dnaism.v1.min.js

(function(exports){var dnaism=exports.dnaism={version:"0.1.0"};var dnaism_id=0;function dnaism_identity(d){return d}dnaism.context=function(){var context=new dnaism_context,step=1e4,size=1440,chrm,start,stop,event=d3.dispatch("focus","change","prepare","beforechange"),scale=context.scale=d3.scale.linear().range([0,size]),focus;function update(){scale.domain([start,stop]);return context}context.chrm=function(_){if(!arguments.length)return chrm;chrm=_;return update()};context.start=function(_){if(!arguments.length)return start;start=+_;return update()};context.stop=function(_){if(!arguments.length)return stop;stop=+_;return update()};context.step=function(_){if(!arguments.length)return step;step=+_;return update()};context.size=function(_){if(!arguments.length)return size;scale.range([0,size=+_]);return update()};context.focus=function(i){event.focus.call(context,focus=i);return context};context.on=function(type,listener){if(arguments.length<2)return event.on(type);event.on(type,listener);if(listener!==null){if(/^focus(\.|$)/.test(type))listener.call(context,focus);if(/^change(\.|$)/.test(type))listener.call(context,start,stop);if(/^prepare(\.|$)/.test(type))listener.call(context,start,stop);if(/^beforechange(\.|$)/.test(type))listener.call(context,start,stop)}return context};return update()};function dnaism_context(){}var dnaism_contextPrototype=dnaism.context.prototype=dnaism_context.prototype;function dnaism_metric(context){if(!(context instanceof dnaism_context))throw new Error("invalid context");this.context=context}var dnaism_metricPrototype=dnaism_metric.prototype;dnaism.metric=dnaism_metric;dnaism_metricPrototype.valueAt=function(){return NaN};dnaism_metricPrototype.alias=function(name){this.toString=function(){return name};return this};dnaism_metricPrototype.extent=function(){var i=0,n=this.context.size(),value,min=Infinity,max=-Infinity;while(++i<n){value=this.valueAt(i);if(value<min)min=value;if(value>max)max=value}return[min,max]};dnaism_metricPrototype.on=function(type,listener){return arguments.length<2?null:this};dnaism_metricPrototype.shift=function(){return this};dnaism_metricPrototype.on=function(){return arguments.length<2?null:this};dnaism_contextPrototype.metric=function(request,name){var context=this,metric=new dnaism_metric(context),id=".metric-"+ ++dnaism_id,start=-Infinity,stop,step=context.step(),size=context.size(),chrm=context.chrm(),values=[],event=d3.dispatch("change"),listening=0,fetching;function prepare(start1,stop){var steps=Math.min(size,Math.round((start1-start)/step));if(!steps||fetching)return;fetching=true;console.log("Requesting ..."+chrm+":"+start1+","+stop);request(start1,stop,chrm,step,function(error,data){fetching=false;if(error)return console.warn(error);var i=isFinite(start)?Math.round((start1-start)/step):0;for(var j=0,m=data.length;j<m;++j)values[j+i]=data[j];event.change.call(metric,start,stop)})}function beforechange(start1,stop1){if(!isFinite(start))start=start1;values.splice(0,Math.max(0,Math.min(size,Math.round((start1-start)/step))));start=start1;stop=stop1}metric.valueAt=function(i){return values[i]};metric.values=function(){return values};metric.shift=function(offset){return context.metric(dnaism_metricShift(request,+offset))};metric.on=function(type,listener){if(!arguments.length)return event.on(type);if(listener==null){if(event.on(type)!=null&&--listening==0){context.on("prepare"+id,null).on("beforechange"+id,null)}}else{if(event.on(type)==null&&++listening==1){context.on("prepare"+id,prepare).on("beforechange"+id,beforechange)}}event.on(type,listener);if(listener!=null){if(/^change(\.|$)/.test(type))listener.call(context,start,stop)}return metric};if(arguments.length>1)metric.toString=function(){return name};return metric};var dnaism_metricOverlap=6;function dnaism_metricShift(request,offset){return function(start,stop,step,callback){request(+start+offset,+stop+offset,chrm,step,callback)}}dnaism_contextPrototype.horizon=function(){var context=this,mode="offset",buffer=document.createElement("canvas"),width=buffer.width=context.size(),height=buffer.height=30,scale=d3.scale.linear().interpolate(d3.interpolateRound),metric=dnaism_identity,extent=null,title=dnaism_identity,format=d3.format(".2s"),colors=["#08519c","#3182bd","#6baed6","#bdd7e7","#bae4b3","#74c476","#31a354","#006d2c"];function horizon(selection){selection.on("mousemove.horizon",function(){context.focus(Math.round(d3.mouse(this)[0]))}).on("mouseout.horizon",function(){context.focus(null)});selection.append("canvas").attr("width",width).attr("height",height);selection.append("span").attr("class","title").text(title);selection.append("span").attr("class","value");selection.each(function(d,i){var that=this,id=++dnaism_id,metric_=typeof metric==="function"?metric.call(that,d,i):metric,colors_=typeof colors==="function"?colors.call(that,d,i):colors,extent_=typeof extent==="function"?extent.call(that,d,i):extent,start=-Infinity,step=context.step(),canvas=d3.select(that).select("canvas"),span=d3.select(that).select(".value"),max_,m=colors_.length>>1,ready;canvas.datum({id:id,metric:metric_});canvas=canvas.node().getContext("2d");function change(start1,stop){canvas.save();var extent=metric_.extent();ready=extent.every(isFinite);if(extent_!=null)extent=extent_;var i0=0,max=Math.max(-extent[0],extent[1]);if(this===context){if(max==max_){i0=width-dnaism_metricOverlap;var dx=(start1-start)/step;if(dx<width){var canvas0=buffer.getContext("2d");canvas0.clearRect(0,0,width,height);canvas0.drawImage(canvas.canvas,dx,0,width-dx,height,0,0,width-dx,height);canvas.clearRect(0,0,width,height);canvas.drawImage(canvas0.canvas,0,0)}}start=start1}scale.domain([0,max_=max]);canvas.clearRect(i0,0,width-i0,height);var negative;for(var j=0;j<m;++j){canvas.fillStyle=colors_[m+j];var y0=(j-m+1)*height;scale.range([m*height+y0,y0]);y0=scale(0);for(var i=i0,n=width,y1;i<n;++i){y1=metric_.valueAt(i);if(y1<=0){negative=true;continue}if(y1===undefined)continue;canvas.fillRect(i,y1=scale(y1),1,y0-y1)}}if(negative){if(mode==="offset"){canvas.translate(0,height);canvas.scale(1,-1)}for(var j=0;j<m;++j){canvas.fillStyle=colors_[m-1-j];var y0=(j-m+1)*height;scale.range([m*height+y0,y0]);y0=scale(0);for(var i=i0,n=width,y1;i<n;++i){y1=metric_.valueAt(i);if(y1>=0)continue;canvas.fillRect(i,scale(-y1),1,y0-scale(-y1))}}}canvas.restore()}function focus(i){if(i==null)i=width-1;var value=metric_.valueAt(i);span.datum(value).text(isNaN(value)?null:format);if(i===width-1)span.datum(value).text(null)}context.on("change.horizon-"+id,change);context.on("focus.horizon-"+id,focus);metric_.on("change.horizon-"+id,function(start,stop){change(start,stop),focus();if(ready)metric_.on("change.horizon-"+id,dnaism_identity)})})}horizon.remove=function(selection){selection.on("mousemove.horizon",null).on("mouseout.horizon",null);selection.selectAll("canvas").each(remove).remove();selection.selectAll(".title,.value").remove();function remove(d){d.metric.on("change.horizon-"+d.id,null);context.on("change.horizon-"+d.id,null);context.on("focus.horizon-"+d.id,null)}};horizon.mode=function(_){if(!arguments.length)return mode;mode=_+"";return horizon};horizon.height=function(_){if(!arguments.length)return height;buffer.height=height=+_;return horizon};horizon.metric=function(_){if(!arguments.length)return metric;metric=_;return horizon};horizon.scale=function(_){if(!arguments.length)return scale;scale=_;return horizon};horizon.extent=function(_){if(!arguments.length)return extent;extent=_;return horizon};horizon.title=function(_){if(!arguments.length)return title;title=_;return horizon};horizon.format=function(_){if(!arguments.length)return format;format=_;return horizon};horizon.colors=function(_){if(!arguments.length)return colors;colors=_;return horizon};return horizon};dnaism_contextPrototype.axis=function(){var context=this,scale=context.scale,axis_=d3.svg.axis().scale(scale);var format=function(d){return context.chrm()+":"+d3.format("s")(d)};var format_log=function(d){return context.chrm()+":"+Math.round(d)};function axis(selection){var id=++dnaism_id,tick;var g=selection.append("svg").datum({id:id}).attr("width",context.size()).attr("height",Math.max(28,-axis.tickSize())).append("g").attr("transform","translate(0,"+(axis_.orient()==="top"?27:4)+")").call(axis_);context.on("change.axis-"+id,function(){g.call(axis_);if(!tick)tick=d3.select(g.node().appendChild(g.selectAll("text").node().cloneNode(true))).style("display","none").text(null)});context.on("focus.axis-"+id,function(i){if(tick){if(i==null){tick.style("display","none");g.selectAll("text").style("fill-opacity",null)}else{tick.style("display",null).attr("x",i).text(format(scale.invert(i)));var dx=tick.node().getComputedTextLength()+6;g.selectAll("text").style("fill-opacity",function(d){return Math.abs(scale(d)-i)<dx?0:1})}}})}axis.remove=function(selection){selection.selectAll("svg").each(remove).remove();function remove(d){context.on("change.axis-"+d.id,null);context.on("focus.axis-"+d.id,null)}};return d3.rebind(axis,axis_,"orient","ticks","tickSubdivide","tickSize","tickPadding","tickFormat").tickFormat(format)};dnaism_contextPrototype.rule=function(){var context=this,metric=dnaism_identity;function rule(selection){var id=++dnaism_id;var line=selection.append("div").datum({id:id}).attr("class","line").call(dnaism_ruleStyle);selection.each(function(d,i){var that=this,id=++dnaism_id,metric_=typeof metric==="function"?metric.call(that,d,i):metric;if(!metric_)return;function change(start,stop){var values=[];for(var i=0,n=context.size();i<n;++i){if(metric_.valueAt(i)){values.push(i)}}var lines=selection.selectAll(".metric").data(values);lines.exit().remove();lines.enter().append("div").attr("class","metric line").call(dnaism_ruleStyle);lines.style("left",dnaism_ruleLeft)}context.on("change.rule-"+id,change);metric_.on("change.rule-"+id,change)});context.on("focus.rule-"+id,function(i){line.datum(i).style("display",i==null?"none":null).style("left",i==null?null:dnaism_ruleLeft)})}rule.remove=function(selection){selection.selectAll(".line").each(remove).remove();function remove(d){context.on("focus.rule-"+d.id,null)}};rule.metric=function(_){if(!arguments.length)return metric;metric=_;return rule};return rule};function dnaism_ruleStyle(line){line.style("position","absolute").style("top",0).style("bottom",0).style("width","1px").style("pointer-events","none")}function dnaism_ruleLeft(i){return i+"px"}dnaism_contextPrototype.bedfile=function(){var source={},context=this,compute_average;compute_average=function(arr){var sum=0,i;for(i=0;i<arr.length;i++)sum=sum+arr[i];return+(sum/arr.length).toFixed(2)};source.metric=function(file_name){return context.metric(function(start,stop,chrm,step,callback){d3.text(file_name,function(contents){var final_data_points=[],size=context.size(),interval_size=(stop-start)/size,int_mark=start+interval_size,sum=0,int_vals=[],_n_plus;d3.tsv.parseRows(contents,function(a_row){var _chrm=a_row[0],coor=+a_row[1],value=+a_row[3];if(chrm===_chrm&&coor<int_mark){int_vals.push(value)}else{if(coor<int_mark+interval_size){final_data_points.push(compute_average(int_vals));int_mark=int_mark+interval_size}else{_n_plus=~~((coor-int_mark)/interval_size);int_mark+=interval_size*_n_plus;while(_n_plus--)final_data_points.push(0)}int_vals=[value]}return null});callback(null,final_data_points.slice(-context.size()))})},file_name)};return source};dnaism_contextPrototype.bedserver=function(host){if(!arguments.length)host="";var source={},context=this;source.metric=function(project,sample){return context.metric(function(start,stop,chrm,step,callback){var url=host+"/bedserver/api/v1.0/samples/"+project+"/"+sample+"?start="+start+"&stop="+stop+"&chrm="+context.chrm()+"&size="+context.size()+"&step="+step;console.log("bedserver; url= "+url);d3.json(url,function(data){if(!data)return callback(new Error("unable to load data"));callback(null,data)})},project+":"+sample)};source.toString=function(){return host};return source}})(this);