)*A);if(H>=0&&(D===null||D<C)){M.fillRect(H,0,x_minus_scaled-H+1,2);H=-1}else{if(w>=0&&(D===null||D>F)){M.fillRect(w,J-2,x_minus_scaled-w+1,2);w=-1}}if(D!==null&&D>C&&H<0){H=P}else{if(D!==null&&D<F&&w<0){w=P}}}M.restore()};var n=function(y,A,w,x,z){l.call(this,y,A,w,x,z)};n.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(n.prototype,{get_required_height:function(x){var w=y_scale=this.get_row_height(),y=this.mode;if(y==="no_detail"||y==="Squish"||y==="Pack"){w=x*y_scale}return w+Math.max(Math.round(y_scale/2),5)},draw:function(I,z,H,E){var C=this.data,F=this.view_start,J=this.view_end;I.save();I.fillStyle=this.prefs.block_color;I.textAlign="right";var M=this.view_end-this.view_start,L=z/M,y=this.get_row_height();for(var B=0,D=C.length;B<D;B++){var K=C[B],A=K[0],w=K[1],x=K[2],G=(E&&E[A]!==undefined?E[A]:null);if((w<J&&x>F)&&(this.mode=="Dense"||G!==null)){this.draw_element(I,this.mode,K,G,F,J,L,y,z)}}I.restore()}});var d=10,h=3,k=5,u=10,f=1,r=3,e=3,a=9,m=2,g="#ccc";var q=function(y,A,w,x,z){n.call(this,y,A,w,x,z)};extend(q.prototype,n.prototype,{get_row_height:function(){var x=this.mode,w;if(x==="Dense"){w=d}else{if(x==="no_detail"){w=h}else{if(x==="Squish"){w=k}else{w=u}}}return w},draw_element:function(I,B,Q,D,K,aa,ae,af,w){var N=Q[0],ac=Q[1],U=Q[2],L=Q[3],V=Math.floor(Math.max(0,(ac-K)*ae)),J=Math.ceil(Math.min(w,Math.max(0,(U-K)*ae))),T=(B==="Dense"?0:(0+D))*af,H,Y,M=null,ag=null,z=this.prefs.block_color,X=this.prefs.label_color;if(B=="Dense"){D=1}if(B==="no_detail"){I.fillStyle=z;I.fillRect(V,T+5,J-V,f)}else{var G=Q[4],S=Q[5],W=Q[6],A=Q[7];if(S&&W){M=Math.floor(Math.max(0,(S-K)*ae));ag=Math.ceil(Math.min(w,Math.max(0,(W-K)*ae)))}var ad,O;if(B==="Squish"||B==="Dense"){ad=1;O=e}else{ad=5;O=a}if(!A){if(Q.strand){if(Q.strand==="+"){I.fillStyle=I.canvas.manager.get_pattern("right_strand_inv")}else{if(Q.strand==="-"){I.fillStyle=I.canvas.manager.get_pattern("left_strand_inv")}}}else{I.fillStyle=z}I.fillRect(V,T,J-V,O)}else{var F,P;if(B==="Squish"||B==="Dense"){I.fillStyle=g;F=T+Math.floor(e/2)+1;P=1}else{if(G){var F=T;var P=O;if(G==="+"){I.fillStyle=I.canvas.manager.get_pattern("right_strand")}else{if(G==="-"){I.fillStyle=I.canvas.manager.get_pattern("left_strand")}}}else{I.fillStyle=g;F+=(e/2)+1;P=1}}I.fillRect(V,F,J-V,P);for(var ab=0,y=A.length;ab<y;ab++){var C=A[ab],x=Math.floor(Math.max(0,(C[0]-K)*ae)),R=Math.ceil(Math.min(w,Math.max((C[1]-K)*ae)));if(x>R){continue}I.fillStyle=z;I.fillRect(x,T+(O-ad)/2+1,R-x,ad);if(M!==undefined&&W>S&&!(x>ag||R<M)){var Z=Math.max(x,M),E=Math.min(R,ag);I.fillRect(Z,T+1,E-Z,O);if(A.length==1&&B=="Pack"){if(G==="+"){I.fillStyle=I.canvas.manager.get_pattern("right_strand_inv")}else{if(G==="-"){I.fillStyle=I.canvas.manager.get_pattern("left_strand_inv")}}if(Z+14<E){Z+=2;E-=2}I.fillRect(Z,T+1,E-Z,O)}}}}if(B==="Pack"&&ac>K){I.fillStyle=X;if(K===0&&V-I.measureText(L).width<0){I.textAlign="left";I.fillText(L,J+m,T+8)}else{I.textAlign="right";I.fillText(L,V-m,T+8)}I.fillStyle=z}}}});var b=function(y,A,w,x,z){n.call(this,y,A,w,x,z)};extend(b.prototype,n.prototype,{draw_element:function(P,K,E,A,S,y,H,Q,N){var E=data[i],G=E[0],O=E[1],z=E[2],J=E[3],C=Math.floor(Math.max(0,(O-S)*H)),F=Math.ceil(Math.min(N,Math.max(0,(z-S)*H))),B=(K==="Dense"?0:(0+A))*Q,w,T,x=null,I=null;if(no_label){P.fillStyle=block_color;P.fillRect(C+left_offset,B+5,F-C,1)}else{var R=E[4],M=E[5],D=E[6];w=9;T=1;P.fillRect(C+left_offset,B,F-C,w);if(K!=="Dense"&&J!==undefined&&O>S){P.fillStyle=label_color;if(S===0&&C-P.measureText(J).width<0){P.textAlign="left";P.fillText(J,F+2+left_offset,B+8)}else{P.textAlign="right";P.fillText(J,C-2+left_offset,B+8)}P.fillStyle=block_color}var L=R+" / "+M;if(O>S&&P.measureText(L).width<(F-C)){P.fillStyle="white";P.textAlign="center";P.fillText(L,left_offset+C+(F-C)/2,B+8);P.fillStyle=block_color}}}});var s=function(z,B,w,y,A,x){n.call(this,z,B,w,y,A);this.ref_seq=x};s.prototype.default_prefs=extend({},n.prototype.default_prefs,{show_insertions:false});extend(s.prototype,n.prototype,{get_row_height:function(){var w,x=this.mode;if(x==="Dense"){w=d}else{if(x==="Squish"){w=k}else{w=u;if(this.prefs.show_insertions){w*=2}}}return w},draw_read:function(S,N,J,X,y,R,G,D,C){S.textAlign="center";var Q=this,x=[X,y],M=0,T=0,P=0;ref_seq=this.ref_seq,char_width_px=S.canvas.manager.char_width_px;var ac=[];if((N==="Pack"||this.mode==="Auto")&&D!==undefined&&J>char_width_px){P=Math.round(J/2)}if(!G){G=[[0,D.length]]}for(var K=0,V=G.length;K<V;K++){var H=G[K],z="MIDNSHP=X"[H[0]],L=H[1];if(z==="H"||z==="S"){M-=L}var E=R+M,ab=Math.floor(Math.max(0,(E-X)*J)),F=Math.floor(Math.max(0,(E+L-X)*J));if(ab===F){F+=1}switch(z){case"H":break;case"S":case"M":case"=":if(is_overlap([E,E+L],x)){var O=D.slice(T,T+L);if(P>0){S.fillStyle=this.prefs.block_color;S.fillRect(ab-P,C+1,F-ab,9);S.fillStyle=g;for(var Z=0,w=O.length;Z<w;Z++){if(this.prefs.show_differences&&ref_seq){var I=ref_seq[E-X+Z];if(!I||I.toLowerCase()===O[Z].toLowerCase()){continue}}if(E+Z>=X&&E+Z<=y){var aa=Math.floor(Math.max(0,(E+Z-X)*J));S.fillText(O[Z],aa,C+9)}}}else{S.fillStyle=this.prefs.block_color;S.fillRect(ab,C+4,F-ab,e)}}T+=L;M+=L;break;case"N":S.fillStyle=g;S.fillRect(ab-P,C+5,F-ab,1);M+=L;break;case"D":S.fillStyle="red";S.fillRect(ab-P,C+4,F-ab,3);M+=L;break;case"P":break;case"I":var W=ab-P;if(is_overlap([E,E+L],x)){var O=D.slice(T,T+L);if(this.prefs.show_insertions){var B=ab-(F-ab)/2;if((N==="Pack"||this.mode==="Auto")&&D!==undefined&&J>char_width_px){S.fillStyle="yellow";S.fillRect(B-P,C-9,F-ab,9);ac[ac.length]={type:"triangle",data:[W,C+4,5]};S.fillStyle=g;switch(seq_tile_overlap){case (OVERLAP_START):O=O.slice(X-E);break;case (OVERLAP_END):O=O.slice(0,E-y);break;case (CONTAINED_BY):break;case (CONTAINS):O=O.slice(X-E,E-y);break}for(var Z=0,w=O.length;Z<w;Z++){var aa=Math.floor(Math.max(0,(E+Z-X)*J));S.fillText(O[Z],aa-(F-ab)/2,C)}}else{S.fillStyle="yellow";S.fillRect(B,C+(this.mode!=="Dense"?2:5),F-ab,(N!=="Dense"?e:r))}}else{if((N==="Pack"||this.mode==="Auto")&&D!==undefined&&J>char_width_px){ac[ac.length]={type:"text",data:[O.length,W,C+9]}}else{}}}T+=L;break;case"X":T+=L;break}}S.fillStyle="yellow";var Y,A,ad;for(var U=0;U<ac.length;U++){Y=ac[U];A=Y.type;ad=Y.data;if(A==="text"){S.save();S.font="bold "+S.font;S.fillText(ad[0],ad[1],ad[2]);S.restore()}else{if(A=="triangle"){p(S,ad[0],ad[1],ad[2])}}}},draw_element:function(P,K,C,z,S,x,G,Q,N){var F=C[0],O=C[1],y=C[2],H=C[3],B=Math.floor(Math.max(0,(O-S)*G)),D=Math.ceil(Math.min(N,Math.max(0,(y-S)*G))),A=(K==="Dense"?0:(0+z))*Q,T=this.prefs.block_color,E=this.prefs.label_color,M=0;if((K==="Pack"||this.mode==="Auto")&&G>P.canvas.manager.char_width_px){var M=Math.round(G/2)}P.fillStyle=T;if(C[5] instanceof Array){var L=Math.floor(Math.max(0,(C[4][0]-S)*G)),J=Math.ceil(Math.min(N,Math.max(0,(C[4][1]-S)*G))),I=Math.floor(Math.max(0,(C[5][0]-S)*G)),w=Math.ceil(Math.min(N,Math.max(0,(C[5][1]-S)*G)));if(C[4][1]>=S&&C[4][0]<=x&&C[4][2]){this.draw_read(P,K,G,S,x,C[4][0],C[4][2],C[4][3],A)}if(C[5][1]>=S&&C[5][0]<=x&&C[5][2]){this.draw_read(P,K,G,S,x,C[5][0],C[5][2],C[5][3],A)}if(I>J){P.fillStyle=g;o(P,J-M,A+5,I-M,A+5)}}else{P.fillStyle=T;this.draw_read(P,K,G,S,x,O,C[4],C[5],A)}if(K==="Pack"&&O>S){P.fillStyle=this.prefs.label_color;var R=1;if(R===0&&B-P.measureText(H).width<0){P.textAlign="left";P.fillText(H,D+m-M,A+8)}else{P.textAlign="right";P.fillText(H,B-m-M,A+8)}P.fillStyle=T}}});v.SummaryTreePainter=t;v.LinePainter=c;v.LinkedFeaturePainter=q;v.ReadPainter=s;v.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("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;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var 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=$(this).parent();var ad=ae.children();var ac;for(ac=0;ac<ad.length;ac++){if(ag.offsetY<$(ad.get(ac)).position().top){break}}if(ac===ad.length){if(this!==ad.get(ac-1)){ae.append(this)}}else{if(this!==ad.get(ac)){$(this).insertBefore(ad.get(ac))}}})};T.sortable=C;var h=function(ac,aa){var ab=aa-ac;return(ab<=2?0.01:(ab<=100?1:(ab<=1000?5:10)))};var D=9,A=10,O=D+2,x=100,F=12000,M=200,t=10,H=5000,u=100,n="There was an error in indexing this dataset. ",G="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",B="No data for this chrom/contig.",r="Currently indexing... please wait",w="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",d=10,s=5,z=5;function v(aa){return Math.round(aa*1000)/1000}var c=function(aa){this.num_elements=aa;this.clear()};o(c.prototype,{get:function(ab){var aa=this.key_ary.indexOf(ab);if(aa!==-1){this.move_key_to_end(ab,aa)}return this.obj_cache[ab]},set:function(ab,ac){if(!this.obj_cache[ab]){if(this.key_ary.length>=this.num_elements){var aa=this.key_ary.shift();delete this.obj_cache[aa]}this.key_ary.push(ab)}this.obj_cache[ab]=ac;return ac},move_key_to_end:function(ab,aa){this.key_ary.splice(aa,1);this.key_ary.push(ab)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var N=function(ab,aa,ac){c.call(this,ab);this.track=aa;this.subset=(ac!==undefined?ac:true)};o(N.prototype,c.prototype,{load_data:function(ai,aj,ae,ah,ab,ag){var ad={chrom:ai,low:aj,high:ae,mode:ah,resolution:ab,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ad,ag);if(this.track.filters_manager){var ak=[];var aa=this.track.filters_manager.filters;for(var af=0;af<aa.length;af++){ak[ak.length]=aa[af].name}ad.filter_cols=JSON.stringify(ak)}var ac=this;return $.getJSON(this.track.data_url,ad,function(al){ac.set_data(aj,ae,ah,al)})},get_data:function(ac,aa,af,ag,ab,ae){var ad=this.get(this.gen_key(aa,af,ag));if(ad){return ad}ad=this.load_data(ac,aa,af,ag,ab,ae);this.set_data(aa,af,ag,ad);return ad},set_data:function(ab,ac,ad,aa){return this.set(this.gen_key(ab,ac,ad),aa)},gen_key:function(aa,ac,ad){var ab=aa+"_"+ac+"_"+ad;return ab},split_key:function(aa){return aa.split("_")}});var E=function(ab,aa,ac){N.call(this,ab,aa,ac)};o(E.prototype,N.prototype,c.prototype,{load_data:function(ac,aa,ae,af,ab,ad){if(ab>1){return}return N.prototype.load_data.call(this,ac,aa,ae,af,ab,ad)}});var Y=function(aa,ad,ac,ab,ae){this.container=aa;this.chrom=null;this.vis_id=ac;this.dbkey=ab;this.title=ad;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(ae);this.canvas_manager=new Z(aa.get(0).ownerDocument);this.reset()};o(Y.prototype,{init:function(ad){var ac=this.container,aa=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ac);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ac);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ac);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ab=function(ae){if(ae.type==="focusout"||(ae.keyCode||ae.which)===13||(ae.keyCode||ae.which)===27){if((ae.keyCode||ae.which)!==27){aa.go_to($(this).val())}$(this).hide();$(this).val("");aa.location_span.show();aa.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ab).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.bind("click",function(){aa.location_span.hide();aa.chrom_select.hide();aa.nav_input.val(aa.chrom+":"+aa.low+"-"+aa.high);aa.nav_input.css("display","inline-block");aa.nav_input.select();aa.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){aa.zoom_out();aa.redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){aa.zoom_in();aa.redraw()}).appendTo(this.nav_controls);this.load_chroms({low:0},ad);this.chrom_select.bind("change",function(){aa.change_chrom(aa.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(ae){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(ae){aa.zoom_in(ae.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ae,af){this.current_x=af.offsetX}).bind("drag",function(ae,ag){var ah=ag.offsetX-this.current_x;this.current_x=ag.offsetX;var af=Math.round(ah/aa.viewport_container.width()*(aa.max_high-aa.max_low));aa.move_delta(-af)});this.overview_close.bind("click",function(){for(var af=0,ae=aa.tracks.length;af<ae;af++){aa.tracks[af].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",aa.overview_box.height());aa.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(ae,af){if(ae.clientX>aa.viewport_container.width()-16){return false}}).bind("dragstart",function(ae,af){af.original_low=aa.low;af.current_height=ae.clientY;af.current_x=af.offsetX}).bind("drag",function(ag,ai){var ae=$(this);var aj=ai.offsetX-ai.current_x;var af=ae.scrollTop()-(ag.clientY-ai.current_height);ae.scrollTop(af);ai.current_height=ag.clientY;ai.current_x=ai.offsetX;var ah=Math.round(aj/aa.viewport_container.width()*(aa.high-aa.low));aa.move_delta(ah)}).bind("mousewheel",function(ag,ai,af,ae){if(af){var ah=Math.round(-af/aa.viewport_container.width()*(aa.high-aa.low));aa.move_delta(ah)}});this.top_labeltrack.bind("dragstart",function(ae,af){return $("<div />").css({height:aa.content_div.height()+aa.top_labeltrack.height()+aa.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ai,aj){$(aj.proxy).css({left:Math.min(ai.pageX,aj.startX),width:Math.abs(ai.pageX-aj.startX)});var af=Math.min(ai.pageX,aj.startX)-aa.container.offset().left,ae=Math.max(ai.pageX,aj.startX)-aa.container.offset().left,ah=(aa.high-aa.low),ag=aa.viewport_container.width();aa.update_location(Math.round(af/ag*ah)+aa.low,Math.round(ae/ag*ah)+aa.low)}).bind("dragend",function(aj,ak){var af=Math.min(aj.pageX,ak.startX),ae=Math.max(aj.pageX,ak.startX),ah=(aa.high-aa.low),ag=aa.viewport_container.width(),ai=aa.low;aa.low=Math.round(af/ag*ah)+ai;aa.high=Math.round(ae/ag*ah)+ai;$(ak.proxy).remove();aa.redraw()});this.add_label_track(new X(this,this.top_labeltrack));this.add_label_track(new X(this,this.nav_labeltrack));$(window).bind("resize",function(){aa.resize_window()});$(document).bind("redraw",function(){aa.redraw()});this.reset();$(window).trigger("resize")},update_location:function(aa,ab){this.location_span.text(commatize(aa)+" - "+commatize(ab));this.nav_input.val(this.chrom+":"+commatize(aa)+"-"+commatize(ab))},load_chroms:function(ab,ac){ab.num=u;$.extend(ab,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var aa=this;$.ajax({url:chrom_url,data:ab,dataType:"json",success:function(ae){if(ae.chrom_info.length===0){alert("Invalid chromosome: "+ab.chrom);return}if(ae.reference){aa.add_label_track(new y(aa))}aa.chrom_data=ae.chrom_info;var ah='<option value="">Select Chrom/Contig</option>';for(var ag=0,ad=aa.chrom_data.length;ag<ad;ag++){var af=aa.chrom_data[ag].chrom;ah+='<option value="'+af+'">'+af+"</option>"}if(ae.prev_chroms){ah+='<option value="previous">Previous '+u+"</option>"}if(ae.next_chroms){ah+='<option value="next">Next '+u+"</option>"}aa.chrom_select.html(ah);if(ac){ac()}aa.chrom_start_index=ae.start_index},error:function(){alert("Could not load chroms for this dbkey:",aa.dbkey)}})},change_chrom:function(ae,ab,ag){if(!ae||ae==="None"){return}var ad=this;if(ae==="previous"){ad.load_chroms({low:this.chrom_start_index-u});return}if(ae==="next"){ad.load_chroms({low:this.chrom_start_index+u});return}var af=$.grep(ad.chrom_data,function(ai,aj){return ai.chrom===ae})[0];if(af===undefined){ad.load_chroms({chrom:ae},function(){ad.change_chrom(ae,ab,ag)});return}else{if(ae!==ad.chrom){ad.chrom=ae;if(!ad.chrom){ad.intro_div.show()}else{ad.intro_div.hide()}ad.chrom_select.val(ad.chrom);ad.max_high=af.len-1;ad.reset();ad.redraw(true);for(var ah=0,aa=ad.tracks.length;ah<aa;ah++){var ac=ad.tracks[ah];if(ac.init){ac.init()}}}if(ab!==undefined&&ag!==undefined){ad.low=Math.max(ab,0);ad.high=Math.min(ag,ad.max_high)}ad.reset_overview();ad.redraw()}},go_to:function(ae){var ai=this,aa,ad,ab=ae.split(":"),ag=ab[0],ah=ab[1];if(ah!==undefined){try{var af=ah.split("-");aa=parseInt(af[0].replace(/,/g,""),10);ad=parseInt(af[1].replace(/,/g,""),10)}catch(ac){return false}}ai.change_chrom(ag,aa,ad)},move_fraction:function(ac){var aa=this;var ab=aa.high-aa.low;this.move_delta(ac*ab)},move_delta:function(ac){var aa=this;var ab=aa.high-aa.low;if(aa.low-ac<aa.max_low){aa.low=aa.max_low;aa.high=aa.max_low+ab}else{if(aa.high-ac>aa.max_high){aa.high=aa.max_high;aa.low=aa.max_high-ab}else{aa.high-=ac;aa.low-=ac}}aa.redraw()},add_track:function(aa){aa.view=this;aa.track_id=this.track_id_counter;this.tracks.push(aa);if(aa.init){aa.init()}aa.container_div.attr("id","track_"+aa.track_id);C(aa.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(aa){aa.view=this;this.label_tracks.push(aa)},remove_track:function(aa){this.has_changes=true;aa.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(aa)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(ah){var ag=this.high-this.low,af=this.low,ab=this.high;if(af<this.max_low){af=this.max_low}if(ab>this.max_high){ab=this.max_high}if(this.high!==0&&ag<this.min_separation){ab=af+this.min_separation}this.low=Math.floor(af);this.high=Math.ceil(ab);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/M)/Math.LN10));this.zoom_res=Math.pow(t,Math.max(0,Math.ceil(Math.log(this.resolution,t)/Math.log(t))));var aa=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=13;this.overview_box.css({left:aa,width:Math.max(ai,ae)}).show();if(ae<ai){this.overview_box.css("left",aa-(ai-ae)/2)}if(this.overview_highlight){this.overview_highlight.css({left:aa,width:ae})}this.update_location(this.low,this.high);if(!ah){for(var ac=0,ad=this.tracks.length;ac<ad;ac++){if(this.tracks[ac]&&this.tracks[ac].enabled){this.tracks[ac].draw()}}for(ac=0,ad=this.label_tracks.length;ac<ad;ac++){this.label_tracks[ac].draw()}}},zoom_in:function(ab,ac){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ad=this.high-this.low,ae=ad/2+this.low,aa=(ad/this.zoom_factor)/2;if(ab){ae=ab/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ae-aa);this.high=Math.round(ae+aa);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var ab=this.high-this.low,ac=ab/2+this.low,aa=(ab*this.zoom_factor)/2;this.low=Math.round(ac-aa);this.high=Math.round(ac+aa);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var p=function(ab,ae){this.track=ab;this.name=ae.name;this.params=[];var am=ae.params;for(var ac=0;ac<am.length;ac++){var ah=am[ac],aa=ah.name,al=ah.label,ad=unescape(ah.html),aj=ah.type;if(aj==="number"){this.params[this.params.length]=new g(aa,al,ad,ah.min,ah.max)}else{if(aj=="select"){this.params[this.params.length]=new K(aa,al,ad)}else{console.log("WARNING: unrecognized tool parameter type:",aa,aj)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ao){ao.stopPropagation()}).bind("click",function(ao){ao.stopPropagation()}).bind("dblclick",function(ao){ao.stopPropagation()});var ak=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ai=this.params;var af=this;$.each(this.params,function(ap,at){var ar=$("<div>").addClass("param-row").appendTo(af.parent_div);var ao=$("<div>").addClass("param-label").text(at.label).appendTo(ar);var aq=$("<div/>").addClass("slider").html(at.html).appendTo(ar);$("<div style='clear: both;'/>").appendTo(ar)});this.parent_div.find("input").click(function(){$(this).select()});var an=$("<div>").addClass("slider-row").appendTo(this.parent_div);var ag=$("<input type='submit'>").attr("value","Run").appendTo(an);var af=this;ag.click(function(){af.run()})};o(p.prototype,{get_param_values_dict:function(){var aa={};this.parent_div.find(":input").each(function(){var ab=$(this).attr("name"),ac=$(this).val();aa[ab]=JSON.stringify(ac)});return aa},get_param_values:function(){var ab=[];var aa={};this.parent_div.find(":input").each(function(){var ac=$(this).attr("name"),ad=$(this).val();if(ac){ab[ab.length]=ad}});return ab},run:function(){var ab={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name};$.extend(ab,this.get_param_values_dict());var ad=this.track,ac=ab.tool_id+ad.tool_region_and_parameters_str(ab.chrom,ab.low,ab.high),ae;if(ad.track_type==="FeatureTrack"){ae=new Q(ac,view,ad.hda_ldda,undefined,{},{},ad)}this.track.add_track(ae);ae.content_div.text("Starting job.");var aa=function(){$.getJSON(run_tool_url,ab,function(af){if(af==="no converter"){ae.container_div.addClass("error");ae.content_div.text(G)}else{if(af.error){ae.container_div.addClass("error");ae.content_div.text(w+af.message)}else{if(af==="pending"){ae.container_div.addClass("pending");ae.content_div.text("Converting input data so that it can be easily reused.");setTimeout(aa,2000)}else{ae.dataset_id=af.dataset_id;ae.content_div.text("Running job.");ae.init()}}}})};aa()}});var K=function(ab,aa,ac){this.name=ab;this.label=aa;this.html=ac};var g=function(ac,ab,ae,ad,aa){K.call(this,ac,ab,ae);this.min=ad;this.max=aa};var j=function(ab,aa,ac){this.name=ab;this.index=aa;this.value=ac};var R=function(ab,aa){this.name=ab;this.index=aa;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};o(R.prototype,{applies_to:function(aa){if(aa.length>this.index){return true}return false},keep:function(aa){if(!this.applies_to(aa)){return true}var ab=parseInt(aa[this.index]);return(isNaN(ab)||(ab>=this.low&&ab<=this.high))},update_attrs:function(ab){var aa=false;if(!this.applies_to(ab)){return aa}if(ab[this.index]<this.min){this.min=Math.floor(ab[this.index]);aa=true}if(ab[this.index]>this.max){this.max=Math.ceil(ab[this.index]);aa=true}return aa},update_ui_elt:function(){var ab=this.slider.slider("option","min"),aa=this.slider.slider("option","max");if(this.min<ab||this.max>aa){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",h(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var W=function(ac,ai){this.track=ac;this.filters=[];for(var ae=0;ae<ai.length;ae++){var aa=ai[ae];var ab=aa.name,ah=aa.type,af=aa.index;if(ah==="int"||ah==="float"){this.filters[ae]=new R(ab,af)}else{this.filters[ae]=new j(ab,af,ah)}}var ag=function(aj,ak,al){aj.click(function(){var am=ak.text();max=parseFloat(al.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(al.slider("option","values")){input_size=2*input_size+1;multi_value=true}ak.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",am).appendTo(ak).focus().select().click(function(an){an.stopPropagation()}).blur(function(){$(this).remove();ak.text(am)}).keyup(function(ar){if(ar.keyCode===27){$(this).trigger("blur")}else{if(ar.keyCode===13){var ap=al.slider("option","min"),an=al.slider("option","max"),aq=function(at){return(isNaN(at)||at>an||at<ap)},ao=$(this).val();if(!multi_value){ao=parseFloat(ao);if(aq(ao)){alert("Parameter value must be in the range ["+ap+"-"+an+"]");return $(this)}}else{ao=ao.split("-");ao=[parseFloat(ao[0]),parseFloat(ao[1])];if(aq(ao[0])||aq(ao[1])){alert("Parameter value must be in the range ["+ap+"-"+an+"]");return $(this)}}al.slider((multi_value?"values":"value"),ao)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aj){aj.stopPropagation()}).bind("click",function(aj){aj.stopPropagation()}).bind("dblclick",function(aj){aj.stopPropagation()});var ad=this;$.each(this.filters,function(ap,ak){var am=$("<div/>").addClass("slider-row").appendTo(ad.parent_div);var aj=$("<div/>").addClass("slider-label").appendTo(am);var ar=$("<span/>").addClass("slider-name").text(ak.name+" ").appendTo(aj);var al=$("<span/>");var an=$("<span/>").addClass("slider-value").appendTo(aj).append("[").append(al).append("]");var aq=$("<div/>").addClass("slider").appendTo(am);ak.control_element=$("<div/>").attr("id",ak.name+"-filter-control").appendTo(aq);var ao=[0,0];ak.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(at,au){ao=au.values;al.text(au.values[0]+"-"+au.values[1]);setTimeout(function(){if(au.values[0]==ao[0]&&au.values[1]==ao[1]){var av=au.values;al.text(av[0]+"-"+av[1]);ak.low=av[0];ak.high=av[1];ad.track.draw(true,true)}},50)},change:function(at,au){ak.control_element.slider("option","slide").call(ak.control_element,at,au)}});ak.slider=ak.control_element;ak.slider_label=al;ag(an,al,ak.control_element);$("<div style='clear: both;'/>").appendTo(am)})};var V=function(aa){this.track=aa.track;this.params=aa.params;this.values={};if(aa.saved_values){this.restore_values(aa.saved_values)}this.onchange=aa.onchange};o(V.prototype,{restore_values:function(aa){var ab=this;$.each(this.params,function(ac,ad){if(aa[ad.key]!==undefined){ab.values[ad.key]=aa[ad.key]}else{ab.values[ad.key]=ad.default_value}})},build_form:function(){var ab=this;var aa=$("<div />");$.each(this.params,function(af,ad){if(!ad.hidden){var ac="param_"+af;var ak=$("<div class='form-row' />").appendTo(aa);ak.append($("<label />").attr("for",ac).text(ad.label+":"));if(ad.type==="bool"){ak.append($('<input type="checkbox" />').attr("id",ac).attr("name",ac).attr("checked",ab.values[ad.key]))}else{if(ad.type==="color"){var ah=ab.values[ad.key];var ag=$("<input />").attr("id",ac).attr("name",ac).val(ah);var ai=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var ae=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ai);var aj=$("<div/>").appendTo(ae).farbtastic({width:100,height:100,callback:ag,color:ah});$("<div />").append(ag).append(ai).appendTo(ak).bind("click",function(al){ai.css({left:$(this).position().left+($(ag).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ai.hide();$(document).unbind("click.color-picker")});al.stopPropagation()})}else{ak.append($("<input />").attr("id",ac).attr("name",ac).val(ab.values[ad.key]))}}}});return aa},update_from_form:function(aa){var ac=this;var ab=false;$.each(this.params,function(ad,af){if(!af.hidden){var ag="param_"+ad;var ae=aa.find("#"+ag).val();if(af.type==="float"){ae=parseFloat(ae)}else{if(af.type==="int"){ae=parseInt(ae)}else{if(af.type==="bool"){ae=aa.find("#"+ag).is(":checked")}}}if(ae!==ac.values[af.key]){ac.values[af.key]=ae;ab=true}}});if(ab){this.onchange()}}});var b=function(ac,ab,aa){this.index=ac;this.resolution=ab;this.canvas=$("<div class='track-tile'/>").append(aa)};var m=function(ac,ab,aa,ad){b.call(this,ac,ab,aa);this.max_val=ad};var L=function(ac,ab,aa){b.call(this,ac,ab,aa)};var k=function(ab,aa,ae,ac,ad){this.name=ab;this.view=aa;this.parent_element=ae;this.data_url=(ac?ac:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ad?ad:H);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};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}$.getJSON(converted_datasets_state_url,{hda_ldda:aa.hda_ldda,dataset_id:aa.dataset_id,chrom:aa.view.chrom},function(ab){if(!ab||ab==="error"||ab.kind==="error"){aa.container_div.addClass("error");aa.content_div.text(n);if(ab.message){var ad=aa.view.tracks.indexOf(aa);var ac=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+ab.message+"</pre>",{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;$.when(aa.predraw_init()).done(function(){aa.container_div.removeClass("nodata error pending");aa.draw()})}}}}}}})},predraw_init:function(){},update_name:function(aa){this.old_name=this.name;this.name=aa;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var J=function(ai,ag,aj){var ab=this,ak=ab.view;this.filters_manager=(ai!==undefined?new W(this,ai):undefined);this.filters_available=false;this.filters_visible=false;this.tool=(ag!==undefined&&obj_length(ag)>0?new p(this,ag):undefined);this.parent_track=aj;this.child_tracks=[];if(ab.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}ab.child_tracks_container=$("<div/>").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=$("<div class='right-float menubutton popup' />").appendTo(ab.header_div);var ad=(ab.track_config&&ab.track_config.values.mode?ab.track_config.values.mode:ab.display_modes[0]);ab.mode=ad;ab.mode_div.text(ad);var ac=function(al){ab.mode_div.text(al);ab.mode=al;ab.track_config.values.mode=al;ab.tile_cache.clear();ab.draw()};var aa={};for(var ae=0,ah=ab.display_modes.length;ae<ah;ae++){var af=ab.display_modes[ae];aa[af]=function(al){return function(){ac(al)}}(af)}make_popupmenu(ab.mode_div,aa)}else{ab.mode_div.hide()}}this.make_name_popup_menu()};o(J.prototype,k.prototype,{make_name_popup_menu:function(){var ab=this;var aa={};aa["Edit configuration"]=function(){var ah=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(){ab.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){af()}}};$(window).bind("keypress.check_enter_esc",ag);show_modal("Configure Track",ab.track_config.build_form(),{Cancel:ah,OK:af})};if(ab.filters_available>0){var ae=(ab.filters_div.is(":visible")?"Hide filters":"Show filters");aa[ae]=function(){ab.filters_visible=(ab.filters_div.is(":visible"));ab.filters_div.toggle();ab.make_name_popup_menu()}}if(ab.tool){var ae=(ab.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");aa[ae]=function(){if(!ab.dynamic_tool_div.is(":visible")){ab.update_name(ab.name+ab.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ab.revert_name()}ab.dynamic_tool_div.toggle();ab.make_name_popup_menu()}}if(ab.valid_chroms){aa["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+ab.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var ac=view;var ad=function(){$("#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=$("<div style='position: relative;'></div>"),am=function(aw,ax,av){return aw+"_"+ax+"_"+av};if(!ac){this.content_div.children().remove()}this.content_div.append(ad);this.max_height=0;var ao=Math.floor(au/al/M);var af=[];var ap=0;while((ao*M*al)<ag){var at=am(ak,ae,ao);var ah=this.tile_cache.get(at);var aq=ao*M*this.view.resolution;var ab=aq+M*this.view.resolution;if(!aa&&ah){af[af.length]=ah;this.show_tile(ah,ad,aq,ae)}else{this.delayed_draw(aa,at,ao,al,ad,ae,af)}ao+=1;ap++}var aj=this;var ar=setInterval(function(){if(af.length===ap){clearInterval(ar);if(ac){var ay=aj.content_div.children();var az=false;for(var ax=ay.length-1,aD=0;ax>=aD;ax--){var aw=$(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;ax<af.length;ax++){var aF=af[ax].max_val;if(aF>aC){aC=aF}}for(var ax=0;ax<af.length;ax++){if(af[ax].max_val!==aC){var aE=af[ax];aE.canvas.remove();aj.delayed_draw(true,am(ak,ae,aE.index),aE.index,aE.resolution,ad,ae,[],{max:aC})}}}if(aj.filters_manager){var av=aj.filters_manager.filters;for(var aB=0;aB<av.length;aB++){av[aB].update_ui_elt()}var aA=false;if(aj.example_feature){for(var aB=0;aB<av.length;aB++){if(av[aB].applies_to(aj.example_feature)){aA=true;break}}}if(aj.filters_available!==aA){aj.filters_available=aA;if(!aj.filters_available){aj.filters_div.hide()}aj.make_name_popup_menu()}}}},50);for(var an=0;an<this.child_tracks.length;an++){this.child_tracks[an].draw(aa,ac)}},delayed_draw:function(ab,ai,ac,ae,aj,am,ak,af){var ad=this,ag=ac*M*ae,al=ag+M*ae;var ah=function(av,an,ap,ao,at,au,aq){var ar=ad.draw_tile(an,ap,ao,au,aq);ad.tile_cache.set(ai,ar);ad.show_tile(ar,at,ag,au);ak[ak.length]=ar};var aa=setTimeout(function(){if(ag<=ad.view.high&&al>=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(){$(this).remove()})}});var X=function(aa,ab){this.track_type="LabelTrack";this.hidden=true;k.call(this,null,aa,ab);this.container_div.addClass("label-track")};o(X.prototype,k.prototype,{draw:function(){var ac=this.view,ad=ac.high-ac.low,ag=Math.floor(Math.pow(10,Math.floor(Math.log(ad)/Math.log(10)))),aa=Math.floor(ac.low/ag)*ag,ae=this.view.container.width(),ab=$("<div style='position: relative; height: 1.3em;'></div>");while(aa<ac.high){var af=(aa-ac.low)/ad*ae;ab.append($("<div class='label'>"+commatize(aa)+"</div>").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<ah;ag++){var aa=Math.round(ag*ak);aj.fillText(ai[ag],aa+ae.left_offset,10)}return new b(ab,af,ad)}this.content_div.css("height","0px")}});var l=function(ae,ac,af,aa,ad){var ab=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";k.call(this,ae,ac,ac.viewport_container);J.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=af;this.dataset_id=aa;this.original_dataset_id=aa;this.data_cache=new N(z,this);this.tile_cache=new c(s);this.track_config=new V({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:ad,onchange:function(){ab.vertical_range=ab.prefs.max_value-ab.prefs.min_value;$("#linetrack_"+ab.track_id+"_minval").text(ab.prefs.min_value);$("#linetrack_"+ab.track_id+"_maxval").text(ab.prefs.max_value);ab.tile_cache.clear();ab.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;this.add_resize_handle()};o(l.prototype,J.prototype,{add_resize_handle:function(){var aa=this;var ad=false;var ac=false;var ab=$("<div class='track-resize'>");$(aa.container_div).hover(function(){ad=true;ab.show()},function(){ad=false;if(!ac){ab.hide()}});ab.hide().bind("dragstart",function(ae,af){ac=true;af.original_height=$(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);$("#track_"+ab+"_maxval").val(aa.prefs.max_value)}aa.vertical_range=aa.prefs.max_value-aa.prefs.min_value;aa.total_frequency=ae.total_frequency;aa.container_div.find(".yaxislabel").remove();var af=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ab+"_minval").text(v(aa.prefs.min_value));var ad=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ab+"_maxval").text(v(aa.prefs.max_value));ad.css({position:"absolute",top:"24px",left:"10px"});ad.prependTo(aa.container_div);af.css({position:"absolute",bottom:"2px",left:"10px"});af.prependTo(aa.container_div)})},draw_tile:function(ak,ae,ab,aj){if(this.vertical_range===undefined){return}var af=ab*M*ae,ad=M*ae,aa=Math.ceil(ad*aj),ah=this.height_px;var ac=this.view.canvas_manager.new_canvas();ac.width=aa,ac.height=ah;var ai=ac.getContext("2d");var ag=new I.LinePainter(ak.data,af,af+ad,this.prefs,this.mode);ag.draw(ai,aa,ah);return new b(ad,ae,ac)}});var e=function(aa,af,ae,ai,ah,ac,ad,ag){var ab=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];this.track_config=new V({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ah,onchange:function(){ab.tile_cache.clear();ab.draw()}});this.prefs=this.track_config.values;k.call(this,aa,af,af.viewport_container);J.call(this,ac,ad,ag);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=ae;this.dataset_id=ai;this.original_dataset_id=ai;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_cache=new N(20,this);this.left_offset=200;this.painter=I.LinkedFeaturePainter};o(e.prototype,J.prototype,{update_auto_mode:function(aa){if(this.mode=="Auto"){if(aa=="no_detail"){aa="feature spans"}else{if(aa=="summary_tree"){aa="coverage histogram"}}this.mode_div.text("Auto ("+aa+")")}},incremental_slots:function(ae,ab,ad){var ac=this.view.canvas_manager.dummy_context,aa=this.inc_slots[ae];if(!aa||(aa.mode!==ad)){aa=new (q.FeatureSlotter)(ae,ad==="Pack",x,function(af){return ac.measureText(af)});aa.mode=ad;this.inc_slots[ae]=aa}return aa.slot_features(ab)},get_summary_tree_data:function(ae,ah,ac,ap){if(ap>ac-ah){ap=ac-ah}var al=Math.floor((ac-ah)/ap),ao=[],ad=0;var af=0,ag=0,ak,an=0,ai=[],am,aj;var ab=function(at,ar,au,aq){at[0]=ar+au*aq;at[1]=ar+(au+1)*aq};while(an<ap&&af!==ae.length){var aa=false;for(;an<ap&&!aa;an++){ab(ai,ah,an,al);for(ag=af;ag<ae.length;ag++){ak=ae[ag].slice(1,3);if(is_overlap(ak,ai)){aa=true;break}}if(aa){break}}data_start_index=ag;ao[ao.length]=am=[ai[0],0];for(;ag<ae.length;ag++){ak=ae[ag].slice(1,3);if(is_overlap(ak,ai)){am[1]++}else{break}}if(am[1]>ad){ad=am[1]}an++}return{max:ad,delta:al,data:ao}},draw_tile:function(an,aw,aA,aj,ad){var at=this,aC=aA*M*aw,ab=(aA+1)*M*aw,ap=ab-aC,au=Math.ceil(ap*aj),ar=this.mode,aG=25,ae=this.left_offset,ao,af;if(ar==="Auto"){if(an.dataset_type==="summary_tree"){ar=an.dataset_type}else{if(an.extra_info==="no_detail"){ar="no_detail"}else{var aF=an.data;if(this.view.high-this.view.low>F){ar="Squish"}else{ar="Pack"}}}this.update_auto_mode(ar)}if(ar==="summary_tree"||ar==="Histogram"){af=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var aa=$("<div />").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;ax<az;ax++){var ag=an.data[ax];var ay=false;var am;for(var aB=0,aE=al.length;aB<aE;aB++){am=al[aB];am.update_attrs(ag);if(!am.keep(ag)){ay=true;break}}if(!ay){ai.push(ag)}}}var aD=new (this.painter)(ai,aC,ab,this.prefs,ar,ad);var af=aD.get_required_height(ah)+A;var ac=this.view.canvas_manager.new_canvas();ac.width=au+ae;ac.height=af;var av=ac.getContext("2d");av.fillStyle=this.prefs.block_color;av.font=av.canvas.manager.default_font;av.textAlign="right";this.container_div.find(".yaxislabel").remove();if(an.message){$(ac).css({"border-top":"1px solid red"});av.fillStyle="red";av.textAlign="left";var aq=av.textBaseline;av.textBaseline="top";av.fillText(an.message,ae,0);av.textBaseline=aq;if(!an.data){return new b(aA,aw,ac,af)}}this.example_feature=(an.data.length?an.data[0]:undefined);av.translate(ae,A);aD.draw(av,au,af,ao);return new L(aA,aw,ac)}});var P=function(ad,ab,af,aa,ac,ae){e.call(this,ad,ab,af,aa,ac,ae);this.track_type="VcfTrack";this.painter=I.VariantPainter};o(P.prototype,J.prototype,e.prototype);var S=function(ad,ab,af,aa,ac,ae){e.call(this,ad,ab,af,aa,ac,ae);this.track_config=new V({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ac,onchange:function(){this.track.tile_cache.clear();this.track.draw()}});this.prefs=this.track_config.values;this.track_type="ReadTrack";this.painter=I.ReadPainter;this.make_name_popup_menu()};o(S.prototype,J.prototype,e.prototype);var Q=function(ae,ac,ag,aa,ad,af,ab){e.call(this,ae,ac,ag,aa,ad,af,{},ab);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};o(Q.prototype,J.prototype,e.prototype,{predraw_init:function(){var ab=this;var aa=function(){if(ab.data_cache.size()===0){setTimeout(aa,300)}else{ab.data_url=default_data_url;ab.data_query_wait=H;ab.dataset_state_url=converted_datasets_state_url;$.getJSON(ab.dataset_state_url,{dataset_id:ab.dataset_id,hda_ldda:ab.hda_ldda},function(ac){})}};aa()}});T.View=Y;T.LineTrack=l;T.FeatureTrack=e;T.ReadTrack=S};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=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;x<D;x++,z+=I,F+=G){if(x%2!==0){continue}H.fillRect(z,F,C,1)}};var p=function(A,z,x,D){var C=z-D/2,B=z+D/2,E=x-Math.sqrt(D*3/2);A.beginPath();A.moveTo(C,E);A.lineTo(B,E);A.lineTo(z,x);A.lineTo(C,E);A.strokeStyle=this.fillStyle;A.fill();A.stroke();A.closePath()};var m=function(z,B,x,y,A){this.data=z;this.view_start=B;this.view_end=x;this.prefs=t({},this.default_prefs,y);this.mode=A};m.prototype.default_prefs={};var u=function(z,B,x,y,A){m.call(this,z,B,x,y,A)};u.prototype.default_prefs={show_counts:false};u.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle="black";M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle="#666";M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var c=function(z,B,x,y,A){m.call(this,z,B,x,y,A)};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(O,N,L){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,K=D-H,z=L,A=this.view_start,M=this.view_end-this.view_start,B=N/M,I=this.mode,S=this.data;O.save();var T=Math.round(L+H/K*L);if(I!=="Intensity"){O.fillStyle="#aaa";O.fillRect(0,T,N,1)}O.beginPath();O.fillStyle=this.prefs.color;var R,E,C;if(S.length>1){C=Math.ceil((S[1][0]-S[0][0])*B)}else{C=10}for(var P=0,Q=S.length;P<Q;P++){R=Math.round((S[P][0]-A)*B);E=S[P][1];if(E===null){if(F&&I==="Filled"){O.lineTo(R,z)}F=false;continue}if(E<H){E=H}else{if(E>D){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<Q;P++){E=S[P][1];R=Math.round((S[P][0]-A)*B);if(J>=0&&(E===null||E<D)){O.fillRect(J,0,G+C-J,2);J=-1}else{if(x>=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&&E<H&&x<0){x=R}}G=R}O.restore()};var n=function(z,B,x,y,A){m.call(this,z,B,x,y,A)};n.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};t(n.prototype,{get_required_height:function(y){var x=y_scale=this.get_row_height(),z=this.mode;if(z==="no_detail"||z==="Squish"||z==="Pack"){x=y*y_scale}return x+Math.max(Math.round(y_scale/2),5)},draw:function(J,A,I,F){var D=this.data,G=this.view_start,K=this.view_end;J.save();J.fillStyle=this.prefs.block_color;J.textAlign="right";var N=this.view_end-this.view_start,M=A/N,z=this.get_row_height();for(var C=0,E=D.length;C<E;C++){var L=D[C],B=L[0],x=L[1],y=L[2],H=(F&&F[B]!==undefined?F[B]:null);if((x<K&&y>G)&&(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 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c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file --- a/static/scripts/trackster.js Thu Apr 14 16:51:40 2011 -0400 +++ b/static/scripts/trackster.js Thu Apr 14 20:25:54 2011 -0400 @@ -155,6 +155,7 @@ } }); }; +exports.sortable = sortable; /** * Calculates step for slider with a given min, max. --- a/templates/library/common/browse_library.mako Thu Apr 14 16:51:40 2011 -0400 +++ b/templates/library/common/browse_library.mako Thu Apr 14 20:25:54 2011 -0400 @@ -48,14 +48,14 @@ <%def name="javascripts()"> ${parent.javascripts()} - ${h.js("json2", "jstorage")} + ${h.js("jstorage")} ${common_javascripts()} ${self.grid_javascripts()} </%def><%def name="grid_javascripts()"><script type="text/javascript"> - $(function() { + var init_libraries = function() { var storage_id = "library-expand-state-${trans.security.encode_id(library.id)}"; var restore_folder_state = function() { @@ -151,6 +151,9 @@ }); restore_folder_state(); + }; + $(function() { + init_libraries(); }); // Looks for changes in dataset state using an async request. Keeps --- a/templates/tracks/browser.mako Thu Apr 14 16:51:40 2011 -0400 +++ b/templates/tracks/browser.mako Thu Apr 14 20:25:54 2011 -0400 @@ -12,7 +12,7 @@ <%def name="stylesheets()"> ${parent.stylesheets()} - ${h.css( "history", "autocomplete_tagging", "trackster", "overcast/jquery-ui-1.8.5.custom" )} + ${h.css( "history", "autocomplete_tagging", "trackster", "overcast/jquery-ui-1.8.5.custom", "library" )} <style type="text/css"> #browser-container { @@ -55,7 +55,7 @@ <script type='text/javascript' src="${h.url_for('/static/scripts/excanvas.js')}"></script><![endif]--> -${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jquery.event.drag", "jquery.mousewheel", "jquery.autocomplete", "trackster", "jquery.ui.sortable.slider", "jquery.scrollTo", "farbtastic" )} +${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.event.drag", "jquery.mousewheel", "jquery.autocomplete", "trackster", "jquery.ui.sortable.slider", "jquery.scrollTo", "farbtastic" )} <script type="text/javascript"> @@ -148,7 +148,7 @@ track_data.name, view, track_data.hda_ldda, track_data.dataset_id, track_data.prefs, track_data.filters, track_data.tool ); view.add_track(new_track); - ## Should replace with live event but can't get working + // Should replace with live event but can't get working sortable( new_track.container_div, ".draghandle" ); view.has_changes = true; $("#no-tracks").hide(); @@ -172,9 +172,8 @@ error: function() { alert( "Grid failed" ); }, success: function(table_html) { show_modal( - "Add Track — Select history/library, then datasets", - table_html, - { + "Select datasets for new tracks", + table_html, { "Cancel": function() { hide_modal(); }, --- a/templates/tracks/history_datasets_select_grid.mako Thu Apr 14 16:51:40 2011 -0400 +++ b/templates/tracks/history_datasets_select_grid.mako Thu Apr 14 20:25:54 2011 -0400 @@ -1,15 +1,5 @@ <%inherit file="/tracks/history_select_grid.mako"/><%def name="title()"> - ## - ## Provide link to go back to histories grid. - ## - <% - url_dict = dict( action="list_histories" ) - for filter, value in grid.cur_filter_dict.iteritems(): - url_dict[ "f-" + filter ] = value - %> - ## Use class 'label' to piggyback on URL functionality in parent template. - <a class="label" href="${h.url_for( **url_dict )}">Back to histories</a><h2>History '${grid.get_current_item( trans, **kwargs ).name}'</h2></%def> \ No newline at end of file --- a/templates/tracks/history_select_grid.mako Thu Apr 14 16:51:40 2011 -0400 +++ b/templates/tracks/history_select_grid.mako Thu Apr 14 20:25:54 2011 -0400 @@ -5,41 +5,78 @@ ## <%namespace file="../grid_base.mako" import="*" /> +${stylesheets()} +${grid_javascripts()} + +<%def name="select_header()"> + <script type="text/javascript"> + // Handle all label clicks. + var f = function() { + $(".addtracktab, #grid-table-body a").click(function() { + var parent_body = $(".divider").parent(); + if (parent_body.length !== 0) { + parent_body.load($(this).attr("href")); + f(); + return false; + } + }); + }; + // Need to process label URLs when document loaded and when grid changes. + $(document).ready(function() { + f(); + // $('#grid-table-body').bind('update', f); + }); + </script> + <style> + .addtracktab { + margin: 0px 5px; + padding: 5px; + display: block; + width: 35%; + text-align: center; + float: left; + background-color: #ccc; + border-bottom: 0px; + -webkit-border-top-left-radius: 10px; + -webkit-border-top-right-radius: 10px; + -moz-border-radius-topleft: 10px; + -moz-border-radius-topright: 10px; + border-top-left-radius: 10px; + border-top-right-radius: 10px; + } + .activetab { + border: 1px solid #aaa; + border-bottom: 0px; + background-color: white; + margin-bottom: -2px; + } + .divider { + clear: both; + border-top: 1px solid #aaa; + margin-bottom: 5px; + } + + </style> + + <% histories_active = data_libraries_active = "" %> + %if getattr(grid, "datasets_param", None): + %if grid.datasets_param == "f-history": + <% histories_active = " activetab" %> + %else: + <% data_libraries_active = " activetab" %> + %endif + %endif + <a class="addtracktab${histories_active}" href="${h.url_for( action='list_histories' )}">Histories</a> + <a class="addtracktab${data_libraries_active}" href="${h.url_for( action='list_libraries' )}">Data Libraries</a> + <div class="divider"></div> +</%def> + +${select_header()} ## Need to define title so that it can be overridden by child templates. <%def name="title()"></%def> ${self.title()} -${stylesheets()} -${grid_javascripts()} -## -## Load grid label and page links within a modal window. -## -<script type="text/javascript"> - // Handle all label clicks. - var f = function() { - $("a.label,.page-link>a").click(function() { - var parent_body = $(this).parents("div.body"); - if (parent_body.length !== 0) { - parent_body.load($(this).attr("href")); - return false; - } - }); - }; - // Need to process label URLs when document loaded and when grid changes. - $(document).ready(function() { - f(); - $('#grid-table-body').bind('update', f); - }); -</script> - -%if getattr(grid, "datasets_param", None): - %if grid.datasets_param == "f-history": - <a class="label" href="${h.url_for( action='list_libraries' )}">Show Data Libraries</a> - %else: - <a class="label" href="${h.url_for( action='list_histories' )}">Show Histories</a> - %endif - <br /><br /> -%endif ${render_grid_header( grid, False )} -${render_grid_table( grid, show_item_checkboxes=show_item_checkboxes )} \ No newline at end of file +${render_grid_table( grid, show_item_checkboxes=show_item_checkboxes )} + Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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1 0

commit/galaxy-central: 7 new changesets
by Bitbucket 14 Apr '11

14 Apr '11

7 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/4730f4406ee7/ changeset: r5392:4730f4406ee7 user: james_taylor date: 2011-04-12 02:55:39 summary: trackster: pull out a class module for the ubiquitous extend method, this should be augmented with a more complete inheritence framework affected #: 1 file (338 bytes) --- a/static/scripts/trackster.js Fri Apr 08 16:43:45 2011 -0400 +++ b/static/scripts/trackster.js Mon Apr 11 20:55:39 2011 -0400 @@ -2,6 +2,10 @@ 2010-2011: James Taylor, Kanwei Li, Jeremy Goecks */ +var class_module = function(require, exports) { + +// Module is a placeholder for a more complete inheritence approach + /** Simple extend function for inheritence */ var extend = function() { var target = arguments[0]; @@ -14,12 +18,20 @@ return target; }; +exports.extend = extend; + +// end class_module encapsulation +}; + + // Encapsulate -- anything to be availabe outside this block is added to exports -var trackster_module = function(require, exports){ +var trackster_module = function(require, exports) { -var slotting = require('slotting'), +var extend = require('class').extend, + slotting = require('slotting'), painters = require('painters'); + // ---- Canvas management and extensions ---- /** @@ -2076,7 +2088,6 @@ this.hda_ldda = hda_ldda; this.dataset_id = dataset_id; this.original_dataset_id = dataset_id; - this.zo_slots = {}; this.show_labels_scale = 0.001; this.showing_details = false; this.summary_draw_height = 30; @@ -2361,6 +2372,8 @@ // Encapsulation var slotting_module = function(require, exports) { + +var extend = require('class').extend; // HACK: LABEL_SPACING is currently duplicated between here and painters var LABEL_SPACING = 2, @@ -2526,6 +2539,8 @@ // ---- Painters ---- var painters_module = function(require, exports){ + +var extend = require('class').extend; /** * Draw a dashed line on a canvas using filled rectangles. This function is based on: @@ -3420,6 +3435,7 @@ modules[key] = exports; }; // Run all modules + run_module( 'class', class_module ); run_module( 'slotting', slotting_module ); run_module( 'painters', painters_module ); run_module( 'trackster', trackster_module ); http://bitbucket.org/galaxy/galaxy-central/changeset/f6050dc1bb64/ changeset: r5393:f6050dc1bb64 user: james_taylor date: 2011-04-12 02:55:51 summary: Automated merge with https://bitbucket.org/galaxy/galaxy-central affected #: 1 file (338 bytes) --- a/static/scripts/trackster.js Mon Apr 11 14:17:35 2011 -0400 +++ b/static/scripts/trackster.js Mon Apr 11 20:55:51 2011 -0400 @@ -2,6 +2,10 @@ 2010-2011: James Taylor, Kanwei Li, Jeremy Goecks */ +var class_module = function(require, exports) { + +// Module is a placeholder for a more complete inheritence approach + /** Simple extend function for inheritence */ var extend = function() { var target = arguments[0]; @@ -14,12 +18,20 @@ return target; }; +exports.extend = extend; + +// end class_module encapsulation +}; + + // Encapsulate -- anything to be availabe outside this block is added to exports -var trackster_module = function(require, exports){ +var trackster_module = function(require, exports) { -var slotting = require('slotting'), +var extend = require('class').extend, + slotting = require('slotting'), painters = require('painters'); + // ---- Canvas management and extensions ---- /** @@ -2093,7 +2105,6 @@ this.hda_ldda = hda_ldda; this.dataset_id = dataset_id; this.original_dataset_id = dataset_id; - this.zo_slots = {}; this.show_labels_scale = 0.001; this.showing_details = false; this.summary_draw_height = 30; @@ -2379,6 +2390,8 @@ // Encapsulation var slotting_module = function(require, exports) { + +var extend = require('class').extend; // HACK: LABEL_SPACING is currently duplicated between here and painters var LABEL_SPACING = 2, @@ -2544,6 +2557,8 @@ // ---- Painters ---- var painters_module = function(require, exports){ + +var extend = require('class').extend; /** * Draw a dashed line on a canvas using filled rectangles. This function is based on: @@ -3438,6 +3453,7 @@ modules[key] = exports; }; // Run all modules + run_module( 'class', class_module ); run_module( 'slotting', slotting_module ); run_module( 'painters', painters_module ); run_module( 'trackster', trackster_module ); http://bitbucket.org/galaxy/galaxy-central/changeset/ffbec3713bc0/ changeset: r5394:ffbec3713bc0 user: james_taylor date: 2011-04-14 20:07:22 summary: Automated merge with https://bitbucket.org/galaxy/galaxy-central affected #: 1 file (0 bytes) http://bitbucket.org/galaxy/galaxy-central/changeset/e8f720f2e0f8/ changeset: r5395:e8f720f2e0f8 user: james_taylor date: 2011-04-14 20:32:37 summary: merging affected #: 1 file (334 bytes) --- a/static/scripts/trackster.js Thu Apr 14 14:07:22 2011 -0400 +++ b/static/scripts/trackster.js Thu Apr 14 14:32:37 2011 -0400 @@ -2,6 +2,10 @@ 2010-2011: James Taylor, Kanwei Li, Jeremy Goecks */ +var class_module = function(require, exports) { + +// Module is a placeholder for a more complete inheritence approach + /** Simple extend function for inheritence */ var extend = function() { var target = arguments[0]; @@ -14,6 +18,12 @@ return target; }; +exports.extend = extend; + +// end class_module encapsulation +}; + + /** * Compute the type of overlap between two regions. They are assumed to be on the same chrom/contig. * The overlap is computed relative to the second region; hence, OVERLAP_START indicates that the first @@ -59,11 +69,13 @@ }; // Encapsulate -- anything to be availabe outside this block is added to exports -var trackster_module = function(require, exports){ +var trackster_module = function(require, exports) { -var slotting = require('slotting'), +var extend = require('class').extend, + slotting = require('slotting'), painters = require('painters'); + // ---- Canvas management and extensions ---- /** @@ -2183,7 +2195,6 @@ this.hda_ldda = hda_ldda; this.dataset_id = dataset_id; this.original_dataset_id = dataset_id; - this.zo_slots = {}; this.show_labels_scale = 0.001; this.showing_details = false; this.summary_draw_height = 30; @@ -2558,6 +2569,8 @@ // Encapsulation var slotting_module = function(require, exports) { + +var extend = require('class').extend; // HACK: LABEL_SPACING is currently duplicated between here and painters var LABEL_SPACING = 2, @@ -2724,6 +2737,8 @@ var painters_module = function(require, exports){ +var extend = require('class').extend; + /** * Draw a dashed line on a canvas using filled rectangles. This function is based on: * http://vetruvet.blogspot.com/2010/10/drawing-dashed-lines-on-html5-canvas.h… @@ -3573,6 +3588,7 @@ modules[key] = exports; }; // Run all modules + run_module( 'class', class_module ); run_module( 'slotting', slotting_module ); run_module( 'painters', painters_module ); run_module( 'trackster', trackster_module ); http://bitbucket.org/galaxy/galaxy-central/changeset/45298d68ad5b/ changeset: r5396:45298d68ad5b user: james_taylor date: 2011-04-14 20:32:44 summary: Automated merge with https://bitbucket.org/galaxy/galaxy-central affected #: 1 file (334 bytes) --- a/static/scripts/trackster.js Thu Apr 14 14:29:32 2011 -0400 +++ b/static/scripts/trackster.js Thu Apr 14 14:32:44 2011 -0400 @@ -2,6 +2,10 @@ 2010-2011: James Taylor, Kanwei Li, Jeremy Goecks */ +var class_module = function(require, exports) { + +// Module is a placeholder for a more complete inheritence approach + /** Simple extend function for inheritence */ var extend = function() { var target = arguments[0]; @@ -14,6 +18,12 @@ return target; }; +exports.extend = extend; + +// end class_module encapsulation +}; + + /** * Compute the type of overlap between two regions. They are assumed to be on the same chrom/contig. * The overlap is computed relative to the second region; hence, OVERLAP_START indicates that the first @@ -59,11 +69,13 @@ }; // Encapsulate -- anything to be availabe outside this block is added to exports -var trackster_module = function(require, exports){ +var trackster_module = function(require, exports) { -var slotting = require('slotting'), +var extend = require('class').extend, + slotting = require('slotting'), painters = require('painters'); + // ---- Canvas management and extensions ---- /** @@ -2185,7 +2197,6 @@ this.hda_ldda = hda_ldda; this.dataset_id = dataset_id; this.original_dataset_id = dataset_id; - this.zo_slots = {}; this.show_labels_scale = 0.001; this.showing_details = false; this.summary_draw_height = 30; @@ -2557,6 +2568,8 @@ // Encapsulation var slotting_module = function(require, exports) { + +var extend = require('class').extend; // HACK: LABEL_SPACING is currently duplicated between here and painters var LABEL_SPACING = 2, @@ -2723,6 +2736,8 @@ var painters_module = function(require, exports){ +var extend = require('class').extend; + /** * Draw a dashed line on a canvas using filled rectangles. This function is based on: * http://vetruvet.blogspot.com/2010/10/drawing-dashed-lines-on-html5-canvas.h… @@ -3572,6 +3587,7 @@ modules[key] = exports; }; // Run all modules + run_module( 'class', class_module ); run_module( 'slotting', slotting_module ); run_module( 'painters', painters_module ); run_module( 'trackster', trackster_module ); http://bitbucket.org/galaxy/galaxy-central/changeset/d4ede96517d0/ changeset: r5397:d4ede96517d0 user: james_taylor date: 2011-04-14 22:51:26 summary: trackster: fix problem with drawing bounderies of overflow bars for line tracks affected #: 1 file (5 bytes) --- a/static/scripts/trackster.js Thu Apr 14 14:32:44 2011 -0400 +++ b/static/scripts/trackster.js Thu Apr 14 16:51:26 2011 -0400 @@ -2941,19 +2941,19 @@ var overflow_min_start = -1, overflow_max_start = -1; ctx.fillStyle = this.prefs.overflow_color; + var last_x_scaled; for (var i = 0, len = data.length; i < len; i++) { y = data[i][1]; x_scaled = Math.round((data[i][0] - view_start) * w_scale); - x_minus_scaled = Math.round((data[i][0] - 1 - view_start) * w_scale); // If we are in a min/max run, check if it should be ended if ( overflow_max_start >= 0 && ( y === null || y < max_value ) ) { // Value does not exist or is in valid range, any overflow ends - ctx.fillRect( overflow_max_start, 0, x_minus_scaled - overflow_max_start + 1, 2 ); + ctx.fillRect( overflow_max_start, 0, last_x_scaled + delta_x_px - overflow_max_start, 2 ); overflow_max_start = -1; } else if ( overflow_min_start >= 0 && ( y === null || y > min_value ) ) { // Draw bottom overflow bar - ctx.fillRect( overflow_min_start, height - 2, x_minus_scaled - overflow_min_start + 1, 2 ); + ctx.fillRect( overflow_min_start, height - 2, last_x_scaled + delta_x_px - overflow_min_start, 2 ); overflow_min_start = -1; } @@ -2966,6 +2966,7 @@ // Bottom overflows and we are not already in a run overflow_min_start = x_scaled; } + last_x_scaled = x_scaled; } ctx.restore(); http://bitbucket.org/galaxy/galaxy-central/changeset/c792f5cc9efd/ changeset: r5398:c792f5cc9efd user: james_taylor date: 2011-04-14 22:51:40 summary: Automated merge with https://bitbucket.org/galaxy/galaxy-central affected #: 1 file (329 bytes) --- a/static/scripts/trackster.js Thu Apr 14 16:42:12 2011 -0400 +++ b/static/scripts/trackster.js Thu Apr 14 16:51:40 2011 -0400 @@ -2,6 +2,10 @@ 2010-2011: James Taylor, Kanwei Li, Jeremy Goecks */ +var class_module = function(require, exports) { + +// Module is a placeholder for a more complete inheritence approach + /** Simple extend function for inheritence */ var extend = function() { var target = arguments[0]; @@ -14,6 +18,12 @@ return target; }; +exports.extend = extend; + +// end class_module encapsulation +}; + + /** * Compute the type of overlap between two regions. They are assumed to be on the same chrom/contig. * The overlap is computed relative to the second region; hence, OVERLAP_START indicates that the first @@ -59,11 +69,13 @@ }; // Encapsulate -- anything to be availabe outside this block is added to exports -var trackster_module = function(require, exports){ +var trackster_module = function(require, exports) { -var slotting = require('slotting'), +var extend = require('class').extend, + slotting = require('slotting'), painters = require('painters'); + // ---- Canvas management and extensions ---- /** @@ -2194,7 +2206,6 @@ this.hda_ldda = hda_ldda; this.dataset_id = dataset_id; this.original_dataset_id = dataset_id; - this.zo_slots = {}; this.show_labels_scale = 0.001; this.showing_details = false; this.summary_draw_height = 30; @@ -2566,6 +2577,8 @@ // Encapsulation var slotting_module = function(require, exports) { + +var extend = require('class').extend; // HACK: LABEL_SPACING is currently duplicated between here and painters var LABEL_SPACING = 2, @@ -2732,6 +2745,8 @@ var painters_module = function(require, exports){ +var extend = require('class').extend; + /** * Draw a dashed line on a canvas using filled rectangles. This function is based on: * http://vetruvet.blogspot.com/2010/10/drawing-dashed-lines-on-html5-canvas.h… @@ -2935,19 +2950,19 @@ var overflow_min_start = -1, overflow_max_start = -1; ctx.fillStyle = this.prefs.overflow_color; + var last_x_scaled; for (var i = 0, len = data.length; i < len; i++) { y = data[i][1]; x_scaled = Math.round((data[i][0] - view_start) * w_scale); - x_minus_scaled = Math.round((data[i][0] - 1 - view_start) * w_scale); // If we are in a min/max run, check if it should be ended if ( overflow_max_start >= 0 && ( y === null || y < max_value ) ) { // Value does not exist or is in valid range, any overflow ends - ctx.fillRect( overflow_max_start, 0, x_minus_scaled - overflow_max_start + 1, 2 ); + ctx.fillRect( overflow_max_start, 0, last_x_scaled + delta_x_px - overflow_max_start, 2 ); overflow_max_start = -1; } else if ( overflow_min_start >= 0 && ( y === null || y > min_value ) ) { // Draw bottom overflow bar - ctx.fillRect( overflow_min_start, height - 2, x_minus_scaled - overflow_min_start + 1, 2 ); + ctx.fillRect( overflow_min_start, height - 2, last_x_scaled + delta_x_px - overflow_min_start, 2 ); overflow_min_start = -1; } @@ -2960,6 +2975,7 @@ // Bottom overflows and we are not already in a run overflow_min_start = x_scaled; } + last_x_scaled = x_scaled; } ctx.restore(); @@ -3581,6 +3597,7 @@ modules[key] = exports; }; // Run all modules + run_module( 'class', class_module ); run_module( 'slotting', slotting_module ); run_module( 'painters', painters_module ); run_module( 'trackster', trackster_module ); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Fixes for transferring files from external services using the http protocol. Automatic file transfers from Pac Bio SMRT Portal are functional for version 1.1.0.
by Bitbucket 14 Apr '11

14 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/5affe61170f7/ changeset: r5391:5affe61170f7 user: greg date: 2011-04-14 22:42:12 summary: Fixes for transferring files from external services using the http protocol. Automatic file transfers from Pac Bio SMRT Portal are functional for version 1.1.0. affected #: 8 files (2.5 KB) --- a/external_service_types/pacific_biosciences_smrt_portal.xml Thu Apr 14 14:34:39 2011 -0400 +++ b/external_service_types/pacific_biosciences_smrt_portal.xml Thu Apr 14 16:42:12 2011 -0400 @@ -2,9 +2,6 @@ <description></description><version>1</version><data_transfer_settings> - <data_transfer protocol='http' automatic_transfer='True' /></data_transfer_settings><run_details> --- a/lib/galaxy/jobs/deferred/data_transfer.py Thu Apr 14 14:34:39 2011 -0400 +++ b/lib/galaxy/jobs/deferred/data_transfer.py Thu Apr 14 16:42:12 2011 -0400 @@ -4,8 +4,6 @@ import logging, urllib2, re, shutil from galaxy import eggs -from galaxy.util import json -from string import Template from sqlalchemy import and_ from galaxy.util.odict import odict @@ -19,6 +17,8 @@ log = logging.getLogger( __name__ ) +__all__ = [ 'DataTransfer' ] + class DataTransfer( object ): check_interval = 15 dataset_name_re = re.compile( '(dataset\d+)_(name)' ) @@ -36,7 +36,10 @@ if job.params[ 'protocol' ] in [ 'http', 'https' ]: results = [] for result in job.params[ 'results' ].values(): - result[ 'transfer_job' ] = self.app.transfer_manager.new( protocol=job.params[ 'protocol' ], url=result[ 'url' ] ) + result[ 'transfer_job' ] = self.app.transfer_manager.new( protocol=job.params[ 'protocol' ], + name=result[ 'name' ], + datatype=result[ 'datatype' ], + url=result[ 'url' ] ) results.append( result ) elif job.params[ 'protocol' ] == 'scp': results = [] @@ -83,9 +86,9 @@ # Update the state of the relevant SampleDataset new_status = self.app.model.SampleDataset.transfer_status.ADD_TO_LIBRARY if protocol in [ 'http', 'https' ]: - result_dict = job.params[ 'results' ] - library_dataset_name = job.params[ 'result' ][ 'name' ] - extension = job.params[ 'result' ][ 'datatype' ] + result_dict = job.params[ 'result' ] + library_dataset_name = result_dict[ 'name' ] + extension = result_dict[ 'datatype' ] elif protocol in [ 'scp' ]: # In this case, job.params will be a dictionary that contains a key named 'result'. The value # of the result key is a dictionary that looks something like: --- a/lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py Thu Apr 14 14:34:39 2011 -0400 +++ b/lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py Thu Apr 14 16:42:12 2011 -0400 @@ -3,6 +3,9 @@ produced by SMRT Portal. """ import logging, urllib2, re, shutil +from string import Template +from galaxy.util import json + from data_transfer import * log = logging.getLogger( __name__ ) @@ -18,9 +21,16 @@ sample = kwd[ 'sample' ] smrt_job_id = kwd[ 'secondary_analysis_job_id' ] external_service = sample.request.type.get_external_service( 'pacific_biosciences_smrt_portal' ) + external_service.load_data_transfer_settings( trans ) + http_configs = external_service.data_transfer[ trans.model.ExternalService.data_transfer_protocol.HTTP ] + if not http_configs[ 'automatic_transfer' ]: + raise Exception( "Manual data transfer using http is not yet supported." ) smrt_host = external_service.form_values.content[ 'host' ] - external_service_type_id = external_service.external_service_type_id - external_service_type = self.app.external_service_types.all_external_service_types[ external_service_type_id ] + external_service_type = external_service.get_external_service_type( trans ) + # TODO: is there a better way to store the protocol? + # external_service_type.data_transfer looks somethng like + # {'http': <galaxy.sample_tracking.data_transfer.HttpDataTransferFactory object at 0x1064239d0>} + protocol = external_service_type.data_transfer.keys()[0] results = {} for k, v in external_service.form_values.content.items(): match = self.dataset_name_re.match( k ) or self.dataset_datatype_re.match( k ) @@ -42,6 +52,7 @@ self.sa_session.add(sample) self.sa_session.flush() params = { 'type' : 'init_transfer', + 'protocol' : protocol, 'sample_id' : sample.id, 'results' : results, 'smrt_host' : smrt_host, @@ -50,6 +61,7 @@ self._associate_untransferred_datasets_with_sample( sample, external_service, results ) elif 'transfer_job_id' in kwd: params = { 'type' : 'finish_transfer', + 'protocol' : kwd[ 'result' ][ 'protocol' ], 'sample_id' : kwd[ 'sample_id' ], 'result' : kwd[ 'result' ], 'transfer_job_id' : kwd[ 'transfer_job_id' ] } --- a/lib/galaxy/jobs/transfer_manager.py Thu Apr 14 14:34:39 2011 -0400 +++ b/lib/galaxy/jobs/transfer_manager.py Thu Apr 14 16:42:12 2011 -0400 @@ -30,14 +30,13 @@ if protocol in [ 'http', 'https' ]: if 'url' not in kwd: raise Exception( 'Missing required parameter "url".' ) - transfer_job = self.app.model.TransferJob( state=self.app.model.TransferJob.states.NEW, params=kwd ) elif protocol == 'scp': # TODO: add more checks here? if 'sample_dataset_id' not in kwd: raise Exception( 'Missing required parameter "sample_dataset_id".' ) if 'file_path' not in kwd: raise Exception( 'Missing required parameter "file_path".' ) - transfer_job = self.app.model.TransferJob( state=self.app.model.TransferJob.states.NEW, params=kwd ) + transfer_job = self.app.model.TransferJob( state=self.app.model.TransferJob.states.NEW, params=kwd ) self.sa_session.add( transfer_job ) self.sa_session.flush() return transfer_job --- a/lib/galaxy/model/__init__.py Thu Apr 14 14:34:39 2011 -0400 +++ b/lib/galaxy/model/__init__.py Thu Apr 14 16:42:12 2011 -0400 @@ -1825,6 +1825,11 @@ scp_configs[ 'data_location' ] = self.form_values.content.get( data_transfer_obj.config.get( 'data_location', '' ), '' ) scp_configs[ 'rename_dataset' ] = self.form_values.content.get( data_transfer_obj.config.get( 'rename_dataset', '' ), '' ) self.data_transfer[ self.data_transfer_protocol.SCP ] = scp_configs + if data_transfer_protocol == self.data_transfer_protocol.HTTP: + http_configs = {} + automatic_transfer = data_transfer_obj.config.get( 'automatic_transfer', 'false' ) + http_configs[ 'automatic_transfer' ] = util.string_as_bool( automatic_transfer ) + self.data_transfer[ self.data_transfer_protocol.HTTP ] = http_configs def populate_actions( self, trans, item, param_dict=None ): return self.get_external_service_type( trans ).actions.populate( self, item, param_dict=param_dict ) --- a/lib/galaxy/sample_tracking/data_transfer.py Thu Apr 14 14:34:39 2011 -0400 +++ b/lib/galaxy/sample_tracking/data_transfer.py Thu Apr 14 16:42:12 2011 -0400 @@ -27,12 +27,23 @@ # Validate for name, value in self.config.items(): assert value, "'%s' attribute missing in 'data_transfer' element of type 'scp' in external_service_type xml config file: '%s'." % ( name, config_file ) - + +class HttpDataTransferFactory( DataTransferFactory ): + type = 'http' + def __init__( self ): + pass + def parse( self, config_file, elem ): + self.config = {} + self.config[ 'automatic_transfer' ] = elem.get( 'automatic_transfer' ) + # Validate + for name, value in self.config.items(): + assert value, "'%s' attribute missing in 'data_transfer' element of type 'http' in external_service_type xml config file: '%s'." % ( name, config_file ) + class FtpDataTransferFactory( DataTransferFactory ): type = 'ftp' def __init__( self ): pass def parse( self, elem ): pass - -data_transfer_factories = dict( [ ( data_transfer.type, data_transfer() ) for data_transfer in [ ScpDataTransferFactory, FtpDataTransferFactory ] ] ) + +data_transfer_factories = dict( [ ( data_transfer.type, data_transfer() ) for data_transfer in [ ScpDataTransferFactory, HttpDataTransferFactory, FtpDataTransferFactory ] ] ) --- a/lib/galaxy/sample_tracking/external_service_types.py Thu Apr 14 14:34:39 2011 -0400 +++ b/lib/galaxy/sample_tracking/external_service_types.py Thu Apr 14 16:42:12 2011 -0400 @@ -84,12 +84,16 @@ def parse_data_transfer_settings( self, root ): self.data_transfer = {} data_transfer_settings_elem = root.find( 'data_transfer_settings' ) - # Currently only data transfer using scp is supported. + # Currently only data transfer using scp or http is supported. for data_transfer_elem in data_transfer_settings_elem.findall( "data_transfer" ): if data_transfer_elem.get( 'protocol' ) == model.ExternalService.data_transfer_protocol.SCP: scp_data_transfer = data_transfer_factories[ model.ExternalService.data_transfer_protocol.SCP ] scp_data_transfer.parse( self.config_file, data_transfer_elem ) self.data_transfer[ model.ExternalService.data_transfer_protocol.SCP ] = scp_data_transfer + if data_transfer_elem.get( 'protocol' ) == model.ExternalService.data_transfer_protocol.HTTP: + http_data_transfer = data_transfer_factories[ model.ExternalService.data_transfer_protocol.HTTP ] + http_data_transfer.parse( self.config_file, data_transfer_elem ) + self.data_transfer[ model.ExternalService.data_transfer_protocol.HTTP ] = http_data_transfer def parse_run_details( self, root ): self.run_details = {} run_details_elem = root.find( 'run_details' ) --- a/lib/galaxy/web/controllers/requests_admin.py Thu Apr 14 14:34:39 2011 -0400 +++ b/lib/galaxy/web/controllers/requests_admin.py Thu Apr 14 16:42:12 2011 -0400 @@ -671,7 +671,7 @@ if not scp_configs[ 'automatic_transfer' ]: deferred_plugin = 'ManualDataTransferPlugin' else: - raise Exception( "Automatic data transfer using scp is not yet suppored." ) + raise Exception( "Automatic data transfer using scp is not yet supported." ) trans.app.job_manager.deferred_job_queue.plugins[ deferred_plugin ].create_job( trans, sample=sample, sample_datasets=sample_datasets, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Create and use ReferenceTrackDataManager to fetch ReferenceTrack data.
by Bitbucket 14 Apr '11

14 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/b20ed3ccbba2/ changeset: r5390:b20ed3ccbba2 user: jgoecks date: 2011-04-14 20:34:39 summary: Create and use ReferenceTrackDataManager to fetch ReferenceTrack data. affected #: 1 file (383 bytes) --- a/static/scripts/trackster.js Thu Apr 14 14:29:32 2011 -0400 +++ b/static/scripts/trackster.js Thu Apr 14 14:34:39 2011 -0400 @@ -244,11 +244,6 @@ * Load data from server; returns AJAX object so that use of Deferred is possible. */ load_data: function(chrom, low, high, mode, resolution, extra_params) { - if (this.track.track_type == "ReferenceTrack" && resolution > 1) { - // Now that data is pre-fetched before draw, we don't load reference tracks - // unless it's at the bottom level - return; - } // Setup data request params. var params = {"chrom": chrom, "low": low, "high": high, "mode": mode, "resolution": resolution, "dataset_id" : this.track.dataset_id, @@ -346,6 +341,20 @@ } }); +var ReferenceTrackDataManager = function(num_elements, track, subset) { + DataManager.call(this, num_elements, track, subset); +}; +extend(ReferenceTrackDataManager.prototype, DataManager.prototype, Cache.prototype, { + load_data: function(chrom, low, high, mode, resolution, extra_params) { + if (resolution > 1) { + // Now that data is pre-fetched before draw, we don't load reference tracks + // unless it's at the bottom level + return; + } + return DataManager.prototype.load_data.call(this, chrom, low, high, mode, resolution, extra_params); + } +}); + /** * View object manages complete viz view, including tracks and user interactions. */ @@ -1979,7 +1988,7 @@ this.content_div.css("border", "none"); this.data_url = reference_url; this.data_url_extra_params = {dbkey: view.dbkey}; - this.data_cache = new DataManager(CACHED_DATA, this, false); + this.data_cache = new ReferenceTrackDataManager(CACHED_DATA, this, false); this.tile_cache = new Cache(CACHED_TILES_LINE); }; extend(ReferenceTrack.prototype, TiledTrack.prototype, { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Trackster: (a) fix bug in acee660871cd that prevented line tracks from displaying properly and (b) set track height in show_tile rather than draw_tile, which obviates the need for parent_element to be passed to draw_tile.
by Bitbucket 14 Apr '11

14 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/49e97cc2ac1f/ changeset: r5389:49e97cc2ac1f user: jgoecks date: 2011-04-14 20:29:32 summary: Trackster: (a) fix bug in acee660871cd that prevented line tracks from displaying properly and (b) set track height in show_tile rather than draw_tile, which obviates the need for parent_element to be passed to draw_tile. affected #: 2 files (1.8 KB) --- a/static/scripts/packed/trackster.js Thu Apr 14 10:37:42 2011 -0400 +++ b/static/scripts/packed/trackster.js Thu Apr 14 14:29:32 2011 -0400 @@ -1,1 +1,1 @@ -var extend=function(){var c=arguments[0];for(var b=1;b<arguments.length;b++){var a=arguments[b];for(key in a){c[key]=a[key]}}return c};var trackster_module=function(f,P){var o=f("slotting"),F=f("painters");var V=function(W,X){this.document=W;this.default_font=X!==undefined?X:"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")};extend(V.prototype,{load_pattern:function(W,aa){var X=this.patterns,Y=this.dummy_context,Z=new Image();Z.src=image_path+aa;Z.onload=function(){X[W]=Y.createPattern(Z,"repeat")}},get_pattern:function(W){return this.patterns[W]},new_canvas:function(){var W=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(W)}W.manager=this;return W}});var A=function(W,X){W.bind("drag",{handle:X,relative:true},function(ab,ac){var aa=$(this).parent();var Z=aa.children();var Y;for(Y=0;Y<Z.length;Y++){if(ac.offsetY<$(Z.get(Y)).position().top){break}}if(Y===Z.length){if(this!==Z.get(Y-1)){aa.append(this)}}else{if(this!==Z.get(Y)){$(this).insertBefore(Z.get(Y))}}})};var h=function(Y,W){var X=W-Y;return(X<=2?0.01:(X<=100?1:(X<=1000?5:10)))};var B=9,y=10,K=B+2,v=100,C=12000,I=200,r=10,E=5000,s=100,m="There was an error in indexing this dataset. ",D="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",z="No data for this chrom/contig.",p="Currently indexing... please wait",u="Tool cannot be rerun: ",a="Loading data...",Q="Ready for display",d=10,q=5,x=5;function t(W){return Math.round(W*1000)/1000}var c=function(W){this.num_elements=W;this.clear()};extend(c.prototype,{get:function(X){var W=this.key_ary.indexOf(X);if(W!==-1){this.move_key_to_end(X,W)}return this.obj_cache[X]},set:function(X,Y){if(!this.obj_cache[X]){if(this.key_ary.length>=this.num_elements){var W=this.key_ary.shift();delete this.obj_cache[W]}this.key_ary.push(X)}this.obj_cache[X]=Y;return Y},move_key_to_end:function(X,W){this.key_ary.splice(W,1);this.key_ary.push(X)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var J=function(X,W,Y){c.call(this,X);this.track=W;this.subset=(Y!==undefined?Y:true)};extend(J.prototype,c.prototype,{load_data:function(ae,af,aa,ad,X,ac){var Z={chrom:ae,low:af,high:aa,mode:ad,resolution:X,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(Z,ac);if(this.track.filters_manager){var ag=[];var W=this.track.filters_manager.filters;for(var ab=0;ab<W.length;ab++){ag[ag.length]=W[ab].name}Z.filter_cols=JSON.stringify(ag)}var Y=this;return $.getJSON(this.track.data_url,Z,function(ah){Y.set_data(af,aa,ad,ah)})},get_data:function(Y,W,ab,ac,X,aa){var Z=this.get(this.gen_key(W,ab,ac));if(Z){return Z}Z=this.load_data(Y,W,ab,ac,X,aa);this.set_data(W,ab,ac,Z);return Z},set_data:function(X,Y,Z,W){return this.set(this.gen_key(X,Y,Z),W)},gen_key:function(W,Y,Z){var X=W+"_"+Y+"_"+Z;return X},split_key:function(W){return W.split("_")}});var U=function(W,Z,Y,X,aa){this.container=W;this.chrom=null;this.vis_id=Y;this.dbkey=X;this.title=Z;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(aa);this.canvas_manager=new V(W.get(0).ownerDocument);this.reset()};extend(U.prototype,{init:function(Z){var Y=this.container,W=this;this.top_container=$("<div/>").addClass("top-container").appendTo(Y);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(Y);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(Y);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var X=function(aa){if(aa.type==="focusout"||(aa.keyCode||aa.which)===13||(aa.keyCode||aa.which)===27){if((aa.keyCode||aa.which)!==27){W.go_to($(this).val())}$(this).hide();$(this).val("");W.location_span.show();W.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",X).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.bind("click",function(){W.location_span.hide();W.chrom_select.hide();W.nav_input.val(W.chrom+":"+W.low+"-"+W.high);W.nav_input.css("display","inline-block");W.nav_input.select();W.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){W.zoom_out();W.redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){W.zoom_in();W.redraw()}).appendTo(this.nav_controls);this.load_chroms({low:0},Z);this.chrom_select.bind("change",function(){W.change_chrom(W.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(aa){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(aa){W.zoom_in(aa.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(aa,ab){this.current_x=ab.offsetX}).bind("drag",function(aa,ac){var ad=ac.offsetX-this.current_x;this.current_x=ac.offsetX;var ab=Math.round(ad/W.viewport_container.width()*(W.max_high-W.max_low));W.move_delta(-ab)});this.overview_close.bind("click",function(){for(var ab=0,aa=W.tracks.length;ab<aa;ab++){W.tracks[ab].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",W.overview_box.height());W.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(aa,ab){if(aa.clientX>W.viewport_container.width()-16){return false}}).bind("dragstart",function(aa,ab){ab.original_low=W.low;ab.current_height=aa.clientY;ab.current_x=ab.offsetX}).bind("drag",function(ac,ae){var aa=$(this);var af=ae.offsetX-ae.current_x;var ab=aa.scrollTop()-(ac.clientY-ae.current_height);aa.scrollTop(ab);ae.current_height=ac.clientY;ae.current_x=ae.offsetX;var ad=Math.round(af/W.viewport_container.width()*(W.high-W.low));W.move_delta(ad)}).bind("mousewheel",function(ac,ae,ab,aa){if(ab){var ad=Math.round(-ab/W.viewport_container.width()*(W.high-W.low));W.move_delta(ad)}});this.top_labeltrack.bind("dragstart",function(aa,ab){return $("<div />").css({height:W.content_div.height()+W.top_labeltrack.height()+W.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ae,af){$(af.proxy).css({left:Math.min(ae.pageX,af.startX),width:Math.abs(ae.pageX-af.startX)});var ab=Math.min(ae.pageX,af.startX)-W.container.offset().left,aa=Math.max(ae.pageX,af.startX)-W.container.offset().left,ad=(W.high-W.low),ac=W.viewport_container.width();W.update_location(Math.round(ab/ac*ad)+W.low,Math.round(aa/ac*ad)+W.low)}).bind("dragend",function(af,ag){var ab=Math.min(af.pageX,ag.startX),aa=Math.max(af.pageX,ag.startX),ad=(W.high-W.low),ac=W.viewport_container.width(),ae=W.low;W.low=Math.round(ab/ac*ad)+ae;W.high=Math.round(aa/ac*ad)+ae;$(ag.proxy).remove();W.redraw()});this.add_label_track(new T(this,this.top_labeltrack));this.add_label_track(new T(this,this.nav_labeltrack));$(window).bind("resize",function(){W.resize_window()});$(document).bind("redraw",function(){W.redraw()});this.reset();$(window).trigger("resize")},update_location:function(W,X){this.location_span.text(commatize(W)+" - "+commatize(X));this.nav_input.val(this.chrom+":"+commatize(W)+"-"+commatize(X))},load_chroms:function(X,Y){X.num=s;$.extend(X,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var W=this;$.ajax({url:chrom_url,data:X,dataType:"json",success:function(aa){if(aa.chrom_info.length===0){alert("Invalid chromosome: "+X.chrom);return}if(aa.reference){W.add_label_track(new w(W))}W.chrom_data=aa.chrom_info;var ad='<option value="">Select Chrom/Contig</option>';for(var ac=0,Z=W.chrom_data.length;ac<Z;ac++){var ab=W.chrom_data[ac].chrom;ad+='<option value="'+ab+'">'+ab+"</option>"}if(aa.prev_chroms){ad+='<option value="previous">Previous '+s+"</option>"}if(aa.next_chroms){ad+='<option value="next">Next '+s+"</option>"}W.chrom_select.html(ad);if(Y){Y()}W.chrom_start_index=aa.start_index},error:function(){alert("Could not load chroms for this dbkey:",W.dbkey)}})},change_chrom:function(aa,X,ac){if(!aa||aa==="None"){return}var Z=this;if(aa==="previous"){Z.load_chroms({low:this.chrom_start_index-s});return}if(aa==="next"){Z.load_chroms({low:this.chrom_start_index+s});return}var ab=$.grep(Z.chrom_data,function(ae,af){return ae.chrom===aa})[0];if(ab===undefined){Z.load_chroms({chrom:aa},function(){Z.change_chrom(aa,X,ac)});return}else{if(aa!==Z.chrom){Z.chrom=aa;if(!Z.chrom){Z.intro_div.show()}else{Z.intro_div.hide()}Z.chrom_select.val(Z.chrom);Z.max_high=ab.len-1;Z.reset();Z.redraw(true);for(var ad=0,W=Z.tracks.length;ad<W;ad++){var Y=Z.tracks[ad];if(Y.init){Y.init()}}}if(X!==undefined&&ac!==undefined){Z.low=Math.max(X,0);Z.high=Math.min(ac,Z.max_high)}Z.reset_overview();Z.redraw()}},go_to:function(aa){var ae=this,W,Z,X=aa.split(":"),ac=X[0],ad=X[1];if(ad!==undefined){try{var ab=ad.split("-");W=parseInt(ab[0].replace(/,/g,""),10);Z=parseInt(ab[1].replace(/,/g,""),10)}catch(Y){return false}}ae.change_chrom(ac,W,Z)},move_fraction:function(Y){var W=this;var X=W.high-W.low;this.move_delta(Y*X)},move_delta:function(Y){var W=this;var X=W.high-W.low;if(W.low-Y<W.max_low){W.low=W.max_low;W.high=W.max_low+X}else{if(W.high-Y>W.max_high){W.high=W.max_high;W.low=W.max_high-X}else{W.high-=Y;W.low-=Y}}W.redraw()},add_track:function(W){W.view=this;W.track_id=this.track_id_counter;this.tracks.push(W);if(W.init){W.init()}W.container_div.attr("id","track_"+W.track_id);A(W.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(W){W.view=this;this.label_tracks.push(W)},remove_track:function(W){this.has_changes=true;W.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(W)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(ad){var ac=this.high-this.low,ab=this.low,X=this.high;if(ab<this.max_low){ab=this.max_low}if(X>this.max_high){X=this.max_high}if(this.high!==0&&ac<this.min_separation){X=ab+this.min_separation}this.low=Math.floor(ab);this.high=Math.ceil(X);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(r,Math.max(0,Math.ceil(Math.log(this.resolution,r)/Math.log(r))));var W=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var aa=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=13;this.overview_box.css({left:W,width:Math.max(ae,aa)}).show();if(aa<ae){this.overview_box.css("left",W-(ae-aa)/2)}if(this.overview_highlight){this.overview_highlight.css({left:W,width:aa})}this.update_location(this.low,this.high);if(!ad){for(var Y=0,Z=this.tracks.length;Y<Z;Y++){if(this.tracks[Y]&&this.tracks[Y].enabled){this.tracks[Y].draw()}}for(Y=0,Z=this.label_tracks.length;Y<Z;Y++){this.label_tracks[Y].draw()}}},zoom_in:function(X,Y){if(this.max_high===0||this.high-this.low<this.min_separation){return}var Z=this.high-this.low,aa=Z/2+this.low,W=(Z/this.zoom_factor)/2;if(X){aa=X/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(aa-W);this.high=Math.round(aa+W);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var X=this.high-this.low,Y=X/2+this.low,W=(X*this.zoom_factor)/2;this.low=Math.round(Y-W);this.high=Math.round(Y+W);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var n=function(X,aa){this.track=X;this.name=aa.name;this.params=[];var ai=aa.params;for(var Y=0;Y<ai.length;Y++){var ad=ai[Y],W=ad.name,ah=ad.label,Z=unescape(ad.html),af=ad.type;if(af==="number"){this.params[this.params.length]=new g(W,ah,Z,ad.min,ad.max)}else{if(af=="select"){this.params[this.params.length]=new H(W,ah,Z)}else{console.log("WARNING: unrecognized tool parameter type:",W,af)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ak){ak.stopPropagation()}).bind("click",function(ak){ak.stopPropagation()}).bind("dblclick",function(ak){ak.stopPropagation()});var ag=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ae=this.params;var ab=this;$.each(this.params,function(al,ao){var an=$("<div>").addClass("param-row").appendTo(ab.parent_div);var ak=$("<div>").addClass("param-label").text(ao.label).appendTo(an);var am=$("<div/>").addClass("slider").html(ao.html).appendTo(an);$("<div style='clear: both;'/>").appendTo(an)});this.parent_div.find("input").click(function(){$(this).select()});var aj=$("<div>").addClass("slider-row").appendTo(this.parent_div);var ac=$("<input type='submit'>").attr("value","Run").appendTo(aj);var ab=this;ac.click(function(){ab.run()})};extend(n.prototype,{get_param_values_dict:function(){var W={};this.parent_div.find(":input").each(function(){var X=$(this).attr("name"),Y=$(this).val();W[X]=JSON.stringify(Y)});return W},get_param_values:function(){var X=[];var W={};this.parent_div.find(":input").each(function(){var Y=$(this).attr("name"),Z=$(this).val();if(Y){X[X.length]=Z}});return X},run:function(){var X={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name};$.extend(X,this.get_param_values_dict());var Z=this.track,Y=X.tool_id+Z.tool_region_and_parameters_str(X.chrom,X.low,X.high),aa;if(Z.track_type==="FeatureTrack"){aa=new M(Y,view,Z.hda_ldda,undefined,{},{},Z)}this.track.add_track(aa);aa.content_div.text("Starting job.");var W=function(){$.getJSON(run_tool_url,X,function(ab){if(ab==="no converter"){aa.container_div.addClass("error");aa.content_div.text(D)}else{if(ab.error){aa.container_div.addClass("error");aa.content_div.text(u+ab.message)}else{if(ab==="pending"){aa.container_div.addClass("pending");aa.content_div.text("Converting input data so that it can be easily reused.");setTimeout(W,2000)}else{aa.dataset_id=ab.dataset_id;aa.content_div.text("Running job.");aa.init()}}}})};W()}});var H=function(X,W,Y){this.name=X;this.label=W;this.html=Y};var g=function(Y,X,aa,Z,W){H.call(this,Y,X,aa);this.min=Z;this.max=W};var j=function(X,W,Y){this.name=X;this.index=W;this.value=Y};var N=function(X,W){this.name=X;this.index=W;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};extend(N.prototype,{applies_to:function(W){if(W.length>this.index){return true}return false},keep:function(W){if(!this.applies_to(W)){return true}return(W[this.index]>=this.low&&W[this.index]<=this.high)},update_attrs:function(X){var W=false;if(!this.applies_to(X)){return W}if(X[this.index]<this.min){this.min=Math.floor(X[this.index]);W=true}if(X[this.index]>this.max){this.max=Math.ceil(X[this.index]);W=true}return W},update_ui_elt:function(){var X=this.slider.slider("option","min"),W=this.slider.slider("option","max");if(this.min<X||this.max>W){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",h(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var S=function(Y,ae){this.track=Y;this.filters=[];for(var aa=0;aa<ae.length;aa++){var W=ae[aa];var X=W.name,ad=W.type,ab=W.index;if(ad==="int"||ad==="float"){this.filters[aa]=new N(X,ab)}else{this.filters[aa]=new j(X,ab,ad)}}var ac=function(af,ag,ah){af.click(function(){var ai=ag.text();max=parseFloat(ah.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(ah.slider("option","values")){input_size=2*input_size+1;multi_value=true}ag.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",ai).appendTo(ag).focus().select().click(function(aj){aj.stopPropagation()}).blur(function(){$(this).remove();ag.text(ai)}).keyup(function(an){if(an.keyCode===27){$(this).trigger("blur")}else{if(an.keyCode===13){var al=ah.slider("option","min"),aj=ah.slider("option","max"),am=function(ao){return(isNaN(ao)||ao>aj||ao<al)},ak=$(this).val();if(!multi_value){ak=parseFloat(ak);if(am(ak)){alert("Parameter value must be in the range ["+al+"-"+aj+"]");return $(this)}}else{ak=ak.split("-");ak=[parseFloat(ak[0]),parseFloat(ak[1])];if(am(ak[0])||am(ak[1])){alert("Parameter value must be in the range ["+al+"-"+aj+"]");return $(this)}}ah.slider((multi_value?"values":"value"),ak)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(af){af.stopPropagation()}).bind("click",function(af){af.stopPropagation()}).bind("dblclick",function(af){af.stopPropagation()});var Z=this;$.each(this.filters,function(al,ag){var ai=$("<div/>").addClass("slider-row").appendTo(Z.parent_div);var af=$("<div/>").addClass("slider-label").appendTo(ai);var an=$("<span/>").addClass("slider-name").text(ag.name+" ").appendTo(af);var ah=$("<span/>");var aj=$("<span/>").addClass("slider-value").appendTo(af).append("[").append(ah).append("]");var am=$("<div/>").addClass("slider").appendTo(ai);ag.control_element=$("<div/>").attr("id",ag.name+"-filter-control").appendTo(am);var ak=[0,0];ag.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(ao,ap){ak=ap.values;ah.text(ap.values[0]+"-"+ap.values[1]);setTimeout(function(){if(ap.values[0]==ak[0]&&ap.values[1]==ak[1]){var aq=ap.values;ah.text(aq[0]+"-"+aq[1]);ag.low=aq[0];ag.high=aq[1];Z.track.draw(true,true)}},50)},change:function(ao,ap){ag.control_element.slider("option","slide").call(ag.control_element,ao,ap)}});ag.slider=ag.control_element;ag.slider_label=ah;ac(aj,ah,ag.control_element);$("<div style='clear: both;'/>").appendTo(ai)})};var R=function(W){this.track=W.track;this.params=W.params;this.values={};if(W.saved_values){this.restore_values(W.saved_values)}this.onchange=W.onchange};extend(R.prototype,{restore_values:function(W){var X=this;$.each(this.params,function(Y,Z){if(W[Z.key]!==undefined){X.values[Z.key]=W[Z.key]}else{X.values[Z.key]=Z.default_value}})},build_form:function(){var X=this;var W=$("<div />");$.each(this.params,function(ab,Z){if(!Z.hidden){var Y="param_"+ab;var ag=$("<div class='form-row' />").appendTo(W);ag.append($("<label />").attr("for",Y).text(Z.label+":"));if(Z.type==="bool"){ag.append($('<input type="checkbox" />').attr("id",Y).attr("name",Y).attr("checked",X.values[Z.key]))}else{if(Z.type==="color"){var ad=X.values[Z.key];var ac=$("<input />").attr("id",Y).attr("name",Y).val(ad);var ae=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var aa=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ae);var af=$("<div/>").appendTo(aa).farbtastic({width:100,height:100,callback:ac,color:ad});$("<div />").append(ac).append(ae).appendTo(ag).bind("click",function(ah){ae.css({left:$(this).position().left+($(ac).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ae.hide();$(document).unbind("click.color-picker")});ah.stopPropagation()})}else{ag.append($("<input />").attr("id",Y).attr("name",Y).val(X.values[Z.key]))}}}});return W},update_from_form:function(W){var Y=this;var X=false;$.each(this.params,function(Z,ab){if(!ab.hidden){var ac="param_"+Z;var aa=W.find("#"+ac).val();if(ab.type==="float"){aa=parseFloat(aa)}else{if(ab.type==="int"){aa=parseInt(aa)}else{if(ab.type==="bool"){aa=W.find("#"+ac).is(":checked")}}}if(aa!==Y.values[ab.key]){Y.values[ab.key]=aa;X=true}}});if(X){this.onchange()}}});var b=function(W,X){this.track=W;this.canvas=X};var k=function(X,W,aa,Y,Z){this.name=X;this.view=W;this.parent_element=aa;this.data_url=(Y?Y:default_data_url);this.data_url_extra_params={};this.data_query_wait=(Z?Z:E);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};extend(k.prototype,{init:function(){var W=this;W.enabled=false;W.tile_cache.clear();W.data_cache.clear();W.initial_canvas=undefined;W.content_div.css("height","auto");W.container_div.removeClass("nodata error pending");if(!W.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:W.hda_ldda,dataset_id:W.dataset_id,chrom:W.view.chrom},function(X){if(!X||X==="error"||X.kind==="error"){W.container_div.addClass("error");W.content_div.text(m);if(X.message){var Z=W.view.tracks.indexOf(W);var Y=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+X.message+"</pre>",{Close:hide_modal})});W.content_div.append(Y)}}else{if(X==="no converter"){W.container_div.addClass("error");W.content_div.text(D)}else{if(X==="no data"||(X.data!==undefined&&(X.data===null||X.data.length===0))){W.container_div.addClass("nodata");W.content_div.text(z)}else{if(X==="pending"){W.container_div.addClass("pending");W.content_div.text(p);setTimeout(function(){W.init()},W.data_query_wait)}else{if(X.status==="data"){if(X.valid_chroms){W.valid_chroms=X.valid_chroms;W.make_name_popup_menu()}W.content_div.text(Q);if(W.view.chrom){W.content_div.text("");W.content_div.css("height",W.height_px+"px");W.enabled=true;$.when(W.predraw_init()).done(function(){W.container_div.removeClass("nodata error pending");W.draw()})}}}}}}})},predraw_init:function(){},update_name:function(W){this.old_name=this.name;this.name=W;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var G=function(ae,ac,af){var X=this,ag=X.view;this.filters_manager=(ae!==undefined?new S(this,ae):undefined);this.filters_available=false;this.filters_visible=false;this.tool=(ac!==undefined&&obj_length(ac)>0?new n(this,ac):undefined);this.parent_track=af;this.child_tracks=[];if(X.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}X.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();X.container_div.append(X.child_tracks_container);if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(X.display_modes!==undefined){if(X.mode_div===undefined){X.mode_div=$("<div class='right-float menubutton popup' />").appendTo(X.header_div);var Z=(X.track_config&&X.track_config.values.mode?X.track_config.values.mode:X.display_modes[0]);X.mode=Z;X.mode_div.text(Z);var Y=function(ah){X.mode_div.text(ah);X.mode=ah;X.track_config.values.mode=ah;X.tile_cache.clear();X.draw()};var W={};for(var aa=0,ad=X.display_modes.length;aa<ad;aa++){var ab=X.display_modes[aa];W[ab]=function(ah){return function(){Y(ah)}}(ab)}make_popupmenu(X.mode_div,W)}else{X.mode_div.hide()}}this.make_name_popup_menu()};extend(G.prototype,k.prototype,{make_name_popup_menu:function(){var X=this;var W={};W["Edit configuration"]=function(){var ad=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ab=function(){X.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ac=function(ae){if((ae.keyCode||ae.which)===27){ad()}else{if((ae.keyCode||ae.which)===13){ab()}}};$(window).bind("keypress.check_enter_esc",ac);show_modal("Configure Track",X.track_config.build_form(),{Cancel:ad,OK:ab})};if(X.filters_available>0){var aa=(X.filters_div.is(":visible")?"Hide filters":"Show filters");W[aa]=function(){X.filters_visible=(X.filters_div.is(":visible"));X.filters_div.toggle();X.make_name_popup_menu()}}if(X.tool){var aa=(X.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");W[aa]=function(){if(!X.dynamic_tool_div.is(":visible")){X.update_name(X.name+X.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";X.revert_name()}X.dynamic_tool_div.toggle();X.make_name_popup_menu()}}if(X.valid_chroms){W["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+X.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var Y=view;var Z=function(){$("#no-tracks").show()};if(this.parent_track){Y=this.parent_track;Z=function(){}}W.Remove=function(){Y.remove_track(X);if(Y.num_tracks===0){Z()}};make_popupmenu(X.name_div,W)},draw:function(W,Z){var an=this.view.low,ac=this.view.high,ae=ac-an,ag=this.view.container.width(),ab=ag/ae,ah=this.view.resolution,aa=$("<div style='position: relative;'></div>");if(!Z){this.content_div.children().remove()}this.content_div.append(aa);this.max_height=0;var aj=Math.floor(an/ah/I);var Y={};while((aj*I*ah)<ac){var am=ag+"_"+ab+"_"+aj;var ad=this.tile_cache.get(am);var ak=aj*I*this.view.resolution;var X=ak+I*this.view.resolution;if(!W&&ad){this.show_tile(ad,aa,ak,ab)}else{this.delayed_draw(W,am,ak,X,aj,ah,aa,ab,Y)}aj+=1}var af=this;var al=setInterval(function(){if(obj_length(Y)===0){clearInterval(al);if(Z){var aq=af.content_div.children();var ap=false;for(var ar=aq.length-1,ao=0;ar>=ao;ar--){var aw=$(aq[ar]);if(ap){aw.remove()}else{if(aw.children().length!==0){ap=true}}}}if(af.filters_manager){var au=af.filters_manager.filters;for(var av=0;av<au.length;av++){au[av].update_ui_elt()}var at=false;if(af.example_feature){for(var av=0;av<au.length;av++){if(au[av].applies_to(af.example_feature)){at=true;break}}}if(af.filters_available!==at){af.filters_available=at;if(!af.filters_available){af.filters_div.hide()}af.make_name_popup_menu()}}}},50);for(var ai=0;ai<this.child_tracks.length;ai++){this.child_tracks[ai].draw(W,Z)}},delayed_draw:function(X,ae,ac,ag,Y,aa,af,ah,ab){var Z=this;var ad=function(ap,ai,ak,aj,an,ao,al){returned_tile=Z.draw_tile(ai,ak,aj,an,ao,al);var am=$("<div class='track-tile'>").prepend(returned_tile);tile_element=am;Z.tile_cache.set(ae,tile_element);Z.show_tile(tile_element,an,ac,ao);delete ab[ap]};var W=setTimeout(function(){if(ac<=Z.view.high&&ag>=Z.view.low){var ai=(X?undefined:Z.tile_cache.get(ae));if(ai){Z.show_tile(ai,af,ac,ah);delete ab[W]}else{$.when(Z.data_cache.get_data(view.chrom,ac,ag,Z.mode,aa,Z.data_url_extra_params)).then(function(aj){if(view.reference_track&&ah>view.canvas_manager.char_width_px){$.when(view.reference_track.data_cache.get_data(view.chrom,ac,ag,Z.mode,aa,view.reference_track.data_url_extra_params)).then(function(ak){ad(W,aj,aa,Y,af,ah,ak)})}else{ad(W,aj,aa,Y,af,ah)}})}}},50);ab[W]=true},show_tile:function(W,ab,Z,ac){var X=this;var Y=this.view.high-this.view.low,aa=(Z-this.view.low)*ac;if(this.left_offset){aa-=this.left_offset}W.css({position:"absolute",top:0,left:aa,height:""});ab.append(W);X.max_height=Math.max(X.max_height,W.height());X.content_div.css("height",X.max_height+"px");ab.children().css("height",X.max_height+"px")},set_overview:function(){var W=this.view;if(this.initial_canvas&&this.is_overview){W.overview_close.show();W.overview_viewport.append(this.initial_canvas);W.overview_highlight.show().height(this.initial_canvas.height());W.overview_viewport.height(this.initial_canvas.height()+W.overview_box.height())}$(window).trigger("resize")},tool_region_and_parameters_str:function(Y,W,Z){var X=this,aa=(Y!==undefined&&W!==undefined&&Z!==undefined?Y+":"+W+"-"+Z:"all");return" - region=["+aa+"], parameters=["+X.tool.get_param_values().join(", ")+"]"},add_track:function(W){W.track_id=this.track_id+"_"+this.child_tracks.length;W.container_div.attr("id","track_"+W.track_id);this.child_tracks_container.append(W.container_div);A(W.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(W);this.view.has_changes=true},remove_track:function(W){W.container_div.fadeOut("slow",function(){$(this).remove()})}});var T=function(W,X){this.track_type="LabelTrack";this.hidden=true;k.call(this,null,W,X);this.container_div.addClass("label-track")};extend(T.prototype,k.prototype,{draw:function(){var Y=this.view,Z=Y.high-Y.low,ac=Math.floor(Math.pow(10,Math.floor(Math.log(Z)/Math.log(10)))),W=Math.floor(Y.low/ac)*ac,aa=this.view.container.width(),X=$("<div style='position: relative; height: 1.3em;'></div>");while(W<Y.high){var ab=(W-Y.low)/Z*aa;X.append($("<div class='label'>"+commatize(W)+"</div>").css({position:"absolute",left:ab-1}));W+=ac}this.content_div.children(":first").remove();this.content_div.append(X)}});var w=function(W){this.track_type="ReferenceTrack";this.hidden=true;k.call(this,null,W,W.top_labeltrack);G.call(this);W.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:W.dbkey};this.data_cache=new J(x,this,false);this.tile_cache=new c(q)};extend(w.prototype,G.prototype,{draw_tile:function(ag,ab,X,ad,ah){var aa=this,Y=I*ab;if(ah>this.view.canvas_manager.char_width_px){if(ag===null){aa.content_div.css("height","0px");return}var Z=this.view.canvas_manager.new_canvas();var af=Z.getContext("2d");Z.width=Math.ceil(Y*ah+aa.left_offset);Z.height=aa.height_px;af.font=af.canvas.manager.default_font;af.textAlign="center";for(var ac=0,ae=ag.length;ac<ae;ac++){var W=Math.round(ac*ah);af.fillText(ag[ac],W+aa.left_offset,10)}return Z}this.content_div.css("height","0px")}});var l=function(aa,Y,ab,W,Z){var X=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";k.call(this,aa,Y,Y.viewport_container);G.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=ab;this.dataset_id=W;this.original_dataset_id=W;this.data_cache=new J(x,this);this.tile_cache=new c(q);this.track_config=new R({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:Z,onchange:function(){X.vertical_range=X.prefs.max_value-X.prefs.min_value;$("#linetrack_"+X.track_id+"_minval").text(X.prefs.min_value);$("#linetrack_"+X.track_id+"_maxval").text(X.prefs.max_value);X.tile_cache.clear();X.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;this.add_resize_handle()};extend(l.prototype,G.prototype,{add_resize_handle:function(){var W=this;var Z=false;var Y=false;var X=$("<div class='track-resize'>");$(W.container_div).hover(function(){Z=true;X.show()},function(){Z=false;if(!Y){X.hide()}});X.hide().bind("dragstart",function(aa,ab){Y=true;ab.original_height=$(W.content_div).height()}).bind("drag",function(ab,ac){var aa=Math.min(Math.max(ac.original_height+ac.deltaY,W.min_height_px),W.max_height_px);$(W.content_div).css("height",aa);W.height_px=aa;W.draw(true)}).bind("dragend",function(aa,ab){W.tile_cache.clear();Y=false;if(!Z){X.hide()}W.track_config.values.height=W.height_px}).appendTo(W.container_div)},predraw_init:function(){var W=this,X=W.view.tracks.indexOf(W);W.vertical_range=undefined;return $.getJSON(W.data_url,{stats:true,chrom:W.view.chrom,low:null,high:null,hda_ldda:W.hda_ldda,dataset_id:W.dataset_id},function(Y){W.container_div.addClass("line-track");var aa=Y.data;if(isNaN(parseFloat(W.prefs.min_value))||isNaN(parseFloat(W.prefs.max_value))){W.prefs.min_value=aa.min;W.prefs.max_value=aa.max;$("#track_"+X+"_minval").val(W.prefs.min_value);$("#track_"+X+"_maxval").val(W.prefs.max_value)}W.vertical_range=W.prefs.max_value-W.prefs.min_value;W.total_frequency=aa.total_frequency;W.container_div.find(".yaxislabel").remove();var ab=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+X+"_minval").text(t(W.prefs.min_value));var Z=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+X+"_maxval").text(t(W.prefs.max_value));Z.css({position:"absolute",top:"24px",left:"10px"});Z.prependTo(W.container_div);ab.css({position:"absolute",bottom:"2px",left:"10px"});ab.prependTo(W.container_div)})},draw_tile:function(ah,aa,X,ae,ag){if(this.vertical_range===undefined){return}var ab=X*I*aa,Z=I*aa,W=Math.ceil(Z*ag),ad=this.height_px;var Y=this.view.canvas_manager.new_canvas();Y.width=W,Y.height=ad;var af=Y.getContext("2d");var ac=new F.LinePainter(ah.data,ab,ab+Z,this.prefs,this.mode);ac.draw(af,W,ad);return Y}});var e=function(W,ab,aa,ae,ad,Y,Z,ac){var X=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];this.track_config=new R({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ad,onchange:function(){X.tile_cache.clear();X.draw()}});this.prefs=this.track_config.values;k.call(this,W,ab,ab.viewport_container);G.call(this,Y,Z,ac);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=aa;this.dataset_id=ae;this.original_dataset_id=ae;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_cache=new J(20,this);this.left_offset=200;this.painter=F.LinkedFeaturePainter};extend(e.prototype,G.prototype,{update_auto_mode:function(W){if(this.mode=="Auto"){if(W=="no_detail"){W="feature spans"}else{if(W=="summary_tree"){W="coverage histogram"}}this.mode_div.text("Auto ("+W+")")}},incremental_slots:function(aa,X,Z){var Y=this.view.canvas_manager.dummy_context,W=this.inc_slots[aa];if(!W||(W.mode!==Z)){W=new (o.FeatureSlotter)(aa,Z==="Pack",v,function(ab){return Y.measureText(ab)});W.mode=Z;this.inc_slots[aa]=W}return W.slot_features(X)},draw_tile:function(aj,ar,aw,ae,ag,Z){var ao=this,ay=aw*I*ar,X=(aw+1)*I*ar,al=X-ay,ap=Math.ceil(al*ag),an=this.mode,aC=25,aa=this.left_offset,ak,ab;if(an==="Auto"){if(aj.dataset_type==="summary_tree"){an=aj.dataset_type}else{if(aj.extra_info==="no_detail"){an="no_detail"}else{var aB=aj.data;if(this.view.high-this.view.low>C){an="Squish"}else{an="Pack"}}}this.update_auto_mode(an)}if(an==="summary_tree"){ab=this.summary_draw_height;ae.parent().css("height",Math.max(this.height_px,ab)+"px");this.container_div.find(".yaxislabel").remove();var W=$("<div />").addClass("yaxislabel");W.text(aj.max);W.css({position:"absolute",top:"22px",left:"10px"});W.prependTo(this.container_div);var Y=this.view.canvas_manager.new_canvas();Y.width=ap+aa;Y.height=ab+K;var az=new F.SummaryTreePainter(aj,ay,X,this.prefs);var aq=Y.getContext("2d");aq.translate(aa,K);az.draw(aq,ap,ab);return Y}var ak,ad=1;if(an==="no_detail"||an==="Squish"||an==="Pack"){ad=this.incremental_slots(ag,aj.data,an);ak=this.inc_slots[ag].slots}var af=[];if(aj.data){var ah=this.filters_manager.filters;for(var at=0,av=aj.data.length;at<av;at++){var ac=aj.data[at];var au=false;var ai;for(var ax=0,aA=ah.length;ax<aA;ax++){ai=ah[ax];ai.update_attrs(ac);if(!ai.keep(ac)){au=true;break}}if(!au){af.push(ac)}}}var az=new (this.painter)(af,ay,X,this.prefs,an,Z);var ab=az.get_required_height(ad)+y;var Y=this.view.canvas_manager.new_canvas();Y.width=ap+aa;Y.height=ab;ae.parent().css("height",Math.max(this.height_px,ab)+"px");var aq=Y.getContext("2d");aq.fillStyle=this.prefs.block_color;aq.font=aq.canvas.manager.default_font;aq.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aj.message){$(Y).css({"border-top":"1px solid red"});aq.fillStyle="red";aq.textAlign="left";var am=aq.textBaseline;aq.textBaseline="top";aq.fillText(aj.message,aa,0);aq.textBaseline=am;if(!aj.data){return Y}}this.example_feature=(aj.data.length?aj.data[0]:undefined);aq.translate(aa,y);az.draw(aq,ap,ab,ak);return Y}});var L=function(Z,X,ab,W,Y,aa){e.call(this,Z,X,ab,W,Y,aa);this.track_type="VcfTrack";this.painter=F.VariantPainter};extend(L.prototype,G.prototype,e.prototype);var O=function(Z,X,ab,W,Y,aa){e.call(this,Z,X,ab,W,Y,aa);this.track_config=new R({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:Y,onchange:function(){this.track.tile_cache.clear();this.track.draw()}});this.prefs=this.track_config.values;this.track_type="ReadTrack";this.painter=F.ReadPainter;this.make_name_popup_menu()};extend(O.prototype,G.prototype,e.prototype);var M=function(aa,Y,ac,W,Z,ab,X){e.call(this,aa,Y,ac,W,Z,ab,{},X);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};extend(M.prototype,G.prototype,e.prototype,{predraw_init:function(){var X=this;var W=function(){if(X.data_cache.size()===0){setTimeout(W,300)}else{X.data_url=default_data_url;X.data_query_wait=E;X.dataset_state_url=converted_datasets_state_url;$.getJSON(X.dataset_state_url,{dataset_id:X.dataset_id,hda_ldda:X.hda_ldda},function(Y){})}};W()}});P.View=U;P.LineTrack=l;P.FeatureTrack=e;P.ReadTrack=O};var slotting_module=function(c,b){var d=2,a=5;b.FeatureSlotter=function(h,g,e,f){this.slots={};this.start_end_dct={};this.w_scale=h;this.include_label=g;this.max_rows=e;this.measureText=f};extend(b.FeatureSlotter.prototype,{slot_features:function(l){var o=this.w_scale,r=this.slots,g=this.start_end_dct,x=[],z=[],m=0,y=this.max_rows;for(var v=0,w=l.length;v<w;v++){var k=l[v],n=k[0];if(r[n]!==undefined){m=Math.max(m,r[n]);z.push(r[n])}else{x.push(v)}}var p=function(F,G){for(var E=0;E<=y;E++){var C=false,H=g[E];if(H!==undefined){for(var B=0,D=H.length;B<D;B++){var A=H[B];if(G>A[0]&&F<A[1]){C=true;break}}}if(!C){return E}}return -1};for(var v=0,w=x.length;v<w;v++){var k=l[x[v]],n=k[0],t=k[1],e=k[2],q=k[3],f=Math.floor(t*o),j=Math.ceil(e*o),u=this.measureText(q).width,h;if(q!==undefined&&this.include_label){u+=(d+a);if(f-u>=0){f-=u;h="left"}else{j+=u;h="right"}}var s=p(f,j);if(s>=0){if(g[s]===undefined){g[s]=[]}g[s].push([f,j]);r[n]=s;m=Math.max(m,s)}else{}}return m+1}})};var painters_module=function(k,B){var r=function(M,E,K,D,J,H){if(H===undefined){H=4}var G=D-E;var F=J-K;var I=Math.floor(Math.sqrt(G*G+F*F)/H);var N=G/I;var L=F/I;var C;for(C=0;C<I;C++,E+=N,K+=L){if(C%2!==0){continue}M.fillRect(E,K,H,1)}};var s=function(E,D,C,H){var G=D-H/2,F=D+H/2,I=C-Math.sqrt(H*3/2);E.beginPath();E.moveTo(G,I);E.lineTo(F,I);E.lineTo(D,C);E.lineTo(G,I);E.strokeStyle=this.fillStyle;E.fill();E.stroke();E.closePath()};var o=function(E,G,C,D,F){this.data=E;this.view_start=G;this.view_end=C;this.prefs=extend({},this.default_prefs,D);this.mode=F};o.prototype.default_prefs={};var w=function(E,G,C,D,F){o.call(this,E,G,C,D,F)};w.prototype.default_prefis={show_counts:false};w.prototype.draw=function(P,C,O){var H=this.view_start,R=this.view_end-this.view_start,Q=C/R;var M=this.data.data,L=this.data.delta,J=this.data.max,E=O;delta_x_px=Math.ceil(L*Q);P.save();for(var F=0,G=M.length;F<G;F++){var K=Math.floor((M[F][0]-H)*Q);var I=M[F][1];if(!I){continue}var N=I/J*O;P.fillStyle="black";P.fillRect(K,E-N,delta_x_px,N);var D=4;if(this.prefs.show_counts&&(P.measureText(I).width+D)<delta_x_px){P.fillStyle="#666";P.textAlign="center";P.fillText(I,K+(delta_x_px/2),10)}}P.restore()};var c=function(E,G,C,D,F){o.call(this,E,G,C,D,F)};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(R,Q,O){var J=false,K=this.prefs.min_value,H=this.prefs.max_value,N=H-K,D=O,E=this.view_start,P=this.view_end-this.view_start,F=Q/P,L=this.mode,V=this.data;R.save();var W=Math.round(O+K/N*O);if(L!=="Intensity"){R.fillStyle="#aaa";R.fillRect(0,W,Q,1)}R.beginPath();R.fillStyle=this.prefs.color;var U,I,G;if(V.length>1){G=Math.ceil((V[1][0]-V[0][0])*F)}else{G=10}for(var S=0,T=V.length;S<T;S++){U=Math.round((V[S][0]-E)*F);I=V[S][1];if(I===null){if(J&&L==="Filled"){R.lineTo(U,D)}J=false;continue}if(I<K){I=K}else{if(I>H){I=H}}if(L==="Histogram"){I=Math.round(I/N*D);R.fillRect(U,W,G,-I)}else{if(L==="Intensity"){I=255-Math.floor((I-K)/N*255);R.fillStyle="rgb("+I+","+I+","+I+")";R.fillRect(U,0,G,D)}else{I=Math.round(D-(I-K)/N*D);if(J){R.lineTo(U,I)}else{J=true;if(L==="Filled"){R.moveTo(U,D);R.lineTo(U,I)}else{R.moveTo(U,I)}}}}}if(L==="Filled"){if(J){R.lineTo(U,W);R.lineTo(0,W)}R.fill()}else{R.stroke()}var C=-1,M=-1;R.fillStyle=this.prefs.overflow_color;for(var S=0,T=V.length;S<T;S++){I=V[S][1];U=Math.round((V[S][0]-E)*F);x_minus_scaled=Math.round((V[S][0]-1-E)*F);if(M>=0&&(I===null||I<H)){R.fillRect(M,0,x_minus_scaled-M+1,2);M=-1}else{if(C>=0&&(I===null||I>K)){R.fillRect(C,O-2,x_minus_scaled-C+1,2);C=-1}}if(I!==null&&I>H&&M<0){M=U}else{if(I!==null&&I<K&&C<0){C=U}}}R.restore()};var q=function(E,G,C,D,F){o.call(this,E,G,C,D,F)};q.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(q.prototype,{get_required_height:function(D){var C=y_scale=this.get_row_height(),E=this.mode;if(E==="no_detail"||E==="Squish"||E==="Pack"){C=D*y_scale}return C+Math.max(Math.round(y_scale/2),5)},draw:function(O,F,N,K){var I=this.data,L=this.view_start,P=this.view_end;O.save();O.fillStyle=this.prefs.block_color;O.textAlign="right";var S=this.view_end-this.view_start,R=F/S,E=this.get_row_height();for(var H=0,J=I.length;H<J;H++){var Q=I[H],G=Q[0],C=Q[1],D=Q[2],M=(K&&K[G]!==undefined?K[G]:null);if((C<P&&D>L)&&(this.mode=="Dense"||M!==null)){this.draw_element(O,this.mode,Q,M,L,P,R,E,F)}}O.restore()}});var d=10,j=3,n=5,A=10,g=1,u=3,f=3,a=9,p=2,h="#ccc";var t=function(E,G,C,D,F){q.call(this,E,G,C,D,F)};extend(t.prototype,q.prototype,{get_row_height:function(){var D=this.mode,C;if(D==="Dense"){C=d}else{if(D==="no_detail"){C=j}else{if(D==="Squish"){C=n}else{C=A}}}return C},draw_element:function(O,H,W,J,Q,ag,ak,al,C){var T=W[0],ai=W[1],aa=W[2]-1,R=W[3],ab=Math.floor(Math.max(0,(ai-Q)*ak)),P=Math.ceil(Math.min(C,Math.max(0,(aa-Q)*ak))),Z=(H==="Dense"?0:(0+J))*al,N,ae,S=null,am=null,F=this.prefs.block_color,ad=this.prefs.label_color;if(H=="Dense"){J=1}if(H==="no_detail"){O.fillStyle=F;O.fillRect(ab,Z+5,P-ab,g)}else{var M=W[4],Y=W[5],ac=W[6],G=W[7];if(Y&&ac){S=Math.floor(Math.max(0,(Y-Q)*ak));am=Math.ceil(Math.min(C,Math.max(0,(ac-Q)*ak)))}var aj,U;if(H==="Squish"||H==="Dense"){aj=1;U=f}else{aj=5;U=a}if(!G){if(W.strand){if(W.strand==="+"){O.fillStyle=O.canvas.manager.get_pattern("right_strand_inv")}else{if(W.strand==="-"){O.fillStyle=O.canvas.manager.get_pattern("left_strand_inv")}}}else{O.fillStyle=F}O.fillRect(ab,Z,P-ab,U)}else{var L,V;if(H==="Squish"||H==="Dense"){O.fillStyle=h;L=Z+Math.floor(f/2)+1;V=1}else{if(M){var L=Z;var V=U;if(M==="+"){O.fillStyle=O.canvas.manager.get_pattern("right_strand")}else{if(M==="-"){O.fillStyle=O.canvas.manager.get_pattern("left_strand")}}}else{O.fillStyle=h;L+=(f/2)+1;V=1}}O.fillRect(ab,L,P-ab,V);for(var ah=0,E=G.length;ah<E;ah++){var I=G[ah],D=Math.floor(Math.max(0,(I[0]-Q)*ak)),X=Math.ceil(Math.min(C,Math.max((I[1]-1-Q)*ak)));if(D>X){continue}O.fillStyle=F;O.fillRect(D,Z+(U-aj)/2+1,X-D,aj);if(S!==undefined&&ac>Y&&!(D>am||X<S)){var af=Math.max(D,S),K=Math.min(X,am);O.fillRect(af,Z+1,K-af,U);if(G.length==1&&H=="Pack"){if(M==="+"){O.fillStyle=O.canvas.manager.get_pattern("right_strand_inv")}else{if(M==="-"){O.fillStyle=O.canvas.manager.get_pattern("left_strand_inv")}}if(af+14<K){af+=2;K-=2}O.fillRect(af,Z+1,K-af,U)}}}}if(H==="Pack"&&ai>Q){O.fillStyle=ad;if(Q===0&&ab-O.measureText(R).width<0){O.textAlign="left";O.fillText(R,P+p,Z+8)}else{O.textAlign="right";O.fillText(R,ab-p,Z+8)}O.fillStyle=F}}}});var b=function(E,G,C,D,F){q.call(this,E,G,C,D,F)};extend(b.prototype,q.prototype,{draw_element:function(V,Q,K,G,Y,E,N,W,T){var K=data[i],M=K[0],U=K[1],F=K[2]-1,P=K[3],I=Math.floor(Math.max(0,(U-Y)*N)),L=Math.ceil(Math.min(T,Math.max(0,(F-Y)*N))),H=(Q==="Dense"?0:(0+G))*W,C,Z,D=null,O=null;if(no_label){V.fillStyle=block_color;V.fillRect(I+left_offset,H+5,L-I,1)}else{var X=K[4],S=K[5],J=K[6];C=9;Z=1;V.fillRect(I+left_offset,H,L-I,C);if(Q!=="Dense"&&P!==undefined&&U>Y){V.fillStyle=label_color;if(Y===0&&I-V.measureText(P).width<0){V.textAlign="left";V.fillText(P,L+2+left_offset,H+8)}else{V.textAlign="right";V.fillText(P,I-2+left_offset,H+8)}V.fillStyle=block_color}var R=X+" / "+S;if(U>Y&&V.measureText(R).width<(L-I)){V.fillStyle="white";V.textAlign="center";V.fillText(R,left_offset+I+(L-I)/2,H+8);V.fillStyle=block_color}}}});var z=1001,m=1002,e=1003,y=1004,l=1005;var x=function(G,D){var I=G[0],H=G[1],F=D[0],E=D[1],C;if(I<F){if(H<F){C=z}else{if(H<=E){C=e}else{C=m}}}else{if(I>E){C=z}else{if(H<=E){C=l}else{C=y}}}return C};var v=function(F,H,C,E,G,D){q.call(this,F,H,C,E,G);this.ref_seq=D};v.prototype.default_prefs=extend({},q.prototype.default_prefs,{show_insertions:false});extend(v.prototype,q.prototype,{get_row_height:function(){var C,D=this.mode;if(D==="Dense"){C=d}else{if(D==="Squish"){C=n}else{C=A;if(this.prefs.show_insertions){C*=2}}}return C},draw_read:function(Z,U,P,ae,E,Y,M,J,I){Z.textAlign="center";var X=this,D=[ae,E],S=0,aa=0,W=0;ref_seq=this.ref_seq,char_width_px=Z.canvas.manager.char_width_px;var aj=[];if((U==="Pack"||this.mode==="Auto")&&J!==undefined&&P>char_width_px){W=Math.round(P/2)}if(!M){M=[[0,J.length]]}for(var Q=0,ac=M.length;Q<ac;Q++){var N=M[Q],F="MIDNSHP=X"[N[0]],R=N[1];if(F==="H"||F==="S"){S-=R}var K=Y+S,ai=Math.floor(Math.max(0,(K-ae)*P)),L=Math.floor(Math.max(0,(K+R-ae)*P));if(ai===L){L+=1}switch(F){case"H":break;case"S":case"M":case"=":var T=x([K,K+R],D);if(T!==z){var V=J.slice(aa,aa+R);if(W>0){Z.fillStyle=this.prefs.block_color;Z.fillRect(ai-W,I+1,L-ai,9);Z.fillStyle=h;for(var ag=0,C=V.length;ag<C;ag++){if(this.prefs.show_differences&&ref_seq){var O=ref_seq[K-ae+ag];if(!O||O.toLowerCase()===V[ag].toLowerCase()){continue}}if(K+ag>=ae&&K+ag<=E){var ah=Math.floor(Math.max(0,(K+ag-ae)*P));Z.fillText(V[ag],ah,I+9)}}}else{Z.fillStyle=this.prefs.block_color;Z.fillRect(ai,I+4,L-ai,f)}}aa+=R;S+=R;break;case"N":Z.fillStyle=h;Z.fillRect(ai-W,I+5,L-ai,1);S+=R;break;case"D":Z.fillStyle="red";Z.fillRect(ai-W,I+4,L-ai,3);S+=R;break;case"P":break;case"I":var T=x([K,K+R],D),ad=ai-W;if(T!==z){var V=J.slice(aa,aa+R);if(this.prefs.show_insertions){var H=ai-(L-ai)/2;if((U==="Pack"||this.mode==="Auto")&&J!==undefined&&P>char_width_px){Z.fillStyle="yellow";Z.fillRect(H-W,I-9,L-ai,9);aj[aj.length]={type:"triangle",data:[ad,I+4,5]};Z.fillStyle=h;switch(T){case (e):V=V.slice(ae-K);break;case (y):V=V.slice(0,K-E);break;case (l):break;case (m):V=V.slice(ae-K,K-E);break}for(var ag=0,C=V.length;ag<C;ag++){var ah=Math.floor(Math.max(0,(K+ag-ae)*P));Z.fillText(V[ag],ah-(L-ai)/2,I)}}else{Z.fillStyle="yellow";Z.fillRect(H,I+(this.mode!=="Dense"?2:5),L-ai,(U!=="Dense"?f:u))}}else{if((U==="Pack"||this.mode==="Auto")&&J!==undefined&&P>char_width_px){aj[aj.length]={type:"text",data:[V.length,ad,I+9]}}else{}}}aa+=R;break;case"X":aa+=R;break}}Z.fillStyle="yellow";var af,G,ak;for(var ab=0;ab<aj.length;ab++){af=aj[ab];G=af.type;ak=af.data;if(G==="text"){Z.save();Z.font="bold "+Z.font;Z.fillText(ak[0],ak[1],ak[2]);Z.restore()}else{if(G=="triangle"){s(Z,ak[0],ak[1],ak[2])}}}},draw_element:function(V,Q,I,F,Y,D,M,W,T){var L=I[0],U=I[1],E=I[2],N=I[3],H=Math.floor(Math.max(0,(U-Y)*M)),J=Math.ceil(Math.min(T,Math.max(0,(E-Y)*M))),G=(Q==="Dense"?0:(0+F))*W,Z=this.prefs.block_color,K=this.prefs.label_color,S=0;if((Q==="Pack"||this.mode==="Auto")&&M>V.canvas.manager.char_width_px){var S=Math.round(M/2)}V.fillStyle=Z;if(I[5] instanceof Array){var R=Math.floor(Math.max(0,(I[4][0]-Y)*M)),P=Math.ceil(Math.min(T,Math.max(0,(I[4][1]-Y)*M))),O=Math.floor(Math.max(0,(I[5][0]-Y)*M)),C=Math.ceil(Math.min(T,Math.max(0,(I[5][1]-Y)*M)));if(I[4][1]>=Y&&I[4][0]<=D&&I[4][2]){this.draw_read(V,Q,M,Y,D,I[4][0],I[4][2],I[4][3],G)}if(I[5][1]>=Y&&I[5][0]<=D&&I[5][2]){this.draw_read(V,Q,M,Y,D,I[5][0],I[5][2],I[5][3],G)}if(O>P){V.fillStyle=h;r(V,P-S,G+5,O-S,G+5)}}else{V.fillStyle=Z;this.draw_read(V,Q,M,Y,D,U,I[4],I[5],G)}if(Q==="Pack"&&U>Y){V.fillStyle=this.prefs.label_color;var X=1;if(X===0&&H-V.measureText(N).width<0){V.textAlign="left";V.fillText(N,J+p-S,G+8)}else{V.textAlign="right";V.fillText(N,H-p-S,G+8)}V.fillStyle=Z}}});B.SummaryTreePainter=w;B.LinePainter=c;B.LinkedFeaturePainter=t;B.ReadPainter=v;B.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("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 extend=function(){var c=arguments[0];for(var b=1;b<arguments.length;b++){var a=arguments[b];for(key in a){c[key]=a[key]}}return c};var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var trackster_module=function(f,R){var p=f("slotting"),G=f("painters");var X=function(Y,Z){this.document=Y;this.default_font=Z!==undefined?Z:"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")};extend(X.prototype,{load_pattern:function(Y,ac){var Z=this.patterns,aa=this.dummy_context,ab=new Image();ab.src=image_path+ac;ab.onload=function(){Z[Y]=aa.createPattern(ab,"repeat")}},get_pattern:function(Y){return this.patterns[Y]},new_canvas:function(){var Y=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(Y)}Y.manager=this;return Y}});var B=function(Y,Z){Y.bind("drag",{handle:Z,relative:true},function(ad,ae){var ac=$(this).parent();var ab=ac.children();var aa;for(aa=0;aa<ab.length;aa++){if(ae.offsetY<$(ab.get(aa)).position().top){break}}if(aa===ab.length){if(this!==ab.get(aa-1)){ac.append(this)}}else{if(this!==ab.get(aa)){$(this).insertBefore(ab.get(aa))}}})};var h=function(aa,Y){var Z=Y-aa;return(Z<=2?0.01:(Z<=100?1:(Z<=1000?5:10)))};var C=9,z=10,M=C+2,w=100,D=12000,K=200,s=10,F=5000,t=100,n="There was an error in indexing this dataset. ",E="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",A="No data for this chrom/contig.",q="Currently indexing... please wait",v="Tool cannot be rerun: ",a="Loading data...",S="Ready for display",d=10,r=5,y=5;function u(Y){return Math.round(Y*1000)/1000}var c=function(Y){this.num_elements=Y;this.clear()};extend(c.prototype,{get:function(Z){var Y=this.key_ary.indexOf(Z);if(Y!==-1){this.move_key_to_end(Z,Y)}return this.obj_cache[Z]},set:function(Z,aa){if(!this.obj_cache[Z]){if(this.key_ary.length>=this.num_elements){var Y=this.key_ary.shift();delete this.obj_cache[Y]}this.key_ary.push(Z)}this.obj_cache[Z]=aa;return aa},move_key_to_end:function(Z,Y){this.key_ary.splice(Y,1);this.key_ary.push(Z)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var L=function(Z,Y,aa){c.call(this,Z);this.track=Y;this.subset=(aa!==undefined?aa:true)};extend(L.prototype,c.prototype,{load_data:function(ag,ah,ac,af,Z,ae){if(this.track.track_type=="ReferenceTrack"&&Z>1){return}var ab={chrom:ag,low:ah,high:ac,mode:af,resolution:Z,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ab,ae);if(this.track.filters_manager){var ai=[];var Y=this.track.filters_manager.filters;for(var ad=0;ad<Y.length;ad++){ai[ai.length]=Y[ad].name}ab.filter_cols=JSON.stringify(ai)}var aa=this;return $.getJSON(this.track.data_url,ab,function(aj){aa.set_data(ah,ac,af,aj)})},get_data:function(aa,Y,ad,ae,Z,ac){var ab=this.get(this.gen_key(Y,ad,ae));if(ab){return ab}ab=this.load_data(aa,Y,ad,ae,Z,ac);this.set_data(Y,ad,ae,ab);return ab},set_data:function(Z,aa,ab,Y){return this.set(this.gen_key(Z,aa,ab),Y)},gen_key:function(Y,aa,ab){var Z=Y+"_"+aa+"_"+ab;return Z},split_key:function(Y){return Y.split("_")}});var W=function(Y,ab,aa,Z,ac){this.container=Y;this.chrom=null;this.vis_id=aa;this.dbkey=Z;this.title=ab;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(ac);this.canvas_manager=new X(Y.get(0).ownerDocument);this.reset()};extend(W.prototype,{init:function(ab){var aa=this.container,Y=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aa);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aa);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aa);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var Z=function(ac){if(ac.type==="focusout"||(ac.keyCode||ac.which)===13||(ac.keyCode||ac.which)===27){if((ac.keyCode||ac.which)!==27){Y.go_to($(this).val())}$(this).hide();$(this).val("");Y.location_span.show();Y.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",Z).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.bind("click",function(){Y.location_span.hide();Y.chrom_select.hide();Y.nav_input.val(Y.chrom+":"+Y.low+"-"+Y.high);Y.nav_input.css("display","inline-block");Y.nav_input.select();Y.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){Y.zoom_out();Y.redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){Y.zoom_in();Y.redraw()}).appendTo(this.nav_controls);this.load_chroms({low:0},ab);this.chrom_select.bind("change",function(){Y.change_chrom(Y.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(ac){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(ac){Y.zoom_in(ac.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ac,ad){this.current_x=ad.offsetX}).bind("drag",function(ac,ae){var af=ae.offsetX-this.current_x;this.current_x=ae.offsetX;var ad=Math.round(af/Y.viewport_container.width()*(Y.max_high-Y.max_low));Y.move_delta(-ad)});this.overview_close.bind("click",function(){for(var ad=0,ac=Y.tracks.length;ad<ac;ad++){Y.tracks[ad].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",Y.overview_box.height());Y.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(ac,ad){if(ac.clientX>Y.viewport_container.width()-16){return false}}).bind("dragstart",function(ac,ad){ad.original_low=Y.low;ad.current_height=ac.clientY;ad.current_x=ad.offsetX}).bind("drag",function(ae,ag){var ac=$(this);var ah=ag.offsetX-ag.current_x;var ad=ac.scrollTop()-(ae.clientY-ag.current_height);ac.scrollTop(ad);ag.current_height=ae.clientY;ag.current_x=ag.offsetX;var af=Math.round(ah/Y.viewport_container.width()*(Y.high-Y.low));Y.move_delta(af)}).bind("mousewheel",function(ae,ag,ad,ac){if(ad){var af=Math.round(-ad/Y.viewport_container.width()*(Y.high-Y.low));Y.move_delta(af)}});this.top_labeltrack.bind("dragstart",function(ac,ad){return $("<div />").css({height:Y.content_div.height()+Y.top_labeltrack.height()+Y.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ag,ah){$(ah.proxy).css({left:Math.min(ag.pageX,ah.startX),width:Math.abs(ag.pageX-ah.startX)});var ad=Math.min(ag.pageX,ah.startX)-Y.container.offset().left,ac=Math.max(ag.pageX,ah.startX)-Y.container.offset().left,af=(Y.high-Y.low),ae=Y.viewport_container.width();Y.update_location(Math.round(ad/ae*af)+Y.low,Math.round(ac/ae*af)+Y.low)}).bind("dragend",function(ah,ai){var ad=Math.min(ah.pageX,ai.startX),ac=Math.max(ah.pageX,ai.startX),af=(Y.high-Y.low),ae=Y.viewport_container.width(),ag=Y.low;Y.low=Math.round(ad/ae*af)+ag;Y.high=Math.round(ac/ae*af)+ag;$(ai.proxy).remove();Y.redraw()});this.add_label_track(new V(this,this.top_labeltrack));this.add_label_track(new V(this,this.nav_labeltrack));$(window).bind("resize",function(){Y.resize_window()});$(document).bind("redraw",function(){Y.redraw()});this.reset();$(window).trigger("resize")},update_location:function(Y,Z){this.location_span.text(commatize(Y)+" - "+commatize(Z));this.nav_input.val(this.chrom+":"+commatize(Y)+"-"+commatize(Z))},load_chroms:function(Z,aa){Z.num=t;$.extend(Z,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var Y=this;$.ajax({url:chrom_url,data:Z,dataType:"json",success:function(ac){if(ac.chrom_info.length===0){alert("Invalid chromosome: "+Z.chrom);return}if(ac.reference){Y.add_label_track(new x(Y))}Y.chrom_data=ac.chrom_info;var af='<option value="">Select Chrom/Contig</option>';for(var ae=0,ab=Y.chrom_data.length;ae<ab;ae++){var ad=Y.chrom_data[ae].chrom;af+='<option value="'+ad+'">'+ad+"</option>"}if(ac.prev_chroms){af+='<option value="previous">Previous '+t+"</option>"}if(ac.next_chroms){af+='<option value="next">Next '+t+"</option>"}Y.chrom_select.html(af);if(aa){aa()}Y.chrom_start_index=ac.start_index},error:function(){alert("Could not load chroms for this dbkey:",Y.dbkey)}})},change_chrom:function(ac,Z,ae){if(!ac||ac==="None"){return}var ab=this;if(ac==="previous"){ab.load_chroms({low:this.chrom_start_index-t});return}if(ac==="next"){ab.load_chroms({low:this.chrom_start_index+t});return}var ad=$.grep(ab.chrom_data,function(ag,ah){return ag.chrom===ac})[0];if(ad===undefined){ab.load_chroms({chrom:ac},function(){ab.change_chrom(ac,Z,ae)});return}else{if(ac!==ab.chrom){ab.chrom=ac;if(!ab.chrom){ab.intro_div.show()}else{ab.intro_div.hide()}ab.chrom_select.val(ab.chrom);ab.max_high=ad.len-1;ab.reset();ab.redraw(true);for(var af=0,Y=ab.tracks.length;af<Y;af++){var aa=ab.tracks[af];if(aa.init){aa.init()}}}if(Z!==undefined&&ae!==undefined){ab.low=Math.max(Z,0);ab.high=Math.min(ae,ab.max_high)}ab.reset_overview();ab.redraw()}},go_to:function(ac){var ag=this,Y,ab,Z=ac.split(":"),ae=Z[0],af=Z[1];if(af!==undefined){try{var ad=af.split("-");Y=parseInt(ad[0].replace(/,/g,""),10);ab=parseInt(ad[1].replace(/,/g,""),10)}catch(aa){return false}}ag.change_chrom(ae,Y,ab)},move_fraction:function(aa){var Y=this;var Z=Y.high-Y.low;this.move_delta(aa*Z)},move_delta:function(aa){var Y=this;var Z=Y.high-Y.low;if(Y.low-aa<Y.max_low){Y.low=Y.max_low;Y.high=Y.max_low+Z}else{if(Y.high-aa>Y.max_high){Y.high=Y.max_high;Y.low=Y.max_high-Z}else{Y.high-=aa;Y.low-=aa}}Y.redraw()},add_track:function(Y){Y.view=this;Y.track_id=this.track_id_counter;this.tracks.push(Y);if(Y.init){Y.init()}Y.container_div.attr("id","track_"+Y.track_id);B(Y.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(Y){Y.view=this;this.label_tracks.push(Y)},remove_track:function(Y){this.has_changes=true;Y.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(Y)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(af){var ae=this.high-this.low,ad=this.low,Z=this.high;if(ad<this.max_low){ad=this.max_low}if(Z>this.max_high){Z=this.max_high}if(this.high!==0&&ae<this.min_separation){Z=ad+this.min_separation}this.low=Math.floor(ad);this.high=Math.ceil(Z);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/K)/Math.LN10));this.zoom_res=Math.pow(s,Math.max(0,Math.ceil(Math.log(this.resolution,s)/Math.log(s))));var Y=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ac=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ag=13;this.overview_box.css({left:Y,width:Math.max(ag,ac)}).show();if(ac<ag){this.overview_box.css("left",Y-(ag-ac)/2)}if(this.overview_highlight){this.overview_highlight.css({left:Y,width:ac})}this.update_location(this.low,this.high);if(!af){for(var aa=0,ab=this.tracks.length;aa<ab;aa++){if(this.tracks[aa]&&this.tracks[aa].enabled){this.tracks[aa].draw()}}for(aa=0,ab=this.label_tracks.length;aa<ab;aa++){this.label_tracks[aa].draw()}}},zoom_in:function(Z,aa){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ab=this.high-this.low,ac=ab/2+this.low,Y=(ab/this.zoom_factor)/2;if(Z){ac=Z/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ac-Y);this.high=Math.round(ac+Y);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var Z=this.high-this.low,aa=Z/2+this.low,Y=(Z*this.zoom_factor)/2;this.low=Math.round(aa-Y);this.high=Math.round(aa+Y);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var o=function(Z,ac){this.track=Z;this.name=ac.name;this.params=[];var ak=ac.params;for(var aa=0;aa<ak.length;aa++){var af=ak[aa],Y=af.name,aj=af.label,ab=unescape(af.html),ah=af.type;if(ah==="number"){this.params[this.params.length]=new g(Y,aj,ab,af.min,af.max)}else{if(ah=="select"){this.params[this.params.length]=new I(Y,aj,ab)}else{console.log("WARNING: unrecognized tool parameter type:",Y,ah)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(am){am.stopPropagation()}).bind("click",function(am){am.stopPropagation()}).bind("dblclick",function(am){am.stopPropagation()});var ai=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ag=this.params;var ad=this;$.each(this.params,function(an,aq){var ap=$("<div>").addClass("param-row").appendTo(ad.parent_div);var am=$("<div>").addClass("param-label").text(aq.label).appendTo(ap);var ao=$("<div/>").addClass("slider").html(aq.html).appendTo(ap);$("<div style='clear: both;'/>").appendTo(ap)});this.parent_div.find("input").click(function(){$(this).select()});var al=$("<div>").addClass("slider-row").appendTo(this.parent_div);var ae=$("<input type='submit'>").attr("value","Run").appendTo(al);var ad=this;ae.click(function(){ad.run()})};extend(o.prototype,{get_param_values_dict:function(){var Y={};this.parent_div.find(":input").each(function(){var Z=$(this).attr("name"),aa=$(this).val();Y[Z]=JSON.stringify(aa)});return Y},get_param_values:function(){var Z=[];var Y={};this.parent_div.find(":input").each(function(){var aa=$(this).attr("name"),ab=$(this).val();if(aa){Z[Z.length]=ab}});return Z},run:function(){var Z={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name};$.extend(Z,this.get_param_values_dict());var 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 O(aa,view,ab.hda_ldda,undefined,{},{},ab)}this.track.add_track(ac);ac.content_div.text("Starting job.");var Y=function(){$.getJSON(run_tool_url,Z,function(ad){if(ad==="no converter"){ac.container_div.addClass("error");ac.content_div.text(E)}else{if(ad.error){ac.container_div.addClass("error");ac.content_div.text(v+ad.message)}else{if(ad==="pending"){ac.container_div.addClass("pending");ac.content_div.text("Converting input data so that it can be easily reused.");setTimeout(Y,2000)}else{ac.dataset_id=ad.dataset_id;ac.content_div.text("Running job.");ac.init()}}}})};Y()}});var I=function(Z,Y,aa){this.name=Z;this.label=Y;this.html=aa};var g=function(aa,Z,ac,ab,Y){I.call(this,aa,Z,ac);this.min=ab;this.max=Y};var j=function(Z,Y,aa){this.name=Z;this.index=Y;this.value=aa};var P=function(Z,Y){this.name=Z;this.index=Y;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};extend(P.prototype,{applies_to:function(Y){if(Y.length>this.index){return true}return false},keep:function(Y){if(!this.applies_to(Y)){return true}var Z=parseInt(Y[this.index]);return(isNaN(Z)||(Z>=this.low&&Z<=this.high))},update_attrs:function(Z){var Y=false;if(!this.applies_to(Z)){return Y}if(Z[this.index]<this.min){this.min=Math.floor(Z[this.index]);Y=true}if(Z[this.index]>this.max){this.max=Math.ceil(Z[this.index]);Y=true}return Y},update_ui_elt:function(){var Z=this.slider.slider("option","min"),Y=this.slider.slider("option","max");if(this.min<Z||this.max>Y){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",h(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var U=function(aa,ag){this.track=aa;this.filters=[];for(var ac=0;ac<ag.length;ac++){var Y=ag[ac];var Z=Y.name,af=Y.type,ad=Y.index;if(af==="int"||af==="float"){this.filters[ac]=new P(Z,ad)}else{this.filters[ac]=new j(Z,ad,af)}}var ae=function(ah,ai,aj){ah.click(function(){var ak=ai.text();max=parseFloat(aj.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aj.slider("option","values")){input_size=2*input_size+1;multi_value=true}ai.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",ak).appendTo(ai).focus().select().click(function(al){al.stopPropagation()}).blur(function(){$(this).remove();ai.text(ak)}).keyup(function(ap){if(ap.keyCode===27){$(this).trigger("blur")}else{if(ap.keyCode===13){var an=aj.slider("option","min"),al=aj.slider("option","max"),ao=function(aq){return(isNaN(aq)||aq>al||aq<an)},am=$(this).val();if(!multi_value){am=parseFloat(am);if(ao(am)){alert("Parameter value must be in the range ["+an+"-"+al+"]");return $(this)}}else{am=am.split("-");am=[parseFloat(am[0]),parseFloat(am[1])];if(ao(am[0])||ao(am[1])){alert("Parameter value must be in the range ["+an+"-"+al+"]");return $(this)}}aj.slider((multi_value?"values":"value"),am)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(ah){ah.stopPropagation()}).bind("click",function(ah){ah.stopPropagation()}).bind("dblclick",function(ah){ah.stopPropagation()});var ab=this;$.each(this.filters,function(an,ai){var ak=$("<div/>").addClass("slider-row").appendTo(ab.parent_div);var ah=$("<div/>").addClass("slider-label").appendTo(ak);var ap=$("<span/>").addClass("slider-name").text(ai.name+" ").appendTo(ah);var aj=$("<span/>");var al=$("<span/>").addClass("slider-value").appendTo(ah).append("[").append(aj).append("]");var ao=$("<div/>").addClass("slider").appendTo(ak);ai.control_element=$("<div/>").attr("id",ai.name+"-filter-control").appendTo(ao);var am=[0,0];ai.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aq,ar){am=ar.values;aj.text(ar.values[0]+"-"+ar.values[1]);setTimeout(function(){if(ar.values[0]==am[0]&&ar.values[1]==am[1]){var at=ar.values;aj.text(at[0]+"-"+at[1]);ai.low=at[0];ai.high=at[1];ab.track.draw(true,true)}},50)},change:function(aq,ar){ai.control_element.slider("option","slide").call(ai.control_element,aq,ar)}});ai.slider=ai.control_element;ai.slider_label=aj;ae(al,aj,ai.control_element);$("<div style='clear: both;'/>").appendTo(ak)})};var T=function(Y){this.track=Y.track;this.params=Y.params;this.values={};if(Y.saved_values){this.restore_values(Y.saved_values)}this.onchange=Y.onchange};extend(T.prototype,{restore_values:function(Y){var Z=this;$.each(this.params,function(aa,ab){if(Y[ab.key]!==undefined){Z.values[ab.key]=Y[ab.key]}else{Z.values[ab.key]=ab.default_value}})},build_form:function(){var Z=this;var Y=$("<div />");$.each(this.params,function(ad,ab){if(!ab.hidden){var aa="param_"+ad;var ai=$("<div class='form-row' />").appendTo(Y);ai.append($("<label />").attr("for",aa).text(ab.label+":"));if(ab.type==="bool"){ai.append($('<input type="checkbox" />').attr("id",aa).attr("name",aa).attr("checked",Z.values[ab.key]))}else{if(ab.type==="color"){var af=Z.values[ab.key];var ae=$("<input />").attr("id",aa).attr("name",aa).val(af);var ag=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var ac=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ag);var ah=$("<div/>").appendTo(ac).farbtastic({width:100,height:100,callback:ae,color:af});$("<div />").append(ae).append(ag).appendTo(ai).bind("click",function(aj){ag.css({left:$(this).position().left+($(ae).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ag.hide();$(document).unbind("click.color-picker")});aj.stopPropagation()})}else{ai.append($("<input />").attr("id",aa).attr("name",aa).val(Z.values[ab.key]))}}}});return Y},update_from_form:function(Y){var aa=this;var Z=false;$.each(this.params,function(ab,ad){if(!ad.hidden){var ae="param_"+ab;var ac=Y.find("#"+ae).val();if(ad.type==="float"){ac=parseFloat(ac)}else{if(ad.type==="int"){ac=parseInt(ac)}else{if(ad.type==="bool"){ac=Y.find("#"+ae).is(":checked")}}}if(ac!==aa.values[ad.key]){aa.values[ad.key]=ac;Z=true}}});if(Z){this.onchange()}}});var b=function(aa,Z,Y){this.index=aa;this.resolution=Z;this.canvas=$("<div class='track-tile'/>").append(Y)};var m=function(aa,Z,Y,ab){b.call(this,aa,Z,Y);this.max_val=ab};var J=function(aa,Z,Y){b.call(this,aa,Z,Y)};var k=function(Z,Y,ac,aa,ab){this.name=Z;this.view=Y;this.parent_element=ac;this.data_url=(aa?aa:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ab?ab:F);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};extend(k.prototype,{init:function(){var Y=this;Y.enabled=false;Y.tile_cache.clear();Y.data_cache.clear();Y.initial_canvas=undefined;Y.content_div.css("height","auto");Y.container_div.removeClass("nodata error pending");if(!Y.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:Y.hda_ldda,dataset_id:Y.dataset_id,chrom:Y.view.chrom},function(Z){if(!Z||Z==="error"||Z.kind==="error"){Y.container_div.addClass("error");Y.content_div.text(n);if(Z.message){var ab=Y.view.tracks.indexOf(Y);var aa=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+Z.message+"</pre>",{Close:hide_modal})});Y.content_div.append(aa)}}else{if(Z==="no converter"){Y.container_div.addClass("error");Y.content_div.text(E)}else{if(Z==="no data"||(Z.data!==undefined&&(Z.data===null||Z.data.length===0))){Y.container_div.addClass("nodata");Y.content_div.text(A)}else{if(Z==="pending"){Y.container_div.addClass("pending");Y.content_div.text(q);setTimeout(function(){Y.init()},Y.data_query_wait)}else{if(Z.status==="data"){if(Z.valid_chroms){Y.valid_chroms=Z.valid_chroms;Y.make_name_popup_menu()}Y.content_div.text(S);if(Y.view.chrom){Y.content_div.text("");Y.content_div.css("height",Y.height_px+"px");Y.enabled=true;$.when(Y.predraw_init()).done(function(){Y.container_div.removeClass("nodata error pending");Y.draw()})}}}}}}})},predraw_init:function(){},update_name:function(Y){this.old_name=this.name;this.name=Y;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var H=function(ag,ae,ah){var Z=this,ai=Z.view;this.filters_manager=(ag!==undefined?new U(this,ag):undefined);this.filters_available=false;this.filters_visible=false;this.tool=(ae!==undefined&&obj_length(ae)>0?new o(this,ae):undefined);this.parent_track=ah;this.child_tracks=[];if(Z.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}Z.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();Z.container_div.append(Z.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(Z.display_modes!==undefined){if(Z.mode_div===undefined){Z.mode_div=$("<div class='right-float menubutton popup' />").appendTo(Z.header_div);var ab=(Z.track_config&&Z.track_config.values.mode?Z.track_config.values.mode:Z.display_modes[0]);Z.mode=ab;Z.mode_div.text(ab);var aa=function(aj){Z.mode_div.text(aj);Z.mode=aj;Z.track_config.values.mode=aj;Z.tile_cache.clear();Z.draw()};var Y={};for(var ac=0,af=Z.display_modes.length;ac<af;ac++){var ad=Z.display_modes[ac];Y[ad]=function(aj){return function(){aa(aj)}}(ad)}make_popupmenu(Z.mode_div,Y)}else{Z.mode_div.hide()}}this.make_name_popup_menu()};extend(H.prototype,k.prototype,{make_name_popup_menu:function(){var Z=this;var Y={};Y["Edit configuration"]=function(){var af=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ad=function(){Z.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(ag){if((ag.keyCode||ag.which)===27){af()}else{if((ag.keyCode||ag.which)===13){ad()}}};$(window).bind("keypress.check_enter_esc",ae);show_modal("Configure Track",Z.track_config.build_form(),{Cancel:af,OK:ad})};if(Z.filters_available>0){var ac=(Z.filters_div.is(":visible")?"Hide filters":"Show filters");Y[ac]=function(){Z.filters_visible=(Z.filters_div.is(":visible"));Z.filters_div.toggle();Z.make_name_popup_menu()}}if(Z.tool){var ac=(Z.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");Y[ac]=function(){if(!Z.dynamic_tool_div.is(":visible")){Z.update_name(Z.name+Z.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";Z.revert_name()}Z.dynamic_tool_div.toggle();Z.make_name_popup_menu()}}if(Z.valid_chroms){Y["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+Z.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var aa=view;var ab=function(){$("#no-tracks").show()};if(this.parent_track){aa=this.parent_track;ab=function(){}}Y.Remove=function(){aa.remove_track(Z);if(aa.num_tracks===0){ab()}};make_popupmenu(Z.name_div,Y)},draw:function(Y,aa){var ar=this.view.low,ae=this.view.high,ag=ae-ar,ai=this.view.container.width(),ac=ai/ag,aj=this.view.resolution,ab=$("<div style='position: relative;'></div>"),ak=function(au,av,at){return au+"_"+av+"_"+at};if(!aa){this.content_div.children().remove()}this.content_div.append(ab);this.max_height=0;var am=Math.floor(ar/aj/K);var ad=[];var an=0;while((am*K*aj)<ae){var aq=ak(ai,ac,am);var af=this.tile_cache.get(aq);var ao=am*K*this.view.resolution;var Z=ao+K*this.view.resolution;if(!Y&&af){ad[ad.length]=af;this.show_tile(af,ab,ao,ac)}else{this.delayed_draw(Y,aq,am,aj,ab,ac,ad)}am+=1;an++}var ah=this;var ap=setInterval(function(){if(ad.length===an){clearInterval(ap);if(aa){var aw=ah.content_div.children();var ax=false;for(var av=aw.length-1,aB=0;av>=aB;av--){var au=$(aw[av]);if(ax){au.remove()}else{if(au.children().length!==0){ax=true}}}}if(ah.track_type=="FeatureTrack"&&ah.mode=="Histogram"){var aA=-1;for(var av=0;av<ad.length;av++){var aD=ad[av].max_val;if(aD>aA){aA=aD}}for(var av=0;av<ad.length;av++){if(ad[av].max_val!==aA){var aC=ad[av];aC.canvas.remove();ah.delayed_draw(true,ak(ai,ac,aC.index),aC.index,aC.resolution,ab,ac,[],{max:aA})}}}if(ah.filters_manager){var at=ah.filters_manager.filters;for(var az=0;az<at.length;az++){at[az].update_ui_elt()}var ay=false;if(ah.example_feature){for(var az=0;az<at.length;az++){if(at[az].applies_to(ah.example_feature)){ay=true;break}}}if(ah.filters_available!==ay){ah.filters_available=ay;if(!ah.filters_available){ah.filters_div.hide()}ah.make_name_popup_menu()}}}},50);for(var al=0;al<this.child_tracks.length;al++){this.child_tracks[al].draw(Y,aa)}},delayed_draw:function(Z,ag,aa,ac,ah,ak,ai,ad){var ab=this,ae=aa*K*ac,aj=ae+K*ac;var af=function(at,al,an,am,aq,ar,ao){var ap=ab.draw_tile(al,an,am,ar,ao);ab.tile_cache.set(ag,ap);ab.show_tile(ap,aq,ae,ar);ai[ai.length]=ap};var Y=setTimeout(function(){if(ae<=ab.view.high&&aj>=ab.view.low){var al=(Z?undefined:ab.tile_cache.get(ag));if(al){ab.show_tile(al,ah,ae,ak);ai[ai.length]=al}else{$.when(ab.data_cache.get_data(view.chrom,ae,aj,ab.mode,ac,ab.data_url_extra_params)).then(function(am){extend(am,ad);if(view.reference_track&&ak>view.canvas_manager.char_width_px){$.when(view.reference_track.data_cache.get_data(view.chrom,ae,aj,ab.mode,ac,view.reference_track.data_url_extra_params)).then(function(an){af(Y,am,ac,aa,ah,ak,an)})}else{af(Y,am,ac,aa,ah,ak)}})}}},50)},show_tile:function(ab,ae,ac,af){var Z=this;var aa=this.view.high-this.view.low,ad=(ac-this.view.low)*af;if(this.left_offset){ad-=this.left_offset}var Y=ab.canvas;Y.css({position:"absolute",top:0,left:ad,height:""});ae.append(Y);Z.max_height=Math.max(Z.max_height,Y.height());Z.content_div.css("height",Z.max_height+"px");ae.children().css("height",Z.max_height+"px")},set_overview:function(){var Y=this.view;if(this.initial_canvas&&this.is_overview){Y.overview_close.show();Y.overview_viewport.append(this.initial_canvas);Y.overview_highlight.show().height(this.initial_canvas.height());Y.overview_viewport.height(this.initial_canvas.height()+Y.overview_box.height())}$(window).trigger("resize")},tool_region_and_parameters_str:function(aa,Y,ab){var Z=this,ac=(aa!==undefined&&Y!==undefined&&ab!==undefined?aa+":"+Y+"-"+ab:"all");return" - region=["+ac+"], parameters=["+Z.tool.get_param_values().join(", ")+"]"},add_track:function(Y){Y.track_id=this.track_id+"_"+this.child_tracks.length;Y.container_div.attr("id","track_"+Y.track_id);this.child_tracks_container.append(Y.container_div);B(Y.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(Y);this.view.has_changes=true},remove_track:function(Y){Y.container_div.fadeOut("slow",function(){$(this).remove()})}});var V=function(Y,Z){this.track_type="LabelTrack";this.hidden=true;k.call(this,null,Y,Z);this.container_div.addClass("label-track")};extend(V.prototype,k.prototype,{draw:function(){var aa=this.view,ab=aa.high-aa.low,ae=Math.floor(Math.pow(10,Math.floor(Math.log(ab)/Math.log(10)))),Y=Math.floor(aa.low/ae)*ae,ac=this.view.container.width(),Z=$("<div style='position: relative; height: 1.3em;'></div>");while(Y<aa.high){var ad=(Y-aa.low)/ab*ac;Z.append($("<div class='label'>"+commatize(Y)+"</div>").css({position:"absolute",left:ad-1}));Y+=ae}this.content_div.children(":first").remove();this.content_div.append(Z)}});var x=function(Y){this.track_type="ReferenceTrack";this.hidden=true;k.call(this,null,Y,Y.top_labeltrack);H.call(this);Y.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:Y.dbkey};this.data_cache=new L(y,this,false);this.tile_cache=new c(r)};extend(x.prototype,H.prototype,{draw_tile:function(ag,ad,Z,ai){var ac=this,aa=K*ad;if(ai>this.view.canvas_manager.char_width_px){if(ag===null){ac.content_div.css("height","0px");return}var ab=this.view.canvas_manager.new_canvas();var ah=ab.getContext("2d");ab.width=Math.ceil(aa*ai+ac.left_offset);ab.height=ac.height_px;ah.font=ah.canvas.manager.default_font;ah.textAlign="center";for(var ae=0,af=ag.length;ae<af;ae++){var Y=Math.round(ae*ai);ah.fillText(ag[ae],Y+ac.left_offset,10)}return new b(Z,ad,ab)}this.content_div.css("height","0px")}});var l=function(ac,aa,ad,Y,ab){var Z=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";k.call(this,ac,aa,aa.viewport_container);H.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=ad;this.dataset_id=Y;this.original_dataset_id=Y;this.data_cache=new L(y,this);this.tile_cache=new c(r);this.track_config=new T({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:ab,onchange:function(){Z.vertical_range=Z.prefs.max_value-Z.prefs.min_value;$("#linetrack_"+Z.track_id+"_minval").text(Z.prefs.min_value);$("#linetrack_"+Z.track_id+"_maxval").text(Z.prefs.max_value);Z.tile_cache.clear();Z.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;this.add_resize_handle()};extend(l.prototype,H.prototype,{add_resize_handle:function(){var Y=this;var ab=false;var aa=false;var Z=$("<div class='track-resize'>");$(Y.container_div).hover(function(){ab=true;Z.show()},function(){ab=false;if(!aa){Z.hide()}});Z.hide().bind("dragstart",function(ac,ad){aa=true;ad.original_height=$(Y.content_div).height()}).bind("drag",function(ad,ae){var ac=Math.min(Math.max(ae.original_height+ae.deltaY,Y.min_height_px),Y.max_height_px);$(Y.content_div).css("height",ac);Y.height_px=ac;Y.draw(true)}).bind("dragend",function(ac,ad){Y.tile_cache.clear();aa=false;if(!ab){Z.hide()}Y.track_config.values.height=Y.height_px}).appendTo(Y.container_div)},predraw_init:function(){var Y=this,Z=Y.view.tracks.indexOf(Y);Y.vertical_range=undefined;return $.getJSON(Y.data_url,{stats:true,chrom:Y.view.chrom,low:null,high:null,hda_ldda:Y.hda_ldda,dataset_id:Y.dataset_id},function(aa){Y.container_div.addClass("line-track");var ac=aa.data;if(isNaN(parseFloat(Y.prefs.min_value))||isNaN(parseFloat(Y.prefs.max_value))){Y.prefs.min_value=ac.min;Y.prefs.max_value=ac.max;$("#track_"+Z+"_minval").val(Y.prefs.min_value);$("#track_"+Z+"_maxval").val(Y.prefs.max_value)}Y.vertical_range=Y.prefs.max_value-Y.prefs.min_value;Y.total_frequency=ac.total_frequency;Y.container_div.find(".yaxislabel").remove();var ad=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+Z+"_minval").text(u(Y.prefs.min_value));var ab=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+Z+"_maxval").text(u(Y.prefs.max_value));ab.css({position:"absolute",top:"24px",left:"10px"});ab.prependTo(Y.container_div);ad.css({position:"absolute",bottom:"2px",left:"10px"});ad.prependTo(Y.container_div)})},draw_tile:function(ai,ac,Z,ah){if(this.vertical_range===undefined){return}var ad=Z*K*ac,ab=K*ac,Y=Math.ceil(ab*ah),af=this.height_px;var aa=this.view.canvas_manager.new_canvas();aa.width=Y,aa.height=af;var ag=aa.getContext("2d");var ae=new G.LinePainter(ai.data,ad,ad+ab,this.prefs,this.mode);ae.draw(ag,Y,af);return new b(ab,ac,aa)}});var e=function(Y,ad,ac,ag,af,aa,ab,ae){var Z=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];this.track_config=new T({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:af,onchange:function(){Z.tile_cache.clear();Z.draw()}});this.prefs=this.track_config.values;k.call(this,Y,ad,ad.viewport_container);H.call(this,aa,ab,ae);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=ac;this.dataset_id=ag;this.original_dataset_id=ag;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_cache=new L(20,this);this.left_offset=200;this.painter=G.LinkedFeaturePainter};extend(e.prototype,H.prototype,{update_auto_mode:function(Y){if(this.mode=="Auto"){if(Y=="no_detail"){Y="feature spans"}else{if(Y=="summary_tree"){Y="coverage histogram"}}this.mode_div.text("Auto ("+Y+")")}},incremental_slots:function(ac,Z,ab){var aa=this.view.canvas_manager.dummy_context,Y=this.inc_slots[ac];if(!Y||(Y.mode!==ab)){Y=new (p.FeatureSlotter)(ac,ab==="Pack",w,function(ad){return aa.measureText(ad)});Y.mode=ab;this.inc_slots[ac]=Y}return Y.slot_features(Z)},get_summary_tree_data:function(ac,af,aa,an){if(an>aa-af){an=aa-af}var aj=Math.floor((aa-af)/an),am=[],ab=0;var ad=0,ae=0,ai,al=0,ag=[],ak,ah;var Z=function(aq,ap,ar,ao){aq[0]=ap+ar*ao;aq[1]=ap+(ar+1)*ao};while(al<an&&ad!==ac.length){var Y=false;for(;al<an&&!Y;al++){Z(ag,af,al,aj);for(ae=ad;ae<ac.length;ae++){ai=ac[ae].slice(1,3);if(is_overlap(ai,ag)){Y=true;break}}if(Y){break}}data_start_index=ae;am[am.length]=ak=[ag[0],0];for(;ae<ac.length;ae++){ai=ac[ae].slice(1,3);if(is_overlap(ai,ag)){ak[1]++}else{break}}if(ak[1]>ab){ab=ak[1]}al++}return{max:ab,delta:aj,data:am}},draw_tile:function(al,au,ay,ah,ab){var aq=this,aA=ay*K*au,Z=(ay+1)*K*au,an=Z-aA,ar=Math.ceil(an*ah),ap=this.mode,aE=25,ac=this.left_offset,am,ad;if(ap==="Auto"){if(al.dataset_type==="summary_tree"){ap=al.dataset_type}else{if(al.extra_info==="no_detail"){ap="no_detail"}else{var aD=al.data;if(this.view.high-this.view.low>D){ap="Squish"}else{ap="Pack"}}}this.update_auto_mode(ap)}if(ap==="summary_tree"||ap==="Histogram"){ad=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var Y=$("<div />").addClass("yaxislabel");Y.text(al.max);Y.css({position:"absolute",top:"22px",left:"10px"});Y.prependTo(this.container_div);var aa=this.view.canvas_manager.new_canvas();aa.width=ar+ac;aa.height=ad+M;if(al.dataset_type!="summary_tree"){var ai=this.get_summary_tree_data(al.data,aA,Z,200);if(al.max){ai.max=al.max}al=ai}var aB=new G.SummaryTreePainter(al,aA,Z,this.prefs);var at=aa.getContext("2d");at.translate(ac,M);aB.draw(at,ar,ad);return new m(ay,au,aa,al.max)}var am,af=1;if(ap==="no_detail"||ap==="Squish"||ap==="Pack"){af=this.incremental_slots(ah,al.data,ap);am=this.inc_slots[ah].slots}var ag=[];if(al.data){var aj=this.filters_manager.filters;for(var av=0,ax=al.data.length;av<ax;av++){var ae=al.data[av];var aw=false;var ak;for(var az=0,aC=aj.length;az<aC;az++){ak=aj[az];ak.update_attrs(ae);if(!ak.keep(ae)){aw=true;break}}if(!aw){ag.push(ae)}}}var aB=new (this.painter)(ag,aA,Z,this.prefs,ap,ab);var ad=aB.get_required_height(af)+z;var aa=this.view.canvas_manager.new_canvas();aa.width=ar+ac;aa.height=ad;var at=aa.getContext("2d");at.fillStyle=this.prefs.block_color;at.font=at.canvas.manager.default_font;at.textAlign="right";this.container_div.find(".yaxislabel").remove();if(al.message){$(aa).css({"border-top":"1px solid red"});at.fillStyle="red";at.textAlign="left";var ao=at.textBaseline;at.textBaseline="top";at.fillText(al.message,ac,0);at.textBaseline=ao;if(!al.data){return new b(ay,au,aa,ad)}}this.example_feature=(al.data.length?al.data[0]:undefined);at.translate(ac,z);aB.draw(at,ar,ad,am);return new J(ay,au,aa)}});var N=function(ab,Z,ad,Y,aa,ac){e.call(this,ab,Z,ad,Y,aa,ac);this.track_type="VcfTrack";this.painter=G.VariantPainter};extend(N.prototype,H.prototype,e.prototype);var Q=function(ab,Z,ad,Y,aa,ac){e.call(this,ab,Z,ad,Y,aa,ac);this.track_config=new T({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:aa,onchange:function(){this.track.tile_cache.clear();this.track.draw()}});this.prefs=this.track_config.values;this.track_type="ReadTrack";this.painter=G.ReadPainter;this.make_name_popup_menu()};extend(Q.prototype,H.prototype,e.prototype);var O=function(ac,aa,ae,Y,ab,ad,Z){e.call(this,ac,aa,ae,Y,ab,ad,{},Z);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};extend(O.prototype,H.prototype,e.prototype,{predraw_init:function(){var Z=this;var Y=function(){if(Z.data_cache.size()===0){setTimeout(Y,300)}else{Z.data_url=default_data_url;Z.data_query_wait=F;Z.dataset_state_url=converted_datasets_state_url;$.getJSON(Z.dataset_state_url,{dataset_id:Z.dataset_id,hda_ldda:Z.hda_ldda},function(aa){})}};Y()}});R.View=W;R.LineTrack=l;R.FeatureTrack=e;R.ReadTrack=Q};var slotting_module=function(c,b){var d=2,a=5;b.FeatureSlotter=function(h,g,e,f){this.slots={};this.start_end_dct={};this.w_scale=h;this.include_label=g;this.max_rows=e;this.measureText=f};extend(b.FeatureSlotter.prototype,{slot_features:function(l){var o=this.w_scale,r=this.slots,g=this.start_end_dct,x=[],z=[],m=0,y=this.max_rows;for(var v=0,w=l.length;v<w;v++){var k=l[v],n=k[0];if(r[n]!==undefined){m=Math.max(m,r[n]);z.push(r[n])}else{x.push(v)}}var p=function(F,G){for(var E=0;E<=y;E++){var C=false,H=g[E];if(H!==undefined){for(var B=0,D=H.length;B<D;B++){var A=H[B];if(G>A[0]&&F<A[1]){C=true;break}}}if(!C){return E}}return -1};for(var v=0,w=x.length;v<w;v++){var k=l[x[v]],n=k[0],t=k[1],e=k[2],q=k[3],f=Math.floor(t*o),j=Math.ceil(e*o),u=this.measureText(q).width,h;if(q!==undefined&&this.include_label){u+=(d+a);if(f-u>=0){f-=u;h="left"}else{j+=u;h="right"}}var s=p(f,j);if(s>=0){if(g[s]===undefined){g[s]=[]}g[s].push([f,j]);r[n]=s;m=Math.max(m,s)}else{}}return m+1}})};var painters_module=function(j,v){var o=function(G,y,E,x,D,B){if(B===undefined){B=4}var A=x-y;var z=D-E;var C=Math.floor(Math.sqrt(A*A+z*z)/B);var H=A/C;var F=z/C;var w;for(w=0;w<C;w++,y+=H,E+=F){if(w%2!==0){continue}G.fillRect(y,E,B,1)}};var p=function(z,x,w,C){var B=x-C/2,A=x+C/2,D=w-Math.sqrt(C*3/2);z.beginPath();z.moveTo(B,D);z.lineTo(A,D);z.lineTo(x,w);z.lineTo(B,D);z.strokeStyle=this.fillStyle;z.fill();z.stroke();z.closePath()};var l=function(y,A,w,x,z){this.data=y;this.view_start=A;this.view_end=w;this.prefs=extend({},this.default_prefs,x);this.mode=z};l.prototype.default_prefs={};var t=function(y,A,w,x,z){l.call(this,y,A,w,x,z)};t.prototype.default_prefs={show_counts:false};t.prototype.draw=function(L,w,K){var D=this.view_start,N=this.view_end-this.view_start,M=w/N;var I=this.data.data,H=this.data.delta,F=this.data.max,A=K;delta_x_px=Math.ceil(H*M);L.save();for(var B=0,C=I.length;B<C;B++){var G=Math.floor((I[B][0]-D)*M);var E=I[B][1];if(!E){continue}var J=E/F*K;if(E!==0&&J<1){J=1}L.fillStyle="black";L.fillRect(G,A-J,delta_x_px,J);var z=4;if(this.prefs.show_counts&&(L.measureText(E).width+z)<delta_x_px){L.fillStyle="#666";L.textAlign="center";L.fillText(E,G+(delta_x_px/2),10)}}L.restore()};var c=function(y,A,w,x,z){l.call(this,y,A,w,x,z)};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(M,L,J){var E=false,F=this.prefs.min_value,C=this.prefs.max_value,I=C-F,x=J,z=this.view_start,K=this.view_end-this.view_start,A=L/K,G=this.mode,Q=this.data;M.save();var R=Math.round(J+F/I*J);if(G!=="Intensity"){M.fillStyle="#aaa";M.fillRect(0,R,L,1)}M.beginPath();M.fillStyle=this.prefs.color;var P,D,B;if(Q.length>1){B=Math.ceil((Q[1][0]-Q[0][0])*A)}else{B=10}for(var N=0,O=Q.length;N<O;N++){P=Math.round((Q[N][0]-z)*A);D=Q[N][1];if(D===null){if(E&&G==="Filled"){M.lineTo(P,x)}E=false;continue}if(D<F){D=F}else{if(D>C){D=C}}if(G==="Histogram"){D=Math.round(D/I*x);M.fillRect(P,R,B,-D)}else{if(G==="Intensity"){D=255-Math.floor((D-F)/I*255);M.fillStyle="rgb("+D+","+D+","+D+")";M.fillRect(P,0,B,x)}else{D=Math.round(x-(D-F)/I*x);if(E){M.lineTo(P,D)}else{E=true;if(G==="Filled"){M.moveTo(P,x);M.lineTo(P,D)}else{M.moveTo(P,D)}}}}}if(G==="Filled"){if(E){M.lineTo(P,R);M.lineTo(0,R)}M.fill()}else{M.stroke()}var w=-1,H=-1;M.fillStyle=this.prefs.overflow_color;for(var N=0,O=Q.length;N<O;N++){D=Q[N][1];P=Math.round((Q[N][0]-z)*A);x_minus_scaled=Math.round((Q[N][0]-1-z)*A);if(H>=0&&(D===null||D<C)){M.fillRect(H,0,x_minus_scaled-H+1,2);H=-1}else{if(w>=0&&(D===null||D>F)){M.fillRect(w,J-2,x_minus_scaled-w+1,2);w=-1}}if(D!==null&&D>C&&H<0){H=P}else{if(D!==null&&D<F&&w<0){w=P}}}M.restore()};var n=function(y,A,w,x,z){l.call(this,y,A,w,x,z)};n.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(n.prototype,{get_required_height:function(x){var w=y_scale=this.get_row_height(),y=this.mode;if(y==="no_detail"||y==="Squish"||y==="Pack"){w=x*y_scale}return w+Math.max(Math.round(y_scale/2),5)},draw:function(I,z,H,E){var C=this.data,F=this.view_start,J=this.view_end;I.save();I.fillStyle=this.prefs.block_color;I.textAlign="right";var M=this.view_end-this.view_start,L=z/M,y=this.get_row_height();for(var B=0,D=C.length;B<D;B++){var K=C[B],A=K[0],w=K[1],x=K[2],G=(E&&E[A]!==undefined?E[A]:null);if((w<J&&x>F)&&(this.mode=="Dense"||G!==null)){this.draw_element(I,this.mode,K,G,F,J,L,y,z)}}I.restore()}});var d=10,h=3,k=5,u=10,f=1,r=3,e=3,a=9,m=2,g="#ccc";var q=function(y,A,w,x,z){n.call(this,y,A,w,x,z)};extend(q.prototype,n.prototype,{get_row_height:function(){var x=this.mode,w;if(x==="Dense"){w=d}else{if(x==="no_detail"){w=h}else{if(x==="Squish"){w=k}else{w=u}}}return w},draw_element:function(I,B,Q,D,K,aa,ae,af,w){var N=Q[0],ac=Q[1],U=Q[2],L=Q[3],V=Math.floor(Math.max(0,(ac-K)*ae)),J=Math.ceil(Math.min(w,Math.max(0,(U-K)*ae))),T=(B==="Dense"?0:(0+D))*af,H,Y,M=null,ag=null,z=this.prefs.block_color,X=this.prefs.label_color;if(B=="Dense"){D=1}if(B==="no_detail"){I.fillStyle=z;I.fillRect(V,T+5,J-V,f)}else{var G=Q[4],S=Q[5],W=Q[6],A=Q[7];if(S&&W){M=Math.floor(Math.max(0,(S-K)*ae));ag=Math.ceil(Math.min(w,Math.max(0,(W-K)*ae)))}var ad,O;if(B==="Squish"||B==="Dense"){ad=1;O=e}else{ad=5;O=a}if(!A){if(Q.strand){if(Q.strand==="+"){I.fillStyle=I.canvas.manager.get_pattern("right_strand_inv")}else{if(Q.strand==="-"){I.fillStyle=I.canvas.manager.get_pattern("left_strand_inv")}}}else{I.fillStyle=z}I.fillRect(V,T,J-V,O)}else{var F,P;if(B==="Squish"||B==="Dense"){I.fillStyle=g;F=T+Math.floor(e/2)+1;P=1}else{if(G){var F=T;var P=O;if(G==="+"){I.fillStyle=I.canvas.manager.get_pattern("right_strand")}else{if(G==="-"){I.fillStyle=I.canvas.manager.get_pattern("left_strand")}}}else{I.fillStyle=g;F+=(e/2)+1;P=1}}I.fillRect(V,F,J-V,P);for(var ab=0,y=A.length;ab<y;ab++){var C=A[ab],x=Math.floor(Math.max(0,(C[0]-K)*ae)),R=Math.ceil(Math.min(w,Math.max((C[1]-K)*ae)));if(x>R){continue}I.fillStyle=z;I.fillRect(x,T+(O-ad)/2+1,R-x,ad);if(M!==undefined&&W>S&&!(x>ag||R<M)){var Z=Math.max(x,M),E=Math.min(R,ag);I.fillRect(Z,T+1,E-Z,O);if(A.length==1&&B=="Pack"){if(G==="+"){I.fillStyle=I.canvas.manager.get_pattern("right_strand_inv")}else{if(G==="-"){I.fillStyle=I.canvas.manager.get_pattern("left_strand_inv")}}if(Z+14<E){Z+=2;E-=2}I.fillRect(Z,T+1,E-Z,O)}}}}if(B==="Pack"&&ac>K){I.fillStyle=X;if(K===0&&V-I.measureText(L).width<0){I.textAlign="left";I.fillText(L,J+m,T+8)}else{I.textAlign="right";I.fillText(L,V-m,T+8)}I.fillStyle=z}}}});var b=function(y,A,w,x,z){n.call(this,y,A,w,x,z)};extend(b.prototype,n.prototype,{draw_element:function(P,K,E,A,S,y,H,Q,N){var E=data[i],G=E[0],O=E[1],z=E[2],J=E[3],C=Math.floor(Math.max(0,(O-S)*H)),F=Math.ceil(Math.min(N,Math.max(0,(z-S)*H))),B=(K==="Dense"?0:(0+A))*Q,w,T,x=null,I=null;if(no_label){P.fillStyle=block_color;P.fillRect(C+left_offset,B+5,F-C,1)}else{var R=E[4],M=E[5],D=E[6];w=9;T=1;P.fillRect(C+left_offset,B,F-C,w);if(K!=="Dense"&&J!==undefined&&O>S){P.fillStyle=label_color;if(S===0&&C-P.measureText(J).width<0){P.textAlign="left";P.fillText(J,F+2+left_offset,B+8)}else{P.textAlign="right";P.fillText(J,C-2+left_offset,B+8)}P.fillStyle=block_color}var L=R+" / "+M;if(O>S&&P.measureText(L).width<(F-C)){P.fillStyle="white";P.textAlign="center";P.fillText(L,left_offset+C+(F-C)/2,B+8);P.fillStyle=block_color}}}});var s=function(z,B,w,y,A,x){n.call(this,z,B,w,y,A);this.ref_seq=x};s.prototype.default_prefs=extend({},n.prototype.default_prefs,{show_insertions:false});extend(s.prototype,n.prototype,{get_row_height:function(){var w,x=this.mode;if(x==="Dense"){w=d}else{if(x==="Squish"){w=k}else{w=u;if(this.prefs.show_insertions){w*=2}}}return w},draw_read:function(S,N,J,X,y,R,G,D,C){S.textAlign="center";var Q=this,x=[X,y],M=0,T=0,P=0;ref_seq=this.ref_seq,char_width_px=S.canvas.manager.char_width_px;var ac=[];if((N==="Pack"||this.mode==="Auto")&&D!==undefined&&J>char_width_px){P=Math.round(J/2)}if(!G){G=[[0,D.length]]}for(var K=0,V=G.length;K<V;K++){var H=G[K],z="MIDNSHP=X"[H[0]],L=H[1];if(z==="H"||z==="S"){M-=L}var E=R+M,ab=Math.floor(Math.max(0,(E-X)*J)),F=Math.floor(Math.max(0,(E+L-X)*J));if(ab===F){F+=1}switch(z){case"H":break;case"S":case"M":case"=":if(is_overlap([E,E+L],x)){var O=D.slice(T,T+L);if(P>0){S.fillStyle=this.prefs.block_color;S.fillRect(ab-P,C+1,F-ab,9);S.fillStyle=g;for(var Z=0,w=O.length;Z<w;Z++){if(this.prefs.show_differences&&ref_seq){var I=ref_seq[E-X+Z];if(!I||I.toLowerCase()===O[Z].toLowerCase()){continue}}if(E+Z>=X&&E+Z<=y){var aa=Math.floor(Math.max(0,(E+Z-X)*J));S.fillText(O[Z],aa,C+9)}}}else{S.fillStyle=this.prefs.block_color;S.fillRect(ab,C+4,F-ab,e)}}T+=L;M+=L;break;case"N":S.fillStyle=g;S.fillRect(ab-P,C+5,F-ab,1);M+=L;break;case"D":S.fillStyle="red";S.fillRect(ab-P,C+4,F-ab,3);M+=L;break;case"P":break;case"I":var W=ab-P;if(is_overlap([E,E+L],x)){var O=D.slice(T,T+L);if(this.prefs.show_insertions){var B=ab-(F-ab)/2;if((N==="Pack"||this.mode==="Auto")&&D!==undefined&&J>char_width_px){S.fillStyle="yellow";S.fillRect(B-P,C-9,F-ab,9);ac[ac.length]={type:"triangle",data:[W,C+4,5]};S.fillStyle=g;switch(seq_tile_overlap){case (OVERLAP_START):O=O.slice(X-E);break;case (OVERLAP_END):O=O.slice(0,E-y);break;case (CONTAINED_BY):break;case (CONTAINS):O=O.slice(X-E,E-y);break}for(var Z=0,w=O.length;Z<w;Z++){var aa=Math.floor(Math.max(0,(E+Z-X)*J));S.fillText(O[Z],aa-(F-ab)/2,C)}}else{S.fillStyle="yellow";S.fillRect(B,C+(this.mode!=="Dense"?2:5),F-ab,(N!=="Dense"?e:r))}}else{if((N==="Pack"||this.mode==="Auto")&&D!==undefined&&J>char_width_px){ac[ac.length]={type:"text",data:[O.length,W,C+9]}}else{}}}T+=L;break;case"X":T+=L;break}}S.fillStyle="yellow";var Y,A,ad;for(var U=0;U<ac.length;U++){Y=ac[U];A=Y.type;ad=Y.data;if(A==="text"){S.save();S.font="bold "+S.font;S.fillText(ad[0],ad[1],ad[2]);S.restore()}else{if(A=="triangle"){p(S,ad[0],ad[1],ad[2])}}}},draw_element:function(P,K,C,z,S,x,G,Q,N){var F=C[0],O=C[1],y=C[2],H=C[3],B=Math.floor(Math.max(0,(O-S)*G)),D=Math.ceil(Math.min(N,Math.max(0,(y-S)*G))),A=(K==="Dense"?0:(0+z))*Q,T=this.prefs.block_color,E=this.prefs.label_color,M=0;if((K==="Pack"||this.mode==="Auto")&&G>P.canvas.manager.char_width_px){var M=Math.round(G/2)}P.fillStyle=T;if(C[5] instanceof Array){var L=Math.floor(Math.max(0,(C[4][0]-S)*G)),J=Math.ceil(Math.min(N,Math.max(0,(C[4][1]-S)*G))),I=Math.floor(Math.max(0,(C[5][0]-S)*G)),w=Math.ceil(Math.min(N,Math.max(0,(C[5][1]-S)*G)));if(C[4][1]>=S&&C[4][0]<=x&&C[4][2]){this.draw_read(P,K,G,S,x,C[4][0],C[4][2],C[4][3],A)}if(C[5][1]>=S&&C[5][0]<=x&&C[5][2]){this.draw_read(P,K,G,S,x,C[5][0],C[5][2],C[5][3],A)}if(I>J){P.fillStyle=g;o(P,J-M,A+5,I-M,A+5)}}else{P.fillStyle=T;this.draw_read(P,K,G,S,x,O,C[4],C[5],A)}if(K==="Pack"&&O>S){P.fillStyle=this.prefs.label_color;var R=1;if(R===0&&B-P.measureText(H).width<0){P.textAlign="left";P.fillText(H,D+m-M,A+8)}else{P.textAlign="right";P.fillText(H,B-m-M,A+8)}P.fillStyle=T}}});v.SummaryTreePainter=t;v.LinePainter=c;v.LinkedFeaturePainter=q;v.ReadPainter=s;v.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("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 --- a/static/scripts/trackster.js Thu Apr 14 10:37:42 2011 -0400 +++ b/static/scripts/trackster.js Thu Apr 14 14:29:32 2011 -0400 @@ -1311,9 +1311,9 @@ * Tiles drawn by tracks. */ var Tile = function(index, resolution, canvas) { - // Wrap element in div for background this.index = index; this.resolution = resolution; + // Wrap element in div for background. this.canvas = $("<div class='track-tile'/>").append(canvas); }; @@ -1743,7 +1743,9 @@ // // If mode is Histogram and tiles do not share max, redraw tiles as necessary using new max. // - if (track.mode == "Histogram") { + // HACK: use track type b/c LineTrack histograms are different; what's needed is different + // post-draw actions for different line tracks. + if (track.track_type == "FeatureTrack" && track.mode == "Histogram") { // Get global max. var global_max = -1; for (var i = 0; i < drawn_tiles.length; i++) { @@ -1826,7 +1828,7 @@ var draw_and_show_tile = function(id, result, resolution, tile_index, parent_element, w_scale, seq_data) { // DEBUG: this is still called too many times when moving slowly, // console.log( "draw_and_show_tile", resolution, tile_index, w_scale ); - var tile = track.draw_tile(result, resolution, tile_index, parent_element, w_scale, seq_data); + var tile = track.draw_tile(result, resolution, tile_index, w_scale, seq_data); track.tile_cache.set(key, tile); track.show_tile(tile, parent_element, tile_low, w_scale); drawn_tiles[drawn_tiles.length] = tile; @@ -1882,9 +1884,9 @@ } var tile_element = tile.canvas; tile_element.css({ position: 'absolute', top: 0, left: left, height: '' }); - - // Setup and show tile element. parent_element.append(tile_element); + + // Set track height. track.max_height = Math.max(track.max_height, tile_element.height()); track.content_div.css("height", track.max_height + "px"); parent_element.children().css("height", track.max_height + "px"); @@ -1984,7 +1986,7 @@ /** * Draw ReferenceTrack tile. */ - draw_tile: function(seq, resolution, tile_index, parent_element, w_scale) { + draw_tile: function(seq, resolution, tile_index, w_scale) { var track = this, tile_length = DENSITY * resolution; @@ -2122,7 +2124,7 @@ /** * Draw LineTrack tile. */ - draw_tile: function(result, resolution, tile_index, parent_element, w_scale) { + draw_tile: function(result, resolution, tile_index, w_scale) { if (this.vertical_range === undefined) { return; } @@ -2312,7 +2314,7 @@ /** * Draw FeatureTrack tile. */ - draw_tile: function(result, resolution, tile_index, parent_element, w_scale, ref_seq) { + draw_tile: function(result, resolution, tile_index, w_scale, ref_seq) { var track = this, tile_low = tile_index * DENSITY * resolution, tile_high = ( tile_index + 1 ) * DENSITY * resolution, @@ -2343,7 +2345,7 @@ var data = result.data; // if ( (data.length && data.length < 4) || // (this.view.high - this.view.low > MIN_SQUISH_VIEW_WIDTH) ) { - if ( this.view.high - this.view.low > MIN_SQUISH_VIEW_WIDTH ) { + if ( this.view.high - this.view.low > MIN_SQUISH_VIEW_WIDTH ) { mode = "Squish"; } else { mode = "Pack"; @@ -2354,9 +2356,7 @@ // Drawing the summary tree (feature coverage histogram) if (mode === "summary_tree" || mode === "Histogram") { - // Set height of parent_element required_height = this.summary_draw_height; - parent_element.parent().css("height", Math.max(this.height_px, required_height) + "px"); // Add label to container div showing maximum count // TODO: this shouldn't be done at the tile level this.container_div.find(".yaxislabel").remove(); @@ -2428,7 +2428,6 @@ canvas.width = width + left_offset; canvas.height = required_height; - parent_element.parent().css("height", Math.max(this.height_px, required_height) + "px"); // console.log(( tile_low - this.view.low ) * w_scale, tile_index, w_scale); var ctx = canvas.getContext("2d"); ctx.fillStyle = this.prefs.block_color; @@ -2452,7 +2451,7 @@ // If there's no data, return. if (!result.data) { - return new Tile(tile_index, resolution, canvas); + return new Tile(tile_index, resolution, canvas, required_height); } } @@ -2460,8 +2459,8 @@ this.example_feature = (result.data.length ? result.data[0] : undefined); // Draw features - ctx.translate( left_offset, ERROR_PADDING ); - painter.draw( ctx, width, required_height, slots ); + ctx.translate(left_offset, ERROR_PADDING); + painter.draw(ctx, width, required_height, slots); return new FeatureTrackTile(tile_index, resolution, canvas); } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Trackster: refactor so that summary_tree and Histogram modes use the same code.
by Bitbucket 14 Apr '11

14 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/9203be6a16b3/ changeset: r5388:9203be6a16b3 user: jgoecks date: 2011-04-14 16:37:42 summary: Trackster: refactor so that summary_tree and Histogram modes use the same code. affected #: 1 file (1.3 KB) --- a/static/scripts/trackster.js Thu Apr 14 10:05:00 2011 -0400 +++ b/static/scripts/trackster.js Thu Apr 14 10:37:42 2011 -0400 @@ -2353,7 +2353,7 @@ } // Drawing the summary tree (feature coverage histogram) - if ( mode === "summary_tree" ) { + if (mode === "summary_tree" || mode === "Histogram") { // Set height of parent_element required_height = this.summary_draw_height; parent_element.parent().css("height", Math.max(this.height_px, required_height) + "px"); @@ -2369,44 +2369,22 @@ canvas.width = width + left_offset; // Extra padding at top of summary tree canvas.height = required_height + SUMMARY_TREE_TOP_PADDING; + + // Get summary tree data if necessary and set max if there is one. + if (result.dataset_type != "summary_tree") { + var st_data = this.get_summary_tree_data(result.data, tile_low, tile_high, 200); + if (result.max) { + st_data.max = result.max; + } + result = st_data; + } // Paint summary tree into canvas - var painter = new painters.SummaryTreePainter( result, tile_low, tile_high, this.prefs ); - var ctx = canvas.getContext("2d"); - // Deal with left_offset by translating - ctx.translate( left_offset, SUMMARY_TREE_TOP_PADDING ); - painter.draw( ctx, width, required_height ); - return new SummaryTreeTile(tile_index, resolution, canvas, result.max); - } - - // Drawing coverage histogram. This is different from summary tree because data can feature - // details, but user has requested a histogram. - if (mode === "Histogram") { - // Set height of parent_element - required_height = this.summary_draw_height; - parent_element.parent().css("height", Math.max(this.height_px, required_height) + "px"); - // Add label to container div showing maximum count - // TODO: this shouldn't be done at the tile level - this.container_div.find(".yaxislabel").remove(); - var max_label = $("<div />").addClass('yaxislabel'); - max_label.text( result.max ); - max_label.css({ position: "absolute", top: "22px", left: "10px" }); - max_label.prependTo(this.container_div); - // Create canvas - var canvas = this.view.canvas_manager.new_canvas(); - canvas.width = width + left_offset; - // Extra padding at top of summary tree - canvas.height = required_height + SUMMARY_TREE_TOP_PADDING; - // Paint summary tree into canvas. - var binned_data = this.get_summary_tree_data(result.data, tile_low, tile_high, 200); - if (result.max) { - binned_data.max = result.max; - } - var painter = new painters.SummaryTreePainter(binned_data, tile_low, tile_high, this.prefs); + var painter = new painters.SummaryTreePainter(result, tile_low, tile_high, this.prefs); var ctx = canvas.getContext("2d"); // Deal with left_offset by translating ctx.translate(left_offset, SUMMARY_TREE_TOP_PADDING); painter.draw(ctx, width, required_height); - return new SummaryTreeTile(tile_index, resolution, canvas, binned_data.max); + return new SummaryTreeTile(tile_index, resolution, canvas, result.max); } // Start dealing with row-by-row tracks Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Fix bug that prevented workflows with runtime parameters from being exported.
by Bitbucket 14 Apr '11

14 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/835656900dd0/ changeset: r5387:835656900dd0 user: jgoecks date: 2011-04-14 16:05:00 summary: Fix bug that prevented workflows with runtime parameters from being exported. affected #: 1 file (5 bytes) --- a/lib/galaxy/web/controllers/workflow.py Thu Apr 14 09:02:20 2011 -0400 +++ b/lib/galaxy/web/controllers/workflow.py Thu Apr 14 10:05:00 2011 -0400 @@ -1587,7 +1587,7 @@ for name, val in module.state.inputs.items(): input_type = type( val ) if input_type == RuntimeValue: - step['inputs'].append( { "name" : name, "description" : "runtime parameter for tool %s" % module.get_name() } ) + step_dict['inputs'].append( { "name" : name, "description" : "runtime parameter for tool %s" % module.get_name() } ) elif input_type == dict: # Input type is described by a dict, e.g. indexed parameters. for partname, partval in val.items(): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by Bitbucket 14 Apr '11

14 Apr '11

3 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/3504e971d8b8/ changeset: r5384:3504e971d8b8 user: Martijn Vermaat date: 2011-04-14 12:14:30 summary: Adds filtering to input selection on run workflow page. affected #: 2 files (2.3 KB) --- a/static/june_2007_style/blue/base.css Thu Apr 14 01:13:10 2011 +0200 +++ b/static/june_2007_style/blue/base.css Thu Apr 14 12:14:30 2011 +0200 @@ -172,4 +172,4 @@ .text-and-autocomplete-select{background:url(fugue.png) no-repeat right -364px;} .icon-button.multiinput{background:url(../images/documents-stack.png) no-repeat;cursor:pointer;float:none;display:inline-block;margin-left:10px;} .icon-button.multiinput.disabled{background:url(../images/documents-stack-faded.png) no-repeat;cursor:auto;} -.workflow-invocation-complete{border:solid 1px #6A6;border-left-width:5px;margin:10px 0;} +.workflow-invocation-complete{border:solid 1px #6A6;border-left-width:5px;margin:10px 0;padding-left:5px;} --- a/templates/workflow/run.mako Thu Apr 14 01:13:10 2011 +0200 +++ b/templates/workflow/run.mako Thu Apr 14 12:14:30 2011 +0200 @@ -21,6 +21,7 @@ } } function toggle_multiinput(select) { + var placeholder; if (select.attr('multiple')) { $('.multiinput').removeClass('disabled'); if (select.val()) { @@ -28,12 +29,16 @@ } else { select.val($('option:last', select).val()); } - select.removeAttr('multiple'); + select.removeAttr('multiple').removeAttr('size'); + placeholder = 'type to filter'; } else { $('.multiinput').addClass('disabled'); $('.multiinput', select.parent().prev()).removeClass('disabled'); - select.attr('multiple', 'multiple'); + select.attr('multiple', 'multiple').attr('size', 8); + placeholder = 'type to filter, [enter] to select all'; } + $('input.multiinput-filter', select.parent()).attr( + 'placeholder', placeholder); } $( "select[refresh_on_change='true']").change( function() { $( "#tool_form" ).submit(); @@ -58,6 +63,7 @@ }); $('select[name*="|input"]').removeAttr('multiple').each(function(i, s) { var select = $(s); + var new_width = select.width() + 20; select.parent().prev().append( $('<span class="icon-button multiinput"></span>').click(function() { if ($(this).hasClass('disabled')) return; @@ -68,6 +74,44 @@ 'files. Each selected file will have an ' + 'instance of the workflow.').tipsy({gravity:'s'}) ); + var filter = $('<input type="text" class="multiinput-filter" ' + + 'placeholder="type to filter">'); + var filter_timeout = false; + var original_rows = select.find('option'); + var previous_filter = ''; + // Todo: might have to choose keypress, depending on browser + filter.keydown(function(e) { + var filter_select = function() { + var f = $.trim(filter.val()); + var filtered_rows = original_rows; + if (f.length >= 1) { + filtered_rows = original_rows.filter(function() { + return new RegExp(f, 'ig').test($(this).text()); + }); + } + select.html(''); + select.html(filtered_rows); + }; + if (e.which == 13) { // 13 = enter key + e.preventDefault(); + multi = select.attr('multiple'); + if (typeof multi !== 'undefined' && multi !== false) { + if (!select.find('option:not(:selected)').length) { + select.find('option').removeAttr('selected'); + } else { + select.find('option').attr('selected', 'selected'); + } + } + return; + } + if (filter.val() != previous_filter) { + if (filter_timeout) clearTimeout(filter_timeout); + timeout = setTimeout(filter_select, 300); + previous_filter = filter.val(); + } + }).width(new_width).css('display', 'block'); + select.after(filter); + select.width(new_width); }); }); </script> http://bitbucket.org/galaxy/galaxy-central/changeset/d6fda5e30200/ changeset: r5385:d6fda5e30200 user: Martijn Vermaat date: 2011-04-14 14:23:28 summary: Give input selection and filtering a minimum width (run tool form). affected #: 1 file (15 bytes) --- a/templates/workflow/run.mako Thu Apr 14 12:14:30 2011 +0200 +++ b/templates/workflow/run.mako Thu Apr 14 14:23:28 2011 +0200 @@ -63,7 +63,7 @@ }); $('select[name*="|input"]').removeAttr('multiple').each(function(i, s) { var select = $(s); - var new_width = select.width() + 20; + var new_width = Math.max(200, select.width()) + 20; select.parent().prev().append( $('<span class="icon-button multiinput"></span>').click(function() { if ($(this).hasClass('disabled')) return; http://bitbucket.org/galaxy/galaxy-central/changeset/67a19816034b/ changeset: r5386:67a19816034b user: dannon date: 2011-04-14 15:02:20 summary: Merge! affected #: 2 files (2.3 KB) --- a/static/june_2007_style/blue/base.css Thu Apr 14 08:09:48 2011 -0400 +++ b/static/june_2007_style/blue/base.css Thu Apr 14 09:02:20 2011 -0400 @@ -172,4 +172,4 @@ .text-and-autocomplete-select{background:url(fugue.png) no-repeat right -364px;} .icon-button.multiinput{background:url(../images/documents-stack.png) no-repeat;cursor:pointer;float:none;display:inline-block;margin-left:10px;} .icon-button.multiinput.disabled{background:url(../images/documents-stack-faded.png) no-repeat;cursor:auto;} -.workflow-invocation-complete{border:solid 1px #6A6;border-left-width:5px;margin:10px 0;} +.workflow-invocation-complete{border:solid 1px #6A6;border-left-width:5px;margin:10px 0;padding-left:5px;} --- a/templates/workflow/run.mako Thu Apr 14 08:09:48 2011 -0400 +++ b/templates/workflow/run.mako Thu Apr 14 09:02:20 2011 -0400 @@ -21,6 +21,7 @@ } } function toggle_multiinput(select) { + var placeholder; if (select.attr('multiple')) { $('.multiinput').removeClass('disabled'); if (select.val()) { @@ -28,12 +29,16 @@ } else { select.val($('option:last', select).val()); } - select.removeAttr('multiple'); + select.removeAttr('multiple').removeAttr('size'); + placeholder = 'type to filter'; } else { $('.multiinput').addClass('disabled'); $('.multiinput', select.parent().prev()).removeClass('disabled'); - select.attr('multiple', 'multiple'); + select.attr('multiple', 'multiple').attr('size', 8); + placeholder = 'type to filter, [enter] to select all'; } + $('input.multiinput-filter', select.parent()).attr( + 'placeholder', placeholder); } $( "select[refresh_on_change='true']").change( function() { $( "#tool_form" ).submit(); @@ -58,6 +63,7 @@ }); $('select[name*="|input"]').removeAttr('multiple').each(function(i, s) { var select = $(s); + var new_width = Math.max(200, select.width()) + 20; select.parent().prev().append( $('<span class="icon-button multiinput"></span>').click(function() { if ($(this).hasClass('disabled')) return; @@ -68,6 +74,44 @@ 'files. Each selected file will have an ' + 'instance of the workflow.').tipsy({gravity:'s'}) ); + var filter = $('<input type="text" class="multiinput-filter" ' + + 'placeholder="type to filter">'); + var filter_timeout = false; + var original_rows = select.find('option'); + var previous_filter = ''; + // Todo: might have to choose keypress, depending on browser + filter.keydown(function(e) { + var filter_select = function() { + var f = $.trim(filter.val()); + var filtered_rows = original_rows; + if (f.length >= 1) { + filtered_rows = original_rows.filter(function() { + return new RegExp(f, 'ig').test($(this).text()); + }); + } + select.html(''); + select.html(filtered_rows); + }; + if (e.which == 13) { // 13 = enter key + e.preventDefault(); + multi = select.attr('multiple'); + if (typeof multi !== 'undefined' && multi !== false) { + if (!select.find('option:not(:selected)').length) { + select.find('option').removeAttr('selected'); + } else { + select.find('option').attr('selected', 'selected'); + } + } + return; + } + if (filter.val() != previous_filter) { + if (filter_timeout) clearTimeout(filter_timeout); + timeout = setTimeout(filter_select, 300); + previous_filter = filter.val(); + } + }).width(new_width).css('display', 'block'); + select.after(filter); + select.width(new_width); }); }); </script> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: fubar: Changes to allow all test outputs generated by twill to be saved to a folder pointed to by
by Bitbucket 14 Apr '11

14 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/b9cff3fbd170/ changeset: r5383:b9cff3fbd170 user: fubar date: 2011-04-14 14:09:48 summary: Changes to allow all test outputs generated by twill to be saved to a folder pointed to by an environment variable "GALAXY_TEST_SAVE" if defined before running functional tests If the environment variable is empty, all tests procede as usual and test outputs are deleted without saving affected #: 3 files (770 bytes) --- a/scripts/functional_tests.py Wed Apr 13 19:14:21 2011 -0400 +++ b/scripts/functional_tests.py Thu Apr 14 08:09:48 2011 -0400 @@ -47,6 +47,8 @@ galaxy_test_host = os.environ.get( 'GALAXY_TEST_HOST', default_galaxy_test_host ) galaxy_test_port = os.environ.get( 'GALAXY_TEST_PORT', None ) + galaxy_test_save = os.environ.get( 'GALAXY_TEST_SAVE', None) + if 'HTTP_ACCEPT_LANGUAGE' not in os.environ: os.environ['HTTP_ACCEPT_LANGUAGE'] = default_galaxy_locales galaxy_test_file_dir = os.environ.get( 'GALAXY_TEST_FILE_DIR', default_galaxy_test_file_dir ) @@ -126,10 +128,14 @@ print "Database connection:", database_connection - # What requires these? + # What requires these? + # handy for (eg) functional tests to save outputs? + if galaxy_test_save: + os.environ['GALAXY_TEST_SAVE'] = galaxy_test_save + # pass in through script setenv + # will leave a copy of ALL test validate files os.environ['GALAXY_TEST_HOST'] = galaxy_test_host os.environ['GALAXY_TEST_FILE_DIR'] = galaxy_test_file_dir - # ---- Build Application -------------------------------------------------- app = None --- a/test/base/twilltestcase.py Wed Apr 13 19:14:21 2011 -0400 +++ b/test/base/twilltestcase.py Thu Apr 14 08:09:48 2011 -0400 @@ -32,7 +32,14 @@ self.port = os.environ.get( 'GALAXY_TEST_PORT' ) self.url = "http://%s:%s" % ( self.host, self.port ) self.file_dir = os.environ.get( 'GALAXY_TEST_FILE_DIR' ) + self.keepOutdir = os.environ.get( 'GALAXY_TEST_SAVE', '' ) + if self.keepOutdir > '': + try: + os.makedirs(self.keepOutdir) + except: + pass self.home() + #self.set_history() # Functions associated with files @@ -632,6 +639,10 @@ self.visit_page( "display?hid=" + hid ) data = self.last_page() file( temp_name, 'wb' ).write(data) + if self.keepOutdir > '': + ofn = os.path.join(self.keepOutdir,os.path.basename(local_name)) + shutil.copy(temp_name,ofn) + log.debug('## GALAXY_TEST_SAVE=%s. saved %s' % (self.keepOutdir,ofn)) try: # have to nest try-except in try-finally to handle 2.4 try: --- a/tools/rgenetics/rgQC.xml Wed Apr 13 19:14:21 2011 -0400 +++ b/tools/rgenetics/rgQC.xml Thu Apr 14 08:09:48 2011 -0400 @@ -28,6 +28,7 @@ </param><param name='title' value='rgQCtest1' /><output name='html_file' file='rgtestouts/rgQC/rgQCtest1.html' ftype='html' lines_diff='300'> + <param name="dbkey" value="hg18" /><extra_files type="file" name='tinywga_All_Paged.pdf' value="rgtestouts/rgQC/tinywga_All_Paged.pdf" compare="sim_size" delta = "100000"/><extra_files type="file" name='tinywga.log' value="rgtestouts/rgQC/tinywga.log" compare="diff" lines_diff="15"/><extra_files type="file" name='tinywga.frq' value="rgtestouts/rgQC/tinywga.frq" compare="diff" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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