[galaxy-commits] commit/galaxy-central: carlfeberhard: scatterplot: improved adj. for varying y-axis sizes; pack scripts

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/369a94139390/ changeset: 369a94139390 user: carlfeberhard date: 2012-10-02 21:36:56 summary: scatterplot: improved adj. for varying y-axis sizes; pack scripts affected #: 8 files diff -r 80251cd7f94d64295ef6e64412f895d268ab988d -r 369a941393909434e0efb5c84dd831e5ab096095 static/scripts/packed/libs/underscore.js --- a/static/scripts/packed/libs/underscore.js +++ b/static/scripts/packed/libs/underscore.js @@ -1,1 +1,1 @@ -(function(){var w=this;var k=w._;var E={};var D=Array.prototype,g=Object.prototype,r=Function.prototype;var I=D.push,o=D.slice,y=D.concat,B=D.unshift,d=g.toString,j=g.hasOwnProperty;var M=D.forEach,q=D.map,F=D.reduce,c=D.reduceRight,b=D.filter,C=D.every,p=D.some,n=D.indexOf,l=D.lastIndexOf,u=Array.isArray,f=Object.keys,G=r.bind;var N=function(O){if(O instanceof N){return O}if(!(this instanceof N)){return new N(O)}this._wrapped=O};if(typeof exports!=="undefined"){if(typeof 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0}}));return{min:i.min(m),max:i.max(m)}}});return{CircsterView:b}}); \ No newline at end of file +define(["libs/underscore","libs/d3","viz/visualization"],function(i,k,j){var f=function(){this.initialize&&this.initialize.apply(this,arguments)};f.extend=Backbone.Model.extend;var l=Backbone.Model.extend({is_visible:function(p,m){var n=p.getBoundingClientRect(),o=$("svg")[0].getBoundingClientRect();if(n.right<0||n.left>o.right||n.bottom<0||n.top>o.bottom){return false}return true}});var e=Backbone.Model.extend({defaults:{prefs:{color:"#ccc"}}});var b=Backbone.View.extend({className:"circster",initialize:function(m){this.total_gap=m.total_gap;this.genome=m.genome;this.dataset_arc_height=m.dataset_arc_height;this.track_gap=5;this.label_arc_height=20;this.scale=1},render:function(){var v=this,s=this.dataset_arc_height,m=v.$el.width(),u=v.$el.height(),n=Math.min(m,u)/2-this.model.get("tracks").length*(this.dataset_arc_height+this.track_gap)-(this.label_arc_height+this.track_gap),t=this.model.get("tracks"),p=t.map(function(w,y){var z=n+y*(s+v.track_gap),x=(w.get("track_type")==="LineTrack"?g:h);return new x({track:w,track_index:y,radius_bounds:[z,z+s],genome:v.genome,total_gap:v.total_gap})});var q=k.select(v.$el[0]).append("svg").attr("width",m).attr("height",u).attr("pointer-events","all").append("svg:g").call(k.behavior.zoom().on("zoom",function(){var w=k.event.scale;q.attr("transform","translate("+k.event.translate+") scale("+w+")");if(v.scale!==w){if(v.zoom_drag_timeout){clearTimeout(v.zoom_drag_timeout)}v.zoom_drag_timeout=setTimeout(function(){i.each(p,function(x){x.update_scale(w)})},400)}})).attr("transform","translate("+m/2+","+u/2+")").append("svg:g");i.each(p,function(w){w.render(q)});var r=n+t.length*(s+v.track_gap)+v.track_gap;var o=new a({track:new e(),track_index:t.length,radius_bounds:[r,r],genome:v.genome,total_gap:v.total_gap});o.render(q)}});var c=f.extend({initialize:function(m){this.options=m;this.options.bg_stroke="ccc";this.options.bg_fill="ccc";this.options.chroms_layout=this._chroms_layout();this.options.data_bounds=this.get_data_bounds(this.options.track.get_genome_wide_data(this.options.genome));this.options.scale=1;this.options.parent_elt=null},render:function(q){this.options.parent_elt=q.append("g").attr("id","parent-"+this.options.track_index);var p=this.options.parent_elt;var o=this.options.chroms_layout,s=k.svg.arc().innerRadius(this.options.radius_bounds[0]).outerRadius(this.options.radius_bounds[1]),m=p.selectAll("g").data(o).enter().append("svg:g");m.append("path").attr("d",s).style("stroke",this.options.bg_stroke).style("fill",this.options.bg_fill).append("title").text(function(t){return t.data.chrom});this._render_data(p);var n=this.options.track.get("prefs"),r=n.block_color;if(!r){r=n.color}p.selectAll("path.chrom-data").style("stroke",r).style("fill",r)},update_scale:function(p){var o=this.options.scale;this.options.scale=p;if(p<=o){return}var n=this,m=new l();this.options.parent_elt.selectAll("path.chrom-data").filter(function(r,q){return m.is_visible(this)}).each(function(v,s){var u=k.select(this),r=u.attr("chrom"),t=n.options.genome.get_chrom_region(r),q=n.options.track.get("data_manager").get_more_detailed_data(t,"Coverage",0,p);$.when(q).then(function(z){u.remove();n._update_data_bounds();var y=i.find(n.options.chroms_layout,function(A){return A.data.chrom===r});var w=n.options.track.get("prefs"),x=w.block_color;if(!x){x=w.color}n._render_chrom_data(n.options.parent_elt,y,z).style("stroke",x).style("fill",x)})});return n},_update_data_bounds:function(){this.options.data_bounds=this.get_data_bounds(this.options.track.get_genome_wide_data(this.options.genome))},_render_data:function(p){var o=this,n=this.options.chroms_layout,m=this.options.track,s=m.get_genome_wide_data(this.options.genome),q=i.zip(n,s),r=i.map(q,function(t){var u=t[0],v=t[1];return o._render_chrom_data(p,u,v)});return p},_render_chrom_data:function(m,n,o){},_compute_path_data:function(m,n){},_chroms_layout:function(){var n=this.options.genome.get_chroms_info(),p=k.layout.pie().value(function(r){return r.len}).sort(null),q=p(n),m=this.options.total_gap/n.length,o=i.map(q,function(t,s){var r=t.endAngle-m;t.endAngle=(r>t.startAngle?r:t.startAngle);return t});return o}});var a=c.extend({initialize:function(m){this.options=m;this.options.bg_stroke="fff";this.options.bg_fill="fff";this.options.chroms_layout=this._chroms_layout()},_render_data:function(n){var m=n.selectAll("g");m.selectAll("path").attr("id",function(o){return"label-"+o.data.chrom});m.append("svg:text").filter(function(o){return o.endAngle-o.startAngle>0.08}).attr("text-anchor","middle").append("svg:textPath").attr("xlink:href",function(o){return"#label-"+o.data.chrom}).attr("startOffset","25%").text(function(o){return o.data.chrom})}});var d=c.extend({_render_chrom_data:function(m,p,n){if(!n||typeof n==="string"||n.data.length===0){return null}var q=this._compute_path_data(p,n.data);var o=m.datum(n.data),r=o.append("path").attr("class","chrom-data").attr("chrom",p.data.chrom).attr("d",q);return r},_compute_path_data:function(o,p){var m=k.scale.linear().domain(this.options.data_bounds).range(this.options.radius_bounds);var q=k.scale.linear().domain([0,p.length]).range([o.startAngle,o.endAngle]);var n=k.svg.line.radial().interpolate("linear").radius(function(r){return m(r[1])}).angle(function(s,r){return q(r)});return k.svg.area.radial().interpolate(n.interpolate()).innerRadius(m(0)).outerRadius(n.radius()).angle(n.angle())},get_data_bounds:function(m){}});var h=d.extend({get_data_bounds:function(n){var m=i.map(n,function(o){if(!o||typeof o==="string"){return 0}return o.max});return[0,(m&&typeof m!=="string"?i.max(m):0)]}});var g=d.extend({get_data_bounds:function(n){var m=i.flatten(i.map(n,function(o){if(o){return i.map(o.data,function(q){return q[1]})}else{return 0}}));return[i.min(m),i.max(m)]}});return{CircsterView:b}}); \ No newline at end of file diff -r 80251cd7f94d64295ef6e64412f895d268ab988d -r 369a941393909434e0efb5c84dd831e5ab096095 static/scripts/packed/viz/scatterplot.js --- a/static/scripts/packed/viz/scatterplot.js +++ b/static/scripts/packed/viz/scatterplot.js @@ -1,1 +1,1 @@ -define(["../libs/underscore","../libs/d3","../mvc/base-mvc"],function(){function b(e){var h=this,g=10,f=12,d=8,c=5;this.log=function(){if(this.debugging&&console&&console.debug){var i=Array.prototype.slice.call(arguments);i.unshift(this.toString());console.debug.apply(null,i)}};this.log("new TwoVarScatterplot:",e);this.defaults={id:"TwoVarScatterplot",containerSelector:"body",maxDataPoints:30000,bubbleRadius:4,entryAnimDuration:500,xNumTicks:10,yNumTicks:10,xAxisLabelBumpY:40,yAxisLabelBumpX:-35,width:500,height:500,marginTop:50,marginRight:50,marginBottom:50,marginLeft:50,xMin:null,xMax:null,yMin:null,yMax:null,xLabel:"X",yLabel:"Y"};this.config=_.extend({},this.defaults,e);this.updateConfig=function(i){_.extend(this.config,i)};this.toString=function(){return this.config.id};this.translateStr=function(i,j){return"translate("+i+","+j+")"};this.rotateStr=function(j,i,k){return"rotate("+j+","+i+","+k+")"};this.svg=d3.select(this.config.containerSelector).append("svg:svg").attr("class","chart").style("display","none");this.content=this.svg.append("svg:g").attr("class","content");this.xAxis=this.content.append("g").attr("class","axis").attr("id","x-axis");this.xAxisLabel=this.xAxis.append("text").attr("class","axis-label").attr("id","x-axis-label");this.yAxis=this.content.append("g").attr("class","axis").attr("id","y-axis");this.yAxisLabel=this.yAxis.append("text").attr("class","axis-label").attr("id","y-axis-label");this.log("built svg:",d3.selectAll("svg"));this.adjustChartDimensions=function(){this.svg.attr("width",this.config.width+(this.config.marginRight+this.config.marginLeft)).attr("height",this.config.height+(this.config.marginTop+this.config.marginBottom)).style("display","block");this.content=this.svg.select("g.content").attr("transform",this.translateStr(this.config.marginLeft,this.config.marginTop))};this.preprocessData=function(i){return i.slice(0,this.config.maxDataPoints)};this.setUpDomains=function(i,j){this.xMin=this.config.xMin||d3.min(i);this.xMax=this.config.xMax||d3.max(i);this.yMin=this.config.yMin||d3.min(j);this.yMax=this.config.yMax||d3.max(j)};this.setUpScales=function(){this.xScale=d3.scale.linear().domain([this.xMin,this.xMax]).range([0,this.config.width]),this.yScale=d3.scale.linear().domain([this.yMin,this.yMax]).range([this.config.height,0])};this.setUpXAxis=function(){this.xAxisFn=d3.svg.axis().scale(this.xScale).ticks(this.config.xNumTicks).orient("bottom");this.xAxis.attr("transform",this.translateStr(0,this.config.height)).call(this.xAxisFn);this.log("xAxis:",this.xAxis);this.xLongestLabel=d3.max(_.map([this.xMin,this.xMax],function(i){return(String(i)).length}));this.log("xLongestLabel:",this.xLongestLabel);if(this.xLongestLabel>=c){this.xAxis.selectAll("g").filter(":nth-child(odd)").style("display","none")}this.xAxisLabel.attr("x",this.config.width/2).attr("y",this.config.xAxisLabelBumpY).attr("text-anchor","middle").text(this.config.xLabel);this.log("xAxisLabel:",this.xAxisLabel)};this.setUpYAxis=function(){this.yAxisFn=d3.svg.axis().scale(this.yScale).ticks(this.config.yNumTicks).orient("left");this.yAxis.call(this.yAxisFn);this.log("yAxis:",this.yAxis);this.yLongestLabel=d3.max(_.map([this.yMin,this.yMax],function(j){return(String(j)).length}));this.log("yLongestLabel:",this.yLongestLabel);var i=this.yLongestLabel*g+(d);if(this.config.yAxisLabelBumpX>-(i)){this.config.yAxisLabelBumpX=-(i)}if(this.config.marginLeft<i){this.config.marginLeft=i+f;this.adjustChartDimensions()}this.log("this.config.yAxisLableBumpx, this.config.marginLeft:",this.config.yAxisLabelBumpX,this.config.marginLeft);this.yAxisLabel.attr("x",this.config.yAxisLabelBumpX).attr("y",this.config.height/2).attr("text-anchor","middle").attr("transform",this.rotateStr(-90,this.config.yAxisLabelBumpX,this.config.height/2)).text(this.config.yLabel);this.log("yAxisLabel:",this.yAxisLabel)};this.renderGrid=function(){this.vGridLines=this.content.selectAll("line.v-grid-line").data(this.xScale.ticks(this.xAxisFn.ticks()[0]));this.vGridLines.enter().append("svg:line").classed("grid-line v-grid-line",true);this.vGridLines.attr("x1",this.xScale).attr("y1",0).attr("x2",this.xScale).attr("y2",this.config.height);this.vGridLines.exit().remove();this.log("vGridLines:",this.vGridLines);this.hGridLines=this.content.selectAll("line.h-grid-line").data(this.yScale.ticks(this.yAxisFn.ticks()[0]));this.hGridLines.enter().append("svg:line").classed("grid-line h-grid-line",true);this.hGridLines.attr("x1",0).attr("y1",this.yScale).attr("x2",this.config.width).attr("y2",this.yScale);this.hGridLines.exit().remove();this.log("hGridLines:",this.hGridLines)};this.glyphEnterState=function(i){};this.glyphFinalState=function(i){};this.glyphExitState=function(i){};this.renderDatapoints=function(i,l){var k=function(n,m){return h.xScale(i[m])};var j=function(n,m){return h.yScale(l[m])};this.datapoints=this.content.selectAll(".glyph").data(i);this.datapoints.enter().append("svg:circle").attr("class","glyph").attr("cx",k).attr("cy",0).attr("r",0);this.datapoints.transition().duration(this.config.entryAnimDuration).attr("cx",k).attr("cy",j).attr("r",this.config.bubbleRadius);this.datapoints.exit().transition().duration(this.config.entryAnimDuration).attr("cy",this.config.height).attr("r",0).style("fill-opacity",0).remove();this.log(this.datapoints,"glyphs rendered")};this.render=function(i,j){this.log("renderScatterplot",i.length,j.length,this.config);i=this.preprocessData(i);j=this.preprocessData(j);this.log("xCol len",i.length,"yCol len",j.length);this.setUpDomains(i,j);this.log("xMin, xMax, yMin, yMax:",this.xMin,this.xMax,this.yMin,this.yMax);this.setUpScales();this.adjustChartDimensions();this.setUpXAxis();this.setUpYAxis();this.renderGrid();this.renderDatapoints(i,j)}}var a=BaseView.extend(LoggableMixin).extend({tagName:"form",className:"scatterplot-settings-form",events:{"click #render-button":"renderScatterplot"},initialize:function(c){if(!c||!c.dataset){throw ("ScatterplotView requires a dataset")}else{this.dataset=c.dataset}this.apiDatasetsURL=c.apiDatasetsURL;this.chartConfig=c.chartConfig||{};this.log("this.chartConfig:",this.chartConfig);this.plot=new b(this.chartConfig)},render:function(){var c=this,e="",d="";this.dataset.metadata_column_types=this.dataset.metadata_column_types.split(", ");_.each(this.dataset.metadata_column_types,function(h,g){if(h==="int"||h==="float"){var f="column "+g;if(c.dataset.metadata_column_names){f=c.dataset.metadata_column_names[g]}d+='<option value="'+g+'">'+f+"</column>"}});e+='<div id="x-column-input">';e+='<label for="">Data column for X: </label><select name="x-column">'+d+"</select>";e+="</div>";e+='<div id="y-column-input">';e+='<label for="">Data column for Y: </label><select name="y-column">'+d+"</select>";e+="</div>";e+='<input id="render-button" type="button" value="Draw" />';e+='<div class="clear"></div>';this.$el.append(e);this.$el.find("#render-button");return this},renderScatterplot:function(){var d=this,e=this.apiDatasetsURL+"/"+this.dataset.id+"?data_type=raw_data&",i=this.$el.find('[name="x-column"]'),j=i.val(),g=i.children('[value="'+j+'"]').text(),h=this.$el.find('[name="y-column"]'),f=h.val(),c=h.children('[value="'+f+'"]').text();this.log(g,c);this.chartConfig.xLabel=g;this.chartConfig.yLabel=c;d.plot.updateConfig(this.chartConfig);e+=jQuery.param({columns:"["+[j,f]+"]"});this.log("url:",e);jQuery.ajax({url:e,dataType:"json",success:function(k){d.endpoint=k.endpoint;d.plot.render(_.map(k.data,function(l){return l[0]}),_.map(k.data,function(l){return l[1]}))},error:function(m,k,l){alert("ERROR:"+k+"\n"+l)}})}});return{ScatterplotView:a}}); \ No newline at end of file +define(["../libs/underscore","../libs/d3","../mvc/base-mvc"],function(){function b(f){var i=this,d=10,h=7,g=10,e=8,c=5;this.log=function(){if(this.debugging&&console&&console.debug){var j=Array.prototype.slice.call(arguments);j.unshift(this.toString());console.debug.apply(null,j)}};this.log("new TwoVarScatterplot:",f);this.defaults={id:"TwoVarScatterplot",containerSelector:"body",maxDataPoints:30000,bubbleRadius:4,entryAnimDuration:500,xNumTicks:10,yNumTicks:10,xAxisLabelBumpY:40,yAxisLabelBumpX:-35,width:500,height:500,marginTop:50,marginRight:50,marginBottom:50,marginLeft:50,xMin:null,xMax:null,yMin:null,yMax:null,xLabel:"X",yLabel:"Y"};this.config=_.extend({},this.defaults,f);this.updateConfig=function(j){_.extend(this.config,j)};this.toString=function(){return this.config.id};this.translateStr=function(j,k){return"translate("+j+","+k+")"};this.rotateStr=function(k,j,l){return"rotate("+k+","+j+","+l+")"};this.svg=d3.select(this.config.containerSelector).append("svg:svg").attr("class","chart").style("display","none");this.content=this.svg.append("svg:g").attr("class","content");this.xAxis=this.content.append("g").attr("class","axis").attr("id","x-axis");this.xAxisLabel=this.xAxis.append("text").attr("class","axis-label").attr("id","x-axis-label");this.yAxis=this.content.append("g").attr("class","axis").attr("id","y-axis");this.yAxisLabel=this.yAxis.append("text").attr("class","axis-label").attr("id","y-axis-label");this.log("built svg:",d3.selectAll("svg"));this.adjustChartDimensions=function(m,k,j,l){m=m||0;k=k||0;j=j||0;l=l||0;this.svg.attr("width",this.config.width+(this.config.marginRight+k)+(this.config.marginLeft+l)).attr("height",this.config.height+(this.config.marginTop+m)+(this.config.marginBottom+j)).style("display","block");this.content=this.svg.select("g.content").attr("transform",this.translateStr(this.config.marginLeft+l,this.config.marginTop+m))};this.preprocessData=function(j){return j.slice(0,this.config.maxDataPoints)};this.setUpDomains=function(j,k){this.xMin=this.config.xMin||d3.min(j);this.xMax=this.config.xMax||d3.max(j);this.yMin=this.config.yMin||d3.min(k);this.yMax=this.config.yMax||d3.max(k)};this.setUpScales=function(){this.xScale=d3.scale.linear().domain([this.xMin,this.xMax]).range([0,this.config.width]),this.yScale=d3.scale.linear().domain([this.yMin,this.yMax]).range([this.config.height,0])};this.setUpXAxis=function(){this.xAxisFn=d3.svg.axis().scale(this.xScale).ticks(this.config.xNumTicks).orient("bottom");this.xAxis.attr("transform",this.translateStr(0,this.config.height)).call(this.xAxisFn);this.xLongestLabel=d3.max(_.map([this.xMin,this.xMax],function(j){return(String(j)).length}));if(this.xLongestLabel>=c){this.xAxis.selectAll("g").filter(":nth-child(odd)").style("display","none")}this.xAxisLabel.attr("x",this.config.width/2).attr("y",this.config.xAxisLabelBumpY).attr("text-anchor","middle").text(this.config.xLabel)};this.setUpYAxis=function(){this.yAxisFn=d3.svg.axis().scale(this.yScale).ticks(this.config.yNumTicks).orient("left");this.yAxis.call(this.yAxisFn);this.log("yAxis:",this.yAxis);var j=this.yAxis.selectAll("text").filter(function(n,m){return m!==0});this.yLongestLabel=d3.max(j[0].map(function(n,m){return(d3.select(n).text()).length}))||0;var k=d+(this.yLongestLabel*h)+e+g;this.config.yAxisLabelBumpX=-(k-g);if(this.config.marginLeft<k){var l=(k)-this.config.marginLeft;l=(l<0)?(0):(l);this.log("adjusting:",l);this.adjustChartDimensions(0,0,0,l)}this.yAxisLabel.attr("x",this.config.yAxisLabelBumpX).attr("y",this.config.height/2).attr("text-anchor","middle").attr("transform",this.rotateStr(-90,this.config.yAxisLabelBumpX,this.config.height/2)).text(this.config.yLabel)};this.renderGrid=function(){this.vGridLines=this.content.selectAll("line.v-grid-line").data(this.xScale.ticks(this.xAxisFn.ticks()[0]));this.vGridLines.enter().append("svg:line").classed("grid-line v-grid-line",true);this.vGridLines.attr("x1",this.xScale).attr("y1",0).attr("x2",this.xScale).attr("y2",this.config.height);this.vGridLines.exit().remove();this.hGridLines=this.content.selectAll("line.h-grid-line").data(this.yScale.ticks(this.yAxisFn.ticks()[0]));this.hGridLines.enter().append("svg:line").classed("grid-line h-grid-line",true);this.hGridLines.attr("x1",0).attr("y1",this.yScale).attr("x2",this.config.width).attr("y2",this.yScale);this.hGridLines.exit().remove()};this.glyphEnterState=function(j){};this.glyphFinalState=function(j){};this.glyphExitState=function(j){};this.renderDatapoints=function(j,m){var l=function(o,n){return i.xScale(j[n])};var k=function(o,n){return i.yScale(m[n])};this.datapoints=this.content.selectAll(".glyph").data(j);this.datapoints.enter().append("svg:circle").attr("class","glyph").attr("cx",l).attr("cy",0).attr("r",0);this.datapoints.transition().duration(this.config.entryAnimDuration).attr("cx",l).attr("cy",k).attr("r",this.config.bubbleRadius);this.datapoints.exit().transition().duration(this.config.entryAnimDuration).attr("cy",this.config.height).attr("r",0).style("fill-opacity",0).remove()};this.render=function(j,k){this.log("renderScatterplot",j.length,k.length,this.config);j=this.preprocessData(j);k=this.preprocessData(k);this.setUpDomains(j,k);this.setUpScales();this.adjustChartDimensions();this.setUpXAxis();this.setUpYAxis();this.renderGrid();this.renderDatapoints(j,k)}}var a=BaseView.extend(LoggableMixin).extend({tagName:"form",className:"scatterplot-settings-form",loadingIndicatorImagePath:(galaxy_paths.get("image_path")+"/loading_large_white_bg.gif"),events:{"click #render-button":"renderScatterplot"},initialize:function(c){if(!c||!c.dataset){throw ("ScatterplotView requires a dataset")}else{this.dataset=c.dataset}this.apiDatasetsURL=c.apiDatasetsURL;this.chartConfig=c.chartConfig||{};this.log("this.chartConfig:",this.chartConfig);this.plot=new b(this.chartConfig)},render:function(){var c=this,e="",d="";this.dataset.metadata_column_types=this.dataset.metadata_column_types.split(", ");_.each(this.dataset.metadata_column_types,function(h,g){if(h==="int"||h==="float"){var f="column "+g;if(c.dataset.metadata_column_names){f=c.dataset.metadata_column_names[g]}d+='<option value="'+g+'">'+f+"</option>"}});e+='<div id="loading-indicator" style="display: none;">';e+='<img class="loading-img" src='+this.loadingIndicatorImagePath+" />";e+='<span class="loading-message"></span>';e+="</div>";e+='<div id="x-column-input">';e+='<label for="">Data column for X: </label><select name="x-column">'+d+"</select>";e+="</div>";e+='<div id="y-column-input">';e+='<label for="">Data column for Y: </label><select name="y-column">'+d+"</select>";e+="</div>";e+='<input id="render-button" type="button" value="Draw" />';e+='<div class="clear"></div>';this.$el.append(e);this.$el.find("#render-button");return this},showLoadingIndicator:function(c){c=c||"";this.$el.find("div#loading-indicator").children(".loading-message").text(c);this.$el.find("div#loading-indicator").show("fast")},hideLoadingIndicator:function(){this.$el.find("div#loading-indicator").hide("fast")},renderScatterplot:function(){var d=this,e=this.apiDatasetsURL+"/"+this.dataset.id+"?data_type=raw_data&",i=this.$el.find('[name="x-column"]'),j=i.val(),g=i.children('[value="'+j+'"]').text(),h=this.$el.find('[name="y-column"]'),f=h.val(),c=h.children('[value="'+f+'"]').text();this.log(g,c);this.chartConfig.xLabel=g;this.chartConfig.yLabel=c;d.plot.updateConfig(this.chartConfig);e+=jQuery.param({columns:"["+[j,f]+"]"});this.log("url:",e);this.showLoadingIndicator("Fetching data...");jQuery.ajax({url:e,dataType:"json",success:function(k){d.showLoadingIndicator("Rendering...");d.endpoint=k.endpoint;d.plot.render(_.map(k.data,function(l){return l[0]}),_.map(k.data,function(l){return l[1]}));d.hideLoadingIndicator()},error:function(m,k,l){d.hideLoadingIndicator();alert("ERROR:"+k+"\n"+l)}})}});return{ScatterplotView:a}}); \ No newline at end of file diff -r 80251cd7f94d64295ef6e64412f895d268ab988d -r 369a941393909434e0efb5c84dd831e5ab096095 static/scripts/packed/viz/sweepster.js --- a/static/scripts/packed/viz/sweepster.js +++ b/static/scripts/packed/viz/sweepster.js @@ -1,1 +1,1 @@ -define(["libs/d3","viz/trackster/util","viz/visualization","viz/trackster/tracks","mvc/tools","mvc/data"],function(o,f,n,h,g,d){var m=Backbone.Model.extend({defaults:{inputs:null,values:null}});var p=Backbone.RelationalModel.extend({defaults:{tool:null,tree_data:null},initialize:function(r){var q=this;this.get("tool").get("inputs").each(function(s){if(!s.get_samples()){return}s.on("change:min change:max change:num_samples",function(t){if(t.get("in_ptree")){q.set_tree_data()}},q);s.on("change:in_ptree",function(t){if(t.get("in_ptree")){q.add_param(t)}else{q.remove_param(t)}q.set_tree_data()},q)});if(r.config){_.each(r.config,function(t){var s=q.get("tool").get("inputs").find(function(u){return u.get("name")===t.name});q.add_param(s);s.set(t)})}},add_param:function(q){if(q.get("ptree_index")){return}q.set("in_ptree",true);q.set("ptree_index",this.get_tree_params().length)},remove_param:function(q){q.set("in_ptree",false);q.set("ptree_index",null);_(this.get_tree_params()).each(function(r,s){r.set("ptree_index",s+1)})},set_tree_data:function(){var r=_.map(this.get_tree_params(),function(t){return{param:t,samples:t.get_samples()}});var q=0,s=function(w,t){var y=w[t],x=y.param,v=x.get("label"),u=y.samples;if(w.length-1===t){return _.map(u,function(z){return{id:q++,name:z,param:x,value:z}})}return _.map(u,function(z){return{id:q++,name:z,param:x,value:z,children:s(w,t+1)}})};this.set("tree_data",{name:"Root",id:q++,children:(r.length!==0?s(r,0):null)})},get_tree_params:function(){return _(this.get("tool").get("inputs").where({in_ptree:true})).sortBy(function(q){return q.get("ptree_index")})},get_num_leaves:function(){return this.get_tree_params().reduce(function(q,r){return q*r.get_samples().length},1)},get_node_settings:function(u){var s=this.get("tool").get_inputs_dict();var v=u.parent;if(v){while(v.depth!==0){s[v.param.get("name")]=v.value;v=v.parent}}var q=this,r=function(x,w){if(x.param){w[x.param.get("name")]=x.value}if(!x.children){return new m({inputs:q.get("tool").get("inputs"),values:w})}else{return _.flatten(_.map(x.children,function(y){return r(y,_.clone(w))}))}},t=r(u,s);if(!_.isArray(t)){t=[t]}return t},get_connected_nodes:function(s){var t=function(u){if(!u.children){return u}else{return _.flatten([u,_.map(u.children,function(v){return t(v)})])}};var r=[],q=s.parent;while(q){r.push(q);q=q.parent}return _.flatten([r,t(s)])},get_leaf:function(r){var s=this.get("tree_data"),q=function(t){return _.find(t,function(u){return r[u.param.get("name")]===u.value})};while(s.children){s=q(s.children)}return s},toJSON:function(){return this.get_tree_params().map(function(q){return{name:q.get("name"),min:q.get("min"),max:q.get("max"),num_samples:q.get("num_samples")}})}});var c=Backbone.RelationalModel.extend({defaults:{track:null,mode:"Pack",settings:null,regions:null},relations:[{type:Backbone.HasMany,key:"regions",relatedModel:n.GenomeRegion}],initialize:function(q){if(q.track){var r=_.extend({data_url:galaxy_paths.get("raw_data_url"),converted_datasets_state_url:galaxy_paths.get("dataset_state_url")},q.track);this.set("track",h.object_from_template(r,{},null))}},same_settings:function(q){var r=this.get("settings"),s=q.get("settings");for(var t in r){if(!s[t]||r[t]!==s[t]){return false}}return true},toJSON:function(){return{track:this.get("track").to_dict(),settings:this.get("settings"),regions:this.get("regions")}}});var a=Backbone.Collection.extend({model:c});var i=n.Visualization.extend({defaults:_.extend({},n.Visualization.prototype.defaults,{dataset:null,tool:null,parameter_tree:null,regions:null,tracks:null,default_mode:"Pack"}),relations:[{type:Backbone.HasOne,key:"dataset",relatedModel:d.Dataset},{type:Backbone.HasOne,key:"tool",relatedModel:g.Tool},{type:Backbone.HasMany,key:"regions",relatedModel:n.GenomeRegion},{type:Backbone.HasMany,key:"tracks",relatedModel:c}],initialize:function(q){var r=this.get("tool").copy(true);this.set("tool_with_samplable_inputs",r);this.set("parameter_tree",new p({tool:r,config:q.tree_config}))},add_track:function(q){this.get("tracks").add(q)},toJSON:function(){return{id:this.get("id"),title:"Parameter exploration for dataset '"+this.get("dataset").get("name")+"'",type:"sweepster",dataset_id:this.get("dataset").id,tool_id:this.get("tool").id,regions:this.get("regions").toJSON(),tree_config:this.get("parameter_tree").toJSON(),tracks:this.get("tracks").toJSON()}}});var l=Backbone.View.extend({tagName:"tr",TILE_LEN:250,initialize:function(q){this.canvas_manager=q.canvas_manager;this.render();this.model.on("change:track change:mode",this.draw_tiles,this)},render:function(){var v=this.model.get("settings"),r=v.get("values"),t=$("<td/>").addClass("settings").appendTo(this.$el),s=$("<div/>").addClass("track-info").hide().appendTo(t);s.append($("<div/>").css("font-weight","bold").text("Track Settings"));v.get("inputs").each(function(x){s.append(x.get("label")+": "+r[x.get("name")]+"<br/>")});var q=this,w=$("<button/>").appendTo(s).text("Run on complete dataset").click(function(){s.toggle();q.trigger("run_on_dataset",v)});var u=create_icon_buttons_menu([{title:"Settings",icon_class:"gear track-settings",on_click:function(){s.toggle()}},{title:"Remove",icon_class:"cross-circle",on_click:function(){q.$el.remove();$(".bs-tooltip").remove()}}]);t.prepend(u.$el);this.model.get("regions").each(function(){q.$el.append($("<td/>").addClass("tile").html($("<img/>").attr("src",galaxy_paths.get("image_path")+"/loading_large_white_bg.gif")))});if(this.model.get("track")){this.draw_tiles()}},draw_tiles:function(){var r=this,q=this.model.get("track"),t=this.model.get("regions"),s=this.$el.find("td.tile");if(!q){return}$.when(q.data_manager.data_is_ready()).then(function(u){t.each(function(x,w){var v=x.length()/r.TILE_LEN,z=1/v,y=r.model.get("mode");$.when(q.data_manager.get_data(x,y,v,{})).then(function(B){var A=r.canvas_manager.new_canvas();A.width=r.TILE_LEN;A.height=q.get_canvas_height(B,y,z,A.width);q.draw_tile(B,A.getContext("2d"),y,v,x,z);$(s[w]).empty().append(A)})})})}});var b=Backbone.View.extend({number_input_template:'<div class="form-row-input sweep"><input class="min" type="text" size="6" value="<%= min %>"> - <input class="max" type="text" size="6" value="<%= max %>"> samples: <input class="num_samples" type="text" size="1" value="<%= num_samples %>"></div>',select_input_template:'<div class="form-row-input sweep"><%= options %></div>',initialize:function(q){this.$el=q.tool_row;this.render()},render:function(){var r=this.model,v=r.get("type"),x=this.$el.find(".form-row-input"),t=null;x.find(":input").change(function(){r.set("value",$(this).val())});if(v==="number"){t=$(_.template(this.number_input_template,this.model.toJSON()))}else{if(v==="select"){var s=_.map(this.$el.find("select option"),function(y){return $(y).val()}),u=s.join(", ");t=$(_.template(this.select_input_template,{options:u}))}}t.insertAfter(x);var q=this,w=create_icon_buttons_menu([{title:"Add parameter to tree",icon_class:"plus-button",on_click:function(){r.set("in_ptree",true);x.hide();t.show();$(this).hide();q.$el.find(".icon-button.toggle").show()}},{title:"Remove parameter from tree",icon_class:"toggle",on_click:function(){r.set("in_ptree",false);t.hide();x.show();$(this).hide();q.$el.find(".icon-button.plus-button").show()}}],{});this.$el.prepend(w.$el);if(r.get("in_ptree")){x.hide();q.$el.find(".icon-button.plus-button").hide()}else{q.$el.find(".icon-button.toggle").hide();t.hide()}_.each(["min","max","num_samples"],function(y){t.find("."+y).change(function(){r.set(y,parseFloat($(this).val()))})})}});var k=Backbone.View.extend({className:"tree-design",initialize:function(q){this.render()},render:function(){var s=new g.ToolFormView({model:this.model.get("tool")});s.render();this.$el.append(s.$el);var r=this,q=r.model.get("tool").get("inputs");this.$el.find(".form-row").not(".form-actions").each(function(t){var u=new b({model:q.at(t),tool_row:$(this)})})}});var j=Backbone.View.extend({className:"tool-parameter-tree",initialize:function(q){this.model.on("change:tree_data",this.render,this)},render:function(){this.$el.children().remove();var y=this.model.get_tree_params();if(!y.length){return}this.width=100*(2+y.length);this.height=15*this.model.get_num_leaves();var x=this;var w=o.layout.cluster().size([this.height,this.width-160]);var s=o.svg.diagonal().projection(function(z){return[z.y,z.x]});var q=w.nodes(this.model.get("tree_data"));var t=_.uniq(_.pluck(q,"y"));_.each(y,function(B,A){var z=t[A+1],C=$("#center").position().left;x.$el.append($("<div>").addClass("label").text(B.get("label")).css("left",z+C))});var r=o.select(this.$el[0]).append("svg").attr("width",this.width).attr("height",this.height+30).append("g").attr("transform","translate(40, 20)");var v=r.selectAll("path.link").data(w.links(q)).enter().append("path").attr("class","link").attr("d",s);var u=r.selectAll("g.node").data(q).enter().append("g").attr("class","node").attr("transform",function(z){return"translate("+z.y+","+z.x+")"}).on("mouseover",function(A){var z=_.pluck(x.model.get_connected_nodes(A),"id");u.filter(function(B){return _.find(z,function(C){return C===B.id})!==undefined}).style("fill","#f00")}).on("mouseout",function(){u.style("fill","#000")});u.append("circle").attr("r",9);u.append("text").attr("dx",function(z){return z.children?-12:12}).attr("dy",3).attr("text-anchor",function(z){return z.children?"end":"start"}).text(function(z){return z.name})}});var e=Backbone.View.extend({className:"Sweepster",helpText:"<div><h4>Getting Started</h4><ol><li>Create a parameter tree by using the icons next to the tool's parameter names to add or remove parameters.<li>Adjust the tree by using parameter inputs to select min, max, and number of samples<li>Run the tool with different settings by clicking on tree nodes</ol></div>",initialize:function(r){this.canvas_manager=new n.CanvasManager(this.$el.parents("body"));this.tool_param_tree_view=new j({model:this.model.get("parameter_tree")});this.track_collection_container=$("<table/>").addClass("tracks");this.model.get("parameter_tree").on("change:tree_data",this.handle_node_clicks,this);var q=this;this.model.get("tracks").each(function(s){s.get("track").view=q});this.block_color=f.get_random_color();this.reverse_strand_color=f.get_random_color([this.block_color,"#ffffff"])},render:function(){var w=new k({model:this.model.get("parameter_tree")});$("#left").append(w.$el);var z=this,t=z.model.get("regions"),x=$("<tr/>").appendTo(this.track_collection_container);t.each(function(A){x.append($("<th>").text(A.toString()))});x.children().first().attr("colspan",2);var u=$("<div>").addClass("tiles");$("#right").append(u.append(this.track_collection_container));z.model.get("tracks").each(function(A){z.add_track(A)});var y=$(this.helpText).addClass("help"),v=create_icon_buttons_menu([{title:"Close",icon_class:"cross-circle",on_click:function(){$(".bs-tooltip").remove();y.remove()}}]);y.prepend(v.$el.css("float","right"));$("#center").append(y);this.tool_param_tree_view.render();$("#center").append(this.tool_param_tree_view.$el);this.handle_node_clicks();var s=create_icon_buttons_menu([{icon_class:"chevron-expand",title:"Set display mode"},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location="${h.url_for( controller='visualization', action='list' )}"}}],{tooltip_config:{placement:"bottom"}});var r=["Squish","Pack"],q={};_.each(r,function(A){q[A]=function(){z.model.set("default_mode",A);z.model.get("tracks").each(function(B){B.set("mode",A)})}});make_popupmenu(s.$el.find(".chevron-expand"),q);s.$el.attr("style","float: right");$("#right .unified-panel-header-inner").append(s.$el)},run_tool_on_dataset:function(r){var q=this.model.get("tool"),t=q.get("name"),s=this.model.get("dataset");q.set_input_values(r.get("values"));$.when(q.rerun(s)).then(function(u){});show_modal("Running "+t+" on complete dataset",t+" is running on dataset '"+s.get("name")+"'. Outputs are in the dataset's history.",{Ok:function(){hide_modal()}})},add_track:function(t){var r=this,s=this.model.get("parameter_tree");r.model.add_track(t);var q=new l({model:t,canvas_manager:r.canvas_manager});q.on("run_on_dataset",r.run_tool_on_dataset,r);r.track_collection_container.append(q.$el);q.$el.hover(function(){var v=s.get_leaf(t.get("settings").get("values"));var u=_.pluck(s.get_connected_nodes(v),"id");o.select(r.tool_param_tree_view.$el[0]).selectAll("g.node").filter(function(w){return _.find(u,function(x){return x===w.id})!==undefined}).style("fill","#f00")},function(){o.select(r.tool_param_tree_view.$el[0]).selectAll("g.node").style("fill","#000")});return t},handle_node_clicks:function(){var q=this,r=this.model.get("parameter_tree"),t=this.model.get("regions"),s=o.select(this.tool_param_tree_view.$el[0]).selectAll("g.node");s.on("click",function(z,w){var v=q.model.get("tool"),y=q.model.get("dataset"),x=r.get_node_settings(z),u=$.Deferred();if(x.length>=10){show_modal("Whoa there cowboy!","You clicked on a node to try "+q.model.get("tool").get("name")+" with "+x.length+" different combinations of settings. You can only run 10 jobs at a time.",{Ok:function(){hide_modal();u.resolve(false)}})}else{u.resolve(true)}$.when(u).then(function(A){if(!A){return}var B=_.map(x,function(C){var D=new c({settings:C,regions:t,mode:q.model.get("default_mode")});q.add_track(D);return D});_.each(B,function(D,C){setTimeout(function(){v.set_input_values(D.get("settings").get("values"));$.when(v.rerun(y,t)).then(function(F){var G=_.extend({data_url:galaxy_paths.get("raw_data_url"),converted_datasets_state_url:galaxy_paths.get("dataset_state_url")},F.first().get("track_config")),E=h.object_from_template(G,q,null);E.data_manager.set("data_type","raw_data");E.prefs.block_color=q.block_color;E.prefs.reverse_strand_color=q.reverse_strand_color;D.set("track",E)})},C*10000)})})})}});return{SweepsterVisualization:i,SweepsterVisualizationView:e}}); \ No newline at end of file +define(["libs/underscore","libs/d3","viz/trackster/util","viz/visualization","viz/trackster/tracks","mvc/tools","mvc/data"],function(m,q,f,o,h,g,d){var n=Backbone.Model.extend({defaults:{inputs:null,values:null}});var p=Backbone.RelationalModel.extend({defaults:{tool:null,tree_data:null},initialize:function(s){var r=this;this.get("tool").get("inputs").each(function(t){if(!t.get_samples()){return}t.on("change:min change:max change:num_samples",function(u){if(u.get("in_ptree")){r.set_tree_data()}},r);t.on("change:in_ptree",function(u){if(u.get("in_ptree")){r.add_param(u)}else{r.remove_param(u)}r.set_tree_data()},r)});if(s.config){m.each(s.config,function(u){var t=r.get("tool").get("inputs").find(function(v){return v.get("name")===u.name});r.add_param(t);t.set(u)})}},add_param:function(r){if(r.get("ptree_index")){return}r.set("in_ptree",true);r.set("ptree_index",this.get_tree_params().length)},remove_param:function(r){r.set("in_ptree",false);r.set("ptree_index",null);m(this.get_tree_params()).each(function(s,t){s.set("ptree_index",t+1)})},set_tree_data:function(){var s=m.map(this.get_tree_params(),function(u){return{param:u,samples:u.get_samples()}});var r=0,t=function(x,u){var z=x[u],y=z.param,w=y.get("label"),v=z.samples;if(x.length-1===u){return m.map(v,function(A){return{id:r++,name:A,param:y,value:A}})}return m.map(v,function(A){return{id:r++,name:A,param:y,value:A,children:t(x,u+1)}})};this.set("tree_data",{name:"Root",id:r++,children:(s.length!==0?t(s,0):null)})},get_tree_params:function(){return m(this.get("tool").get("inputs").where({in_ptree:true})).sortBy(function(r){return r.get("ptree_index")})},get_num_leaves:function(){return this.get_tree_params().reduce(function(r,s){return r*s.get_samples().length},1)},get_node_settings:function(v){var t=this.get("tool").get_inputs_dict();var w=v.parent;if(w){while(w.depth!==0){t[w.param.get("name")]=w.value;w=w.parent}}var r=this,s=function(y,x){if(y.param){x[y.param.get("name")]=y.value}if(!y.children){return new n({inputs:r.get("tool").get("inputs"),values:x})}else{return m.flatten(m.map(y.children,function(z){return s(z,m.clone(x))}))}},u=s(v,t);if(!m.isArray(u)){u=[u]}return u},get_connected_nodes:function(t){var u=function(v){if(!v.children){return v}else{return m.flatten([v,m.map(v.children,function(w){return u(w)})])}};var s=[],r=t.parent;while(r){s.push(r);r=r.parent}return m.flatten([s,u(t)])},get_leaf:function(s){var t=this.get("tree_data"),r=function(u){return m.find(u,function(v){return s[v.param.get("name")]===v.value})};while(t.children){t=r(t.children)}return t},toJSON:function(){return this.get_tree_params().map(function(r){return{name:r.get("name"),min:r.get("min"),max:r.get("max"),num_samples:r.get("num_samples")}})}});var c=Backbone.RelationalModel.extend({defaults:{track:null,mode:"Pack",settings:null,regions:null},relations:[{type:Backbone.HasMany,key:"regions",relatedModel:o.GenomeRegion}],initialize:function(r){if(r.track){var s=m.extend({data_url:galaxy_paths.get("raw_data_url"),converted_datasets_state_url:galaxy_paths.get("dataset_state_url")},r.track);this.set("track",h.object_from_template(s,{},null))}},same_settings:function(r){var s=this.get("settings"),t=r.get("settings");for(var u in s){if(!t[u]||s[u]!==t[u]){return false}}return true},toJSON:function(){return{track:this.get("track").to_dict(),settings:this.get("settings"),regions:this.get("regions")}}});var a=Backbone.Collection.extend({model:c});var i=o.Visualization.extend({defaults:m.extend({},o.Visualization.prototype.defaults,{dataset:null,tool:null,parameter_tree:null,regions:null,tracks:null,default_mode:"Pack"}),relations:[{type:Backbone.HasOne,key:"dataset",relatedModel:d.Dataset},{type:Backbone.HasOne,key:"tool",relatedModel:g.Tool},{type:Backbone.HasMany,key:"regions",relatedModel:o.GenomeRegion},{type:Backbone.HasMany,key:"tracks",relatedModel:c}],initialize:function(r){var s=this.get("tool").copy(true);this.set("tool_with_samplable_inputs",s);this.set("parameter_tree",new p({tool:s,config:r.tree_config}))},add_track:function(r){this.get("tracks").add(r)},toJSON:function(){return{id:this.get("id"),title:"Parameter exploration for dataset '"+this.get("dataset").get("name")+"'",type:"sweepster",dataset_id:this.get("dataset").id,tool_id:this.get("tool").id,regions:this.get("regions").toJSON(),tree_config:this.get("parameter_tree").toJSON(),tracks:this.get("tracks").toJSON()}}});var l=Backbone.View.extend({tagName:"tr",TILE_LEN:250,initialize:function(r){this.canvas_manager=r.canvas_manager;this.render();this.model.on("change:track change:mode",this.draw_tiles,this)},render:function(){var w=this.model.get("settings"),s=w.get("values"),u=$("<td/>").addClass("settings").appendTo(this.$el),t=$("<div/>").addClass("track-info").hide().appendTo(u);t.append($("<div/>").css("font-weight","bold").text("Track Settings"));w.get("inputs").each(function(y){t.append(y.get("label")+": "+s[y.get("name")]+"<br/>")});var r=this,x=$("<button/>").appendTo(t).text("Run on complete dataset").click(function(){t.toggle();r.trigger("run_on_dataset",w)});var v=create_icon_buttons_menu([{title:"Settings",icon_class:"gear track-settings",on_click:function(){t.toggle()}},{title:"Remove",icon_class:"cross-circle",on_click:function(){r.$el.remove();$(".bs-tooltip").remove()}}]);u.prepend(v.$el);this.model.get("regions").each(function(){r.$el.append($("<td/>").addClass("tile").html($("<img/>").attr("src",galaxy_paths.get("image_path")+"/loading_large_white_bg.gif")))});if(this.model.get("track")){this.draw_tiles()}},draw_tiles:function(){var s=this,r=this.model.get("track"),u=this.model.get("regions"),t=this.$el.find("td.tile");if(!r){return}$.when(r.data_manager.data_is_ready()).then(function(v){u.each(function(y,x){var w=y.length()/s.TILE_LEN,A=1/w,z=s.model.get("mode");$.when(r.data_manager.get_data(y,z,w,{})).then(function(C){var B=s.canvas_manager.new_canvas();B.width=s.TILE_LEN;B.height=r.get_canvas_height(C,z,A,B.width);r.draw_tile(C,B.getContext("2d"),z,w,y,A);$(t[x]).empty().append(B)})})})}});var b=Backbone.View.extend({number_input_template:'<div class="form-row-input sweep"><input class="min" type="text" size="6" value="<%= min %>"> - <input class="max" type="text" size="6" value="<%= max %>"> samples: <input class="num_samples" type="text" size="1" value="<%= num_samples %>"></div>',select_input_template:'<div class="form-row-input sweep"><%= options %></div>',initialize:function(r){this.$el=r.tool_row;this.render()},render:function(){var s=this.model,w=s.get("type"),y=this.$el.find(".form-row-input"),u=null;y.find(":input").change(function(){s.set("value",$(this).val())});if(w==="number"){u=$(m.template(this.number_input_template,this.model.toJSON()))}else{if(w==="select"){var t=m.map(this.$el.find("select option"),function(z){return $(z).val()}),v=t.join(", ");u=$(m.template(this.select_input_template,{options:v}))}}u.insertAfter(y);var r=this,x=create_icon_buttons_menu([{title:"Add parameter to tree",icon_class:"plus-button",on_click:function(){s.set("in_ptree",true);y.hide();u.show();$(this).hide();r.$el.find(".icon-button.toggle").show()}},{title:"Remove parameter from tree",icon_class:"toggle",on_click:function(){s.set("in_ptree",false);u.hide();y.show();$(this).hide();r.$el.find(".icon-button.plus-button").show()}}],{});this.$el.prepend(x.$el);if(s.get("in_ptree")){y.hide();r.$el.find(".icon-button.plus-button").hide()}else{r.$el.find(".icon-button.toggle").hide();u.hide()}m.each(["min","max","num_samples"],function(z){u.find("."+z).change(function(){s.set(z,parseFloat($(this).val()))})})}});var k=Backbone.View.extend({className:"tree-design",initialize:function(r){this.render()},render:function(){var t=new g.ToolFormView({model:this.model.get("tool")});t.render();this.$el.append(t.$el);var s=this,r=s.model.get("tool").get("inputs");this.$el.find(".form-row").not(".form-actions").each(function(u){var v=new b({model:r.at(u),tool_row:$(this)})})}});var j=Backbone.View.extend({className:"tool-parameter-tree",initialize:function(r){this.model.on("change:tree_data",this.render,this)},render:function(){this.$el.children().remove();var z=this.model.get_tree_params();if(!z.length){return}this.width=100*(2+z.length);this.height=15*this.model.get_num_leaves();var y=this;var x=q.layout.cluster().size([this.height,this.width-160]);var t=q.svg.diagonal().projection(function(A){return[A.y,A.x]});var r=x.nodes(this.model.get("tree_data"));var u=m.uniq(m.pluck(r,"y"));m.each(z,function(C,B){var A=u[B+1],D=$("#center").position().left;y.$el.append($("<div>").addClass("label").text(C.get("label")).css("left",A+D))});var s=q.select(this.$el[0]).append("svg").attr("width",this.width).attr("height",this.height+30).append("g").attr("transform","translate(40, 20)");var w=s.selectAll("path.link").data(x.links(r)).enter().append("path").attr("class","link").attr("d",t);var v=s.selectAll("g.node").data(r).enter().append("g").attr("class","node").attr("transform",function(A){return"translate("+A.y+","+A.x+")"}).on("mouseover",function(B){var A=m.pluck(y.model.get_connected_nodes(B),"id");v.filter(function(C){return m.find(A,function(D){return D===C.id})!==undefined}).style("fill","#f00")}).on("mouseout",function(){v.style("fill","#000")});v.append("circle").attr("r",9);v.append("text").attr("dx",function(A){return A.children?-12:12}).attr("dy",3).attr("text-anchor",function(A){return A.children?"end":"start"}).text(function(A){return A.name})}});var e=Backbone.View.extend({className:"Sweepster",helpText:"<div><h4>Getting Started</h4><ol><li>Create a parameter tree by using the icons next to the tool's parameter names to add or remove parameters.<li>Adjust the tree by using parameter inputs to select min, max, and number of samples<li>Run the tool with different settings by clicking on tree nodes</ol></div>",initialize:function(s){this.canvas_manager=new o.CanvasManager(this.$el.parents("body"));this.tool_param_tree_view=new j({model:this.model.get("parameter_tree")});this.track_collection_container=$("<table/>").addClass("tracks");this.model.get("parameter_tree").on("change:tree_data",this.handle_node_clicks,this);var r=this;this.model.get("tracks").each(function(t){t.get("track").view=r});this.block_color=f.get_random_color();this.reverse_strand_color=f.get_random_color([this.block_color,"#ffffff"])},render:function(){var x=new k({model:this.model.get("parameter_tree")});$("#left").append(x.$el);var A=this,u=A.model.get("regions"),y=$("<tr/>").appendTo(this.track_collection_container);u.each(function(B){y.append($("<th>").text(B.toString()))});y.children().first().attr("colspan",2);var v=$("<div>").addClass("tiles");$("#right").append(v.append(this.track_collection_container));A.model.get("tracks").each(function(B){A.add_track(B)});var z=$(this.helpText).addClass("help"),w=create_icon_buttons_menu([{title:"Close",icon_class:"cross-circle",on_click:function(){$(".bs-tooltip").remove();z.remove()}}]);z.prepend(w.$el.css("float","right"));$("#center").append(z);this.tool_param_tree_view.render();$("#center").append(this.tool_param_tree_view.$el);this.handle_node_clicks();var t=create_icon_buttons_menu([{icon_class:"chevron-expand",title:"Set display mode"},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location="${h.url_for( controller='visualization', action='list' )}"}}],{tooltip_config:{placement:"bottom"}});var s=["Squish","Pack"],r={};m.each(s,function(B){r[B]=function(){A.model.set("default_mode",B);A.model.get("tracks").each(function(C){C.set("mode",B)})}});make_popupmenu(t.$el.find(".chevron-expand"),r);t.$el.attr("style","float: right");$("#right .unified-panel-header-inner").append(t.$el)},run_tool_on_dataset:function(s){var r=this.model.get("tool"),u=r.get("name"),t=this.model.get("dataset");r.set_input_values(s.get("values"));$.when(r.rerun(t)).then(function(v){});show_modal("Running "+u+" on complete dataset",u+" is running on dataset '"+t.get("name")+"'. Outputs are in the dataset's history.",{Ok:function(){hide_modal()}})},add_track:function(u){var s=this,t=this.model.get("parameter_tree");s.model.add_track(u);var r=new l({model:u,canvas_manager:s.canvas_manager});r.on("run_on_dataset",s.run_tool_on_dataset,s);s.track_collection_container.append(r.$el);r.$el.hover(function(){var w=t.get_leaf(u.get("settings").get("values"));var v=m.pluck(t.get_connected_nodes(w),"id");q.select(s.tool_param_tree_view.$el[0]).selectAll("g.node").filter(function(x){return m.find(v,function(y){return y===x.id})!==undefined}).style("fill","#f00")},function(){q.select(s.tool_param_tree_view.$el[0]).selectAll("g.node").style("fill","#000")});return u},handle_node_clicks:function(){var r=this,s=this.model.get("parameter_tree"),u=this.model.get("regions"),t=q.select(this.tool_param_tree_view.$el[0]).selectAll("g.node");t.on("click",function(A,x){var w=r.model.get("tool"),z=r.model.get("dataset"),y=s.get_node_settings(A),v=$.Deferred();if(y.length>=10){show_modal("Whoa there cowboy!","You clicked on a node to try "+r.model.get("tool").get("name")+" with "+y.length+" different combinations of settings. You can only run 10 jobs at a time.",{Ok:function(){hide_modal();v.resolve(false)}})}else{v.resolve(true)}$.when(v).then(function(B){if(!B){return}var C=m.map(y,function(D){var E=new c({settings:D,regions:u,mode:r.model.get("default_mode")});r.add_track(E);return E});m.each(C,function(E,D){setTimeout(function(){w.set_input_values(E.get("settings").get("values"));$.when(w.rerun(z,u)).then(function(G){var H=m.extend({data_url:galaxy_paths.get("raw_data_url"),converted_datasets_state_url:galaxy_paths.get("dataset_state_url")},G.first().get("track_config")),F=h.object_from_template(H,r,null);F.data_manager.set("data_type","raw_data");F.prefs.block_color=r.block_color;F.prefs.reverse_strand_color=r.reverse_strand_color;E.set("track",F)})},D*10000)})})})}});return{SweepsterVisualization:i,SweepsterVisualizationView:e}}); \ No newline at end of file diff -r 80251cd7f94d64295ef6e64412f895d268ab988d -r 369a941393909434e0efb5c84dd831e5ab096095 static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","mvc/data","viz/trackster/filters","viz/trackster_ui"],function(ad,y,l,v,M,ab,i,q){var r=ad.extend;var R=l.get_random_color;var ae=function(af,ah,ag){$.ajax({url:af,data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(ai){show_modal("Select datasets for new tracks",ai,{Cancel:function(){hide_modal()},Add:function(){var aj=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var ak={data_type:"track_config",hda_ldda:"hda"},al=$(this).val();if($(this).attr("name")!=="id"){ak.hda_ldda="ldda"}aj[aj.length]=$.ajax({url:ah+"/"+al,data:ak,dataType:"json"})});$.when.apply($,aj).then(function(){var ak=(arguments[0] instanceof Array?$.map(arguments,function(al){return al[0]}):[arguments[0]]);ag(ak)});hide_modal()}})}})};var X=function(af){return("isResolved" in af)};var n={};var k=function(af,ag){n[af.attr("id")]=ag};var m=function(af,ah,aj,ai){aj=".group";var ag={};n[af.attr("id")]=ai;af.bind("drag",{handle:"."+ah,relative:true},function(ar,at){var aq=$(this),aw=$(this).parent(),an=aw.children(),ap=n[$(this).attr("id")],am,al,au,ak,ao;al=$(this).parents(aj);if(al.length!==0){au=al.position().top;ak=au+al.outerHeight();if(at.offsetY<au){$(this).insertBefore(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable_before(ap,av);return}else{if(at.offsetY>ak){$(this).insertAfter(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable(ap);return}}}al=null;for(ao=0;ao<an.length;ao++){am=$(an.get(ao));au=am.position().top;ak=au+am.outerHeight();if(am.is(aj)&&this!==am.get(0)&&at.offsetY>=au&&at.offsetY<=ak){if(at.offsetY-au<ak-at.offsetY){am.find(".content-div").prepend(this)}else{am.find(".content-div").append(this)}if(ap.container){ap.container.remove_drawable(ap)}n[am.attr("id")].add_drawable(ap);return}}for(ao=0;ao<an.length;ao++){am=$(an.get(ao));if(at.offsetY<am.position().top&&!(am.hasClass("reference-track")||am.hasClass("intro"))){break}}if(ao===an.length){if(this!==an.get(ao-1)){aw.append(this);n[aw.attr("id")].move_drawable(ap,ao)}}else{if(this!==an.get(ao)){$(this).insertBefore(an.get(ao));n[aw.attr("id")].move_drawable(ap,(at.deltaY>0?ao-1:ao))}}}).bind("dragstart",function(){ag["border-top"]=af.css("border-top");ag["border-bottom"]=af.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ag)})};exports.moveable=m;var ac=16,H=9,E=20,B=100,J=12000,U=400,L=5000,x=100,o="There was an error in indexing this dataset. ",K="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",F="No data for this chrom/contig.",w="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",z="Tool cannot be rerun: ",a="Loading data...",W="Ready for display",S=10,I=20;function Y(ag,af){if(!af){af=0}var ah=Math.pow(10,af);return Math.round(ag*ah)/ah}var s=function(ag,af,ai){if(!s.id_counter){s.id_counter=0}this.id=s.id_counter++;this.name=ai.name;this.view=ag;this.container=af;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ai.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ai.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(aj){aj.stopPropagation()});var ah=this;this.container_div.hover(function(){ah.icons_div.show()},function(){ah.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};s.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(af){if(af.content_visible){af.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");af.hide_contents();af.content_visible=false}else{af.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");af.content_visible=true;af.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ag){var ai=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(){ag.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ah=function(aj){if((aj.keyCode||aj.which)===27){ai()}else{if((aj.keyCode||aj.which)===13){af()}}};$(window).bind("keypress.check_enter_esc",ah);show_modal("Configure",ag.config.build_form(),{Cancel:ai,OK:af})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(af){$(".bs-tooltip").remove();af.remove()}}];r(s.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(af){this.old_name=this.name;this.name=af;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var af=this.view;this.container_div.hide(0,function(){$(this).remove();af.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ag,al,ak,aj,af,ai){var ah=this;this.action_icons[ag]=$("<a/>").attr("href","javascript:void(0);").attr("title",al).addClass("icon-button").addClass(ak).tooltip().click(function(){aj(ah)}).appendTo(this.icons_div);if(ai){this.action_icons[ag].hide()}},build_action_icons:function(af){var ah;for(var ag=0;ag<af.length;ag++){ah=af[ag];this.add_action_icon(ah.name,ah.title,ah.css_class,ah.on_click_fn,ah.prepend,ah.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var A=function(ag,af,ah){s.call(this,ag,af,ah);this.obj_type=ah.obj_type;this.drawables=[]};r(A.prototype,s.prototype,{unpack_drawables:function(ah){this.drawables=[];var ag;for(var af=0;af<ah.length;af++){ag=p(ah[af],this.view,this);this.add_drawable(ag)}},init:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af].init()}},_draw:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af]._draw()}},to_dict:function(){var ag=[];for(var af=0;af<this.drawables.length;af++){ag.push(this.drawables[af].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ag}},add_drawable:function(af){this.drawables.push(af);af.container=this;this.changed()},add_drawable_before:function(ah,af){this.changed();var ag=this.drawables.indexOf(af);if(ag!==-1){this.drawables.splice(ag,0,ah);return true}return false},replace_drawable:function(ah,af,ag){var ai=this.drawables.indexOf(ah);if(ai!==-1){this.drawables[ai]=af;if(ag){ah.container_div.replaceWith(af.container_div)}this.changed()}return ai},remove_drawable:function(ag){var af=this.drawables.indexOf(ag);if(af!==-1){this.drawables.splice(af,1);ag.container=null;this.changed();return true}return false},move_drawable:function(ag,ah){var af=this.drawables.indexOf(ag);if(af!==-1){this.drawables.splice(af,1);this.drawables.splice(ah,0,ag);this.changed();return true}return false},get_drawables:function(){return this.drawables}});var Q=function(ag,af,ai){r(ai,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});A.call(this,ag,af,ai);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ai){this.unpack_drawables(ai.drawables)}if("filters" in ai){var ah=this.filters_manager;this.filters_manager=new i.FiltersManager(this,ai.filters);ah.parent_div.replaceWith(this.filters_manager.parent_div);if(ai.filters.visible){this.setup_multitrack_filtering()}}};r(Q.prototype,s.prototype,A.prototype,{action_icons_def:[s.prototype.action_icons_def[0],s.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(af){$(".bs-tooltip").remove();af.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(af){if(af.filters_manager.visible()){af.filters_manager.clear_filters();af._restore_filter_managers()}else{af.setup_multitrack_filtering();af.request_draw(true)}af.filters_manager.toggle()}},s.prototype.action_icons_def[2]],build_container_div:function(){var af=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(af)}return af},build_header_div:function(){var af=$("<div/>").addClass("track-header");af.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(af);return af},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ah=this.drawables.length;if(ah===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ah===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ao,an,al,ar=true,aj=this.drawables[0].get_type(),af=0;for(ao=0;ao<ah;ao++){al=this.drawables[ao];if(al.get_type()!==aj){can_composite=false;break}if(al instanceof c){af++}}if(ar||af===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(af>1&&af===this.drawables.length){var at={},ag;al=this.drawables[0];for(an=0;an<al.filters_manager.filters.length;an++){ag=al.filters_manager.filters[an];at[ag.name]=[ag]}for(ao=1;ao<this.drawables.length;ao++){al=this.drawables[ao];for(an=0;an<al.filters_manager.filters.length;an++){ag=al.filters_manager.filters[an];if(ag.name in at){at[ag.name].push(ag)}}}this.filters_manager.remove_all();var ai,ak,am,ap;for(var aq in at){ai=at[aq];if(ai.length===af){ak=new i.NumberFilter({name:ai[0].name,index:ai[0].index});this.filters_manager.add_filter(ak)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af].filters_manager=this.saved_filters_managers[af]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var af=0;af<this.drawables.length;af++){drawable=this.drawables[af];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var aj=[];for(var ag=0;ag<this.drawables.length;ag++){aj.push(this.drawables[ag].name)}var ah="Composite Track of "+this.drawables.length+" tracks ("+aj.join(", ")+")";var ai=new f(this.view,this.view,{name:ah,drawables:this.drawables});var af=this.container.replace_drawable(this,ai,true);ai.request_draw()},add_drawable:function(af){A.prototype.add_drawable.call(this,af);this.update_icons()},remove_drawable:function(af){A.prototype.remove_drawable.call(this,af);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var af=r(A.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return af},request_draw:function(af,ah){for(var ag=0;ag<this.drawables.length;ag++){this.drawables[ag].request_draw(af,ah)}}});var aa=function(af){r(af,{obj_type:"View"});A.call(this,"View",af.container,af);this.chrom=null;this.vis_id=af.vis_id;this.dbkey=af.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new y.CanvasManager(this.container.get(0).ownerDocument);this.reset()};ad.extend(aa.prototype,Backbone.Events);r(aa.prototype,A.prototype,{init:function(){this.requested_redraw=false;var ah=this.container,af=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ah);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ah);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ah);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,af);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ai=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){ae(add_datasets_url,add_track_async_url,function(aj){ad.each(aj,function(ak){af.add_drawable(p(ak,af,af))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-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=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<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").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ag=function(aj){if(aj.type==="focusout"||(aj.keyCode||aj.which)===13||(aj.keyCode||aj.which)===27){if((aj.keyCode||aj.which)!==27){af.go_to($(this).val())}$(this).hide();$(this).val("");af.location_span.show();af.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ag).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){af.location_span.hide();af.chrom_select.hide();af.nav_input.val(af.chrom+":"+af.low+"-"+af.high);af.nav_input.css("display","inline-block");af.nav_input.select();af.nav_input.focus();af.nav_input.autocomplete({source:function(al,aj){var am=[],ak=$.map(af.get_drawables(),function(an){return an.data_manager.search_features(al.term).success(function(ao){am=am.concat(ao)})});$.when.apply($,ak).done(function(){aj($.map(am,function(an){return{label:an[0],value:an[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){af.zoom_out();af.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){af.zoom_in();af.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){af.change_chrom(af.chrom_select.val())});this.browser_content_div.click(function(aj){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(aj){af.zoom_in(aj.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(aj,ak){this.current_x=ak.offsetX}).bind("drag",function(aj,al){var am=al.offsetX-this.current_x;this.current_x=al.offsetX;var ak=Math.round(am/af.viewport_container.width()*(af.max_high-af.max_low));af.move_delta(-ak)});this.overview_close.click(function(){af.reset_overview()});this.viewport_container.bind("draginit",function(aj,ak){if(aj.clientX>af.viewport_container.width()-16){return false}}).bind("dragstart",function(aj,ak){ak.original_low=af.low;ak.current_height=aj.clientY;ak.current_x=ak.offsetX}).bind("drag",function(al,an){var aj=$(this);var ao=an.offsetX-an.current_x;var ak=aj.scrollTop()-(al.clientY-an.current_height);aj.scrollTop(ak);an.current_height=al.clientY;an.current_x=an.offsetX;var am=Math.round(ao/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}).bind("mousewheel",function(al,an,ak,aj){if(ak){ak*=50;var am=Math.round(-ak/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}});this.top_labeltrack.bind("dragstart",function(aj,ak){return $("<div />").css({height:af.browser_content_div.height()+af.top_labeltrack.height()+af.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(an,ao){$(ao.proxy).css({left:Math.min(an.pageX,ao.startX)-af.container.offset().left,width:Math.abs(an.pageX-ao.startX)});var ak=Math.min(an.pageX,ao.startX)-af.container.offset().left,aj=Math.max(an.pageX,ao.startX)-af.container.offset().left,am=(af.high-af.low),al=af.viewport_container.width();af.update_location(Math.round(ak/al*am)+af.low,Math.round(aj/al*am)+af.low)}).bind("dragend",function(ao,ap){var ak=Math.min(ao.pageX,ap.startX),aj=Math.max(ao.pageX,ap.startX),am=(af.high-af.low),al=af.viewport_container.width(),an=af.low;af.low=Math.round(ak/al*am)+an;af.high=Math.round(aj/al*am)+an;$(ap.proxy).remove();af.request_redraw()});this.add_label_track(new Z(this,{content_div:this.top_labeltrack}));this.add_label_track(new Z(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){af.resize_window()},500)});$(document).bind("redraw",function(){af.redraw()});this.reset();$(window).trigger("resize")},changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ag,ai,af,aj){if(this.timer){clearTimeout(this.timer)}if(aj){var ah=this;this.timer=setTimeout(function(){ah.trigger("navigate",ag+":"+ai+"-"+af)},500)}else{view.trigger("navigate",ag+":"+ai+"-"+af)}},update_location:function(af,ah){this.location_span.text(commatize(af)+" - "+commatize(ah));this.nav_input.val(this.chrom+":"+commatize(af)+"-"+commatize(ah));var ag=view.chrom_select.val();if(ag!==""){this.trigger_navigate(ag,view.low,view.high,true)}},load_chroms:function(ah){ah.num=x;var af=this,ag=$.Deferred();$.ajax({url:chrom_url+"/"+this.dbkey,data:ah,dataType:"json",success:function(aj){if(aj.chrom_info.length===0){return}if(aj.reference){af.add_label_track(new C(af))}af.chrom_data=aj.chrom_info;var am='<option value="">Select Chrom/Contig</option>';for(var al=0,ai=af.chrom_data.length;al<ai;al++){var ak=af.chrom_data[al].chrom;am+='<option value="'+ak+'">'+ak+"</option>"}if(aj.prev_chroms){am+='<option value="previous">Previous '+x+"</option>"}if(aj.next_chroms){am+='<option value="next">Next '+x+"</option>"}af.chrom_select.html(am);af.chrom_start_index=aj.start_index;ag.resolve(aj)},error:function(){alert("Could not load chroms for this dbkey:",af.dbkey)}});return ag},change_chrom:function(ak,ag,am){var ah=this;if(!ah.chrom_data){ah.load_chroms_deferred.then(function(){ah.change_chrom(ak,ag,am)});return}if(!ak||ak==="None"){return}if(ak==="previous"){ah.load_chroms({low:this.chrom_start_index-x});return}if(ak==="next"){ah.load_chroms({low:this.chrom_start_index+x});return}var al=$.grep(ah.chrom_data,function(an,ao){return an.chrom===ak})[0];if(al===undefined){ah.load_chroms({chrom:ak},function(){ah.change_chrom(ak,ag,am)});return}else{if(ak!==ah.chrom){ah.chrom=ak;ah.chrom_select.val(ah.chrom);ah.max_high=al.len-1;ah.reset();ah.request_redraw(true);for(var aj=0,af=ah.drawables.length;aj<af;aj++){var ai=ah.drawables[aj];if(ai.init){ai.init()}}if(ah.reference_track){ah.reference_track.init()}}if(ag!==undefined&&am!==undefined){ah.low=Math.max(ag,0);ah.high=Math.min(am,ah.max_high)}else{ah.low=0;ah.high=ah.max_high}ah.reset_overview();ah.request_redraw()}},go_to:function(aj){aj=aj.replace(/ |,/g,"");var an=this,af,ai,ag=aj.split(":"),al=ag[0],am=ag[1];if(am!==undefined){try{var ak=am.split("-");af=parseInt(ak[0],10);ai=parseInt(ak[1],10)}catch(ah){return false}}an.change_chrom(al,af,ai)},move_fraction:function(ah){var af=this;var ag=af.high-af.low;this.move_delta(ah*ag)},move_delta:function(ai){var af=this;var ah=af.high-af.low;if(af.low-ai<af.max_low){af.low=af.max_low;af.high=af.max_low+ah}else{if(af.high-ai>af.max_high){af.high=af.max_high;af.low=af.max_high-ah}else{af.high-=ai;af.low-=ai}}af.request_redraw();var ag=af.chrom_select.val();this.trigger_navigate(ag,af.low,af.high,true)},add_drawable:function(af){A.prototype.add_drawable.call(this,af);af.init();this.changed();this.update_intro_div()},add_label_track:function(af){af.view=this;af.init();this.label_tracks.push(af)},remove_drawable:function(ah,ag){A.prototype.remove_drawable.call(this,ah);if(ag){var af=this;ah.container_div.hide(0,function(){$(this).remove();af.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(an,af,am,ao){var al=this,ak=(ao?[ao]:al.drawables),ah;var ag;for(var aj=0;aj<ak.length;aj++){ag=ak[aj];ah=-1;for(var ai=0;ai<al.tracks_to_be_redrawn.length;ai++){if(al.tracks_to_be_redrawn[ai][0]===ag){ah=ai;break}}if(ah<0){al.tracks_to_be_redrawn.push([ag,af,am])}else{al.tracks_to_be_redrawn[aj][1]=af;al.tracks_to_be_redrawn[aj][2]=am}}if(!this.requested_redraw){requestAnimationFrame(function(){al._redraw(an)});this.requested_redraw=true}},_redraw:function(ap){this.requested_redraw=false;var am=this.low,ai=this.high;if(am<this.max_low){am=this.max_low}if(ai>this.max_high){ai=this.max_high}var ao=this.high-this.low;if(this.high!==0&&ao<this.min_separation){ai=am+this.min_separation}this.low=Math.floor(am);this.high=Math.ceil(ai);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var al=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var aq=13;this.overview_box.css({left:af,width:Math.max(aq,al)}).show();if(al<aq){this.overview_box.css("left",af-(aq-al)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:al})}if(!ap){var ah,ag,an;for(var aj=0,ak=this.tracks_to_be_redrawn.length;aj<ak;aj++){ah=this.tracks_to_be_redrawn[aj][0];ag=this.tracks_to_be_redrawn[aj][1];an=this.tracks_to_be_redrawn[aj][2];if(ah){ah._draw(ag,an)}}this.tracks_to_be_redrawn=[];for(aj=0,ak=this.label_tracks.length;aj<ak;aj++){this.label_tracks[aj]._draw()}}},zoom_in:function(ag,ah){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ai=this.high-this.low,aj=ai/2+this.low,af=(ai/this.zoom_factor)/2;if(ag){aj=ag/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(aj-af);this.high=Math.round(aj+af);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ag=this.high-this.low,ah=ag/2+this.low,af=(ag*this.zoom_factor)/2;this.low=Math.round(ah-af);this.high=Math.round(ah+af);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ah){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ah.dataset_id){return}this.overview_viewport.find(".track").remove()}var ag=ah.copy({content_div:this.overview_viewport}),af=this;ag.header_div.hide();ag.is_overview=true;af.overview_drawable=ag;this.overview_drawable.postdraw_actions=function(){af.overview_highlight.show().height(af.overview_drawable.content_div.height());af.overview_viewport.height(af.overview_drawable.content_div.height()+af.overview_box.outerHeight());af.overview_close.show();af.resize_window()};af.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var t=function(ah,am,ai){this.track=ah;this.name=am.name;this.params=[];var au=am.params;for(var aj=0;aj<au.length;aj++){var ao=au[aj],ag=ao.name,at=ao.label,ak=unescape(ao.html),av=ao.value,aq=ao.type;if(aq==="number"){this.params.push(new e(ag,at,ak,(ag in ai?ai[ag]:av),ao.min,ao.max))}else{if(aq==="select"){this.params.push(new O(ag,at,ak,(ag in ai?ai[ag]:av)))}else{console.log("WARNING: unrecognized tool parameter type:",ag,aq)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ax){ax.stopPropagation()}).click(function(ax){ax.stopPropagation()}).bind("dblclick",function(ax){ax.stopPropagation()});var ar=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ap=this.params;var an=this;$.each(this.params,function(ay,aB){var aA=$("<div>").addClass("param-row").appendTo(an.parent_div);var ax=$("<div>").addClass("param-label").text(aB.label).appendTo(aA);var az=$("<div/>").addClass("param-input").html(aB.html).appendTo(aA);az.find(":input").val(aB.value);$("<div style='clear: both;'/>").appendTo(aA)});this.parent_div.find("input").click(function(){$(this).select()});var aw=$("<div>").addClass("param-row").appendTo(this.parent_div);var al=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(aw);var af=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(aw);af.click(function(){an.run_on_region()});al.click(function(){an.run_on_dataset()});if("visible" in ai&&ai.visible){this.parent_div.show()}};r(t.prototype,{update_params:function(){for(var af=0;af<this.params.length;af++){this.params[af].update_value()}},state_dict:function(){var ag={};for(var af=0;af<this.params.length;af++){ag[this.params[af].name]=this.params[af].value}ag.visible=this.parent_div.is(":visible");return ag},get_param_values_dict:function(){var af={};this.parent_div.find(":input").each(function(){var ag=$(this).attr("name"),ah=$(this).val();af[ag]=ah});return af},get_param_values:function(){var af=[];this.parent_div.find(":input").each(function(){var ag=$(this).attr("name"),ah=$(this).val();if(ag){af[af.length]=ah}});return af},run_on_dataset:function(){var af=this;af.run({target_dataset_id:this.track.original_dataset_id,tool_id:af.name},null,function(ag){show_modal(af.name+" is Running",af.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ag={target_dataset_id:this.track.original_dataset_id,action:"rerun",tool_id:this.name,regions:[{chrom:this.track.view.chrom,start:this.track.view.low,end:this.track.view.high}]},ak=this.track,ah=ag.tool_id+ak.tool_region_and_parameters_str(ag.chrom,ag.low,ag.high),af;if(ak.container===view){var aj=new Q(view,view,{name:this.name});var ai=ak.container.replace_drawable(ak,aj,false);aj.container_div.insertBefore(ak.view.content_div.children()[ai]);aj.add_drawable(ak);ak.container_div.appendTo(aj.content_div);af=aj}else{af=ak.container}var al=new ak.constructor(view,af,{name:ah,hda_ldda:"hda"});al.init_for_tool_data();al.change_mode(ak.mode);al.set_filters_manager(ak.filters_manager.copy(al));al.update_icons();af.add_drawable(al);al.tiles_div.text("Starting job.");this.update_params();this.run(ag,al,function(am){al.set_dataset(new ab.Dataset(am));al.tiles_div.text("Running job.");al.init()})},run:function(af,ah,ai){af.inputs=this.get_param_values_dict();var ag=new l.ServerStateDeferred({ajax_settings:{url:galaxy_paths.get("tool_url"),data:JSON.stringify(af),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(aj){return aj!=="pending"}});$.when(ag.go()).then(function(aj){if(aj==="no converter"){ah.container_div.addClass("error");ah.content_div.text(K)}else{if(aj.error){ah.container_div.addClass("error");ah.content_div.text(z+aj.message)}else{ai(aj)}}})}});var O=function(ag,af,ah,ai){this.name=ag;this.label=af;this.html=$(ah);this.value=ai};r(O.prototype,{update_value:function(){this.value=$(this.html).val()}});var e=function(ah,ag,aj,ak,ai,af){O.call(this,ah,ag,aj,ak);this.min=ai;this.max=af};r(e.prototype,O.prototype,{update_value:function(){O.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var D=function(af,ag){M.Scaler.call(this,ag);this.filter=af};D.prototype.gen_val=function(af){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(af[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var G=function(af){this.track=af.track;this.params=af.params;this.values={};this.restore_values((af.saved_values?af.saved_values:{}));this.onchange=af.onchange};r(G.prototype,{restore_values:function(af){var ag=this;$.each(this.params,function(ah,ai){if(af[ai.key]!==undefined){ag.values[ai.key]=af[ai.key]}else{ag.values[ai.key]=ai.default_value}})},build_form:function(){var ai=this;var af=$("<div />");var ah;function ag(an,aj){for(var ar=0;ar<an.length;ar++){ah=an[ar];if(ah.hidden){continue}var al="param_"+ar;var aw=ai.values[ah.key];var ay=$("<div class='form-row' />").appendTo(aj);ay.append($("<label />").attr("for",al).text(ah.label+":"));if(ah.type==="bool"){ay.append($('<input type="checkbox" />').attr("id",al).attr("name",al).attr("checked",aw))}else{if(ah.type==="text"){ay.append($('<input type="text"/>').attr("id",al).val(aw).click(function(){$(this).select()}))}else{if(ah.type==="select"){var au=$("<select />").attr("id",al);for(var ap=0;ap<ah.options.length;ap++){$("<option/>").text(ah.options[ap].label).attr("value",ah.options[ap].value).appendTo(au)}au.val(aw);ay.append(au)}else{if(ah.type==="color"){var ax=$("<div/>").appendTo(ay),at=$("<input />").attr("id",al).attr("name",al).val(aw).css("float","left").appendTo(ax).click(function(aA){$(".bs-tooltip").removeClass("in");var az=$(this).siblings(".bs-tooltip").addClass("in");az.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(az).height()/2)+($(this).height()/2)}).show();az.click(function(aB){aB.stopPropagation()});$(document).bind("click.color-picker",function(){az.hide();$(document).unbind("click.color-picker")});aA.stopPropagation()}),aq=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(ax).attr("title","Set new random color").tooltip(),av=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(ax).hide(),am=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(av),ak=$("<div class='tooltip-arrow'></div>").appendTo(av),ao=$.farbtastic(am,{width:100,height:100,callback:at,color:aw});ax.append($("<div/>").css("clear","both"));(function(az){aq.click(function(){az.setColor(R())})})(ao)}else{ay.append($("<input />").attr("id",al).attr("name",al).val(aw))}}}}if(ah.help){ay.append($("<div class='help'/>").text(ah.help))}}}ag(this.params,af);return af},update_from_form:function(af){var ah=this;var ag=false;$.each(this.params,function(ai,ak){if(!ak.hidden){var al="param_"+ai;var aj=af.find("#"+al).val();if(ak.type==="float"){aj=parseFloat(aj)}else{if(ak.type==="int"){aj=parseInt(aj)}else{if(ak.type==="bool"){aj=af.find("#"+al).is(":checked")}}}if(aj!==ah.values[ak.key]){ah.values[ak.key]=aj;ag=true}}});if(ag){this.onchange();this.track.changed()}}});var b=function(af,aj,ah,ag,ai){this.track=af;this.region=aj;this.low=aj.get("start");this.high=aj.get("end");this.resolution=ah;this.html_elt=$("<div class='track-tile'/>").append(ag).height($(ag).attr("height"));this.data=ai;this.stale=false};b.prototype.predisplay_actions=function(){};var j=function(af,ak,ah,ag,ai,aj){b.call(this,af,ak,ah,ag,ai);this.max_val=aj};r(j.prototype,b.prototype);var P=function(ai,aq,aj,ah,al,at,am,au,ag,ap){b.call(this,ai,aq,aj,ah,al);this.mode=am;this.all_slotted=ag;this.feature_mapper=ap;this.has_icons=false;if(au){this.has_icons=true;var an=this;ah=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:E-1,width:ah.width}).prependTo(this.html_elt);var ao=new y.GenomeRegion({chrom:ai.view.chrom,start:this.low,end:this.high}),ar=al.length,ak=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ar+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),af=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ar+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ak.click(function(){an.stale=true;ai.data_manager.get_more_data(ao,ai.mode,an.resolution,{},ai.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();ai.request_draw(true)}).dblclick(function(av){av.stopPropagation()});af.click(function(){an.stale=true;ai.data_manager.get_more_data(ao,ai.mode,an.resolution,{},ai.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();ai.request_draw(true)}).dblclick(function(av){av.stopPropagation()})}};r(P.prototype,b.prototype);P.prototype.predisplay_actions=function(){var ag=this,af={};if(ag.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ar){if(!this.hovered){return}var am=$(this).offset(),aq=ar.pageX-am.left,ap=ar.pageY-am.top,aw=ag.feature_mapper.get_feature_data(aq,ap),an=(aw?aw[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!an||$(this).attr("id")!==an.toString()){$(this).remove()}});if(aw){var ai=af[an];if(!ai){var an=aw[0],at={name:aw[3],start:aw[1],end:aw[2],strand:aw[4]},al=ag.track.filters_manager.filters,ak;for(var ao=0;ao<al.length;ao++){ak=al[ao];at[ak.name]=aw[ak.index]}var ai=$("<div/>").attr("id",an).addClass("feature-popup"),ax=$("<table/>"),av,au,ay;for(av in at){au=at[av];ay=$("<tr/>").appendTo(ax);$("<th/>").appendTo(ay).text(av);$("<td/>").attr("align","left").appendTo(ay).text(typeof(au)==="number"?Y(au,2):au)}ai.append($("<div class='feature-popup-inner'>").append(ax));af[an]=ai}ai.appendTo($(this).parents(".track-content").children(".overlay"));var aj=aq+parseInt(ag.html_elt.css("left"))-ai.width()/2,ah=ap+parseInt(ag.html_elt.css("top"))+7;ai.css("left",aj+"px").css("top",ah+"px")}else{if(!ar.isPropagationStopped()){ar.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ar)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ag,af,ah){r(ah,{drag_handle_class:"draghandle"});s.call(this,ag,af,ah);this.dataset=new ab.Dataset({id:ah.dataset_id,hda_ldda:ah.hda_ldda});this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ah?ah.data_query_wait:L);this.data_manager=("data_manager" in ah?ah.data_manager:new y.GenomeDataManager({dataset:this.dataset,data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ah)||ah.resize){this.add_resize_handle()}}};r(g.prototype,s.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},s.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(af){af.view.set_overview(af)}},s.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(af){if(af.filters_manager.visible()){af.filters_manager.clear_filters()}else{af.filters_manager.init_filters()}af.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(af){af.dynamic_tool_div.toggle();if(af.dynamic_tool_div.is(":visible")){af.set_name(af.name+af.tool_region_and_parameters_str())}else{af.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(af){var ai='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ah=ad.template(ai,{track:af});var ak=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ag=function(){var am=$('select[name="regions"] option:selected').val(),ao,al=new y.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),an=ad.map($(".bookmark"),function(ap){return new y.GenomeRegion({from_str:$(ap).children(".position").text()})});if(am==="cur"){ao=[al]}else{if(am==="bookmarks"){ao=an}else{ao=[al].concat(an)}}hide_modal();window.location.href=galaxy_paths.get("sweepster_url")+"?"+$.param({dataset_id:af.dataset_id,hda_ldda:af.hda_ldda,regions:JSON.stringify(new Backbone.Collection(ao).toJSON())})},aj=function(al){if((al.keyCode||al.which)===27){ak()}else{if((al.keyCode||al.which)===13){ag()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",ah,{No:ak,Yes:ag})}},s.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&s.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var af=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(af)}this.name_div=$("<div/>").addClass("track-name").appendTo(af).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return af},on_resize:function(){},add_resize_handle:function(){var af=this;var ai=false;var ah=false;var ag=$("<div class='track-resize'>");$(af.container_div).hover(function(){if(af.content_visible){ai=true;ag.show()}},function(){ai=false;if(!ah){ag.hide()}});ag.hide().bind("dragstart",function(aj,ak){ah=true;ak.original_height=$(af.content_div).height()}).bind("drag",function(ak,al){var aj=Math.min(Math.max(al.original_height+al.deltaY,af.min_height_px),af.max_height_px);$(af.tiles_div).css("height",aj);af.visible_height_px=(af.max_height_px===aj?0:aj);af.on_resize()}).bind("dragend",function(aj,ak){af.tile_cache.clear();ah=false;if(!ai){ag.hide()}af.config.values.height=af.visible_height_px;af.changed()}).appendTo(af.container_div)},set_display_modes:function(ai,al){this.display_modes=ai;this.mode=(al?al:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ag=this,aj={};for(var ah=0,af=ag.display_modes.length;ah<af;ah++){var ak=ag.display_modes[ah];aj[ak]=function(am){return function(){ag.change_mode(am);ag.icons_div.show();ag.container_div.mouseleave(function(){ag.icons_div.hide()})}}(ak)}make_popupmenu(this.action_icons.mode_icon,aj)},build_action_icons:function(){s.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof Z){return"LabelTrack"}else{if(this instanceof C){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof V){return"ReadTrack"}else{if(this instanceof T){return"VcfTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(){var ag=this;ag.enabled=false;ag.tile_cache.clear();ag.data_manager.clear();ag.content_div.css("height","auto");ag.tiles_div.children().remove();ag.container_div.removeClass("nodata error pending");if(!ag.dataset_id){return}var af=$.Deferred(),ah={hda_ldda:ag.hda_ldda,data_type:this.dataset_check_type,chrom:ag.view.chrom};$.getJSON(this.dataset.url(),ah,function(ai){if(!ai||ai==="error"||ai.kind==="error"){ag.container_div.addClass("error");ag.tiles_div.text(o);if(ai.message){var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ag.tiles_div.append(aj)}}else{if(ai==="no converter"){ag.container_div.addClass("error");ag.tiles_div.text(K)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ag.container_div.addClass("nodata");ag.tiles_div.text(F)}else{if(ai==="pending"){ag.container_div.addClass("pending");ag.tiles_div.html(w);setTimeout(function(){ag.init()},ag.data_query_wait)}else{if(ai==="data"||ai.status==="data"){if(ai.valid_chroms){ag.valid_chroms=ai.valid_chroms;ag.update_icons()}ag.tiles_div.text(W);if(ag.view.chrom){ag.tiles_div.text("");ag.tiles_div.css("height",ag.visible_height_px+"px");ag.enabled=true;$.when(ag.predraw_init()).done(function(){af.resolve();ag.container_div.removeClass("nodata error pending");ag.request_draw()})}else{af.resolve()}}}}}}});this.update_icons();return af},predraw_init:function(){},get_drawables:function(){return this}});var N=function(ah,ag,ai){g.call(this,ah,ag,ai);var af=this;m(af.container_div,af.drag_handle_class,".group",af);this.filters_manager=new i.FiltersManager(this,("filters" in ai?ai.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in ai&&ai.tool?new t(this,ai.tool,ai.tool_state):null);this.tile_cache=new y.Cache(S);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ai.mode){this.change_mode(ai.mode)}};r(N.prototype,s.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(af){$(".bs-tooltip").remove();af.slotters[af.view.resolution_px_b].max_rows*=2;af.request_draw(true)},hide:true}]),copy:function(af){var ag=this.to_dict();r(ag,{data_manager:this.data_manager});var ah=new this.constructor(this.view,af,ag);ah.change_mode(this.mode);ah.enabled=this.enabled;return ah},set_filters_manager:function(af){this.filters_manager=af;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(ag){var af=this;af.mode=ag;af.config.values.mode=ag;af.tile_cache.clear();af.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+af.mode+")");return af},update_icons:function(){var af=this;if(af.filters_available){af.action_icons.filters_icon.show()}else{af.action_icons.filters_icon.hide()}if(af.tool){af.action_icons.tools_icon.show();af.action_icons.param_space_viz_icon.show()}else{af.action_icons.tools_icon.hide();af.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ag,ah,af){return ag+"_"+ah+"_"+af},request_draw:function(ag,af){this.view.request_redraw(false,ag,af,this)},before_draw:function(){},_draw:function(ag,aq){if(!this.can_draw()){return}var ao=this.view.low,ak=this.view.high,am=ak-ao,ah=this.view.container.width(),at=this.view.resolution_px_b,aj=this.view.resolution_b_px;if(this.is_overview){ao=this.view.max_low;ak=this.view.max_high;aj=(view.max_high-view.max_low)/ah;at=1/aj}this.before_draw();this.tiles_div.children().addClass("remove");var af=Math.floor(ao/(aj*U)),an=true,ar=[],al=function(au){return(au&&"track" in au)};while((af*U*aj)<ak){var ap=this.draw_helper(ag,ah,af,aj,this.tiles_div,at);if(al(ap)){ar.push(ap)}else{an=false}af+=1}if(!aq){this.tiles_div.children(".remove").removeClass("remove").remove()}var ai=this;if(an){this.tiles_div.children(".remove").remove();ai.postdraw_actions(ar,ah,at,aq)}},postdraw_actions:function(ah,ai,ak,af){var aj=false;for(var ag=0;ag<ah.length;ag++){if(ah[ag].has_icons){aj=true;break}}if(aj){for(var ag=0;ag<ah.length;ag++){tile=ah[ag];if(!tile.has_icons){tile.html_elt.css("padding-top",E)}}}},draw_helper:function(af,ar,ax,av,ak,al,at){var aq=this,aA=this._gen_tile_cache_key(ar,al,ax),ai=this._get_tile_bounds(ax,av);if(!at){at={}}var az=(af?undefined:aq.tile_cache.get_elt(aA));if(az){aq.show_tile(az,ak,al);return az}var ao=true;var aw=aq.data_manager.get_data(ai,aq.mode,av,aq.data_url_extra_params);if(X(aw)){ao=false}var am;if(view.reference_track&&al>view.canvas_manager.char_width_px){am=view.reference_track.data_manager.get_data(ai,aq.mode,av,view.reference_track.data_url_extra_params);if(X(am)){ao=false}}if(ao){r(aw,at.more_tile_data);var an=aq.mode;if(an==="Auto"){an=aq.get_mode(aw);aq.update_auto_mode(an)}var ah=aq.view.canvas_manager.new_canvas(),ay=ai.get("start"),ag=ai.get("end"),ar=Math.ceil((ag-ay)*al)+aq.left_offset,ap=aq.get_canvas_height(aw,an,al,ar);ah.width=ar;ah.height=ap;var au=ah.getContext("2d");au.translate(this.left_offset,0);var az=aq.draw_tile(aw,au,an,av,ai,al,am);if(az!==undefined){aq.tile_cache.set_elt(aA,az);aq.show_tile(az,ak,al)}return az}var aj=$.Deferred();$.when(aw,am).then(function(){view.request_redraw(false,false,false,aq);aj.resolve()});return aj},get_canvas_height:function(af,ah,ai,ag){return this.visible_height_px},draw_tile:function(af,ag,ak,ai,aj,al,ah){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ah,aj,ak){var ag=this,af=ah.html_elt;ah.predisplay_actions();var ai=(ah.low-(this.is_overview?this.view.max_low:this.view.low))*ak;if(this.left_offset){ai-=this.left_offset}af.css({position:"absolute",top:0,left:ai});if(af.hasClass("remove")){af.removeClass("remove")}else{aj.append(af)}ag.after_show_tile(ah)},after_show_tile:function(af){this.max_height_px=Math.max(this.max_height_px,af.html_elt.height());af.html_elt.parent().children().css("height",this.max_height_px+"px");var ag=this.max_height_px;if(this.visible_height_px!==0){ag=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ag+"px")},_get_tile_bounds:function(af,ag){var ai=Math.floor(af*U*ag),aj=Math.ceil(U*ag),ah=(ai+aj<=this.view.max_high?ai+aj:this.view.max_high);return new y.GenomeRegion({chrom:this.view.chrom,start:ai,end:ah})},tool_region_and_parameters_str:function(ah,af,ai){var ag=this,aj=(ah!==undefined&&af!==undefined&&ai!==undefined?ah+":"+af+"-"+ai:"all");return" - region=["+aj+"], parameters=["+ag.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(af,ag){return true},can_subset:function(af){return false},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ah,ai,ak,af){var ag=this;ag.normal_postdraw_actions(ah,ai,ak,af);ag.dataset_check_type="converted_datasets_state";ag.data_query_wait=L;var aj=new l.ServerStateDeferred({url:ag.dataset_state_url,url_params:{dataset_id:ag.dataset_id,hda_ldda:ag.hda_ldda},interval:ag.data_query_wait,success_fn:function(al){return al!=="pending"}});$.when(aj.go()).then(function(){ag.data_manager.set("data_type","data")});ag.postdraw_actions=ag.normal_postdraw_actions}}});var Z=function(ag,af){var ah={resize:false};g.call(this,ag,af,ah);this.container_div.addClass("label-track")};r(Z.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ah=this.view,ai=ah.high-ah.low,al=Math.floor(Math.pow(10,Math.floor(Math.log(ai)/Math.log(10)))),af=Math.floor(ah.low/al)*al,aj=this.view.container.width(),ag=$("<div style='position: relative; height: 1.3em;'></div>");while(af<ah.high){var ak=(af-ah.low)/ai*aj;ag.append($("<div class='label'>"+commatize(af)+"</div>").css({position:"absolute",left:ak-1}));af+=al}this.content_div.children(":first").remove();this.content_div.append(ag)}});var f=function(ag,af,aj){N.call(this,ag,af,aj);this.drawables=[];this.left_offset=0;if("drawables" in aj){var ai;for(var ah=0;ah<aj.drawables.length;ah++){ai=aj.drawables[ah];this.drawables[ah]=p(ai,ag,null);if(ai.left_offset>this.left_offset){this.left_offset=ai.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};r(f.prototype,N.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(af){$(".bs-tooltip").remove();af.show_group()}}].concat(N.prototype.action_icons_def),to_dict:A.prototype.to_dict,add_drawable:A.prototype.add_drawable,unpack_drawables:A.prototype.unpack_drawables,change_mode:function(af){N.prototype.change_mode.call(this,af);for(var ag=0;ag<this.drawables.length;ag++){this.drawables[ag].change_mode(af)}},init:function(){var ah=[];for(var ag=0;ag<this.drawables.length;ag++){ah.push(this.drawables[ag].init())}var af=this;$.when.apply($,ah).then(function(){af.enabled=true;af.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:s.prototype.can_draw,draw_helper:function(ag,aw,aC,az,an,ap,ax){var av=this,aG=this._gen_tile_cache_key(aw,ap,aC),ak=this._get_tile_bounds(aC,az);if(!ax){ax={}}var aF=(ag?undefined:av.tile_cache.get_elt(aG));if(aF){av.show_tile(aF,an,ap);return aF}var ao=[],av,at=true,aA,aq;for(var aB=0;aB<this.drawables.length;aB++){av=this.drawables[aB];aA=av.data_manager.get_data(ak,av.mode,az,av.data_url_extra_params);if(X(aA)){at=false}ao.push(aA);aq=null;if(view.reference_track&&ap>view.canvas_manager.char_width_px){aq=view.reference_track.data_manager.get_data(ak,av.mode,az,view.reference_track.data_url_extra_params);if(X(aq)){at=false}}ao.push(aq)}if(at){r(aA,ax.more_tile_data);this.tile_predraw_init();var aj=av.view.canvas_manager.new_canvas(),al=av._get_tile_bounds(aC,az),aD=ak.get("start"),ah=ak.get("end"),aE=0,aw=Math.ceil((ah-aD)*ap)+this.left_offset,au=0,ai=[],aB;var af=0;for(aB=0;aB<this.drawables.length;aB++,aE+=2){av=this.drawables[aB];aA=ao[aE];var ar=av.mode;if(ar==="Auto"){ar=av.get_mode(aA);av.update_auto_mode(ar)}ai.push(ar);af=av.get_canvas_height(aA,ar,ap,aw);if(af>au){au=af}}aj.width=aw;aj.height=(ax.height?ax.height:au);aE=0;var ay=aj.getContext("2d");ay.translate(this.left_offset,0);ay.globalAlpha=0.5;ay.globalCompositeOperation="source-over";for(aB=0;aB<this.drawables.length;aB++,aE+=2){av=this.drawables[aB];aA=ao[aE];aq=ao[aE+1];aF=av.draw_tile(aA,ay,ai[aB],az,ak,ap,aq)}this.tile_cache.set_elt(aG,aF);this.show_tile(aF,an,ap);return aF}var am=$.Deferred(),av=this;$.when.apply($,ao).then(function(){view.request_redraw(false,false,false,av);am.resolve()});return am},show_group:function(){var ai=new Q(this.view,this.container,{name:this.name}),af;for(var ah=0;ah<this.drawables.length;ah++){af=this.drawables[ah];af.update_icons();ai.add_drawable(af);af.container=ai;ai.content_div.append(af.container_div)}var ag=this.container.replace_drawable(this,ai,true);ai.request_draw()},tile_predraw_init:function(){var ai=Number.MAX_VALUE,af=-ai,ag;for(var ah=0;ah<this.drawables.length;ah++){ag=this.drawables[ah];if(ag instanceof h){if(ag.prefs.min_value<ai){ai=ag.prefs.min_value}if(ag.prefs.max_value>af){af=ag.prefs.max_value}}}for(var ah=0;ah<this.drawables.length;ah++){ag=this.drawables[ah];ag.prefs.min_value=ai;ag.prefs.max_value=af}},postdraw_actions:function(ah,ak,am,ag){N.prototype.postdraw_actions.call(this,ah,ak,am,ag);var aj=-1;for(var ai=0;ai<ah.length;ai++){var af=ah[ai].html_elt.find("canvas").height();if(af>aj){aj=af}}for(var ai=0;ai<ah.length;ai++){var al=ah[ai];if(al.html_elt.find("canvas").height()!==aj){this.draw_helper(true,ak,al.index,al.resolution,al.html_elt.parent(),am,{height:aj});al.html_elt.remove()}}}});var C=function(af){N.call(this,af,{content_div:af.top_labeltrack},{resize:false});af.reference_track=this;this.left_offset=200;this.visible_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.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new y.ReferenceTrackDataManager({data_url:this.data_url});this.hide_contents()};r(C.prototype,s.prototype,N.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:s.prototype.can_draw,draw_helper:function(aj,ah,af,ag,ak,al,ai){if(al>this.view.canvas_manager.char_width_px){return N.prototype.draw_helper.call(this,aj,ah,af,ag,ak,al,ai)}else{this.hide_contents();return null}},draw_tile:function(an,ao,aj,ai,al,ap){var ah=this;if(ap>this.view.canvas_manager.char_width_px){if(an.data===null){this.hide_contents();return}var ag=ao.canvas;ao.font=ao.canvas.manager.default_font;ao.textAlign="center";an=an.data;for(var ak=0,am=an.length;ak<am;ak++){var af=Math.floor(ak*ap);ao.fillText(an[ak],af,10)}this.show_contents();return new b(ah,al,ai,ag,an)}this.hide_contents()}});var h=function(ah,ag,ai){var af=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";N.call(this,ah,ag,ai);this.hda_ldda=ai.hda_ldda;this.dataset_id=ai.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:R()},{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:32,hidden:true}],saved_values:ai.prefs,onchange:function(){af.set_name(af.prefs.name);af.vertical_range=af.prefs.max_value-af.prefs.min_value;af.set_min_value(af.prefs.min_value);af.set_max_value(af.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};r(h.prototype,s.prototype,N.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(af){this.prefs.min_value=af;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(af){this.prefs.max_value=af;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var af=this;af.vertical_range=undefined;return $.getJSON(af.dataset.url(),{data_type:"data",stats:true,chrom:af.view.chrom,low:0,high:af.view.max_high,hda_ldda:af.hda_ldda},function(ag){af.container_div.addClass("line-track");var aj=ag.data;if(isNaN(parseFloat(af.prefs.min_value))||isNaN(parseFloat(af.prefs.max_value))){var ah=aj.min,al=aj.max;ah=Math.floor(Math.min(0,Math.max(ah,aj.mean-2*aj.sd)));al=Math.ceil(Math.max(0,Math.min(al,aj.mean+2*aj.sd)));af.prefs.min_value=ah;af.prefs.max_value=al;$("#track_"+af.dataset_id+"_minval").val(af.prefs.min_value);$("#track_"+af.dataset_id+"_maxval").val(af.prefs.max_value)}af.vertical_range=af.prefs.max_value-af.prefs.min_value;af.total_frequency=aj.total_frequency;af.container_div.find(".yaxislabel").remove();var ak=$("<div/>").text(Y(af.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(am){$(".bs-tooltip").remove();var am=parseFloat(am);if(!isNaN(am)){af.set_min_value(am)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+af.dataset_id+"_minval").prependTo(af.container_div),ai=$("<div/>").text(Y(af.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(am){$(".bs-tooltip").remove();var am=parseFloat(am);if(!isNaN(am)){af.set_max_value(am)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+af.dataset_id+"_maxval").prependTo(af.container_div)})},draw_tile:function(ao,am,ah,ag,aj,an){var af=am.canvas,ai=aj.get("start"),al=aj.get("end"),ak=new M.LinePainter(ao.data,ai,al,this.prefs,ah);ak.draw(am,af.width,af.height,an);return new b(this,aj,ag,af,ao.data)},can_subset:function(af){return false}});var u=function(ah,ag,ai){var af=this;this.display_modes=["Heatmap"];this.mode="Heatmap";N.call(this,ah,ag,ai);this.hda_ldda=ai.hda_ldda;this.dataset_id=ai.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"4169E1"},{key:"negative_color",label:"Negative Color",type:"color",default_value:"FF8C00"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:ai.prefs,onchange:function(){af.set_name(af.prefs.name);af.vertical_range=af.prefs.max_value-af.prefs.min_value;af.set_min_value(af.prefs.min_value);af.set_max_value(af.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};r(u.prototype,s.prototype,N.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(af){this.prefs.min_value=af;this.tile_cache.clear();this.request_draw()},set_max_value:function(af){this.prefs.max_value=af;this.tile_cache.clear();this.request_draw()},draw_tile:function(ap,an,ak,ai,ag,ao){var ah=an.canvas,af=this._get_tile_bounds(ag,ai),aj=af[0],am=af[1],al=new M.DiagonalHeatmapPainter(ap.data,aj,am,this.prefs,ak);al.draw(an,ah.width,ah.height,ao);return new b(this,ag,ai,ah,ap.data)}});var c=function(ai,ah,ak){var ag=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ai,ah,ak);var aj=R(),af=R([aj,"#ffffff"]);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:aj},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:af},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:ak.prefs,onchange:function(){ag.set_name(ag.prefs.name);ag.tile_cache.clear();ag.set_painter_from_config();ag.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=ak.hda_ldda;this.dataset_id=ak.dataset_id;this.original_dataset_id=ak.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};r(c.prototype,s.prototype,N.prototype,{set_dataset:function(af){this.dataset_id=af.get("id");this.hda_ldda=af.get("hda_ldda");this.dataset=af;this.data_manager.set("dataset",af)},set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=M.ArcLinkedFeaturePainter}else{this.painter=M.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},postdraw_actions:function(av,ap,ak,aj){N.prototype.postdraw_actions.call(this,av,aj);var ao=this,ar;if(ao.mode==="Coverage"){var ag=-1;for(ar=0;ar<av.length;ar++){var aq=av[ar].max_val;if(aq>ag){ag=aq}}for(ar=0;ar<av.length;ar++){var ax=av[ar];if(ax.max_val!==ag){ax.html_elt.remove();ao.draw_helper(true,ap,ax.index,ax.resolution,ax.html_elt.parent(),ak,{more_tile_data:{max:ag}})}}}if(ao.filters_manager){var al=ao.filters_manager.filters;for(var au=0;au<al.length;au++){al[au].update_ui_elt()}var aw=false,af,am;for(ar=0;ar<av.length;ar++){if(av[ar].data.length){af=av[ar].data[0];for(var au=0;au<al.length;au++){am=al[au];if(am.applies_to(af)&&am.min!==am.max){aw=true;break}}}}if(ao.filters_available!==aw){ao.filters_available=aw;if(!ao.filters_available){ao.filters_manager.hide()}ao.update_icons()}}this.container_div.find(".yaxislabel").remove();var ai=av[0];if(ai instanceof j){var an=(this.prefs.histogram_max?this.prefs.histogram_max:ai.max_val),ah=$("<div/>").text(an).make_text_editable({num_cols:12,on_finish:function(ay){$(".bs-tooltip").remove();var ay=parseFloat(ay);ao.prefs.histogram_max=(!isNaN(ay)?ay:null);ao.tile_cache.clear();ao.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ah)}if(ai instanceof P){var at=true;for(ar=0;ar<av.length;ar++){if(!av[ar].all_slotted){at=false;break}}if(!at){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(af){var af;if(this.mode==="Auto"){if(af==="no_detail"){af="feature spans"}else{if(af==="summary_tree"){af="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+af+")")}},incremental_slots:function(aj,af,ai){var ag=this.view.canvas_manager.dummy_context,ah=this.slotters[aj];if(!ah||(ah.mode!==ai)){ah=new (v.FeatureSlotter)(aj,ai,B,function(ak){return ag.measureText(ak)});this.slotters[aj]=ah}return ah.slot_features(af)},get_mode:function(af){if(af.dataset_type==="summary_tree"){mode="summary_tree"}else{if(af.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>J){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(af,aj,ak,ag){if(aj==="summary_tree"||aj==="Coverage"){return this.summary_draw_height}else{var ai=this.incremental_slots(ak,af.data,aj);var ah=new (this.painter)(null,null,null,this.prefs,aj);return Math.max(ac,ah.get_required_height(ai,ag))}},draw_tile:function(ap,au,ar,av,ai,am,ah){var at=this,ag=au.canvas,aB=ai.get("start"),af=ai.get("end"),aj=this.left_offset;if(ar==="summary_tree"||ar==="Coverage"){var aD=new M.SummaryTreePainter(ap,aB,af,this.prefs);aD.draw(au,ag.width,ag.height,am);return new j(at,ai,av,ag,ap.data,ap.max)}var al=[],aq=this.slotters[am].slots;all_slotted=true;if(ap.data){var an=this.filters_manager.filters;for(var aw=0,ay=ap.data.length;aw<ay;aw++){var ak=ap.data[aw];var ax=false;var ao;for(var aA=0,aF=an.length;aA<aF;aA++){ao=an[aA];ao.update_attrs(ak);if(!ao.keep(ak)){ax=true;break}}if(!ax){al.push(ak);if(!(ak[0] in aq)){all_slotted=false}}}}var aE=(this.filters_manager.alpha_filter?new D(this.filters_manager.alpha_filter):null);var aC=(this.filters_manager.height_filter?new D(this.filters_manager.height_filter):null);var aD=new (this.painter)(al,aB,af,this.prefs,ar,aE,aC,ah);var az=null;au.fillStyle=this.prefs.block_color;au.font=au.canvas.manager.default_font;au.textAlign="right";if(ap.data){az=aD.draw(au,ag.width,ag.height,am,aq);az.translation=-aj}return new P(at,ai,av,ag,ap.data,am,ar,ap.message,all_slotted,az)},data_and_mode_compatible:function(af,ag){if(ag==="Auto"){return true}else{if(ag==="Coverage"){return af.dataset_type==="summary_tree"}else{if(af.extra_info==="no_detail"||af.dataset_type==="summary_tree"){return false}else{return true}}}},can_subset:function(af){if(af.dataset_type==="summary_tree"||af.message||af.extra_info==="no_detail"){return false}return true}});var T=function(ag,af,ah){c.call(this,ag,af,ah);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:R()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ah.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter};r(T.prototype,s.prototype,N.prototype,c.prototype);var V=function(ah,ag,aj){c.call(this,ah,ag,aj);var ai=R(),af=R([ai,"#ffffff"]);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ai},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:af},{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:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:aj.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter;this.update_icons()};r(V.prototype,s.prototype,N.prototype,c.prototype);var d={LineTrack:h,FeatureTrack:c,VcfTrack:T,ReadTrack:V,CompositeTrack:f,DrawableGroup:Q};var p=function(ah,ag,af){if("copy" in ah){return ah.copy(af)}else{var ai=ah.obj_type;if(!ai){ai=ah.track_type}return new d[ai](ag,af,ah)}};return{View:aa,DrawableGroup:Q,LineTrack:h,FeatureTrack:c,DiagonalHeatmapTrack:u,ReadTrack:V,VcfTrack:T,CompositeTrack:f,object_from_template:p,add_datasets:ae}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","mvc/data","viz/trackster/filters"],function(ac,x,l,u,L,aa,i){var q=ac.extend;var Q=l.get_random_color;var ad=function(ae,ag,af){$.ajax({url:ae,data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(ah){show_modal("Select datasets for new tracks",ah,{Cancel:function(){hide_modal()},Add:function(){var ai=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var aj={data_type:"track_config",hda_ldda:"hda"},ak=$(this).val();if($(this).attr("name")!=="id"){aj.hda_ldda="ldda"}ai[ai.length]=$.ajax({url:ag+"/"+ak,data:aj,dataType:"json"})});$.when.apply($,ai).then(function(){var aj=(arguments[0] instanceof Array?$.map(arguments,function(ak){return ak[0]}):[arguments[0]]);af(aj)});hide_modal()}})}})};var W=function(ae){return("isResolved" in ae)};var n={};var k=function(ae,af){n[ae.attr("id")]=af};var m=function(ae,ag,ai,ah){ai=".group";var af={};n[ae.attr("id")]=ah;ae.bind("drag",{handle:"."+ag,relative:true},function(aq,ar){var ap=$(this),av=$(this).parent(),am=av.children(),ao=n[$(this).attr("id")],al,ak,at,aj,an;ak=$(this).parents(ai);if(ak.length!==0){at=ak.position().top;aj=at+ak.outerHeight();if(ar.offsetY<at){$(this).insertBefore(ak);var au=n[ak.attr("id")];au.remove_drawable(ao);au.container.add_drawable_before(ao,au);return}else{if(ar.offsetY>aj){$(this).insertAfter(ak);var au=n[ak.attr("id")];au.remove_drawable(ao);au.container.add_drawable(ao);return}}}ak=null;for(an=0;an<am.length;an++){al=$(am.get(an));at=al.position().top;aj=at+al.outerHeight();if(al.is(ai)&&this!==al.get(0)&&ar.offsetY>=at&&ar.offsetY<=aj){if(ar.offsetY-at<aj-ar.offsetY){al.find(".content-div").prepend(this)}else{al.find(".content-div").append(this)}if(ao.container){ao.container.remove_drawable(ao)}n[al.attr("id")].add_drawable(ao);return}}for(an=0;an<am.length;an++){al=$(am.get(an));if(ar.offsetY<al.position().top&&!(al.hasClass("reference-track")||al.hasClass("intro"))){break}}if(an===am.length){if(this!==am.get(an-1)){av.append(this);n[av.attr("id")].move_drawable(ao,an)}}else{if(this!==am.get(an)){$(this).insertBefore(am.get(an));n[av.attr("id")].move_drawable(ao,(ar.deltaY>0?an-1:an))}}}).bind("dragstart",function(){af["border-top"]=ae.css("border-top");af["border-bottom"]=ae.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(af)})};exports.moveable=m;var ab=16,G=9,D=20,A=100,I=12000,T=400,K=5000,w=100,o="There was an error in indexing this dataset. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",v="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",y="Tool cannot be rerun: ",a="Loading data...",V="Ready for display",R=10,H=20;function X(af,ae){if(!ae){ae=0}var ag=Math.pow(10,ae);return Math.round(af*ag)/ag}var r=function(af,ae,ah){if(!r.id_counter){r.id_counter=0}this.id=r.id_counter++;this.name=ah.name;this.view=af;this.container=ae;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ah.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ah.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ai){ai.stopPropagation()});var ag=this;this.container_div.hover(function(){ag.icons_div.show()},function(){ag.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};r.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ae){if(ae.content_visible){ae.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ae.hide_contents();ae.content_visible=false}else{ae.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ae.content_visible=true;ae.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(af){var ah=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(){af.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ae()}}};$(window).bind("keypress.check_enter_esc",ag);show_modal("Configure",af.config.build_form(),{Cancel:ah,OK:ae})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ae){$(".bs-tooltip").remove();ae.remove()}}];q(r.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(ae){this.old_name=this.name;this.name=ae;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ae=this.view;this.container_div.hide(0,function(){$(this).remove();ae.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(af,ak,aj,ai,ae,ah){var ag=this;this.action_icons[af]=$("<a/>").attr("href","javascript:void(0);").attr("title",ak).addClass("icon-button").addClass(aj).tooltip().click(function(){ai(ag)}).appendTo(this.icons_div);if(ah){this.action_icons[af].hide()}},build_action_icons:function(ae){var ag;for(var af=0;af<ae.length;af++){ag=ae[af];this.add_action_icon(ag.name,ag.title,ag.css_class,ag.on_click_fn,ag.prepend,ag.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var z=function(af,ae,ag){r.call(this,af,ae,ag);this.obj_type=ag.obj_type;this.drawables=[]};q(z.prototype,r.prototype,{unpack_drawables:function(ag){this.drawables=[];var af;for(var ae=0;ae<ag.length;ae++){af=p(ag[ae],this.view,this);this.add_drawable(af)}},init:function(){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].init()}},_draw:function(){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae]._draw()}},to_dict:function(){var af=[];for(var ae=0;ae<this.drawables.length;ae++){af.push(this.drawables[ae].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:af}},add_drawable:function(ae){this.drawables.push(ae);ae.container=this;this.changed()},add_drawable_before:function(ag,ae){this.changed();var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables.splice(af,0,ag);return true}return false},replace_drawable:function(ag,ae,af){var ah=this.drawables.indexOf(ag);if(ah!==-1){this.drawables[ah]=ae;if(af){ag.container_div.replaceWith(ae.container_div)}this.changed()}return ah},remove_drawable:function(af){var ae=this.drawables.indexOf(af);if(ae!==-1){this.drawables.splice(ae,1);af.container=null;this.changed();return true}return false},move_drawable:function(af,ag){var ae=this.drawables.indexOf(af);if(ae!==-1){this.drawables.splice(ae,1);this.drawables.splice(ag,0,af);this.changed();return true}return false},get_drawables:function(){return this.drawables}});var P=function(af,ae,ah){q(ah,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});z.call(this,af,ae,ah);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ah){this.unpack_drawables(ah.drawables)}if("filters" in ah){var ag=this.filters_manager;this.filters_manager=new i.FiltersManager(this,ah.filters);ag.parent_div.replaceWith(this.filters_manager.parent_div);if(ah.filters.visible){this.setup_multitrack_filtering()}}};q(P.prototype,r.prototype,z.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ae){$(".bs-tooltip").remove();ae.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ae){if(ae.filters_manager.visible()){ae.filters_manager.clear_filters();ae._restore_filter_managers()}else{ae.setup_multitrack_filtering();ae.request_draw(true)}ae.filters_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div:function(){var ae=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ae)}return ae},build_header_div:function(){var ae=$("<div/>").addClass("track-header");ae.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ae);return ae},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ag=this.drawables.length;if(ag===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ag===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var an,am,ak,aq=true,ai=this.drawables[0].get_type(),ae=0;for(an=0;an<ag;an++){ak=this.drawables[an];if(ak.get_type()!==ai){can_composite=false;break}if(ak instanceof c){ae++}}if(aq||ae===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(ae>1&&ae===this.drawables.length){var ar={},af;ak=this.drawables[0];for(am=0;am<ak.filters_manager.filters.length;am++){af=ak.filters_manager.filters[am];ar[af.name]=[af]}for(an=1;an<this.drawables.length;an++){ak=this.drawables[an];for(am=0;am<ak.filters_manager.filters.length;am++){af=ak.filters_manager.filters[am];if(af.name in ar){ar[af.name].push(af)}}}this.filters_manager.remove_all();var ah,aj,al,ao;for(var ap in ar){ah=ar[ap];if(ah.length===ae){aj=new i.NumberFilter({name:ah[0].name,index:ah[0].index});this.filters_manager.add_filter(aj)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].filters_manager=this.saved_filters_managers[ae]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ae=0;ae<this.drawables.length;ae++){drawable=this.drawables[ae];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ai=[];for(var af=0;af<this.drawables.length;af++){ai.push(this.drawables[af].name)}var ag="Composite Track of "+this.drawables.length+" tracks ("+ai.join(", ")+")";var ah=new f(this.view,this.view,{name:ag,drawables:this.drawables});var ae=this.container.replace_drawable(this,ah,true);ah.request_draw()},add_drawable:function(ae){z.prototype.add_drawable.call(this,ae);this.update_icons()},remove_drawable:function(ae){z.prototype.remove_drawable.call(this,ae);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ae=q(z.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ae},request_draw:function(ae,ag){for(var af=0;af<this.drawables.length;af++){this.drawables[af].request_draw(ae,ag)}}});var Z=function(ae){q(ae,{obj_type:"View"});z.call(this,"View",ae.container,ae);this.chrom=null;this.vis_id=ae.vis_id;this.dbkey=ae.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new x.CanvasManager(this.container.get(0).ownerDocument);this.reset()};ac.extend(Z.prototype,Backbone.Events);q(Z.prototype,z.prototype,{init:function(){this.requested_redraw=false;var ag=this.container,ae=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ag);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ag);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ag);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,ae);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ah=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){ad(add_datasets_url,add_track_async_url,function(ai){ac.each(ai,function(aj){ae.add_drawable(p(aj,ae,ae))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").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=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var af=function(ai){if(ai.type==="focusout"||(ai.keyCode||ai.which)===13||(ai.keyCode||ai.which)===27){if((ai.keyCode||ai.which)!==27){ae.go_to($(this).val())}$(this).hide();$(this).val("");ae.location_span.show();ae.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",af).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ae.location_span.hide();ae.chrom_select.hide();ae.nav_input.val(ae.chrom+":"+ae.low+"-"+ae.high);ae.nav_input.css("display","inline-block");ae.nav_input.select();ae.nav_input.focus();ae.nav_input.autocomplete({source:function(ak,ai){var al=[],aj=$.map(ae.get_drawables(),function(am){return am.data_manager.search_features(ak.term).success(function(an){al=al.concat(an)})});$.when.apply($,aj).done(function(){ai($.map(al,function(am){return{label:am[0],value:am[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ae.zoom_out();ae.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ae.zoom_in();ae.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ae.change_chrom(ae.chrom_select.val())});this.browser_content_div.click(function(ai){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ai){ae.zoom_in(ai.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ai,aj){this.current_x=aj.offsetX}).bind("drag",function(ai,ak){var al=ak.offsetX-this.current_x;this.current_x=ak.offsetX;var aj=Math.round(al/ae.viewport_container.width()*(ae.max_high-ae.max_low));ae.move_delta(-aj)});this.overview_close.click(function(){ae.reset_overview()});this.viewport_container.bind("draginit",function(ai,aj){if(ai.clientX>ae.viewport_container.width()-16){return false}}).bind("dragstart",function(ai,aj){aj.original_low=ae.low;aj.current_height=ai.clientY;aj.current_x=aj.offsetX}).bind("drag",function(ak,am){var ai=$(this);var an=am.offsetX-am.current_x;var aj=ai.scrollTop()-(ak.clientY-am.current_height);ai.scrollTop(aj);am.current_height=ak.clientY;am.current_x=am.offsetX;var al=Math.round(an/ae.viewport_container.width()*(ae.high-ae.low));ae.move_delta(al)}).bind("mousewheel",function(ak,am,aj,ai){if(aj){aj*=50;var al=Math.round(-aj/ae.viewport_container.width()*(ae.high-ae.low));ae.move_delta(al)}});this.top_labeltrack.bind("dragstart",function(ai,aj){return $("<div />").css({height:ae.browser_content_div.height()+ae.top_labeltrack.height()+ae.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(am,an){$(an.proxy).css({left:Math.min(am.pageX,an.startX)-ae.container.offset().left,width:Math.abs(am.pageX-an.startX)});var aj=Math.min(am.pageX,an.startX)-ae.container.offset().left,ai=Math.max(am.pageX,an.startX)-ae.container.offset().left,al=(ae.high-ae.low),ak=ae.viewport_container.width();ae.update_location(Math.round(aj/ak*al)+ae.low,Math.round(ai/ak*al)+ae.low)}).bind("dragend",function(an,ao){var aj=Math.min(an.pageX,ao.startX),ai=Math.max(an.pageX,ao.startX),al=(ae.high-ae.low),ak=ae.viewport_container.width(),am=ae.low;ae.low=Math.round(aj/ak*al)+am;ae.high=Math.round(ai/ak*al)+am;$(ao.proxy).remove();ae.request_redraw()});this.add_label_track(new Y(this,{content_div:this.top_labeltrack}));this.add_label_track(new Y(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ae.resize_window()},500)});$(document).bind("redraw",function(){ae.redraw()});this.reset();$(window).trigger("resize")},changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(af,ah,ae,ai){if(this.timer){clearTimeout(this.timer)}if(ai){var ag=this;this.timer=setTimeout(function(){ag.trigger("navigate",af+":"+ah+"-"+ae)},500)}else{view.trigger("navigate",af+":"+ah+"-"+ae)}},update_location:function(ae,ag){this.location_span.text(commatize(ae)+" - "+commatize(ag));this.nav_input.val(this.chrom+":"+commatize(ae)+"-"+commatize(ag));var af=view.chrom_select.val();if(af!==""){this.trigger_navigate(af,view.low,view.high,true)}},load_chroms:function(ag){ag.num=w;var ae=this,af=$.Deferred();$.ajax({url:chrom_url+"/"+this.dbkey,data:ag,dataType:"json",success:function(ai){if(ai.chrom_info.length===0){return}if(ai.reference){ae.add_label_track(new B(ae))}ae.chrom_data=ai.chrom_info;var al='<option value="">Select Chrom/Contig</option>';for(var ak=0,ah=ae.chrom_data.length;ak<ah;ak++){var aj=ae.chrom_data[ak].chrom;al+='<option value="'+aj+'">'+aj+"</option>"}if(ai.prev_chroms){al+='<option value="previous">Previous '+w+"</option>"}if(ai.next_chroms){al+='<option value="next">Next '+w+"</option>"}ae.chrom_select.html(al);ae.chrom_start_index=ai.start_index;af.resolve(ai)},error:function(){alert("Could not load chroms for this dbkey:",ae.dbkey)}});return af},change_chrom:function(aj,af,al){var ag=this;if(!ag.chrom_data){ag.load_chroms_deferred.then(function(){ag.change_chrom(aj,af,al)});return}if(!aj||aj==="None"){return}if(aj==="previous"){ag.load_chroms({low:this.chrom_start_index-w});return}if(aj==="next"){ag.load_chroms({low:this.chrom_start_index+w});return}var ak=$.grep(ag.chrom_data,function(am,an){return am.chrom===aj})[0];if(ak===undefined){ag.load_chroms({chrom:aj},function(){ag.change_chrom(aj,af,al)});return}else{if(aj!==ag.chrom){ag.chrom=aj;ag.chrom_select.val(ag.chrom);ag.max_high=ak.len-1;ag.reset();ag.request_redraw(true);for(var ai=0,ae=ag.drawables.length;ai<ae;ai++){var ah=ag.drawables[ai];if(ah.init){ah.init()}}if(ag.reference_track){ag.reference_track.init()}}if(af!==undefined&&al!==undefined){ag.low=Math.max(af,0);ag.high=Math.min(al,ag.max_high)}else{ag.low=0;ag.high=ag.max_high}ag.reset_overview();ag.request_redraw()}},go_to:function(ai){ai=ai.replace(/ |,/g,"");var am=this,ae,ah,af=ai.split(":"),ak=af[0],al=af[1];if(al!==undefined){try{var aj=al.split("-");ae=parseInt(aj[0],10);ah=parseInt(aj[1],10)}catch(ag){return false}}am.change_chrom(ak,ae,ah)},move_fraction:function(ag){var ae=this;var af=ae.high-ae.low;this.move_delta(ag*af)},move_delta:function(ah){var ae=this;var ag=ae.high-ae.low;if(ae.low-ah<ae.max_low){ae.low=ae.max_low;ae.high=ae.max_low+ag}else{if(ae.high-ah>ae.max_high){ae.high=ae.max_high;ae.low=ae.max_high-ag}else{ae.high-=ah;ae.low-=ah}}ae.request_redraw();var af=ae.chrom_select.val();this.trigger_navigate(af,ae.low,ae.high,true)},add_drawable:function(ae){z.prototype.add_drawable.call(this,ae);ae.init();this.changed();this.update_intro_div()},add_label_track:function(ae){ae.view=this;ae.init();this.label_tracks.push(ae)},remove_drawable:function(ag,af){z.prototype.remove_drawable.call(this,ag);if(af){var ae=this;ag.container_div.hide(0,function(){$(this).remove();ae.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(am,ae,al,an){var ak=this,aj=(an?[an]:ak.drawables),ag;var af;for(var ai=0;ai<aj.length;ai++){af=aj[ai];ag=-1;for(var ah=0;ah<ak.tracks_to_be_redrawn.length;ah++){if(ak.tracks_to_be_redrawn[ah][0]===af){ag=ah;break}}if(ag<0){ak.tracks_to_be_redrawn.push([af,ae,al])}else{ak.tracks_to_be_redrawn[ai][1]=ae;ak.tracks_to_be_redrawn[ai][2]=al}}if(!this.requested_redraw){requestAnimationFrame(function(){ak._redraw(am)});this.requested_redraw=true}},_redraw:function(ao){this.requested_redraw=false;var al=this.low,ah=this.high;if(al<this.max_low){al=this.max_low}if(ah>this.max_high){ah=this.max_high}var an=this.high-this.low;if(this.high!==0&&an<this.min_separation){ah=al+this.min_separation}this.low=Math.floor(al);this.high=Math.ceil(ah);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ae=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ak=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ap=13;this.overview_box.css({left:ae,width:Math.max(ap,ak)}).show();if(ak<ap){this.overview_box.css("left",ae-(ap-ak)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ae,width:ak})}if(!ao){var ag,af,am;for(var ai=0,aj=this.tracks_to_be_redrawn.length;ai<aj;ai++){ag=this.tracks_to_be_redrawn[ai][0];af=this.tracks_to_be_redrawn[ai][1];am=this.tracks_to_be_redrawn[ai][2];if(ag){ag._draw(af,am)}}this.tracks_to_be_redrawn=[];for(ai=0,aj=this.label_tracks.length;ai<aj;ai++){this.label_tracks[ai]._draw()}}},zoom_in:function(af,ag){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ah=this.high-this.low,ai=ah/2+this.low,ae=(ah/this.zoom_factor)/2;if(af){ai=af/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ai-ae);this.high=Math.round(ai+ae);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var af=this.high-this.low,ag=af/2+this.low,ae=(af*this.zoom_factor)/2;this.low=Math.round(ag-ae);this.high=Math.round(ag+ae);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ag){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ag.dataset_id){return}this.overview_viewport.find(".track").remove()}var af=ag.copy({content_div:this.overview_viewport}),ae=this;af.header_div.hide();af.is_overview=true;ae.overview_drawable=af;this.overview_drawable.postdraw_actions=function(){ae.overview_highlight.show().height(ae.overview_drawable.content_div.height());ae.overview_viewport.height(ae.overview_drawable.content_div.height()+ae.overview_box.outerHeight());ae.overview_close.show();ae.resize_window()};ae.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=function(ag,al,ah){this.track=ag;this.name=al.name;this.params=[];var at=al.params;for(var ai=0;ai<at.length;ai++){var an=at[ai],af=an.name,ar=an.label,aj=unescape(an.html),au=an.value,ap=an.type;if(ap==="number"){this.params.push(new e(af,ar,aj,(af in ah?ah[af]:au),an.min,an.max))}else{if(ap==="select"){this.params.push(new N(af,ar,aj,(af in ah?ah[af]:au)))}else{console.log("WARNING: unrecognized tool parameter type:",af,ap)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aw){aw.stopPropagation()}).click(function(aw){aw.stopPropagation()}).bind("dblclick",function(aw){aw.stopPropagation()});var aq=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ao=this.params;var am=this;$.each(this.params,function(ax,aA){var az=$("<div>").addClass("param-row").appendTo(am.parent_div);var aw=$("<div>").addClass("param-label").text(aA.label).appendTo(az);var ay=$("<div/>").addClass("param-input").html(aA.html).appendTo(az);ay.find(":input").val(aA.value);$("<div style='clear: both;'/>").appendTo(az)});this.parent_div.find("input").click(function(){$(this).select()});var av=$("<div>").addClass("param-row").appendTo(this.parent_div);var ak=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(av);var ae=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(av);ae.click(function(){am.run_on_region()});ak.click(function(){am.run_on_dataset()});if("visible" in ah&&ah.visible){this.parent_div.show()}};q(s.prototype,{update_params:function(){for(var ae=0;ae<this.params.length;ae++){this.params[ae].update_value()}},state_dict:function(){var af={};for(var ae=0;ae<this.params.length;ae++){af[this.params[ae].name]=this.params[ae].value}af.visible=this.parent_div.is(":visible");return af},get_param_values_dict:function(){var ae={};this.parent_div.find(":input").each(function(){var af=$(this).attr("name"),ag=$(this).val();ae[af]=ag});return ae},get_param_values:function(){var ae=[];this.parent_div.find(":input").each(function(){var af=$(this).attr("name"),ag=$(this).val();if(af){ae[ae.length]=ag}});return ae},run_on_dataset:function(){var ae=this;ae.run({target_dataset_id:this.track.original_dataset_id,tool_id:ae.name},null,function(af){show_modal(ae.name+" is Running",ae.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var af={target_dataset_id:this.track.original_dataset_id,action:"rerun",tool_id:this.name,regions:[{chrom:this.track.view.chrom,start:this.track.view.low,end:this.track.view.high}]},aj=this.track,ag=af.tool_id+aj.tool_region_and_parameters_str(af.chrom,af.low,af.high),ae;if(aj.container===view){var ai=new P(view,view,{name:this.name});var ah=aj.container.replace_drawable(aj,ai,false);ai.container_div.insertBefore(aj.view.content_div.children()[ah]);ai.add_drawable(aj);aj.container_div.appendTo(ai.content_div);ae=ai}else{ae=aj.container}var ak=new aj.constructor(view,ae,{name:ag,hda_ldda:"hda"});ak.init_for_tool_data();ak.change_mode(aj.mode);ak.set_filters_manager(aj.filters_manager.copy(ak));ak.update_icons();ae.add_drawable(ak);ak.tiles_div.text("Starting job.");this.update_params();this.run(af,ak,function(al){ak.set_dataset(new aa.Dataset(al));ak.tiles_div.text("Running job.");ak.init()})},run:function(ae,ag,ah){ae.inputs=this.get_param_values_dict();var af=new l.ServerStateDeferred({ajax_settings:{url:galaxy_paths.get("tool_url"),data:JSON.stringify(ae),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ai){return ai!=="pending"}});$.when(af.go()).then(function(ai){if(ai==="no converter"){ag.container_div.addClass("error");ag.content_div.text(J)}else{if(ai.error){ag.container_div.addClass("error");ag.content_div.text(y+ai.message)}else{ah(ai)}}})}});var N=function(af,ae,ag,ah){this.name=af;this.label=ae;this.html=$(ag);this.value=ah};q(N.prototype,{update_value:function(){this.value=$(this.html).val()}});var e=function(ag,af,ai,aj,ah,ae){N.call(this,ag,af,ai,aj);this.min=ah;this.max=ae};q(e.prototype,N.prototype,{update_value:function(){N.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var C=function(ae,af){L.Scaler.call(this,af);this.filter=ae};C.prototype.gen_val=function(ae){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ae[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ae){this.track=ae.track;this.params=ae.params;this.values={};this.restore_values((ae.saved_values?ae.saved_values:{}));this.onchange=ae.onchange};q(F.prototype,{restore_values:function(ae){var af=this;$.each(this.params,function(ag,ah){if(ae[ah.key]!==undefined){af.values[ah.key]=ae[ah.key]}else{af.values[ah.key]=ah.default_value}})},build_form:function(){var ah=this;var ae=$("<div />");var ag;function af(am,ai){for(var aq=0;aq<am.length;aq++){ag=am[aq];if(ag.hidden){continue}var ak="param_"+aq;var av=ah.values[ag.key];var ax=$("<div class='form-row' />").appendTo(ai);ax.append($("<label />").attr("for",ak).text(ag.label+":"));if(ag.type==="bool"){ax.append($('<input type="checkbox" />').attr("id",ak).attr("name",ak).attr("checked",av))}else{if(ag.type==="text"){ax.append($('<input type="text"/>').attr("id",ak).val(av).click(function(){$(this).select()}))}else{if(ag.type==="select"){var at=$("<select />").attr("id",ak);for(var ao=0;ao<ag.options.length;ao++){$("<option/>").text(ag.options[ao].label).attr("value",ag.options[ao].value).appendTo(at)}at.val(av);ax.append(at)}else{if(ag.type==="color"){var aw=$("<div/>").appendTo(ax),ar=$("<input />").attr("id",ak).attr("name",ak).val(av).css("float","left").appendTo(aw).click(function(az){$(".bs-tooltip").removeClass("in");var ay=$(this).siblings(".bs-tooltip").addClass("in");ay.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(ay).height()/2)+($(this).height()/2)}).show();ay.click(function(aA){aA.stopPropagation()});$(document).bind("click.color-picker",function(){ay.hide();$(document).unbind("click.color-picker")});az.stopPropagation()}),ap=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(aw).attr("title","Set new random color").tooltip(),au=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(aw).hide(),al=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(au),aj=$("<div class='tooltip-arrow'></div>").appendTo(au),an=$.farbtastic(al,{width:100,height:100,callback:ar,color:av});aw.append($("<div/>").css("clear","both"));(function(ay){ap.click(function(){ay.setColor(Q())})})(an)}else{ax.append($("<input />").attr("id",ak).attr("name",ak).val(av))}}}}if(ag.help){ax.append($("<div class='help'/>").text(ag.help))}}}af(this.params,ae);return ae},update_from_form:function(ae){var ag=this;var af=false;$.each(this.params,function(ah,aj){if(!aj.hidden){var ak="param_"+ah;var ai=ae.find("#"+ak).val();if(aj.type==="float"){ai=parseFloat(ai)}else{if(aj.type==="int"){ai=parseInt(ai)}else{if(aj.type==="bool"){ai=ae.find("#"+ak).is(":checked")}}}if(ai!==ag.values[aj.key]){ag.values[aj.key]=ai;af=true}}});if(af){this.onchange();this.track.changed()}}});var b=function(ae,ai,ag,af,ah){this.track=ae;this.region=ai;this.low=ai.get("start");this.high=ai.get("end");this.resolution=ag;this.html_elt=$("<div class='track-tile'/>").append(af).height($(af).attr("height"));this.data=ah;this.stale=false};b.prototype.predisplay_actions=function(){};var j=function(ae,aj,ag,af,ah,ai){b.call(this,ae,aj,ag,af,ah);this.max_val=ai};q(j.prototype,b.prototype);var O=function(ah,ap,ai,ag,ak,ar,al,at,af,ao){b.call(this,ah,ap,ai,ag,ak);this.mode=al;this.all_slotted=af;this.feature_mapper=ao;this.has_icons=false;if(at){this.has_icons=true;var am=this;ag=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:ag.width}).prependTo(this.html_elt);var an=new x.GenomeRegion({chrom:ah.view.chrom,start:this.low,end:this.high}),aq=ak.length,aj=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+aq+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ae=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+aq+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);aj.click(function(){am.stale=true;ah.data_manager.get_more_data(an,ah.mode,am.resolution,{},ah.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();ah.request_draw(true)}).dblclick(function(au){au.stopPropagation()});ae.click(function(){am.stale=true;ah.data_manager.get_more_data(an,ah.mode,am.resolution,{},ah.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();ah.request_draw(true)}).dblclick(function(au){au.stopPropagation()})}};q(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var af=this,ae={};if(af.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(aq){if(!this.hovered){return}var al=$(this).offset(),ap=aq.pageX-al.left,ao=aq.pageY-al.top,av=af.feature_mapper.get_feature_data(ap,ao),am=(av?av[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!am||$(this).attr("id")!==am.toString()){$(this).remove()}});if(av){var ah=ae[am];if(!ah){var am=av[0],ar={name:av[3],start:av[1],end:av[2],strand:av[4]},ak=af.track.filters_manager.filters,aj;for(var an=0;an<ak.length;an++){aj=ak[an];ar[aj.name]=av[aj.index]}var ah=$("<div/>").attr("id",am).addClass("feature-popup"),aw=$("<table/>"),au,at,ax;for(au in ar){at=ar[au];ax=$("<tr/>").appendTo(aw);$("<th/>").appendTo(ax).text(au);$("<td/>").attr("align","left").appendTo(ax).text(typeof(at)==="number"?X(at,2):at)}ah.append($("<div class='feature-popup-inner'>").append(aw));ae[am]=ah}ah.appendTo($(this).parents(".track-content").children(".overlay"));var ai=ap+parseInt(af.html_elt.css("left"))-ah.width()/2,ag=ao+parseInt(af.html_elt.css("top"))+7;ah.css("left",ai+"px").css("top",ag+"px")}else{if(!aq.isPropagationStopped()){aq.stopPropagation();$(this).siblings().each(function(){$(this).trigger(aq)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(af,ae,ag){q(ag,{drag_handle_class:"draghandle"});r.call(this,af,ae,ag);this.dataset=new aa.Dataset({id:ag.dataset_id,hda_ldda:ag.hda_ldda});this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ag?ag.data_query_wait:K);this.data_manager=("data_manager" in ag?ag.data_manager:new x.GenomeDataManager({dataset:this.dataset,data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ag)||ag.resize){this.add_resize_handle()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ae){ae.view.set_overview(ae)}},r.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ae){if(ae.filters_manager.visible()){ae.filters_manager.clear_filters()}else{ae.filters_manager.init_filters()}ae.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ae){ae.dynamic_tool_div.toggle();if(ae.dynamic_tool_div.is(":visible")){ae.set_name(ae.name+ae.tool_region_and_parameters_str())}else{ae.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ae){var ah='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ag=ac.template(ah,{track:ae});var aj=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(){var al=$('select[name="regions"] option:selected').val(),an,ak=new x.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),am=ac.map($(".bookmark"),function(ao){return new x.GenomeRegion({from_str:$(ao).children(".position").text()})});if(al==="cur"){an=[ak]}else{if(al==="bookmarks"){an=am}else{an=[ak].concat(am)}}hide_modal();window.location.href=galaxy_paths.get("sweepster_url")+"?"+$.param({dataset_id:ae.dataset_id,hda_ldda:ae.hda_ldda,regions:JSON.stringify(new Backbone.Collection(an).toJSON())})},ai=function(ak){if((ak.keyCode||ak.which)===27){aj()}else{if((ak.keyCode||ak.which)===13){af()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",ag,{No:aj,Yes:af})}},r.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&r.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ae=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ae)}this.name_div=$("<div/>").addClass("track-name").appendTo(ae).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ae},on_resize:function(){},add_resize_handle:function(){var ae=this;var ah=false;var ag=false;var af=$("<div class='track-resize'>");$(ae.container_div).hover(function(){if(ae.content_visible){ah=true;af.show()}},function(){ah=false;if(!ag){af.hide()}});af.hide().bind("dragstart",function(ai,aj){ag=true;aj.original_height=$(ae.content_div).height()}).bind("drag",function(aj,ak){var ai=Math.min(Math.max(ak.original_height+ak.deltaY,ae.min_height_px),ae.max_height_px);$(ae.tiles_div).css("height",ai);ae.visible_height_px=(ae.max_height_px===ai?0:ai);ae.on_resize()}).bind("dragend",function(ai,aj){ae.tile_cache.clear();ag=false;if(!ah){af.hide()}ae.config.values.height=ae.visible_height_px;ae.changed()}).appendTo(ae.container_div)},set_display_modes:function(ah,ak){this.display_modes=ah;this.mode=(ak?ak:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var af=this,ai={};for(var ag=0,ae=af.display_modes.length;ag<ae;ag++){var aj=af.display_modes[ag];ai[aj]=function(al){return function(){af.change_mode(al);af.icons_div.show();af.container_div.mouseleave(function(){af.icons_div.hide()})}}(aj)}make_popupmenu(this.action_icons.mode_icon,ai)},build_action_icons:function(){r.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof Y){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof U){return"ReadTrack"}else{if(this instanceof S){return"VcfTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(){var af=this;af.enabled=false;af.tile_cache.clear();af.data_manager.clear();af.content_div.css("height","auto");af.tiles_div.children().remove();af.container_div.removeClass("nodata error pending");if(!af.dataset_id){return}var ae=$.Deferred(),ag={hda_ldda:af.hda_ldda,data_type:this.dataset_check_type,chrom:af.view.chrom};$.getJSON(this.dataset.url(),ag,function(ah){if(!ah||ah==="error"||ah.kind==="error"){af.container_div.addClass("error");af.tiles_div.text(o);if(ah.message){var ai=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ah.message+"</pre>",{Close:hide_modal})});af.tiles_div.append(ai)}}else{if(ah==="no converter"){af.container_div.addClass("error");af.tiles_div.text(J)}else{if(ah==="no data"||(ah.data!==undefined&&(ah.data===null||ah.data.length===0))){af.container_div.addClass("nodata");af.tiles_div.text(E)}else{if(ah==="pending"){af.container_div.addClass("pending");af.tiles_div.html(v);setTimeout(function(){af.init()},af.data_query_wait)}else{if(ah==="data"||ah.status==="data"){if(ah.valid_chroms){af.valid_chroms=ah.valid_chroms;af.update_icons()}af.tiles_div.text(V);if(af.view.chrom){af.tiles_div.text("");af.tiles_div.css("height",af.visible_height_px+"px");af.enabled=true;$.when(af.predraw_init()).done(function(){ae.resolve();af.container_div.removeClass("nodata error pending");af.request_draw()})}else{ae.resolve()}}}}}}});this.update_icons();return ae},predraw_init:function(){},get_drawables:function(){return this}});var M=function(ag,af,ah){g.call(this,ag,af,ah);var ae=this;m(ae.container_div,ae.drag_handle_class,".group",ae);this.filters_manager=new i.FiltersManager(this,("filters" in ah?ah.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in ah&&ah.tool?new s(this,ah.tool,ah.tool_state):null);this.tile_cache=new x.Cache(R);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ah.mode){this.change_mode(ah.mode)}};q(M.prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ae){$(".bs-tooltip").remove();ae.slotters[ae.view.resolution_px_b].max_rows*=2;ae.request_draw(true)},hide:true}]),copy:function(ae){var af=this.to_dict();q(af,{data_manager:this.data_manager});var ag=new this.constructor(this.view,ae,af);ag.change_mode(this.mode);ag.enabled=this.enabled;return ag},set_filters_manager:function(ae){this.filters_manager=ae;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(af){var ae=this;ae.mode=af;ae.config.values.mode=af;ae.tile_cache.clear();ae.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+ae.mode+")");return ae},update_icons:function(){var ae=this;if(ae.filters_available){ae.action_icons.filters_icon.show()}else{ae.action_icons.filters_icon.hide()}if(ae.tool){ae.action_icons.tools_icon.show();ae.action_icons.param_space_viz_icon.show()}else{ae.action_icons.tools_icon.hide();ae.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(af,ag,ae){return af+"_"+ag+"_"+ae},request_draw:function(af,ae){this.view.request_redraw(false,af,ae,this)},before_draw:function(){},_draw:function(af,ap){if(!this.can_draw()){return}var an=this.view.low,aj=this.view.high,al=aj-an,ag=this.view.container.width(),ar=this.view.resolution_px_b,ai=this.view.resolution_b_px;if(this.is_overview){an=this.view.max_low;aj=this.view.max_high;ai=(view.max_high-view.max_low)/ag;ar=1/ai}this.before_draw();this.tiles_div.children().addClass("remove");var ae=Math.floor(an/(ai*T)),am=true,aq=[],ak=function(at){return(at&&"track" in at)};while((ae*T*ai)<aj){var ao=this.draw_helper(af,ag,ae,ai,this.tiles_div,ar);if(ak(ao)){aq.push(ao)}else{am=false}ae+=1}if(!ap){this.tiles_div.children(".remove").removeClass("remove").remove()}var ah=this;if(am){this.tiles_div.children(".remove").remove();ah.postdraw_actions(aq,ag,ar,ap)}},postdraw_actions:function(ag,ah,aj,ae){var ai=false;for(var af=0;af<ag.length;af++){if(ag[af].has_icons){ai=true;break}}if(ai){for(var af=0;af<ag.length;af++){tile=ag[af];if(!tile.has_icons){tile.html_elt.css("padding-top",D)}}}},draw_helper:function(ae,aq,aw,au,aj,ak,ar){var ap=this,az=this._gen_tile_cache_key(aq,ak,aw),ah=this._get_tile_bounds(aw,au);if(!ar){ar={}}var ay=(ae?undefined:ap.tile_cache.get_elt(az));if(ay){ap.show_tile(ay,aj,ak);return ay}var an=true;var av=ap.data_manager.get_data(ah,ap.mode,au,ap.data_url_extra_params);if(W(av)){an=false}var al;if(view.reference_track&&ak>view.canvas_manager.char_width_px){al=view.reference_track.data_manager.get_data(ah,ap.mode,au,view.reference_track.data_url_extra_params);if(W(al)){an=false}}if(an){q(av,ar.more_tile_data);var am=ap.mode;if(am==="Auto"){am=ap.get_mode(av);ap.update_auto_mode(am)}var ag=ap.view.canvas_manager.new_canvas(),ax=ah.get("start"),af=ah.get("end"),aq=Math.ceil((af-ax)*ak)+ap.left_offset,ao=ap.get_canvas_height(av,am,ak,aq);ag.width=aq;ag.height=ao;var at=ag.getContext("2d");at.translate(this.left_offset,0);var ay=ap.draw_tile(av,at,am,au,ah,ak,al);if(ay!==undefined){ap.tile_cache.set_elt(az,ay);ap.show_tile(ay,aj,ak)}return ay}var ai=$.Deferred();$.when(av,al).then(function(){view.request_redraw(false,false,false,ap);ai.resolve()});return ai},get_canvas_height:function(ae,ag,ah,af){return this.visible_height_px},draw_tile:function(ae,af,aj,ah,ai,ak,ag){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ag,ai,aj){var af=this,ae=ag.html_elt;ag.predisplay_actions();var ah=(ag.low-(this.is_overview?this.view.max_low:this.view.low))*aj;if(this.left_offset){ah-=this.left_offset}ae.css({position:"absolute",top:0,left:ah});if(ae.hasClass("remove")){ae.removeClass("remove")}else{ai.append(ae)}af.after_show_tile(ag)},after_show_tile:function(ae){this.max_height_px=Math.max(this.max_height_px,ae.html_elt.height());ae.html_elt.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},_get_tile_bounds:function(ae,af){var ah=Math.floor(ae*T*af),ai=Math.ceil(T*af),ag=(ah+ai<=this.view.max_high?ah+ai:this.view.max_high);return new x.GenomeRegion({chrom:this.view.chrom,start:ah,end:ag})},tool_region_and_parameters_str:function(ag,ae,ah){var af=this,ai=(ag!==undefined&&ae!==undefined&&ah!==undefined?ag+":"+ae+"-"+ah:"all");return" - region=["+ai+"], parameters=["+af.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ae,af){return true},can_subset:function(ae){return false},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ag,ah,aj,ae){var af=this;af.normal_postdraw_actions(ag,ah,aj,ae);af.dataset_check_type="converted_datasets_state";af.data_query_wait=K;var ai=new l.ServerStateDeferred({url:af.dataset_state_url,url_params:{dataset_id:af.dataset_id,hda_ldda:af.hda_ldda},interval:af.data_query_wait,success_fn:function(ak){return ak!=="pending"}});$.when(ai.go()).then(function(){af.data_manager.set("data_type","data")});af.postdraw_actions=af.normal_postdraw_actions}}});var Y=function(af,ae){var ag={resize:false};g.call(this,af,ae,ag);this.container_div.addClass("label-track")};q(Y.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ag=this.view,ah=ag.high-ag.low,ak=Math.floor(Math.pow(10,Math.floor(Math.log(ah)/Math.log(10)))),ae=Math.floor(ag.low/ak)*ak,ai=this.view.container.width(),af=$("<div style='position: relative; height: 1.3em;'></div>");while(ae<ag.high){var aj=(ae-ag.low)/ah*ai;af.append($("<div class='label'>"+commatize(ae)+"</div>").css({position:"absolute",left:aj-1}));ae+=ak}this.content_div.children(":first").remove();this.content_div.append(af)}});var f=function(af,ae,ai){M.call(this,af,ae,ai);this.drawables=[];this.left_offset=0;if("drawables" in ai){var ah;for(var ag=0;ag<ai.drawables.length;ag++){ah=ai.drawables[ag];this.drawables[ag]=p(ah,af,null);if(ah.left_offset>this.left_offset){this.left_offset=ah.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,M.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ae){$(".bs-tooltip").remove();ae.show_group()}}].concat(M.prototype.action_icons_def),to_dict:z.prototype.to_dict,add_drawable:z.prototype.add_drawable,unpack_drawables:z.prototype.unpack_drawables,change_mode:function(ae){M.prototype.change_mode.call(this,ae);for(var af=0;af<this.drawables.length;af++){this.drawables[af].change_mode(ae)}},init:function(){var ag=[];for(var af=0;af<this.drawables.length;af++){ag.push(this.drawables[af].init())}var ae=this;$.when.apply($,ag).then(function(){ae.enabled=true;ae.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw,draw_helper:function(af,av,aB,ay,am,ao,aw){var au=this,aF=this._gen_tile_cache_key(av,ao,aB),aj=this._get_tile_bounds(aB,ay);if(!aw){aw={}}var aE=(af?undefined:au.tile_cache.get_elt(aF));if(aE){au.show_tile(aE,am,ao);return aE}var an=[],au,ar=true,az,ap;for(var aA=0;aA<this.drawables.length;aA++){au=this.drawables[aA];az=au.data_manager.get_data(aj,au.mode,ay,au.data_url_extra_params);if(W(az)){ar=false}an.push(az);ap=null;if(view.reference_track&&ao>view.canvas_manager.char_width_px){ap=view.reference_track.data_manager.get_data(aj,au.mode,ay,view.reference_track.data_url_extra_params);if(W(ap)){ar=false}}an.push(ap)}if(ar){q(az,aw.more_tile_data);this.tile_predraw_init();var ai=au.view.canvas_manager.new_canvas(),ak=au._get_tile_bounds(aB,ay),aC=aj.get("start"),ag=aj.get("end"),aD=0,av=Math.ceil((ag-aC)*ao)+this.left_offset,at=0,ah=[],aA;var ae=0;for(aA=0;aA<this.drawables.length;aA++,aD+=2){au=this.drawables[aA];az=an[aD];var aq=au.mode;if(aq==="Auto"){aq=au.get_mode(az);au.update_auto_mode(aq)}ah.push(aq);ae=au.get_canvas_height(az,aq,ao,av);if(ae>at){at=ae}}ai.width=av;ai.height=(aw.height?aw.height:at);aD=0;var ax=ai.getContext("2d");ax.translate(this.left_offset,0);ax.globalAlpha=0.5;ax.globalCompositeOperation="source-over";for(aA=0;aA<this.drawables.length;aA++,aD+=2){au=this.drawables[aA];az=an[aD];ap=an[aD+1];aE=au.draw_tile(az,ax,ah[aA],ay,aj,ao,ap)}this.tile_cache.set_elt(aF,aE);this.show_tile(aE,am,ao);return aE}var al=$.Deferred(),au=this;$.when.apply($,an).then(function(){view.request_redraw(false,false,false,au);al.resolve()});return al},show_group:function(){var ah=new P(this.view,this.container,{name:this.name}),ae;for(var ag=0;ag<this.drawables.length;ag++){ae=this.drawables[ag];ae.update_icons();ah.add_drawable(ae);ae.container=ah;ah.content_div.append(ae.container_div)}var af=this.container.replace_drawable(this,ah,true);ah.request_draw()},tile_predraw_init:function(){var ah=Number.MAX_VALUE,ae=-ah,af;for(var ag=0;ag<this.drawables.length;ag++){af=this.drawables[ag];if(af instanceof h){if(af.prefs.min_value<ah){ah=af.prefs.min_value}if(af.prefs.max_value>ae){ae=af.prefs.max_value}}}for(var ag=0;ag<this.drawables.length;ag++){af=this.drawables[ag];af.prefs.min_value=ah;af.prefs.max_value=ae}},postdraw_actions:function(ag,aj,al,af){M.prototype.postdraw_actions.call(this,ag,aj,al,af);var ai=-1;for(var ah=0;ah<ag.length;ah++){var ae=ag[ah].html_elt.find("canvas").height();if(ae>ai){ai=ae}}for(var ah=0;ah<ag.length;ah++){var ak=ag[ah];if(ak.html_elt.find("canvas").height()!==ai){this.draw_helper(true,aj,ak.index,ak.resolution,ak.html_elt.parent(),al,{height:ai});ak.html_elt.remove()}}}});var B=function(ae){M.call(this,ae,{content_div:ae.top_labeltrack},{resize:false});ae.reference_track=this;this.left_offset=200;this.visible_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.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new x.ReferenceTrackDataManager({data_url:this.data_url});this.hide_contents()};q(B.prototype,r.prototype,M.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:r.prototype.can_draw,draw_helper:function(ai,ag,ae,af,aj,ak,ah){if(ak>this.view.canvas_manager.char_width_px){return M.prototype.draw_helper.call(this,ai,ag,ae,af,aj,ak,ah)}else{this.hide_contents();return null}},draw_tile:function(am,an,ai,ah,ak,ao){var ag=this;if(ao>this.view.canvas_manager.char_width_px){if(am.data===null){this.hide_contents();return}var af=an.canvas;an.font=an.canvas.manager.default_font;an.textAlign="center";am=am.data;for(var aj=0,al=am.length;aj<al;aj++){var ae=Math.floor(aj*ao);an.fillText(am[aj],ae,10)}this.show_contents();return new b(ag,ak,ah,af,am)}this.hide_contents()}});var h=function(ag,af,ah){var ae=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";M.call(this,ag,af,ah);this.hda_ldda=ah.hda_ldda;this.dataset_id=ah.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:Q()},{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:32,hidden:true}],saved_values:ah.prefs,onchange:function(){ae.set_name(ae.prefs.name);ae.vertical_range=ae.prefs.max_value-ae.prefs.min_value;ae.set_min_value(ae.prefs.min_value);ae.set_max_value(ae.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};q(h.prototype,r.prototype,M.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ae){this.prefs.min_value=ae;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(ae){this.prefs.max_value=ae;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var ae=this;ae.vertical_range=undefined;return $.getJSON(ae.dataset.url(),{data_type:"data",stats:true,chrom:ae.view.chrom,low:0,high:ae.view.max_high,hda_ldda:ae.hda_ldda},function(af){ae.container_div.addClass("line-track");var ai=af.data;if(isNaN(parseFloat(ae.prefs.min_value))||isNaN(parseFloat(ae.prefs.max_value))){var ag=ai.min,ak=ai.max;ag=Math.floor(Math.min(0,Math.max(ag,ai.mean-2*ai.sd)));ak=Math.ceil(Math.max(0,Math.min(ak,ai.mean+2*ai.sd)));ae.prefs.min_value=ag;ae.prefs.max_value=ak;$("#track_"+ae.dataset_id+"_minval").val(ae.prefs.min_value);$("#track_"+ae.dataset_id+"_maxval").val(ae.prefs.max_value)}ae.vertical_range=ae.prefs.max_value-ae.prefs.min_value;ae.total_frequency=ai.total_frequency;ae.container_div.find(".yaxislabel").remove();var aj=$("<div/>").text(X(ae.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(al){$(".bs-tooltip").remove();var al=parseFloat(al);if(!isNaN(al)){ae.set_min_value(al)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+ae.dataset_id+"_minval").prependTo(ae.container_div),ah=$("<div/>").text(X(ae.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(al){$(".bs-tooltip").remove();var al=parseFloat(al);if(!isNaN(al)){ae.set_max_value(al)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+ae.dataset_id+"_maxval").prependTo(ae.container_div)})},draw_tile:function(an,al,ag,af,ai,am){var ae=al.canvas,ah=ai.get("start"),ak=ai.get("end"),aj=new L.LinePainter(an.data,ah,ak,this.prefs,ag);aj.draw(al,ae.width,ae.height,am);return new b(this,ai,af,ae,an.data)},can_subset:function(ae){return false}});var t=function(ag,af,ah){var ae=this;this.display_modes=["Heatmap"];this.mode="Heatmap";M.call(this,ag,af,ah);this.hda_ldda=ah.hda_ldda;this.dataset_id=ah.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"4169E1"},{key:"negative_color",label:"Negative Color",type:"color",default_value:"FF8C00"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:ah.prefs,onchange:function(){ae.set_name(ae.prefs.name);ae.vertical_range=ae.prefs.max_value-ae.prefs.min_value;ae.set_min_value(ae.prefs.min_value);ae.set_max_value(ae.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};q(t.prototype,r.prototype,M.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ae){this.prefs.min_value=ae;this.tile_cache.clear();this.request_draw()},set_max_value:function(ae){this.prefs.max_value=ae;this.tile_cache.clear();this.request_draw()},draw_tile:function(ao,am,aj,ah,af,an){var ag=am.canvas,ae=this._get_tile_bounds(af,ah),ai=ae[0],al=ae[1],ak=new L.DiagonalHeatmapPainter(ao.data,ai,al,this.prefs,aj);ak.draw(am,ag.width,ag.height,an);return new b(this,af,ah,ag,ao.data)}});var c=function(ah,ag,aj){var af=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];M.call(this,ah,ag,aj);var ai=Q(),ae=Q([ai,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ai},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ae},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:aj.prefs,onchange:function(){af.set_name(af.prefs.name);af.tile_cache.clear();af.set_painter_from_config();af.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=aj.hda_ldda;this.dataset_id=aj.dataset_id;this.original_dataset_id=aj.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};q(c.prototype,r.prototype,M.prototype,{set_dataset:function(ae){this.dataset_id=ae.get("id");this.hda_ldda=ae.get("hda_ldda");this.dataset=ae;this.data_manager.set("dataset",ae)},set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},postdraw_actions:function(au,ao,aj,ai){M.prototype.postdraw_actions.call(this,au,ai);var an=this,aq;if(an.mode==="Coverage"){var af=-1;for(aq=0;aq<au.length;aq++){var ap=au[aq].max_val;if(ap>af){af=ap}}for(aq=0;aq<au.length;aq++){var aw=au[aq];if(aw.max_val!==af){aw.html_elt.remove();an.draw_helper(true,ao,aw.index,aw.resolution,aw.html_elt.parent(),aj,{more_tile_data:{max:af}})}}}if(an.filters_manager){var ak=an.filters_manager.filters;for(var at=0;at<ak.length;at++){ak[at].update_ui_elt()}var av=false,ae,al;for(aq=0;aq<au.length;aq++){if(au[aq].data.length){ae=au[aq].data[0];for(var at=0;at<ak.length;at++){al=ak[at];if(al.applies_to(ae)&&al.min!==al.max){av=true;break}}}}if(an.filters_available!==av){an.filters_available=av;if(!an.filters_available){an.filters_manager.hide()}an.update_icons()}}this.container_div.find(".yaxislabel").remove();var ah=au[0];if(ah instanceof j){var am=(this.prefs.histogram_max?this.prefs.histogram_max:ah.max_val),ag=$("<div/>").text(am).make_text_editable({num_cols:12,on_finish:function(ax){$(".bs-tooltip").remove();var ax=parseFloat(ax);an.prefs.histogram_max=(!isNaN(ax)?ax:null);an.tile_cache.clear();an.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ag)}if(ah instanceof O){var ar=true;for(aq=0;aq<au.length;aq++){if(!au[aq].all_slotted){ar=false;break}}if(!ar){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ae){var ae;if(this.mode==="Auto"){if(ae==="no_detail"){ae="feature spans"}else{if(ae==="summary_tree"){ae="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ae+")")}},incremental_slots:function(ai,ae,ah){var af=this.view.canvas_manager.dummy_context,ag=this.slotters[ai];if(!ag||(ag.mode!==ah)){ag=new (u.FeatureSlotter)(ai,ah,A,function(aj){return af.measureText(aj)});this.slotters[ai]=ag}return ag.slot_features(ae)},get_mode:function(ae){if(ae.dataset_type==="summary_tree"){mode="summary_tree"}else{if(ae.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(ae,ai,aj,af){if(ai==="summary_tree"||ai==="Coverage"){return this.summary_draw_height}else{var ah=this.incremental_slots(aj,ae.data,ai);var ag=new (this.painter)(null,null,null,this.prefs,ai);return Math.max(ab,ag.get_required_height(ah,af))}},draw_tile:function(ao,at,aq,au,ah,al,ag){var ar=this,af=at.canvas,aA=ah.get("start"),ae=ah.get("end"),ai=this.left_offset;if(aq==="summary_tree"||aq==="Coverage"){var aC=new L.SummaryTreePainter(ao,aA,ae,this.prefs);aC.draw(at,af.width,af.height,al);return new j(ar,ah,au,af,ao.data,ao.max)}var ak=[],ap=this.slotters[al].slots;all_slotted=true;if(ao.data){var am=this.filters_manager.filters;for(var av=0,ax=ao.data.length;av<ax;av++){var aj=ao.data[av];var aw=false;var an;for(var az=0,aE=am.length;az<aE;az++){an=am[az];an.update_attrs(aj);if(!an.keep(aj)){aw=true;break}}if(!aw){ak.push(aj);if(!(aj[0] in ap)){all_slotted=false}}}}var aD=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null);var aB=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null);var aC=new (this.painter)(ak,aA,ae,this.prefs,aq,aD,aB,ag);var ay=null;at.fillStyle=this.prefs.block_color;at.font=at.canvas.manager.default_font;at.textAlign="right";if(ao.data){ay=aC.draw(at,af.width,af.height,al,ap);ay.translation=-ai}return new O(ar,ah,au,af,ao.data,al,aq,ao.message,all_slotted,ay)},data_and_mode_compatible:function(ae,af){if(af==="Auto"){return true}else{if(af==="Coverage"){return ae.dataset_type==="summary_tree"}else{if(ae.extra_info==="no_detail"||ae.dataset_type==="summary_tree"){return false}else{return true}}}},can_subset:function(ae){if(ae.dataset_type==="summary_tree"||ae.message||ae.extra_info==="no_detail"){return false}return true}});var S=function(af,ae,ag){c.call(this,af,ae,ag);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:Q()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter};q(S.prototype,r.prototype,M.prototype,c.prototype);var U=function(ag,af,ai){c.call(this,ag,af,ai);var ah=Q(),ae=Q([ah,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ah},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ae},{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:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ai.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter;this.update_icons()};q(U.prototype,r.prototype,M.prototype,c.prototype);var d={LineTrack:h,FeatureTrack:c,VcfTrack:S,ReadTrack:U,CompositeTrack:f,DrawableGroup:P};var p=function(ag,af,ae){if("copy" in ag){return ag.copy(ae)}else{var ah=ag.obj_type;if(!ah){ah=ag.track_type}return new d[ah](af,ae,ag)}};return{View:Z,DrawableGroup:P,LineTrack:h,FeatureTrack:c,DiagonalHeatmapTrack:t,ReadTrack:U,VcfTrack:S,CompositeTrack:f,object_from_template:p,add_datasets:ad}}); \ No newline at end of file diff -r 80251cd7f94d64295ef6e64412f895d268ab988d -r 369a941393909434e0efb5c84dd831e5ab096095 static/scripts/packed/viz/visualization.js --- a/static/scripts/packed/viz/visualization.js +++ b/static/scripts/packed/viz/visualization.js @@ -1,1 +1,1 @@ -define(["libs/underscore","mvc/data","viz/trackster/util"],function(q,h,j){var i=function(s){return("isResolved" in s)};var e=function(s){this.default_font=s!==undefined?s:"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")};q.extend(e.prototype,{load_pattern:function(s,w){var t=this.patterns,u=this.dummy_context,v=new Image();v.src=galaxy_paths.attributes.image_path+w;v.onload=function(){t[s]=u.createPattern(v,"repeat")}},get_pattern:function(s){return this.patterns[s]},new_canvas:function(){var s=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(s)}s.manager=this;return s}});var o=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(s){this.clear()},get_elt:function(t){var u=this.attributes.obj_cache,v=this.attributes.key_ary,s=v.indexOf(t);if(s!==-1){if(u[t].stale){v.splice(s,1);delete u[t]}else{this.move_key_to_end(t,s)}}return u[t]},set_elt:function(t,v){var w=this.attributes.obj_cache,x=this.attributes.key_ary,u=this.attributes.num_elements;if(!w[t]){if(x.length>=u){var s=x.shift();delete w[s]}x.push(t)}w[t]=v;return v},move_key_to_end:function(t,s){this.attributes.key_ary.splice(s,1);this.attributes.key_ary.push(t)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length}});var c=o.extend({defaults:q.extend({},o.prototype.defaults,{dataset:null,filters_manager:null,data_type:"data",data_mode_compatible:function(s,t){return true},can_subset:function(s){return false}}),data_is_ready:function(){var u=this.get("dataset"),t=$.Deferred(),s=new j.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:u.get("hda_ldda"),data_type:"state"},dataType:"json"},interval:5000,success_fn:function(v){return v!=="pending"}});$.when(s.go()).then(function(v){t.resolve(v==="ok"||v==="data")});return t},search_features:function(s){var t=this.get("dataset"),u={query:s,hda_ldda:t.get("hda_ldda"),data_type:"features"};return $.getJSON(t.url(),u)},load_data:function(A,z,t,y){var w=this.get("dataset"),v={data_type:this.get("data_type"),chrom:A.get("chrom"),low:A.get("start"),high:A.get("end"),mode:z,resolution:t,hda_ldda:w.get("hda_ldda")};$.extend(v,y);var C=this.get("filters_manager");if(C){var D=[];var s=C.filters;for(var x=0;x<s.length;x++){D.push(s[x].name)}v.filter_cols=JSON.stringify(D)}var u=this,B=$.getJSON(w.url(),v,function(E){u.set_data(A,E)});this.set_data(A,B);return B},get_data:function(y,x,u,w){var z=this.get_elt(y);if(z&&(i(z)||this.get("data_mode_compatible")(z,x))){return z}var A=this.get("key_ary"),t=this.get("obj_cache"),B,s;for(var v=0;v<A.length;v++){B=A[v];s=new f({from_str:B});if(s.contains(y)){z=t[B];if(i(z)||(this.get("data_mode_compatible")(z,x)&&this.get("can_subset")(z))){this.move_key_to_end(B,v);return z}}}return this.load_data(y,x,u,w)},set_data:function(t,s){this.set_elt(t,s)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(A,z,v,y,w){var C=this._mark_stale(A);if(!(C&&this.get("data_mode_compatible")(C,z))){console.log("ERROR: problem with getting more data: current data is not compatible");return}var u=A.get("start");if(w===this.DEEP_DATA_REQ){$.extend(y,{start_val:C.data.length+1})}else{if(w===this.BROAD_DATA_REQ){u=(C.max_high?C.max_high:C.data[C.data.length-1][2])+1}}var B=A.copy().set("start",u);var t=this,x=this.load_data(B,z,v,y),s=$.Deferred();this.set_data(A,s);$.when(x).then(function(D){if(D.data){D.data=C.data.concat(D.data);if(D.max_low){D.max_low=C.max_low}if(D.message){D.message=D.message.replace(/[0-9]+/,D.data.length)}}t.set_data(A,D);s.resolve(D)});return s},get_more_detailed_data:function(v,x,t,w,u){var s=this._mark_stale(v);if(!s){console.log("ERROR getting more detailed data: no current data");return}if(!u){u={}}var x;if(s.dataset_type==="bigwig"){u.num_samples=s.data.length*w}else{if(s.dataset_type==="summary_tree"){u.level=s.level+1}}return this.load_data(v,x,t,u)},_mark_stale:function(t){var s=this.get_elt(t);if(!s){console.log("ERROR: no data to mark as stale: ",this.get("dataset"),t.toString())}s.stale=true;return s},get_elt:function(s){return o.prototype.get_elt.call(this,s.toString())},set_elt:function(t,s){return o.prototype.set_elt.call(this,t.toString(),s)}});var m=c.extend({initialize:function(s){var t=new Backbone.Model();t.urlRoot=s.data_url;this.set("dataset",t)},load_data:function(u,v,s,t){console.log(u,v,s);if(s>1){return{data:null}}return c.prototype.load_data.call(this,u,v,s,t)}});var b=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(s){this.id=s.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(s){var t=q.find(this.get_chroms_info(),function(u){return u.chrom==s});return new f({chrom:t.chrom,end:t.len})}});var f=Backbone.RelationalModel.extend({defaults:{chrom:null,start:0,end:0,DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006},initialize:function(t){if(t.from_str){var v=t.from_str.split(":"),u=v[0],s=v[1].split("-");this.set({chrom:u,start:parseInt(s[0],10),end:parseInt(s[1],10)})}},copy:function(){return new f({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(z){var t=this.get("chrom"),y=z.get("chrom"),x=this.get("start"),v=z.get("start"),w=this.get("end"),u=z.get("end"),s;if(t&&y&&t!==y){return this.get("DIF_CHROMS")}if(x<v){if(w<v){s=this.get("BEFORE")}else{if(w<=u){s=this.get("OVERLAP_START")}else{s=this.get("CONTAINS")}}}else{if(x>u){s=this.get("AFTER")}else{if(w<=u){s=this.get("CONTAINED_BY")}else{s=this.get("OVERLAP_END")}}}return s},contains:function(s){return this.compute_overlap(s)===this.get("CONTAINS")},overlaps:function(s){return q.intersection([this.compute_overlap(s)],[this.get("DIF_CHROMS"),this.get("BEFORE"),this.get("AFTER")]).length===0}});var l=Backbone.Collection.extend({model:f});var d=Backbone.RelationalModel.extend({defaults:{region:null,note:""},relations:[{type:Backbone.HasOne,key:"region",relatedModel:f}]});var p=Backbone.Collection.extend({model:d});var r=h.Dataset.extend({initialize:function(s){this.set("id",s.dataset_id);var t=new c({dataset:this});this.set("data_manager",t);var u=this.get("preloaded_data");if(u){t.set("num_elements",u.data.length);q.each(u.data,function(v){t.set_data(v.region,v)})}},get_genome_wide_data:function(s){var t=this.get("data_manager");return q.map(s.get("chroms_info").chrom_info,function(u){return t.get_elt(new f({chrom:u.chrom,start:0,end:u.len}))})}});var n=Backbone.RelationalModel.extend({defaults:{id:"",title:"",type:"",dbkey:"",tracks:null},relations:[{type:Backbone.HasMany,key:"tracks",relatedModel:r}],url:function(){return galaxy_paths.get("visualization_url")},save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var k=n.extend({defaults:q.extend({},n.prototype.defaults,{bookmarks:null,viewport:null})});var a=Backbone.Model.extend({});var g=Backbone.Router.extend({initialize:function(t){this.view=t.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var s=this;s.view.on("navigate",function(u){s.navigate(u)})},change_location:function(s){this.view.go_to(s)}});return{BrowserBookmark:d,BrowserBookmarkCollection:p,Cache:o,CanvasManager:e,Genome:b,GenomeDataManager:c,GenomeRegion:f,GenomeRegionCollection:l,GenomeVisualization:k,ReferenceTrackDataManager:m,TrackBrowserRouter:g,TrackConfig:a,Visualization:n}}); \ No newline at end of file +define(["libs/underscore","mvc/data","viz/trackster/util"],function(q,h,j){var i=function(s){return("isResolved" in s)};var e=function(s){this.default_font=s!==undefined?s:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};q.extend(e.prototype,{load_pattern:function(s,w){var t=this.patterns,u=this.dummy_context,v=new Image();v.src=galaxy_paths.attributes.image_path+w;v.onload=function(){t[s]=u.createPattern(v,"repeat")}},get_pattern:function(s){return this.patterns[s]},new_canvas:function(){var s=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(s)}s.manager=this;return s}});var o=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(s){this.clear()},get_elt:function(t){var u=this.attributes.obj_cache,v=this.attributes.key_ary,s=v.indexOf(t);if(s!==-1){if(u[t].stale){v.splice(s,1);delete u[t]}else{this.move_key_to_end(t,s)}}return u[t]},set_elt:function(t,v){var w=this.attributes.obj_cache,x=this.attributes.key_ary,u=this.attributes.num_elements;if(!w[t]){if(x.length>=u){var s=x.shift();delete w[s]}x.push(t)}w[t]=v;return v},move_key_to_end:function(t,s){this.attributes.key_ary.splice(s,1);this.attributes.key_ary.push(t)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length}});var c=o.extend({defaults:q.extend({},o.prototype.defaults,{dataset:null,filters_manager:null,data_type:"data",data_mode_compatible:function(s,t){return true},can_subset:function(s){return false}}),data_is_ready:function(){var u=this.get("dataset"),t=$.Deferred(),s=new j.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:u.get("hda_ldda"),data_type:"state"},dataType:"json"},interval:5000,success_fn:function(v){return v!=="pending"}});$.when(s.go()).then(function(v){t.resolve(v==="ok"||v==="data")});return t},search_features:function(s){var t=this.get("dataset"),u={query:s,hda_ldda:t.get("hda_ldda"),data_type:"features"};return $.getJSON(t.url(),u)},load_data:function(A,z,t,y){var w=this.get("dataset"),v={data_type:this.get("data_type"),chrom:A.get("chrom"),low:A.get("start"),high:A.get("end"),mode:z,resolution:t,hda_ldda:w.get("hda_ldda")};$.extend(v,y);var C=this.get("filters_manager");if(C){var D=[];var s=C.filters;for(var x=0;x<s.length;x++){D.push(s[x].name)}v.filter_cols=JSON.stringify(D)}var u=this,B=$.getJSON(w.url(),v,function(E){u.set_data(A,E)});this.set_data(A,B);return B},get_data:function(y,x,u,w){var z=this.get_elt(y);if(z&&(i(z)||this.get("data_mode_compatible")(z,x))){return z}var A=this.get("key_ary"),t=this.get("obj_cache"),B,s;for(var v=0;v<A.length;v++){B=A[v];s=new f({from_str:B});if(s.contains(y)){z=t[B];if(i(z)||(this.get("data_mode_compatible")(z,x)&&this.get("can_subset")(z))){this.move_key_to_end(B,v);return z}}}return this.load_data(y,x,u,w)},set_data:function(t,s){this.set_elt(t,s)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(A,z,v,y,w){var C=this._mark_stale(A);if(!(C&&this.get("data_mode_compatible")(C,z))){console.log("ERROR: problem with getting more data: current data is not compatible");return}var u=A.get("start");if(w===this.DEEP_DATA_REQ){$.extend(y,{start_val:C.data.length+1})}else{if(w===this.BROAD_DATA_REQ){u=(C.max_high?C.max_high:C.data[C.data.length-1][2])+1}}var B=A.copy().set("start",u);var t=this,x=this.load_data(B,z,v,y),s=$.Deferred();this.set_data(A,s);$.when(x).then(function(D){if(D.data){D.data=C.data.concat(D.data);if(D.max_low){D.max_low=C.max_low}if(D.message){D.message=D.message.replace(/[0-9]+/,D.data.length)}}t.set_data(A,D);s.resolve(D)});return s},get_more_detailed_data:function(v,x,t,w,u){var s=this._mark_stale(v);if(!s){console.log("ERROR getting more detailed data: no current data");return}if(!u){u={}}var x;if(s.dataset_type==="bigwig"){u.num_samples=s.data.length*w}else{if(s.dataset_type==="summary_tree"){u.level=Math.min(s.level-1,2)}}return this.load_data(v,x,t,u)},_mark_stale:function(t){var s=this.get_elt(t);if(!s){console.log("ERROR: no data to mark as stale: ",this.get("dataset"),t.toString())}s.stale=true;return s},get_elt:function(s){return o.prototype.get_elt.call(this,s.toString())},set_elt:function(t,s){return o.prototype.set_elt.call(this,t.toString(),s)}});var m=c.extend({initialize:function(s){var t=new Backbone.Model();t.urlRoot=s.data_url;this.set("dataset",t)},load_data:function(u,v,s,t){console.log(u,v,s);if(s>1){return{data:null}}return c.prototype.load_data.call(this,u,v,s,t)}});var b=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(s){this.id=s.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(s){var t=q.find(this.get_chroms_info(),function(u){return u.chrom==s});return new f({chrom:t.chrom,end:t.len})}});var f=Backbone.RelationalModel.extend({defaults:{chrom:null,start:0,end:0,DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006},initialize:function(t){if(t.from_str){var v=t.from_str.split(":"),u=v[0],s=v[1].split("-");this.set({chrom:u,start:parseInt(s[0],10),end:parseInt(s[1],10)})}},copy:function(){return new f({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(z){var t=this.get("chrom"),y=z.get("chrom"),x=this.get("start"),v=z.get("start"),w=this.get("end"),u=z.get("end"),s;if(t&&y&&t!==y){return this.get("DIF_CHROMS")}if(x<v){if(w<v){s=this.get("BEFORE")}else{if(w<=u){s=this.get("OVERLAP_START")}else{s=this.get("CONTAINS")}}}else{if(x>u){s=this.get("AFTER")}else{if(w<=u){s=this.get("CONTAINED_BY")}else{s=this.get("OVERLAP_END")}}}return s},contains:function(s){return this.compute_overlap(s)===this.get("CONTAINS")},overlaps:function(s){return q.intersection([this.compute_overlap(s)],[this.get("DIF_CHROMS"),this.get("BEFORE"),this.get("AFTER")]).length===0}});var l=Backbone.Collection.extend({model:f});var d=Backbone.RelationalModel.extend({defaults:{region:null,note:""},relations:[{type:Backbone.HasOne,key:"region",relatedModel:f}]});var p=Backbone.Collection.extend({model:d});var r=h.Dataset.extend({initialize:function(s){this.set("id",s.dataset_id);var t=new c({dataset:this});this.set("data_manager",t);var u=this.get("preloaded_data");if(u){t.set("num_elements",u.data.length);q.each(u.data,function(v){t.set_data(v.region,v)})}},get_genome_wide_data:function(s){var t=this.get("data_manager");return q.map(s.get("chroms_info").chrom_info,function(u){return t.get_elt(new f({chrom:u.chrom,start:0,end:u.len}))})}});var n=Backbone.RelationalModel.extend({defaults:{id:"",title:"",type:"",dbkey:"",tracks:null},relations:[{type:Backbone.HasMany,key:"tracks",relatedModel:r}],url:function(){return galaxy_paths.get("visualization_url")},save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var k=n.extend({defaults:q.extend({},n.prototype.defaults,{bookmarks:null,viewport:null})});var a=Backbone.Model.extend({});var g=Backbone.Router.extend({initialize:function(t){this.view=t.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var s=this;s.view.on("navigate",function(u){s.navigate(u)})},change_location:function(s){this.view.go_to(s)}});return{BrowserBookmark:d,BrowserBookmarkCollection:p,Cache:o,CanvasManager:e,Genome:b,GenomeDataManager:c,GenomeRegion:f,GenomeRegionCollection:l,GenomeVisualization:k,ReferenceTrackDataManager:m,TrackBrowserRouter:g,TrackConfig:a,Visualization:n}}); \ No newline at end of file diff -r 80251cd7f94d64295ef6e64412f895d268ab988d -r 369a941393909434e0efb5c84dd831e5ab096095 static/scripts/viz/scatterplot.js --- a/static/scripts/viz/scatterplot.js +++ b/static/scripts/viz/scatterplot.js @@ -61,8 +61,9 @@ */ function TwoVarScatterplot( config ){ var plot = this, - GUESS_AT_SVG_CHAR_WIDTH = 10, - GUESS_AT_SVG_CHAR_HEIGHT = 12, + TICK_LINE_AND_PADDING = 10, + GUESS_AT_SVG_CHAR_WIDTH = 7, + GUESS_AT_SVG_CHAR_HEIGHT = 10, PADDING = 8, X_LABEL_TOO_LONG_AT = 5; @@ -135,16 +136,23 @@ this.log( 'built svg:', d3.selectAll( 'svg' ) ); - this.adjustChartDimensions = function(){ + this.adjustChartDimensions = function( top, right, bottom, left ){ + top = top || 0; + right = right || 0; + bottom = bottom || 0; + left = left || 0; this.svg - .attr( "width", this.config.width + ( this.config.marginRight + this.config.marginLeft ) ) - .attr( "height", this.config.height + ( this.config.marginTop + this.config.marginBottom ) ) + .attr( "width", this.config.width + ( this.config.marginRight + right ) + + ( this.config.marginLeft + left ) ) + .attr( "height", this.config.height + ( this.config.marginTop + top ) + + ( this.config.marginBottom + bottom ) ) // initial is hidden - show it .style( 'display', 'block' ); // move content group away from margins + //TODO: allow top, right axis this.content = this.svg.select( "g.content" ) - .attr( "transform", this.translateStr( this.config.marginLeft, this.config.marginTop ) ); + .attr( "transform", this.translateStr( this.config.marginLeft + left, this.config.marginTop + top ) ); }; // ........................................................ data and scales @@ -208,29 +216,38 @@ .orient( 'left' ); this.yAxis// = content.select( 'g#y-axis' ) .call( this.yAxisFn ); - //this.log( 'yAxis:', this.yAxis ); + this.log( 'yAxis:', this.yAxis ); - //TODO: this isn't reliable with -/+ ranges - better to go thru each tick - this.yLongestLabel = d3.max( _.map( [ this.yMin, this.yMax ], - function( number ){ return ( String( number ) ).length; } ) ); - this.log( 'yLongestLabel:', this.yLongestLabel ); + // get the tick labels for the y axis + var yTickLabels = this.yAxis.selectAll( 'text' ).filter( function( e, i ){ return i !== 0; } ); + //this.log( 'yTickLabels:', yTickLabels ); - //TODO: ugh ... so clumsy - //TODO: this isn't reliable with -/+ ranges - better to go thru each tick - var neededY = this.yLongestLabel * GUESS_AT_SVG_CHAR_WIDTH + ( PADDING ); + // get the longest label length (or 0 if no labels) + this.yLongestLabel = d3.max( + //NOTE: d3 returns an nested array - use the plain array inside ([0]) + yTickLabels[0].map( function( e, i ){ + return ( d3.select( e ).text() ).length; + }) + ) || 0; + //this.log( 'yLongestLabel:', this.yLongestLabel ); + //TODO: lose the guessing if possible + var neededY = TICK_LINE_AND_PADDING + ( this.yLongestLabel * GUESS_AT_SVG_CHAR_WIDTH ) + + PADDING + GUESS_AT_SVG_CHAR_HEIGHT; + //this.log( 'neededY:', neededY ); // increase width for yLongerStr, increase margin for y //TODO??: (or transform each number: 2k) - if( this.config.yAxisLabelBumpX > -( neededY ) ){ - this.config.yAxisLabelBumpX = -( neededY ); + this.config.yAxisLabelBumpX = -( neededY - GUESS_AT_SVG_CHAR_HEIGHT ); + if( this.config.marginLeft < neededY ){ + var adjusting = ( neededY ) - this.config.marginLeft; + adjusting = ( adjusting < 0 )?( 0 ):( adjusting ); + this.log( 'adjusting:', adjusting ); + + // update dimensions, translations + this.adjustChartDimensions( 0, 0, 0, adjusting ); } - if( this.config.marginLeft < neededY ){ - this.config.marginLeft = neededY + GUESS_AT_SVG_CHAR_HEIGHT; - // update dimensions, translations - this.adjustChartDimensions(); - } - this.log( 'this.config.yAxisLableBumpx, this.config.marginLeft:', - this.config.yAxisLabelBumpX, this.config.marginLeft ); + //this.log( 'this.config.yAxisLableBumpx, this.config.marginLeft:', + // this.config.yAxisLabelBumpX, this.config.marginLeft ); this.yAxisLabel// = yAxis.select( 'text#y-axis-label' ) .attr( 'x', this.config.yAxisLabelBumpX ) @@ -367,7 +384,7 @@ * */ var ScatterplotView = BaseView.extend( LoggableMixin ).extend({ - logger : console, + //logger : console, tagName : 'form', className : 'scatterplot-settings-form', @@ -444,12 +461,10 @@ message = message || ''; this.$el.find( 'div#loading-indicator' ).children( '.loading-message' ).text( message ); this.$el.find( 'div#loading-indicator' ).show( 'fast' ); - console.debug( 'showing:', this.$el.find( 'div#loading-indicator' ), message ); }, hideLoadingIndicator : function(){ this.$el.find( 'div#loading-indicator' ).hide( 'fast' ); - console.debug( 'hiding:', this.$el.find( 'div#loading-indicator' ) ); }, renderScatterplot : function(){ diff -r 80251cd7f94d64295ef6e64412f895d268ab988d -r 369a941393909434e0efb5c84dd831e5ab096095 templates/visualization/scatterplot.mako --- a/templates/visualization/scatterplot.mako +++ b/templates/visualization/scatterplot.mako @@ -60,9 +60,15 @@ stroke: black; shape-rendering: crispEdges; } + svg .axis text { + font-family: monospace; + font-size: 12px; +} + +svg #x-axis-label, svg #y-axis-label { font-family: sans-serif; - font-size: 12px; + font-size: 10px; } svg .glyph { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from 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