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/

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